Starting phenix.real_space_refine
on Wed Feb 12 10:32:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lly_0915/02_2025/6lly_0915.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lly_0915/02_2025/6lly_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lly_0915/02_2025/6lly_0915.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lly_0915/02_2025/6lly_0915.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lly_0915/02_2025/6lly_0915.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lly_0915/02_2025/6lly_0915.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.28, per 1000 atoms: 0.55
  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: 1.97
  Conformation dependent library (CDL) restraints added in 778.1 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: 1.11
  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: 2.79

  Time building geometry restraints manager: 2.27 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:             0.280
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:11.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.820
-------------------------------------------------------------------------------
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      :  0.003   0.083   7918  Z= 0.216
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.011   0.001   TRP A1041 
 HIS   0.003   0.001   HIS A 682 
 PHE   0.016   0.001   PHE A 759 
 TYR   0.015   0.001   TYR A 836 
 ARG   0.003   0.000   ARG A 821 

*********************** 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  : 0.870 
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: 0.6817 (OUTLIER) cc_final: 0.6459 (m-30)
REVERT: A  176 ASP cc_start: 0.7391 (t70) cc_final: 0.7010 (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: 0.8494 (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: 1.3915
  time to fit residues: 222.7284
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  : 0.906 
-------------------------------------------------------------------------------
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 84 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0270
   chunk 90 optimal weight:    6.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 472 ASN
A 477 GLN
A 615 GLN
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 = 0.4037 r_free = 0.4037 target = 0.187717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.147205 restraints weight = 7655.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 1.60
r_work: 0.3447 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7918  Z= 0.174
  Angle     :  0.555   6.330  10745  Z= 0.297
  Chirality :  0.042   0.148   1264
  Planarity :  0.005   0.049   1366
  Dihedral  :  4.373  22.597   1065
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 10.48 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.25), residues: 998
  helix: -0.44 (0.22), residues: 485
  sheet: -0.96 (0.54), residues: 94
  loop : -1.19 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 854 
 HIS   0.002   0.001   HIS A 682 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.018   0.002   TYR A 867 
 ARG   0.006   0.000   ARG A 139 

*********************** 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
  139 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7089 (mp0) cc_final: 0.6861 (mp0)
REVERT: A   41 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7686 (mm)
REVERT: A   58 GLU cc_start: 0.7360 (tt0) cc_final: 0.6538 (tp30)
REVERT: A  107 TRP cc_start: 0.8239 (t60) cc_final: 0.7940 (t60)
REVERT: A  120 LYS cc_start: 0.7343 (mptm) cc_final: 0.6958 (mptm)
REVERT: A  126 MET cc_start: 0.8367 (mmt) cc_final: 0.7755 (mmt)
REVERT: A  134 ARG cc_start: 0.7083 (ptp-110) cc_final: 0.6770 (pmm-80)
REVERT: A  207 MET cc_start: 0.8542 (mmt) cc_final: 0.8240 (tpp)
REVERT: A  412 GLU cc_start: 0.7988 (tt0) cc_final: 0.7744 (tt0)
REVERT: A  479 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6449 (tpp)
REVERT: A  536 MET cc_start: 0.6871 (ttp) cc_final: 0.6472 (ttp)
REVERT: A  575 MET cc_start: 0.3083 (mmt) cc_final: 0.2009 (mmt)
REVERT: A  836 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5928 (p90)
REVERT: A  968 MET cc_start: 0.8270 (tpp) cc_final: 0.7994 (tpp)
REVERT: A  978 LEU cc_start: 0.8246 (tp) cc_final: 0.7856 (tm)
  outliers start: 17
  outliers final: 5
  residues processed: 130
  average time/residue: 1.2375
  time to fit residues: 170.5908
Evaluate side-chains
  114 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LEU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  836 TYR
Chi-restraints excluded: chain A residue  930 ILE
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 66 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.186314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145816 restraints weight = 7821.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.61
r_work: 0.3463 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7918  Z= 0.186
  Angle     :  0.534   6.204  10745  Z= 0.281
  Chirality :  0.041   0.160   1264
  Planarity :  0.004   0.046   1366
  Dihedral  :  4.261  15.775   1063
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 11.76 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.26), residues: 998
  helix:  0.74 (0.23), residues: 486
  sheet: -0.66 (0.53), residues: 93
  loop : -0.88 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 526 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 130 
 ARG   0.004   0.000   ARG A 139 

