Starting phenix.real_space_refine
on Sat Jul 26 23:44:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bv2_30210/07_2025/7bv2_30210.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bv2_30210/07_2025/7bv2_30210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bv2_30210/07_2025/7bv2_30210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bv2_30210/07_2025/7bv2_30210.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bv2_30210/07_2025/7bv2_30210.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bv2_30210/07_2025/7bv2_30210.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      28      5.49       5
     Mg      2      5.21       5
     S      58      5.16       5
     C    5407      2.51       5
     N    1437      2.21       5
     O    1696      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8630
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 834, 6712
          Classifications: {'peptide': 834}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 805}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 871
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 481
          Classifications: {'peptide': 63}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 62}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "P"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 234
          Classifications: {'RNA': 11}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 1, 'rna3p': 9}
    Chain: "T"
      Number of atoms: 290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 290
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 9}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 13
          Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "P"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'F86': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1816  SG  CYS A 301      49.560  64.092  38.924  1.00 12.33           S
  ATOM   1857  SG  CYS A 306      49.369  63.471  35.242  1.00 10.05           S
  ATOM   1889  SG  CYS A 310      52.744  63.249  37.074  1.00  9.56           S
  ATOM   3297  SG  CYS A 487      31.730  59.229  47.521  1.00 11.38           S
  ATOM   4550  SG  CYS A 645      30.654  59.341  44.075  1.00 12.29           S
  ATOM   4556  SG  CYS A 646      33.652  60.861  45.159  1.00 10.15           S

  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" O   POP A1003 " occ=0.50
      ... (7 atoms not shown)
      pdb=" P2  POP A1003 " occ=0.50
    residue:
      pdb="MG    MG A1004 " occ=0.50
    residue:
      pdb="MG    MG A1005 " occ=0.50
    residue:
      pdb=" C1  F86 P 101 " occ=0.50
      ... (22 atoms not shown)
      pdb=" P1  F86 P 101 " occ=0.50
  Time building chain proxies: 9.42, per 1000 atoms: 1.09
  Number of scatterers: 8630
  At special positions: 0
  Unit cell: (95.316, 93.288, 106.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      58     16.00
     P      28     15.00
     Mg      2     11.99
     O    1696      8.00
     N    1437      7.00
     C    5407      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.63
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 301 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 306 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
      Number of angles added : 6


  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 8 sheets defined
      56.4% alpha, 13.4% beta
      9 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 3.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 90
    Processing helix  chain 'A' and resid 123 through 133
      removed outlier: 3.534A  pdb=" N   LEU A 127 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 153 through 159
      removed outlier: 3.682A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 178 through 200
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 234 through 248
      Proline residue:  A 243  - end of helix
      removed outlier: 4.045A  pdb=" N   THR A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.327A  pdb=" N   ALA A 253 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   VAL A 257 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ASP A 258 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.522A  pdb=" N   PHE A 313 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
    Processing helix  chain 'A' and resid 367 through 377
    Processing helix  chain 'A' and resid 377 through 385
      removed outlier: 4.541A  pdb=" N   HIS A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 426
    Processing helix  chain 'A' and resid 447 through 454
    Processing helix  chain 'A' and resid 455 through 459
    Processing helix  chain 'A' and resid 465 through 477
      removed outlier: 3.853A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 489 through 493
