Starting phenix.real_space_refine
on Tue Mar  3 17:52:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lly_0915/03_2026/6lly_0915.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lly_0915/03_2026/6lly_0915.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lly_0915/03_2026/6lly_0915.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lly_0915/03_2026/6lly_0915.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lly_0915/03_2026/6lly_0915.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lly_0915/03_2026/6lly_0915.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      58      5.16       5
     Be      1      3.05       5
     C    4958      2.51       5
     N    1299      2.21       5
     O    1454      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 7774
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1006, 7769
          Classifications: {'peptide': 1006}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 960}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" F1  BEF A2001 " occ=0.00
      ... (2 atoms not shown)
      pdb="BE   BEF A2001 " occ=0.00
  Time building chain proxies: 1.80, per 1000 atoms: 0.23
  Number of scatterers: 7774
  At special positions: 0
  Unit cell: (88.395, 97.11, 145.665, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      58     16.00
     Mg      1     11.99
     F       3      9.00
     O    1454      8.00
     N    1299      7.00
     C    4958      6.00
     Be      1      4.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 317.7 milliseconds
  

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      55.7% alpha, 15.0% 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 3 through 7
    Processing helix  chain 'A' and resid 8 through 16
      removed outlier: 3.604A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.518A  pdb=" N   ARG A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
      removed outlier: 3.720A  pdb=" N   ILE A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 78
    Processing helix  chain 'A' and resid 85 through 87
      No H-bonds generated for 'chain 'A' and resid 85 through 87'
    Processing helix  chain 'A' and resid 88 through 117
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 226 through 229
    Processing helix  chain 'A' and resid 230 through 242
    Processing helix  chain 'A' and resid 247 through 275
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 4.103A  pdb=" N   ILE A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 329
      removed outlier: 3.663A  pdb=" N   LYS A 329 " --> pdb=" O   ARG A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 345
      removed outlier: 3.898A  pdb=" N   THR A 341 " --> pdb=" O   SER A 338 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   LEU A 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR A 345 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 406
      removed outlier: 4.058A  pdb=" N   GLN A 406 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 403 through 406'
    Processing helix  chain 'A' and resid 407 through 421
      removed outlier: 3.974A  pdb=" N   ASN A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
      removed outlier: 3.687A  pdb=" N   LEU A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 3.619A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 478
    Processing helix  chain 'A' and resid 516 through 523
      removed outlier: 3.928A  pdb=" N   ARG A 523 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.530A  pdb=" N   GLY A 554 " --> pdb=" O   GLU A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 575
    Processing helix  chain 'A' and resid 579 through 587
      removed outlier: 3.758A  pdb=" N   PHE A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLU A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.693A  pdb=" N   LYS A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.767A  pdb=" N   ASP A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.947A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 730
      removed outlier: 3.500A  pdb=" N   ALA A 729 " --> pdb=" O   VAL A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 4.009A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 797
      removed outlier: 3.698A  pdb=" N   TRP A 793 " --> pdb=" O   VAL A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 806
    Processing helix  chain 'A' and resid 807 through 809
      No H-bonds generated for 'chain 'A' and resid 807 through 809'
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.503A  pdb=" N   ILE A 839 " --> pdb=" O   ARG A 835 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 871
    Processing helix  chain 'A' and resid 872 through 875
      removed outlier: 4.042A  pdb=" N   CYS A 875 " --> pdb=" O   PHE A 872 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 872 through 875'
    Processing helix  chain 'A' and resid 887 through 892
    Processing helix  chain 'A' and resid 893 through 913
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 949
      removed outlier: 3.543A  pdb=" N   LEU A 947 " --> pdb=" O   HIS A 943 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 948 " --> pdb=" O   PHE A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 956
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.881A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1031
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141
      removed outlier: 4.531A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189
      removed outlier: 4.630A  pdb=" N   LEU A 173 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.195A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.463A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   PHE A 652 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 401
      removed outlier: 6.553A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.261A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.857A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.699A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   SER A 493 " --> pdb=" O   GLU A 486 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   GLU A 486 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   SER A 495 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   THR A 484 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   TYR A 497 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 401
      removed outlier: 6.553A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.950A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 9.261A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.857A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.699A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 525 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   ILE A 527 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 9.217A  pdb=" N   GLY A 594 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
      removed outlier: 11.271A  pdb=" N   VAL A 529 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 17.355A  pdb=" N   VAL A 596 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 428

    434 hydrogen bonds defined for protein.
