Starting phenix.real_space_refine
on Fri Sep 11 12:01:03 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7l1f_23109/09_2026/7l1f_23109.cif"
  }
  resolution = 3.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.021 sd=   0.103
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      35      5.49       5
     S      58      5.16       5
     C    5504      2.51       5
     N    1473      2.21       5
     O    1755      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8825
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 832, 6708
          Classifications: {'peptide': 832}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 803}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 883
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
    Chain: "D"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 486
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 62}
    Chain: "P"
      Number of atoms: 276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 276
          Classifications: {'RNAv2': 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: {'RNAv2': 18}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 16}
  Time building chain proxies: 1.97, per 1000 atoms: 0.22
  Number of scatterers: 8825
  At special positions: 0
  Unit cell: (86.9, 99, 122.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P      35     15.00
     O    1755      8.00
     N    1473      7.00
     C    5504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 327.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 9 sheets defined
      46.3% alpha, 7.1% beta
      9 base pairs and 23 stacking pairs defined.
    Time for finding SS restraints: 0.82
  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: 1.48

  Time building geometry restraints manager: 1.12 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: 12056
        3.23 -     6.47: 358
        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 -    16.09: 4650
       16.09 -    32.17: 501
       32.17 -    48.26: 106
       48.26 -    64.34: 15
       64.34 -    80.43: 7
  Dihedral angle restraints: 5279
    sinusoidal: 2286
      harmonic: 2993
  Sorted by residual:
  dihedral pdb=" C4'   A T   0 "
           pdb=" C3'   A T   0 "
           pdb=" C2'   A T   0 "
           pdb=" C1'   A T   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -32.98   69.32     1      3.10e+00 1.04e-01 6.46e+02
  dihedral pdb=" O4'   A T   0 "
           pdb=" C4'   A T   0 "
           pdb=" C3'   A T   0 "
           pdb=" C2'   A T   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.15   20.43  -55.58     1      4.00e+00 6.25e-02 2.61e+02
  dihedral pdb=" O4'   A T   0 "
           pdb=" C2'   A T   0 "
           pdb=" C1'   A T   0 "
           pdb=" C3'   A T   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -94.41  -35.03  -59.38     3      3.80e+00 6.93e-02 1.48e+02
  ... (remaining 5276 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1223
       0.105 -    0.210: 143
       0.210 -    0.315: 55
       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:             0.060
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.960
  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:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.117   9097  Z= 0.516
  Angle     :  1.379  16.168  12497  Z= 0.739
  Chirality :  0.083   0.524   1426
  Planarity :  0.008   0.087   1466
  Dihedral  : 13.898  80.426   3347
  Min Nonbonded Distance : 2.323

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

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

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00835 /  0.52 ( 9093)
  covalent geometry    : angle       1.37899 /  0.74 (12497)
  hydrogen bonds       : bond        0.20481 / 12.50 (  303)
  hydrogen bonds       : angle       8.13057 /  5.53 (  855)
  Misc. bond           : bond        0.00127 /  0.06 (    4)

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

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.256 
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: 0.0914
  time to fit residues: 31.6798
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  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    6.9990

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.157464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135221 restraints weight = 15001.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.139338 restraints weight = 8124.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142050 restraints weight = 5138.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.143894 restraints weight = 3637.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.145171 restraints weight = 2800.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9097  Z= 0.280
  Angle     :  0.787   8.068  12497  Z= 0.409
  Chirality :  0.053   0.309   1426
  Planarity :  0.006   0.087   1466
  Dihedral  : 10.200 135.705   1475
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.44 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.24 (0.22), residues: 997
  helix: -1.82 (0.21), residues: 439
  sheet: -2.60 (0.56), residues: 67
  loop : -2.36 (0.23), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 249 
 TYR   0.026   0.002   TYR A 273 
 PHE   0.042   0.002   PHE A 157 
 TRP   0.015   0.002   TRP C 154 
 HIS   0.005   0.001   HIS A 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00574 /  0.28 ( 9093)
  covalent geometry    : angle       0.78673 /  0.41 (12497)
  hydrogen bonds       : bond        0.06635 /  4.12 (  303)
  hydrogen bonds       : angle       4.94218 /  3.36 (  855)
  Misc. bond           : bond        0.00140 /  0.07 (    4)

