Starting phenix.real_space_refine
on Wed Feb 12 13:09:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ln7_0926/02_2025/6ln7_0926.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ln7_0926/02_2025/6ln7_0926.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/6ln7_0926/02_2025/6ln7_0926.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ln7_0926/02_2025/6ln7_0926.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ln7_0926/02_2025/6ln7_0926.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ln7_0926/02_2025/6ln7_0926.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
     Ca      2      9.91       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      57      5.16       5
     C    4988      2.51       5
     N    1311      2.21       5
     O    1478      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7840
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1011, 7806
          Classifications: {'peptide': 1011}
          Link IDs: {'PTRANS': 46, 'TRANS': 964}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 4.73, per 1000 atoms: 0.60
  Number of scatterers: 7840
  At special positions: 0
  Unit cell: (103.335, 80.925, 139.44, 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)
     Ca      2     19.99
     S      57     16.00
     P       3     15.00
     Mg      1     11.99
     O    1478      8.00
     N    1311      7.00
     C    4988      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 779.2 milliseconds
  

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      53.7% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
      removed outlier: 3.618A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 48 through 55
    Processing helix  chain 'A' and resid 56 through 58
      No H-bonds generated for 'chain 'A' and resid 56 through 58'
    Processing helix  chain 'A' and resid 59 through 79
      removed outlier: 3.897A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 87
    Processing helix  chain 'A' and resid 88 through 118
      removed outlier: 3.815A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    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 235
      removed outlier: 3.501A  pdb=" N   ILE A 235 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 275
      removed outlier: 3.541A  pdb=" N   ASN A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 280
      removed outlier: 3.586A  pdb=" N   PHE A 279 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 276 through 280'
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 287 through 307
    Processing helix  chain 'A' and resid 310 through 328
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 407 through 420
    Processing helix  chain 'A' and resid 439 through 452
      removed outlier: 3.650A  pdb=" N   LEU A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 477
      removed outlier: 3.569A  pdb=" N   VAL A 474 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 475 " --> pdb=" O   CYS A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 522
    Processing helix  chain 'A' and resid 537 through 553
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.656A  pdb=" N   TYR A 586 " --> pdb=" O   ASN A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.806A  pdb=" N   CYS A 669 " --> pdb=" O   GLN A 665 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU A 670 " --> pdb=" O   ARG A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.679A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE A 693 " --> pdb=" O   PHE A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 711
    Processing helix  chain 'A' and resid 723 through 729
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 4.004A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 799
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.648A  pdb=" N   ALA A 851 " --> pdb=" O   THR A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
    Processing helix  chain 'A' and resid 886 through 891
      removed outlier: 3.579A  pdb=" N   PHE A 890 " --> pdb=" O   CYS A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.348A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 949
    Processing helix  chain 'A' and resid 951 through 957
      removed outlier: 3.772A  pdb=" N   ILE A 955 " --> pdb=" O   PRO A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 974
    Processing helix  chain 'A' and resid 974 through 992
      removed outlier: 3.797A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU A 992 " --> pdb=" O   ARG A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      removed outlier: 3.621A  pdb=" N   LEU A1021 " --> pdb=" O   PRO A1017 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141
      removed outlier: 4.321A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 6.855A  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: 4.748A  pdb=" N   LEU A 173 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ARG A 174 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.342A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 350
      removed outlier: 8.131A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   PHE A 652 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.615A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 19.652A  pdb=" N   CYS A 524 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 17.375A  pdb=" N   PHE A 367 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 14.855A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
      removed outlier: 10.400A  pdb=" N   LEU A 369 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ARG A 528 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   ARG A 371 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 532 through 535
      removed outlier: 5.774A  pdb=" N   LEU A 590 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   GLY A 594 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
      removed outlier: 16.175A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 14.534A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.615A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.534A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 16.175A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   SER A 493 " --> pdb=" O   GLU A 486 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   GLU A 486 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   SER A 495 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   THR A 484 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   TYR A 497 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 428

    443 hydrogen bonds defined for protein.
