Starting phenix.real_space_refine
on Wed Mar  4 05:36:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dth_27698/03_2026/8dth_27698.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dth_27698/03_2026/8dth_27698.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dth_27698/03_2026/8dth_27698.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dth_27698/03_2026/8dth_27698.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dth_27698/03_2026/8dth_27698.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dth_27698/03_2026/8dth_27698.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      88      5.16       5
     C    7126      2.51       5
     N    1848      2.21       5
     O    2091      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11153
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 736, 5732
          Classifications: {'peptide': 736}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 701}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 5421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5421
          Classifications: {'peptide': 701}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 667}
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 37
  Time building chain proxies: 2.58, per 1000 atoms: 0.23
  Number of scatterers: 11153
  At special positions: 0
  Unit cell: (97.68, 101.2, 160.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      88     16.00
     O    2091      8.00
     N    1848      7.00
     C    7126      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: 0.76
  Conformation dependent library (CDL) restraints added in 572.9 milliseconds
  

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2710

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 4 sheets defined
      69.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 111 through 124
      removed outlier: 3.531A  pdb=" N   GLU A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 141
      removed outlier: 3.696A  pdb=" N   ALA A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 165
    Processing helix  chain 'A' and resid 167 through 182
    Processing helix  chain 'A' and resid 185 through 199
      removed outlier: 3.852A  pdb=" N   TYR A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 216
    Processing helix  chain 'A' and resid 219 through 233
      removed outlier: 3.803A  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 274
    Processing helix  chain 'A' and resid 276 through 291
    Processing helix  chain 'A' and resid 294 through 308
    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 410
      removed outlier: 3.539A  pdb=" N   PHE A 400 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 427
    Processing helix  chain 'A' and resid 430 through 442
    Processing helix  chain 'A' and resid 450 through 466
      removed outlier: 3.521A  pdb=" N   GLU A 454 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 508
      removed outlier: 5.161A  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 538
    Processing helix  chain 'A' and resid 549 through 560
    Processing helix  chain 'A' and resid 576 through 582
      removed outlier: 3.523A  pdb=" N   CYS A 582 " --> pdb=" O   GLY A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 653
      removed outlier: 4.001A  pdb=" N   SER A 651 " --> pdb=" O   THR A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 681
    Processing helix  chain 'A' and resid 691 through 694
      removed outlier: 3.907A  pdb=" N   CYS A 694 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 691 through 694'
    Processing helix  chain 'A' and resid 695 through 709
      removed outlier: 3.589A  pdb=" N   LEU A 709 " --> pdb=" O   THR A 705 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 767 through 781
      removed outlier: 5.294A  pdb=" N   GLY A 773 " --> pdb=" O   ALA A 769 " (cutoff:3.500A)
      removed outlier: 4.719A  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: 3.754A  pdb=" N   ASP A 803 " --> pdb=" O   ASP A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 820
      removed outlier: 4.465A  pdb=" N   ARG A 815 " --> pdb=" O   ARG A 811 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   ASP A 816 " --> pdb=" O   MET A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 824
    Processing helix  chain 'A' and resid 825 through 846
    Processing helix  chain 'B' and resid 147 through 165
    Processing helix  chain 'B' and resid 167 through 182
    Processing helix  chain 'B' and resid 185 through 199
      removed outlier: 3.599A  pdb=" N   TYR B 189 " --> pdb=" O   TYR B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 216
    Processing helix  chain 'B' and resid 219 through 234
    Processing helix  chain 'B' and resid 236 through 250
    Processing helix  chain 'B' and resid 253 through 275
    Processing helix  chain 'B' and resid 276 through 291
      removed outlier: 3.541A  pdb=" N   TYR B 290 " --> pdb=" O   LYS B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 309
    Processing helix  chain 'B' and resid 310 through 325
    Processing helix  chain 'B' and resid 328 through 341
    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 410
    Processing helix  chain 'B' and resid 412 through 427
    Processing helix  chain 'B' and resid 430 through 444
      removed outlier: 3.708A  pdb=" N   TYR B 443 " --> pdb=" O   LEU B 439 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ILE B 444 " --> pdb=" O   ALA B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 466
    Processing helix  chain 'B' and resid 497 through 507
      removed outlier: 5.238A  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 537
    Processing helix  chain 'B' and resid 549 through 560
