Starting phenix.real_space_refine
on Wed Mar 12 14:44:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lle_0912/03_2025/6lle_0912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lle_0912/03_2025/6lle_0912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2025/6lle_0912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2025/6lle_0912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2025/6lle_0912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2025/6lle_0912.cif"
  }
  resolution = 2.9
  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=   0.020
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      58      5.16       5
     C    5038      2.51       5
     N    1319      2.21       5
     O    1495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7916
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1020, 7882
          Classifications: {'peptide': 1020}
          Link IDs: {'PTRANS': 46, 'TRANS': 973}
          Chain breaks: 2
    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: 4.59, per 1000 atoms: 0.58
  Number of scatterers: 7916
  At special positions: 0
  Unit cell: (93.375, 78.435, 141.93, 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      58     16.00
     P       3     15.00
     Mg      1     11.99
     O    1495      8.00
     N    1319      7.00
     C    5038      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: 1.96
  Conformation dependent library (CDL) restraints added in 887.6 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      52.6% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
      removed outlier: 3.874A  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 76
    Processing helix  chain 'A' and resid 88 through 120
      removed outlier: 3.801A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.603A  pdb=" N   THR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 274
    Processing helix  chain 'A' and resid 276 through 280
      removed outlier: 3.631A  pdb=" N   PHE A 279 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 4.229A  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 287 through 307
      removed outlier: 3.512A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 328
    Processing helix  chain 'A' and resid 335 through 344
      removed outlier: 3.715A  pdb=" N   GLU A 340 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR A 341 " --> pdb=" O   SER A 338 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   LEU A 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 420
      removed outlier: 3.732A  pdb=" N   GLU A 412 " --> pdb=" O   ASP A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 516 through 523
      removed outlier: 3.602A  pdb=" N   ARG A 523 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.687A  pdb=" N   LYS A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   MET A 545 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 575
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 4.110A  pdb=" N   ILE A 584 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.511A  pdb=" N   LYS A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
    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: 4.005A  pdb=" N   CYS A 669 " --> pdb=" O   GLN A 665 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A 670 " --> pdb=" O   ARG A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.640A  pdb=" N   VAL A 687 " --> pdb=" O   LYS A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 713
      removed outlier: 3.513A  pdb=" N   LYS A 712 " --> pdb=" O   PRO A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 729
    Processing helix  chain 'A' and resid 740 through 781
      removed outlier: 3.543A  pdb=" N   ALA A 744 " --> pdb=" O   SER A 740 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.827A  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: 3.683A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (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 890
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.329A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 912 " --> pdb=" O   MET A 908 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASN A 913 " --> pdb=" O   CYS A 909 " (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 952 through 957
    Processing helix  chain 'A' and resid 962 through 974
      removed outlier: 3.641A  pdb=" N   MET A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.915A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      removed outlier: 3.638A  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: 4.556A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 7.137A  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 188