      removed outlier: 3.519A  pdb=" N   VAL A 493 " --> pdb=" O   ALA A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 511 through 519
      removed outlier: 3.726A  pdb=" N   TYR A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 561 through 582
      removed outlier: 3.710A  pdb=" N   THR A 567 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 606
    Processing helix  chain 'A' and resid 621 through 626
      removed outlier: 3.656A  pdb=" N   MET A 626 " --> pdb=" O   CYS A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 640 through 642
      No H-bonds generated for 'chain 'A' and resid 640 through 642'
    Processing helix  chain 'A' and resid 647 through 663
    Processing helix  chain 'A' and resid 686 through 709
    Processing helix  chain 'A' and resid 711 through 715
    Processing helix  chain 'A' and resid 717 through 733
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 773
    Processing helix  chain 'A' and resid 778 through 790
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 833 through 842
    Processing helix  chain 'A' and resid 846 through 850
    Processing helix  chain 'A' and resid 851 through 867
      removed outlier: 3.958A  pdb=" N   GLU A 857 " --> pdb=" O   THR A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 874 through 895
      removed outlier: 4.207A  pdb=" N   VAL A 880 " --> pdb=" O   GLU A 876 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   PHE A 881 " --> pdb=" O   TYR A 877 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   HIS A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 923
      removed outlier: 4.306A  pdb=" N   TYR A 921 " --> pdb=" O   GLU A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 924 through 926
      No H-bonds generated for 'chain 'A' and resid 924 through 926'
    Processing helix  chain 'B' and resid 79 through 94
    Processing helix  chain 'B' and resid 95 through 97
      No H-bonds generated for 'chain 'B' and resid 95 through 97'
    Processing helix  chain 'B' and resid 100 through 109
      removed outlier: 4.036A  pdb=" N   ASN B 109 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 125
      removed outlier: 4.168A  pdb=" N   LEU B 122 " --> pdb=" O   ASN B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 142
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'C' and resid 3 through 20
    Processing helix  chain 'C' and resid 21 through 24
    Processing helix  chain 'C' and resid 25 through 42
      removed outlier: 4.043A  pdb=" N   GLN C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 62
      removed outlier: 3.827A  pdb=" N   VAL C  58 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET C  62 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38
    Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224
      removed outlier: 7.094A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   VAL A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLY A 203 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.653A  pdb=" N   LEU A 329 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   TYR A 346 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   GLY A 327 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 9.413A  pdb=" N   SER A 363 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   PHE A 334 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.653A  pdb=" N   LEU A 329 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   TYR A 346 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   GLY A 327 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559
      removed outlier: 6.653A  pdb=" N   THR A 540 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN B 158 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU B 189 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 189 " (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 753 through 758
    Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822
      removed outlier: 3.688A  pdb=" N   ASP A 825 " --> pdb=" O   GLN A 822 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      40 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 3.71

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1344
        1.29 -     1.43: 2552
        1.43 -     1.56: 4834
        1.56 -     1.70: 49
        1.70 -     1.83: 88
  Bond restraints: 8867
  Sorted by residual:
  bond pdb=" O4  F86 P 101 "
       pdb=" P1  F86 P 101 "
    ideal  model  delta    sigma   weight residual
    1.601  1.704 -0.103 1.00e-02 1.00e+04 1.06e+02
  bond pdb=" C12 F86 P 101 "
       pdb=" N2  F86 P 101 "
    ideal  model  delta    sigma   weight residual
    1.293  1.359 -0.066 1.00e-02 1.00e+04 4.38e+01
  bond pdb=" P     U P  20 "
       pdb=" O5'   U P  20 "
    ideal  model  delta    sigma   weight residual
    1.593  1.676 -0.083 1.50e-02 4.44e+03 3.08e+01
