Starting phenix.real_space_refine
on Wed Mar  4 06:36:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mkw_48340/03_2026/9mkw_48340.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mkw_48340/03_2026/9mkw_48340.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mkw_48340/03_2026/9mkw_48340.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mkw_48340/03_2026/9mkw_48340.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mkw_48340/03_2026/9mkw_48340.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mkw_48340/03_2026/9mkw_48340.map"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=  -0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      64      5.49       5
     S      20      5.16       5
     C    6967      2.51       5
     N    1850      2.21       5
     O    2289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11190
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1189, 9852
          Classifications: {'peptide': 1189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 1162}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 764
          Classifications: {'RNA': 36}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 11, 'rna3p': 24}
    Chain: "C"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 407
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "D"
      Number of atoms: 167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 167
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
  Time building chain proxies: 2.50, per 1000 atoms: 0.22
  Number of scatterers: 11190
  At special positions: 0
  Unit cell: (109.22, 104.06, 134.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P      64     15.00
     O    2289      8.00
     N    1850      7.00
     C    6967      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 465.2 milliseconds
  

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 9 sheets defined
      54.0% alpha, 8.4% beta
      20 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 4.299A  pdb=" N   GLU A   6 " --> pdb=" O   ILE A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 35
      removed outlier: 4.251A  pdb=" N   ASN A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 67
      removed outlier: 3.742A  pdb=" N   ASP A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TYR A  57 " --> pdb=" O   ILE A  53 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A  65 " --> pdb=" O   PHE A  61 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   SER A  67 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 87
      removed outlier: 3.642A  pdb=" N   LEU A  76 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LYS A  87 " --> pdb=" O   TYR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 116
      removed outlier: 3.632A  pdb=" N   SER A 116 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 4.411A  pdb=" N   LYS A 120 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ASN A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 121'
    Processing helix  chain 'A' and resid 137 through 148
    Processing helix  chain 'A' and resid 152 through 157
      removed outlier: 3.954A  pdb=" N   ASN A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 171
      removed outlier: 3.707A  pdb=" N   ALA A 165 " --> pdb=" O   ASP A 161 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 191
      removed outlier: 4.469A  pdb=" N   PHE A 182 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ASN A 185 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG A 186 " --> pdb=" O   PHE A 182 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   VAL A 189 " --> pdb=" O   ASN A 185 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 206
    Processing helix  chain 'A' and resid 206 through 225
      removed outlier: 3.830A  pdb=" N   ASP A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 260 through 264
      removed outlier: 3.503A  pdb=" N   PHE A 264 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 272
    Processing helix  chain 'A' and resid 274 through 287
    Processing helix  chain 'A' and resid 299 through 312
    Processing helix  chain 'A' and resid 313 through 319
      removed outlier: 3.819A  pdb=" N   LYS A 317 " --> pdb=" O   ASP A 313 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TYR A 319 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 362
      removed outlier: 3.549A  pdb=" N   VAL A 348 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 383
    Processing helix  chain 'A' and resid 397 through 407
    Processing helix  chain 'A' and resid 412 through 423
      removed outlier: 3.627A  pdb=" N   THR A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 467
    Processing helix  chain 'A' and resid 474 through 506
      Proline residue:  A 486  - end of helix
      removed outlier: 3.797A  pdb=" N   GLN A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 540
      removed outlier: 3.847A  pdb=" N   VAL A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 573
    Processing helix  chain 'A' and resid 574 through 586
      removed outlier: 3.779A  pdb=" N   LEU A 578 " --> pdb=" O   ASN A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 618
    Processing helix  chain 'A' and resid 642 through 649
    Processing helix  chain 'A' and resid 668 through 674
    Processing helix  chain 'A' and resid 678 through 683
      removed outlier: 4.316A  pdb=" N   TYR A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 695
      removed outlier: 3.502A  pdb=" N   LEU A 689 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 731
    Processing helix  chain 'A' and resid 733 through 738