*********************** 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
  141 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7061 (mp0) cc_final: 0.6835 (mp0)
REVERT: A   40 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8311 (pt0)
REVERT: A   58 GLU cc_start: 0.7278 (tt0) cc_final: 0.6561 (tp30)
REVERT: A  107 TRP cc_start: 0.8230 (t60) cc_final: 0.7980 (t60)
REVERT: A  120 LYS cc_start: 0.7418 (mptm) cc_final: 0.7088 (mptm)
REVERT: A  126 MET cc_start: 0.8207 (mmt) cc_final: 0.7720 (mmt)
REVERT: A  134 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6992 (pmm-80)
REVERT: A  207 MET cc_start: 0.8505 (mmt) cc_final: 0.8210 (tpp)
REVERT: A  220 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8246 (mtt)
REVERT: A  245 GLU cc_start: 0.6797 (pt0) cc_final: 0.6440 (pm20)
REVERT: A  412 GLU cc_start: 0.8021 (tt0) cc_final: 0.7413 (tt0)
REVERT: A  439 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6637 (tm-30)
REVERT: A  466 GLU cc_start: 0.7374 (tp30) cc_final: 0.7171 (tp30)
REVERT: A  479 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6506 (tpp)
REVERT: A  536 MET cc_start: 0.6811 (ttp) cc_final: 0.6486 (ttp)
REVERT: A  575 MET cc_start: 0.3089 (mmt) cc_final: 0.2048 (mmt)
REVERT: A  756 MET cc_start: 0.8470 (ttm) cc_final: 0.7959 (ttp)
REVERT: A  836 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6006 (p90)
REVERT: A  896 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8317 (tpp)
REVERT: A  968 MET cc_start: 0.8284 (tpp) cc_final: 0.8005 (tpp)
REVERT: A  978 LEU cc_start: 0.8267 (tp) cc_final: 0.7906 (tm)
  outliers start: 29
  outliers final: 9
  residues processed: 123
  average time/residue: 1.2955
  time to fit residues: 168.4167
Evaluate side-chains
  118 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  220 MET
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  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
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 87 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 98 optimal weight:    0.4980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 661 ASN
** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.185403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.144762 restraints weight = 7724.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.60
r_work: 0.3364 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7918  Z= 0.193
  Angle     :  0.534   6.228  10745  Z= 0.279
  Chirality :  0.042   0.166   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  4.235  16.594   1063
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.27 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.27), residues: 998
  helix:  1.21 (0.24), residues: 487
  sheet: -0.49 (0.53), residues: 93
  loop : -0.69 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 927 
 HIS   0.002   0.001   HIS A 396 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.019   0.002   TYR A 867 
 ARG   0.003   0.000   ARG A 139 

*********************** 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
  144 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7085 (mp0) cc_final: 0.6759 (mp0)
REVERT: A  120 LYS cc_start: 0.7369 (mptm) cc_final: 0.7098 (mptm)
REVERT: A  126 MET cc_start: 0.8392 (mmt) cc_final: 0.7917 (mmt)
REVERT: A  132 GLN cc_start: 0.8231 (mt0) cc_final: 0.8023 (mt0)
REVERT: A  134 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6829 (pmm-80)
REVERT: A  207 MET cc_start: 0.8553 (mmt) cc_final: 0.8230 (tpp)
REVERT: A  220 MET cc_start: 0.8525 (mtp) cc_final: 0.8262 (mtt)
REVERT: A  245 GLU cc_start: 0.6769 (pt0) cc_final: 0.6414 (pm20)
REVERT: A  412 GLU cc_start: 0.7991 (tt0) cc_final: 0.7438 (tt0)
REVERT: A  419 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7756 (tp)
REVERT: A  439 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6537 (tm-30)
REVERT: A  466 GLU cc_start: 0.7553 (tp30) cc_final: 0.7323 (tp30)
REVERT: A  479 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6359 (tpp)
REVERT: A  494 MET cc_start: 0.7758 (tmt) cc_final: 0.7473 (tmt)
REVERT: A  536 MET cc_start: 0.6289 (ttp) cc_final: 0.6078 (ttp)
REVERT: A  575 MET cc_start: 0.3056 (mmt) cc_final: 0.2106 (mmt)
REVERT: A  836 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.5892 (p90)
REVERT: A  968 MET cc_start: 0.8289 (tpp) cc_final: 0.7994 (tpp)
REVERT: A  978 LEU cc_start: 0.8222 (tp) cc_final: 0.7860 (tm)
  outliers start: 28
  outliers final: 12
  residues processed: 128
  average time/residue: 1.2844
  time to fit residues: 173.9460
Evaluate side-chains
  128 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  419 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  649 SER
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  836 TYR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0670
   overall best weight:    0.7322

