Starting phenix.real_space_refine
on Fri Jul 25 19:43:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lle_0912/07_2025/6lle_0912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lle_0912/07_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_0912/07_2025/6lle_0912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lle_0912/07_2025/6lle_0912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lle_0912/07_2025/6lle_0912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lle_0912/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.08, per 1000 atoms: 0.64
  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: 2.22
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.94
  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: 2.63

  Time building geometry restraints manager: 2.61 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:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.990
  Find NCS groups from input model:        0.230
  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:12.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.050
-------------------------------------------------------------------------------
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= 0.260
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14837 (  415)
  hydrogen bonds       : angle       6.66692 ( 1209)
  covalent geometry    : bond        0.00540 ( 8064)
  covalent geometry    : angle       0.63241 (10951)

*********************** 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  : 1.087 
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: 1.3203
  time to fit residues: 255.3265
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  : 0.881 
-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.143406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.112333 restraints weight = 8333.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.66
r_work: 0.2954 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1412

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= 0.111
  Angle     :  0.512   6.638  10951  Z= 0.264
  Chirality :  0.042   0.150   1283
  Planarity :  0.004   0.036   1390
  Dihedral  :  7.990 144.284   1110
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.49 %
    Favored  : 85.22 %
  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: -0.45 (0.26), residues: 1014
  helix:  0.61 (0.24), residues: 480
  sheet: -0.86 (0.44), residues: 118
  loop : -1.13 (0.30), residues: 416

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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  415)
  hydrogen bonds       : angle       4.54578 ( 1209)
  covalent geometry    : bond        0.00248 ( 8064)
  covalent geometry    : angle       0.51242 (10951)

*********************** 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
  149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7458 (ttmt)
REVERT: A   51 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7501 (pt0)
REVERT: A  135 LYS cc_start: 0.8722 (tptp) cc_final: 0.8282 (mtpp)
REVERT: A  251 GLN cc_start: 0.7970 (mt0) cc_final: 0.7692 (mt0)
REVERT: A  280 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7817 (p0)
REVERT: A  309 GLU cc_start: 0.8770 (pm20) cc_final: 0.8556 (pm20)
REVERT: A  394 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: A  456 ASP cc_start: 0.7994 (m-30) cc_final: 0.7708 (m-30)
REVERT: A  479 MET cc_start: 0.7237 (mtt) cc_final: 0.6942 (mtp)
REVERT: A  531 SER cc_start: 0.9144 (p) cc_final: 0.8925 (p)
REVERT: A  545 MET cc_start: 0.8292 (mmm) cc_final: 0.7855 (mmm)
REVERT: A  572 ARG cc_start: 0.6816 (tpt90) cc_final: 0.6585 (tpt-90)
REVERT: A  575 MET cc_start: 0.9164 (mtt) cc_final: 0.8744 (mtt)
REVERT: A  599 LEU cc_start: 0.8923 (pp) cc_final: 0.8597 (pt)
REVERT: A  816 MET cc_start: 0.8901 (mmm) cc_final: 0.8560 (mmm)
REVERT: A  940 MET cc_start: 0.8681 (mmm) cc_final: 0.8392 (mmm)
REVERT: A  979 MET cc_start: 0.8631 (ttm) cc_final: 0.8333 (ttm)
  outliers start: 20
  outliers final: 4
  residues processed: 138
  average time/residue: 1.1362
  time to fit residues: 167.2476
Evaluate side-chains
  114 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0980
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.146564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.116053 restraints weight = 8535.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.62
r_work: 0.2984 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8064  Z= 0.115
  Angle     :  0.516   6.871  10951  Z= 0.262
  Chirality :  0.042   0.188   1283
  Planarity :  0.003   0.037   1390
  Dihedral  :  8.036 144.834   1110
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.63 %
    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:  0.20 (0.27), residues: 1014
  helix:  1.18 (0.24), residues: 481
  sheet: -0.46 (0.46), residues: 114
  loop : -0.89 (0.30), residues: 419