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

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 236
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7551 (tpt) cc_final: 0.6948 (tpt)
REVERT: A  143 LYS cc_start: 0.7884 (tppp) cc_final: 0.7682 (tptt)
REVERT: A  150 ASN cc_start: 0.7967 (m110) cc_final: 0.7619 (m110)
REVERT: A  167 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7020 (tm-30)
REVERT: A  242 MET cc_start: 0.7275 (mtp) cc_final: 0.6924 (mtp)
REVERT: A  365 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6990 (mtt90)
REVERT: A  395 CYS cc_start: 0.7277 (m) cc_final: 0.7068 (m)
REVERT: A  454 ASP cc_start: 0.7496 (t0) cc_final: 0.7118 (t0)
REVERT: A  463 MET cc_start: 0.6285 (ppp) cc_final: 0.5949 (ppp)
REVERT: A  703 ASN cc_start: 0.8233 (m110) cc_final: 0.7811 (m110)
REVERT: A  765 CYS cc_start: 0.8560 (t) cc_final: 0.8297 (t)
REVERT: A  766 PHE cc_start: 0.8687 (p90) cc_final: 0.7816 (p90)
REVERT: A  782 PHE cc_start: 0.7438 (m-80) cc_final: 0.6977 (t80)
REVERT: A  855 MET cc_start: 0.6609 (mtm) cc_final: 0.6021 (mtm)
REVERT: A  889 ARG cc_start: 0.7647 (tmm160) cc_final: 0.7141 (tmm160)
REVERT: A  892 HIS cc_start: 0.7783 (t70) cc_final: 0.7556 (t70)
REVERT: A  919 GLU cc_start: 0.7771 (mp0) cc_final: 0.7360 (mp0)
REVERT: A  924 MET cc_start: 0.7410 (tpp) cc_final: 0.7059 (ttm)
REVERT: C  129 MET cc_start: 0.7007 (ppp) cc_final: 0.6429 (ppp)
REVERT: C  157 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8077 (tm-30)
REVERT: D    2 LYS cc_start: 0.6520 (pttp) cc_final: 0.6060 (pttm)
REVERT: D   51 LYS cc_start: 0.7581 (mptt) cc_final: 0.7378 (tptt)
  outliers start: 20
  outliers final: 14
  residues processed: 238
  average time/residue: 0.0934
  time to fit residues: 30.2682
Evaluate side-chains
  231 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 216
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  492 GLN
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.4980
   chunk 26 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    3.4988

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.159742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137411 restraints weight = 15106.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141531 restraints weight = 8246.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144263 restraints weight = 5240.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.146146 restraints weight = 3714.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.147378 restraints weight = 2862.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9097  Z= 0.160
  Angle     :  0.648   7.864  12497  Z= 0.336
  Chirality :  0.047   0.325   1426
  Planarity :  0.005   0.046   1466
  Dihedral  :  9.851 141.678   1475
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.03 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.24), residues: 997
  helix: -0.83 (0.23), residues: 432
  sheet: -2.80 (0.50), 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   0.031   0.002   TYR A 129 
 PHE   0.028   0.002   PHE A 415 
 TRP   0.008   0.001   TRP A 268 
 HIS   0.004   0.001   HIS A 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.16 ( 9093)
  covalent geometry    : angle       0.64825 /  0.34 (12497)
  hydrogen bonds       : bond        0.04693 /  2.92 (  303)
  hydrogen bonds       : angle       4.40941 /  2.97 (  855)
  Misc. bond           : bond        0.00071 /  0.03 (    4)

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

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 223
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7510 (tpt) cc_final: 0.7164 (tpt)
REVERT: A  150 ASN cc_start: 0.7786 (m110) cc_final: 0.7466 (m110)
REVERT: A  249 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7295 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7196 (mtt90) cc_final: 0.6934 (mtt90)
REVERT: A  454 ASP cc_start: 0.7437 (t0) cc_final: 0.7096 (t0)
REVERT: A  703 ASN cc_start: 0.8060 (m110) cc_final: 0.7657 (m110)
REVERT: A  765 CYS cc_start: 0.8407 (t) cc_final: 0.8010 (t)
REVERT: A  782 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6869 (t80)
REVERT: A  807 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8177 (pttm)
REVERT: A  855 MET cc_start: 0.6469 (mtm) cc_final: 0.5838 (mtm)
REVERT: A  889 ARG cc_start: 0.7658 (tmm160) cc_final: 0.7040 (tmm160)
REVERT: A  917 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7269 (mm-30)
REVERT: A  919 GLU cc_start: 0.7574 (mp0) cc_final: 0.7264 (mp0)
REVERT: C  129 MET cc_start: 0.6877 (ppp) cc_final: 0.6331 (ppp)
REVERT: C  157 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: D   51 LYS cc_start: 0.7569 (mptt) cc_final: 0.7336 (tptt)
  outliers start: 28
  outliers final: 23
  residues processed: 229
  average time/residue: 0.0907
  time to fit residues: 28.0527
Evaluate side-chains
  239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 215
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  492 GLN
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue    3 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:    0.2980
   chunk 53 optimal weight:    8.9990
   chunk 85 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 16 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0980
   chunk 52 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.6786