    1233 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: 1.26

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2534
        1.34 -     1.46: 1323
        1.46 -     1.57: 3971
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 7918
  Sorted by residual:
  bond pdb=" F2  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.559 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" F3  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.544 -0.068 2.00e-02 2.50e+03 1.17e+01
  bond pdb=" F1  BEF A2001 "
       pdb="BE   BEF A2001 "
    ideal  model  delta    sigma   weight residual
    1.476  1.532 -0.056 2.00e-02 2.50e+03 7.95e+00
  bond pdb=" CA  ASP A 556 "
       pdb=" CB  ASP A 556 "
    ideal  model  delta    sigma   weight residual
    1.522  1.538 -0.016 1.32e-02 5.74e+03 1.45e+00
  bond pdb=" CA  LYS A 400 "
       pdb=" CB  LYS A 400 "
    ideal  model  delta    sigma   weight residual
    1.534  1.550 -0.016 1.57e-02 4.06e+03 1.06e+00
  ... (remaining 7913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 10679
        2.63 -     5.27: 61
        5.27 -     7.90: 3
        7.90 -    10.54: 0
       10.54 -    13.17: 2
  Bond angle restraints: 10745
  Sorted by residual:
  angle pdb=" F2  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     119.96  106.79   13.17 3.00e+00 1.11e-01 1.93e+01
  angle pdb=" F1  BEF A2001 "
        pdb="BE   BEF A2001 "
        pdb=" F3  BEF A2001 "
      ideal   model   delta    sigma   weight residual
     120.12  109.35   10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" C   PHE A1040 "
        pdb=" N   TRP A1041 "
        pdb=" CA  TRP A1041 "
      ideal   model   delta    sigma   weight residual
     120.82  126.14   -5.32 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" N   LYS A 876 "
        pdb=" CA  LYS A 876 "
        pdb=" C   LYS A 876 "
      ideal   model   delta    sigma   weight residual
     113.20  109.26    3.94 1.21e+00 6.83e-01 1.06e+01
  angle pdb=" N   ASP A 881 "
        pdb=" CA  ASP A 881 "
        pdb=" C   ASP A 881 "
      ideal   model   delta    sigma   weight residual
     114.09  109.45    4.64 1.55e+00 4.16e-01 8.95e+00
  ... (remaining 10740 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 4463
       17.70 -    35.40: 274
       35.40 -    53.10: 44
       53.10 -    70.79: 6
       70.79 -    88.49: 6
  Dihedral angle restraints: 4793
    sinusoidal: 1886
      harmonic: 2907
  Sorted by residual:
  dihedral pdb=" CB  GLU A 113 "
           pdb=" CG  GLU A 113 "
           pdb=" CD  GLU A 113 "
           pdb=" OE1 GLU A 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.49  -88.49     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  LYS A 876 "
           pdb=" C   LYS A 876 "
           pdb=" N   GLU A 877 "
           pdb=" CA  GLU A 877 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.30   15.70     0      5.00e+00 4.00e-02 9.86e+00
  dihedral pdb=" CA  ALA A 216 "
           pdb=" C   ALA A 216 "
           pdb=" N   GLY A 217 "
           pdb=" CA  GLY A 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.83  -15.17     0      5.00e+00 4.00e-02 9.21e+00
  ... (remaining 4790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 721
       0.027 -    0.054: 336
       0.054 -    0.081: 121
       0.081 -    0.107: 62
       0.107 -    0.134: 24
  Chirality restraints: 1264
  Sorted by residual:
  chirality pdb=" CA  VAL A 283 "
            pdb=" N   VAL A 283 "
            pdb=" C   VAL A 283 "
            pdb=" CB  VAL A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" CA  ILE A 392 "
            pdb=" N   ILE A 392 "
            pdb=" C   ILE A 392 "
            pdb=" CB  ILE A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  VAL A 534 "
            pdb=" N   VAL A 534 "
            pdb=" C   VAL A 534 "
            pdb=" CB  VAL A 534 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1261 not shown)

  Planarity restraints: 1366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 952 "    0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO A 953 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 953 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 953 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 975 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 801 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO A 802 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 802 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 802 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1363 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 71
        2.61 -     3.19: 6860
        3.19 -     3.76: 11913