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   0.014   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  415)
  hydrogen bonds       : angle       4.36206 ( 1209)
  covalent geometry    : bond        0.00266 ( 8064)
  covalent geometry    : angle       0.51570 (10951)

*********************** 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: 25
    poor density    : 122
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7537 (mtmt)
REVERT: A   51 GLU cc_start: 0.7958 (tt0) cc_final: 0.7544 (pt0)
REVERT: A  135 LYS cc_start: 0.8721 (tptp) cc_final: 0.8311 (mtmt)
REVERT: A  251 GLN cc_start: 0.8035 (mt0) cc_final: 0.7811 (mt0)
REVERT: A  309 GLU cc_start: 0.8818 (pm20) cc_final: 0.8563 (pm20)
REVERT: A  394 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7582 (mt-10)
REVERT: A  476 LYS cc_start: 0.8281 (mttt) cc_final: 0.8079 (mttm)
REVERT: A  479 MET cc_start: 0.7256 (mtt) cc_final: 0.6945 (mtp)
REVERT: A  531 SER cc_start: 0.9150 (p) cc_final: 0.8933 (p)
REVERT: A  545 MET cc_start: 0.8358 (mmm) cc_final: 0.7995 (mmm)
REVERT: A  575 MET cc_start: 0.9128 (mtt) cc_final: 0.8788 (mtt)
REVERT: A  599 LEU cc_start: 0.8829 (pp) cc_final: 0.8455 (pt)
REVERT: A  816 MET cc_start: 0.8904 (mmm) cc_final: 0.8616 (mmm)
REVERT: A  940 MET cc_start: 0.8674 (mmm) cc_final: 0.8320 (mmm)
  outliers start: 25
  outliers final: 11
  residues processed: 139
  average time/residue: 1.0655
  time to fit residues: 158.3288
Evaluate side-chains
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  499 THR
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  967 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3501 r_free = 0.3501 target = 0.138025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.105944 restraints weight = 8431.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.68
r_work: 0.2898 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8064  Z= 0.137
  Angle     :  0.534   7.426  10951  Z= 0.271
  Chirality :  0.043   0.188   1283
  Planarity :  0.004   0.036   1390
  Dihedral  :  8.233 150.205   1110
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 13.97 %
    Favored  : 82.13 %
  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:  0.25 (0.27), residues: 1014
  helix:  1.21 (0.24), residues: 493
  sheet: -0.55 (0.46), residues: 117
  loop : -0.88 (0.31), residues: 404

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   0.019   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 572 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03604 (  415)
  hydrogen bonds       : angle       4.30490 ( 1209)
  covalent geometry    : bond        0.00328 ( 8064)
  covalent geometry    : angle       0.53368 (10951)

*********************** 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
  152 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: A   31 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7441 (mtmt)
REVERT: A   51 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7608 (pt0)
REVERT: A  135 LYS cc_start: 0.8720 (tptp) cc_final: 0.8288 (mtpp)
REVERT: A  198 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7403 (mmp80)
REVERT: A  251 GLN cc_start: 0.7975 (mt0) cc_final: 0.7736 (mt0)
REVERT: A  280 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7903 (p0)
REVERT: A  309 GLU cc_start: 0.8857 (pm20) cc_final: 0.8527 (pm20)
REVERT: A  394 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7605 (mt-10)
REVERT: A  479 MET cc_start: 0.7238 (mtt) cc_final: 0.6914 (mtp)
REVERT: A  531 SER cc_start: 0.9156 (p) cc_final: 0.8939 (p)
REVERT: A  545 MET cc_start: 0.8305 (mmm) cc_final: 0.7938 (mmm)
REVERT: A  575 MET cc_start: 0.9106 (mtt) cc_final: 0.8745 (mtt)
REVERT: A  623 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8827 (mt)
REVERT: A  816 MET cc_start: 0.8883 (mmm) cc_final: 0.8614 (mmm)
  outliers start: 34
  outliers final: 16
  residues processed: 138
  average time/residue: 1.0582
  time to fit residues: 156.1124
Evaluate side-chains
  132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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  207 MET
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  369 LEU
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  499 THR
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  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:    7.9990
   chunk 4 optimal weight:    0.0770
   chunk 92 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.142786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.111600 restraints weight = 8511.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.65
r_work: 0.2972 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8064  Z= 0.107
  Angle     :  0.508   7.692  10951  Z= 0.257
  Chirality :  0.041   0.156   1283
  Planarity :  0.003   0.036   1390
  Dihedral  :  8.194 150.921   1110
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 15.23 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 1014
  helix:  1.59 (0.24), residues: 486
  sheet: -0.44 (0.47), residues: 117
  loop : -0.74 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 HIS   0.003   0.001   HIS A 566 
 PHE   0.016   0.001   PHE A 367 
 TYR   0.013   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 572 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  415)
  hydrogen bonds       : angle       4.14137 ( 1209)
  covalent geometry    : bond        0.00248 ( 8064)
  covalent geometry    : angle       0.50801 (10951)