  bond pdb=" C11 F86 P 101 "
       pdb=" N5  F86 P 101 "
    ideal  model  delta    sigma   weight residual
    1.337  1.392 -0.055 1.00e-02 1.00e+04 3.07e+01
  bond pdb=" O5  F86 P 101 "
       pdb=" P1  F86 P 101 "
    ideal  model  delta    sigma   weight residual
    1.533  1.483  0.050 1.50e-02 4.44e+03 1.11e+01
  ... (remaining 8862 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 12102
        3.75 -     7.50: 47
        7.50 -    11.25: 5
       11.25 -    15.00: 0
       15.00 -    18.75: 1
  Bond angle restraints: 12155
  Sorted by residual:
  angle pdb=" C10 F86 P 101 "
        pdb=" C9  F86 P 101 "
        pdb=" C11 F86 P 101 "
      ideal   model   delta    sigma   weight residual
     136.68  128.29    8.39 1.00e+00 1.00e+00 7.04e+01
  angle pdb=" C10 F86 P 101 "
        pdb=" C9  F86 P 101 "
        pdb=" N1  F86 P 101 "
      ideal   model   delta    sigma   weight residual
     107.41  115.10   -7.69 1.00e+00 1.00e+00 5.91e+01
  angle pdb=" C7  F86 P 101 "
        pdb=" C10 F86 P 101 "
        pdb=" C9  F86 P 101 "
      ideal   model   delta    sigma   weight residual
     107.84  100.22    7.62 1.00e+00 1.00e+00 5.81e+01
  angle pdb=" P1  POP A1003 "
        pdb=" O   POP A1003 "
        pdb=" P2  POP A1003 "
      ideal   model   delta    sigma   weight residual
     139.66  120.91   18.75 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" C5  F86 P 101 "
        pdb=" N1  F86 P 101 "
        pdb=" C9  F86 P 101 "
      ideal   model   delta    sigma   weight residual
     109.66  105.27    4.39 1.00e+00 1.00e+00 1.93e+01
  ... (remaining 12150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4697
       17.97 -    35.93: 426
       35.93 -    53.90: 99
       53.90 -    71.87: 33
       71.87 -    89.84: 9
  Dihedral angle restraints: 5264
    sinusoidal: 2265
      harmonic: 2999
  Sorted by residual:
  dihedral pdb=" CA  TYR A 606 "
           pdb=" C   TYR A 606 "
           pdb=" N   SER A 607 "
           pdb=" CA  SER A 607 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.17  -31.83     0      5.00e+00 4.00e-02 4.05e+01
  dihedral pdb=" CA  PRO A 612 "
           pdb=" C   PRO A 612 "
           pdb=" N   HIS A 613 "
           pdb=" CA  HIS A 613 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASN A 611 "
           pdb=" C   ASN A 611 "
           pdb=" N   PRO A 612 "
           pdb=" CA  PRO A 612 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.80  -22.20     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 5261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1063
       0.052 -    0.103: 258
       0.103 -    0.155: 52
       0.155 -    0.207: 8
       0.207 -    0.258: 6
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" CA  ARG B 111 "
            pdb=" N   ARG B 111 "
            pdb=" C   ARG B 111 "
            pdb=" CB  ARG B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ASP A 258 "
            pdb=" N   ASP A 258 "
            pdb=" C   ASP A 258 "
            pdb=" CB  ASP A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  LYS A 676 "
            pdb=" N   LYS A 676 "
            pdb=" C   LYS A 676 "
            pdb=" CB  LYS A 676 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1384 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U P  20 "    0.066 2.00e-02 2.50e+03   3.19e-02 2.29e+01
        pdb=" N1    U P  20 "   -0.052 2.00e-02 2.50e+03
        pdb=" C2    U P  20 "   -0.025 2.00e-02 2.50e+03
        pdb=" O2    U P  20 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U P  20 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    U P  20 "    0.009 2.00e-02 2.50e+03
        pdb=" O4    U P  20 "    0.030 2.00e-02 2.50e+03
        pdb=" C5    U P  20 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U P  20 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C  36 "    0.017 2.00e-02 2.50e+03   1.80e-02 4.84e+00
        pdb=" CG  HIS C  36 "   -0.039 2.00e-02 2.50e+03
        pdb=" ND1 HIS C  36 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 HIS C  36 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS C  36 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS C  36 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 532 "    0.011 2.00e-02 2.50e+03   2.07e-02 4.27e+00
        pdb=" C   LYS A 532 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LYS A 532 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A 533 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 31
        2.53 -     3.12: 6388
        3.12 -     3.72: 13413
        3.72 -     4.31: 20117
        4.31 -     4.90: 32232
  Nonbonded interactions: 72181
  Sorted by model distance:
  nonbonded pdb=" O4    U P  12 "
            pdb=" N1    A T  19 "
     model   vdw
     1.942 2.496