    Processing helix  chain 'B' and resid 576 through 582
    Processing helix  chain 'B' and resid 647 through 653
      removed outlier: 3.684A  pdb=" N   SER B 651 " --> pdb=" O   THR B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 666
    Processing helix  chain 'B' and resid 667 through 681
      removed outlier: 3.763A  pdb=" N   VAL B 673 " --> pdb=" O   LYS B 669 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 691 through 694
    Processing helix  chain 'B' and resid 695 through 710
      removed outlier: 3.566A  pdb=" N   ARG B 699 " --> pdb=" O   CYS B 695 " (cutoff:3.500A)
    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
      removed outlier: 3.653A  pdb=" N   MET B 735 " --> pdb=" O   TYR B 732 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 732 through 735'
    Processing helix  chain 'B' and resid 747 through 756
    Processing helix  chain 'B' and resid 767 through 781
      removed outlier: 5.173A  pdb=" N   GLY B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
      removed outlier: 4.642A  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: 3.633A  pdb=" N   ASP B 803 " --> pdb=" O   ASP B 799 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 820
      removed outlier: 4.222A  pdb=" N   ARG B 815 " --> pdb=" O   ARG B 811 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   ASP B 816 " --> pdb=" O   MET B 812 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 824
    Processing helix  chain 'B' and resid 825 through 846
    Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544
      removed outlier: 8.803A  pdb=" N   VAL A 541 " --> pdb=" O   TYR A 513 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL A 515 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   LYS A 543 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL A 517 " --> pdb=" O   LYS A 543 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE A 483 " --> pdb=" O   LYS A 514 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   VAL A 516 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE A 485 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   TYR A 518 " --> pdb=" O   ILE A 485 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TYR A 487 " --> pdb=" O   TYR A 518 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   THR A 484 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   VAL A 566 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   GLY A 486 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLN A 588 " --> pdb=" O   TYR A 605 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE A 607 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   THR A 590 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 9.769A  pdb=" N   ASP A 609 " --> pdb=" O   THR A 590 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719
      removed outlier: 6.406A  pdb=" N   LEU A 686 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   LEU A 719 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 688 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   THR A 656 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   LEU A 739 " --> pdb=" O   THR A 656 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   GLY A 658 " --> pdb=" O   LEU A 739 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   SER A 738 " --> pdb=" O   VAL A 761 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   MET A 763 " --> pdb=" O   SER A 738 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   ALA A 787 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)
      removed outlier: 6.588A  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: 6.262A  pdb=" N   ILE B 483 " --> pdb=" O   LYS B 514 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B 516 " --> pdb=" O   ILE B 483 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ILE B 485 " --> pdb=" O   VAL B 516 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   TYR B 518 " --> pdb=" O   ILE B 485 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   TYR B 487 " --> pdb=" O   TYR B 518 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   THR B 484 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   VAL B 566 " --> pdb=" O   THR B 484 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLY B 486 " --> pdb=" O   VAL B 566 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   GLN B 588 " --> pdb=" O   TYR B 605 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   ILE B 607 " --> pdb=" O   GLN B 588 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   THR B 590 " --> pdb=" O   ILE B 607 " (cutoff:3.500A)
      removed outlier: 9.735A  pdb=" N   ASP B 609 " --> pdb=" O   THR B 590 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 716 through 719
      removed outlier: 8.165A  pdb=" N   ASP B 717 " --> pdb=" O   SER B 684 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LEU B 686 " --> pdb=" O   ASP B 717 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   LEU B 719 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   VAL B 688 " --> pdb=" O   LEU B 719 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   THR B 656 " --> pdb=" O   ILE B 737 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   LEU B 739 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY B 658 " --> pdb=" O   LEU B 739 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   SER B 738 " --> pdb=" O   VAL B 761 " (cutoff:3.500A)
      removed outlier: 8.679A  pdb=" N   MET B 763 " --> pdb=" O   SER B 738 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   ALA B 787 " --> pdb=" O   CYS B 760 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR B 762 " --> pdb=" O   ALA B 787 " (cutoff:3.500A)

    697 hydrogen bonds defined for protein.