*********************** 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
  155 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A   31 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7476 (mtmt)
REVERT: A   51 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7595 (pt0)
REVERT: A   77 TRP cc_start: 0.6727 (OUTLIER) cc_final: 0.6047 (m100)
REVERT: A  135 LYS cc_start: 0.8717 (tptp) cc_final: 0.8304 (mtmt)
REVERT: A  153 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7060 (mt)
REVERT: A  198 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7425 (mmp80)
REVERT: A  251 GLN cc_start: 0.8002 (mt0) cc_final: 0.7789 (mt0)
REVERT: A  280 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7925 (p0)
REVERT: A  309 GLU cc_start: 0.8847 (pm20) cc_final: 0.8581 (pm20)
REVERT: A  394 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7572 (mt-10)
REVERT: A  479 MET cc_start: 0.7211 (mtt) cc_final: 0.6884 (mtp)
REVERT: A  531 SER cc_start: 0.9164 (p) cc_final: 0.8949 (p)
REVERT: A  545 MET cc_start: 0.8338 (mmm) cc_final: 0.7962 (mmm)
REVERT: A  575 MET cc_start: 0.9105 (mtt) cc_final: 0.8748 (mtt)
REVERT: A  623 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8803 (mt)
REVERT: A  816 MET cc_start: 0.8885 (mmm) cc_final: 0.8590 (mmm)
REVERT: A  979 MET cc_start: 0.8641 (ttm) cc_final: 0.8358 (ttm)
  outliers start: 34
  outliers final: 14
  residues processed: 141
  average time/residue: 1.0720
  time to fit residues: 161.7049
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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  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  207 MET
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  499 THR
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  681 SER
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:    0.6980
   chunk 52 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.148166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.117363 restraints weight = 8422.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.64
r_work: 0.2976 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8064  Z= 0.114
  Angle     :  0.510   7.847  10951  Z= 0.259
  Chirality :  0.042   0.158   1283
  Planarity :  0.003   0.035   1390
  Dihedral  :  8.216 151.635   1110
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 15.35 %
    Favored  : 80.76 %
  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:  0.77 (0.27), residues: 1014
  helix:  1.71 (0.24), residues: 487
  sheet: -0.34 (0.46), residues: 118
  loop : -0.66 (0.31), residues: 409

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   0.017   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 122 
 ARG   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03284 (  415)
  hydrogen bonds       : angle       4.14449 ( 1209)
  covalent geometry    : bond        0.00270 ( 8064)
  covalent geometry    : angle       0.51045 (10951)