-------------------------------------------------------------------------------
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 = 0.4025 r_free = 0.4025 target = 0.186629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.146238 restraints weight = 7689.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.60
r_work: 0.3492 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
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   0.033   7918  Z= 0.168
  Angle     :  0.518   5.679  10745  Z= 0.270
  Chirality :  0.041   0.162   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  4.115  16.530   1063
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.85 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 998
  helix:  1.53 (0.24), residues: 486
  sheet: -0.46 (0.54), residues: 93
  loop : -0.58 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.028   0.001   PHE A 759 
 TYR   0.016   0.001   TYR A 990 
 ARG   0.002   0.000   ARG A 761 

*********************** 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
  142 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.6901 (mp0) cc_final: 0.6498 (mp0)
REVERT: A  120 LYS cc_start: 0.7336 (mptm) cc_final: 0.7125 (mptm)
REVERT: A  126 MET cc_start: 0.8272 (mmt) cc_final: 0.7783 (mmt)
REVERT: A  134 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7031 (pmm-80)
REVERT: A  207 MET cc_start: 0.8510 (mmt) cc_final: 0.8167 (tpp)
REVERT: A  220 MET cc_start: 0.8438 (mtp) cc_final: 0.8172 (mtt)
REVERT: A  245 GLU cc_start: 0.6724 (pt0) cc_final: 0.6407 (pm20)
REVERT: A  412 GLU cc_start: 0.7933 (tt0) cc_final: 0.7625 (tt0)
REVERT: A  466 GLU cc_start: 0.7547 (tp30) cc_final: 0.7275 (tp30)
REVERT: A  479 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6393 (tpp)
REVERT: A  575 MET cc_start: 0.3097 (mmt) cc_final: 0.2190 (mmt)
REVERT: A  599 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8008 (pt)
REVERT: A  719 MET cc_start: 0.8615 (mmm) cc_final: 0.8373 (mmt)
REVERT: A  756 MET cc_start: 0.8437 (ttm) cc_final: 0.7947 (ttp)
REVERT: A  775 PHE cc_start: 0.7112 (t80) cc_final: 0.6911 (t80)
REVERT: A  836 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.5781 (p90)
REVERT: A  968 MET cc_start: 0.8252 (tpp) cc_final: 0.7927 (tpp)
REVERT: A  978 LEU cc_start: 0.8185 (tp) cc_final: 0.7826 (tm)
  outliers start: 27
  outliers final: 14
  residues processed: 128
  average time/residue: 1.1726
  time to fit residues: 159.7602
Evaluate side-chains
  126 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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  152 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  179 ILE
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  479 MET
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  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 94 optimal weight:    0.5980
   chunk 57 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 51 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0070
   chunk 66 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.188376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.147759 restraints weight = 7753.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.62
r_work: 0.3444 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7918  Z= 0.163
  Angle     :  0.512   5.694  10745  Z= 0.266
  Chirality :  0.041   0.161   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  4.071  16.777   1063
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.32 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.27), residues: 998
  helix:  1.66 (0.24), residues: 488
  sheet: -0.36 (0.54), residues: 93
  loop : -0.51 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 836 
 ARG   0.006   0.000   ARG A 290 