  nonbonded pdb=" O   ASN A 790 "
            pdb=" OD1 ASN A 790 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" O   GLU A 144 "
            pdb=" OG1 THR A 148 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE A 494 "
            pdb=" NE2 GLN A 573 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OG  SER A 239 "
            pdb=" OD1 ASP A 465 "
     model   vdw
     2.284 3.040
  ... (remaining 72176 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             77.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.900
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:85.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  197.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
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      :  0.006   0.200   8876  Z= 0.350
  Angle     :  0.785  18.748  12161  Z= 0.454
  Chirality :  0.050   0.258   1387
  Planarity :  0.004   0.044   1452
  Dihedral  : 15.369  89.836   3328
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.26), residues: 999
  helix: -0.10 (0.23), residues: 472
  sheet: -0.43 (0.47), residues: 97
  loop :  0.56 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 916 
 HIS   0.019   0.002   HIS C  36 
 PHE   0.027   0.002   PHE A 652 
 TYR   0.024   0.002   TYR A 289 
 ARG   0.009   0.001   ARG A 914 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17649 (  429)
  hydrogen bonds       : angle       6.48694 ( 1147)
  metal coordination   : bond        0.07948 (    8)
  metal coordination   : angle      11.40962 (    6)
  covalent geometry    : bond        0.00491 ( 8867)
  covalent geometry    : angle       0.74356 (12155)
  Misc. bond           : bond        0.15822 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 2.038 
Fit side-chains
REVERT: A  160 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7251 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 1.4427
  time to fit residues: 236.3837
Evaluate side-chains
  130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0980
   chunk 26 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 552 ASN
A 705 ASN
A 790 ASN
B 176 ASN
** C  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.164229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.120785 restraints weight = 8546.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.97
r_work: 0.3256 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8876  Z= 0.113
  Angle     :  0.520   7.639  12161  Z= 0.281
  Chirality :  0.041   0.188   1387
  Planarity :  0.004   0.043   1452
  Dihedral  : 10.471  73.176   1474
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.94 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 999
  helix:  0.61 (0.24), residues: 466
  sheet:  0.27 (0.52), residues: 86
  loop :  0.54 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 916 
 HIS   0.013   0.001   HIS C  36 
 PHE   0.020   0.001   PHE A 652 
 TYR   0.015   0.001   TYR A 289 
 ARG   0.004   0.000   ARG A 750 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  429)
  hydrogen bonds       : angle       4.34378 ( 1147)
  metal coordination   : bond        0.00754 (    8)
  metal coordination   : angle       2.41905 (    6)
  covalent geometry    : bond        0.00240 ( 8867)
  covalent geometry    : angle       0.51776 (12155)
  Misc. bond           : bond        0.00069 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  144 GLU cc_start: 0.8101 (tp30) cc_final: 0.7630 (tm-30)
REVERT: A  158 ASN cc_start: 0.8107 (m-40) cc_final: 0.7820 (m-40)
REVERT: C   62 MET cc_start: 0.6932 (ptp) cc_final: 0.6596 (ptp)
  outliers start: 9
  outliers final: 2
  residues processed: 147
  average time/residue: 1.1583
  time to fit residues: 182.2493
Evaluate side-chains
  133 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  610 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
A 191 GLN
A 468 GLN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A 724 GLN
A 790 ASN
A 875 GLN
B 176 ASN
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.158207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.112418 restraints weight = 8643.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.81
r_work: 0.3156 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8876  Z= 0.223
  Angle     :  0.605   6.658  12161  Z= 0.329
  Chirality :  0.046   0.165   1387
  Planarity :  0.004   0.045   1452
  Dihedral  : 10.681  72.945   1474
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 11.98 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 999
  helix:  0.53 (0.24), residues: 469
  sheet: -0.04 (0.48), residues: 98
  loop :  0.31 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 290 
 HIS   0.012   0.002   HIS C  36 
 PHE   0.025   0.002   PHE A 652 
 TYR   0.019   0.002   TYR A 788 