      removed outlier: 3.791A  pdb=" N   ASP A 736 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE A 737 " --> pdb=" O   TRP A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 760
      removed outlier: 3.968A  pdb=" N   PHE A 753 " --> pdb=" O   SER A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 780
      removed outlier: 3.532A  pdb=" N   GLN A 780 " --> pdb=" O   SER A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 794
      removed outlier: 3.796A  pdb=" N   PHE A 793 " --> pdb=" O   ASN A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 812
      removed outlier: 4.320A  pdb=" N   PHE A 812 " --> pdb=" O   TRP A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 819
      removed outlier: 3.512A  pdb=" N   ASP A 819 " --> pdb=" O   ARG A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 875
    Processing helix  chain 'A' and resid 897 through 907
      removed outlier: 3.647A  pdb=" N   LEU A 903 " --> pdb=" O   GLU A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 961
    Processing helix  chain 'A' and resid 977 through 997
      removed outlier: 3.729A  pdb=" N   HIS A 990 " --> pdb=" O   SER A 986 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE A 997 " --> pdb=" O   ALA A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1036
      removed outlier: 4.156A  pdb=" N   LYS A1026 " --> pdb=" O   GLN A1022 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A1027 " --> pdb=" O   VAL A1023 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLU A1028 " --> pdb=" O   TYR A1024 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS A1029 " --> pdb=" O   GLN A1025 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1067
    Processing helix  chain 'A' and resid 1101 through 1109
    Processing helix  chain 'A' and resid 1129 through 1133
      removed outlier: 3.553A  pdb=" N   PHE A1133 " --> pdb=" O   TYR A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1172 through 1180
      removed outlier: 4.162A  pdb=" N   LYS A1176 " --> pdb=" O   LYS A1172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1184 through 1188
      removed outlier: 4.159A  pdb=" N   GLY A1188 " --> pdb=" O   TYR A1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1190 through 1198
      removed outlier: 4.038A  pdb=" N   ALA A1194 " --> pdb=" O   CYS A1190 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU A1198 " --> pdb=" O   ALA A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1200 through 1215
      removed outlier: 3.595A  pdb=" N   SER A1209 " --> pdb=" O   ALA A1205 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL A1210 " --> pdb=" O   LYS A1206 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   THR A1213 " --> pdb=" O   SER A1209 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU A1215 " --> pdb=" O   LEU A1211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1253 through 1267
    Processing helix  chain 'A' and resid 1270 through 1275
    Processing helix  chain 'A' and resid 1287 through 1299
      removed outlier: 3.623A  pdb=" N   ASN A1299 " --> pdb=" O   VAL A1295 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 597
      removed outlier: 5.100A  pdb=" N   PHE A 878 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE A 788 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   TYR A 628 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   LEU A 621 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ILE A 657 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 596 through 597
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394
    Processing sheet with id=AA4, first strand: chain 'A' and resid 848 through 850
    Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 940
      removed outlier: 6.717A  pdb=" N   LEU A 928 " --> pdb=" O   ILE A 936 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLN A 938 " --> pdb=" O   TYR A 926 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TYR A 926 " --> pdb=" O   GLN A 938 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 943 through 944
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1004 through 1006
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1118
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1127 through 1128

    446 hydrogen bonds defined for protein.
    1245 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2557
        1.33 -     1.45: 2685
        1.45 -     1.57: 6142
        1.57 -     1.69: 125
        1.69 -     1.81: 32
  Bond restraints: 11541
  Sorted by residual:
  bond pdb=" P    DT D  -4 "
       pdb=" OP1  DT D  -4 "
    ideal  model  delta    sigma   weight residual
    1.480  1.517 -0.037 2.00e-02 2.50e+03 3.45e+00
  bond pdb=" P    DT D  -3 "
       pdb=" OP2  DT D  -3 "
    ideal  model  delta    sigma   weight residual
    1.480  1.516 -0.036 2.00e-02 2.50e+03 3.17e+00
  bond pdb=" P    DT D  -3 "
       pdb=" OP1  DT D  -3 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" P    DT D  -4 "
       pdb=" OP2  DT D  -4 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.03e+00
  bond pdb=" C   VAL A 576 "
       pdb=" N   PRO A 577 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.49e+00
  ... (remaining 11536 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 15339
        1.45 -     2.90: 393
        2.90 -     4.35: 41
        4.35 -     5.80: 12
        5.80 -     7.25: 5
  Bond angle restraints: 15790
  Sorted by residual:
  angle pdb=" N   PHE A 543 "
        pdb=" CA  PHE A 543 "
        pdb=" C   PHE A 543 "
      ideal   model   delta    sigma   weight residual
     113.72  109.41    4.31 1.52e+00 4.33e-01 8.04e+00
  angle pdb=" C3'  DA C   2 "
        pdb=" C2'  DA C   2 "