        3.76 -     4.33: 17604
        4.33 -     4.90: 28227
  Nonbonded interactions: 64675
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.043 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.075 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" OD2 ASP A 351 "
            pdb=" F1  BEF A2001 "
     model   vdw
     2.129 2.990
  nonbonded pdb=" O   VAL A 969 "
            pdb=" OG  SER A 973 "
     model   vdw
     2.226 3.040
  ... (remaining 64670 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.330
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.320
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
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      :  0.010   0.887   7919  Z= 1.009
  Angle     :  0.603  13.174  10745  Z= 0.355
  Chirality :  0.040   0.134   1264
  Planarity :  0.004   0.043   1366
  Dihedral  : 12.235  88.493   2907
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.38 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.03 (0.21), residues: 998
  helix: -3.45 (0.15), residues: 481
  sheet: -1.54 (0.50), residues: 106
  loop : -1.70 (0.26), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 821 
 TYR   0.015   0.001   TYR A 836 
 PHE   0.016   0.001   PHE A 759 
 TRP   0.011   0.001   TRP A1041 
 HIS   0.003   0.001   HIS A 682 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7918)
  covalent geometry    : angle       0.60256 (10745)
  hydrogen bonds       : bond        0.27751 (  420)
  hydrogen bonds       : angle       9.03703 ( 1233)
  Misc. bond           : bond        0.88732 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.7725 (t60) cc_final: 0.7489 (t60)
REVERT: A  126 MET cc_start: 0.7771 (mmt) cc_final: 0.7310 (mmt)
REVERT: A  133 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6459 (m-30)
REVERT: A  176 ASP cc_start: 0.7391 (t70) cc_final: 0.7011 (t70)
REVERT: A  207 MET cc_start: 0.8345 (mmt) cc_final: 0.8102 (tpp)
REVERT: A  441 THR cc_start: 0.8745 (p) cc_final: 0.8495 (p)
REVERT: A  467 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.6989 (mmm160)
REVERT: A  550 GLU cc_start: 0.7149 (tt0) cc_final: 0.6929 (mt-10)
REVERT: A  575 MET cc_start: 0.3524 (mmt) cc_final: 0.2153 (mmt)
REVERT: A  600 ASP cc_start: 0.8156 (t0) cc_final: 0.7481 (t70)
REVERT: A  756 MET cc_start: 0.8282 (ttm) cc_final: 0.8008 (ttm)
REVERT: A  968 MET cc_start: 0.8232 (tpp) cc_final: 0.7889 (tpp)
REVERT: A  978 LEU cc_start: 0.8441 (tp) cc_final: 0.8178 (tm)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.6158
  time to fit residues: 98.4174
Evaluate side-chains
  111 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 177 GLN
A 275 ASN
A 278 HIS
A 469 ASN
A 477 GLN
A 615 GLN
A 661 ASN
A 671 ASN
A 682 HIS
A 767 ASN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 822 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.184527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.143847 restraints weight = 7741.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.59
r_work: 0.3348 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7919  Z= 0.158
  Angle     :  0.590   6.526  10745  Z= 0.315
  Chirality :  0.043   0.155   1264
  Planarity :  0.005   0.048   1366
  Dihedral  :  4.541  21.601   1065
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.36 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.25), residues: 998
  helix: -0.61 (0.22), residues: 486
  sheet: -0.57 (0.54), residues: 100
  loop : -1.17 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 139 
 TYR   0.017   0.002   TYR A 867 
 PHE   0.028   0.001   PHE A 759 
 TRP   0.007   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 682 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7918)
  covalent geometry    : angle       0.58995 (10745)
  hydrogen bonds       : bond        0.06000 (  420)
  hydrogen bonds       : angle       4.67183 ( 1233)
  Misc. bond           : bond        0.00167 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   26 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6978 (mm)
REVERT: A   58 GLU cc_start: 0.7453 (tt0) cc_final: 0.6645 (tp30)
REVERT: A  107 TRP cc_start: 0.8248 (t60) cc_final: 0.7973 (t60)
REVERT: A  120 LYS cc_start: 0.7428 (mptm) cc_final: 0.7048 (mptm)
REVERT: A  126 MET cc_start: 0.8338 (mmt) cc_final: 0.7846 (mmt)
REVERT: A  134 ARG cc_start: 0.7232 (ptp-110) cc_final: 0.6900 (pmm-80)
REVERT: A  141 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8449 (mtmp)
REVERT: A  207 MET cc_start: 0.8589 (mmt) cc_final: 0.8301 (tpp)
REVERT: A  245 GLU cc_start: 0.6854 (pt0) cc_final: 0.6578 (pt0)
REVERT: A  412 GLU cc_start: 0.8011 (tt0) cc_final: 0.7770 (tt0)
