Starting phenix.real_space_refine
on Wed Mar  4 00:46:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dti_27699/03_2026/8dti_27699.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dti_27699/03_2026/8dti_27699.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dti_27699/03_2026/8dti_27699.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dti_27699/03_2026/8dti_27699.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dti_27699/03_2026/8dti_27699.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dti_27699/03_2026/8dti_27699.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.976
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      63      5.16       5
     C    6018      2.51       5
     N    1594      2.21       5
     O    1776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9455
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 629, 4684
          Classifications: {'peptide': 629}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 598}
          Unresolved non-hydrogen bonds: 268
          Unresolved non-hydrogen angles: 321
          Unresolved non-hydrogen dihedrals: 226
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 14, 'ASN:plan1': 1, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 134
    Chain: "B"
      Number of atoms: 4695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 629, 4695
          Classifications: {'peptide': 629}
          Incomplete info: {'truncation_to_alanine': 70}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 598}
          Unresolved non-hydrogen bonds: 257
          Unresolved non-hydrogen angles: 309
          Unresolved non-hydrogen dihedrals: 216
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 13, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 5, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 125
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 38
          Unusual residues: {'GFB': 1}
          Classifications: {'RNA_mixed': 1}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 38
          Unusual residues: {'GFB': 1}
          Classifications: {'RNA_mixed': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.24
  Number of scatterers: 9455
  At special positions: 0
  Unit cell: (156.6, 78.84, 78.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P       4     15.00
     O    1776      8.00
     N    1594      7.00
     C    6018      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 526.2 milliseconds
  

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2372

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 4 sheets defined
      66.0% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 219 through 234
      removed outlier: 3.707A  pdb=" N   TYR A 223 " --> pdb=" O   TYR A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 250
    Processing helix  chain 'A' and resid 253 through 275
    Processing helix  chain 'A' and resid 276 through 291
    Processing helix  chain 'A' and resid 294 through 308
      removed outlier: 3.620A  pdb=" N   MET A 298 " --> pdb=" O   TYR A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 325
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 344 through 359
    Processing helix  chain 'A' and resid 362 through 377
    Processing helix  chain 'A' and resid 378 through 393
    Processing helix  chain 'A' and resid 396 through 411
      removed outlier: 4.051A  pdb=" N   PHE A 400 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 427
    Processing helix  chain 'A' and resid 430 through 442
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 450 through 467
    Processing helix  chain 'A' and resid 495 through 508
      removed outlier: 4.323A  pdb=" N   ALA A 503 " --> pdb=" O   TYR A 499 " (cutoff:3.500A)
      Proline residue:  A 504  - end of helix
    Processing helix  chain 'A' and resid 525 through 539
    Processing helix  chain 'A' and resid 549 through 560
    Processing helix  chain 'A' and resid 576 through 581
      removed outlier: 3.955A  pdb=" N   MET A 580 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
    Processing helix  chain 'A' and resid 662 through 666
    Processing helix  chain 'A' and resid 667 through 681
      removed outlier: 3.574A  pdb=" N   VAL A 681 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 709
    Processing helix  chain 'A' and resid 712 through 714
      No H-bonds generated for 'chain 'A' and resid 712 through 714'
    Processing helix  chain 'A' and resid 724 through 731
    Processing helix  chain 'A' and resid 732 through 735
    Processing helix  chain 'A' and resid 747 through 756
      removed outlier: 3.638A  pdb=" N   CYS A 751 " --> pdb=" O   THR A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 781
      removed outlier: 4.728A  pdb=" N   GLY A 773 " --> pdb=" O   ALA A 769 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   VAL A 774 " --> pdb=" O   HIS A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 784
      No H-bonds generated for 'chain 'A' and resid 782 through 784'
    Processing helix  chain 'A' and resid 789 through 803
      removed outlier: 4.208A  pdb=" N   ASP A 803 " --> pdb=" O   ASP A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 820
      removed outlier: 4.203A  pdb=" N   ARG A 815 " --> pdb=" O   ARG A 811 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   ASP A 816 " --> pdb=" O   MET A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 846
      removed outlier: 3.955A  pdb=" N   PHE A 829 " --> pdb=" O   ASN A 825 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 234
      removed outlier: 3.709A  pdb=" N   TYR B 223 " --> pdb=" O   TYR B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 250
    Processing helix  chain 'B' and resid 253 through 275
    Processing helix  chain 'B' and resid 276 through 291
    Processing helix  chain 'B' and resid 294 through 308
      removed outlier: 3.621A  pdb=" N   MET B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 325
    Processing helix  chain 'B' and resid 328 through 342
    Processing helix  chain 'B' and resid 344 through 359
    Processing helix  chain 'B' and resid 362 through 377
    Processing helix  chain 'B' and resid 378 through 393
    Processing helix  chain 'B' and resid 396 through 411
      removed outlier: 4.050A  pdb=" N   PHE B 400 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 427