    2070 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: 1.82

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3598
        1.34 -     1.46: 2113
        1.46 -     1.58: 5573
        1.58 -     1.69: 0
        1.69 -     1.81: 132
  Bond restraints: 11416
  Sorted by residual:
  bond pdb=" CB  PRO A 743 "
       pdb=" CG  PRO A 743 "
    ideal  model  delta    sigma   weight residual
    1.506  1.463  0.043 3.90e-02 6.57e+02 1.24e+00
  bond pdb=" CG  PRO A 692 "
       pdb=" CD  PRO A 692 "
    ideal  model  delta    sigma   weight residual
    1.503  1.473  0.030 3.40e-02 8.65e+02 7.99e-01
  bond pdb=" CG1 ILE A 677 "
       pdb=" CD1 ILE A 677 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 7.35e-01
  bond pdb=" CB  PRO B 743 "
       pdb=" CG  PRO B 743 "
    ideal  model  delta    sigma   weight residual
    1.506  1.473  0.033 3.90e-02 6.57e+02 7.12e-01
  bond pdb=" CA  TRP A 459 "
       pdb=" C   TRP A 459 "
    ideal  model  delta    sigma   weight residual
    1.524  1.513  0.011 1.29e-02 6.01e+03 6.99e-01
  ... (remaining 11411 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 15280
        1.94 -     3.87: 228
        3.87 -     5.81: 26
        5.81 -     7.74: 3
        7.74 -     9.68: 1
  Bond angle restraints: 15538
  Sorted by residual:
  angle pdb=" CA  LEU B 734 "
        pdb=" CB  LEU B 734 "
        pdb=" CG  LEU B 734 "
      ideal   model   delta    sigma   weight residual
     116.30  125.98   -9.68 3.50e+00 8.16e-02 7.65e+00
  angle pdb=" N   GLU A 350 "
        pdb=" CA  GLU A 350 "
        pdb=" CB  GLU A 350 "
      ideal   model   delta    sigma   weight residual
     110.12  114.09   -3.97 1.47e+00 4.63e-01 7.31e+00
  angle pdb=" N   PHE A 463 "
        pdb=" CA  PHE A 463 "
        pdb=" CB  PHE A 463 "
      ideal   model   delta    sigma   weight residual
     110.16  106.48    3.68 1.48e+00 4.57e-01 6.19e+00
  angle pdb=" N   TRP B 591 "
        pdb=" CA  TRP B 591 "
        pdb=" C   TRP B 591 "
      ideal   model   delta    sigma   weight residual
     110.80  116.05   -5.25 2.13e+00 2.20e-01 6.08e+00
  angle pdb=" N   LYS A 691 "
        pdb=" CA  LYS A 691 "
        pdb=" C   LYS A 691 "
      ideal   model   delta    sigma   weight residual
     113.57  116.74   -3.17 1.38e+00 5.25e-01 5.27e+00
  ... (remaining 15533 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.24: 6305
       17.24 -    34.48: 413
       34.48 -    51.72: 90
       51.72 -    68.97: 10
       68.97 -    86.21: 5
  Dihedral angle restraints: 6823
    sinusoidal: 2589
      harmonic: 4234
  Sorted by residual:
  dihedral pdb=" CA  VAL A 589 "
           pdb=" C   VAL A 589 "
           pdb=" N   THR A 590 "
           pdb=" CA  THR A 590 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  THR A 506 "
           pdb=" C   THR A 506 "
           pdb=" N   HIS A 507 "
           pdb=" CA  HIS A 507 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CG  ARG A 685 "
           pdb=" CD  ARG A 685 "
           pdb=" NE  ARG A 685 "
           pdb=" CZ  ARG A 685 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.62   44.62     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 6820 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1343
       0.042 -    0.085: 293
       0.085 -    0.127: 100
       0.127 -    0.170: 7
       0.170 -    0.212: 2
  Chirality restraints: 1745
  Sorted by residual:
  chirality pdb=" CB  THR A 464 "
            pdb=" CA  THR A 464 "
            pdb=" OG1 THR A 464 "
            pdb=" CG2 THR A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  VAL B 716 "
            pdb=" N   VAL B 716 "
            pdb=" C   VAL B 716 "
            pdb=" CB  VAL B 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.84e-01
  chirality pdb=" CA  PRO A 479 "
            pdb=" N   PRO A 479 "
            pdb=" C   PRO A 479 "
            pdb=" CB  PRO A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.86e-01
  ... (remaining 1742 not shown)

  Planarity restraints: 1993
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 427 "    0.051 5.00e-02 4.00e+02   7.79e-02 9.70e+00
        pdb=" N   PRO B 428 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 428 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 428 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 250 "   -0.046 5.00e-02 4.00e+02   6.98e-02 7.80e+00
        pdb=" N   PRO A 251 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 251 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 251 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 145 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.59e+00
        pdb=" N   PRO A 146 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1990 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 995
        2.74 -     3.28: 12189
        3.28 -     3.82: 19446
        3.82 -     4.36: 23021
        4.36 -     4.90: 38825
  Nonbonded interactions: 94476
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 346 "
            pdb=" OE1 GLU A 350 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OH  TYR B 635 "
            pdb=" OE2 GLU B 752 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   MET A 238 "
            pdb=" OG1 THR A 241 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD1 ASN B 442 "