      removed outlier: 6.294A  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: 6.331A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   PHE A 652 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.927A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.085A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.739A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   SER A 493 " --> pdb=" O   GLU A 486 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   GLU A 486 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER A 495 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   THR A 484 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   TYR A 497 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.927A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.085A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.739A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LEU A 590 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLY A 594 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 428

    427 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 2.34 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: 2592
        1.35 -     1.48: 1830
        1.48 -     1.61: 3546
        1.61 -     1.73: 4
        1.73 -     1.86: 92
  Bond restraints: 8064
  Sorted by residual:
  bond pdb=" C1' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.390  1.617 -0.227 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C1' ACP A2001 "
       pdb=" C2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.527  1.306  0.221 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" C4' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.428  1.299  0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C6  ACP A2001 "
       pdb=" N6  ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.335  1.451 -0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" C2' ACP A2001 "
       pdb=" O2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.401  1.493 -0.092 2.00e-02 2.50e+03 2.13e+01
  ... (remaining 8059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 10885
        3.05 -     6.10: 56
        6.10 -     9.14: 5
        9.14 -    12.19: 4
       12.19 -    15.24: 1
  Bond angle restraints: 10951
  Sorted by residual:
  angle pdb=" O3A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O5' ACP A2001 "
      ideal   model   delta    sigma   weight residual
      93.75  108.99  -15.24 3.00e+00 1.11e-01 2.58e+01
  angle pdb=" C3B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O3A ACP A2001 "
      ideal   model   delta    sigma   weight residual
      98.05  110.24  -12.19 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" O1B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O2B ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.60  109.22   10.38 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N1  ACP A2001 "
        pdb=" C6  ACP A2001 "
        pdb=" N6  ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.32  109.04   10.28 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" O1A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O2A ACP A2001 "
      ideal   model   delta    sigma   weight residual
     118.95  108.80   10.15 3.00e+00 1.11e-01 1.14e+01
  ... (remaining 10946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.50: 4684
       23.50 -    47.00: 182
       47.00 -    70.49: 20
       70.49 -    93.99: 10
       93.99 -   117.49: 1
  Dihedral angle restraints: 4897
    sinusoidal: 1951
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  ILE A 153 "
           pdb=" C   ILE A 153 "
           pdb=" N   ALA A 154 "
           pdb=" CA  ALA A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.82   27.18     0      5.00e+00 4.00e-02 2.95e+01
  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   68.74 -117.49     1      3.00e+01 1.11e-03 1.56e+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 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 4894 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1184
       0.079 -    0.158: 97
       0.158 -    0.237: 1
       0.237 -    0.316: 0
       0.316 -    0.395: 1
  Chirality restraints: 1283
  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   -0.40 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" CB  ILE A 153 "
            pdb=" CA  ILE A 153 "
            pdb=" CG1 ILE A 153 "
            pdb=" CG2 ILE A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.37e-01