 ARG   0.004   0.001   ARG A 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05327 (  429)
  hydrogen bonds       : angle       4.46537 ( 1147)
  metal coordination   : bond        0.01732 (    8)
  metal coordination   : angle       2.92480 (    6)
  covalent geometry    : bond        0.00532 ( 8867)
  covalent geometry    : angle       0.60135 (12155)
  Misc. bond           : bond        0.00193 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.865 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6582 (pp20)
REVERT: A  158 ASN cc_start: 0.8160 (m-40) cc_final: 0.7956 (m-40)
REVERT: A  452 ASP cc_start: 0.8405 (t70) cc_final: 0.8200 (t0)
REVERT: A  856 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7855 (mm)
REVERT: A  885 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7123 (mp)
REVERT: B  174 MET cc_start: 0.7817 (tpp) cc_final: 0.7442 (tpt)
REVERT: C   27 LYS cc_start: 0.7799 (ttpp) cc_final: 0.7569 (mtpp)
REVERT: C   62 MET cc_start: 0.6881 (ptp) cc_final: 0.6547 (ptp)
  outliers start: 21
  outliers final: 9
  residues processed: 129
  average time/residue: 1.2510
  time to fit residues: 171.8677
Evaluate side-chains
  129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  291 ASP
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  568 ASN
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.2980
   chunk 36 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   chunk 7 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** 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 = 0.3895 r_free = 0.3895 target = 0.163177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.120017 restraints weight = 8595.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.04
r_work: 0.3240 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8876  Z= 0.104
  Angle     :  0.475   7.224  12161  Z= 0.256
  Chirality :  0.040   0.183   1387
  Planarity :  0.004   0.041   1452
  Dihedral  : 10.440  73.306   1474
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.11 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.26), residues: 999
  helix:  0.98 (0.24), residues: 471
  sheet:  0.20 (0.50), residues: 86
  loop :  0.27 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 916 
 HIS   0.010   0.001   HIS C  36 
 PHE   0.016   0.001   PHE A 652 
 TYR   0.014   0.001   TYR A 788 
 ARG   0.005   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  429)
  hydrogen bonds       : angle       4.09336 ( 1147)
  metal coordination   : bond        0.00666 (    8)
  metal coordination   : angle       2.05987 (    6)
  covalent geometry    : bond        0.00229 ( 8867)
  covalent geometry    : angle       0.47332 (12155)
  Misc. bond           : bond        0.00086 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  144 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7660 (tm-30)
REVERT: A  542 MET cc_start: 0.8153 (mtm) cc_final: 0.7892 (mmm)
REVERT: A  796 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6507 (mt-10)
REVERT: A  885 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.6991 (mp)
REVERT: B  174 MET cc_start: 0.7858 (tpp) cc_final: 0.7527 (tpt)
REVERT: C   27 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7575 (mtpp)
REVERT: C   62 MET cc_start: 0.6679 (ptp) cc_final: 0.6401 (ptp)
  outliers start: 15
  outliers final: 5
  residues processed: 140
  average time/residue: 1.2808
  time to fit residues: 190.6767
Evaluate side-chains
  123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0030
   chunk 50 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.162842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.117618 restraints weight = 8630.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.80
r_work: 0.3222 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3095
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3095 r_free = 0.3095    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8876  Z= 0.108
  Angle     :  0.474   6.973  12161  Z= 0.254
  Chirality :  0.039   0.152   1387
  Planarity :  0.003   0.039   1452
  Dihedral  : 10.417  73.372   1474
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 14.12 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 999
  helix:  1.11 (0.24), residues: 471
  sheet:  0.19 (0.51), residues: 86
  loop :  0.28 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 916 
 HIS   0.009   0.001   HIS C  36 
 PHE   0.016   0.001   PHE A 741 
 TYR   0.015   0.001   TYR B 135 
 ARG   0.005   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  429)
  hydrogen bonds       : angle       4.06898 ( 1147)
  metal coordination   : bond        0.00851 (    8)
  metal coordination   : angle       1.98488 (    6)
  covalent geometry    : bond        0.00240 ( 8867)
  covalent geometry    : angle       0.47202 (12155)