    1275 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: 3.27

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2578
        1.35 -     1.48: 1791
        1.48 -     1.61: 3522
        1.61 -     1.73: 4
        1.73 -     1.86: 90
  Bond restraints: 7985
  Sorted by residual:
  bond pdb=" C1' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.390  1.618 -0.228 2.00e-02 2.50e+03 1.30e+02
  bond pdb=" C1' ACP A2001 "
       pdb=" C2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.527  1.307  0.220 2.00e-02 2.50e+03 1.21e+02
  bond pdb=" C4' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.428  1.301  0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C6  ACP A2001 "
       pdb=" N6  ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.335  1.449 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C2' ACP A2001 "
       pdb=" O2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.401  1.494 -0.093 2.00e-02 2.50e+03 2.16e+01
  ... (remaining 7980 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 10786
        3.15 -     6.30: 49
        6.30 -     9.45: 4
        9.45 -    12.60: 4
       12.60 -    15.75: 1
  Bond angle restraints: 10844
  Sorted by residual:
  angle pdb=" O3A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O5' ACP A2001 "
      ideal   model   delta    sigma   weight residual
      93.75  109.50  -15.75 3.00e+00 1.11e-01 2.76e+01
  angle pdb=" C3B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O3A ACP A2001 "
      ideal   model   delta    sigma   weight residual
      98.05  110.64  -12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" N1  ACP A2001 "
        pdb=" C6  ACP A2001 "
        pdb=" N6  ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.32  108.35   10.97 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" O1B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O2B ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.60  108.99   10.61 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" O1A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O2A ACP A2001 "
      ideal   model   delta    sigma   weight residual
     118.95  108.65   10.30 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 10839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.02: 4714
       26.02 -    52.04: 129
       52.04 -    78.06: 12
       78.06 -   104.08: 2
      104.08 -   130.10: 1
  Dihedral angle restraints: 4858
    sinusoidal: 1938
      harmonic: 2920
  Sorted by residual:
  dihedral pdb=" O1A ACP A2001 "
           pdb=" O3A ACP A2001 "
           pdb=" PA  ACP A2001 "
           pdb=" PB  ACP A2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -48.75   81.35 -130.10     1      3.00e+01 1.11e-03 1.75e+01
  dihedral pdb=" CA  VAL A 949 "
           pdb=" C   VAL A 949 "
           pdb=" N   GLU A 950 "
           pdb=" CA  GLU A 950 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.81  -19.19     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ASP A 370 "
           pdb=" CB  ASP A 370 "
           pdb=" CG  ASP A 370 "
           pdb=" OD1 ASP A 370 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.58   57.58     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 4855 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1184
       0.078 -    0.155: 88
       0.155 -    0.233: 0
       0.233 -    0.310: 0
       0.310 -    0.388: 1
  Chirality restraints: 1273
  Sorted by residual:
  chirality pdb=" C2' ACP A2001 "
            pdb=" C1' ACP A2001 "
            pdb=" C3' ACP A2001 "
            pdb=" O2' ACP A2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.36   -0.39 2.00e-01 2.50e+01 3.76e+00
  chirality pdb=" CA  ILE A 623 "
            pdb=" N   ILE A 623 "
            pdb=" C   ILE A 623 "
            pdb=" CB  ILE A 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CG  LEU A 806 "
            pdb=" CB  LEU A 806 "
            pdb=" CD1 LEU A 806 "
            pdb=" CD2 LEU A 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.47   -0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 1270 not shown)

  Planarity restraints: 1377
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A1016 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO A1017 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A1017 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1017 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO A 975 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 194 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.77e+00