REVERT: A  441 THR cc_start: 0.8568 (p) cc_final: 0.8022 (p)
REVERT: A  494 MET cc_start: 0.7444 (ttt) cc_final: 0.6943 (tmt)
REVERT: A  536 MET cc_start: 0.6633 (ttp) cc_final: 0.6236 (ttp)
REVERT: A  575 MET cc_start: 0.3135 (mmt) cc_final: 0.2064 (mmt)
REVERT: A  836 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.5970 (p90)
REVERT: A  942 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7595 (mt)
REVERT: A  968 MET cc_start: 0.8304 (tpp) cc_final: 0.8060 (tpp)
REVERT: A  978 LEU cc_start: 0.8359 (tp) cc_final: 0.7995 (tm)
REVERT: A  979 MET cc_start: 0.8443 (ttt) cc_final: 0.8223 (ttt)
  outliers start: 22
  outliers final: 8
  residues processed: 135
  average time/residue: 0.5379
  time to fit residues: 77.0044
Evaluate side-chains
  123 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    0.0570
   chunk 9 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.1500

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 469 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.184794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.144057 restraints weight = 7688.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 1.59
r_work: 0.3376 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7919  Z= 0.146
  Angle     :  0.559   6.243  10745  Z= 0.294
  Chirality :  0.042   0.163   1264
  Planarity :  0.004   0.046   1366
  Dihedral  :  4.413  15.893   1063
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.92 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.26), residues: 998
  helix:  0.58 (0.23), residues: 486
  sheet: -0.94 (0.53), residues: 97
  loop : -0.85 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.010   0.002   TYR A 130 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.008   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7918)
  covalent geometry    : angle       0.55910 (10745)
  hydrogen bonds       : bond        0.05162 (  420)
  hydrogen bonds       : angle       4.36271 ( 1233)
  Misc. bond           : bond        0.00135 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8356 (pt0)
REVERT: A   58 GLU cc_start: 0.7370 (tt0) cc_final: 0.6620 (tp30)
REVERT: A  107 TRP cc_start: 0.8198 (t60) cc_final: 0.7978 (t60)
REVERT: A  120 LYS cc_start: 0.7412 (mptm) cc_final: 0.7138 (mptm)
REVERT: A  126 MET cc_start: 0.8395 (mmt) cc_final: 0.7913 (mmt)
REVERT: A  134 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7067 (pmm-80)
REVERT: A  141 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8428 (mtmp)
REVERT: A  207 MET cc_start: 0.8573 (mmt) cc_final: 0.8280 (tpp)
REVERT: A  220 MET cc_start: 0.8535 (mtp) cc_final: 0.8217 (mtt)
REVERT: A  412 GLU cc_start: 0.8055 (tt0) cc_final: 0.7566 (tt0)
REVERT: A  466 GLU cc_start: 0.7403 (tp30) cc_final: 0.7193 (tp30)
REVERT: A  494 MET cc_start: 0.7579 (ttt) cc_final: 0.6986 (tmt)
REVERT: A  536 MET cc_start: 0.6702 (ttp) cc_final: 0.6443 (ttp)
REVERT: A  575 MET cc_start: 0.3148 (mmt) cc_final: 0.2109 (mmt)
REVERT: A  836 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.5963 (p90)
REVERT: A  896 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8244 (tpp)
REVERT: A  968 MET cc_start: 0.8282 (tpp) cc_final: 0.8015 (tpp)
REVERT: A  978 LEU cc_start: 0.8191 (tp) cc_final: 0.7809 (tm)
  outliers start: 27
  outliers final: 10
  residues processed: 127
  average time/residue: 0.5299
  time to fit residues: 71.3335
Evaluate side-chains
  125 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  134 ARG
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 469 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.185939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.145398 restraints weight = 7823.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.64
r_work: 0.3453 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7919  Z= 0.125
  Angle     :  0.529   6.047  10745  Z= 0.278
  Chirality :  0.041   0.163   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  4.265  16.284   1063
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.09 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.27), residues: 998
  helix:  1.14 (0.24), residues: 487
  sheet: -0.57 (0.54), residues: 93
  loop : -0.73 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 164 
 TYR   0.020   0.002   TYR A 867 
 PHE   0.028   0.001   PHE A 759 
 TRP   0.008   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7918)
  covalent geometry    : angle       0.52914 (10745)
  hydrogen bonds       : bond        0.04650 (  420)
  hydrogen bonds       : angle       4.15408 ( 1233)
  Misc. bond           : bond        0.00094 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8319 (pt0)