            pdb=" OH  TYR B 594 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   PRO A 682 "
            pdb=" OD1 ASN A 683 "
     model   vdw
     2.313 3.040
  ... (remaining 94471 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 146 through 154 or (resid 155 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 156 through 179 or (resid 180 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 181 through 195 or (resid  \ 
196 and (name N or name CA or name C or name O or name CB )) or resid 197 throug \ 
h 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 219 through 285 or (resid 286 through 287 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 288 through 386 or (resid 387 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 388 through 447 or (resid 448  \ 
and (name N or name CA or name C or name O or name CB )) or resid 449 through 46 \ 
1 or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 463 through 511 or (resid 512 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 513 or (resid 514 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 515 through 522 or (resid 523 through 524 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 525 through 542 or (resid 543  \ 
and (name N or name CA or name C or name O or name CB )) or resid 544 through 56 \ 
6 or (resid 567 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 568 through 668 or (resid 669 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 670 through 722 or (resid 723 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 724 through 794 or (resid 795 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 796 through 815 or (resid 816  \ 
and (name N or name CA or name C or name O or name CB )) or resid 817 through 83 \ 
7 or (resid 838 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 839 or (resid 840 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 841 through 846))
  selection = (chain 'B' and (resid 146 through 414 or (resid 415 through 416 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 417 through 420 or (resid 421  \ 
and (name N or name CA or name C or name O or name CB )) or resid 422 through 42 \ 
8 or (resid 429 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 430 through 706 or (resid 707 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 708 through 846))
}

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:             3.650
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.940
  Find NCS groups from input model:        0.180
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11416  Z= 0.154
  Angle     :  0.604   9.678  15538  Z= 0.324
  Chirality :  0.041   0.212   1745
  Planarity :  0.006   0.078   1993
  Dihedral  : 12.279  86.208   4113
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.22), residues: 1433
  helix:  0.80 (0.16), residues: 945
  sheet: -0.83 (0.50), residues: 121
  loop : -1.98 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 701 
 TYR   0.034   0.002   TYR A 134 
 PHE   0.040   0.003   PHE A 829 
 TRP   0.022   0.001   TRP B 841 
 HIS   0.005   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11416)
  covalent geometry    : angle       0.60439 (15538)
  hydrogen bonds       : bond        0.11880 (  697)
  hydrogen bonds       : angle       5.44687 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  553 ILE cc_start: 0.8808 (mm) cc_final: 0.8339 (mm)
REVERT: B  211 LYS cc_start: 0.9125 (mttm) cc_final: 0.8759 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0783
  time to fit residues: 16.4051
Evaluate side-chains
  97 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 ASN
A 467 HIS
A 662 ASN
B 201 GLN
B 367 ASN
B 402 ASN
B 442 ASN
B 730 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.123315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.086894 restraints weight = 25624.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.088884 restraints weight = 15851.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.089583 restraints weight = 11233.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.089946 restraints weight = 9305.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090161 restraints weight = 8922.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11416  Z= 0.174
  Angle     :  0.575  10.546  15538  Z= 0.294
  Chirality :  0.041   0.174   1745
  Planarity :  0.005   0.052   1993
  Dihedral  :  3.852  16.360   1571
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.64 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  1.58 (0.23), residues: 1433
  helix:  2.03 (0.17), residues: 950
  sheet: -0.70 (0.47), residues: 131
  loop : -0.97 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 462 
 TYR   0.018   0.002   TYR A 793 
 PHE   0.028   0.002   PHE A 829 
 TRP   0.011   0.001   TRP B 591 
 HIS   0.005   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11416)
  covalent geometry    : angle       0.57463 (15538)
  hydrogen bonds       : bond        0.04063 (  697)
  hydrogen bonds       : angle       4.16644 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A  489 SER cc_start: 0.9463 (t) cc_final: 0.8729 (m)
REVERT: B  580 MET cc_start: 0.8586 (mmp) cc_final: 0.8144 (mmm)