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.157990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.135472 restraints weight = 15268.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.139619 restraints weight = 8318.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.142356 restraints weight = 5299.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.144189 restraints weight = 3763.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.145483 restraints weight = 2911.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2557

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= 0.194
  Angle     :  0.655  10.179  12497  Z= 0.338
  Chirality :  0.048   0.310   1426
  Planarity :  0.004   0.053   1466
  Dihedral  :  9.735 138.533   1475
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.27 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.25), residues: 997
  helix: -0.44 (0.24), residues: 435
  sheet: -2.88 (0.48), residues: 79
  loop : -1.94 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 183 
 TYR   0.024   0.002   TYR A 129 
 PHE   0.028   0.002   PHE A 415 
 TRP   0.009   0.002   TRP D  29 
 HIS   0.003   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.19 ( 9093)
  covalent geometry    : angle       0.65508 /  0.34 (12497)
  hydrogen bonds       : bond        0.05015 /  3.15 (  303)
  hydrogen bonds       : angle       4.40128 /  2.97 (  855)
  Misc. bond           : bond        0.00074 /  0.04 (    4)

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

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 218
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7573 (tpt) cc_final: 0.7210 (tpt)
REVERT: A  150 ASN cc_start: 0.7847 (m110) cc_final: 0.7545 (m110)
REVERT: A  249 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7432 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7174 (mtt90) cc_final: 0.6937 (mtt90)
REVERT: A  380 MET cc_start: 0.7318 (tmm) cc_final: 0.7029 (tmm)
REVERT: A  438 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8110 (mmtt)
REVERT: A  454 ASP cc_start: 0.7478 (t0) cc_final: 0.7195 (t0)
REVERT: A  513 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7902 (ttm-80)
REVERT: A  703 ASN cc_start: 0.8122 (m110) cc_final: 0.7704 (m110)
REVERT: A  765 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7964 (t)
REVERT: A  782 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6942 (t80)
REVERT: A  807 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8368 (pttm)
REVERT: A  855 MET cc_start: 0.6527 (mtm) cc_final: 0.5817 (mtm)
REVERT: A  881 PHE cc_start: 0.7358 (t80) cc_final: 0.7149 (t80)
REVERT: A  889 ARG cc_start: 0.7650 (tmm160) cc_final: 0.7001 (tmm160)
REVERT: A  917 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7444 (mm-30)
REVERT: A  919 GLU cc_start: 0.7863 (mp0) cc_final: 0.7342 (mp0)
REVERT: C  129 MET cc_start: 0.6932 (ppp) cc_final: 0.6329 (ppp)
REVERT: C  157 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: D   51 LYS cc_start: 0.7569 (mptt) cc_final: 0.7337 (tptt)
  outliers start: 36
  outliers final: 26
  residues processed: 227
  average time/residue: 0.0926
  time to fit residues: 28.9987
Evaluate side-chains
  243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 215
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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  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  477 ASP
Chi-restraints excluded: chain A residue  563 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 642 HIS
** 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 = 0.4000 r_free = 0.4000 target = 0.158651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.136704 restraints weight = 15117.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.140621 restraints weight = 8513.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.143222 restraints weight = 5506.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.145026 restraints weight = 3955.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.146230 restraints weight = 3069.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9097  Z= 0.170
  Angle     :  0.634   9.659  12497  Z= 0.324
  Chirality :  0.047   0.292   1426
  Planarity :  0.004   0.054   1466
  Dihedral  :  9.573 137.681   1475
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 17.73 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.25), residues: 997
  helix: -0.17 (0.25), residues: 435
  sheet: -2.69 (0.48), residues: 73
  loop : -1.92 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 183 
 TYR   0.027   0.002   TYR A 129 
 PHE   0.026   0.002   PHE A 415 
 TRP   0.012   0.002   TRP D  29 
 HIS   0.003   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 ( 9093)
  covalent geometry    : angle       0.63351 /  0.32 (12497)
  hydrogen bonds       : bond        0.04625 /  2.91 (  303)
  hydrogen bonds       : angle       4.33029 /  2.91 (  855)
  Misc. bond           : bond        0.00075 /  0.04 (    4)

