Starting phenix.real_space_refine
on Thu Jul  2 16:14:43 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l1f_23109/07_2026/7l1f_23109.cif"
  }
  resolution = 3.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.021 sd=   0.103
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: 5
    Type Number    sf(0)   Gaussians
     P      35      5.49       5
     S      58      5.16       5
     C    5504      2.51       5
     N    1473      2.21       5
     O    1755      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8825
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 832, 6708
          Classifications: {'peptide': 832}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 803}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 883
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
    Chain: "D"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 486
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "P"
      Number of atoms: 276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 276
          Classifications: {'RNA': 13}
          Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 6}
          Link IDs: {'rna3p': 12}
    Chain: "P"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 96
          Unusual residues: {'F86': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 12
    Chain: "T"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 376
          Classifications: {'RNA': 18}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 16}
  Time building chain proxies: 1.42, per 1000 atoms: 0.16
  Number of scatterers: 8825
  At special positions: 0
  Unit cell: (86.9, 99, 122.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P      35     15.00
     O    1755      8.00
     N    1473      7.00
     C    5504      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 252.6 milliseconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      46.3% alpha, 7.1% beta
      9 base pairs and 23 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 130
      removed outlier: 3.877A  pdb=" N   LEU A 127 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 3.585A  pdb=" N   LYS A 143 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   TYR A 149 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 176
      removed outlier: 4.418A  pdb=" N   VAL A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 200
      removed outlier: 3.690A  pdb=" N   VAL A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A 199 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 210
      removed outlier: 3.576A  pdb=" N   ASN A 209 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN A 210 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 206 through 210'
    Processing helix  chain 'A' and resid 234 through 249
      removed outlier: 3.733A  pdb=" N   TYR A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      Proline residue:  A 243  - end of helix
      removed outlier: 4.335A  pdb=" N   THR A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   LEU A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 305 through 318
      removed outlier: 3.930A  pdb=" N   HIS A 309 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 318 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 377
      removed outlier: 3.655A  pdb=" N   ASP A 377 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 383
      removed outlier: 3.656A  pdb=" N   ALA A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 424
    Processing helix  chain 'A' and resid 447 through 454
      removed outlier: 3.666A  pdb=" N   SER A 451 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 459
      removed outlier: 4.144A  pdb=" N   TYR A 458 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 476
      removed outlier: 3.978A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 480
    Processing helix  chain 'A' and resid 489 through 493
      removed outlier: 3.568A  pdb=" N   GLN A 492 " --> pdb=" O   ASN A 489 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL A 493 " --> pdb=" O   ALA A 490 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 489 through 493'
    Processing helix  chain 'A' and resid 505 through 509
      removed outlier: 4.138A  pdb=" N   LYS A 508 " --> pdb=" O   PRO A 505 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TRP A 509 " --> pdb=" O   PHE A 506 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 505 through 509'
    Processing helix  chain 'A' and resid 513 through 518
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 561 through 580
      removed outlier: 4.103A  pdb=" N   THR A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLN A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA A 580 " --> pdb=" O   LEU A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 606
      removed outlier: 3.809A  pdb=" N   ASN A 600 " --> pdb=" O   GLY A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
      removed outlier: 3.606A  pdb=" N   ARG A 631 " --> pdb=" O   PRO A 627 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 663
      removed outlier: 3.638A  pdb=" N   ARG A 651 " --> pdb=" O   SER A 647 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 663 " --> pdb=" O   CYS A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 709
      removed outlier: 3.538A  pdb=" N   ALA A 690 " --> pdb=" O   THR A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 733
    Processing helix  chain 'A' and resid 738 through 752
      removed outlier: 3.772A  pdb=" N   VAL A 742 " --> pdb=" O   ASP A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 789
      removed outlier: 3.906A  pdb=" N   PHE A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 842
      removed outlier: 3.567A  pdb=" N   ILE A 837 " --> pdb=" O   ASP A 833 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLY A 841 " --> pdb=" O   ILE A 837 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   CYS A 842 " --> pdb=" O   LEU A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 850
    Processing helix  chain 'A' and resid 851 through 866
      removed outlier: 4.190A  pdb=" N   MET A 855 " --> pdb=" O   ASP A 851 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   GLU A 857 " --> pdb=" O   THR A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 895
      removed outlier: 4.382A  pdb=" N   ALA A 878 " --> pdb=" O   ASN A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 925
      removed outlier: 4.312A  pdb=" N   TYR A 921 " --> pdb=" O   GLU A 917 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A 923 " --> pdb=" O   GLU A 919 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET A 924 " --> pdb=" O   PHE A 920 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TYR A 925 " --> pdb=" O   TYR A 921 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 94
      removed outlier: 3.978A  pdb=" N   MET C  94 " --> pdb=" O   MET C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 108
      removed outlier: 4.219A  pdb=" N   ASN C 104 " --> pdb=" O   ASN C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 118
      No H-bonds generated for 'chain 'C' and resid 116 through 118'
    Processing helix  chain 'C' and resid 119 through 125
      removed outlier: 3.608A  pdb=" N   THR C 123 " --> pdb=" O   ILE C 119 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   THR C 124 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 142
      removed outlier: 3.758A  pdb=" N   TYR C 138 " --> pdb=" O   ASP C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 177
      removed outlier: 4.047A  pdb=" N   ASN C 176 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 19
      removed outlier: 3.977A  pdb=" N   LYS D   7 " --> pdb=" O   MET D   3 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN D  19 " --> pdb=" O   SER D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 40
      removed outlier: 3.756A  pdb=" N   TRP D  29 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLN D  31 " --> pdb=" O   LYS D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 62
      removed outlier: 3.554A  pdb=" N   MET D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38
      removed outlier: 3.524A  pdb=" N   ALA A  46 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224
      removed outlier: 7.296A  pdb=" N   VAL A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   GLY A 203 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 328
    Processing sheet with id=AA4, first strand: chain 'A' and resid 332 through 335
      removed outlier: 3.806A  pdb=" N   ILE A 333 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 674
      removed outlier: 7.215A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN A 386 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET C 129 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL C 131 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU C 128 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL C 130 " --> pdb=" O   VAL C 186 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLN C 158 " --> pdb=" O   THR C 187 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   LEU C 189 " --> pdb=" O   ILE C 156 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   ILE C 156 " --> pdb=" O   LEU C 189 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   PHE C 147 " --> pdb=" O   TRP C 154 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415
    Processing sheet with id=AA7, first strand: chain 'A' and resid 612 through 614
      removed outlier: 3.818A  pdb=" N   HIS A 613 " --> pdb=" O   PHE A 766 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A 766 " --> pdb=" O   HIS A 613 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASP A 761 " --> pdb=" O   LEU A 758 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER A 754 " --> pdb=" O   CYS A 765 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 817
    Processing sheet with id=AA9, first strand: chain 'A' and resid 820 through 822
      removed outlier: 3.767A  pdb=" N   ASP A 825 " --> pdb=" O   GLN A 822 " (cutoff:3.500A)

    282 hydrogen bonds defined for protein.