        pdb=" C1'  DA C   2 "
      ideal   model   delta    sigma   weight residual
     101.60  105.44   -3.84 1.50e+00 4.44e-01 6.54e+00
  angle pdb=" C4   DT D  -3 "
        pdb=" C5   DT D  -3 "
        pdb=" C7   DT D  -3 "
      ideal   model   delta    sigma   weight residual
     122.40  118.59    3.81 1.50e+00 4.44e-01 6.46e+00
  angle pdb=" N   ILE A 542 "
        pdb=" CA  ILE A 542 "
        pdb=" C   ILE A 542 "
      ideal   model   delta    sigma   weight residual
     109.45  105.93    3.52 1.39e+00 5.18e-01 6.40e+00
  angle pdb=" C4   DT D  -4 "
        pdb=" C5   DT D  -4 "
        pdb=" C7   DT D  -4 "
      ideal   model   delta    sigma   weight residual
     122.40  118.69    3.71 1.50e+00 4.44e-01 6.11e+00
  ... (remaining 15785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.22: 6410
       26.22 -    52.43: 444
       52.43 -    78.65: 107
       78.65 -   104.87: 7
      104.87 -   131.09: 1
  Dihedral angle restraints: 6969
    sinusoidal: 3436
      harmonic: 3533
  Sorted by residual:
  dihedral pdb=" C4'  DA C -14 "
           pdb=" C3'  DA C -14 "
           pdb=" O3'  DA C -14 "
           pdb=" P    DT C -13 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   -8.91 -131.09     1      3.50e+01 8.16e-04 1.30e+01
  dihedral pdb=" CA  TYR A 392 "
           pdb=" C   TYR A 392 "
           pdb=" N   PHE A 393 "
           pdb=" CA  PHE A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  LYS A 541 "
           pdb=" C   LYS A 541 "
           pdb=" N   ILE A 542 "
           pdb=" CA  ILE A 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.15   16.85     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 1720
       0.124 -    0.247: 6
       0.247 -    0.371: 0
       0.371 -    0.494: 0
       0.494 -    0.618: 2
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" P    DT D  -4 "
            pdb=" OP1  DT D  -4 "
            pdb=" OP2  DT D  -4 "
            pdb=" O5'  DT D  -4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.62 2.00e-01 2.50e+01 9.55e+00
  chirality pdb=" P    DT D  -3 "
            pdb=" OP1  DT D  -3 "
            pdb=" OP2  DT D  -3 "
            pdb=" O5'  DT D  -3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.86   -0.52 2.00e-01 2.50e+01 6.67e+00
  chirality pdb=" CA  VAL A 576 "
            pdb=" N   VAL A 576 "
            pdb=" C   VAL A 576 "
            pdb=" CB  VAL A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.29    0.15 2.00e-01 2.50e+01 5.46e-01
  ... (remaining 1725 not shown)

  Planarity restraints: 1786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A1029 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.30e+00
        pdb=" C   LYS A1029 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   LYS A1029 "    0.012 2.00e-02 2.50e+03
        pdb=" N   MET A1030 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  12 "    0.022 2.00e-02 2.50e+03   9.81e-03 2.65e+00
        pdb=" N9    A B  12 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    A B  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A B  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A B  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A B  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A B  12 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A B  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A B  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A B  12 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A B  12 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 485 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO A 486 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 486 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 486 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1783 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 719
        2.73 -     3.27: 11797
        3.27 -     3.81: 18835
        3.81 -     4.36: 22095
        4.36 -     4.90: 34758
  Nonbonded interactions: 88204
  Sorted by model distance:
  nonbonded pdb=" O2'   A B  15 "
            pdb=" O4'   A B  16 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   ASN A 952 "
            pdb=" NZ  LYS A 956 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OE1 GLN A1094 "
            pdb=" OH  TYR A1130 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   ILE A 113 "
            pdb=" OG  SER A 116 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" N   TYR A 248 "
            pdb=" OD1 ASN A 268 "
     model   vdw
     2.233 3.120
  ... (remaining 88199 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.110
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.870
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
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      :  0.004   0.037  11541  Z= 0.170
  Angle     :  0.569   7.254  15790  Z= 0.312
  Chirality :  0.043   0.618   1728
  Planarity :  0.003   0.040   1786
  Dihedral  : 17.578 131.086   4681
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.24), residues: 1167
  helix:  0.80 (0.23), residues: 542
  sheet: -0.36 (0.52), residues: 103
  loop : -1.26 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 186 
 TYR   0.023   0.002   TYR A1169 
 PHE   0.026   0.002   PHE A 244 
 TRP   0.022   0.002   TRP A1142 
 HIS   0.003   0.001   HIS A 843 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11541)
  covalent geometry    : angle       0.56911 (15790)
  hydrogen bonds       : bond        0.14926 (  484)
  hydrogen bonds       : angle       5.91151 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 ASP cc_start: 0.7777 (m-30) cc_final: 0.7570 (m-30)