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

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7920 (mttm) cc_final: 0.7593 (mttt)
REVERT: A   86 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.5243 (mt)
REVERT: A  124 MET cc_start: 0.7479 (tpt) cc_final: 0.7169 (tpt)
REVERT: A  150 ASN cc_start: 0.7785 (m110) cc_final: 0.7495 (m110)
REVERT: A  249 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7460 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7146 (mtt90) cc_final: 0.6887 (mtt90)
REVERT: A  380 MET cc_start: 0.7330 (tmm) cc_final: 0.7111 (tmm)
REVERT: A  454 ASP cc_start: 0.7383 (t0) cc_final: 0.7086 (t0)
REVERT: A  572 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6463 (m-70)
REVERT: A  576 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8150 (mm)
REVERT: A  694 PHE cc_start: 0.7593 (t80) cc_final: 0.7242 (t80)
REVERT: A  703 ASN cc_start: 0.8031 (m110) cc_final: 0.7563 (m110)
REVERT: A  765 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7910 (t)
REVERT: A  782 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6941 (t80)
REVERT: A  807 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8345 (pttm)
REVERT: A  855 MET cc_start: 0.6402 (mtm) cc_final: 0.5673 (mtm)
REVERT: A  889 ARG cc_start: 0.7662 (tmm160) cc_final: 0.6989 (tmm160)
REVERT: A  919 GLU cc_start: 0.7892 (mp0) cc_final: 0.7417 (mp0)
REVERT: C  129 MET cc_start: 0.6912 (ppp) cc_final: 0.6338 (ppp)
REVERT: C  157 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: D   51 LYS cc_start: 0.7567 (mptt) cc_final: 0.7315 (tptt)
  outliers start: 38
  outliers final: 31
  residues processed: 228
  average time/residue: 0.0928
  time to fit residues: 29.2509
Evaluate side-chains
  249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 213
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  190 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  473 VAL
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  572 HIS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  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:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    2.5386