    813 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      21 hydrogen bonds
      42 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      23 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1364
        1.27 -     1.41: 2436
        1.41 -     1.55: 5044
        1.55 -     1.68: 162
        1.68 -     1.82: 87
  Bond restraints: 9093
  Sorted by residual:
  bond pdb=" C11 F86 P  15 "
       pdb=" N5  F86 P  15 "
    ideal  model  delta    sigma   weight residual
    1.337  1.454 -0.117 1.00e-02 1.00e+04 1.37e+02
  bond pdb=" C11 F86 P  16 "
       pdb=" N5  F86 P  16 "
    ideal  model  delta    sigma   weight residual
    1.337  1.452 -0.115 1.00e-02 1.00e+04 1.32e+02
  bond pdb=" C11 F86 P  14 "
       pdb=" N5  F86 P  14 "
    ideal  model  delta    sigma   weight residual
    1.337  1.451 -0.114 1.00e-02 1.00e+04 1.30e+02
  bond pdb=" C11 F86 P  17 "
       pdb=" N5  F86 P  17 "
    ideal  model  delta    sigma   weight residual
    1.337  1.451 -0.114 1.00e-02 1.00e+04 1.30e+02
  bond pdb=" C12 F86 P  15 "
       pdb=" N2  F86 P  15 "
    ideal  model  delta    sigma   weight residual
    1.293  1.358 -0.065 1.00e-02 1.00e+04 4.28e+01
  ... (remaining 9088 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.23: 12063
        3.23 -     6.47: 351
        6.47 -     9.70: 61
        9.70 -    12.93: 16
       12.93 -    16.17: 6
  Bond angle restraints: 12497
  Sorted by residual:
  angle pdb=" C   THR A 556 "
        pdb=" N   VAL A 557 "
        pdb=" CA  VAL A 557 "
      ideal   model   delta    sigma   weight residual
     121.97  137.48  -15.51 1.80e+00 3.09e-01 7.42e+01
  angle pdb=" C   TRP C 182 "
        pdb=" N   PRO C 183 "
        pdb=" CD  PRO C 183 "
      ideal   model   delta    sigma   weight residual
     120.60  104.96   15.64 2.20e+00 2.07e-01 5.06e+01
  angle pdb=" CB  LYS A 411 "
        pdb=" CG  LYS A 411 "
        pdb=" CD  LYS A 411 "
      ideal   model   delta    sigma   weight residual
     111.30  127.43  -16.13 2.30e+00 1.89e-01 4.92e+01
  angle pdb=" C7  F86 P  16 "
        pdb=" C5  F86 P  16 "
        pdb=" N1  F86 P  16 "
      ideal   model   delta    sigma   weight residual
     107.20  113.84   -6.64 1.00e+00 1.00e+00 4.41e+01
  angle pdb=" CA  ASP A 304 "
        pdb=" CB  ASP A 304 "
        pdb=" CG  ASP A 304 "
      ideal   model   delta    sigma   weight residual
     112.60  119.15   -6.55 1.00e+00 1.00e+00 4.28e+01
  ... (remaining 12492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.49: 4975
       23.49 -    46.97: 286
       46.97 -    70.46: 13
       70.46 -    93.94: 4
       93.94 -   117.43: 1
  Dihedral angle restraints: 5279
    sinusoidal: 2286
      harmonic: 2993
  Sorted by residual:
  dihedral pdb=" CA  THR A 556 "
           pdb=" C   THR A 556 "
           pdb=" N   VAL A 557 "
           pdb=" CA  VAL A 557 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.03   31.97     0      5.00e+00 4.00e-02 4.09e+01
  dihedral pdb=" CA  LEU C  98 "
           pdb=" C   LEU C  98 "
           pdb=" N   ASP C  99 "
           pdb=" CA  ASP C  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.78  -30.22     0      5.00e+00 4.00e-02 3.65e+01
  dihedral pdb=" CA  ALA A 762 "
           pdb=" C   ALA A 762 "
           pdb=" N   VAL A 763 "
           pdb=" CA  VAL A 763 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.70   26.30     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 5276 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1257
       0.105 -    0.210: 138
       0.210 -    0.315: 26
       0.315 -    0.419: 3
       0.419 -    0.524: 2
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CB  VAL A 588 "
            pdb=" CA  VAL A 588 "
            pdb=" CG1 VAL A 588 "
            pdb=" CG2 VAL A 588 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.11   -0.52 2.00e-01 2.50e+01 6.87e+00
  chirality pdb=" CB  THR A 556 "
            pdb=" CA  THR A 556 "
            pdb=" OG1 THR A 556 "
            pdb=" CG2 THR A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.03    0.52 2.00e-01 2.50e+01 6.71e+00
  chirality pdb=" CB  VAL A 476 "
            pdb=" CA  VAL A 476 "
            pdb=" CG1 VAL A 476 "
            pdb=" CG2 VAL A 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.22   -0.41 2.00e-01 2.50e+01 4.15e+00
  ... (remaining 1423 not shown)

  Planarity restraints: 1466
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 157 "    0.021 2.00e-02 2.50e+03   3.06e-02 1.64e+01
        pdb=" CG  PHE A 157 "   -0.069 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 157 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 157 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 157 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 157 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 157 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 237 "    0.007 2.00e-02 2.50e+03   2.84e-02 1.62e+01
        pdb=" CG  TYR A 237 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 237 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 237 "    0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 237 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 237 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 237 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 237 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 182 "    0.060 5.00e-02 4.00e+02   8.71e-02 1.21e+01
        pdb=" N   PRO C 183 "   -0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO C 183 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO C 183 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1463 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2804
        2.84 -     3.35: 7268
        3.35 -     3.87: 14457
        3.87 -     4.38: 15613
        4.38 -     4.90: 25841
  Nonbonded interactions: 65983
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 540 "
            pdb=" OE2 GLU A 665 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG1 THR A 246 "
            pdb=" O   PRO A 461 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   THR C  89 "
            pdb=" OG1 THR C  93 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" OG1 THR A 206 "
            pdb=" OD1 ASN A 209 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   GLU A 144 "
            pdb=" OG1 THR A 148 "