REVERT: B  729 MET cc_start: 0.7636 (mmm) cc_final: 0.7407 (mmm)
REVERT: B  730 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8002 (tp40)
  outliers start: 8
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0877
  time to fit residues: 14.6652
Evaluate side-chains
  97 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  346 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0770
   chunk 103 optimal weight:    3.9990
   chunk 104 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 111 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 662 ASN
B 201 GLN
** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 825 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.123840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.087624 restraints weight = 25609.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.089313 restraints weight = 14993.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.089928 restraints weight = 11224.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.090318 restraints weight = 9292.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.090537 restraints weight = 8942.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11416  Z= 0.124
  Angle     :  0.497   7.843  15538  Z= 0.255
  Chirality :  0.039   0.145   1745
  Planarity :  0.004   0.058   1993
  Dihedral  :  3.765  15.633   1571
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  5.82 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.11 (0.23), residues: 1433
  helix:  2.41 (0.17), residues: 951
  sheet: -0.51 (0.47), residues: 131
  loop : -0.67 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 811 
 TYR   0.015   0.001   TYR A 793 
 PHE   0.022   0.001   PHE A 829 
 TRP   0.008   0.001   TRP B 841 
 HIS   0.003   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (11416)
  covalent geometry    : angle       0.49740 (15538)
  hydrogen bonds       : bond        0.03380 (  697)
  hydrogen bonds       : angle       3.75117 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  489 SER cc_start: 0.9439 (t) cc_final: 0.8732 (m)
REVERT: B  192 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8862 (mt)
REVERT: B  580 MET cc_start: 0.8553 (mmp) cc_final: 0.8087 (mmm)
REVERT: B  730 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7997 (tp-100)
  outliers start: 12
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0850
  time to fit residues: 14.7808
Evaluate side-chains
  102 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  346 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0980
   chunk 99 optimal weight:    0.6980
   chunk 22 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 126 optimal weight:    7.9990
   chunk 121 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   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 300 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 571 HIS ** 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 = 0.3817 r_free = 0.3817 target = 0.122954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.089703 restraints weight = 25908.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.087837 restraints weight = 16592.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.089533 restraints weight = 12187.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.089766 restraints weight = 9550.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.089779 restraints weight = 9389.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  11416  Z= 0.142
  Angle     :  0.513  13.062  15538  Z= 0.258
  Chirality :  0.040   0.239   1745
  Planarity :  0.004   0.059   1993
  Dihedral  :  3.761  14.852   1571
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.68 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.22 (0.23), residues: 1433
  helix:  2.44 (0.17), residues: 956
  sheet: -0.45 (0.47), residues: 130
  loop : -0.53 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 606 
 TYR   0.016   0.001   TYR A 793 
 PHE   0.021   0.001   PHE A 829 
 TRP   0.024   0.001   TRP B 841 
 HIS   0.004   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11416)
  covalent geometry    : angle       0.51263 (15538)
  hydrogen bonds       : bond        0.03293 (  697)
  hydrogen bonds       : angle       3.62490 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  489 SER cc_start: 0.9409 (t) cc_final: 0.8746 (m)
REVERT: B  192 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8871 (mt)
REVERT: B  569 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7213 (t)
REVERT: B  580 MET cc_start: 0.8549 (mmp) cc_final: 0.8093 (mmm)
REVERT: B  635 TYR cc_start: 0.6261 (t80) cc_final: 0.5659 (t80)
REVERT: B  730 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7908 (tp-100)
  outliers start: 13
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0793
  time to fit residues: 13.5484
Evaluate side-chains
  107 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  569 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 0 optimal weight:   40.0000
   chunk 84 optimal weight:    0.5980
   chunk 125 optimal weight:    0.5980