    Processing helix  chain 'B' and resid 430 through 442
    Processing helix  chain 'B' and resid 443 through 445
      No H-bonds generated for 'chain 'B' and resid 443 through 445'
    Processing helix  chain 'B' and resid 450 through 467
    Processing helix  chain 'B' and resid 495 through 508
      removed outlier: 4.323A  pdb=" N   ALA B 503 " --> pdb=" O   TYR B 499 " (cutoff:3.500A)
      Proline residue:  B 504  - end of helix
    Processing helix  chain 'B' and resid 525 through 539
    Processing helix  chain 'B' and resid 549 through 560
    Processing helix  chain 'B' and resid 576 through 581
      removed outlier: 3.956A  pdb=" N   MET B 580 " --> pdb=" O   LYS B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 653
    Processing helix  chain 'B' and resid 662 through 666
    Processing helix  chain 'B' and resid 667 through 681
      removed outlier: 3.575A  pdb=" N   VAL B 681 " --> pdb=" O   ILE B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 695 through 709
    Processing helix  chain 'B' and resid 712 through 714
      No H-bonds generated for 'chain 'B' and resid 712 through 714'
    Processing helix  chain 'B' and resid 724 through 731
    Processing helix  chain 'B' and resid 732 through 735
    Processing helix  chain 'B' and resid 747 through 756
      removed outlier: 3.638A  pdb=" N   CYS B 751 " --> pdb=" O   THR B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 767 through 781
      removed outlier: 4.729A  pdb=" N   GLY B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL B 774 " --> pdb=" O   HIS B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 784
      No H-bonds generated for 'chain 'B' and resid 782 through 784'
    Processing helix  chain 'B' and resid 789 through 803
      removed outlier: 4.208A  pdb=" N   ASP B 803 " --> pdb=" O   ASP B 799 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 820
      removed outlier: 4.203A  pdb=" N   ARG B 815 " --> pdb=" O   ARG B 811 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   ASP B 816 " --> pdb=" O   MET B 812 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 846
      removed outlier: 3.954A  pdb=" N   PHE B 829 " --> pdb=" O   ASN B 825 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544
      removed outlier: 6.212A  pdb=" N   THR A 484 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   VAL A 566 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLY A 486 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   GLN A 588 " --> pdb=" O   TYR A 605 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ILE A 607 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   THR A 590 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 9.739A  pdb=" N   ASP A 609 " --> pdb=" O   THR A 590 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ARG A 606 " --> pdb=" O   VAL A 626 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   LEU A 628 " --> pdb=" O   ARG A 606 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   THR A 608 " --> pdb=" O   LEU A 628 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719
      removed outlier: 8.840A  pdb=" N   ASP A 717 " --> pdb=" O   SER A 684 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU A 686 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   LEU A 719 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL A 688 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL A 655 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   VAL A 687 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   PHE A 657 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   LYS A 689 " --> pdb=" O   PHE A 657 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   SER A 659 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ILE A 737 " --> pdb=" O   THR A 656 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   SER A 738 " --> pdb=" O   VAL A 761 " (cutoff:3.500A)
      removed outlier: 8.622A  pdb=" N   MET A 763 " --> pdb=" O   SER A 738 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   ALA A 787 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   THR A 762 " --> pdb=" O   ALA A 787 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 544
      removed outlier: 6.212A  pdb=" N   THR B 484 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL B 566 " --> pdb=" O   THR B 484 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   GLY B 486 " --> pdb=" O   VAL B 566 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   GLN B 588 " --> pdb=" O   TYR B 605 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ILE B 607 " --> pdb=" O   GLN B 588 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   THR B 590 " --> pdb=" O   ILE B 607 " (cutoff:3.500A)
      removed outlier: 9.739A  pdb=" N   ASP B 609 " --> pdb=" O   THR B 590 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ARG B 606 " --> pdb=" O   VAL B 626 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   LEU B 628 " --> pdb=" O   ARG B 606 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   THR B 608 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 716 through 719
      removed outlier: 8.840A  pdb=" N   ASP B 717 " --> pdb=" O   SER B 684 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   LEU B 686 " --> pdb=" O   ASP B 717 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   LEU B 719 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL B 688 " --> pdb=" O   LEU B 719 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL B 655 " --> pdb=" O   ARG B 685 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   VAL B 687 " --> pdb=" O   VAL B 655 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   PHE B 657 " --> pdb=" O   VAL B 687 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   LYS B 689 " --> pdb=" O   PHE B 657 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   SER B 659 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE B 737 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   SER B 738 " --> pdb=" O   VAL B 761 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   MET B 763 " --> pdb=" O   SER B 738 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   ALA B 787 " --> pdb=" O   CYS B 760 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   THR B 762 " --> pdb=" O   ALA B 787 " (cutoff:3.500A)

    582 hydrogen bonds defined for protein.