  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    2.56   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 1280 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A1016 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO A1017 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A1017 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1017 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 661 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 662 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 662 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 662 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO A 975 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 91
        2.62 -     3.19: 6955
        3.19 -     3.76: 12323
        3.76 -     4.33: 17608
        4.33 -     4.90: 29040
  Nonbonded interactions: 66017
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.050 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.114 2.170
  nonbonded pdb=" OD1 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.170 2.170
  nonbonded pdb=" O3G ACP A2001 "
            pdb="MG    MG A2002 "
     model   vdw
     2.171 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.192 2.170
  ... (remaining 66012 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:             0.210
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.610
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
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   0.227   8064  Z= 0.345
  Angle     :  0.632  15.238  10951  Z= 0.315
  Chirality :  0.043   0.395   1283
  Planarity :  0.004   0.036   1390
  Dihedral  : 13.044 117.490   2987
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  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: -1.87 (0.24), residues: 1014
  helix: -0.83 (0.22), residues: 472
  sheet: -1.09 (0.47), residues: 104
  loop : -1.62 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 793 
 HIS   0.007   0.001   HIS A 566 
 PHE   0.012   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.005   0.000   ARG A 677 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  251 GLN cc_start: 0.7762 (mt0) cc_final: 0.7538 (mt0)
REVERT: A  394 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: A  439 GLU cc_start: 0.7554 (tt0) cc_final: 0.7331 (tt0)
REVERT: A  479 MET cc_start: 0.7209 (mtt) cc_final: 0.6970 (mtp)
REVERT: A  531 SER cc_start: 0.9135 (p) cc_final: 0.8890 (p)
REVERT: A  545 MET cc_start: 0.8044 (mmm) cc_final: 0.7714 (mmm)
REVERT: A  572 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6681 (tpt-90)
REVERT: A  575 MET cc_start: 0.9284 (mtt) cc_final: 0.8931 (mtt)
REVERT: A  667 ASP cc_start: 0.7962 (t0) cc_final: 0.7745 (t0)
REVERT: A  816 MET cc_start: 0.8749 (mmm) cc_final: 0.8486 (mmm)
REVERT: A  917 GLU cc_start: 0.7797 (tt0) cc_final: 0.7484 (tt0)
REVERT: A  940 MET cc_start: 0.8639 (mmm) cc_final: 0.8180 (mmm)
REVERT: A 1023 MET cc_start: 0.6803 (tpp) cc_final: 0.6589 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 1.2031
  time to fit residues: 232.8755
Evaluate side-chains
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.0170
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A  15 HIS
A 190 HIS
A 275 ASN
A 469 ASN
A 817 ASN
A 913 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.143276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.112236 restraints weight = 8338.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.65
r_work: 0.2951 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8064  Z= 0.164
  Angle     :  0.514   6.609  10951  Z= 0.265
  Chirality :  0.042   0.150   1283
  Planarity :  0.004   0.036   1390
  Dihedral  :  7.981 143.597   1110
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.03 %
    Favored  : 85.45 %
  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: -0.46 (0.26), residues: 1014
  helix:  0.59 (0.24), residues: 481
  sheet: -0.86 (0.44), residues: 118
  loop : -1.12 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 793 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.017   0.001   PHE A 367 
 TYR   0.014   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 365 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7457 (ttmt)
REVERT: A   51 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7535 (pt0)
REVERT: A  135 LYS cc_start: 0.8717 (tptp) cc_final: 0.8278 (mtpp)
REVERT: A  251 GLN cc_start: 0.7957 (mt0) cc_final: 0.7669 (mt0)
REVERT: A  280 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7790 (p0)
REVERT: A  309 GLU cc_start: 0.8770 (pm20) cc_final: 0.8554 (pm20)
REVERT: A  394 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: A  456 ASP cc_start: 0.7984 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  476 LYS cc_start: 0.8198 (mttt) cc_final: 0.7996 (mttm)
REVERT: A  479 MET cc_start: 0.7237 (mtt) cc_final: 0.6938 (mtp)
REVERT: A  531 SER cc_start: 0.9144 (p) cc_final: 0.8927 (p)
