Starting phenix.real_space_refine
on Thu Jun 12 13:12:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u3y_41867/06_2025/8u3y_41867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u3y_41867/06_2025/8u3y_41867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u3y_41867/06_2025/8u3y_41867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u3y_41867/06_2025/8u3y_41867.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u3y_41867/06_2025/8u3y_41867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u3y_41867/06_2025/8u3y_41867.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.045
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: 6
    Type Number    sf(0)   Gaussians
     P     144      5.49       5
     Mg      5      5.21       5
     S      22      5.16       5
     C    8375      2.51       5
     N    2458      2.21       5
     O    3008      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14012
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 10962
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1336, 10951
          Classifications: {'peptide': 1336}
          Link IDs: {'PTRANS': 35, 'TRANS': 1300}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 1336, 10951
          Classifications: {'peptide': 1336}
          Link IDs: {'PTRANS': 35, 'TRANS': 1300}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 11134
    Chain: "B"
      Number of atoms: 2103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2103
          Classifications: {'RNA': 98}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34}
          Link IDs: {'rna2p': 10, 'rna3p': 87}
    Chain: "C"
      Number of atoms: 325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 325
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "c"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 341
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "D"
      Number of atoms: 271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 271
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "c"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "c"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 783 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 783 " occ=0.50
  Time building chain proxies: 15.34, per 1000 atoms: 1.09
  Number of scatterers: 14012
  At special positions: 0
  Unit cell: (87.465, 128.282, 121.618, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      22     16.00
     P     144     15.00
     Mg      5     11.99
     O    3008      8.00
     N    2458      7.00
     C    8375      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: 3.68
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2548

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 10 sheets defined
      55.6% alpha, 9.6% beta
      48 base pairs and 92 stacking pairs defined.
    Time for finding SS restraints: 5.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 5.086A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.588A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 175 through 179
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 4.086A  pdb=" N   ALA A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 240 through 246
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 276 through 278
      No H-bonds generated for 'chain 'A' and resid 276 through 278'
    Processing helix  chain 'A' and resid 290 through 306
      removed outlier: 4.142A  pdb=" N   LYS A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 4.186A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.039A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.668A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.702A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 553
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 3.506A  pdb=" N   TYR A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 601
      removed outlier: 3.526A  pdb=" N   ILE A 600 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 609
      removed outlier: 3.611A  pdb=" N   LEU A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 711
    Processing helix  chain 'A' and resid 719 through 727
    Processing helix  chain 'A' and resid 731 through 751
      removed outlier: 4.327A  pdb=" N   LYS A 735 " --> pdb=" O   PRO A 731 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 777
    Processing helix  chain 'A' and resid 779 through 792
      removed outlier: 3.617A  pdb=" N   GLY A 787 " --> pdb=" O  AARG A 783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 804 through 807
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 829 through 833
      removed outlier: 3.854A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 866
    Processing helix  chain 'A' and resid 872 through 889
      removed outlier: 5.419A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 902 through 906
      removed outlier: 3.736A  pdb=" N   GLY A 906 " --> pdb=" O   ALA A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
    Processing helix  chain 'A' and resid 917 through 940
      removed outlier: 4.318A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL A 922 " --> pdb=" O   LYS A 918 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLN A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 971
    Processing helix  chain 'A' and resid 980 through 1001
      removed outlier: 4.339A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 3.799A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1043
      removed outlier: 3.554A  pdb=" N   TYR A1039 " --> pdb=" O   LYS A1035 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   MET A1043 " --> pdb=" O   TYR A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1047
    Processing helix  chain 'A' and resid 1078 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.585A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1186
    Processing helix  chain 'A' and resid 1191 through 1195
      removed outlier: 3.707A  pdb=" N   ILE A1195 " --> pdb=" O   LYS A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1240
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1310
    Processing helix  chain 'A' and resid 1311 through 1315
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 3.609A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959
      removed outlier: 7.257A  pdb=" N   TYR A   5 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   VAL A 760 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   LEU A   9 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 10.079A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065
      removed outlier: 6.898A  pdb=" N   GLU A1064 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.613A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.613A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325

    512 hydrogen bonds defined for protein.
    1471 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      119 hydrogen bonds
      234 hydrogen bond angles
      0 basepair planarities
      48 basepair parallelities
      92 stacking parallelities
  Total time for adding SS restraints: 7.57