     model   vdw
     2.349 3.040
  ... (remaining 65978 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.050
  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:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
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      :  0.008   0.117   9097  Z= 0.516
  Angle     :  1.362  16.168  12497  Z= 0.737
  Chirality :  0.075   0.524   1426
  Planarity :  0.008   0.087   1466
  Dihedral  : 13.376 117.425   3347
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.31 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.38 (0.20), residues: 997
  helix: -3.54 (0.15), residues: 411
  sheet: -2.04 (0.65), residues: 61
  loop : -2.45 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.002   ARG A 583 
 TYR   0.064   0.004   TYR A 237 
 PHE   0.069   0.004   PHE A 157 
 TRP   0.030   0.003   TRP D  29 
 HIS   0.017   0.002   HIS A 309 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00833 /  0.52 ( 9093)
  covalent geometry    : angle       1.36162 /  0.74 (12497)
  hydrogen bonds       : bond        0.20481 / 12.50 (  303)
  hydrogen bonds       : angle       8.13057 /  5.53 (  855)
  Misc. bond           : bond        0.00127 /  0.06 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7376 (tpt) cc_final: 0.6950 (tpt)
REVERT: A  129 TYR cc_start: 0.8002 (t80) cc_final: 0.7593 (t80)
REVERT: A  143 LYS cc_start: 0.7914 (tppp) cc_final: 0.7465 (tptt)
REVERT: A  149 TYR cc_start: 0.8083 (m-80) cc_final: 0.7787 (m-10)
REVERT: A  150 ASN cc_start: 0.7788 (m110) cc_final: 0.7510 (m110)
REVERT: A  173 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7809 (ttp80)
REVERT: A  283 PHE cc_start: 0.7485 (t80) cc_final: 0.7060 (t80)
REVERT: A  395 CYS cc_start: 0.7589 (m) cc_final: 0.7326 (m)
REVERT: A  454 ASP cc_start: 0.7414 (t0) cc_final: 0.6993 (t0)
REVERT: A  691 ASN cc_start: 0.8311 (m110) cc_final: 0.8034 (m-40)
REVERT: A  698 GLN cc_start: 0.7715 (mp10) cc_final: 0.7510 (mp10)
REVERT: A  703 ASN cc_start: 0.8006 (m-40) cc_final: 0.7565 (m-40)
REVERT: A  707 LEU cc_start: 0.8546 (tp) cc_final: 0.8321 (tp)
REVERT: A  748 TYR cc_start: 0.7782 (t80) cc_final: 0.7479 (t80)
REVERT: A  815 GLN cc_start: 0.7505 (mm110) cc_final: 0.7222 (mm110)
REVERT: A  855 MET cc_start: 0.6818 (mtm) cc_final: 0.6117 (mtm)
REVERT: A  857 GLU cc_start: 0.7442 (pm20) cc_final: 0.7215 (pm20)
REVERT: A  892 HIS cc_start: 0.7798 (t70) cc_final: 0.7535 (t70)
REVERT: C  129 MET cc_start: 0.6852 (ppp) cc_final: 0.6560 (ppp)
REVERT: C  157 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8211 (tm-30)
REVERT: D    2 LYS cc_start: 0.6639 (pttp) cc_final: 0.6289 (pttm)
REVERT: D   51 LYS cc_start: 0.7629 (mptt) cc_final: 0.7410 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.0757
  time to fit residues: 26.4800
Evaluate side-chains
  215 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    6.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 703 ASN
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.156986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.134744 restraints weight = 14987.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.138876 restraints weight = 8121.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.141622 restraints weight = 5136.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.143432 restraints weight = 3621.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.144728 restraints weight = 2792.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9097  Z= 0.281
  Angle     :  0.751   8.098  12497  Z= 0.405
  Chirality :  0.048   0.320   1426
  Planarity :  0.006   0.085   1466
  Dihedral  :  8.148 126.584   1475
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.66 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.22), residues: 997
  helix: -1.77 (0.21), residues: 441
  sheet: -2.63 (0.56), residues: 67
  loop : -2.34 (0.24), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 249 
 TYR   0.028   0.002   TYR A 273 
 PHE   0.042   0.002   PHE A 157 
 TRP   0.020   0.003   TRP C 154 
 HIS   0.006   0.001   HIS D  36 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00569 /  0.28 ( 9093)
  covalent geometry    : angle       0.75064 /  0.41 (12497)
  hydrogen bonds       : bond        0.06678 /  4.14 (  303)
  hydrogen bonds       : angle       4.90817 /  3.33 (  855)
  Misc. bond           : bond        0.00142 /  0.07 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 236
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7549 (tpt) cc_final: 0.6951 (tpt)
REVERT: A  150 ASN cc_start: 0.7988 (m110) cc_final: 0.7645 (m110)
REVERT: A  242 MET cc_start: 0.7298 (mtp) cc_final: 0.6941 (mtp)
REVERT: A  365 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6984 (mtt90)
REVERT: A  395 CYS cc_start: 0.7277 (m) cc_final: 0.7064 (m)
REVERT: A  454 ASP cc_start: 0.7512 (t0) cc_final: 0.7173 (t0)
REVERT: A  463 MET cc_start: 0.6229 (ppp) cc_final: 0.5896 (ppp)
REVERT: A  703 ASN cc_start: 0.8231 (m110) cc_final: 0.7750 (m110)
REVERT: A  765 CYS cc_start: 0.8568 (t) cc_final: 0.8305 (t)
REVERT: A  766 PHE cc_start: 0.8684 (p90) cc_final: 0.7907 (p90)
REVERT: A  782 PHE cc_start: 0.7446 (m-80) cc_final: 0.6967 (t80)
REVERT: A  855 MET cc_start: 0.6606 (mtm) cc_final: 0.6019 (mtm)
REVERT: A  889 ARG cc_start: 0.7680 (tmm160) cc_final: 0.7156 (tmm160)
REVERT: A  892 HIS cc_start: 0.7787 (t70) cc_final: 0.7568 (t70)
REVERT: A  917 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7251 (mm-30)
REVERT: A  919 GLU cc_start: 0.7768 (mp0) cc_final: 0.7289 (mp0)
REVERT: A  924 MET cc_start: 0.7410 (tpp) cc_final: 0.7033 (ttm)
REVERT: C  129 MET cc_start: 0.7001 (ppp) cc_final: 0.6442 (ppp)
REVERT: C  157 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8088 (tm-30)
REVERT: D    2 LYS cc_start: 0.6542 (pttp) cc_final: 0.6095 (pttm)
REVERT: D   51 LYS cc_start: 0.7592 (mptt) cc_final: 0.7390 (tptt)
  outliers start: 20
  outliers final: 15
  residues processed: 239
  average time/residue: 0.0830
  time to fit residues: 26.9196
Evaluate side-chains
  231 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 216
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  492 GLN
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0060
   chunk 26 optimal weight:    0.1980
   chunk 67 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.4402