  Misc. bond           : bond        0.00105 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6892 (pp20)
REVERT: A  138 ASN cc_start: 0.6709 (t0) cc_final: 0.6492 (t0)
REVERT: A  158 ASN cc_start: 0.8189 (m-40) cc_final: 0.7901 (m-40)
REVERT: A  284 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8019 (t70)
REVERT: A  610 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7219 (mt-10)
REVERT: A  735 ARG cc_start: 0.7394 (mtp180) cc_final: 0.7190 (mtm-85)
REVERT: A  796 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6435 (mt-10)
REVERT: A  885 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.6975 (mp)
REVERT: B  174 MET cc_start: 0.7828 (tpp) cc_final: 0.7510 (tpt)
REVERT: C   27 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7470 (mtpp)
REVERT: C   62 MET cc_start: 0.6515 (ptp) cc_final: 0.6212 (ptp)
  outliers start: 13
  outliers final: 5
  residues processed: 137
  average time/residue: 1.2545
  time to fit residues: 183.0279
Evaluate side-chains
  134 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0050
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
A 381 HIS
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.159385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113775 restraints weight = 8543.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.80
r_work: 0.3175 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8876  Z= 0.182
  Angle     :  0.543   6.989  12161  Z= 0.292
  Chirality :  0.043   0.141   1387
  Planarity :  0.004   0.041   1452
  Dihedral  : 10.601  73.288   1474
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.90 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 999
  helix:  0.91 (0.24), residues: 472
  sheet:  0.17 (0.51), residues: 86
  loop :  0.12 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 916 
 HIS   0.008   0.001   HIS C  36 
 PHE   0.021   0.002   PHE A 741 
 TYR   0.019   0.002   TYR A 788 
 ARG   0.004   0.001   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  429)
  hydrogen bonds       : angle       4.23453 ( 1147)
  metal coordination   : bond        0.01459 (    8)
  metal coordination   : angle       2.40372 (    6)
  covalent geometry    : bond        0.00430 ( 8867)
  covalent geometry    : angle       0.54037 (12155)
  Misc. bond           : bond        0.00174 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6835 (pp20)
REVERT: A  158 ASN cc_start: 0.8182 (m-40) cc_final: 0.7920 (m-40)
REVERT: A  197 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.7141 (ttp-170)
REVERT: A  284 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.8020 (t70)
REVERT: A  417 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7844 (tttm)
REVERT: A  610 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7451 (mt-10)
REVERT: A  629 MET cc_start: 0.8647 (mmm) cc_final: 0.8345 (mmm)
REVERT: A  796 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6568 (mt-10)
REVERT: B  174 MET cc_start: 0.7776 (tpp) cc_final: 0.7455 (tpt)
REVERT: C   23 GLU cc_start: 0.7690 (pt0) cc_final: 0.7265 (tt0)
REVERT: C   27 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7466 (mtpp)
REVERT: C   62 MET cc_start: 0.6653 (ptp) cc_final: 0.6357 (ptp)
  outliers start: 20
  outliers final: 7
  residues processed: 132
  average time/residue: 1.3519
  time to fit residues: 189.3121
Evaluate side-chains
  129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.162062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.116861 restraints weight = 8688.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.81
r_work: 0.3210 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8876  Z= 0.114
  Angle     :  0.482   7.263  12161  Z= 0.257
  Chirality :  0.040   0.157   1387
  Planarity :  0.004   0.040   1452
  Dihedral  : 10.455  73.381   1474
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.92 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 999
  helix:  1.09 (0.24), residues: 471
  sheet:  0.21 (0.52), residues: 86
  loop :  0.17 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 916 
 HIS   0.008   0.001   HIS C  36 
 PHE   0.016   0.001   PHE A 741 
 TYR   0.016   0.001   TYR A 788 
 ARG   0.005   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  429)
  hydrogen bonds       : angle       4.08400 ( 1147)
  metal coordination   : bond        0.00810 (    8)
  metal coordination   : angle       2.07041 (    6)
  covalent geometry    : bond        0.00259 ( 8867)
  covalent geometry    : angle       0.47958 (12155)
  Misc. bond           : bond        0.00108 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6860 (pp20)
REVERT: A  138 ASN cc_start: 0.6665 (t0) cc_final: 0.6451 (t0)
REVERT: A  158 ASN cc_start: 0.8116 (m-40) cc_final: 0.7849 (m-40)
REVERT: A  197 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7061 (ttp-170)