        pdb=" N   PRO A 195 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 195 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 195 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1374 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 119
        2.66 -     3.22: 7357
        3.22 -     3.78: 11988
        3.78 -     4.34: 17673
        4.34 -     4.90: 28382
  Nonbonded interactions: 65519
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.101 2.170
  nonbonded pdb=" OE2 GLU A 309 "
            pdb=" OD1 ASN A 795 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.134 2.170
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.138 2.170
  nonbonded pdb=" O   ILE A 307 "
            pdb=" OE1 GLU A 309 "
     model   vdw
     2.150 3.040
  ... (remaining 65514 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=1.00 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:             0.300
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.330
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:12.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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      :  0.005   0.228   7985  Z= 0.348
  Angle     :  0.647  15.750  10844  Z= 0.341
  Chirality :  0.042   0.388   1273
  Planarity :  0.004   0.041   1377
  Dihedral  : 12.197 130.104   2966
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  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: -3.93 (0.20), residues: 1007
  helix: -3.29 (0.13), residues: 501
  sheet: -1.13 (0.46), residues: 113
  loop : -1.80 (0.25), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 793 
 HIS   0.005   0.001   HIS A 566 
 PHE   0.010   0.001   PHE A 367 
 TYR   0.009   0.001   TYR A 842 
 ARG   0.005   0.000   ARG A 666 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7214 (tpp) cc_final: 0.6660 (tpp)
REVERT: A   33 LYS cc_start: 0.8417 (tmtt) cc_final: 0.7918 (ttmm)
REVERT: A  254 ASP cc_start: 0.7702 (m-30) cc_final: 0.7412 (m-30)
REVERT: A  365 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7414 (mtt180)
REVERT: A  381 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8133 (mt-10)
REVERT: A  494 MET cc_start: 0.8920 (ttt) cc_final: 0.8596 (ttm)
REVERT: A  732 MET cc_start: 0.8595 (ttt) cc_final: 0.8393 (ttp)
REVERT: A  824 LYS cc_start: 0.8486 (mttm) cc_final: 0.8238 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 1.5656
  time to fit residues: 277.0255
Evaluate side-chains
  113 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 GLN
A 190 HIS
A 278 HIS
A 469 ASN
A 472 ASN
A 582 ASN
A 868 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.129332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.098931 restraints weight = 8842.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 1.80
r_work: 0.2829 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7985  Z= 0.231
  Angle     :  0.568   6.417  10844  Z= 0.294
  Chirality :  0.043   0.134   1273
  Planarity :  0.005   0.052   1377
  Dihedral  :  8.432 159.774   1103
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 12.96 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.08 (0.24), residues: 1007
  helix: -0.30 (0.21), residues: 507
  sheet: -0.79 (0.45), residues: 116
  loop : -1.08 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.021   0.001   PHE A 367 
 TYR   0.013   0.002   TYR A 842 
 ARG   0.005   0.001   ARG A 821 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.8569 (tmtt) cc_final: 0.7866 (ttmm)
REVERT: A   51 GLU cc_start: 0.7382 (tp30) cc_final: 0.7064 (tm-30)
REVERT: A  135 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8379 (ttmm)
REVERT: A  246 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6307 (ptm160)
REVERT: A  254 ASP cc_start: 0.7875 (m-30) cc_final: 0.7544 (m-30)
REVERT: A  258 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7349 (mm-30)
REVERT: A  324 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7882 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8168 (mmm-85)
REVERT: A  381 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8258 (mt-10)
REVERT: A  466 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8065 (mp0)
REVERT: A  494 MET cc_start: 0.9204 (ttt) cc_final: 0.8871 (ttm)
REVERT: A  508 MET cc_start: 0.5966 (mpp) cc_final: 0.4382 (tpt)
REVERT: A  754 ASN cc_start: 0.9137 (m-40) cc_final: 0.8908 (m110)
  outliers start: 17
  outliers final: 6
  residues processed: 128
  average time/residue: 1.4044
  time to fit residues: 189.3225
Evaluate side-chains
  119 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  534 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0010
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
