Starting phenix.real_space_refine
on Sat Aug 23 02:46:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7l1f_23109/08_2025/7l1f_23109.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l1f_23109/08_2025/7l1f_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l1f_23109/08_2025/7l1f_23109.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l1f_23109/08_2025/7l1f_23109.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l1f_23109/08_2025/7l1f_23109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l1f_23109/08_2025/7l1f_23109.map"
  }
  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-2.0-5787/lib/python3.9/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: 2.00, per 1000 atoms: 0.23
  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: 1.03
  Conformation dependent library (CDL) restraints added in 327.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.35
  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: 1.74

  Time building geometry restraints manager: 1.26 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: 5007
       23.49 -    46.97: 311
       46.97 -    70.46: 44
       70.46 -    93.94: 8
       93.94 -   117.43: 1
  Dihedral angle restraints: 5371
    sinusoidal: 2378
      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 5368 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:             0.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.040
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
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  : 14.821 117.425   3439
  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 aren 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
  covalent geometry    : bond        0.00833 ( 9093)
  covalent geometry    : angle       1.36162 (12497)
  hydrogen bonds       : bond        0.20481 (  303)
  hydrogen bonds       : angle       8.13057 (  855)
  Misc. bond           : bond        0.00127 (    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  : 0.337 
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: 0.1094
  time to fit residues: 37.4928
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  : 0.249 
-------------------------------------------------------------------------------
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:   30.0000
   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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3975 r_free = 0.3975 target = 0.157109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.134879 restraints weight = 15006.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139000 restraints weight = 8145.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141735 restraints weight = 5152.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143594 restraints weight = 3639.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144869 restraints weight = 2799.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9097  Z= 0.283
  Angle     :  0.746   8.008  12497  Z= 0.404
  Chirality :  0.048   0.327   1426
  Planarity :  0.006   0.085   1466
  Dihedral  : 12.514 126.829   1567
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.55 %
    Favored  : 87.21 %
  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 aren not related in a simple way.
  whole: -3.19 (0.22), residues: 997
  helix: -1.76 (0.21), residues: 440
  sheet: -2.62 (0.56), residues: 67
  loop : -2.35 (0.23), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 249 
 TYR   0.027   0.002   TYR A 273 
 PHE   0.041   0.002   PHE A 157 
 TRP   0.017   0.002   TRP C 154 
 HIS   0.005   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 9093)
  covalent geometry    : angle       0.74568 (12497)
  hydrogen bonds       : bond        0.06518 (  303)
  hydrogen bonds       : angle       4.91796 (  855)
  Misc. bond           : bond        0.00152 (    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
  255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 235
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7550 (tpt) cc_final: 0.6954 (tpt)
REVERT: A  150 ASN cc_start: 0.7980 (m110) cc_final: 0.7639 (m110)
REVERT: A  242 MET cc_start: 0.7291 (mtp) cc_final: 0.6938 (mtp)
REVERT: A  365 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6988 (mtt90)
REVERT: A  395 CYS cc_start: 0.7272 (m) cc_final: 0.7051 (m)
REVERT: A  454 ASP cc_start: 0.7514 (t0) cc_final: 0.7167 (t0)
REVERT: A  463 MET cc_start: 0.6269 (ppp) cc_final: 0.5928 (ppp)
REVERT: A  703 ASN cc_start: 0.8243 (m110) cc_final: 0.7769 (m110)
REVERT: A  765 CYS cc_start: 0.8556 (t) cc_final: 0.8294 (t)
REVERT: A  766 PHE cc_start: 0.8688 (p90) cc_final: 0.7861 (p90)
REVERT: A  782 PHE cc_start: 0.7444 (m-80) cc_final: 0.6980 (t80)
REVERT: A  855 MET cc_start: 0.6620 (mtm) cc_final: 0.6029 (mtm)
REVERT: A  889 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7143 (tmm160)
REVERT: A  892 HIS cc_start: 0.7782 (t70) cc_final: 0.7556 (t70)
REVERT: A  917 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7207 (mm-30)
REVERT: A  919 GLU cc_start: 0.7793 (mp0) cc_final: 0.7283 (mp0)
REVERT: A  924 MET cc_start: 0.7411 (tpp) cc_final: 0.7029 (ttm)
REVERT: C  129 MET cc_start: 0.6993 (ppp) cc_final: 0.6416 (ppp)
REVERT: C  157 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: D    2 LYS cc_start: 0.6531 (pttp) cc_final: 0.6090 (pttm)
REVERT: D   51 LYS cc_start: 0.7584 (mptt) cc_final: 0.7382 (tptt)
  outliers start: 20
  outliers final: 16
  residues processed: 238
  average time/residue: 0.1053
  time to fit residues: 33.7115
Evaluate side-chains
  231 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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  756 MET
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:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 661 GLN
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 815 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.158855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.136593 restraints weight = 15096.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.140707 restraints weight = 8239.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143429 restraints weight = 5239.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145300 restraints weight = 3716.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.146428 restraints weight = 2866.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9097  Z= 0.172
  Angle     :  0.626   7.309  12497  Z= 0.336
  Chirality :  0.044   0.330   1426
  Planarity :  0.005   0.049   1466
  Dihedral  : 12.105 126.588   1567
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 14.25 %
    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 aren not related in a simple way.