REVERT: A   60 PHE cc_start: 0.7972 (m-80) cc_final: 0.7633 (m-80)
REVERT: A   92 ASP cc_start: 0.9323 (m-30) cc_final: 0.8933 (p0)
REVERT: A  117 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7720 (tm-30)
REVERT: A  753 PHE cc_start: 0.8007 (t80) cc_final: 0.7670 (t80)
REVERT: A  899 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7788 (mp0)
REVERT: A  984 TYR cc_start: 0.6796 (t80) cc_final: 0.6251 (t80)
REVERT: A 1031 LEU cc_start: 0.8839 (tp) cc_final: 0.8601 (tp)
REVERT: A 1217 MET cc_start: 0.7881 (mmm) cc_final: 0.7218 (tpp)
REVERT: A 1290 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7752 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1182
  time to fit residues: 30.4503
Evaluate side-chains
  96 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.2980
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    2.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 255 GLN
A 282 ASN
** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 897 ASN
A1036 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.142958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.104416 restraints weight = 47024.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.105998 restraints weight = 25598.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.107197 restraints weight = 17291.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.107774 restraints weight = 13585.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.108160 restraints weight = 11919.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11541  Z= 0.173
  Angle     :  0.610  11.111  15790  Z= 0.330
  Chirality :  0.040   0.173   1728
  Planarity :  0.004   0.045   1786
  Dihedral  : 17.967 134.390   2126
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.61 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.24), residues: 1167
  helix:  0.54 (0.22), residues: 543
  sheet: -0.15 (0.53), residues: 99
  loop : -1.11 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 746 
 TYR   0.021   0.002   TYR A 659 
 PHE   0.021   0.002   PHE A 244 
 TRP   0.006   0.001   TRP A1142 
 HIS   0.009   0.001   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11541)
  covalent geometry    : angle       0.60988 (15790)
  hydrogen bonds       : bond        0.04926 (  484)
  hydrogen bonds       : angle       5.09281 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 ASP cc_start: 0.9503 (m-30) cc_final: 0.9049 (p0)
REVERT: A  112 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (m-80)
REVERT: A  117 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7728 (tm-30)
REVERT: A  301 ASN cc_start: 0.8768 (m-40) cc_final: 0.8542 (m110)
REVERT: A  753 PHE cc_start: 0.7974 (t80) cc_final: 0.7698 (t80)
REVERT: A  941 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7939 (t80)
REVERT: A  984 TYR cc_start: 0.7042 (t80) cc_final: 0.6619 (t80)
REVERT: A 1067 MET cc_start: 0.8425 (ttt) cc_final: 0.8146 (ttt)
REVERT: A 1077 VAL cc_start: 0.8080 (p) cc_final: 0.7711 (m)
REVERT: A 1217 MET cc_start: 0.7508 (mmm) cc_final: 0.6973 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0974
  time to fit residues: 17.1484
Evaluate side-chains
  108 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 120 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    0.1980
   chunk 97 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 881 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.141844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.104558 restraints weight = 48140.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.105417 restraints weight = 27200.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.106251 restraints weight = 17907.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.107148 restraints weight = 14308.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.107603 restraints weight = 12114.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11541  Z= 0.171
  Angle     :  0.589   9.447  15790  Z= 0.320
  Chirality :  0.039   0.182   1728
  Planarity :  0.004   0.057   1786
  Dihedral  : 18.016 136.222   2126
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.93 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.23), residues: 1167
  helix:  0.29 (0.21), residues: 553
  sheet: -0.27 (0.55), residues: 88
  loop : -1.24 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 746 
 TYR   0.015   0.002   TYR A 659 
 PHE   0.017   0.002   PHE A 244 
 TRP   0.008   0.001   TRP A 609 
 HIS   0.006   0.001   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (11541)
  covalent geometry    : angle       0.58881 (15790)
  hydrogen bonds       : bond        0.04862 (  484)
  hydrogen bonds       : angle       4.91137 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ASP cc_start: 0.9490 (m-30) cc_final: 0.9059 (p0)
REVERT: A  117 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7694 (tm-30)
REVERT: A  245 ASP cc_start: 0.7985 (m-30) cc_final: 0.7531 (p0)
REVERT: A  899 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7773 (mt-10)
REVERT: A  941 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8037 (t80)
REVERT: A  984 TYR cc_start: 0.7132 (t80) cc_final: 0.6714 (t80)
REVERT: A 1077 VAL cc_start: 0.8127 (p) cc_final: 0.7735 (m)
REVERT: A 1217 MET cc_start: 0.7547 (mmm) cc_final: 0.7023 (tpp)
REVERT: A 1281 LYS cc_start: 0.8744 (pptt) cc_final: 0.8463 (pptt)
  outliers start: 24
  outliers final: 17
  residues processed: 118
  average time/residue: 0.1047
  time to fit residues: 18.0665
Evaluate side-chains
  108 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  823 LYS
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1031 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    0.1980