REVERT: A  545 MET cc_start: 0.8287 (mmm) cc_final: 0.7849 (mmm)
REVERT: A  572 ARG cc_start: 0.6827 (tpt90) cc_final: 0.6588 (tpt-90)
REVERT: A  575 MET cc_start: 0.9155 (mtt) cc_final: 0.8785 (mtt)
REVERT: A  599 LEU cc_start: 0.8931 (pp) cc_final: 0.8626 (pt)
REVERT: A  816 MET cc_start: 0.8902 (mmm) cc_final: 0.8559 (mmm)
REVERT: A  940 MET cc_start: 0.8676 (mmm) cc_final: 0.8387 (mmm)
REVERT: A  979 MET cc_start: 0.8631 (ttm) cc_final: 0.8333 (ttm)
  outliers start: 22
  outliers final: 5
  residues processed: 140
  average time/residue: 1.0589
  time to fit residues: 158.2328
Evaluate side-chains
  116 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 109
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 80 optimal weight:    0.4980
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.1382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.144888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.114158 restraints weight = 8562.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.62
r_work: 0.2911 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8064  Z= 0.229
  Angle     :  0.547   6.943  10951  Z= 0.278
  Chirality :  0.043   0.220   1283
  Planarity :  0.004   0.038   1390
  Dihedral  :  8.225 148.063   1110
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 13.17 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 1014
  helix:  1.06 (0.24), residues: 486
  sheet: -0.65 (0.45), residues: 117
  loop : -0.94 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 793 
 HIS   0.006   0.001   HIS A 566 
 PHE   0.019   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 677 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7520 (mtmt)
REVERT: A   51 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7591 (pt0)
REVERT: A  135 LYS cc_start: 0.8717 (tptp) cc_final: 0.8296 (mtmt)
REVERT: A  198 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7412 (mmp80)
REVERT: A  251 GLN cc_start: 0.8022 (mt0) cc_final: 0.7799 (mt0)
REVERT: A  280 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7892 (p0)
REVERT: A  309 GLU cc_start: 0.8869 (pm20) cc_final: 0.8558 (pm20)
REVERT: A  394 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7609 (mt-10)
REVERT: A  479 MET cc_start: 0.7226 (mtt) cc_final: 0.6898 (mtp)
REVERT: A  531 SER cc_start: 0.9161 (p) cc_final: 0.8946 (p)
REVERT: A  545 MET cc_start: 0.8311 (mmm) cc_final: 0.7947 (mmm)
REVERT: A  575 MET cc_start: 0.9128 (mtt) cc_final: 0.8717 (mtt)
REVERT: A  623 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8791 (mt)
REVERT: A  816 MET cc_start: 0.8903 (mmm) cc_final: 0.8641 (mmm)
REVERT: A  940 MET cc_start: 0.8674 (mmm) cc_final: 0.8318 (mmm)
  outliers start: 29
  outliers final: 10
  residues processed: 136
  average time/residue: 1.0284
  time to fit residues: 149.7971
Evaluate side-chains
  124 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.136981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.104694 restraints weight = 8463.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.69
r_work: 0.2943 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8064  Z= 0.223
  Angle     :  0.537   7.557  10951  Z= 0.273
  Chirality :  0.043   0.197   1283
  Planarity :  0.004   0.040   1390
  Dihedral  :  8.330 154.175   1110
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 14.09 %
    Favored  : 81.79 %
  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:  0.20 (0.27), residues: 1014
  helix:  1.19 (0.24), residues: 493
  sheet: -0.65 (0.45), residues: 116
  loop : -0.89 (0.30), residues: 405

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   0.018   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.005   0.000   ARG A 572 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7421 (mtmt)
REVERT: A   51 GLU cc_start: 0.7970 (tt0) cc_final: 0.7558 (pt0)
REVERT: A   77 TRP cc_start: 0.6571 (OUTLIER) cc_final: 0.5870 (m100)
REVERT: A  135 LYS cc_start: 0.8743 (tptp) cc_final: 0.8307 (mtpp)
REVERT: A  198 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7448 (mmp80)
REVERT: A  251 GLN cc_start: 0.7913 (mt0) cc_final: 0.7692 (mt0)
REVERT: A  280 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7925 (p0)
REVERT: A  309 GLU cc_start: 0.8854 (pm20) cc_final: 0.8554 (pm20)
REVERT: A  394 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7611 (mt-10)
REVERT: A  479 MET cc_start: 0.7166 (mtt) cc_final: 0.6814 (mtp)
REVERT: A  531 SER cc_start: 0.9161 (p) cc_final: 0.8948 (p)
REVERT: A  545 MET cc_start: 0.8306 (mmm) cc_final: 0.7964 (mmm)
REVERT: A  575 MET cc_start: 0.9093 (mtt) cc_final: 0.8744 (mtt)
REVERT: A  816 MET cc_start: 0.8900 (mmm) cc_final: 0.8630 (mmm)
REVERT: A  940 MET cc_start: 0.8686 (mmm) cc_final: 0.8406 (mmm)