REVERT: A  284 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7991 (t70)
REVERT: A  417 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7843 (tttm)
REVERT: A  610 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7298 (mt-10)
REVERT: A  796 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6526 (mt-10)
REVERT: B  174 MET cc_start: 0.7918 (tpp) cc_final: 0.7617 (tpt)
REVERT: C   23 GLU cc_start: 0.7440 (pt0) cc_final: 0.7045 (tt0)
REVERT: C   27 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7359 (mtpp)
REVERT: C   62 MET cc_start: 0.6484 (ptp) cc_final: 0.6185 (ptp)
  outliers start: 16
  outliers final: 6
  residues processed: 134
  average time/residue: 1.3195
  time to fit residues: 187.7366
Evaluate side-chains
  129 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 32 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.164158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121049 restraints weight = 8819.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.01
r_work: 0.3254 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8876  Z= 0.095
  Angle     :  0.461   6.831  12161  Z= 0.244
  Chirality :  0.038   0.145   1387
  Planarity :  0.003   0.038   1452
  Dihedral  : 10.324  73.434   1474
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.25 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 999
  helix:  1.22 (0.25), residues: 471
  sheet:  0.38 (0.54), residues: 86
  loop :  0.24 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 162 
 HIS   0.008   0.001   HIS C  36 
 PHE   0.015   0.001   PHE A 741 
 TYR   0.015   0.001   TYR B 135 
 ARG   0.007   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  429)
  hydrogen bonds       : angle       3.98394 ( 1147)
  metal coordination   : bond        0.00717 (    8)
  metal coordination   : angle       1.93709 (    6)
  covalent geometry    : bond        0.00206 ( 8867)
  covalent geometry    : angle       0.45902 (12155)
  Misc. bond           : bond        0.00085 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  138 ASN cc_start: 0.6647 (t0) cc_final: 0.6427 (t0)
REVERT: A  158 ASN cc_start: 0.8195 (m-40) cc_final: 0.7926 (m-40)
REVERT: A  284 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (t70)
REVERT: A  610 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7211 (mt-10)
REVERT: A  796 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6526 (mt-10)
REVERT: A  885 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7126 (mp)
REVERT: A  922 GLU cc_start: 0.7863 (tt0) cc_final: 0.7536 (tt0)
REVERT: B  174 MET cc_start: 0.7757 (tpp) cc_final: 0.7484 (tpt)
REVERT: C   27 LYS cc_start: 0.7580 (ttpp) cc_final: 0.7251 (mtpp)
  outliers start: 12
  outliers final: 5
  residues processed: 143
  average time/residue: 1.2796
  time to fit residues: 195.1216
Evaluate side-chains
  136 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  885 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 91 optimal weight:    0.4980
   chunk 73 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 95 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.161453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.116433 restraints weight = 8603.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.78
r_work: 0.3207 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8876  Z= 0.130
  Angle     :  0.493   6.966  12161  Z= 0.262
  Chirality :  0.040   0.138   1387
  Planarity :  0.003   0.038   1452
  Dihedral  : 10.405  73.395   1474
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.50 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 999
  helix:  1.12 (0.24), residues: 471
  sheet:  0.33 (0.54), residues: 86
  loop :  0.18 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 290 
 HIS   0.008   0.001   HIS C  36 
 PHE   0.018   0.001   PHE A 741 
 TYR   0.020   0.001   TYR A 289 
 ARG   0.005   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  429)
  hydrogen bonds       : angle       4.07521 ( 1147)
  metal coordination   : bond        0.01048 (    8)
  metal coordination   : angle       2.01604 (    6)
  covalent geometry    : bond        0.00300 ( 8867)
  covalent geometry    : angle       0.49115 (12155)
  Misc. bond           : bond        0.00129 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A  138 ASN cc_start: 0.6744 (t0) cc_final: 0.6514 (t0)
REVERT: A  158 ASN cc_start: 0.8171 (m-40) cc_final: 0.7900 (m-40)
REVERT: A  197 ARG cc_start: 0.7514 (ttp-170) cc_final: 0.7213 (ttp-170)
REVERT: A  284 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.8001 (t70)
REVERT: A  542 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7863 (mmm)
REVERT: A  796 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6495 (mt-10)
REVERT: A  922 GLU cc_start: 0.7871 (tt0) cc_final: 0.7539 (tt0)