  whole: -2.37 (0.24), residues: 997
  helix: -0.80 (0.23), residues: 432
  sheet: -2.85 (0.49), residues: 79
  loop : -2.05 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 249 
 TYR   0.032   0.002   TYR A 129 
 PHE   0.029   0.002   PHE A 415 
 TRP   0.008   0.002   TRP A 268 
 HIS   0.004   0.001   HIS A 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9093)
  covalent geometry    : angle       0.62638 (12497)
  hydrogen bonds       : bond        0.04955 (  303)
  hydrogen bonds       : angle       4.46280 (  855)
  Misc. bond           : bond        0.00082 (    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
  249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 217
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7890 (mttt) cc_final: 0.7436 (mttp)
REVERT: A  124 MET cc_start: 0.7523 (tpt) cc_final: 0.6924 (tpt)
REVERT: A  150 ASN cc_start: 0.7810 (m110) cc_final: 0.7473 (m110)
REVERT: A  249 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7347 (ttm-80)
REVERT: A  357 GLN cc_start: 0.6725 (mp10) cc_final: 0.6414 (mp10)
REVERT: A  365 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6971 (mtt90)
REVERT: A  438 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8054 (mmtt)
REVERT: A  454 ASP cc_start: 0.7469 (t0) cc_final: 0.7140 (t0)
REVERT: A  703 ASN cc_start: 0.8084 (m110) cc_final: 0.7666 (m110)
REVERT: A  765 CYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8023 (t)
REVERT: A  782 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6886 (t80)
REVERT: A  807 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8190 (pttm)
REVERT: A  855 MET cc_start: 0.6504 (mtm) cc_final: 0.5963 (mtm)
REVERT: A  881 PHE cc_start: 0.7656 (t80) cc_final: 0.7437 (t80)
REVERT: A  889 ARG cc_start: 0.7668 (tmm160) cc_final: 0.7030 (tmm160)
REVERT: A  917 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7408 (mm-30)
REVERT: A  919 GLU cc_start: 0.7840 (mp0) cc_final: 0.7367 (mp0)
REVERT: A  924 MET cc_start: 0.7278 (tpp) cc_final: 0.6918 (ttm)
REVERT: C  129 MET cc_start: 0.6880 (ppp) cc_final: 0.6340 (ppp)
REVERT: C  157 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: D   51 LYS cc_start: 0.7570 (mptt) cc_final: 0.7352 (tptt)
  outliers start: 32
  outliers final: 27
  residues processed: 224
  average time/residue: 0.1004
  time to fit residues: 30.7195
Evaluate side-chains
  241 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 212
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  315 VAL
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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  474 GLU
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  591 THR
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  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
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:    0.0980
   chunk 53 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 88 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   overall best weight:    3.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 642 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.159041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.136571 restraints weight = 15293.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.140730 restraints weight = 8342.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143487 restraints weight = 5315.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145379 restraints weight = 3760.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.146617 restraints weight = 2897.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9097  Z= 0.150
  Angle     :  0.602  11.043  12497  Z= 0.316
  Chirality :  0.043   0.299   1426
  Planarity :  0.004   0.050   1466
  Dihedral  : 11.807 124.597   1567
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.95 %
    Favored  : 79.46 %
  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 aren not related in a simple way.