REVERT: A  979 MET cc_start: 0.8631 (ttm) cc_final: 0.8331 (ttm)
  outliers start: 36
  outliers final: 15
  residues processed: 137
  average time/residue: 1.0583
  time to fit residues: 155.1079
Evaluate side-chains
  130 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.145312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.114598 restraints weight = 8438.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.62
r_work: 0.2950 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8064  Z= 0.190
  Angle     :  0.522   7.793  10951  Z= 0.264
  Chirality :  0.042   0.171   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.296 153.696   1110
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.12 %
    Favored  : 81.21 %
  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:  0.56 (0.27), residues: 1014
  helix:  1.52 (0.24), residues: 487
  sheet: -0.52 (0.46), residues: 116
  loop : -0.72 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 793 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.016   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 572 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7465 (mtmt)
REVERT: A   51 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7579 (pt0)
REVERT: A   77 TRP cc_start: 0.6848 (OUTLIER) cc_final: 0.6254 (m100)
REVERT: A  135 LYS cc_start: 0.8738 (tptp) cc_final: 0.8322 (mtmt)
REVERT: A  153 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6971 (mt)
REVERT: A  198 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7420 (mmp80)
REVERT: A  394 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7612 (mt-10)
REVERT: A  479 MET cc_start: 0.7186 (mtt) cc_final: 0.6829 (mtp)
REVERT: A  531 SER cc_start: 0.9170 (p) cc_final: 0.8943 (p)
REVERT: A  545 MET cc_start: 0.8453 (mmm) cc_final: 0.8090 (mmm)
REVERT: A  575 MET cc_start: 0.9120 (mtt) cc_final: 0.8786 (mtt)
REVERT: A  623 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8846 (mt)
REVERT: A  816 MET cc_start: 0.8902 (mmm) cc_final: 0.8597 (mmm)
REVERT: A  940 MET cc_start: 0.8763 (mmm) cc_final: 0.8524 (mmm)
REVERT: A  979 MET cc_start: 0.8664 (ttm) cc_final: 0.8373 (ttm)
  outliers start: 32
  outliers final: 16
  residues processed: 139
  average time/residue: 1.1462
  time to fit residues: 169.9881
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0030
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 101 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.0392

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 472 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.137939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.105752 restraints weight = 8437.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.69
r_work: 0.2898 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8064  Z= 0.213
  Angle     :  0.531   8.362  10951  Z= 0.270
  Chirality :  0.042   0.165   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.328 154.770   1110
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.04 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 1014
  helix:  1.61 (0.24), residues: 485
  sheet: -0.35 (0.47), residues: 116
  loop : -0.69 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 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   0.004   0.000   ARG A 572 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 1.146 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7405 (mtmt)
REVERT: A   33 LYS cc_start: 0.8012 (tttt) cc_final: 0.7576 (ttmt)
REVERT: A   51 GLU cc_start: 0.8005 (tt0) cc_final: 0.7609 (pt0)
REVERT: A   71 ILE cc_start: 0.8670 (mt) cc_final: 0.8422 (mt)
REVERT: A   77 TRP cc_start: 0.6808 (OUTLIER) cc_final: 0.6318 (m100)
REVERT: A  135 LYS cc_start: 0.8651 (tptp) cc_final: 0.8281 (mtmt)
REVERT: A  198 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7417 (mmp80)
REVERT: A  394 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7617 (mt-10)
REVERT: A  479 MET cc_start: 0.7255 (mtt) cc_final: 0.6874 (mtp)
REVERT: A  531 SER cc_start: 0.9167 (p) cc_final: 0.8938 (p)
REVERT: A  545 MET cc_start: 0.8405 (mmm) cc_final: 0.8045 (mmm)
REVERT: A  575 MET cc_start: 0.9091 (mtt) cc_final: 0.8741 (mtt)
REVERT: A  623 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8840 (mt)
REVERT: A  816 MET cc_start: 0.8892 (mmm) cc_final: 0.8606 (mmm)
REVERT: A  940 MET cc_start: 0.8714 (mmm) cc_final: 0.8480 (mmm)
  outliers start: 31
  outliers final: 17
  residues processed: 137
  average time/residue: 1.1285
  time to fit residues: 164.9653
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0770
   chunk 64 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.0742