   chunk 109 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 ASN
A 649 ASN
** A1261 HIS ** 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 = 0.4394 r_free = 0.4394 target = 0.141901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.103640 restraints weight = 49225.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.105030 restraints weight = 27308.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.105837 restraints weight = 18429.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.106559 restraints weight = 14620.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.106790 restraints weight = 13101.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11541  Z= 0.159
  Angle     :  0.570   8.067  15790  Z= 0.311
  Chirality :  0.039   0.209   1728
  Planarity :  0.004   0.045   1786
  Dihedral  : 18.043 136.277   2126
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.14 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.23), residues: 1167
  helix:  0.21 (0.21), residues: 560
  sheet: -0.38 (0.56), residues: 88
  loop : -1.25 (0.26), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 746 
 TYR   0.022   0.002   TYR A  83 
 PHE   0.028   0.002   PHE A 269 
 TRP   0.007   0.001   TRP A1142 
 HIS   0.010   0.001   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11541)
  covalent geometry    : angle       0.57038 (15790)
  hydrogen bonds       : bond        0.04693 (  484)
  hydrogen bonds       : angle       4.80669 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7727 (tm-30)
REVERT: A  245 ASP cc_start: 0.7937 (m-30) cc_final: 0.7470 (p0)
REVERT: A  899 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7891 (mt-10)
REVERT: A  941 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8152 (t80)
REVERT: A  984 TYR cc_start: 0.7172 (t80) cc_final: 0.6744 (t80)
REVERT: A 1217 MET cc_start: 0.7507 (mmm) cc_final: 0.6975 (tpp)
  outliers start: 28
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1004
  time to fit residues: 17.4983
Evaluate side-chains
  109 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  271 ASN
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  823 LYS
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  910 ASP
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  940 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1031 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 99 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 ASN
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 HIS ** 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 = 0.4356 r_free = 0.4356 target = 0.139048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.102610 restraints weight = 49313.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.102790 restraints weight = 27491.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.103719 restraints weight = 18845.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.104357 restraints weight = 15136.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.104692 restraints weight = 13258.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11541  Z= 0.216
  Angle     :  0.627   7.616  15790  Z= 0.343
  Chirality :  0.041   0.250   1728
  Planarity :  0.004   0.042   1786
  Dihedral  : 18.185 135.538   2126
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.07 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.23), residues: 1167
  helix:  0.02 (0.21), residues: 563
  sheet: -0.48 (0.57), residues: 86
  loop : -1.37 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  18 
 TYR   0.020   0.002   TYR A 659 
 PHE   0.017   0.002   PHE A 211 
 TRP   0.012   0.002   TRP A1142 
 HIS   0.010   0.002   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (11541)
  covalent geometry    : angle       0.62692 (15790)
  hydrogen bonds       : bond        0.05214 (  484)
  hydrogen bonds       : angle       4.99828 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 90
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7741 (tm-30)
REVERT: A  183 HIS cc_start: 0.7990 (m170) cc_final: 0.7667 (m170)
REVERT: A  245 ASP cc_start: 0.8126 (m-30) cc_final: 0.7608 (p0)
REVERT: A  941 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8113 (t80)
REVERT: A  953 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6661 (m-80)
REVERT: A 1067 MET cc_start: 0.8303 (ttt) cc_final: 0.8052 (ttm)
REVERT: A 1217 MET cc_start: 0.7506 (mmm) cc_final: 0.6921 (tpp)
  outliers start: 35
  outliers final: 24
  residues processed: 112
  average time/residue: 0.0956
  time to fit residues: 16.1824
Evaluate side-chains
  113 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  269 PHE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  596 PHE
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  823 LYS
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  910 ASP
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  940 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  953 TYR
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1286 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 112 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 63 optimal weight:    0.5980
   chunk 83 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    5.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 ASN
A 282 ASN
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 942 ASN