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 489 ASN
A 661 GLN
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 815 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.160358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138009 restraints weight = 15072.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.142172 restraints weight = 8216.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.144896 restraints weight = 5219.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.146803 restraints weight = 3701.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148070 restraints weight = 2845.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9097  Z= 0.131
  Angle     :  0.598   7.616  12497  Z= 0.320
  Chirality :  0.042   0.317   1426
  Planarity :  0.004   0.046   1466
  Dihedral  :  7.415 125.023   1475
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.04 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.24), residues: 997
  helix: -0.76 (0.23), residues: 432
  sheet: -2.32 (0.55), residues: 71
  loop : -2.09 (0.24), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 249 
 TYR   0.025   0.001   TYR C 149 
 PHE   0.027   0.001   PHE A 415 
 TRP   0.008   0.001   TRP A 268 
 HIS   0.002   0.001   HIS A 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.13 ( 9093)
  covalent geometry    : angle       0.59809 /  0.32 (12497)
  hydrogen bonds       : bond        0.04375 /  2.74 (  303)
  hydrogen bonds       : angle       4.31883 /  2.91 (  855)
  Misc. bond           : bond        0.00055 /  0.03 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 225
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7493 (tpt) cc_final: 0.7172 (tpt)
REVERT: A  135 ASP cc_start: 0.8033 (p0) cc_final: 0.7800 (p0)
REVERT: A  150 ASN cc_start: 0.7765 (m110) cc_final: 0.7444 (m110)
REVERT: A  183 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.7379 (ttm170)
REVERT: A  248 THR cc_start: 0.8916 (p) cc_final: 0.8685 (t)
REVERT: A  249 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7371 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7213 (mtt90) cc_final: 0.6954 (mtt90)
REVERT: A  380 MET cc_start: 0.7221 (tmm) cc_final: 0.6894 (tmm)
REVERT: A  395 CYS cc_start: 0.7230 (m) cc_final: 0.7015 (m)
REVERT: A  454 ASP cc_start: 0.7438 (t0) cc_final: 0.7090 (t0)
REVERT: A  513 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7855 (ttm-80)
REVERT: A  703 ASN cc_start: 0.8048 (m110) cc_final: 0.7629 (m110)
REVERT: A  765 CYS cc_start: 0.8393 (t) cc_final: 0.7992 (t)
REVERT: A  782 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6900 (t80)
REVERT: A  807 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8162 (pttm)
REVERT: A  855 MET cc_start: 0.6447 (mtm) cc_final: 0.5826 (mtm)
REVERT: A  881 PHE cc_start: 0.7616 (t80) cc_final: 0.7402 (t80)
REVERT: A  889 ARG cc_start: 0.7644 (tmm160) cc_final: 0.6999 (tmm160)
REVERT: A  917 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: A  919 GLU cc_start: 0.7818 (mp0) cc_final: 0.7342 (mp0)
REVERT: A  924 MET cc_start: 0.7269 (tpp) cc_final: 0.6936 (ttm)
REVERT: C  129 MET cc_start: 0.6876 (ppp) cc_final: 0.6365 (ppp)
REVERT: C  157 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: D   51 LYS cc_start: 0.7572 (mptt) cc_final: 0.7335 (tptt)
  outliers start: 25
  outliers final: 19
  residues processed: 230
  average time/residue: 0.0959
  time to fit residues: 30.3836
Evaluate side-chains
  240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 220
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue    3 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 88 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 41 optimal weight:    0.3980
   chunk 14 optimal weight:   10.0000
   overall best weight:    3.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.159318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.136679 restraints weight = 15359.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.140810 restraints weight = 8392.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.143586 restraints weight = 5371.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.145468 restraints weight = 3815.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146690 restraints weight = 2949.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9097  Z= 0.150
  Angle     :  0.578   7.008  12497  Z= 0.309
  Chirality :  0.042   0.293   1426
  Planarity :  0.004   0.050   1466
  Dihedral  :  7.115 124.604   1475
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.94 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.25), residues: 997
  helix: -0.33 (0.25), residues: 437
  sheet: -2.35 (0.52), residues: 71
  loop : -1.95 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 249 
 TYR   0.019   0.001   TYR C 149 
 PHE   0.027   0.002   PHE A 415 
 TRP   0.007   0.001   TRP A 268 
 HIS   0.002   0.001   HIS D  36 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 ( 9093)
  covalent geometry    : angle       0.57823 /  0.31 (12497)
  hydrogen bonds       : bond        0.04425 /  2.79 (  303)
  hydrogen bonds       : angle       4.20460 /  2.84 (  855)
  Misc. bond           : bond        0.00051 /  0.03 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 221
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7879 (mttt) cc_final: 0.7485 (mttt)
REVERT: A  124 MET cc_start: 0.7518 (tpt) cc_final: 0.7250 (tpt)
REVERT: A  150 ASN cc_start: 0.7810 (m110) cc_final: 0.7517 (m110)
REVERT: A  249 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7398 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7171 (mtt90) cc_final: 0.6920 (mtt90)
REVERT: A  380 MET cc_start: 0.7288 (tmm) cc_final: 0.6972 (tmm)
REVERT: A  438 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8023 (mmtt)
REVERT: A  454 ASP cc_start: 0.7441 (t0) cc_final: 0.7115 (t0)
REVERT: A  513 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7860 (ttm-80)
REVERT: A  661 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7502 (mm-40)
REVERT: A  694 PHE cc_start: 0.7695 (t80) cc_final: 0.7332 (t80)
REVERT: A  698 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7836 (mm-40)
REVERT: A  703 ASN cc_start: 0.8109 (m110) cc_final: 0.7681 (m110)
REVERT: A  765 CYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7978 (t)