   chunk 101 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.121881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087945 restraints weight = 25442.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.087357 restraints weight = 14321.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087014 restraints weight = 13897.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.087665 restraints weight = 12741.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.087723 restraints weight = 10954.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11416  Z= 0.157
  Angle     :  0.516  12.342  15538  Z= 0.260
  Chirality :  0.040   0.177   1745
  Planarity :  0.004   0.058   1993
  Dihedral  :  3.788  16.039   1571
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.44 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.36 (0.23), residues: 1433
  helix:  2.53 (0.17), residues: 954
  sheet: -0.40 (0.46), residues: 130
  loop : -0.41 (0.37), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 606 
 TYR   0.017   0.001   TYR A 793 
 PHE   0.021   0.001   PHE A 829 
 TRP   0.011   0.001   TRP B 461 
 HIS   0.006   0.001   HIS A 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (11416)
  covalent geometry    : angle       0.51558 (15538)
  hydrogen bonds       : bond        0.03380 (  697)
  hydrogen bonds       : angle       3.57681 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.8605 (mpp) cc_final: 0.8329 (mpp)
REVERT: A  489 SER cc_start: 0.9397 (t) cc_final: 0.8749 (m)
REVERT: B  192 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8877 (mt)
REVERT: B  580 MET cc_start: 0.8506 (mmp) cc_final: 0.8016 (mmm)
REVERT: B  635 TYR cc_start: 0.6396 (t80) cc_final: 0.5811 (t80)
REVERT: B  729 MET cc_start: 0.7592 (mmm) cc_final: 0.7375 (tmm)
REVERT: B  730 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7782 (tp-100)
  outliers start: 14
  outliers final: 6
  residues processed: 108
  average time/residue: 0.0817
  time to fit residues: 13.7771
Evaluate side-chains
  103 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  569 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 132 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 117 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.122359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087165 restraints weight = 25655.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.087458 restraints weight = 16223.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.087592 restraints weight = 12144.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.087821 restraints weight = 11599.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.088234 restraints weight = 10439.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11416  Z= 0.130
  Angle     :  0.511  14.723  15538  Z= 0.253
  Chirality :  0.039   0.149   1745
  Planarity :  0.004   0.058   1993
  Dihedral  :  3.759  15.660   1571
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.86 %
    Favored  : 90.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.50 (0.23), residues: 1433
  helix:  2.65 (0.17), residues: 953
  sheet: -0.36 (0.47), residues: 130
  loop : -0.36 (0.37), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.015   0.001   TYR A 793 
 PHE   0.020   0.001   PHE A 829 
 TRP   0.011   0.001   TRP B 461 
 HIS   0.003   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11416)
  covalent geometry    : angle       0.51115 (15538)
  hydrogen bonds       : bond        0.03111 (  697)
  hydrogen bonds       : angle       3.46724 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.8628 (ptt) cc_final: 0.8356 (ptt)
REVERT: A  200 MET cc_start: 0.8648 (mpp) cc_final: 0.8365 (mpp)
REVERT: A  489 SER cc_start: 0.9394 (t) cc_final: 0.8762 (m)
REVERT: B  192 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8847 (mt)
REVERT: B  219 TYR cc_start: 0.7159 (m-80) cc_final: 0.6873 (m-80)
REVERT: B  580 MET cc_start: 0.8421 (mmp) cc_final: 0.7933 (mmm)
REVERT: B  635 TYR cc_start: 0.6617 (t80) cc_final: 0.5827 (t80)
REVERT: B  729 MET cc_start: 0.7535 (mmm) cc_final: 0.7210 (tmm)
REVERT: B  818 MET cc_start: 0.8984 (ppp) cc_final: 0.8603 (ppp)
  outliers start: 13
  outliers final: 9
  residues processed: 111
  average time/residue: 0.0873
  time to fit residues: 15.2850
Evaluate side-chains
  109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 106 optimal weight:    8.9990
   chunk 131 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0870
   chunk 1 optimal weight:   30.0000
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.122591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.087425 restraints weight = 25346.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.087716 restraints weight = 16557.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.088321 restraints weight = 12108.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.088774 restraints weight = 10768.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.088705 restraints weight = 10057.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11416  Z= 0.120
  Angle     :  0.512  14.249  15538  Z= 0.251
  Chirality :  0.039   0.141   1745
  Planarity :  0.004   0.057   1993
  Dihedral  :  3.728  15.594   1571
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.62 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.53 (0.23), residues: 1433
  helix:  2.67 (0.17), residues: 961
  sheet: -0.12 (0.50), residues: 119