*********************** 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
  152 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7535 (mtmt)
REVERT: A   51 GLU cc_start: 0.8020 (tt0) cc_final: 0.7620 (pt0)
REVERT: A   77 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.6273 (m100)
REVERT: A  135 LYS cc_start: 0.8648 (tptp) cc_final: 0.8318 (mtmt)
REVERT: A  198 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7410 (mmp80)
REVERT: A  280 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7757 (p0)
REVERT: A  309 GLU cc_start: 0.8889 (pm20) cc_final: 0.8567 (pm20)
REVERT: A  394 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: A  479 MET cc_start: 0.7237 (mtt) cc_final: 0.6878 (mtp)
REVERT: A  531 SER cc_start: 0.9167 (p) cc_final: 0.8953 (p)
REVERT: A  545 MET cc_start: 0.8377 (mmm) cc_final: 0.7998 (mmm)
REVERT: A  575 MET cc_start: 0.9123 (mtt) cc_final: 0.8785 (mtt)
REVERT: A  623 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8827 (mt)
REVERT: A  816 MET cc_start: 0.8900 (mmm) cc_final: 0.8584 (mmm)
  outliers start: 34
  outliers final: 17
  residues processed: 140
  average time/residue: 1.2133
  time to fit residues: 181.1504
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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  207 MET
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  499 THR
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  681 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.147863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.117280 restraints weight = 8467.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.62
r_work: 0.2919 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1987

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= 0.117
  Angle     :  0.520  10.149  10951  Z= 0.263
  Chirality :  0.042   0.162   1283
  Planarity :  0.003   0.035   1390
  Dihedral  :  8.227 152.179   1110
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.95 %
    Favored  : 79.84 %
  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:  0.85 (0.27), residues: 1014
  helix:  1.74 (0.24), residues: 487
  sheet: -0.21 (0.47), residues: 118
  loop : -0.60 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   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   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  415)
  hydrogen bonds       : angle       4.13682 ( 1209)
  covalent geometry    : bond        0.00278 ( 8064)
  covalent geometry    : angle       0.52002 (10951)

*********************** 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
  149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7654 (mtpt) cc_final: 0.7377 (mtmt)
REVERT: A   51 GLU cc_start: 0.7983 (tt0) cc_final: 0.7565 (pt0)
REVERT: A   71 ILE cc_start: 0.8689 (mt) cc_final: 0.8448 (mt)
REVERT: A   77 TRP cc_start: 0.6678 (OUTLIER) cc_final: 0.6293 (m100)
REVERT: A  135 LYS cc_start: 0.8620 (tptp) cc_final: 0.8255 (mtmt)
REVERT: A  198 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7387 (mmp80)
REVERT: A  280 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7705 (p0)
REVERT: A  309 GLU cc_start: 0.8849 (pm20) cc_final: 0.8451 (pm20)
REVERT: A  394 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7541 (mt-10)
REVERT: A  479 MET cc_start: 0.7185 (mtt) cc_final: 0.6812 (mtp)
REVERT: A  531 SER cc_start: 0.9157 (p) cc_final: 0.8940 (p)
REVERT: A  545 MET cc_start: 0.8351 (mmm) cc_final: 0.7974 (mmm)
REVERT: A  575 MET cc_start: 0.9084 (mtt) cc_final: 0.8764 (mtt)
REVERT: A  623 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8805 (mt)
REVERT: A  816 MET cc_start: 0.8846 (mmm) cc_final: 0.8544 (mmm)
REVERT: A  908 MET cc_start: 0.9106 (mpp) cc_final: 0.8854 (mpm)
  outliers start: 28
  outliers final: 16
  residues processed: 138
  average time/residue: 1.1854
  time to fit residues: 175.1014
Evaluate side-chains
  135 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  280 ASN
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  499 THR
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  681 SER
Chi-restraints excluded: chain A residue  702 ASP
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:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 472 ASN
A 566 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.145955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115202 restraints weight = 8481.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.60
r_work: 0.2904 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8064  Z= 0.167
  Angle     :  0.574  10.996  10951  Z= 0.290
  Chirality :  0.044   0.205   1283
  Planarity :  0.004   0.035   1390
  Dihedral  :  8.421 157.644   1110
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 17.30 %
    Favored  : 79.38 %
  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:  0.73 (0.27), residues: 1014
  helix:  1.63 (0.24), residues: 484
  sheet: -0.16 (0.47), residues: 117
  loop : -0.67 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.006   0.001   HIS A 566 
 PHE   0.021   0.001   PHE A 367 
 TYR   0.016   0.002   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  415)
  hydrogen bonds       : angle       4.32528 ( 1209)
  covalent geometry    : bond        0.00410 ( 8064)
  covalent geometry    : angle       0.57432 (10951)