REVERT: A  782 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6897 (t80)
REVERT: A  807 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8439 (pttm)
REVERT: A  855 MET cc_start: 0.6507 (mtm) cc_final: 0.5798 (mtm)
REVERT: A  881 PHE cc_start: 0.7658 (t80) cc_final: 0.7351 (t80)
REVERT: A  889 ARG cc_start: 0.7664 (tmm160) cc_final: 0.6941 (tmm160)
REVERT: A  917 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: A  919 GLU cc_start: 0.7882 (mp0) cc_final: 0.7411 (mp0)
REVERT: A  924 MET cc_start: 0.7217 (tpp) cc_final: 0.6878 (ttm)
REVERT: C  129 MET cc_start: 0.6912 (ppp) cc_final: 0.6331 (ppp)
REVERT: C  157 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8116 (tm-30)
REVERT: D   51 LYS cc_start: 0.7563 (mptt) cc_final: 0.7333 (tptt)
  outliers start: 33
  outliers final: 27
  residues processed: 229
  average time/residue: 0.0974
  time to fit residues: 30.6052
Evaluate side-chains
  244 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 215
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 89 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    4.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 642 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.158041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.135418 restraints weight = 15132.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139556 restraints weight = 8279.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.142335 restraints weight = 5284.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.144188 restraints weight = 3745.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145320 restraints weight = 2894.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9097  Z= 0.188
  Angle     :  0.612  10.378  12497  Z= 0.323
  Chirality :  0.044   0.296   1426
  Planarity :  0.004   0.056   1466
  Dihedral  :  7.057 123.429   1475
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 18.29 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.25), residues: 997
  helix: -0.05 (0.25), residues: 430
  sheet: -2.66 (0.49), residues: 75
  loop : -1.91 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 331 
 TYR   0.022   0.002   TYR A 689 
 PHE   0.026   0.002   PHE A 415 
 TRP   0.010   0.002   TRP D  29 
 HIS   0.004   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 ( 9093)
  covalent geometry    : angle       0.61204 /  0.32 (12497)
  hydrogen bonds       : bond        0.04919 /  3.10 (  303)
  hydrogen bonds       : angle       4.30677 /  2.90 (  855)
  Misc. bond           : bond        0.00083 /  0.04 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7861 (mttt) cc_final: 0.7220 (mttp)
REVERT: A   86 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.5197 (mt)
REVERT: A  124 MET cc_start: 0.7576 (tpt) cc_final: 0.7253 (tpt)
REVERT: A  150 ASN cc_start: 0.7853 (m110) cc_final: 0.7543 (m110)
REVERT: A  249 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7513 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6955 (mtt90)
REVERT: A  380 MET cc_start: 0.7329 (tmm) cc_final: 0.7025 (tmm)
REVERT: A  454 ASP cc_start: 0.7458 (t0) cc_final: 0.7169 (t0)
REVERT: A  513 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7838 (ttm-80)
REVERT: A  703 ASN cc_start: 0.8099 (m110) cc_final: 0.7659 (m110)
REVERT: A  765 CYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7976 (t)
REVERT: A  782 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6934 (t80)
REVERT: A  807 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8369 (pttm)
REVERT: A  855 MET cc_start: 0.6560 (mtm) cc_final: 0.5783 (mtm)
REVERT: A  881 PHE cc_start: 0.7701 (t80) cc_final: 0.7403 (t80)
REVERT: A  886 GLN cc_start: 0.7790 (mm-40) cc_final: 0.6386 (mm-40)
REVERT: A  889 ARG cc_start: 0.7710 (tmm160) cc_final: 0.6969 (tmm160)
REVERT: A  919 GLU cc_start: 0.7900 (mp0) cc_final: 0.7384 (mp0)
REVERT: C  129 MET cc_start: 0.6943 (ppp) cc_final: 0.6337 (ppp)
REVERT: C  157 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: D   51 LYS cc_start: 0.7563 (mptt) cc_final: 0.7331 (tptt)
  outliers start: 39
  outliers final: 30
  residues processed: 226
  average time/residue: 0.1008
  time to fit residues: 31.2897
Evaluate side-chains
  245 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  464 CYS
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   overall best weight:    4.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 543 ASN
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.158317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.135820 restraints weight = 15220.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.139962 restraints weight = 8363.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142691 restraints weight = 5343.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144567 restraints weight = 3794.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.145808 restraints weight = 2930.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9097  Z= 0.180
  Angle     :  0.617   8.802  12497  Z= 0.325
  Chirality :  0.044   0.278   1426
  Planarity :  0.004   0.058   1466
  Dihedral  :  6.941 120.467   1475
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 19.08 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 997
  helix:  0.07 (0.25), residues: 428
  sheet: -2.64 (0.49), residues: 75
  loop : -1.85 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 183 
 TYR   0.017   0.002   TYR A 689 
 PHE   0.024   0.002   PHE A 415 
 TRP   0.013   0.002   TRP D  29 
 HIS   0.003   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.18 ( 9093)
  covalent geometry    : angle       0.61723 /  0.32 (12497)
  hydrogen bonds       : bond        0.04713 /  2.96 (  303)
  hydrogen bonds       : angle       4.29248 /  2.89 (  855)
  Misc. bond           : bond        0.00091 /  0.05 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 226
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7871 (mttt) cc_final: 0.7511 (mttt)
REVERT: A   86 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5136 (mt)
REVERT: A  124 MET cc_start: 0.7555 (tpt) cc_final: 0.7269 (tpt)
REVERT: A  150 ASN cc_start: 0.7831 (m110) cc_final: 0.7514 (m110)
REVERT: A  183 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.7447 (ttm170)
REVERT: A  365 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6936 (mtt90)
REVERT: A  380 MET cc_start: 0.7328 (tmm) cc_final: 0.7074 (tmm)