  loop : -0.53 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.014   0.001   TYR A 793 
 PHE   0.019   0.001   PHE A 829 
 TRP   0.013   0.001   TRP B 461 
 HIS   0.004   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11416)
  covalent geometry    : angle       0.51238 (15538)
  hydrogen bonds       : bond        0.03002 (  697)
  hydrogen bonds       : angle       3.42871 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.8655 (ptt) cc_final: 0.8033 (ptt)
REVERT: A  200 MET cc_start: 0.8648 (mpp) cc_final: 0.8216 (mpp)
REVERT: A  253 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8217 (t80)
REVERT: A  489 SER cc_start: 0.9400 (t) cc_final: 0.8784 (m)
REVERT: B  192 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8845 (mt)
REVERT: B  219 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6978 (m-80)
REVERT: B  450 ASP cc_start: 0.7527 (t0) cc_final: 0.7323 (t0)
REVERT: B  580 MET cc_start: 0.8434 (mmp) cc_final: 0.7947 (mmm)
REVERT: B  635 TYR cc_start: 0.6623 (t80) cc_final: 0.5849 (t80)
REVERT: B  735 MET cc_start: 0.8269 (ptp) cc_final: 0.7780 (ttp)
REVERT: B  818 MET cc_start: 0.9016 (ppp) cc_final: 0.8674 (ppp)
  outliers start: 17
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0835
  time to fit residues: 14.7219
Evaluate side-chains
  113 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 TYR
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  219 TYR
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  597 THR
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0870
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.122418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.088851 restraints weight = 25592.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088253 restraints weight = 14522.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.087858 restraints weight = 14232.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.088263 restraints weight = 12695.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.088291 restraints weight = 12266.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11416  Z= 0.123
  Angle     :  0.510  12.793  15538  Z= 0.251
  Chirality :  0.039   0.130   1745
  Planarity :  0.004   0.058   1993
  Dihedral  :  3.718  15.656   1571
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.21 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.52 (0.23), residues: 1433
  helix:  2.63 (0.17), residues: 967
  sheet: -0.13 (0.51), residues: 110
  loop : -0.48 (0.36), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.014   0.001   TYR A 793 
 PHE   0.018   0.001   PHE A 829 
 TRP   0.015   0.001   TRP B 461 
 HIS   0.004   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11416)
  covalent geometry    : angle       0.50993 (15538)
  hydrogen bonds       : bond        0.03019 (  697)
  hydrogen bonds       : angle       3.42218 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.8650 (ptt) cc_final: 0.8179 (ptt)
REVERT: A  200 MET cc_start: 0.8622 (mpp) cc_final: 0.8245 (mpp)
REVERT: A  253 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8232 (t80)
REVERT: A  489 SER cc_start: 0.9368 (t) cc_final: 0.8732 (m)
REVERT: B  192 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8860 (mt)
REVERT: B  219 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.7056 (m-80)
REVERT: B  450 ASP cc_start: 0.7520 (t0) cc_final: 0.7311 (t0)
REVERT: B  580 MET cc_start: 0.8476 (mmp) cc_final: 0.7978 (mmm)
REVERT: B  729 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6516 (tmm)
REVERT: B  735 MET cc_start: 0.8313 (ptp) cc_final: 0.7871 (ttp)
REVERT: B  818 MET cc_start: 0.8940 (ppp) cc_final: 0.8729 (ppp)
  outliers start: 18
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0935
  time to fit residues: 15.6426
Evaluate side-chains
  111 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 TYR
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  219 TYR
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  597 THR
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  729 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 113 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 138 optimal weight:    5.9990
   chunk 140 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.121791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.084881 restraints weight = 25425.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.086038 restraints weight = 15450.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.086751 restraints weight = 11729.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.086913 restraints weight = 10229.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.087109 restraints weight = 9730.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11416  Z= 0.158
  Angle     :  0.551  13.185  15538  Z= 0.273
  Chirality :  0.040   0.136   1745
  Planarity :  0.004   0.059   1993
  Dihedral  :  3.770  15.481   1571
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.97 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.50 (0.23), residues: 1433
  helix:  2.62 (0.16), residues: 963
  sheet:  0.11 (0.53), residues: 108
  loop : -0.58 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.016   0.001   TYR A 793 
 PHE   0.019   0.001   PHE A 829 
 TRP   0.016   0.001   TRP B 461 