A 868 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.127951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.097139 restraints weight = 8831.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.81
r_work: 0.2825 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7985  Z= 0.186
  Angle     :  0.525   5.917  10844  Z= 0.269
  Chirality :  0.042   0.168   1273
  Planarity :  0.004   0.045   1377
  Dihedral  :  8.432 163.171   1103
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.35 %
    Favored  : 82.99 %
  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:  0.04 (0.26), residues: 1007
  helix:  0.86 (0.23), residues: 509
  sheet: -0.61 (0.46), residues: 116
  loop : -0.81 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.019   0.001   PHE A 367 
 TYR   0.012   0.002   TYR A 842 
 ARG   0.005   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7030 (tpp) cc_final: 0.6333 (tpp)
REVERT: A   33 LYS cc_start: 0.8529 (tmtt) cc_final: 0.7797 (ttmm)
REVERT: A   51 GLU cc_start: 0.7192 (tp30) cc_final: 0.6792 (tm-30)
REVERT: A   59 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6670 (t70)
REVERT: A  135 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8390 (ttmm)
REVERT: A  203 ASP cc_start: 0.8334 (m-30) cc_final: 0.8105 (m-30)
REVERT: A  246 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6432 (ptm160)
REVERT: A  254 ASP cc_start: 0.7855 (m-30) cc_final: 0.7528 (m-30)
REVERT: A  258 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7265 (mm-30)
REVERT: A  309 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8023 (pm20)
REVERT: A  324 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7822 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8500 (mtt90) cc_final: 0.8153 (mmm-85)
REVERT: A  466 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8102 (mt-10)
REVERT: A  494 MET cc_start: 0.9024 (ttt) cc_final: 0.8730 (ttm)
REVERT: A  650 LYS cc_start: 0.8677 (mttt) cc_final: 0.8301 (mttp)
REVERT: A  754 ASN cc_start: 0.8983 (m-40) cc_final: 0.8712 (m110)
REVERT: A  876 LYS cc_start: 0.6487 (mtmm) cc_final: 0.5837 (mtmm)
REVERT: A  945 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8500 (tp)
  outliers start: 23
  outliers final: 6
  residues processed: 134
  average time/residue: 1.3444
  time to fit residues: 190.4848
Evaluate side-chains
  124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0570
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8102

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.130098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.100504 restraints weight = 8687.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.70
r_work: 0.2841 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7985  Z= 0.175
  Angle     :  0.512   6.214  10844  Z= 0.260
  Chirality :  0.041   0.163   1273
  Planarity :  0.004   0.044   1377
  Dihedral  :  8.446 165.342   1103
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.74 %
    Favored  : 81.83 %
  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:  0.52 (0.26), residues: 1007
  helix:  1.29 (0.23), residues: 509
  sheet: -0.44 (0.47), residues: 116
  loop : -0.62 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.8580 (tmtt) cc_final: 0.7846 (ttmm)
REVERT: A   59 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6896 (t70)
REVERT: A  135 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8472 (ttmm)
REVERT: A  172 THR cc_start: 0.8813 (t) cc_final: 0.8511 (p)
REVERT: A  246 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6694 (ptm160)
REVERT: A  254 ASP cc_start: 0.7895 (m-30) cc_final: 0.7633 (m-30)
REVERT: A  309 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8130 (pm20)
REVERT: A  324 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7915 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8602 (mtt90) cc_final: 0.8305 (mmm-85)
REVERT: A  466 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: A  494 MET cc_start: 0.9109 (ttt) cc_final: 0.8786 (ttm)
REVERT: A  508 MET cc_start: 0.5627 (mpp) cc_final: 0.3976 (tpt)
REVERT: A  599 LEU cc_start: 0.8531 (pt) cc_final: 0.8116 (mp)
REVERT: A  650 LYS cc_start: 0.8763 (mttt) cc_final: 0.8426 (mttp)
REVERT: A  754 ASN cc_start: 0.8996 (m-40) cc_final: 0.8750 (m110)
REVERT: A  881 ASP cc_start: 0.8187 (m-30) cc_final: 0.7943 (m-30)
REVERT: A  945 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8479 (tp)
  outliers start: 21
  outliers final: 10
  residues processed: 134
  average time/residue: 1.3404
  time to fit residues: 189.6374
Evaluate side-chains
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  898 MET