*********************** 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
  148 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7045 (mp0) cc_final: 0.6628 (mp0)
REVERT: A   40 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8351 (pt0)
REVERT: A  120 LYS cc_start: 0.7282 (mptm) cc_final: 0.7043 (mptm)
REVERT: A  126 MET cc_start: 0.8383 (mmt) cc_final: 0.7912 (mmt)
REVERT: A  134 ARG cc_start: 0.7282 (ptp-110) cc_final: 0.7055 (pmm-80)
REVERT: A  207 MET cc_start: 0.8554 (mmt) cc_final: 0.8237 (tpp)
REVERT: A  220 MET cc_start: 0.8465 (mtp) cc_final: 0.8219 (mtt)
REVERT: A  245 GLU cc_start: 0.6769 (pt0) cc_final: 0.6456 (pm20)
REVERT: A  290 ARG cc_start: 0.4806 (ttt90) cc_final: 0.4256 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7610 (ttmm)
REVERT: A  466 GLU cc_start: 0.7625 (tp30) cc_final: 0.7403 (tp30)
REVERT: A  494 MET cc_start: 0.7992 (tmt) cc_final: 0.7272 (tmt)
REVERT: A  575 MET cc_start: 0.3147 (mmt) cc_final: 0.2248 (mmt)
REVERT: A  599 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8081 (pt)
REVERT: A  719 MET cc_start: 0.8697 (mmm) cc_final: 0.8420 (mmt)
REVERT: A  836 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.5905 (p90)
REVERT: A  968 MET cc_start: 0.8312 (tpp) cc_final: 0.7973 (tpp)
  outliers start: 29
  outliers final: 14
  residues processed: 133
  average time/residue: 1.2792
  time to fit residues: 181.1308
Evaluate side-chains
  131 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   40 GLU
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  265 SER
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  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  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 56 optimal weight:   20.0000
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.4018 r_free = 0.4018 target = 0.185474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.145139 restraints weight = 7786.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 1.58
r_work: 0.3430 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7918  Z= 0.258
  Angle     :  0.572   5.876  10745  Z= 0.297
  Chirality :  0.044   0.176   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  4.337  17.483   1063
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 14.78 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 998
  helix:  1.46 (0.24), residues: 490
  sheet: -0.39 (0.54), residues: 93
  loop : -0.52 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A  15 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.014   0.002   TYR A 990 
 ARG   0.004   0.000   ARG A 290 

*********************** 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
  147 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 114
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7072 (mp0) cc_final: 0.6648 (mp0)
REVERT: A   58 GLU cc_start: 0.7668 (tt0) cc_final: 0.6873 (tp30)
REVERT: A   97 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8000 (mp)
REVERT: A  120 LYS cc_start: 0.7443 (mptm) cc_final: 0.7220 (mptm)
REVERT: A  126 MET cc_start: 0.8429 (mmt) cc_final: 0.8007 (mmt)
REVERT: A  134 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7228 (pmm-80)
REVERT: A  207 MET cc_start: 0.8599 (mmt) cc_final: 0.8275 (tpp)
REVERT: A  245 GLU cc_start: 0.6992 (pt0) cc_final: 0.6714 (pm20)
REVERT: A  290 ARG cc_start: 0.4989 (ttt90) cc_final: 0.4441 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7699 (ttmm)
REVERT: A  439 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6381 (tm-30)
REVERT: A  441 THR cc_start: 0.8802 (p) cc_final: 0.8139 (p)
REVERT: A  466 GLU cc_start: 0.7644 (tp30) cc_final: 0.7424 (tp30)
REVERT: A  548 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7080 (mp)
REVERT: A  575 MET cc_start: 0.3151 (mmt) cc_final: 0.2280 (mmt)
REVERT: A  599 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8173 (pt)
REVERT: A  836 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6005 (p90)
REVERT: A  924 MET cc_start: 0.8151 (ttp) cc_final: 0.7646 (ttm)
REVERT: A  968 MET cc_start: 0.8333 (tpp) cc_final: 0.8123 (tpp)
REVERT: A  978 LEU cc_start: 0.8335 (tp) cc_final: 0.7966 (tm)
  outliers start: 33
  outliers final: 16
  residues processed: 132
  average time/residue: 1.1157
  time to fit residues: 157.0626
Evaluate side-chains
  135 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
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  103 ILE
Chi-restraints excluded: chain A residue  134 ARG
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  439 GLU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  548 ILE
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  916 SER
Chi-restraints excluded: chain A residue  930 ILE
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 31 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4032 r_free = 0.4032 target = 0.187025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.147001 restraints weight = 7868.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.61
r_work: 0.3429 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7918  Z= 0.185
  Angle     :  0.534   5.755  10745  Z= 0.276
  Chirality :  0.042   0.165   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  4.202  17.384   1063
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.48 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 998
  helix:  1.54 (0.24), residues: 496
  sheet: -0.31 (0.54), residues: 92
  loop : -0.44 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.011   0.001   TYR A 836 
 ARG   0.003   0.000   ARG A 290 