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.160431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.137827 restraints weight = 15191.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.141990 restraints weight = 8371.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144689 restraints weight = 5337.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146593 restraints weight = 3804.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147869 restraints weight = 2945.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9097  Z= 0.129
  Angle     :  0.614   9.902  12497  Z= 0.311
  Chirality :  0.045   0.272   1426
  Planarity :  0.004   0.055   1466
  Dihedral  :  9.358 136.326   1475
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 19.42 %
    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 are not related in a simple way.
  whole: -1.55 (0.25), residues: 997
  helix:  0.06 (0.25), residues: 436
  sheet: -2.45 (0.49), residues: 71
  loop : -1.82 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 183 
 TYR   0.028   0.001   TYR A 129 
 PHE   0.023   0.001   PHE A 415 
 TRP   0.009   0.001   TRP D  29 
 HIS   0.002   0.001   HIS A 642 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 9093)
  covalent geometry    : angle       0.61367 /  0.31 (12497)
  hydrogen bonds       : bond        0.04044 /  2.53 (  303)
  hydrogen bonds       : angle       4.12066 /  2.76 (  855)
  Misc. bond           : bond        0.00069 /  0.03 (    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
  263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 226
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7857 (mttm) cc_final: 0.7324 (mttm)
REVERT: A   86 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.5171 (mt)
REVERT: A  124 MET cc_start: 0.7571 (tpt) cc_final: 0.7232 (tpt)
REVERT: A  150 ASN cc_start: 0.7792 (m110) cc_final: 0.7473 (m110)
REVERT: A  249 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7493 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6939 (mtt90)
REVERT: A  380 MET cc_start: 0.7371 (tmm) cc_final: 0.7089 (tmm)
REVERT: A  395 CYS cc_start: 0.7367 (m) cc_final: 0.7148 (m)
REVERT: A  454 ASP cc_start: 0.7449 (t0) cc_final: 0.7136 (t0)
REVERT: A  645 CYS cc_start: 0.8088 (m) cc_final: 0.6626 (t)
REVERT: A  694 PHE cc_start: 0.7634 (t80) cc_final: 0.7262 (t80)
REVERT: A  703 ASN cc_start: 0.7985 (m110) cc_final: 0.7560 (m110)
REVERT: A  765 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7692 (t)
REVERT: A  782 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6837 (t80)
REVERT: A  783 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7767 (mmpt)
REVERT: A  807 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8318 (pttm)
REVERT: A  855 MET cc_start: 0.6477 (mtm) cc_final: 0.5771 (mtm)
REVERT: A  889 ARG cc_start: 0.7667 (tmm160) cc_final: 0.6991 (tmm160)
REVERT: C  129 MET cc_start: 0.6895 (ppp) cc_final: 0.6341 (ppp)
REVERT: C  157 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: D   51 LYS cc_start: 0.7542 (mptt) cc_final: 0.7286 (tptt)
  outliers start: 37
  outliers final: 26
  residues processed: 242
  average time/residue: 0.0871
  time to fit residues: 29.4991
Evaluate side-chains
  251 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 222
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  477 ASP
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  765 CYS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  782 PHE
Chi-restraints excluded: chain A residue  789 GLN
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9990
   chunk 47 optimal weight:   30.0000
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0980
   chunk 9 optimal weight:    7.9990
   overall best weight:    2.8188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4023 r_free = 0.4023 target = 0.160149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.137583 restraints weight = 15120.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.141783 restraints weight = 8302.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144537 restraints weight = 5280.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.146378 restraints weight = 3758.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.147687 restraints weight = 2906.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9097  Z= 0.137
  Angle     :  0.621   9.329  12497  Z= 0.315
  Chirality :  0.045   0.232   1426
  Planarity :  0.004   0.058   1466
  Dihedral  :  9.303 135.604   1475
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 19.98 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.25), residues: 997
  helix:  0.16 (0.25), residues: 437
  sheet: -2.32 (0.50), residues: 71
  loop : -1.81 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 183 
 TYR   0.027   0.001   TYR A 129 
 PHE   0.025   0.001   PHE A 415 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.14 ( 9093)
  covalent geometry    : angle       0.62084 /  0.31 (12497)
  hydrogen bonds       : bond        0.04141 /  2.63 (  303)
  hydrogen bonds       : angle       4.08967 /  2.74 (  855)
  Misc. bond           : bond        0.00068 /  0.03 (    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
  260 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 223
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7854 (mttm) cc_final: 0.7633 (mttm)
REVERT: A   86 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.5149 (mt)
REVERT: A  124 MET cc_start: 0.7580 (tpt) cc_final: 0.7244 (tpt)
REVERT: A  150 ASN cc_start: 0.7803 (m110) cc_final: 0.7486 (m110)
REVERT: A  219 PHE cc_start: 0.6098 (m-80) cc_final: 0.5891 (m-80)
REVERT: A  249 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7523 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7204 (mtt90) cc_final: 0.6932 (mtt90)
REVERT: A  380 MET cc_start: 0.7346 (tmm) cc_final: 0.7030 (tmm)
REVERT: A  395 CYS cc_start: 0.7406 (m) cc_final: 0.7164 (m)
REVERT: A  454 ASP cc_start: 0.7407 (t0) cc_final: 0.7138 (t0)
REVERT: A  463 MET cc_start: 0.6153 (ptm) cc_final: 0.5772 (ppp)
REVERT: A  645 CYS cc_start: 0.8082 (m) cc_final: 0.6642 (t)
REVERT: A  694 PHE cc_start: 0.7582 (t80) cc_final: 0.7353 (t80)
REVERT: A  703 ASN cc_start: 0.7951 (m110) cc_final: 0.7512 (m110)
REVERT: A  765 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7710 (t)
REVERT: A  782 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6800 (t80)
REVERT: A  783 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7772 (mmpt)
REVERT: A  818 MET cc_start: 0.7401 (ppp) cc_final: 0.6728 (ppp)
REVERT: A  819 LEU cc_start: 0.8098 (tp) cc_final: 0.7038 (mt)
REVERT: A  855 MET cc_start: 0.6488 (mtm) cc_final: 0.5929 (mtm)
REVERT: A  889 ARG cc_start: 0.7665 (tmm160) cc_final: 0.7005 (tmm160)
REVERT: C  129 MET cc_start: 0.6911 (ppp) cc_final: 0.6362 (ppp)
REVERT: C  157 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: D    7 LYS cc_start: 0.7741 (mttm) cc_final: 0.7327 (mttp)
REVERT: D   51 LYS cc_start: 0.7544 (mptt) cc_final: 0.7280 (tptt)
  outliers start: 37
  outliers final: 33
  residues processed: 235
  average time/residue: 0.0880
  time to fit residues: 28.9990
Evaluate side-chains
  256 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 220
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  159 LYS
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  346 TYR
Chi-restraints excluded: chain A residue  355 HIS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  572 HIS
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  744 GLU
Chi-restraints excluded: chain A residue  756 MET
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    3 MET
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   62 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    0.0470
   chunk 16 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0060
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 97 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.4896