REVERT: A  395 CYS cc_start: 0.7368 (m) cc_final: 0.7145 (m)
REVERT: A  438 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8104 (mmtt)
REVERT: A  454 ASP cc_start: 0.7453 (t0) cc_final: 0.7162 (t0)
REVERT: A  513 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7844 (ttm-80)
REVERT: A  645 CYS cc_start: 0.8116 (m) cc_final: 0.6662 (t)
REVERT: A  694 PHE cc_start: 0.7636 (t80) cc_final: 0.7287 (t80)
REVERT: A  698 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7853 (mm-40)
REVERT: A  703 ASN cc_start: 0.8176 (m110) cc_final: 0.7744 (m110)
REVERT: A  763 VAL cc_start: 0.7749 (p) cc_final: 0.7513 (m)
REVERT: A  765 CYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7921 (t)
REVERT: A  782 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6894 (t80)
REVERT: A  783 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7767 (mmpt)
REVERT: A  855 MET cc_start: 0.6457 (mtm) cc_final: 0.5874 (mtm)
REVERT: A  886 GLN cc_start: 0.7783 (mm-40) cc_final: 0.6419 (mm-40)
REVERT: A  889 ARG cc_start: 0.7710 (tmm160) cc_final: 0.7001 (tmm160)
REVERT: C  129 MET cc_start: 0.6913 (ppp) cc_final: 0.6321 (ppp)
REVERT: C  157 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: D   51 LYS cc_start: 0.7561 (mptt) cc_final: 0.7298 (tptt)
  outliers start: 39
  outliers final: 31
  residues processed: 239
  average time/residue: 0.0977
  time to fit residues: 32.1950
Evaluate side-chains
  257 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  789 GLN
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0060
   chunk 47 optimal weight:   30.0000
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    2.3202

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 543 ASN
A 572 HIS
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.160467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137876 restraints weight = 15214.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.142047 restraints weight = 8344.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.144781 restraints weight = 5316.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.146676 restraints weight = 3770.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.147946 restraints weight = 2907.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9097  Z= 0.124
  Angle     :  0.591  10.671  12497  Z= 0.307
  Chirality :  0.042   0.224   1426
  Planarity :  0.004   0.056   1466
  Dihedral  :  6.661 117.443   1475
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 19.98 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.25), residues: 997
  helix:  0.18 (0.25), residues: 432
  sheet: -2.47 (0.49), residues: 73
  loop : -1.81 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 331 
 TYR   0.015   0.001   TYR A 689 
 PHE   0.021   0.001   PHE A 415 
 TRP   0.008   0.001   TRP A 268 
 HIS   0.002   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 9093)
  covalent geometry    : angle       0.59148 /  0.31 (12497)
  hydrogen bonds       : bond        0.03932 /  2.52 (  303)
  hydrogen bonds       : angle       4.04053 /  2.70 (  855)
  Misc. bond           : bond        0.00047 /  0.02 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7886 (mttt) cc_final: 0.7449 (mttt)
REVERT: A   86 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.5138 (mt)
REVERT: A  124 MET cc_start: 0.7578 (tpt) cc_final: 0.7249 (tpt)
REVERT: A  150 ASN cc_start: 0.7788 (m110) cc_final: 0.7476 (m110)
REVERT: A  219 PHE cc_start: 0.6111 (m-80) cc_final: 0.5894 (m-80)
REVERT: A  365 ARG cc_start: 0.7194 (mtt90) cc_final: 0.6927 (mtt90)
REVERT: A  380 MET cc_start: 0.7292 (tmm) cc_final: 0.7073 (tmm)
REVERT: A  395 CYS cc_start: 0.7357 (m) cc_final: 0.7130 (m)
REVERT: A  438 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8078 (mmtt)
REVERT: A  454 ASP cc_start: 0.7386 (t0) cc_final: 0.7108 (t0)
REVERT: A  513 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7885 (ttm-80)
REVERT: A  645 CYS cc_start: 0.8059 (m) cc_final: 0.6644 (t)
REVERT: A  694 PHE cc_start: 0.7609 (t80) cc_final: 0.7219 (t80)
REVERT: A  698 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7734 (mm-40)
REVERT: A  703 ASN cc_start: 0.8035 (m110) cc_final: 0.7570 (m110)
REVERT: A  763 VAL cc_start: 0.7738 (p) cc_final: 0.7530 (m)
REVERT: A  765 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7890 (t)
REVERT: A  782 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6850 (t80)
REVERT: A  783 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7730 (mmpt)
REVERT: A  855 MET cc_start: 0.6459 (mtm) cc_final: 0.5899 (mtm)
REVERT: A  889 ARG cc_start: 0.7674 (tmm160) cc_final: 0.6981 (tmm160)
REVERT: C  129 MET cc_start: 0.6880 (ppp) cc_final: 0.6322 (ppp)
REVERT: C  157 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8163 (tm-30)
REVERT: D   51 LYS cc_start: 0.7536 (mptt) cc_final: 0.7268 (tptt)
  outliers start: 36
  outliers final: 30
  residues processed: 237
  average time/residue: 0.0965
  time to fit residues: 31.7288
Evaluate side-chains
  257 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 224
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  789 GLN
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0470
   chunk 87 optimal weight:    0.0040
   chunk 48 optimal weight:    0.3980
   chunk 42 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    1.4492

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 541 GLN
A 543 ASN
A 572 HIS
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.161905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.139280 restraints weight = 15194.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.143396 restraints weight = 8358.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146180 restraints weight = 5366.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148031 restraints weight = 3819.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.149210 restraints weight = 2961.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9097  Z= 0.110
  Angle     :  0.578  10.142  12497  Z= 0.301
  Chirality :  0.041   0.220   1426
  Planarity :  0.004   0.055   1466
  Dihedral  :  6.467 116.373   1475
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.20 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.25), residues: 997
  helix:  0.34 (0.26), residues: 432
  sheet: -2.34 (0.51), residues: 73