REVERT: A  120 LYS cc_start: 0.7404 (mptm) cc_final: 0.7165 (mptm)
REVERT: A  126 MET cc_start: 0.8396 (mmt) cc_final: 0.7923 (mmt)
REVERT: A  134 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6964 (pmm-80)
REVERT: A  141 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8470 (mtmp)
REVERT: A  207 MET cc_start: 0.8538 (mmt) cc_final: 0.8212 (tpp)
REVERT: A  220 MET cc_start: 0.8560 (mtp) cc_final: 0.8279 (mtt)
REVERT: A  412 GLU cc_start: 0.8012 (tt0) cc_final: 0.7478 (tt0)
REVERT: A  439 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6535 (tm-30)
REVERT: A  466 GLU cc_start: 0.7551 (tp30) cc_final: 0.7345 (tp30)
REVERT: A  494 MET cc_start: 0.7599 (ttt) cc_final: 0.7050 (tmt)
REVERT: A  536 MET cc_start: 0.6425 (ttp) cc_final: 0.6165 (ttp)
REVERT: A  575 MET cc_start: 0.3129 (mmt) cc_final: 0.2173 (mmt)
REVERT: A  599 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8269 (pt)
REVERT: A  836 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.5899 (p90)
REVERT: A  896 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8287 (tpp)
REVERT: A  968 MET cc_start: 0.8274 (tpp) cc_final: 0.7976 (tpp)
REVERT: A  978 LEU cc_start: 0.8228 (tp) cc_final: 0.7819 (tm)
  outliers start: 28
  outliers final: 11
  residues processed: 126
  average time/residue: 0.5458
  time to fit residues: 72.7999
Evaluate side-chains
  130 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  134 ARG
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  439 GLU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 44 optimal weight:    0.3980
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.189017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.149072 restraints weight = 7849.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 1.64
r_work: 0.3442 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7919  Z= 0.119
  Angle     :  0.527   5.909  10745  Z= 0.275
  Chirality :  0.041   0.163   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  4.183  16.357   1063
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 14.20 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.27), residues: 998
  helix:  1.46 (0.24), residues: 486
  sheet: -0.53 (0.54), residues: 93
  loop : -0.62 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 761 
 TYR   0.010   0.001   TYR A 836 
 PHE   0.028   0.001   PHE A 759 
 TRP   0.008   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7918)
  covalent geometry    : angle       0.52657 (10745)
  hydrogen bonds       : bond        0.04407 (  420)
  hydrogen bonds       : angle       4.06379 ( 1233)
  Misc. bond           : bond        0.00077 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.7269 (mptm) cc_final: 0.7018 (mptm)
REVERT: A  126 MET cc_start: 0.8433 (mmt) cc_final: 0.7974 (mmt)
REVERT: A  134 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6948 (pmm-80)
REVERT: A  141 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8564 (mtmp)
REVERT: A  207 MET cc_start: 0.8539 (mmt) cc_final: 0.8232 (tpp)
REVERT: A  220 MET cc_start: 0.8539 (mtp) cc_final: 0.8276 (mtt)
REVERT: A  328 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7633 (ttmm)
REVERT: A  412 GLU cc_start: 0.7973 (tt0) cc_final: 0.7693 (tt0)
REVERT: A  466 GLU cc_start: 0.7528 (tp30) cc_final: 0.7264 (tp30)
REVERT: A  494 MET cc_start: 0.7734 (ttt) cc_final: 0.7142 (tmt)
REVERT: A  575 MET cc_start: 0.3135 (mmt) cc_final: 0.2205 (mmt)
REVERT: A  599 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8289 (pt)
REVERT: A  775 PHE cc_start: 0.7270 (t80) cc_final: 0.7050 (t80)
REVERT: A  836 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.5902 (p90)
REVERT: A  896 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8311 (tpp)
REVERT: A  968 MET cc_start: 0.8305 (tpp) cc_final: 0.7989 (tpp)
REVERT: A  978 LEU cc_start: 0.8242 (tp) cc_final: 0.7878 (tm)
  outliers start: 32
  outliers final: 18
  residues processed: 132
  average time/residue: 0.5246
  time to fit residues: 73.4589
Evaluate side-chains
  134 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  134 ARG
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0020
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 477 GLN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.186402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.145833 restraints weight = 7808.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 1.62
r_work: 0.3407 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7919  Z= 0.143
  Angle     :  0.553   6.008  10745  Z= 0.287
  Chirality :  0.043   0.169   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  4.294  17.033   1063