    1722 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.57

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1952
        1.33 -     1.45: 2285
        1.45 -     1.57: 5347
        1.57 -     1.69: 8
        1.69 -     1.81: 95
  Bond restraints: 9687
  Sorted by residual:
  bond pdb=" C4  GFB A1001 "
       pdb=" N3  GFB A1001 "
    ideal  model  delta    sigma   weight residual
    1.340  1.503 -0.163 2.00e-02 2.50e+03 6.65e+01
  bond pdb=" C4  GFB B1001 "
       pdb=" N3  GFB B1001 "
    ideal  model  delta    sigma   weight residual
    1.340  1.503 -0.163 2.00e-02 2.50e+03 6.63e+01
  bond pdb=" C2  GFB A1001 "
       pdb=" N2  GFB A1001 "
    ideal  model  delta    sigma   weight residual
    1.341  1.491 -0.150 2.00e-02 2.50e+03 5.61e+01
  bond pdb=" C2  GFB B1001 "
       pdb=" N2  GFB B1001 "
    ideal  model  delta    sigma   weight residual
    1.341  1.490 -0.149 2.00e-02 2.50e+03 5.57e+01
  bond pdb=" C2  GFB B1001 "
       pdb=" N3  GFB B1001 "
    ideal  model  delta    sigma   weight residual
    1.310  1.451 -0.141 2.00e-02 2.50e+03 4.98e+01
  ... (remaining 9682 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 13161
        3.10 -     6.21: 83
        6.21 -     9.31: 10
        9.31 -    12.41: 4
       12.41 -    15.51: 4
  Bond angle restraints: 13262
  Sorted by residual:
  angle pdb=" O2P GFB B1001 "
        pdb=" P   GFB B1001 "
        pdb=" O5' GFB B1001 "
      ideal   model   delta    sigma   weight residual
      93.35  108.86  -15.51 3.00e+00 1.11e-01 2.67e+01
  angle pdb=" O2P GFB A1001 "
        pdb=" P   GFB A1001 "
        pdb=" O5' GFB A1001 "
      ideal   model   delta    sigma   weight residual
      93.35  108.84  -15.49 3.00e+00 1.11e-01 2.66e+01
  angle pdb=" O1X GFB A1001 "
        pdb=" P1  GFB A1001 "
        pdb=" O2X GFB A1001 "
      ideal   model   delta    sigma   weight residual
     122.73  109.50   13.23 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" O1X GFB B1001 "
        pdb=" P1  GFB B1001 "
        pdb=" O2X GFB B1001 "
      ideal   model   delta    sigma   weight residual
     122.73  109.55   13.18 3.00e+00 1.11e-01 1.93e+01
  angle pdb=" O1  GFB A1001 "
        pdb=" P1  GFB A1001 "
        pdb=" O2P GFB A1001 "
      ideal   model   delta    sigma   weight residual
      99.26  109.54  -10.28 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 13257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 5124
       15.94 -    31.88: 460
       31.88 -    47.82: 142
       47.82 -    63.76: 34
       63.76 -    79.70: 16
  Dihedral angle restraints: 5776
    sinusoidal: 2082
      harmonic: 3694
  Sorted by residual:
  dihedral pdb=" CG  ARG A 532 "
           pdb=" CD  ARG A 532 "
           pdb=" NE  ARG A 532 "
           pdb=" CZ  ARG A 532 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.41  -42.59     2      1.50e+01 4.44e-03 9.77e+00
  dihedral pdb=" CG  ARG B 532 "
           pdb=" CD  ARG B 532 "
           pdb=" NE  ARG B 532 "
           pdb=" CZ  ARG B 532 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.46  -42.54     2      1.50e+01 4.44e-03 9.75e+00
  dihedral pdb=" CB  MET B 441 "
           pdb=" CG  MET B 441 "
           pdb=" SD  MET B 441 "
           pdb=" CE  MET B 441 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.28  -59.72     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5773 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1368
       0.070 -    0.140: 149
       0.140 -    0.209: 4
       0.209 -    0.279: 0
       0.279 -    0.349: 2
  Chirality restraints: 1523
  Sorted by residual:
  chirality pdb=" C2' GFB B1001 "
            pdb=" C1' GFB B1001 "
            pdb=" C3' GFB B1001 "
            pdb=" O2' GFB B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.91    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" C2' GFB A1001 "
            pdb=" C1' GFB A1001 "
            pdb=" C3' GFB A1001 "
            pdb=" O2' GFB A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.90    0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" C5A GFB B1001 "
            pdb=" C4A GFB B1001 "
            pdb=" C6A GFB B1001 "
            pdb=" O5  GFB B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.63   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1520 not shown)

  Planarity restraints: 1702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 420 "    0.022 2.00e-02 2.50e+03   1.87e-02 7.02e+00
        pdb=" CG  TYR B 420 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 420 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 420 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 420 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 420 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 420 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 420 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 420 "   -0.022 2.00e-02 2.50e+03   1.87e-02 6.97e+00