** A1261 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.136835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.100207 restraints weight = 50462.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.100308 restraints weight = 28819.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.101033 restraints weight = 19523.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.101804 restraints weight = 15913.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.102031 restraints weight = 13880.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  11541  Z= 0.256
  Angle     :  0.687  11.019  15790  Z= 0.373
  Chirality :  0.043   0.299   1728
  Planarity :  0.004   0.042   1786
  Dihedral  : 18.453 134.752   2126
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 18.73 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.23), residues: 1167
  helix: -0.29 (0.21), residues: 556
  sheet: -0.92 (0.54), residues: 91
  loop : -1.50 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  18 
 TYR   0.021   0.002   TYR A 659 
 PHE   0.016   0.002   PHE A 482 
 TRP   0.016   0.003   TRP A1142 
 HIS   0.010   0.002   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (11541)
  covalent geometry    : angle       0.68684 (15790)
  hydrogen bonds       : bond        0.05705 (  484)
  hydrogen bonds       : angle       5.30616 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7791 (tm-30)
REVERT: A  183 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7716 (m90)
REVERT: A  245 ASP cc_start: 0.8052 (m-30) cc_final: 0.7412 (p0)
REVERT: A  895 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8793 (tppp)
REVERT: A  941 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8481 (t80)
REVERT: A 1217 MET cc_start: 0.7290 (mmm) cc_final: 0.6666 (tpp)
REVERT: A 1261 HIS cc_start: 0.7557 (m170) cc_final: 0.7345 (m90)
  outliers start: 38
  outliers final: 28
  residues processed: 113
  average time/residue: 0.1000
  time to fit residues: 17.0265
Evaluate side-chains
  115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  194 ASP
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  596 PHE
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  778 VAL
Chi-restraints excluded: chain A residue  823 LYS
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  876 ASP
Chi-restraints excluded: chain A residue  910 ASP
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  940 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1035 LEU
Chi-restraints excluded: chain A residue 1286 ILE
Chi-restraints excluded: chain A residue 1291 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 84 optimal weight:    0.0170
   chunk 36 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 121 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.4026

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 301 ASN
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 584 ASN
A 825 ASN
** A 897 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 = 0.4377 r_free = 0.4377 target = 0.140656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.103928 restraints weight = 49426.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.104473 restraints weight = 27245.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.105265 restraints weight = 18163.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.105988 restraints weight = 14323.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.106362 restraints weight = 12789.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11541  Z= 0.149
  Angle     :  0.591  10.184  15790  Z= 0.319
  Chirality :  0.040   0.328   1728
  Planarity :  0.003   0.040   1786
  Dihedral  : 18.231 133.962   2126
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.48 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.23), residues: 1167
  helix:  0.04 (0.21), residues: 550
  sheet: -1.01 (0.53), residues: 93
  loop : -1.32 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  18 
 TYR   0.018   0.002   TYR A 659 
 PHE   0.014   0.001   PHE A1240 
 TRP   0.005   0.001   TRP A 141 
 HIS   0.006   0.001   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (11541)
  covalent geometry    : angle       0.59140 (15790)
  hydrogen bonds       : bond        0.04854 (  484)
  hydrogen bonds       : angle       4.96010 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7130 (m-80)
REVERT: A   18 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7645 (mtm180)
REVERT: A   55 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (m-30)
REVERT: A  117 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7778 (tm-30)
REVERT: A  182 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7794 (t80)
REVERT: A  183 HIS cc_start: 0.8028 (m170) cc_final: 0.7633 (m170)
REVERT: A  201 TYR cc_start: 0.9474 (t80) cc_final: 0.9273 (t80)
REVERT: A  245 ASP cc_start: 0.8041 (m-30) cc_final: 0.7396 (p0)
REVERT: A  269 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7626 (m-80)
REVERT: A  895 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8710 (tppp)
REVERT: A  899 GLU cc_start: 0.8128 (pt0) cc_final: 0.7684 (pm20)
REVERT: A  941 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8317 (t80)
REVERT: A 1217 MET cc_start: 0.7503 (mmm) cc_final: 0.7112 (mmm)
REVERT: A 1268 MET cc_start: 0.6437 (mmm) cc_final: 0.5222 (pmm)
  outliers start: 24
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0932
  time to fit residues: 14.5653
Evaluate side-chains
  103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  194 ASP
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  269 PHE
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  596 PHE
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1286 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 110 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 113 optimal weight:    6.9990