REVERT: B  174 MET cc_start: 0.7893 (tpp) cc_final: 0.7556 (tpt)
REVERT: C   23 GLU cc_start: 0.7423 (pt0) cc_final: 0.7077 (tt0)
REVERT: C   27 LYS cc_start: 0.7505 (ttpp) cc_final: 0.7165 (mtpp)
  outliers start: 10
  outliers final: 5
  residues processed: 126
  average time/residue: 1.5177
  time to fit residues: 202.5407
Evaluate side-chains
  123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ASP
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  542 MET
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 8 optimal weight:    0.3980
   chunk 88 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
B 157 GLN
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.166941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123766 restraints weight = 9086.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.88
r_work: 0.3464 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8876  Z= 0.122
  Angle     :  0.497   7.146  12161  Z= 0.263
  Chirality :  0.040   0.139   1387
  Planarity :  0.003   0.038   1452
  Dihedral  : 10.386  73.416   1474
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.84 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 999
  helix:  1.14 (0.24), residues: 471
  sheet:  0.34 (0.54), residues: 86
  loop :  0.18 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 916 
 HIS   0.008   0.001   HIS C  36 
 PHE   0.018   0.001   PHE A 741 
 TYR   0.019   0.001   TYR A 289 
 ARG   0.006   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03690 (  429)
  hydrogen bonds       : angle       4.06854 ( 1147)
  metal coordination   : bond        0.00879 (    8)
  metal coordination   : angle       1.97896 (    6)
  covalent geometry    : bond        0.00280 ( 8867)
  covalent geometry    : angle       0.49550 (12155)
  Misc. bond           : bond        0.00121 (    1)

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

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

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1998 Ramachandran restraints generated.
    999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.983 
Fit side-chains
REVERT: A  138 ASN cc_start: 0.6834 (t0) cc_final: 0.6605 (t0)
REVERT: A  158 ASN cc_start: 0.8367 (m-40) cc_final: 0.8125 (m-40)
REVERT: A  197 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7415 (ttp-170)
REVERT: A  542 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8044 (mmm)
REVERT: A  796 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6544 (mt-10)
REVERT: A  922 GLU cc_start: 0.8048 (tt0) cc_final: 0.7837 (tt0)
REVERT: B  174 MET cc_start: 0.7879 (tpp) cc_final: 0.7574 (tpt)
REVERT: C   23 GLU cc_start: 0.7610 (pt0) cc_final: 0.7282 (tt0)
REVERT: C   27 LYS cc_start: 0.7808 (ttpp) cc_final: 0.7516 (mtpp)
  outliers start: 8
  outliers final: 6
  residues processed: 120
  average time/residue: 1.3922
  time to fit residues: 177.4631
Evaluate side-chains
  123 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  542 MET
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   22 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 87 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 2 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.3362

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

Flipped N/Q/H residues before XYZ refinement:
** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 886 GLN
C  34 GLN
** C  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  37 ASN ** 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 = 0.3982 r_free = 0.3982 target = 0.166706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.123461 restraints weight = 9106.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.87
r_work: 0.3459 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8876  Z= 0.127
  Angle     :  0.496   7.013  12161  Z= 0.262
  Chirality :  0.040   0.138   1387
  Planarity :  0.004   0.038   1452
  Dihedral  : 10.395  73.418   1474
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 16.50 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 999
  helix:  1.12 (0.24), residues: 471
  sheet:  0.32 (0.54), residues: 86
  loop :  0.18 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 916 
 HIS   0.008   0.001   HIS C  36 
 PHE   0.018   0.001   PHE A 741 
 TYR   0.020   0.001   TYR A 289 
 ARG   0.006   0.000   ARG A 555 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  429)
  hydrogen bonds       : angle       4.07908 ( 1147)
  metal coordination   : bond        0.00932 (    8)
  metal coordination   : angle       2.01365 (    6)
  covalent geometry    : bond        0.00292 ( 8867)
  covalent geometry    : angle       0.49387 (12155)
  Misc. bond           : bond        0.00125 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8379.19 seconds
wall clock time: 146 minutes 2.39 seconds (8762.39 seconds total)