        pdb=" CG  TYR A 420 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 420 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 420 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 420 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 420 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 420 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 420 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 420 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.83e+00
        pdb=" C   TYR B 420 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   TYR B 420 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU B 421 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1699 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 731
        2.74 -     3.28: 10009
        3.28 -     3.82: 16216
        3.82 -     4.36: 17902
        4.36 -     4.90: 30474
  Nonbonded interactions: 75332
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 748 "
            pdb=" OE2 GLU A 752 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG1 THR B 748 "
            pdb=" OE2 GLU B 752 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OH  TYR B 518 "
            pdb=" OD2 ASP B 560 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR A 518 "
            pdb=" OD2 ASP A 560 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   LEU A 505 "
            pdb=" OH  TYR A 510 "
     model   vdw
     2.231 3.040
  ... (remaining 75327 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 218 through 226 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 227 or (resid 228 through 231 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 232 through 1001))
  selection = (chain 'B' and (resid 218 through 232 or (resid 233 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 234 through 236 or (resid 237 through 239  \ 
and (name N or name CA or name C or name O or name CB )) or resid 240 through 77 \ 
8 or (resid 779 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 780 through 1001))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.130
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
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      :  0.006   0.163   9687  Z= 0.314
  Angle     :  0.659  15.513  13262  Z= 0.306
  Chirality :  0.041   0.349   1523
  Planarity :  0.003   0.032   1702
  Dihedral  : 14.507  79.702   3404
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.25), residues: 1254
  helix:  2.19 (0.19), residues: 778
  sheet:  0.11 (0.49), residues: 122
  loop : -0.63 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 342 
 TYR   0.045   0.001   TYR B 420 
 PHE   0.018   0.001   PHE A 724 
 TRP   0.007   0.001   TRP B 459 
 HIS   0.003   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00638 ( 9687)
  covalent geometry    : angle       0.65877 (13262)
  hydrogen bonds       : bond        0.14633 (  582)
  hydrogen bonds       : angle       5.03662 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  632 PHE cc_start: 0.6534 (p90) cc_final: 0.6318 (p90)
REVERT: B  632 PHE cc_start: 0.7292 (p90) cc_final: 0.7026 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0631
  time to fit residues: 12.2993
Evaluate side-chains
  98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 467 HIS
A 661 ASN
B 368 ASN
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.117513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.099716 restraints weight = 21362.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.102566 restraints weight = 13092.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.104546 restraints weight = 9228.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.105965 restraints weight = 7100.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.107004 restraints weight = 5814.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9687  Z= 0.153
  Angle     :  0.540   7.452  13262  Z= 0.272
  Chirality :  0.041   0.124   1523
  Planarity :  0.004   0.028   1702
  Dihedral  :  7.500  68.744   1465
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.57 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.25), residues: 1254
  helix:  2.49 (0.19), residues: 780
  sheet: -0.65 (0.43), residues: 140
  loop : -0.61 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 606 
 TYR   0.024   0.002   TYR B 420 
 PHE   0.021   0.002   PHE B 500 
 TRP   0.011   0.001   TRP B 473 
 HIS   0.006   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9687)
  covalent geometry    : angle       0.54004 (13262)
  hydrogen bonds       : bond        0.03929 (  582)
  hydrogen bonds       : angle       4.03863 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.8573 (m-80) cc_final: 0.7816 (m-80)
REVERT: A  632 PHE cc_start: 0.6899 (p90) cc_final: 0.6610 (p90)
REVERT: A  729 MET cc_start: 0.7931 (tpp) cc_final: 0.7123 (tpp)
REVERT: B  290 TYR cc_start: 0.8664 (m-80) cc_final: 0.8435 (m-80)
REVERT: B  508 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7138 (t-90)
REVERT: B  632 PHE cc_start: 0.7685 (p90) cc_final: 0.7079 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 117
  average time/residue: 0.0619
  time to fit residues: 11.7456
Evaluate side-chains