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 566 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.146405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.115805 restraints weight = 8476.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.61
r_work: 0.2939 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8064  Z= 0.218
  Angle     :  0.537   8.493  10951  Z= 0.272
  Chirality :  0.042   0.173   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.394 155.720   1110
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.95 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.71 (0.27), residues: 1014
  helix:  1.65 (0.24), residues: 484
  sheet: -0.31 (0.47), residues: 116
  loop : -0.68 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 HIS   0.004   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7484 (mtmt)
REVERT: A   33 LYS cc_start: 0.8018 (tttt) cc_final: 0.7616 (ttmt)
REVERT: A   51 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7699 (pt0)
REVERT: A   71 ILE cc_start: 0.8754 (mt) cc_final: 0.8515 (mt)
REVERT: A  135 LYS cc_start: 0.8673 (tptp) cc_final: 0.8305 (mtpp)
REVERT: A  198 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7434 (mmp80)
REVERT: A  394 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7630 (mt-10)
REVERT: A  479 MET cc_start: 0.7305 (mtt) cc_final: 0.6928 (mtp)
REVERT: A  531 SER cc_start: 0.9150 (p) cc_final: 0.8927 (p)
REVERT: A  545 MET cc_start: 0.8479 (mmm) cc_final: 0.8117 (mmm)
REVERT: A  575 MET cc_start: 0.9120 (mtt) cc_final: 0.8804 (mtt)
REVERT: A  623 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8869 (mt)
REVERT: A  816 MET cc_start: 0.8911 (mmm) cc_final: 0.8595 (mmm)
REVERT: A  940 MET cc_start: 0.8781 (mmm) cc_final: 0.8563 (mmm)
REVERT: A 1023 MET cc_start: 0.6552 (tpt) cc_final: 0.6212 (tpp)
  outliers start: 30
  outliers final: 16
  residues processed: 140
  average time/residue: 1.1576
  time to fit residues: 173.0694
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 421 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.135813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.103335 restraints weight = 8565.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.70
r_work: 0.3048 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8064  Z= 0.267
  Angle     :  0.564   9.044  10951  Z= 0.286
  Chirality :  0.044   0.194   1283
  Planarity :  0.004   0.040   1390
  Dihedral  :  8.475 158.650   1110
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 17.18 %
    Favored  : 78.92 %
  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:  0.63 (0.27), residues: 1014
  helix:  1.55 (0.24), residues: 484
  sheet: -0.29 (0.47), residues: 116
  loop : -0.70 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.020   0.001   PHE A 367 
 TYR   0.017   0.002   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7303 (mtmt)
REVERT: A   51 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7613 (pt0)
REVERT: A   71 ILE cc_start: 0.8643 (mt) cc_final: 0.8391 (mt)
REVERT: A  135 LYS cc_start: 0.8744 (tptp) cc_final: 0.8345 (mttt)
REVERT: A  198 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7409 (mmp80)
REVERT: A  394 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7611 (mt-10)
REVERT: A  479 MET cc_start: 0.7291 (mtt) cc_final: 0.6914 (mtp)
REVERT: A  531 SER cc_start: 0.9167 (p) cc_final: 0.8955 (p)
REVERT: A  545 MET cc_start: 0.8318 (mmm) cc_final: 0.8002 (mmm)
REVERT: A  575 MET cc_start: 0.9091 (mtt) cc_final: 0.8767 (mtt)
REVERT: A  623 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8870 (mt)
REVERT: A  784 GLU cc_start: 0.8432 (mp0) cc_final: 0.8057 (mt-10)
REVERT: A  816 MET cc_start: 0.8876 (mmm) cc_final: 0.8545 (mmm)
REVERT: A  940 MET cc_start: 0.8688 (mmm) cc_final: 0.8451 (mmm)
REVERT: A 1023 MET cc_start: 0.6581 (tpt) cc_final: 0.6211 (tpp)
  outliers start: 34
  outliers final: 21
  residues processed: 141
  average time/residue: 1.1968
  time to fit residues: 180.6754
Evaluate side-chains
  140 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0470
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.5478

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.144316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113430 restraints weight = 8465.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.63
r_work: 0.3106 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8064  Z= 0.164
  Angle     :  0.519   9.452  10951  Z= 0.263
  Chirality :  0.041   0.132   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.316 156.411   1110
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.67 %
    Favored  : 78.69 %
  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:  0.89 (0.27), residues: 1014
  helix:  1.79 (0.25), residues: 486
  sheet: -0.26 (0.47), residues: 116
  loop : -0.57 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 793 