 HIS   0.004   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (11416)
  covalent geometry    : angle       0.55139 (15538)
  hydrogen bonds       : bond        0.03275 (  697)
  hydrogen bonds       : angle       3.54107 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 MET cc_start: 0.7741 (ptp) cc_final: 0.6955 (tpp)
REVERT: A  199 MET cc_start: 0.8662 (ptt) cc_final: 0.8214 (ptt)
REVERT: A  200 MET cc_start: 0.8642 (mpp) cc_final: 0.8272 (mpp)
REVERT: A  489 SER cc_start: 0.9399 (t) cc_final: 0.8767 (m)
REVERT: B  192 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8850 (mt)
REVERT: B  219 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.7062 (m-80)
REVERT: B  580 MET cc_start: 0.8479 (mmp) cc_final: 0.7977 (mmm)
REVERT: B  735 MET cc_start: 0.8348 (ptp) cc_final: 0.7925 (ttp)
  outliers start: 16
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0836
  time to fit residues: 13.9023
Evaluate side-chains
  109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  219 TYR
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  597 THR
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 GLN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.122279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.088187 restraints weight = 25504.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.087460 restraints weight = 14467.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.087268 restraints weight = 13047.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.087817 restraints weight = 12550.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.087834 restraints weight = 11210.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11416  Z= 0.131
  Angle     :  0.535  11.735  15538  Z= 0.266
  Chirality :  0.039   0.127   1745
  Planarity :  0.004   0.059   1993
  Dihedral  :  3.759  16.422   1571
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.31 %
    Favored  : 87.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.56 (0.23), residues: 1433
  helix:  2.68 (0.17), residues: 957
  sheet:  0.12 (0.53), residues: 108
  loop : -0.52 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.018   0.001   TYR B 755 
 PHE   0.019   0.001   PHE A 829 
 TRP   0.018   0.001   TRP B 461 
 HIS   0.004   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11416)
  covalent geometry    : angle       0.53549 (15538)
  hydrogen bonds       : bond        0.03067 (  697)
  hydrogen bonds       : angle       3.47928 ( 2070)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 MET cc_start: 0.7480 (ptp) cc_final: 0.6782 (tpp)
REVERT: A  199 MET cc_start: 0.8655 (ptt) cc_final: 0.8186 (ptt)
REVERT: A  200 MET cc_start: 0.8628 (mpp) cc_final: 0.8244 (mpp)
REVERT: A  253 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8271 (t80)
REVERT: A  489 SER cc_start: 0.9376 (t) cc_final: 0.8748 (m)
REVERT: B  192 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8818 (mt)
REVERT: B  580 MET cc_start: 0.8526 (mmp) cc_final: 0.8018 (mmm)
REVERT: B  735 MET cc_start: 0.8354 (ptp) cc_final: 0.7986 (ttp)
  outliers start: 14
  outliers final: 12
  residues processed: 105
  average time/residue: 0.0828
  time to fit residues: 13.8730
Evaluate side-chains
  108 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 TYR
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  508 HIS
Chi-restraints excluded: chain A residue  567 GLU
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  728 HIS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  379 MET
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  569 THR
Chi-restraints excluded: chain B residue  597 THR
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0980
   chunk 87 optimal weight:    0.3980
   chunk 131 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.122329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.087894 restraints weight = 25665.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.087558 restraints weight = 14054.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.087367 restraints weight = 12294.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.087663 restraints weight = 12153.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.088013 restraints weight = 10756.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11416  Z= 0.122
  Angle     :  0.535  13.205  15538  Z= 0.266
  Chirality :  0.039   0.125   1745
  Planarity :  0.004   0.059   1993
  Dihedral  :  3.753  15.740   1571
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.22 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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:  2.59 (0.23), residues: 1433
  helix:  2.69 (0.17), residues: 964
  sheet:  0.13 (0.54), residues: 108
  loop : -0.54 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 606 
 TYR   0.027   0.001   TYR B 755 
 PHE   0.019   0.001   PHE A 829 
 TRP   0.017   0.001   TRP B 461 
 HIS   0.004   0.001   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11416)
  covalent geometry    : angle       0.53537 (15538)
  hydrogen bonds       : bond        0.02997 (  697)
  hydrogen bonds       : angle       3.45017 ( 2070)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1701.75 seconds
wall clock time: 30 minutes 19.58 seconds (1819.58 seconds total)