  105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  723 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 105 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0270
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.3042

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 661 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.113836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.095611 restraints weight = 21622.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.098449 restraints weight = 13506.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100415 restraints weight = 9589.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.101772 restraints weight = 7453.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.102680 restraints weight = 6172.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9687  Z= 0.189
  Angle     :  0.554   6.115  13262  Z= 0.283
  Chirality :  0.042   0.125   1523
  Planarity :  0.004   0.034   1702
  Dihedral  :  6.577  72.997   1465
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.90 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.24), residues: 1254
  helix:  2.30 (0.18), residues: 790
  sheet: -0.97 (0.48), residues: 120
  loop : -0.55 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 811 
 TYR   0.026   0.002   TYR B 318 
 PHE   0.040   0.002   PHE A 724 
 TRP   0.009   0.001   TRP A 459 
 HIS   0.005   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 9687)
  covalent geometry    : angle       0.55446 (13262)
  hydrogen bonds       : bond        0.04020 (  582)
  hydrogen bonds       : angle       4.03989 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.8467 (m-80) cc_final: 0.7769 (m-80)
REVERT: A  491 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7484 (p0)
REVERT: A  632 PHE cc_start: 0.6797 (p90) cc_final: 0.6485 (p90)
REVERT: B  290 TYR cc_start: 0.8707 (m-80) cc_final: 0.8504 (m-80)
REVERT: B  508 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7106 (t-90)
REVERT: B  632 PHE cc_start: 0.7510 (p90) cc_final: 0.6868 (p90)
  outliers start: 19
  outliers final: 13
  residues processed: 114
  average time/residue: 0.0597
  time to fit residues: 11.2125
Evaluate side-chains
  112 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  385 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3658 r_free = 0.3658 target = 0.114693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.096527 restraints weight = 21505.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.099391 restraints weight = 13337.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.101405 restraints weight = 9434.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.102819 restraints weight = 7280.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.103749 restraints weight = 5962.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9687  Z= 0.133
  Angle     :  0.511   6.390  13262  Z= 0.256
  Chirality :  0.040   0.150   1523
  Planarity :  0.004   0.034   1702
  Dihedral  :  6.493  73.855   1465
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.40 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.25), residues: 1254
  helix:  2.54 (0.18), residues: 778
  sheet: -0.82 (0.45), residues: 140
  loop : -0.59 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 685 
 TYR   0.016   0.001   TYR A 420 
 PHE   0.018   0.002   PHE A 724 
 TRP   0.007   0.001   TRP A 459 
 HIS   0.004   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9687)
  covalent geometry    : angle       0.51078 (13262)
  hydrogen bonds       : bond        0.03407 (  582)
  hydrogen bonds       : angle       3.77377 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.8458 (m-80) cc_final: 0.7785 (m-80)
REVERT: A  632 PHE cc_start: 0.6641 (p90) cc_final: 0.6399 (p90)
REVERT: B  491 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7157 (p0)
REVERT: B  508 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7083 (t-90)
REVERT: B  632 PHE cc_start: 0.7541 (p90) cc_final: 0.6873 (p90)
  outliers start: 23
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0638
  time to fit residues: 12.2577
Evaluate side-chains
  111 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  762 THR
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 123 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3658 r_free = 0.3658 target = 0.114476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.096000 restraints weight = 21603.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.098949 restraints weight = 13476.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.100967 restraints weight = 9556.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.102372 restraints weight = 7420.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.103400 restraints weight = 6136.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9687  Z= 0.133
  Angle     :  0.504   7.200  13262  Z= 0.254
  Chirality :  0.040   0.122   1523
  Planarity :  0.004   0.034   1702
  Dihedral  :  6.419  69.469   1465