  whole: -1.92 (0.25), residues: 997
  helix: -0.32 (0.25), residues: 428
  sheet: -2.52 (0.50), residues: 73
  loop : -1.94 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 183 
 TYR   0.024   0.001   TYR A 129 
 PHE   0.027   0.001   PHE A 415 
 TRP   0.010   0.001   TRP D  29 
 HIS   0.002   0.001   HIS A 872 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9093)
  covalent geometry    : angle       0.60206 (12497)
  hydrogen bonds       : bond        0.04428 (  303)
  hydrogen bonds       : angle       4.29313 (  855)
  Misc. bond           : bond        0.00048 (    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
  247 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 215
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7856 (mttt) cc_final: 0.7593 (mttt)
REVERT: A  124 MET cc_start: 0.7547 (tpt) cc_final: 0.7207 (tpt)
REVERT: A  150 ASN cc_start: 0.7806 (m110) cc_final: 0.7515 (m110)
REVERT: A  183 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.7441 (ttm170)
REVERT: A  249 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7451 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6924 (mtt90)
REVERT: A  380 MET cc_start: 0.7330 (tmm) cc_final: 0.7091 (tmm)
REVERT: A  454 ASP cc_start: 0.7460 (t0) cc_final: 0.7140 (t0)
REVERT: A  513 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7905 (ttm-80)
REVERT: A  576 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8182 (mm)
REVERT: A  703 ASN cc_start: 0.8085 (m110) cc_final: 0.7636 (m110)
REVERT: A  765 CYS cc_start: 0.8366 (t) cc_final: 0.7949 (t)
REVERT: A  782 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6894 (t80)
REVERT: A  807 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8376 (pttm)
REVERT: A  855 MET cc_start: 0.6521 (mtm) cc_final: 0.5780 (mtm)
REVERT: A  881 PHE cc_start: 0.7664 (t80) cc_final: 0.7368 (t80)
REVERT: A  889 ARG cc_start: 0.7636 (tmm160) cc_final: 0.6917 (tmm160)
REVERT: A  917 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7470 (mm-30)
REVERT: A  919 GLU cc_start: 0.7889 (mp0) cc_final: 0.7417 (mp0)
REVERT: C  129 MET cc_start: 0.6896 (ppp) cc_final: 0.6338 (ppp)
REVERT: C  157 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: D   51 LYS cc_start: 0.7565 (mptt) cc_final: 0.7332 (tptt)
  outliers start: 32
  outliers final: 27
  residues processed: 224
  average time/residue: 0.1003
  time to fit residues: 30.5673
Evaluate side-chains
  241 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 212
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
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  563 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  697 CYS
Chi-restraints excluded: chain A residue  744 GLU
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 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:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3989 r_free = 0.3989 target = 0.157752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.135289 restraints weight = 15109.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139442 restraints weight = 8260.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.142179 restraints weight = 5256.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.144054 restraints weight = 3719.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.145231 restraints weight = 2862.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9097  Z= 0.189
  Angle     :  0.615   9.898  12497  Z= 0.325
  Chirality :  0.044   0.299   1426
  Planarity :  0.004   0.056   1466
  Dihedral  : 11.712 123.940   1567
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 17.51 %
    Favored  : 77.67 %
  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 aren not related in a simple way.
  whole: -1.80 (0.25), residues: 997
  helix: -0.14 (0.25), residues: 434
  sheet: -2.69 (0.48), residues: 73
  loop : -1.93 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 183 
 TYR   0.027   0.002   TYR A 129 
 PHE   0.027   0.002   PHE A 415 
 TRP   0.011   0.002   TRP A 216 
 HIS   0.003   0.001   HIS A 872 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 9093)
  covalent geometry    : angle       0.61473 (12497)
  hydrogen bonds       : bond        0.04949 (  303)
  hydrogen bonds       : angle       4.38134 (  855)
  Misc. bond           : bond        0.00088 (    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
  260 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 217
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7872 (mttt) cc_final: 0.7553 (mttt)
REVERT: A   86 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.5186 (mt)
REVERT: A  124 MET cc_start: 0.7577 (tpt) cc_final: 0.7274 (tpt)
REVERT: A  150 ASN cc_start: 0.7858 (m110) cc_final: 0.7559 (m110)
REVERT: A  249 ARG cc_start: 0.7812 (ttm110) cc_final: 0.7500 (ttm-80)
REVERT: A  271 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5799 (mt)
REVERT: A  365 ARG cc_start: 0.7214 (mtt90) cc_final: 0.6947 (mtt90)
REVERT: A  380 MET cc_start: 0.7421 (tmm) cc_final: 0.7062 (tmm)
REVERT: A  438 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8114 (mmtt)
REVERT: A  454 ASP cc_start: 0.7460 (t0) cc_final: 0.7162 (t0)
REVERT: A  694 PHE cc_start: 0.7741 (t80) cc_final: 0.7316 (t80)
REVERT: A  703 ASN cc_start: 0.8130 (m110) cc_final: 0.7717 (m110)
REVERT: A  729 GLU cc_start: 0.7770 (tp30) cc_final: 0.7496 (tp30)
REVERT: A  765 CYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7922 (t)
REVERT: A  782 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6938 (t80)
REVERT: A  807 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8379 (pttm)
REVERT: A  855 MET cc_start: 0.6576 (mtm) cc_final: 0.5817 (mtm)
REVERT: A  886 GLN cc_start: 0.7782 (mm-40) cc_final: 0.6434 (mm-40)
REVERT: A  889 ARG cc_start: 0.7698 (tmm160) cc_final: 0.7027 (tmm160)
REVERT: A  919 GLU cc_start: 0.7883 (mp0) cc_final: 0.7391 (mp0)
REVERT: C  129 MET cc_start: 0.6935 (ppp) cc_final: 0.6332 (ppp)
REVERT: C  157 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: D   23 GLU cc_start: 0.6904 (tt0) cc_final: 0.6698 (tt0)