  loop : -1.72 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 331 
 TYR   0.024   0.001   TYR A 689 
 PHE   0.024   0.001   PHE A 415 
 TRP   0.009   0.001   TRP D  29 
 HIS   0.009   0.001   HIS A 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 9093)
  covalent geometry    : angle       0.57803 /  0.30 (12497)
  hydrogen bonds       : bond        0.03586 /  2.30 (  303)
  hydrogen bonds       : angle       3.93616 /  2.63 (  855)
  Misc. bond           : bond        0.00022 /  0.01 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 224
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7885 (mttt) cc_final: 0.7406 (mttt)
REVERT: A   86 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.5056 (mt)
REVERT: A  124 MET cc_start: 0.7565 (tpt) cc_final: 0.7238 (tpt)
REVERT: A  150 ASN cc_start: 0.7768 (m110) cc_final: 0.7446 (m110)
REVERT: A  283 PHE cc_start: 0.7340 (t80) cc_final: 0.7127 (t80)
REVERT: A  365 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6914 (mtt90)
REVERT: A  380 MET cc_start: 0.7279 (tmm) cc_final: 0.7070 (tmm)
REVERT: A  395 CYS cc_start: 0.7363 (m) cc_final: 0.7131 (m)
REVERT: A  438 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8065 (mmtt)
REVERT: A  454 ASP cc_start: 0.7378 (t0) cc_final: 0.7167 (t0)
REVERT: A  463 MET cc_start: 0.6272 (ptm) cc_final: 0.5984 (ppp)
REVERT: A  513 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7892 (ttm-80)
REVERT: A  645 CYS cc_start: 0.8035 (m) cc_final: 0.6643 (t)
REVERT: A  694 PHE cc_start: 0.7568 (t80) cc_final: 0.7269 (t80)
REVERT: A  698 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7680 (mm-40)
REVERT: A  703 ASN cc_start: 0.8012 (m110) cc_final: 0.7545 (m110)
REVERT: A  763 VAL cc_start: 0.7737 (p) cc_final: 0.7530 (m)
REVERT: A  765 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7874 (t)
REVERT: A  782 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6781 (t80)
REVERT: A  783 LYS cc_start: 0.8118 (mmpt) cc_final: 0.7750 (mmpt)
REVERT: A  818 MET cc_start: 0.7273 (ppp) cc_final: 0.6549 (ppp)
REVERT: A  819 LEU cc_start: 0.7939 (tp) cc_final: 0.7147 (mt)
REVERT: A  855 MET cc_start: 0.6366 (mtm) cc_final: 0.5846 (mtm)
REVERT: A  881 PHE cc_start: 0.7359 (t80) cc_final: 0.7055 (t80)
REVERT: A  889 ARG cc_start: 0.7659 (tmm160) cc_final: 0.7007 (tmm160)
REVERT: C  129 MET cc_start: 0.6867 (ppp) cc_final: 0.6343 (ppp)
REVERT: C  157 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: D    7 LYS cc_start: 0.7712 (mttm) cc_final: 0.7324 (mttp)
REVERT: D   51 LYS cc_start: 0.7521 (mptt) cc_final: 0.7251 (tptt)
  outliers start: 40
  outliers final: 26
  residues processed: 238
  average time/residue: 0.0959
  time to fit residues: 31.6878
Evaluate side-chains
  253 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 224
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  340 PHE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  789 GLN
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    3 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 53 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    2.1902

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 543 ASN
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.161314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.138776 restraints weight = 15019.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.142967 restraints weight = 8211.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.145748 restraints weight = 5205.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.147626 restraints weight = 3676.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.148880 restraints weight = 2834.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9097  Z= 0.122
  Angle     :  0.589   9.683  12497  Z= 0.308
  Chirality :  0.041   0.213   1426
  Planarity :  0.004   0.058   1466
  Dihedral  :  6.433 116.203   1475
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.32 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.26), residues: 997
  helix:  0.39 (0.26), residues: 432
  sheet: -1.97 (0.58), residues: 63
  loop : -1.73 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 331 
 TYR   0.020   0.001   TYR A 689 
 PHE   0.023   0.001   PHE A 415 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.002   0.000   HIS A 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 9093)
  covalent geometry    : angle       0.58893 /  0.31 (12497)
  hydrogen bonds       : bond        0.03788 /  2.40 (  303)
  hydrogen bonds       : angle       3.90878 /  2.62 (  855)
  Misc. bond           : bond        0.00034 /  0.02 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 231
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7891 (mttt) cc_final: 0.7519 (mttt)
REVERT: A   86 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.5035 (mt)
REVERT: A  124 MET cc_start: 0.7644 (tpt) cc_final: 0.7306 (tpt)
REVERT: A  150 ASN cc_start: 0.7782 (m110) cc_final: 0.7468 (m110)
REVERT: A  365 ARG cc_start: 0.7152 (mtt90) cc_final: 0.6891 (mtt90)
REVERT: A  395 CYS cc_start: 0.7490 (m) cc_final: 0.7242 (m)
REVERT: A  438 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8078 (mmtt)
REVERT: A  454 ASP cc_start: 0.7388 (t0) cc_final: 0.7174 (t0)
REVERT: A  463 MET cc_start: 0.6317 (ptm) cc_final: 0.5985 (ppp)
REVERT: A  513 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7893 (ttm-80)
REVERT: A  645 CYS cc_start: 0.7945 (m) cc_final: 0.6643 (t)
REVERT: A  694 PHE cc_start: 0.7714 (t80) cc_final: 0.7255 (t80)
REVERT: A  698 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7651 (mm-40)
REVERT: A  703 ASN cc_start: 0.8044 (m110) cc_final: 0.7591 (m110)
REVERT: A  765 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7901 (t)
REVERT: A  782 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6796 (t80)
REVERT: A  783 LYS cc_start: 0.8134 (mmpt) cc_final: 0.7779 (mmpt)
REVERT: A  807 LYS cc_start: 0.8504 (pttm) cc_final: 0.8297 (mtmm)
REVERT: A  818 MET cc_start: 0.7435 (ppp) cc_final: 0.6651 (ppp)
REVERT: A  819 LEU cc_start: 0.7981 (tp) cc_final: 0.7047 (mt)
REVERT: A  842 CYS cc_start: 0.7068 (p) cc_final: 0.6846 (p)
REVERT: A  855 MET cc_start: 0.6486 (mtm) cc_final: 0.5880 (mtm)
REVERT: A  881 PHE cc_start: 0.7364 (t80) cc_final: 0.7072 (t80)
REVERT: A  889 ARG cc_start: 0.7681 (tmm160) cc_final: 0.6994 (tmm160)