 HIS   0.001   0.000   HIS A 526 
 PHE   0.015   0.001   PHE A 367 
 TYR   0.014   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.217 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7403 (mtmt)
REVERT: A   33 LYS cc_start: 0.7949 (tttt) cc_final: 0.7536 (ttmt)
REVERT: A   51 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7671 (pt0)
REVERT: A   71 ILE cc_start: 0.8728 (mt) cc_final: 0.8486 (mt)
REVERT: A  117 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7334 (pt0)
REVERT: A  135 LYS cc_start: 0.8787 (tptp) cc_final: 0.8389 (mtpp)
REVERT: A  394 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7558 (mt-10)
REVERT: A  479 MET cc_start: 0.7280 (mtt) cc_final: 0.6884 (mtp)
REVERT: A  531 SER cc_start: 0.9185 (p) cc_final: 0.8977 (p)
REVERT: A  545 MET cc_start: 0.8422 (mmm) cc_final: 0.8064 (mmm)
REVERT: A  575 MET cc_start: 0.9105 (mtt) cc_final: 0.8769 (mtt)
REVERT: A  623 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8826 (mt)
REVERT: A  816 MET cc_start: 0.8877 (mmm) cc_final: 0.8506 (mmm)
REVERT: A  940 MET cc_start: 0.8756 (mmm) cc_final: 0.8550 (mmm)
REVERT: A  979 MET cc_start: 0.8637 (ttm) cc_final: 0.8376 (ttm)
REVERT: A 1023 MET cc_start: 0.6647 (tpt) cc_final: 0.6270 (tpp)
  outliers start: 23
  outliers final: 15
  residues processed: 142
  average time/residue: 1.2886
  time to fit residues: 197.2976
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  806 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0980
   chunk 9 optimal weight:    0.2980
   chunk 83 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0870
   chunk 74 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.4358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.143253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.112016 restraints weight = 8457.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.65
r_work: 0.2993 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8064  Z= 0.154
  Angle     :  0.506   9.036  10951  Z= 0.257
  Chirality :  0.041   0.134   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.204 154.144   1110
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.70 %
    Favored  : 78.12 %
  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 (0.28), residues: 1014
  helix:  1.91 (0.24), residues: 488
  sheet: -0.18 (0.47), residues: 117
  loop : -0.43 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 793 
 HIS   0.001   0.000   HIS A 526 
 PHE   0.016   0.001   PHE A 367 
 TYR   0.014   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7399 (mtmt)
REVERT: A   51 GLU cc_start: 0.8012 (tt0) cc_final: 0.7664 (pt0)
REVERT: A   71 ILE cc_start: 0.8652 (mt) cc_final: 0.8411 (mt)
REVERT: A  135 LYS cc_start: 0.8737 (tptp) cc_final: 0.8358 (mttt)
REVERT: A  394 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7564 (mt-10)
REVERT: A  479 MET cc_start: 0.7252 (mtt) cc_final: 0.6922 (mtp)
REVERT: A  531 SER cc_start: 0.9160 (p) cc_final: 0.8959 (p)
REVERT: A  545 MET cc_start: 0.8437 (mmm) cc_final: 0.8077 (mmm)
REVERT: A  575 MET cc_start: 0.9088 (mtt) cc_final: 0.8770 (mtt)
REVERT: A  623 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8815 (mt)
REVERT: A  682 HIS cc_start: 0.8207 (m-70) cc_final: 0.7794 (m170)
REVERT: A  816 MET cc_start: 0.8830 (mmm) cc_final: 0.8502 (mmm)
REVERT: A  940 MET cc_start: 0.8745 (mmm) cc_final: 0.8448 (mmm)
REVERT: A  979 MET cc_start: 0.8638 (ttm) cc_final: 0.8360 (ttm)
REVERT: A 1023 MET cc_start: 0.6592 (tpt) cc_final: 0.6211 (tpp)
  outliers start: 19
  outliers final: 13
  residues processed: 138
  average time/residue: 1.1582
  time to fit residues: 170.6517
Evaluate side-chains
  128 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  806 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0570
   chunk 36 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.0104

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.147339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.116798 restraints weight = 8522.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.59
r_work: 0.3055 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8064  Z= 0.220
  Angle     :  0.537   8.753  10951  Z= 0.273
  Chirality :  0.042   0.148   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.312 154.799   1110
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.70 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.27), residues: 1014
  helix:  1.82 (0.24), residues: 486
  sheet: -0.21 (0.47), residues: 117
  loop : -0.46 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 572 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5950.64 seconds
wall clock time: 103 minutes 3.70 seconds (6183.70 seconds total)