REVERT: D   51 LYS cc_start: 0.7563 (mptt) cc_final: 0.7323 (tptt)
  outliers start: 43
  outliers final: 33
  residues processed: 231
  average time/residue: 0.0946
  time to fit residues: 29.7716
Evaluate side-chains
  254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 217
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
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  271 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  473 VAL
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  556 THR
Chi-restraints excluded: chain A residue  563 CYS
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  756 MET
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  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:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   chunk 95 optimal weight:    0.0270
   chunk 85 optimal weight:    0.8980
   chunk 68 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    1.7844

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

Flipped N/Q/H residues before XYZ refinement:
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  18 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 = 0.4035 r_free = 0.4035 target = 0.161148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138513 restraints weight = 15200.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.142720 restraints weight = 8359.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145475 restraints weight = 5322.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.147416 restraints weight = 3770.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.148521 restraints weight = 2900.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9097  Z= 0.114
  Angle     :  0.578   9.167  12497  Z= 0.299
  Chirality :  0.042   0.262   1426
  Planarity :  0.004   0.053   1466
  Dihedral  : 11.457 119.657   1567
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 19.53 %
    Favored  : 76.43 %
  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 aren not related in a simple way.
  whole: -1.48 (0.25), residues: 997
  helix:  0.10 (0.25), residues: 435
  sheet: -2.41 (0.49), residues: 71
  loop : -1.78 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 183 
 TYR   0.026   0.001   TYR A 129 
 PHE   0.024   0.001   PHE A 415 
 TRP   0.009   0.001   TRP A 268 
 HIS   0.002   0.000   HIS A 642 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9093)
  covalent geometry    : angle       0.57791 (12497)
  hydrogen bonds       : bond        0.03690 (  303)
  hydrogen bonds       : angle       4.02700 (  855)
  Misc. bond           : bond        0.00049 (    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
  266 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 230
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7874 (mttt) cc_final: 0.7445 (mttm)
REVERT: A   86 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.5181 (mt)
REVERT: A  124 MET cc_start: 0.7530 (tpt) cc_final: 0.7232 (tpt)
REVERT: A  150 ASN cc_start: 0.7762 (m110) cc_final: 0.7450 (m110)
REVERT: A  183 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7453 (ttm170)
REVERT: A  249 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7503 (ttm-80)
REVERT: A  331 ARG cc_start: 0.7140 (tpp80) cc_final: 0.6826 (tpp80)
REVERT: A  365 ARG cc_start: 0.7181 (mtt90) cc_final: 0.6917 (mtt90)
REVERT: A  380 MET cc_start: 0.7381 (tmm) cc_final: 0.7105 (tmm)
REVERT: A  395 CYS cc_start: 0.7345 (m) cc_final: 0.7108 (m)
REVERT: A  454 ASP cc_start: 0.7409 (t0) cc_final: 0.7111 (t0)
REVERT: A  645 CYS cc_start: 0.8053 (m) cc_final: 0.6631 (t)
REVERT: A  694 PHE cc_start: 0.7633 (t80) cc_final: 0.7261 (t80)
REVERT: A  703 ASN cc_start: 0.7943 (m110) cc_final: 0.7529 (m110)
REVERT: A  729 GLU cc_start: 0.7837 (tp30) cc_final: 0.7568 (tp30)
REVERT: A  765 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7658 (t)
REVERT: A  782 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6798 (t80)
REVERT: A  783 LYS cc_start: 0.8162 (mmpt) cc_final: 0.7735 (mmpt)
REVERT: A  855 MET cc_start: 0.6504 (mtm) cc_final: 0.5814 (mtm)
REVERT: A  889 ARG cc_start: 0.7655 (tmm160) cc_final: 0.6920 (tmm160)
REVERT: C  129 MET cc_start: 0.6874 (ppp) cc_final: 0.6320 (ppp)
REVERT: C  157 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: D   51 LYS cc_start: 0.7545 (mptt) cc_final: 0.7291 (tptt)
  outliers start: 36
  outliers final: 23
  residues processed: 244
  average time/residue: 0.0802
  time to fit residues: 26.8846
Evaluate side-chains
  251 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 225
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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  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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
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  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 D residue    2 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 20 optimal weight:    0.3980
   chunk 79 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   overall best weight:    4.2788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4007 r_free = 0.4007 target = 0.158790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136295 restraints weight = 15148.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.140453 restraints weight = 8350.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143233 restraints weight = 5320.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145077 restraints weight = 3766.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.146293 restraints weight = 2911.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9097  Z= 0.178
  Angle     :  0.619  10.362  12497  Z= 0.325
  Chirality :  0.043   0.243   1426
  Planarity :  0.004   0.059   1466
  Dihedral  : 11.512 120.991   1567
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.43 %
    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 aren not related in a simple way.