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 14.09 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.27), residues: 998
  helix:  1.48 (0.24), residues: 484
  sheet: -0.44 (0.54), residues: 93
  loop : -0.58 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 290 
 TYR   0.015   0.002   TYR A 990 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.007   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7918)
  covalent geometry    : angle       0.55264 (10745)
  hydrogen bonds       : bond        0.04729 (  420)
  hydrogen bonds       : angle       4.09632 ( 1233)
  Misc. bond           : bond        0.00128 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 115
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   58 GLU cc_start: 0.7705 (tt0) cc_final: 0.6836 (tp30)
REVERT: A   97 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7990 (mp)
REVERT: A  120 LYS cc_start: 0.7299 (mptm) cc_final: 0.7040 (mptm)
REVERT: A  126 MET cc_start: 0.8473 (mmt) cc_final: 0.8019 (mmt)
REVERT: A  134 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6975 (pmm-80)
REVERT: A  141 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8488 (mtmp)
REVERT: A  207 MET cc_start: 0.8597 (mmt) cc_final: 0.8276 (tpp)
REVERT: A  290 ARG cc_start: 0.5931 (tpt-90) cc_final: 0.5565 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7696 (ttmm)
REVERT: A  466 GLU cc_start: 0.7606 (tp30) cc_final: 0.7381 (tp30)
REVERT: A  575 MET cc_start: 0.3111 (mmt) cc_final: 0.2257 (mmt)
REVERT: A  599 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8325 (pt)
REVERT: A  836 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6001 (p90)
REVERT: A  896 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8350 (tpp)
REVERT: A  968 MET cc_start: 0.8329 (tpp) cc_final: 0.8052 (tpp)
REVERT: A  978 LEU cc_start: 0.8324 (tp) cc_final: 0.7970 (tm)
  outliers start: 37
  outliers final: 16
  residues processed: 131
  average time/residue: 0.5586
  time to fit residues: 77.5616
Evaluate side-chains
  134 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  134 ARG
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 790 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 = 0.4049 r_free = 0.4049 target = 0.188556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.148868 restraints weight = 7821.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.61
r_work: 0.3416 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7919  Z= 0.122
  Angle     :  0.528   5.828  10745  Z= 0.274
  Chirality :  0.041   0.163   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  4.171  16.901   1063
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.37 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.27), residues: 998
  helix:  1.58 (0.24), residues: 493
  sheet: -0.41 (0.54), residues: 93
  loop : -0.53 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.011   0.001   TYR A 836 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.008   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7918)
  covalent geometry    : angle       0.52832 (10745)
  hydrogen bonds       : bond        0.04357 (  420)
  hydrogen bonds       : angle       3.99892 ( 1233)
  Misc. bond           : bond        0.00082 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  120 LYS cc_start: 0.7222 (mptm) cc_final: 0.6992 (mptm)
REVERT: A  126 MET cc_start: 0.8415 (mmt) cc_final: 0.7947 (mmt)
REVERT: A  134 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (pmm-80)
REVERT: A  141 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (mtmp)
REVERT: A  179 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7747 (pp)
REVERT: A  207 MET cc_start: 0.8549 (mmt) cc_final: 0.8223 (tpp)
REVERT: A  220 MET cc_start: 0.8422 (mtp) cc_final: 0.8097 (mtt)
REVERT: A  290 ARG cc_start: 0.5746 (tpt-90) cc_final: 0.5349 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7593 (ttmm)
REVERT: A  466 GLU cc_start: 0.7536 (tp30) cc_final: 0.7254 (tp30)
REVERT: A  575 MET cc_start: 0.3182 (mmt) cc_final: 0.2382 (mmt)
REVERT: A  836 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.5850 (p90)
REVERT: A  896 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8310 (tpp)
REVERT: A  930 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8038 (mm)
REVERT: A  968 MET cc_start: 0.8277 (tpp) cc_final: 0.7956 (tpp)
  outliers start: 32
  outliers final: 16
  residues processed: 133
  average time/residue: 0.5147
  time to fit residues: 72.6904
Evaluate side-chains
  137 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  134 ARG
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  896 MET