*********************** 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
  148 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7047 (mp0) cc_final: 0.6591 (mp0)
REVERT: A   58 GLU cc_start: 0.7614 (tt0) cc_final: 0.6724 (tp30)
REVERT: A  120 LYS cc_start: 0.7269 (mptm) cc_final: 0.7024 (mptm)
REVERT: A  126 MET cc_start: 0.8418 (mmt) cc_final: 0.7948 (mmt)
REVERT: A  134 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7115 (pmm-80)
REVERT: A  179 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7818 (pp)
REVERT: A  207 MET cc_start: 0.8562 (mmt) cc_final: 0.8246 (tpp)
REVERT: A  220 MET cc_start: 0.8438 (mtp) cc_final: 0.8120 (mtt)
REVERT: A  245 GLU cc_start: 0.6978 (pt0) cc_final: 0.6694 (pm20)
REVERT: A  290 ARG cc_start: 0.4776 (ttt90) cc_final: 0.4244 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7651 (ttmm)
REVERT: A  441 THR cc_start: 0.8650 (p) cc_final: 0.8296 (p)
REVERT: A  466 GLU cc_start: 0.7584 (tp30) cc_final: 0.7289 (tp30)
REVERT: A  548 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6991 (mp)
REVERT: A  549 ARG cc_start: 0.6595 (mpp80) cc_final: 0.6292 (mpp80)
REVERT: A  575 MET cc_start: 0.2962 (mmt) cc_final: 0.2097 (mmt)
REVERT: A  599 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8147 (pt)
REVERT: A  775 PHE cc_start: 0.7449 (t80) cc_final: 0.7188 (t80)
REVERT: A  836 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.5882 (p90)
REVERT: A  924 MET cc_start: 0.8039 (ttp) cc_final: 0.7631 (ttm)
REVERT: A  968 MET cc_start: 0.8305 (tpp) cc_final: 0.7984 (tpp)
REVERT: A  978 LEU cc_start: 0.8251 (tp) cc_final: 0.7890 (tm)
  outliers start: 28
  outliers final: 16
  residues processed: 136
  average time/residue: 1.0497
  time to fit residues: 152.9361
Evaluate side-chains
  139 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
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  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  548 ILE
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  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.187978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.147758 restraints weight = 7940.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.64
r_work: 0.3437 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7918  Z= 0.176
  Angle     :  0.528   6.600  10745  Z= 0.273
  Chirality :  0.041   0.162   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  4.121  16.999   1063
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.27), residues: 998
  helix:  1.56 (0.24), residues: 502
  sheet: -0.34 (0.52), residues: 95
  loop : -0.39 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.026   0.001   PHE A 759 
 TYR   0.017   0.001   TYR A 990 
 ARG   0.003   0.000   ARG A 290 

*********************** 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
  141 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.6981 (mp0) cc_final: 0.6490 (mp0)
REVERT: A  120 LYS cc_start: 0.7161 (mptm) cc_final: 0.6898 (mptm)
REVERT: A  126 MET cc_start: 0.8436 (mmt) cc_final: 0.7966 (mmt)
REVERT: A  134 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7216 (pmm-80)
REVERT: A  179 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7795 (pp)
REVERT: A  207 MET cc_start: 0.8557 (mmt) cc_final: 0.8241 (tpp)
REVERT: A  220 MET cc_start: 0.8407 (mtp) cc_final: 0.8110 (mtt)
REVERT: A  245 GLU cc_start: 0.6980 (pt0) cc_final: 0.6696 (pm20)
REVERT: A  290 ARG cc_start: 0.4835 (ttt90) cc_final: 0.4303 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7648 (ttmm)
REVERT: A  466 GLU cc_start: 0.7588 (tp30) cc_final: 0.7351 (tp30)
REVERT: A  548 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6770 (mp)
REVERT: A  575 MET cc_start: 0.3412 (mmt) cc_final: 0.2626 (mmt)
REVERT: A  599 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8116 (pt)
REVERT: A  775 PHE cc_start: 0.7416 (t80) cc_final: 0.7158 (t80)
REVERT: A  836 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.5905 (p90)
REVERT: A  924 MET cc_start: 0.7976 (ttp) cc_final: 0.7600 (ttm)
REVERT: A  930 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (mm)
REVERT: A  968 MET cc_start: 0.8296 (tpp) cc_final: 0.7960 (tpp)
  outliers start: 27
  outliers final: 14
  residues processed: 129
  average time/residue: 1.1421
  time to fit residues: 157.0059
Evaluate side-chains
  133 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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  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  265 SER
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  548 ILE
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  916 SER
Chi-restraints excluded: chain A residue  930 ILE
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 71 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 90 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.188244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.147909 restraints weight = 7866.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 1.63
r_work: 0.3459 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7918  Z= 0.163
  Angle     :  0.524   7.421  10745  Z= 0.270
  Chirality :  0.041   0.159   1264
  Planarity :  0.004   0.044   1366
  Dihedral  :  4.060  17.055   1063
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.00 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 998
  helix:  1.63 (0.24), residues: 504
  sheet: -0.25 (0.53), residues: 95
  loop : -0.34 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A  15 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.022   0.002   TYR A 867 
 ARG   0.006   0.000   ARG A 198 