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    0.0050
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.138514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.111177 restraints weight = 8483.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.55
r_work: 0.2875 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   7985  Z= 0.162
  Angle     :  0.505   6.692  10844  Z= 0.257
  Chirality :  0.041   0.155   1273
  Planarity :  0.004   0.044   1377
  Dihedral  :  8.408 166.376   1103
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.13 %
    Favored  : 80.67 %
  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:  0.82 (0.27), residues: 1007
  helix:  1.53 (0.23), residues: 510
  sheet: -0.43 (0.47), residues: 116
  loop : -0.41 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.012   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.8603 (tmtt) cc_final: 0.7860 (ttmm)
REVERT: A   59 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6902 (t70)
REVERT: A  135 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8388 (ttmm)
REVERT: A  172 THR cc_start: 0.8842 (t) cc_final: 0.8582 (p)
REVERT: A  246 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6758 (ptm160)
REVERT: A  254 ASP cc_start: 0.7865 (m-30) cc_final: 0.7606 (m-30)
REVERT: A  324 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7905 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8298 (mmm-85)
REVERT: A  366 MET cc_start: 0.9057 (ptt) cc_final: 0.8787 (ptt)
REVERT: A  394 GLU cc_start: 0.8332 (tt0) cc_final: 0.7944 (mm-30)
REVERT: A  452 MET cc_start: 0.8559 (ptm) cc_final: 0.8331 (ptp)
REVERT: A  466 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8097 (mt-10)
REVERT: A  473 SER cc_start: 0.8540 (m) cc_final: 0.8240 (m)
REVERT: A  494 MET cc_start: 0.9065 (ttt) cc_final: 0.8798 (ttm)
REVERT: A  508 MET cc_start: 0.5447 (mpp) cc_final: 0.3773 (tpt)
REVERT: A  650 LYS cc_start: 0.8790 (mttt) cc_final: 0.8471 (mttp)
REVERT: A  754 ASN cc_start: 0.8992 (m-40) cc_final: 0.8773 (m110)
REVERT: A  876 LYS cc_start: 0.6586 (mtmm) cc_final: 0.6143 (mtmm)
REVERT: A  945 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8485 (tp)
  outliers start: 19
  outliers final: 9
  residues processed: 134
  average time/residue: 1.3197
  time to fit residues: 187.4810
Evaluate side-chains
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  579 ASP
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 89 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0370
   chunk 18 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9462

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.133876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.106323 restraints weight = 8530.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.52
r_work: 0.2886 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7985  Z= 0.193
  Angle     :  0.531   7.933  10844  Z= 0.266
  Chirality :  0.042   0.175   1273
  Planarity :  0.004   0.043   1377
  Dihedral  :  8.494 166.752   1103
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.59 %
    Favored  : 80.32 %
  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:  0.82 (0.26), residues: 1007
  helix:  1.54 (0.23), residues: 511
  sheet: -0.45 (0.47), residues: 116
  loop : -0.43 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.019   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8621 (tmtt) cc_final: 0.7778 (tppp)
REVERT: A   59 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6871 (t70)
REVERT: A  135 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8390 (ttmm)
REVERT: A  172 THR cc_start: 0.8849 (t) cc_final: 0.8586 (p)
REVERT: A  246 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6725 (ptm160)
REVERT: A  254 ASP cc_start: 0.7899 (m-30) cc_final: 0.7661 (m-30)
REVERT: A  324 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7921 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8307 (mmm-85)
REVERT: A  366 MET cc_start: 0.9116 (ptt) cc_final: 0.8805 (ptt)
REVERT: A  394 GLU cc_start: 0.8340 (tt0) cc_final: 0.7973 (mm-30)
REVERT: A  452 MET cc_start: 0.8551 (ptm) cc_final: 0.8333 (ptp)
REVERT: A  466 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: A  473 SER cc_start: 0.8539 (m) cc_final: 0.8261 (m)
REVERT: A  494 MET cc_start: 0.9081 (ttt) cc_final: 0.8821 (ttm)
REVERT: A  599 LEU cc_start: 0.8495 (pt) cc_final: 0.8154 (mp)
REVERT: A  650 LYS cc_start: 0.8784 (mttt) cc_final: 0.8444 (mttp)
REVERT: A  754 ASN cc_start: 0.8941 (m-40) cc_final: 0.8708 (m110)
REVERT: A  945 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8510 (tp)
  outliers start: 18
  outliers final: 7