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 541 GLN
** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 ASN
** D  18 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 = 0.4065 r_free = 0.4065 target = 0.163634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.140822 restraints weight = 15140.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.144979 restraints weight = 8343.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147786 restraints weight = 5353.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.149658 restraints weight = 3809.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.150955 restraints weight = 2944.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   9097  Z= 0.110
  Angle     :  0.607   8.932  12497  Z= 0.307
  Chirality :  0.044   0.200   1426
  Planarity :  0.004   0.053   1466
  Dihedral  :  9.049 134.665   1475
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.88 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.25), residues: 997
  helix:  0.38 (0.25), residues: 437
  sheet: -2.07 (0.53), residues: 71
  loop : -1.64 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 513 
 TYR   0.027   0.001   TYR A 129 
 PHE   0.022   0.001   PHE A 415 
 TRP   0.010   0.001   TRP A 268 
 HIS   0.002   0.000   HIS A 309 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 ( 9093)
  covalent geometry    : angle       0.60713 /  0.31 (12497)
  hydrogen bonds       : bond        0.03276 /  2.10 (  303)
  hydrogen bonds       : angle       3.83201 /  2.56 (  855)
  Misc. bond           : bond        0.00013 /  0.01 (    4)

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

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 230
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7846 (mttm) cc_final: 0.7407 (mttt)
REVERT: A  124 MET cc_start: 0.7548 (tpt) cc_final: 0.7222 (tpt)
REVERT: A  150 ASN cc_start: 0.7742 (m110) cc_final: 0.7419 (m110)
REVERT: A  173 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7915 (ttp80)
REVERT: A  249 ARG cc_start: 0.7760 (ttm110) cc_final: 0.7476 (ttm-80)
REVERT: A  365 ARG cc_start: 0.7148 (mtt90) cc_final: 0.6886 (mtt90)
REVERT: A  380 MET cc_start: 0.7283 (tmm) cc_final: 0.6927 (tmm)
REVERT: A  395 CYS cc_start: 0.7328 (m) cc_final: 0.7085 (m)
REVERT: A  466 ILE cc_start: 0.7133 (tp) cc_final: 0.6743 (mm)
REVERT: A  488 ILE cc_start: 0.7304 (pt) cc_final: 0.7062 (pt)
REVERT: A  541 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7180 (tp-100)
REVERT: A  645 CYS cc_start: 0.7927 (m) cc_final: 0.6688 (t)
REVERT: A  668 MET cc_start: 0.7641 (tmm) cc_final: 0.7135 (tmm)
REVERT: A  673 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7888 (tp)
REVERT: A  691 ASN cc_start: 0.8317 (m-40) cc_final: 0.8068 (m-40)
REVERT: A  694 PHE cc_start: 0.7678 (t80) cc_final: 0.7252 (t80)
REVERT: A  703 ASN cc_start: 0.7967 (m110) cc_final: 0.7503 (m110)
REVERT: A  765 CYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7626 (t)
REVERT: A  782 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6717 (t80)
REVERT: A  783 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7768 (mmpt)
REVERT: A  807 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8346 (mtmm)
REVERT: A  818 MET cc_start: 0.7403 (ppp) cc_final: 0.6678 (ppp)
REVERT: A  819 LEU cc_start: 0.8017 (tp) cc_final: 0.6900 (mt)
REVERT: A  855 MET cc_start: 0.6411 (mtm) cc_final: 0.5839 (mtm)
REVERT: A  889 ARG cc_start: 0.7630 (tmm160) cc_final: 0.6908 (tmm160)
REVERT: C  129 MET cc_start: 0.6840 (ppp) cc_final: 0.6360 (ppp)
REVERT: C  157 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8130 (tm-30)
REVERT: D    7 LYS cc_start: 0.7687 (mttm) cc_final: 0.7267 (mttp)
REVERT: D   51 LYS cc_start: 0.7508 (mptt) cc_final: 0.7235 (tptt)
  outliers start: 33
  outliers final: 22
  residues processed: 241
  average time/residue: 0.0890
  time to fit residues: 30.2611
Evaluate side-chains
  252 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 226
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  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  477 ASP
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  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
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   62 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0370
   chunk 8 optimal weight:    8.9990
   chunk 101 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   overall best weight:    2.9464