********************** 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
  136 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7019 (mp0) cc_final: 0.6530 (mp0)
REVERT: A  113 GLU cc_start: 0.7767 (mt-10) cc_final: 0.6843 (mp0)
REVERT: A  120 LYS cc_start: 0.7187 (mptm) cc_final: 0.6943 (mptm)
REVERT: A  126 MET cc_start: 0.8466 (mmt) cc_final: 0.8012 (mmt)
REVERT: A  179 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7789 (pp)
REVERT: A  207 MET cc_start: 0.8539 (mmt) cc_final: 0.8211 (tpp)
REVERT: A  220 MET cc_start: 0.8414 (mtp) cc_final: 0.8125 (mtt)
REVERT: A  245 GLU cc_start: 0.7010 (pt0) cc_final: 0.6758 (pm20)
REVERT: A  290 ARG cc_start: 0.4775 (ttt90) cc_final: 0.4215 (ttt-90)
REVERT: A  328 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7630 (ttmm)
REVERT: A  466 GLU cc_start: 0.7693 (tp30) cc_final: 0.7441 (tp30)
REVERT: A  494 MET cc_start: 0.7660 (tmt) cc_final: 0.7412 (ppp)
REVERT: A  549 ARG cc_start: 0.6976 (mpp80) cc_final: 0.6396 (mpp80)
REVERT: A  575 MET cc_start: 0.3200 (mmt) cc_final: 0.2592 (mmt)
REVERT: A  599 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8177 (pt)
REVERT: A  719 MET cc_start: 0.8727 (mmm) cc_final: 0.8420 (mmt)
REVERT: A  775 PHE cc_start: 0.7322 (t80) cc_final: 0.7085 (t80)
REVERT: A  836 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.5975 (p90)
REVERT: A  896 MET cc_start: 0.8735 (tpp) cc_final: 0.8528 (mmm)
REVERT: A  924 MET cc_start: 0.7960 (ttp) cc_final: 0.7662 (ttm)
REVERT: A  930 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (mm)
  outliers start: 22
  outliers final: 15
  residues processed: 128
  average time/residue: 1.1147
  time to fit residues: 152.6351
Evaluate side-chains
  131 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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  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  265 SER
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  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  930 ILE
Chi-restraints excluded: chain A residue  942 LEU
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 67 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0570
   chunk 91 optimal weight:    0.4980
   chunk 88 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 61 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0070
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.4316

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.190015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.149557 restraints weight = 7786.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.66
r_work: 0.3465 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7918  Z= 0.141
  Angle     :  0.503   5.591  10745  Z= 0.259
  Chirality :  0.040   0.154   1264
  Planarity :  0.004   0.045   1366
  Dihedral  :  3.926  16.325   1063
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.69 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.28), residues: 998
  helix:  1.78 (0.24), residues: 503
  sheet: -0.11 (0.54), residues: 95
  loop : -0.26 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 682 
 PHE   0.027   0.001   PHE A 759 
 TYR   0.021   0.002   TYR A 867 
 ARG   0.006   0.000   ARG A 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6604.37 seconds
wall clock time: 117 minutes 11.29 seconds (7031.29 seconds total)