   chunk 90 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.140362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.102520 restraints weight = 49266.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.104082 restraints weight = 27622.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.104808 restraints weight = 18499.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.105737 restraints weight = 15068.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.106127 restraints weight = 13057.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11541  Z= 0.152
  Angle     :  0.597   9.705  15790  Z= 0.322
  Chirality :  0.040   0.333   1728
  Planarity :  0.004   0.040   1786
  Dihedral  : 18.114 133.704   2126
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.94 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.23), residues: 1167
  helix:  0.00 (0.21), residues: 560
  sheet: -0.81 (0.55), residues: 88
  loop : -1.38 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  18 
 TYR   0.017   0.002   TYR A 659 
 PHE   0.015   0.002   PHE A 123 
 TRP   0.005   0.001   TRP A 609 
 HIS   0.005   0.001   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11541)
  covalent geometry    : angle       0.59662 (15790)
  hydrogen bonds       : bond        0.04892 (  484)
  hydrogen bonds       : angle       4.86198 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6994 (m-80)
REVERT: A   92 ASP cc_start: 0.9503 (m-30) cc_final: 0.9102 (p0)
REVERT: A  117 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7770 (tm-30)
REVERT: A  182 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8042 (t80)
REVERT: A  183 HIS cc_start: 0.7875 (m170) cc_final: 0.7559 (m170)
REVERT: A  201 TYR cc_start: 0.9467 (t80) cc_final: 0.9258 (t80)
REVERT: A  245 ASP cc_start: 0.8072 (m-30) cc_final: 0.7467 (p0)
REVERT: A  269 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7560 (m-80)
REVERT: A  895 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8683 (tppp)
REVERT: A  899 GLU cc_start: 0.8032 (pt0) cc_final: 0.7619 (pm20)
REVERT: A  941 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8413 (t80)
REVERT: A 1217 MET cc_start: 0.7643 (mmm) cc_final: 0.7227 (mmm)
REVERT: A 1268 MET cc_start: 0.6538 (mmm) cc_final: 0.5275 (pmm)
  outliers start: 26
  outliers final: 16
  residues processed: 102
  average time/residue: 0.0942
  time to fit residues: 14.5121
Evaluate side-chains
  102 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  269 PHE
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  596 PHE
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  910 ASP
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1286 ILE
Chi-restraints excluded: chain A residue 1291 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 121 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    3.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 ASN
A 282 ASN
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 897 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 = 0.4346 r_free = 0.4346 target = 0.138303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.101811 restraints weight = 49175.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.102350 restraints weight = 28781.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.103176 restraints weight = 19258.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.103917 restraints weight = 14977.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.104396 restraints weight = 13355.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11541  Z= 0.207
  Angle     :  0.645  10.642  15790  Z= 0.350
  Chirality :  0.042   0.375   1728
  Planarity :  0.004   0.039   1786
  Dihedral  : 18.193 133.523   2126
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.66 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.23), residues: 1167
  helix: -0.13 (0.21), residues: 565
  sheet: -0.77 (0.55), residues: 86
  loop : -1.41 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  18 
 TYR   0.020   0.002   TYR A 659 
 PHE   0.018   0.002   PHE A 812 
 TRP   0.009   0.002   TRP A 609 
 HIS   0.006   0.002   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (11541)
  covalent geometry    : angle       0.64542 (15790)
  hydrogen bonds       : bond        0.05341 (  484)
  hydrogen bonds       : angle       5.03833 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7096 (m-80)
REVERT: A   92 ASP cc_start: 0.9500 (m-30) cc_final: 0.9072 (p0)
REVERT: A  117 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7793 (tm-30)
REVERT: A  182 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8142 (t80)
REVERT: A  183 HIS cc_start: 0.8031 (m170) cc_final: 0.7685 (m170)
REVERT: A  201 TYR cc_start: 0.9471 (t80) cc_final: 0.9258 (t80)
REVERT: A  245 ASP cc_start: 0.8220 (m-30) cc_final: 0.7556 (p0)
REVERT: A  895 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8606 (tppp)
REVERT: A  899 GLU cc_start: 0.8157 (pt0) cc_final: 0.7686 (pm20)
REVERT: A  941 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8381 (t80)
REVERT: A 1217 MET cc_start: 0.7469 (mmm) cc_final: 0.6848 (tpp)
REVERT: A 1268 MET cc_start: 0.6546 (mmm) cc_final: 0.5144 (pmm)
  outliers start: 30
  outliers final: 21
  residues processed: 103
  average time/residue: 0.0950
  time to fit residues: 14.5740
Evaluate side-chains
  103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  182 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 ASN
Chi-restraints excluded: chain A residue  487 MET
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  596 PHE
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  778 VAL
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  876 ASP
Chi-restraints excluded: chain A residue  910 ASP