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 541 GLN
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 = 0.4035 r_free = 0.4035 target = 0.161157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.138631 restraints weight = 15040.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.142765 restraints weight = 8237.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.145487 restraints weight = 5259.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.147372 restraints weight = 3744.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.148509 restraints weight = 2891.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9097  Z= 0.144
  Angle     :  0.628   8.399  12497  Z= 0.322
  Chirality :  0.045   0.191   1426
  Planarity :  0.004   0.058   1466
  Dihedral  :  9.178 134.425   1475
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.55 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.26), residues: 997
  helix:  0.41 (0.26), residues: 438
  sheet: -2.11 (0.52), residues: 71
  loop : -1.67 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 513 
 TYR   0.038   0.002   TYR A 156 
 PHE   0.022   0.001   PHE A 415 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.002   0.001   HIS A 872 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 9093)
  covalent geometry    : angle       0.62829 /  0.32 (12497)
  hydrogen bonds       : bond        0.03974 /  2.50 (  303)
  hydrogen bonds       : angle       3.93187 /  2.64 (  855)
  Misc. bond           : bond        0.00065 /  0.03 (    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
  259 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 228
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7861 (mttm) cc_final: 0.7440 (mttp)
REVERT: A  124 MET cc_start: 0.7584 (tpt) cc_final: 0.7269 (tpt)
REVERT: A  150 ASN cc_start: 0.7795 (m110) cc_final: 0.7470 (m110)
REVERT: A  365 ARG cc_start: 0.7187 (mtt90) cc_final: 0.6911 (mtt90)
REVERT: A  380 MET cc_start: 0.7299 (tmm) cc_final: 0.7047 (tmm)
REVERT: A  395 CYS cc_start: 0.7478 (m) cc_final: 0.7260 (m)
REVERT: A  438 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8087 (mmtt)
REVERT: A  645 CYS cc_start: 0.7926 (m) cc_final: 0.6662 (t)
REVERT: A  694 PHE cc_start: 0.7717 (t80) cc_final: 0.7280 (t80)
REVERT: A  703 ASN cc_start: 0.7974 (m110) cc_final: 0.7557 (m110)
REVERT: A  765 CYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7708 (t)
REVERT: A  782 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6813 (t80)
REVERT: A  783 LYS cc_start: 0.8121 (mmpt) cc_final: 0.7827 (mmpt)
REVERT: A  818 MET cc_start: 0.7451 (ppp) cc_final: 0.6746 (ppp)
REVERT: A  819 LEU cc_start: 0.8095 (tp) cc_final: 0.6966 (mt)
REVERT: A  855 MET cc_start: 0.6509 (mtm) cc_final: 0.5913 (mtm)
REVERT: A  889 ARG cc_start: 0.7672 (tmm160) cc_final: 0.6935 (tmm160)
REVERT: C  129 MET cc_start: 0.6896 (ppp) cc_final: 0.6348 (ppp)
REVERT: C  157 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: D    7 LYS cc_start: 0.7773 (mttm) cc_final: 0.7347 (mttp)
REVERT: D   51 LYS cc_start: 0.7526 (mptt) cc_final: 0.7275 (tptt)
  outliers start: 31
  outliers final: 25
  residues processed: 238
  average time/residue: 0.0917
  time to fit residues: 30.6266
Evaluate side-chains
  252 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 225
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
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  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   92 PHE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain D residue    2 LYS
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   62 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 92 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 60 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 572 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 = 0.4005 r_free = 0.4005 target = 0.159484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137925 restraints weight = 15012.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.142044 restraints weight = 8201.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144756 restraints weight = 5175.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.146586 restraints weight = 3630.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.147699 restraints weight = 2772.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3245