  whole: -1.45 (0.25), residues: 997
  helix:  0.16 (0.25), residues: 435
  sheet: -2.40 (0.49), residues: 71
  loop : -1.78 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 183 
 TYR   0.027   0.002   TYR A 129 
 PHE   0.025   0.002   PHE A 415 
 TRP   0.010   0.001   TRP A 216 
 HIS   0.004   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9093)
  covalent geometry    : angle       0.61898 (12497)
  hydrogen bonds       : bond        0.04648 (  303)
  hydrogen bonds       : angle       4.22363 (  855)
  Misc. bond           : bond        0.00099 (    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
  263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 226
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7890 (mttt) cc_final: 0.7468 (mttm)
REVERT: A   86 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.4978 (mt)
REVERT: A  124 MET cc_start: 0.7585 (tpt) cc_final: 0.7255 (tpt)
REVERT: A  150 ASN cc_start: 0.7836 (m110) cc_final: 0.7510 (m110)
REVERT: A  365 ARG cc_start: 0.7211 (mtt90) cc_final: 0.6949 (mtt90)
REVERT: A  380 MET cc_start: 0.7413 (tmm) cc_final: 0.7105 (tmm)
REVERT: A  395 CYS cc_start: 0.7490 (m) cc_final: 0.7263 (m)
REVERT: A  438 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8114 (mmtt)
REVERT: A  454 ASP cc_start: 0.7421 (t0) cc_final: 0.7146 (t0)
REVERT: A  463 MET cc_start: 0.6200 (ptm) cc_final: 0.5929 (ppp)
REVERT: A  645 CYS cc_start: 0.8104 (m) cc_final: 0.6621 (t)
REVERT: A  694 PHE cc_start: 0.7624 (t80) cc_final: 0.7388 (t80)
REVERT: A  703 ASN cc_start: 0.8098 (m110) cc_final: 0.7710 (m110)
REVERT: A  729 GLU cc_start: 0.7910 (tp30) cc_final: 0.7637 (tp30)
REVERT: A  765 CYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7743 (t)
REVERT: A  782 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6861 (t80)
REVERT: A  783 LYS cc_start: 0.8174 (mmpt) cc_final: 0.7800 (mmpt)
REVERT: A  818 MET cc_start: 0.7498 (ppp) cc_final: 0.6838 (ppp)
REVERT: A  819 LEU cc_start: 0.8170 (tp) cc_final: 0.7407 (mt)
REVERT: A  855 MET cc_start: 0.6514 (mtm) cc_final: 0.5985 (mtm)
REVERT: A  889 ARG cc_start: 0.7687 (tmm160) cc_final: 0.6968 (tmm160)
REVERT: C  129 MET cc_start: 0.6924 (ppp) cc_final: 0.6310 (ppp)
REVERT: C  157 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: D    3 MET cc_start: 0.7220 (ppp) cc_final: 0.6871 (ppp)
REVERT: D    7 LYS cc_start: 0.7741 (mttm) cc_final: 0.7335 (mttp)
REVERT: D   51 LYS cc_start: 0.7571 (mptt) cc_final: 0.7310 (tptt)
  outliers start: 37
  outliers final: 27
  residues processed: 238
  average time/residue: 0.0893
  time to fit residues: 29.0532
Evaluate side-chains
  252 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 222
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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  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  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  615 MET
Chi-restraints excluded: chain A residue  629 MET
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 D residue    2 LYS
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:    0.0270
   chunk 16 optimal weight:    0.0030
   chunk 76 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0040
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 97 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.3862

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

Flipped N/Q/H residues before XYZ refinement:
A 541 GLN
A 543 ASN
A 642 HIS
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.163799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.141142 restraints weight = 15078.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.145330 restraints weight = 8313.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.148104 restraints weight = 5308.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.149921 restraints weight = 3771.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.151212 restraints weight = 2929.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.3119

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= 0.108
  Angle     :  0.585  10.750  12497  Z= 0.300
  Chirality :  0.041   0.193   1426
  Planarity :  0.004   0.052   1466
  Dihedral  : 11.253 115.136   1567
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.66 %
    Favored  : 74.75 %
  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 aren not related in a simple way.