*********************** 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
  149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7462 (ttmt)
REVERT: A   33 LYS cc_start: 0.8022 (tttt) cc_final: 0.7601 (ttmt)
REVERT: A   51 GLU cc_start: 0.8082 (tt0) cc_final: 0.7691 (pt0)
REVERT: A   71 ILE cc_start: 0.8732 (mt) cc_final: 0.8485 (mt)
REVERT: A  135 LYS cc_start: 0.8747 (tptp) cc_final: 0.8352 (mtpp)
REVERT: A  198 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7420 (mmp80)
REVERT: A  309 GLU cc_start: 0.8891 (pm20) cc_final: 0.8620 (pm20)
REVERT: A  394 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: A  479 MET cc_start: 0.7271 (mtt) cc_final: 0.6922 (mtp)
REVERT: A  531 SER cc_start: 0.9173 (p) cc_final: 0.8948 (p)
REVERT: A  545 MET cc_start: 0.8394 (mmm) cc_final: 0.8039 (mmm)
REVERT: A  575 MET cc_start: 0.9104 (mtt) cc_final: 0.8765 (mtt)
REVERT: A  623 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8880 (mt)
REVERT: A  784 GLU cc_start: 0.8603 (mp0) cc_final: 0.8199 (mt-10)
REVERT: A  816 MET cc_start: 0.8900 (mmm) cc_final: 0.8582 (mmm)
REVERT: A 1023 MET cc_start: 0.6531 (tpt) cc_final: 0.6184 (tpp)
  outliers start: 29
  outliers final: 18
  residues processed: 141
  average time/residue: 1.1852
  time to fit residues: 177.8010
Evaluate side-chains
  141 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  499 THR
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  967 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    0.4980
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0770
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6340

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.138987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.106694 restraints weight = 8571.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 1.71
r_work: 0.2922 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8064  Z= 0.110
  Angle     :  0.524  11.378  10951  Z= 0.264
  Chirality :  0.041   0.143   1283
  Planarity :  0.003   0.035   1390
  Dihedral  :  8.288 155.110   1110
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.44 %
    Favored  : 79.04 %
  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:  0.91 (0.27), residues: 1014
  helix:  1.76 (0.24), residues: 487
  sheet: -0.10 (0.47), residues: 117
  loop : -0.57 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 793 
 HIS   0.001   0.000   HIS A 566 
 PHE   0.016   0.001   PHE A 367 
 TYR   0.014   0.001   TYR A 295 
 ARG   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  415)
  hydrogen bonds       : angle       4.14590 ( 1209)
  covalent geometry    : bond        0.00257 ( 8064)
  covalent geometry    : angle       0.52405 (10951)