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.22 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.24), residues: 1254
  helix:  2.62 (0.18), residues: 778
  sheet: -0.13 (0.49), residues: 118
  loop : -0.79 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 811 
 TYR   0.018   0.001   TYR B 605 
 PHE   0.020   0.002   PHE A 724 
 TRP   0.007   0.001   TRP A 459 
 HIS   0.004   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9687)
  covalent geometry    : angle       0.50415 (13262)
  hydrogen bonds       : bond        0.03328 (  582)
  hydrogen bonds       : angle       3.59378 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.8415 (m-80) cc_final: 0.7803 (m-80)
REVERT: A  491 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7512 (p0)
REVERT: A  594 TYR cc_start: 0.8225 (t80) cc_final: 0.8023 (t80)
REVERT: B  491 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7223 (p0)
REVERT: B  508 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7190 (t-90)
REVERT: B  632 PHE cc_start: 0.7599 (p90) cc_final: 0.6918 (p90)
  outliers start: 25
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0639
  time to fit residues: 12.3617
Evaluate side-chains
  114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  488 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  588 GLN
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 39 optimal weight:    0.3980
   chunk 111 optimal weight:    0.0020
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0970
   chunk 25 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3684 r_free = 0.3684 target = 0.116401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.098133 restraints weight = 21423.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.101098 restraints weight = 13289.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.103170 restraints weight = 9378.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.104656 restraints weight = 7221.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105672 restraints weight = 5887.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9687  Z= 0.096
  Angle     :  0.483   6.283  13262  Z= 0.241
  Chirality :  0.039   0.121   1523
  Planarity :  0.003   0.032   1702
  Dihedral  :  6.229  64.354   1465
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.86 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.25), residues: 1254
  helix:  2.67 (0.18), residues: 790
  sheet: -0.11 (0.47), residues: 130
  loop : -0.98 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.013   0.001   TYR A 420 
 PHE   0.019   0.001   PHE B 724 
 TRP   0.005   0.001   TRP A 459 
 HIS   0.002   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 9687)
  covalent geometry    : angle       0.48291 (13262)
  hydrogen bonds       : bond        0.02901 (  582)
  hydrogen bonds       : angle       3.36484 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  232 ASN cc_start: 0.7149 (m-40) cc_final: 0.6881 (p0)
REVERT: A  318 TYR cc_start: 0.8386 (m-80) cc_final: 0.7779 (m-80)
REVERT: A  594 TYR cc_start: 0.8087 (t80) cc_final: 0.7843 (t80)
REVERT: B  311 PHE cc_start: 0.7508 (m-10) cc_final: 0.7201 (m-10)
REVERT: B  491 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7112 (p0)
REVERT: B  508 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.7194 (t-90)
REVERT: B  632 PHE cc_start: 0.7582 (p90) cc_final: 0.6866 (p90)
  outliers start: 25
  outliers final: 17
  residues processed: 120
  average time/residue: 0.0555
  time to fit residues: 10.9472
Evaluate side-chains
  117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  488 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0030
   chunk 40 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 101 optimal weight:    8.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 GLN
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3682 r_free = 0.3682 target = 0.116251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.098108 restraints weight = 21364.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.101058 restraints weight = 13290.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.103085 restraints weight = 9367.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.104549 restraints weight = 7236.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105593 restraints weight = 5910.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9687  Z= 0.102
  Angle     :  0.486   6.327  13262  Z= 0.242
  Chirality :  0.039   0.120   1523
  Planarity :  0.003   0.031   1702
  Dihedral  :  6.159  63.764   1465
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.86 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.25), residues: 1254
  helix:  2.69 (0.18), residues: 790
  sheet: -0.10 (0.47), residues: 130
  loop : -0.96 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 437 
 TYR   0.018   0.001   TYR A 299 
 PHE   0.023   0.001   PHE A 724 
 TRP   0.005   0.001   TRP A 459 
 HIS   0.003   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9687)
  covalent geometry    : angle       0.48615 (13262)
  hydrogen bonds       : bond        0.02941 (  582)