  whole: -1.15 (0.25), residues: 997
  helix:  0.37 (0.25), residues: 437
  sheet: -1.99 (0.54), residues: 69
  loop : -1.65 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 331 
 TYR   0.027   0.001   TYR A 294 
 PHE   0.023   0.001   PHE A 415 
 TRP   0.011   0.001   TRP A 268 
 HIS   0.002   0.000   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9093)
  covalent geometry    : angle       0.58538 (12497)
  hydrogen bonds       : bond        0.03237 (  303)
  hydrogen bonds       : angle       3.84302 (  855)
  Misc. bond           : bond        0.00015 (    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
  266 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 234
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7870 (mttt) cc_final: 0.7126 (mttp)
REVERT: A  124 MET cc_start: 0.7562 (tpt) cc_final: 0.7194 (tpt)
REVERT: A  149 TYR cc_start: 0.8061 (m-80) cc_final: 0.7858 (m-80)
REVERT: A  150 ASN cc_start: 0.7735 (m110) cc_final: 0.7429 (m110)
REVERT: A  249 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7489 (ttm-80)
REVERT: A  357 GLN cc_start: 0.6772 (mp10) cc_final: 0.6527 (mp-120)
REVERT: A  365 ARG cc_start: 0.7230 (mtt90) cc_final: 0.6966 (mtt90)
REVERT: A  380 MET cc_start: 0.7339 (tmm) cc_final: 0.6942 (tmm)
REVERT: A  395 CYS cc_start: 0.7310 (m) cc_final: 0.7077 (m)
REVERT: A  454 ASP cc_start: 0.7359 (t0) cc_final: 0.7151 (t0)
REVERT: A  463 MET cc_start: 0.6129 (ptm) cc_final: 0.5839 (ppp)
REVERT: A  541 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7212 (tp-100)
REVERT: A  645 CYS cc_start: 0.7910 (m) cc_final: 0.6518 (t)
REVERT: A  668 MET cc_start: 0.7664 (tmm) cc_final: 0.7167 (tmm)
REVERT: A  673 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7871 (tp)
REVERT: A  691 ASN cc_start: 0.8383 (m-40) cc_final: 0.8124 (m-40)
REVERT: A  694 PHE cc_start: 0.7694 (t80) cc_final: 0.7286 (t80)
REVERT: A  703 ASN cc_start: 0.7890 (m110) cc_final: 0.7456 (m110)
REVERT: A  729 GLU cc_start: 0.7857 (tp30) cc_final: 0.7599 (tp30)
REVERT: A  765 CYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7627 (t)
REVERT: A  782 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6839 (t80)
REVERT: A  783 LYS cc_start: 0.8096 (mmpt) cc_final: 0.7765 (mmpt)
REVERT: A  818 MET cc_start: 0.7589 (ppp) cc_final: 0.6809 (ppp)
REVERT: A  819 LEU cc_start: 0.7989 (tp) cc_final: 0.7120 (mt)
REVERT: A  842 CYS cc_start: 0.7083 (p) cc_final: 0.6814 (p)
REVERT: A  855 MET cc_start: 0.6408 (mtm) cc_final: 0.5846 (mtm)
REVERT: A  889 ARG cc_start: 0.7677 (tmm160) cc_final: 0.6977 (tmm160)
REVERT: C  129 MET cc_start: 0.6833 (ppp) cc_final: 0.6330 (ppp)
REVERT: C  157 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: D    7 LYS cc_start: 0.7603 (mttm) cc_final: 0.7178 (mttp)
REVERT: D   51 LYS cc_start: 0.7504 (mptt) cc_final: 0.7228 (tptt)
  outliers start: 32
  outliers final: 21
  residues processed: 244
  average time/residue: 0.0696
  time to fit residues: 23.5981
Evaluate side-chains
  257 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  541 GLN
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  563 CYS
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 A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 541 GLN
A 543 ASN
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 = 0.3997 r_free = 0.3997 target = 0.158549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137135 restraints weight = 15024.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141257 restraints weight = 8202.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.143876 restraints weight = 5157.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.145784 restraints weight = 3631.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.146989 restraints weight = 2749.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9097  Z= 0.146
  Angle     :  0.613   9.815  12497  Z= 0.320
  Chirality :  0.042   0.183   1426
  Planarity :  0.004   0.058   1466
  Dihedral  : 11.325 118.166   1567
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 22.11 %
    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 aren not related in a simple way.