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= 0.129
  Angle     :  0.626   8.183  12497  Z= 0.320
  Chirality :  0.045   0.192   1426
  Planarity :  0.004   0.059   1466
  Dihedral  :  9.177 134.131   1475
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 21.66 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.26), residues: 997
  helix:  0.38 (0.25), residues: 438
  sheet: -1.83 (0.58), residues: 61
  loop : -1.69 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 513 
 TYR   0.033   0.001   TYR A 156 
 PHE   0.023   0.001   PHE A 283 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.003   0.001   HIS A 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 9093)
  covalent geometry    : angle       0.62584 /  0.32 (12497)
  hydrogen bonds       : bond        0.03795 /  2.40 (  303)
  hydrogen bonds       : angle       3.88950 /  2.60 (  855)
  Misc. bond           : bond        0.00054 /  0.03 (    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
  258 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 228
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LYS cc_start: 0.7822 (mttm) cc_final: 0.7377 (mttp)
REVERT: A  124 MET cc_start: 0.7693 (tpt) cc_final: 0.7315 (tpt)
REVERT: A  150 ASN cc_start: 0.7766 (m110) cc_final: 0.7451 (m110)
REVERT: A  365 ARG cc_start: 0.7196 (mtt90) cc_final: 0.6920 (mtt90)
REVERT: A  380 MET cc_start: 0.7356 (tmm) cc_final: 0.7069 (tmm)
REVERT: A  395 CYS cc_start: 0.7578 (m) cc_final: 0.7324 (m)
REVERT: A  438 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8062 (mmtt)
REVERT: A  645 CYS cc_start: 0.7981 (m) cc_final: 0.6685 (t)
REVERT: A  694 PHE cc_start: 0.7776 (t80) cc_final: 0.7375 (t80)
REVERT: A  703 ASN cc_start: 0.7994 (m110) cc_final: 0.7566 (m110)
REVERT: A  765 CYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7719 (t)
REVERT: A  782 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6794 (t80)
REVERT: A  783 LYS cc_start: 0.8135 (mmpt) cc_final: 0.7835 (mmpt)
REVERT: A  818 MET cc_start: 0.7443 (ppp) cc_final: 0.6704 (ppp)
REVERT: A  819 LEU cc_start: 0.8094 (tp) cc_final: 0.6912 (mt)
REVERT: A  842 CYS cc_start: 0.7065 (p) cc_final: 0.6840 (p)
REVERT: A  855 MET cc_start: 0.6531 (mtm) cc_final: 0.5889 (mtm)
REVERT: A  889 ARG cc_start: 0.7690 (tmm160) cc_final: 0.6942 (tmm160)
REVERT: C  129 MET cc_start: 0.6897 (ppp) cc_final: 0.6319 (ppp)
REVERT: C  157 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8088 (tm-30)
REVERT: D    7 LYS cc_start: 0.7760 (mttm) cc_final: 0.7345 (mttp)
REVERT: D   51 LYS cc_start: 0.7528 (mptt) cc_final: 0.7261 (tptt)
  outliers start: 30
  outliers final: 26
  residues processed: 236
  average time/residue: 0.0885
  time to fit residues: 29.5777
Evaluate side-chains
  254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 226
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  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  462 THR
Chi-restraints excluded: chain A residue  473 VAL
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  572 HIS
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    3 MET
Chi-restraints excluded: chain D residue   28 LEU
Chi-restraints excluded: chain D residue   62 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 69 optimal weight:   20.0000
   chunk 67 optimal weight:    9.9990
   chunk 81 optimal weight:    0.0070
   chunk 44 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 87 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 101 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    2.5604

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 572 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 = 0.4000 r_free = 0.4000 target = 0.159063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.137584 restraints weight = 14888.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.141676 restraints weight = 8171.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144378 restraints weight = 5172.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.146229 restraints weight = 3624.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.147325 restraints weight = 2761.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9097  Z= 0.133
  Angle     :  0.628   7.873  12497  Z= 0.322
  Chirality :  0.045   0.192   1426
  Planarity :  0.004   0.059   1466
  Dihedral  :  9.196 133.998   1475
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.45 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.26), residues: 997
  helix:  0.40 (0.26), residues: 437
  sheet: -1.80 (0.58), residues: 61
  loop : -1.71 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 513 
 TYR   0.033   0.001   TYR A 156 
 PHE   0.030   0.001   PHE A 283 
 TRP   0.008   0.001   TRP A 216 
 HIS   0.006   0.001   HIS A 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 9093)
  covalent geometry    : angle       0.62819 /  0.32 (12497)
  hydrogen bonds       : bond        0.03871 /  2.45 (  303)
  hydrogen bonds       : angle       3.93893 /  2.63 (  855)
  Misc. bond           : bond        0.00060 /  0.03 (    4)

===============================================================================
Job complete
usr+sys time: 1422.43 seconds
wall clock time: 25 minutes 52.19 seconds (1552.19 seconds total)