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.0980
   chunk 61 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0370
   chunk 26 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0570
   chunk 85 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 17 optimal weight:    0.0970
   overall best weight:    0.1974

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 790 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 = 0.4083 r_free = 0.4083 target = 0.192669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.152879 restraints weight = 7851.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.66
r_work: 0.3509 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7919  Z= 0.097
  Angle     :  0.492   5.664  10745  Z= 0.255
  Chirality :  0.040   0.145   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  3.855  15.347   1063
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.95 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.28), residues: 998
  helix:  1.78 (0.24), residues: 501
  sheet: -0.11 (0.54), residues: 91
  loop : -0.33 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.017   0.001   TYR A 990 
 PHE   0.028   0.001   PHE A 759 
 TRP   0.011   0.001   TRP A 854 
 HIS   0.001   0.000   HIS A 682 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 7918)
  covalent geometry    : angle       0.49223 (10745)
  hydrogen bonds       : bond        0.03582 (  420)
  hydrogen bonds       : angle       3.81088 ( 1233)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  110 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7079 (mmt180)
REVERT: A  113 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6798 (mp0)
REVERT: A  120 LYS cc_start: 0.7379 (mptm) cc_final: 0.7174 (mptm)
REVERT: A  126 MET cc_start: 0.8352 (mmt) cc_final: 0.7867 (mmt)
REVERT: A  128 LYS cc_start: 0.8393 (mttt) cc_final: 0.8124 (mttp)
REVERT: A  141 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8625 (mtmp)
REVERT: A  207 MET cc_start: 0.8521 (mmt) cc_final: 0.8316 (tpp)
REVERT: A  220 MET cc_start: 0.8334 (mtp) cc_final: 0.8044 (mtt)
REVERT: A  290 ARG cc_start: 0.5586 (tpt-90) cc_final: 0.5067 (ttt-90)
REVERT: A  466 GLU cc_start: 0.7622 (tp30) cc_final: 0.7408 (tp30)
REVERT: A  479 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6607 (tpp)
REVERT: A  494 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7265 (tmt)
REVERT: A  575 MET cc_start: 0.3179 (mmt) cc_final: 0.2575 (mmt)
REVERT: A  599 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8041 (pt)
REVERT: A  836 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6128 (p90)
REVERT: A  913 ASN cc_start: 0.6860 (p0) cc_final: 0.6658 (t0)
REVERT: A  924 MET cc_start: 0.8128 (ttp) cc_final: 0.7852 (ttp)
  outliers start: 26
  outliers final: 10
  residues processed: 136
  average time/residue: 0.4750
  time to fit residues: 69.1360
Evaluate side-chains
  130 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  916 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0020
   chunk 26 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 177 GLN
A 477 GLN
A 643 GLN
A 671 ASN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.190123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.150233 restraints weight = 7808.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.61
r_work: 0.3445 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7919  Z= 0.116
  Angle     :  0.526   6.655  10745  Z= 0.270
  Chirality :  0.041   0.163   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  3.985  17.005   1063
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.88 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.27), residues: 998
  helix:  1.90 (0.24), residues: 491
  sheet: -0.24 (0.53), residues: 95
  loop : -0.44 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.009   0.001   TYR A 836 
 PHE   0.026   0.001   PHE A 759 
 TRP   0.011   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7918)
  covalent geometry    : angle       0.52587 (10745)
  hydrogen bonds       : bond        0.04047 (  420)
  hydrogen bonds       : angle       3.87024 ( 1233)
  Misc. bond           : bond        0.00080 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   97 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mp)
REVERT: A  120 LYS cc_start: 0.7098 (mptm) cc_final: 0.6877 (mptm)
REVERT: A  126 MET cc_start: 0.8183 (mmt) cc_final: 0.7709 (mmt)
REVERT: A  141 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8538 (mtmp)
REVERT: A  207 MET cc_start: 0.8534 (mmt) cc_final: 0.8319 (tpp)
REVERT: A  220 MET cc_start: 0.8347 (mtp) cc_final: 0.8043 (mtt)
REVERT: A  245 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.4763 (pt0)