  whole: -1.12 (0.26), residues: 997
  helix:  0.39 (0.25), residues: 437
  sheet: -1.62 (0.61), residues: 59
  loop : -1.69 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 183 
 TYR   0.032   0.002   TYR A 294 
 PHE   0.034   0.002   PHE A 283 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.003   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9093)
  covalent geometry    : angle       0.61261 (12497)
  hydrogen bonds       : bond        0.04107 (  303)
  hydrogen bonds       : angle       3.93397 (  855)
  Misc. bond           : bond        0.00063 (    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
  255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 226
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7856 (mttt) cc_final: 0.7487 (mttp)
REVERT: A  124 MET cc_start: 0.7645 (tpt) cc_final: 0.7307 (tpt)
REVERT: A  150 ASN cc_start: 0.7797 (m110) cc_final: 0.7478 (m110)
REVERT: A  173 ARG cc_start: 0.8229 (ttp80) cc_final: 0.8004 (ttp80)
REVERT: A  365 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6918 (mtt90)
REVERT: A  380 MET cc_start: 0.7349 (tmm) cc_final: 0.6891 (tmm)
REVERT: A  395 CYS cc_start: 0.7488 (m) cc_final: 0.7227 (m)
REVERT: A  454 ASP cc_start: 0.7490 (t0) cc_final: 0.7267 (t0)
REVERT: A  645 CYS cc_start: 0.7988 (m) cc_final: 0.6625 (t)
REVERT: A  694 PHE cc_start: 0.7836 (t80) cc_final: 0.7408 (t80)
REVERT: A  703 ASN cc_start: 0.8025 (m110) cc_final: 0.7590 (m110)
REVERT: A  729 GLU cc_start: 0.7961 (tp30) cc_final: 0.7695 (tp30)
REVERT: A  765 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7730 (t)
REVERT: A  782 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6840 (t80)
REVERT: A  783 LYS cc_start: 0.8160 (mmpt) cc_final: 0.7860 (mmpt)
REVERT: A  818 MET cc_start: 0.7434 (ppp) cc_final: 0.6724 (ppp)
REVERT: A  819 LEU cc_start: 0.8036 (tp) cc_final: 0.7233 (mt)
REVERT: A  855 MET cc_start: 0.6529 (mtm) cc_final: 0.5922 (mtm)
REVERT: A  881 PHE cc_start: 0.7589 (t80) cc_final: 0.7184 (t80)
REVERT: A  889 ARG cc_start: 0.7682 (tmm160) cc_final: 0.6969 (tmm160)
REVERT: C  129 MET cc_start: 0.6892 (ppp) cc_final: 0.6281 (ppp)
REVERT: C  157 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8094 (tm-30)
REVERT: D    7 LYS cc_start: 0.7657 (mttm) cc_final: 0.7248 (mttp)
REVERT: D   51 LYS cc_start: 0.7523 (mptt) cc_final: 0.7273 (tptt)
  outliers start: 29
  outliers final: 24
  residues processed: 236
  average time/residue: 0.0877
  time to fit residues: 28.5190
Evaluate side-chains
  250 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 224
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
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  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   92 PHE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 89 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 92 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3965 r_free = 0.3965 target = 0.156173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134755 restraints weight = 15033.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.138811 restraints weight = 8210.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.141531 restraints weight = 5198.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.143337 restraints weight = 3646.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.144544 restraints weight = 2787.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9097  Z= 0.205
  Angle     :  0.665   9.732  12497  Z= 0.349
  Chirality :  0.044   0.208   1426
  Planarity :  0.004   0.064   1466
  Dihedral  : 11.480 116.231   1567
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.00 %
    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 aren not related in a simple way.