  hydrogen bonds       : angle       3.31247 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.8351 (m-80) cc_final: 0.7703 (m-80)
REVERT: A  491 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.6921 (p0)
REVERT: A  594 TYR cc_start: 0.8129 (t80) cc_final: 0.7572 (t80)
REVERT: A  814 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8448 (tt)
REVERT: B  311 PHE cc_start: 0.7516 (m-10) cc_final: 0.7231 (m-10)
REVERT: B  491 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7121 (p0)
REVERT: B  632 PHE cc_start: 0.7553 (p90) cc_final: 0.6837 (p90)
  outliers start: 24
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0628
  time to fit residues: 12.3362
Evaluate side-chains
  117 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  488 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0370
   chunk 64 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 GLN
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3679 r_free = 0.3679 target = 0.116121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.098061 restraints weight = 21327.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.100910 restraints weight = 13306.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.102975 restraints weight = 9492.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.104435 restraints weight = 7287.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.105486 restraints weight = 5947.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
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      :  0.002   0.027   9687  Z= 0.108
  Angle     :  0.498   6.637  13262  Z= 0.249
  Chirality :  0.039   0.119   1523
  Planarity :  0.003   0.031   1702
  Dihedral  :  6.140  63.580   1465
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.08 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.25), residues: 1254
  helix:  2.67 (0.18), residues: 790
  sheet: -0.10 (0.47), residues: 130
  loop : -0.98 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 606 
 TYR   0.028   0.001   TYR B 318 
 PHE   0.024   0.001   PHE A 724 
 TRP   0.005   0.001   TRP A 459 
 HIS   0.002   0.001   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9687)
  covalent geometry    : angle       0.49812 (13262)
  hydrogen bonds       : bond        0.03050 (  582)
  hydrogen bonds       : angle       3.32849 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  318 TYR cc_start: 0.8339 (m-80) cc_final: 0.7708 (m-80)
REVERT: A  491 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.6925 (p0)
REVERT: A  777 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7352 (mm)
REVERT: A  814 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (tt)
REVERT: B  311 PHE cc_start: 0.7526 (m-10) cc_final: 0.7178 (m-10)
REVERT: B  491 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7130 (p0)
REVERT: B  632 PHE cc_start: 0.7535 (p90) cc_final: 0.6784 (p90)
  outliers start: 25
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0630
  time to fit residues: 12.4476
Evaluate side-chains
  124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  488 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0170
   chunk 60 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0010
   overall best weight:    0.5624

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

Flipped N/Q/H residues before XYZ refinement:
A 571 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 GLN
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3676 r_free = 0.3676 target = 0.115956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.098000 restraints weight = 21371.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.100887 restraints weight = 13361.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.102901 restraints weight = 9476.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.104223 restraints weight = 7308.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.105311 restraints weight = 6034.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9687  Z= 0.110
  Angle     :  0.506   6.931  13262  Z= 0.252
  Chirality :  0.039   0.118   1523
  Planarity :  0.003   0.032   1702
  Dihedral  :  6.140  63.335   1465
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.18 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.24), residues: 1254
  helix:  2.53 (0.18), residues: 802
  sheet: -0.22 (0.50), residues: 110
  loop : -0.91 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 606 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.024   0.001   PHE A 724 
 TRP   0.005   0.001   TRP A 459 
 HIS   0.002   0.001   HIS B 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9687)
  covalent geometry    : angle       0.50626 (13262)
  hydrogen bonds       : bond        0.03056 (  582)
  hydrogen bonds       : angle       3.32406 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  232 ASN cc_start: 0.6211 (p0) cc_final: 0.6008 (p0)
REVERT: A  318 TYR cc_start: 0.8343 (m-80) cc_final: 0.7703 (m-80)
REVERT: A  491 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.6915 (p0)