  residues processed: 127
  average time/residue: 1.3297
  time to fit residues: 178.5088
Evaluate side-chains
  128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  898 MET
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 92 optimal weight:    0.4980
   chunk 83 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.136578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.109393 restraints weight = 8563.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.55
r_work: 0.2852 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7985  Z= 0.203
  Angle     :  0.535   8.697  10844  Z= 0.269
  Chirality :  0.042   0.174   1273
  Planarity :  0.004   0.044   1377
  Dihedral  :  8.551 167.634   1103
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.06 %
    Favored  : 79.75 %
  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:  0.88 (0.26), residues: 1007
  helix:  1.55 (0.23), residues: 511
  sheet: -0.31 (0.47), residues: 119
  loop : -0.37 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.019   0.001   PHE A 367 
 TYR   0.015   0.002   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.906 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.8660 (tmtt) cc_final: 0.7789 (tppp)
REVERT: A   59 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6818 (t70)
REVERT: A  135 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8346 (ttmm)
REVERT: A  172 THR cc_start: 0.8832 (t) cc_final: 0.8563 (p)
REVERT: A  246 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6834 (ptm160)
REVERT: A  254 ASP cc_start: 0.7951 (m-30) cc_final: 0.7707 (m-30)
REVERT: A  324 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7907 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8599 (mtt90) cc_final: 0.8317 (mmm-85)
REVERT: A  394 GLU cc_start: 0.8348 (tt0) cc_final: 0.7969 (mm-30)
REVERT: A  452 MET cc_start: 0.8537 (ptm) cc_final: 0.8319 (ptp)
REVERT: A  466 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8021 (mt-10)
REVERT: A  473 SER cc_start: 0.8516 (m) cc_final: 0.8276 (m)
REVERT: A  494 MET cc_start: 0.9089 (ttt) cc_final: 0.8826 (ttm)
REVERT: A  576 HIS cc_start: 0.7414 (m170) cc_final: 0.7107 (m-70)
REVERT: A  599 LEU cc_start: 0.8500 (pt) cc_final: 0.8125 (mp)
REVERT: A  650 LYS cc_start: 0.8778 (mttt) cc_final: 0.8427 (mttp)
REVERT: A  754 ASN cc_start: 0.8945 (m-40) cc_final: 0.8710 (m110)
REVERT: A  876 LYS cc_start: 0.6774 (mtmm) cc_final: 0.6312 (mtmm)
REVERT: A  881 ASP cc_start: 0.8344 (m-30) cc_final: 0.8091 (m-30)
REVERT: A  945 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8547 (tp)
  outliers start: 19
  outliers final: 9
  residues processed: 130
  average time/residue: 1.4507
  time to fit residues: 199.6282
Evaluate side-chains
  129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  898 MET
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 18 optimal weight:    0.2980
   chunk 98 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.137859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.110569 restraints weight = 8598.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.57
r_work: 0.2869 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7985  Z= 0.169
  Angle     :  0.523   9.943  10844  Z= 0.261
  Chirality :  0.041   0.171   1273
  Planarity :  0.004   0.043   1377
  Dihedral  :  8.487 168.472   1103
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.94 %
    Favored  : 79.98 %
  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:  1.00 (0.27), residues: 1007
  helix:  1.62 (0.23), residues: 513
  sheet: -0.34 (0.48), residues: 114
  loop : -0.24 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.8677 (tmtt) cc_final: 0.7810 (tppp)
REVERT: A   59 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6817 (t70)
REVERT: A  135 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8364 (ttmm)
REVERT: A  172 THR cc_start: 0.8841 (t) cc_final: 0.8581 (p)
REVERT: A  180 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8687 (tt)
REVERT: A  254 ASP cc_start: 0.8026 (m-30) cc_final: 0.7771 (m-30)
REVERT: A  324 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7928 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8271 (mmm-85)
REVERT: A  366 MET cc_start: 0.9045 (ptt) cc_final: 0.8769 (ptt)
REVERT: A  394 GLU cc_start: 0.8311 (tt0) cc_final: 0.7988 (mm-30)
REVERT: A  452 MET cc_start: 0.8526 (ptm) cc_final: 0.8315 (ptp)
REVERT: A  465 ILE cc_start: 0.8703 (mt) cc_final: 0.8463 (mp)
REVERT: A  466 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8111 (mt-10)
REVERT: A  473 SER cc_start: 0.8576 (m) cc_final: 0.8302 (m)
REVERT: A  494 MET cc_start: 0.9068 (ttt) cc_final: 0.8822 (ttm)