*********************** 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
  146 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 1.421 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7369 (mtmt)
REVERT: A   51 GLU cc_start: 0.8001 (tt0) cc_final: 0.7627 (pt0)
REVERT: A   71 ILE cc_start: 0.8705 (mt) cc_final: 0.8450 (mt)
REVERT: A  135 LYS cc_start: 0.8741 (tptp) cc_final: 0.8329 (mtpp)
REVERT: A  198 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7390 (mmp80)
REVERT: A  309 GLU cc_start: 0.8841 (pm20) cc_final: 0.8523 (pm20)
REVERT: A  394 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7515 (mt-10)
REVERT: A  479 MET cc_start: 0.7189 (mtt) cc_final: 0.6816 (mtp)
REVERT: A  531 SER cc_start: 0.9153 (p) cc_final: 0.8924 (p)
REVERT: A  545 MET cc_start: 0.8402 (mmm) cc_final: 0.8032 (mmm)
REVERT: A  575 MET cc_start: 0.9079 (mtt) cc_final: 0.8754 (mtt)
REVERT: A  623 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8790 (mt)
REVERT: A  659 GLU cc_start: 0.7836 (mt-10) cc_final: 0.6461 (pp20)
REVERT: A  816 MET cc_start: 0.8866 (mmm) cc_final: 0.8538 (mmm)
REVERT: A  979 MET cc_start: 0.8611 (ttm) cc_final: 0.8331 (ttm)
REVERT: A 1023 MET cc_start: 0.6523 (tpt) cc_final: 0.6139 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 142
  average time/residue: 1.6514
  time to fit residues: 248.9611
Evaluate side-chains
  139 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  499 THR
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  967 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:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 95 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.148474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.117985 restraints weight = 8490.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.61
r_work: 0.2945 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8064  Z= 0.118
  Angle     :  0.543  11.949  10951  Z= 0.273
  Chirality :  0.042   0.163   1283
  Planarity :  0.003   0.035   1390
  Dihedral  :  8.265 153.375   1110
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.79 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 1014
  helix:  1.80 (0.25), residues: 485
  sheet: -0.07 (0.47), residues: 118
  loop : -0.52 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.017   0.001   PHE A 367 
 TYR   0.014   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (  415)
  hydrogen bonds       : angle       4.17330 ( 1209)
  covalent geometry    : bond        0.00281 ( 8064)
  covalent geometry    : angle       0.54285 (10951)

********************** 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
  139 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 1.568 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7462 (mtmt)
REVERT: A   51 GLU cc_start: 0.8056 (tt0) cc_final: 0.7699 (pt0)
REVERT: A   71 ILE cc_start: 0.8754 (mt) cc_final: 0.8517 (mt)
REVERT: A  135 LYS cc_start: 0.8748 (tptp) cc_final: 0.8346 (mtpp)
REVERT: A  198 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7408 (mmp80)
REVERT: A  309 GLU cc_start: 0.8867 (pm20) cc_final: 0.8455 (pm20)
REVERT: A  394 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7524 (mt-10)
REVERT: A  479 MET cc_start: 0.7236 (mtt) cc_final: 0.6893 (mtp)
REVERT: A  545 MET cc_start: 0.8508 (mmm) cc_final: 0.8147 (mmm)
REVERT: A  575 MET cc_start: 0.9102 (mtt) cc_final: 0.8778 (mtt)
REVERT: A  623 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8848 (mt)
REVERT: A  784 GLU cc_start: 0.8582 (mp0) cc_final: 0.8172 (mt-10)
REVERT: A  816 MET cc_start: 0.8904 (mmm) cc_final: 0.8607 (mmm)
REVERT: A 1023 MET cc_start: 0.6618 (tpt) cc_final: 0.6235 (tpp)
  outliers start: 21
  outliers final: 18
  residues processed: 135
  average time/residue: 1.5827
  time to fit residues: 227.4840
Evaluate side-chains
  138 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  499 THR
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  967 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 12 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.141418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.109954 restraints weight = 8493.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.66
r_work: 0.3059 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8064  Z= 0.122
  Angle     :  0.542  11.927  10951  Z= 0.273
  Chirality :  0.042   0.146   1283
  Planarity :  0.003   0.035   1390
  Dihedral  :  8.271 153.429   1110
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.90 %
    Favored  : 78.58 %
  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:  0.95 (0.27), residues: 1014
  helix:  1.74 (0.24), residues: 487
  sheet: -0.03 (0.47), residues: 118
  loop : -0.49 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A 566 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.018   0.001   TYR A 122 
 ARG   0.004   0.000   ARG A 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (  415)
  hydrogen bonds       : angle       4.19268 ( 1209)
  covalent geometry    : bond        0.00293 ( 8064)
  covalent geometry    : angle       0.54247 (10951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6634.62 seconds
wall clock time: 117 minutes 42.28 seconds (7062.28 seconds total)