REVERT: C  129 MET cc_start: 0.6884 (ppp) cc_final: 0.6334 (ppp)
REVERT: C  157 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: D    7 LYS cc_start: 0.7690 (mttm) cc_final: 0.7292 (mttp)
REVERT: D   51 LYS cc_start: 0.7528 (mptt) cc_final: 0.7253 (tptt)
  outliers start: 29
  outliers final: 24
  residues processed: 242
  average time/residue: 0.0934
  time to fit residues: 31.6097
Evaluate side-chains
  255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  340 PHE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   92 PHE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    3 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 89 optimal weight:   20.0000
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 92 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.160454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138149 restraints weight = 15155.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.142390 restraints weight = 8289.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.145250 restraints weight = 5245.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.147003 restraints weight = 3674.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148398 restraints weight = 2832.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9097  Z= 0.113
  Angle     :  0.594   9.039  12497  Z= 0.308
  Chirality :  0.041   0.202   1426
  Planarity :  0.004   0.057   1466
  Dihedral  :  6.303 114.388   1475
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.11 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.26), residues: 997
  helix:  0.44 (0.25), residues: 432
  sheet: -1.78 (0.58), residues: 61
  loop : -1.69 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 331 
 TYR   0.017   0.001   TYR A 689 
 PHE   0.022   0.001   PHE A 283 
 TRP   0.008   0.001   TRP A 268 
 HIS   0.007   0.001   HIS A 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 9093)
  covalent geometry    : angle       0.59407 /  0.31 (12497)
  hydrogen bonds       : bond        0.03487 /  2.24 (  303)
  hydrogen bonds       : angle       3.83124 /  2.54 (  855)
  Misc. bond           : bond        0.00033 /  0.02 (    4)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7866 (mttt) cc_final: 0.7509 (mttt)
REVERT: A   86 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.4897 (mt)
REVERT: A  124 MET cc_start: 0.7694 (tpt) cc_final: 0.7326 (tpt)
REVERT: A  150 ASN cc_start: 0.7793 (m110) cc_final: 0.7489 (m110)
REVERT: A  173 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7966 (ttp80)
REVERT: A  297 ASN cc_start: 0.7796 (p0) cc_final: 0.7323 (p0)
REVERT: A  365 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6958 (mtt90)
REVERT: A  395 CYS cc_start: 0.7556 (m) cc_final: 0.7268 (m)
REVERT: A  438 LYS cc_start: 0.8399 (mmtm) cc_final: 0.8065 (mmtt)
REVERT: A  454 ASP cc_start: 0.7488 (t0) cc_final: 0.7267 (t0)
REVERT: A  463 MET cc_start: 0.6327 (ptm) cc_final: 0.5995 (ppp)
REVERT: A  513 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7890 (ttm-80)
REVERT: A  673 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: A  694 PHE cc_start: 0.7871 (t80) cc_final: 0.7328 (t80)
REVERT: A  698 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7769 (mm-40)
REVERT: A  703 ASN cc_start: 0.8074 (m110) cc_final: 0.7609 (m110)
REVERT: A  765 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7805 (t)
REVERT: A  782 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6795 (t80)
REVERT: A  783 LYS cc_start: 0.8147 (mmpt) cc_final: 0.7790 (mmpt)
REVERT: A  818 MET cc_start: 0.7395 (ppp) cc_final: 0.6581 (ppp)
REVERT: A  819 LEU cc_start: 0.7929 (tp) cc_final: 0.7022 (mt)
REVERT: A  842 CYS cc_start: 0.7071 (p) cc_final: 0.6827 (p)
REVERT: A  855 MET cc_start: 0.6540 (mtm) cc_final: 0.5893 (mtm)
REVERT: A  881 PHE cc_start: 0.7353 (t80) cc_final: 0.7097 (t80)
REVERT: A  889 ARG cc_start: 0.7661 (tmm160) cc_final: 0.7051 (tmm160)
REVERT: C  129 MET cc_start: 0.6884 (ppp) cc_final: 0.6315 (ppp)
REVERT: C  157 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8081 (tm-30)
REVERT: D    7 LYS cc_start: 0.7686 (mttm) cc_final: 0.7301 (mttp)
REVERT: D   51 LYS cc_start: 0.7504 (mptt) cc_final: 0.7228 (tptt)
  outliers start: 30
  outliers final: 24
  residues processed: 246
  average time/residue: 0.0912
  time to fit residues: 31.3341
Evaluate side-chains
  259 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 231
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  340 PHE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  361 LEU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   62 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 67 optimal weight:    6.9990
   chunk 81 optimal weight:    0.1980
   chunk 44 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.160799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138490 restraints weight = 15074.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142732 restraints weight = 8260.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145594 restraints weight = 5231.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.147478 restraints weight = 3668.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.148797 restraints weight = 2801.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9097  Z= 0.111
  Angle     :  0.598   9.000  12497  Z= 0.311
  Chirality :  0.041   0.188   1426
  Planarity :  0.004   0.056   1466
  Dihedral  :  6.236 113.538   1475
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.22 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.26), residues: 997
  helix:  0.51 (0.26), residues: 432
  sheet: -1.64 (0.59), residues: 61
  loop : -1.67 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 331 
 TYR   0.016   0.001   TYR A 689 
 PHE   0.031   0.001   PHE A 283 
 TRP   0.008   0.001   TRP A 268 
 HIS   0.002   0.000   HIS A 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 9093)
  covalent geometry    : angle       0.59771 /  0.31 (12497)
  hydrogen bonds       : bond        0.03424 /  2.19 (  303)
  hydrogen bonds       : angle       3.85152 /  2.55 (  855)
  Misc. bond           : bond        0.00046 /  0.02 (    4)

===============================================================================
Job complete
usr+sys time: 1426.48 seconds
wall clock time: 25 minutes 26.10 seconds (1526.10 seconds total)