REVERT: A  594 TYR cc_start: 0.8150 (t80) cc_final: 0.7562 (t80)
REVERT: A  814 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8518 (tt)
REVERT: B  311 PHE cc_start: 0.7512 (m-10) cc_final: 0.7177 (m-10)
REVERT: B  491 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7104 (p0)
REVERT: B  632 PHE cc_start: 0.7526 (p90) cc_final: 0.6787 (p90)
REVERT: B  752 GLU cc_start: 0.7511 (tt0) cc_final: 0.7204 (mt-10)
  outliers start: 26
  outliers final: 19
  residues processed: 125
  average time/residue: 0.0635
  time to fit residues: 13.0577
Evaluate side-chains
  125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  786 VAL
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  488 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0870
   chunk 57 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 105 optimal weight:    0.0170
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 GLN
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3680 r_free = 0.3680 target = 0.115755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.097581 restraints weight = 21532.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.100536 restraints weight = 13315.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.102558 restraints weight = 9387.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103957 restraints weight = 7259.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.105014 restraints weight = 5973.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9687  Z= 0.109
  Angle     :  0.515   7.290  13262  Z= 0.254
  Chirality :  0.039   0.124   1523
  Planarity :  0.003   0.032   1702
  Dihedral  :  6.136  62.796   1465
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.51 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.24), residues: 1254
  helix:  2.53 (0.18), residues: 802
  sheet: -0.23 (0.50), residues: 110
  loop : -0.94 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 606 
 TYR   0.028   0.001   TYR B 318 
 PHE   0.025   0.001   PHE A 724 
 TRP   0.005   0.001   TRP B 461 
 HIS   0.003   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9687)
  covalent geometry    : angle       0.51457 (13262)
  hydrogen bonds       : bond        0.03062 (  582)
  hydrogen bonds       : angle       3.31433 ( 1722)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  232 ASN cc_start: 0.6317 (p0) cc_final: 0.6103 (p0)
REVERT: A  318 TYR cc_start: 0.8367 (m-80) cc_final: 0.7796 (m-80)
REVERT: A  491 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.6893 (p0)
REVERT: A  814 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8519 (tt)
REVERT: B  491 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7092 (p0)
REVERT: B  580 MET cc_start: 0.8273 (mpp) cc_final: 0.7920 (mmt)
REVERT: B  632 PHE cc_start: 0.7443 (p90) cc_final: 0.6686 (p90)
  outliers start: 23
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0639
  time to fit residues: 12.5610
Evaluate side-chains
  120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  488 ILE
Chi-restraints excluded: chain A residue  491 ASP
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  598 THR
Chi-restraints excluded: chain A residue  748 THR
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  488 ILE
Chi-restraints excluded: chain B residue  491 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  508 HIS
Chi-restraints excluded: chain B residue  589 VAL
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  814 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0010
   chunk 52 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 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 = 0.3679 r_free = 0.3679 target = 0.115744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.097635 restraints weight = 21495.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.100461 restraints weight = 13386.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.102515 restraints weight = 9565.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103951 restraints weight = 7382.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105021 restraints weight = 6058.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.197   9687  Z= 0.230
  Angle     :  0.848  59.165  13262  Z= 0.491
  Chirality :  0.039   0.129   1523
  Planarity :  0.003   0.032   1702
  Dihedral  :  6.131  62.809   1465
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.08 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.24), residues: 1254
  helix:  2.53 (0.18), residues: 802
  sheet: -0.18 (0.51), residues: 110
  loop : -0.94 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 606 
 TYR   0.018   0.001   TYR B 318 
 PHE   0.023   0.001   PHE A 724 
 TRP   0.005   0.001   TRP A 459 
 HIS   0.003   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 9687)
  covalent geometry    : angle       0.84791 (13262)
  hydrogen bonds       : bond        0.03077 (  582)
  hydrogen bonds       : angle       3.31923 ( 1722)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1413.86 seconds
wall clock time: 25 minutes 13.23 seconds (1513.23 seconds total)