REVERT: A  536 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8430 (ttm)
REVERT: A  576 HIS cc_start: 0.7469 (m170) cc_final: 0.7207 (m-70)
REVERT: A  599 LEU cc_start: 0.8522 (pt) cc_final: 0.8148 (mp)
REVERT: A  650 LYS cc_start: 0.8804 (mttt) cc_final: 0.8459 (mttp)
REVERT: A  876 LYS cc_start: 0.6739 (mtmm) cc_final: 0.6295 (mtmm)
REVERT: A  881 ASP cc_start: 0.8337 (m-30) cc_final: 0.8076 (m-30)
REVERT: A  945 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8487 (tp)
  outliers start: 18
  outliers final: 9
  residues processed: 127
  average time/residue: 1.2673
  time to fit residues: 170.4462
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  536 MET
Chi-restraints excluded: chain A residue  898 MET
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 17 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
A 754 ASN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.137997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.110753 restraints weight = 8713.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.57
r_work: 0.2882 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7985  Z= 0.170
  Angle     :  0.526  10.619  10844  Z= 0.261
  Chirality :  0.041   0.172   1273
  Planarity :  0.004   0.041   1377
  Dihedral  :  8.477 168.751   1103
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.29 %
    Favored  : 79.98 %
  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:  1.07 (0.27), residues: 1007
  helix:  1.69 (0.23), residues: 513
  sheet: -0.34 (0.48), residues: 114
  loop : -0.23 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8694 (tmtt) cc_final: 0.7827 (tppp)
REVERT: A   59 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6822 (t70)
REVERT: A  135 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8360 (ttmm)
REVERT: A  172 THR cc_start: 0.8850 (t) cc_final: 0.8576 (p)
REVERT: A  180 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8693 (tt)
REVERT: A  208 LEU cc_start: 0.8762 (mt) cc_final: 0.8543 (mp)
REVERT: A  254 ASP cc_start: 0.8007 (m-30) cc_final: 0.7765 (m-30)
REVERT: A  324 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7930 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8591 (mtt90) cc_final: 0.8339 (mmm-85)
REVERT: A  366 MET cc_start: 0.9090 (ptt) cc_final: 0.8812 (ptt)
REVERT: A  394 GLU cc_start: 0.8288 (tt0) cc_final: 0.7981 (mm-30)
REVERT: A  452 MET cc_start: 0.8499 (ptm) cc_final: 0.8298 (ptp)
REVERT: A  465 ILE cc_start: 0.8736 (mt) cc_final: 0.8520 (mp)
REVERT: A  466 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8110 (mt-10)
REVERT: A  473 SER cc_start: 0.8587 (m) cc_final: 0.8321 (m)
REVERT: A  494 MET cc_start: 0.9070 (ttt) cc_final: 0.8844 (ttm)
REVERT: A  536 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8394 (ttm)
REVERT: A  576 HIS cc_start: 0.7499 (m170) cc_final: 0.7262 (m-70)
REVERT: A  599 LEU cc_start: 0.8520 (pt) cc_final: 0.8145 (mp)
REVERT: A  650 LYS cc_start: 0.8805 (mttt) cc_final: 0.8472 (mttp)
REVERT: A  876 LYS cc_start: 0.6646 (mtmm) cc_final: 0.6258 (mtmm)
REVERT: A  881 ASP cc_start: 0.8283 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  945 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8449 (tp)
REVERT: A  968 MET cc_start: 0.8738 (tpt) cc_final: 0.8515 (tpp)
  outliers start: 15
  outliers final: 9
  residues processed: 125
  average time/residue: 1.2368
  time to fit residues: 164.1679
Evaluate side-chains
  127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  536 MET
Chi-restraints excluded: chain A residue  898 MET
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.133459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.105243 restraints weight = 8728.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.61
r_work: 0.2878 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7985  Z= 0.164
  Angle     :  0.526  11.886  10844  Z= 0.260
  Chirality :  0.041   0.172   1273
  Planarity :  0.004   0.041   1377
  Dihedral  :  8.449 169.070   1103
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.94 %
    Favored  : 79.86 %
  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:  1.14 (0.27), residues: 1007
  helix:  1.75 (0.23), residues: 513
  sheet: -0.31 (0.48), residues: 114
  loop : -0.20 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.019   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 842 
 ARG   0.006   0.000   ARG A 572 

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

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

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2014 Ramachandran restraints generated.