  whole: -1.36 (0.25), residues: 997
  helix:  0.18 (0.25), residues: 436
  sheet: -2.10 (0.47), residues: 81
  loop : -1.71 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 183 
 TYR   0.031   0.002   TYR A 129 
 PHE   0.033   0.002   PHE A 283 
 TRP   0.010   0.002   TRP A 216 
 HIS   0.003   0.001   HIS A 872 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 9093)
  covalent geometry    : angle       0.66467 (12497)
  hydrogen bonds       : bond        0.04960 (  303)
  hydrogen bonds       : angle       4.21021 (  855)
  Misc. bond           : bond        0.00117 (    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
  264 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 234
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   47 LYS cc_start: 0.7834 (mttt) cc_final: 0.7415 (mttp)
REVERT: A  124 MET cc_start: 0.7756 (tpt) cc_final: 0.7163 (tpt)
REVERT: A  150 ASN cc_start: 0.7840 (m110) cc_final: 0.7488 (m110)
REVERT: A  365 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6948 (mtt90)
REVERT: A  380 MET cc_start: 0.7384 (tmm) cc_final: 0.7130 (tmm)
REVERT: A  395 CYS cc_start: 0.7525 (m) cc_final: 0.7284 (m)
REVERT: A  438 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8060 (mmtt)
REVERT: A  454 ASP cc_start: 0.7528 (t0) cc_final: 0.7311 (t0)
REVERT: A  645 CYS cc_start: 0.8042 (m) cc_final: 0.6636 (t)
REVERT: A  694 PHE cc_start: 0.7829 (t80) cc_final: 0.7433 (t80)
REVERT: A  703 ASN cc_start: 0.8144 (m110) cc_final: 0.7752 (m110)
REVERT: A  729 GLU cc_start: 0.7987 (tp30) cc_final: 0.7703 (tp30)
REVERT: A  765 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7893 (t)
REVERT: A  782 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6915 (t80)
REVERT: A  783 LYS cc_start: 0.8198 (mmpt) cc_final: 0.7901 (mmpt)
REVERT: A  818 MET cc_start: 0.7557 (ppp) cc_final: 0.6865 (ppp)
REVERT: A  819 LEU cc_start: 0.8182 (tp) cc_final: 0.7323 (mt)
REVERT: A  842 CYS cc_start: 0.7010 (p) cc_final: 0.6801 (p)
REVERT: A  855 MET cc_start: 0.6576 (mtm) cc_final: 0.5934 (mtm)
REVERT: A  881 PHE cc_start: 0.7584 (t80) cc_final: 0.7204 (t80)
REVERT: A  889 ARG cc_start: 0.7707 (tmm160) cc_final: 0.7020 (tmm160)
REVERT: C  129 MET cc_start: 0.6944 (ppp) cc_final: 0.6269 (ppp)
REVERT: C  157 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: D   51 LYS cc_start: 0.7551 (mptt) cc_final: 0.7261 (tptt)
  outliers start: 30
  outliers final: 24
  residues processed: 243
  average time/residue: 0.0863
  time to fit residues: 29.0496
Evaluate side-chains
  261 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 235
  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  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  372 LEU
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  556 THR
Chi-restraints excluded: chain A residue  563 CYS
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  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   28 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3971 r_free = 0.3971 target = 0.156551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.135321 restraints weight = 14880.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.139428 restraints weight = 8109.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.142131 restraints weight = 5091.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.143996 restraints weight = 3553.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.145219 restraints weight = 2689.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9097  Z= 0.183
  Angle     :  0.652   9.574  12497  Z= 0.342
  Chirality :  0.044   0.203   1426
  Planarity :  0.004   0.061   1466
  Dihedral  : 11.453 112.454   1567
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.01 %
    Favored  : 73.51 %
  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 aren not related in a simple way.
  whole: -1.37 (0.25), residues: 997
  helix:  0.16 (0.25), residues: 436
  sheet: -2.02 (0.57), residues: 60
  loop : -1.77 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 631 
 TYR   0.030   0.002   TYR A 129 
 PHE   0.032   0.002   PHE A 283 
 TRP   0.015   0.002   TRP C 182 
 HIS   0.003   0.001   HIS A 872 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 9093)
  covalent geometry    : angle       0.65233 (12497)
  hydrogen bonds       : bond        0.04629 (  303)
  hydrogen bonds       : angle       4.17661 (  855)
  Misc. bond           : bond        0.00090 (    4)

===============================================================================
Job complete
usr+sys time: 1379.75 seconds
wall clock time: 24 minutes 38.35 seconds (1478.35 seconds total)