REVERT: A  290 ARG cc_start: 0.5596 (tpt-90) cc_final: 0.5327 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7519 (ttmm)
REVERT: A  412 GLU cc_start: 0.7958 (tt0) cc_final: 0.7641 (tt0)
REVERT: A  494 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7206 (ppp)
REVERT: A  575 MET cc_start: 0.3353 (mmt) cc_final: 0.2558 (mmt)
REVERT: A  599 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7984 (pt)
REVERT: A  775 PHE cc_start: 0.6511 (t80) cc_final: 0.6284 (t80)
REVERT: A  836 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.5835 (p90)
REVERT: A  924 MET cc_start: 0.8222 (ttp) cc_final: 0.7933 (ttp)
  outliers start: 26
  outliers final: 13
  residues processed: 130
  average time/residue: 0.5287
  time to fit residues: 73.1775
Evaluate side-chains
  137 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0670
   chunk 79 optimal weight:    0.0980
   chunk 24 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 790 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 = 0.4070 r_free = 0.4070 target = 0.191189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.151315 restraints weight = 7802.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.63
r_work: 0.3478 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7919  Z= 0.108
  Angle     :  0.518   6.063  10745  Z= 0.267
  Chirality :  0.041   0.162   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  3.939  16.488   1063
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.81 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.27), residues: 998
  helix:  2.00 (0.24), residues: 489
  sheet: -0.17 (0.53), residues: 95
  loop : -0.39 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.017   0.001   TYR A 990 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.010   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7918)
  covalent geometry    : angle       0.51763 (10745)
  hydrogen bonds       : bond        0.03895 (  420)
  hydrogen bonds       : angle       3.85166 ( 1233)
  Misc. bond           : bond        0.00048 (    1)

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  126 MET cc_start: 0.8167 (mmt) cc_final: 0.7741 (mmt)
REVERT: A  141 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8594 (mtmp)
REVERT: A  207 MET cc_start: 0.8554 (mmt) cc_final: 0.8348 (tpp)
REVERT: A  220 MET cc_start: 0.8353 (mtp) cc_final: 0.8059 (mtt)
REVERT: A  245 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.4822 (pt0)
REVERT: A  290 ARG cc_start: 0.5557 (tpt-90) cc_final: 0.5294 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7548 (ttmm)
REVERT: A  494 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7150 (tmt)
REVERT: A  575 MET cc_start: 0.3274 (mmt) cc_final: 0.2624 (mmt)
REVERT: A  599 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8332 (pt)
REVERT: A  775 PHE cc_start: 0.6483 (t80) cc_final: 0.6269 (t80)
REVERT: A  836 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.5902 (p90)
REVERT: A  913 ASN cc_start: 0.7209 (p0) cc_final: 0.6623 (t0)
REVERT: A  924 MET cc_start: 0.8166 (ttp) cc_final: 0.7886 (ttp)
  outliers start: 18
  outliers final: 12
  residues processed: 130
  average time/residue: 0.5305
  time to fit residues: 73.4164
Evaluate side-chains
  133 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  864 VAL
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0000
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 790 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 = 0.4054 r_free = 0.4054 target = 0.189659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.149078 restraints weight = 7787.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 1.65
r_work: 0.3439 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7919  Z= 0.117
  Angle     :  0.532   5.948  10745  Z= 0.275
  Chirality :  0.041   0.162   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  3.984  16.869   1063
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.16 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.27), residues: 998
  helix:  1.94 (0.24), residues: 491
  sheet: -0.13 (0.53), residues: 95
  loop : -0.42 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.018   0.001   TYR A 294 
 PHE   0.027   0.001   PHE A 759 
 TRP   0.010   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7918)
  covalent geometry    : angle       0.53189 (10745)
  hydrogen bonds       : bond        0.04066 (  420)
  hydrogen bonds       : angle       3.86440 ( 1233)
  Misc. bond           : bond        0.00068 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3136.14 seconds
wall clock time: 54 minutes 1.01 seconds (3241.01 seconds total)