    1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8700 (tmtt) cc_final: 0.7830 (tppp)
REVERT: A   59 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6906 (t70)
REVERT: A  135 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8379 (ttmm)
REVERT: A  172 THR cc_start: 0.8871 (t) cc_final: 0.8562 (p)
REVERT: A  180 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8698 (tt)
REVERT: A  254 ASP cc_start: 0.8053 (m-30) cc_final: 0.7810 (m-30)
REVERT: A  324 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7937 (ttp-110)
REVERT: A  365 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8389 (mmm-85)
REVERT: A  366 MET cc_start: 0.9107 (ptt) cc_final: 0.8825 (ptt)
REVERT: A  394 GLU cc_start: 0.8286 (tt0) cc_final: 0.7987 (mm-30)
REVERT: A  400 LYS cc_start: 0.7765 (ptmt) cc_final: 0.7264 (ptmm)
REVERT: A  452 MET cc_start: 0.8505 (ptm) cc_final: 0.8305 (ptp)
REVERT: A  465 ILE cc_start: 0.8739 (mt) cc_final: 0.8525 (mp)
REVERT: A  466 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8105 (mt-10)
REVERT: A  473 SER cc_start: 0.8591 (m) cc_final: 0.8327 (m)
REVERT: A  494 MET cc_start: 0.9087 (ttt) cc_final: 0.8845 (ttm)
REVERT: A  576 HIS cc_start: 0.7478 (m170) cc_final: 0.7209 (m-70)
REVERT: A  599 LEU cc_start: 0.8514 (pt) cc_final: 0.8143 (mp)
REVERT: A  650 LYS cc_start: 0.8822 (mttt) cc_final: 0.8491 (mttp)
REVERT: A  876 LYS cc_start: 0.6633 (mtmm) cc_final: 0.6257 (mtmm)
REVERT: A  881 ASP cc_start: 0.8322 (m-30) cc_final: 0.8059 (m-30)
REVERT: A  945 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8428 (tp)
REVERT: A  954 LEU cc_start: 0.8786 (tp) cc_final: 0.8564 (mm)
REVERT: A  968 MET cc_start: 0.8821 (tpt) cc_final: 0.8610 (tpp)
  outliers start: 19
  outliers final: 12
  residues processed: 126
  average time/residue: 1.2131
  time to fit residues: 162.0715
Evaluate side-chains
  132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  898 MET
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.124490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.094602 restraints weight = 8839.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 1.72
r_work: 0.2762 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   7985  Z= 0.406
  Angle     :  0.665  12.287  10844  Z= 0.330
  Chirality :  0.048   0.180   1273
  Planarity :  0.005   0.066   1377
  Dihedral  :  9.064 178.079   1103
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.29 %
    Favored  : 79.75 %
  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:  0.54 (0.26), residues: 1007
  helix:  1.23 (0.23), residues: 514
  sheet: -0.44 (0.45), residues: 124
  loop : -0.49 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 854 
 HIS   0.007   0.001   HIS A 566 
 PHE   0.023   0.002   PHE A 367 
 TYR   0.018   0.003   TYR A 842 
 ARG   0.007   0.001   ARG A 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6046.35 seconds
wall clock time: 107 minutes 15.24 seconds (6435.24 seconds total)