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  940 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1031 LEU
Chi-restraints excluded: chain A residue 1286 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    9.9990
   chunk 117 optimal weight:    0.3980
   chunk 39 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:   20.0000
   chunk 67 optimal weight:    0.3980
   chunk 84 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 94 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
** A 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 942 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.142939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.105488 restraints weight = 48202.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.106321 restraints weight = 26712.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.107155 restraints weight = 17936.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.107950 restraints weight = 13929.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 74)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.108481 restraints weight = 12340.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11541  Z= 0.122
  Angle     :  0.605  11.071  15790  Z= 0.322
  Chirality :  0.041   0.370   1728
  Planarity :  0.003   0.041   1786
  Dihedral  : 18.016 132.362   2126
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.86 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.23), residues: 1167
  helix:  0.10 (0.21), residues: 563
  sheet: -0.96 (0.53), residues: 95
  loop : -1.28 (0.26), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  18 
 TYR   0.026   0.001   TYR A 272 
 PHE   0.015   0.001   PHE A 269 
 TRP   0.010   0.001   TRP A 175 
 HIS   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (11541)
  covalent geometry    : angle       0.60533 (15790)
  hydrogen bonds       : bond        0.04380 (  484)
  hydrogen bonds       : angle       4.70921 ( 1331)

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

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

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2334 Ramachandran restraints generated.
    1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6945 (m-80)
REVERT: A   18 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7489 (mtm-85)
REVERT: A   55 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6498 (t0)
REVERT: A   95 GLN cc_start: 0.9585 (tp-100) cc_final: 0.9334 (mt0)
REVERT: A  117 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7762 (tm-30)
REVERT: A  183 HIS cc_start: 0.7840 (m170) cc_final: 0.7489 (m170)
REVERT: A  245 ASP cc_start: 0.7956 (m-30) cc_final: 0.7342 (p0)
REVERT: A  633 MET cc_start: 0.8626 (pmm) cc_final: 0.8210 (pmm)
REVERT: A  760 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.5806 (mp10)
REVERT: A  895 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8722 (tppp)
REVERT: A  899 GLU cc_start: 0.8073 (pt0) cc_final: 0.7847 (pm20)
REVERT: A  941 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (t80)
REVERT: A 1067 MET cc_start: 0.7813 (ttt) cc_final: 0.7593 (ptm)
REVERT: A 1217 MET cc_start: 0.7759 (mmm) cc_final: 0.7360 (mmm)
REVERT: A 1268 MET cc_start: 0.6590 (mmm) cc_final: 0.5586 (pmm)
  outliers start: 17
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1015
  time to fit residues: 15.4388
Evaluate side-chains
  99 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  112 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  596 PHE
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  760 GLN
Chi-restraints excluded: chain A residue  769 ILE
Chi-restraints excluded: chain A residue  778 VAL
Chi-restraints excluded: chain A residue  927 THR
Chi-restraints excluded: chain A residue  941 PHE
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1002 ILE
Chi-restraints excluded: chain A residue 1031 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 84 optimal weight:    9.9990
   chunk 73 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 116 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 ASN
A 301 ASN
** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
** A 897 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 = 0.4373 r_free = 0.4373 target = 0.139982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.103911 restraints weight = 49955.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.103961 restraints weight = 27937.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.104774 restraints weight = 18835.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.105514 restraints weight = 14685.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.105850 restraints weight = 13227.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11541  Z= 0.178
  Angle     :  0.628  11.656  15790  Z= 0.336
  Chirality :  0.041   0.364   1728
  Planarity :  0.004   0.039   1786
  Dihedral  : 18.080 132.475   2126
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 22.14 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.24), residues: 1167
  helix:  0.10 (0.21), residues: 561
  sheet: -0.73 (0.55), residues: 88
  loop : -1.34 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  18 
 TYR   0.018   0.002   TYR A 659 
 PHE   0.014   0.002   PHE A 123 
 TRP   0.007   0.001   TRP A 609 
 HIS   0.006   0.001   HIS A1261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11541)
  covalent geometry    : angle       0.62780 (15790)
  hydrogen bonds       : bond        0.04893 (  484)
  hydrogen bonds       : angle       4.83297 ( 1331)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4008.56 seconds
wall clock time: 69 minutes 13.33 seconds (4153.33 seconds total)