  Time building geometry restraints manager: 4.37 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2046
        1.31 -     1.43: 4552
        1.43 -     1.56: 7636
        1.56 -     1.68: 284
        1.68 -     1.81: 42
  Bond restraints: 14560
  Sorted by residual:
  bond pdb=" C   PRO A1321 "
       pdb=" O   PRO A1321 "
    ideal  model  delta    sigma   weight residual
    1.233  1.183  0.050 1.34e-02 5.57e+03 1.42e+01
  bond pdb=" O3'  DG D  41 "
       pdb=" P    DT D  42 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 9.78e+00
  bond pdb=" CA  ALA A1217 "
       pdb=" CB  ALA A1217 "
    ideal  model  delta    sigma   weight residual
    1.531  1.479  0.052 1.69e-02 3.50e+03 9.41e+00
  bond pdb=" N   PRO A1321 "
       pdb=" CA  PRO A1321 "
    ideal  model  delta    sigma   weight residual
    1.471  1.434  0.037 1.27e-02 6.20e+03 8.38e+00
  bond pdb=" CA  ALA A1322 "
       pdb=" CB  ALA A1322 "
    ideal  model  delta    sigma   weight residual
    1.531  1.491  0.040 1.48e-02 4.57e+03 7.27e+00
  ... (remaining 14555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 19903
        2.21 -     4.42: 335
        4.42 -     6.63: 27
        6.63 -     8.84: 3
        8.84 -    11.05: 3
  Bond angle restraints: 20271
  Sorted by residual:
  angle pdb=" N   TYR A1326 "
        pdb=" CA  TYR A1326 "
        pdb=" C   TYR A1326 "
      ideal   model   delta    sigma   weight residual
     110.35  102.79    7.56 1.38e+00 5.25e-01 3.00e+01
  angle pdb=" C   THR A1339 "
        pdb=" CA  THR A1339 "
        pdb=" CB  THR A1339 "
      ideal   model   delta    sigma   weight residual
     111.40  104.86    6.54 1.29e+00 6.01e-01 2.57e+01
  angle pdb=" N   LYS A1340 "
        pdb=" CA  LYS A1340 "
        pdb=" C   LYS A1340 "
      ideal   model   delta    sigma   weight residual
     113.88  107.75    6.13 1.23e+00 6.61e-01 2.49e+01
  angle pdb=" CA  TYR A1336 "
        pdb=" C   TYR A1336 "
        pdb=" O   TYR A1336 "
      ideal   model   delta    sigma   weight residual
     122.41  116.40    6.01 1.21e+00 6.83e-01 2.47e+01
  angle pdb=" N   PRO A1321 "
        pdb=" CA  PRO A1321 "
        pdb=" CB  PRO A1321 "
      ideal   model   delta    sigma   weight residual
     103.17   98.83    4.34 8.90e-01 1.26e+00 2.38e+01
  ... (remaining 20266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.24: 8351
       34.24 -    68.47: 440
       68.47 -   102.71: 40
      102.71 -   136.94: 0
      136.94 -   171.18: 5
  Dihedral angle restraints: 8836
    sinusoidal: 4901
      harmonic: 3935
  Sorted by residual:
  dihedral pdb=" O4'   U B  59 "
           pdb=" C1'   U B  59 "
           pdb=" N1    U B  59 "
           pdb=" C2    U B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   28.82  171.18     1      1.50e+01 4.44e-03 8.48e+01
  dihedral pdb=" O4'   C B  70 "
           pdb=" C1'   C B  70 "
           pdb=" N1    C B  70 "
           pdb=" C2    C B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   37.33  162.67     1      1.50e+01 4.44e-03 8.34e+01
  dihedral pdb=" CA  LYS A1153 "
           pdb=" C   LYS A1153 "
           pdb=" N   SER A1154 "
           pdb=" CA  SER A1154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 8833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 2200
       0.089 -    0.179: 113
       0.179 -    0.268: 7
       0.268 -    0.357: 1
       0.357 -    0.447: 1
  Chirality restraints: 2322
  Sorted by residual:
  chirality pdb=" P    DT c  23 "
            pdb=" OP1  DT c  23 "
            pdb=" OP2  DT c  23 "
            pdb=" O5'  DT c  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.79   -0.45 2.00e-01 2.50e+01 4.99e+00
  chirality pdb=" CA  TYR A1336 "
            pdb=" N   TYR A1336 "
            pdb=" C   TYR A1336 "
            pdb=" CB  TYR A1336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C3'   A B   8 "
            pdb=" C4'   A B   8 "
            pdb=" O3'   A B   8 "
            pdb=" C2'   A B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.26   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 2319 not shown)

  Planarity restraints: 2066
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 730 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.48e+00
        pdb=" N   PRO A 731 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 731 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 731 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1228 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO A1229 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A1229 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1229 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1216 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   SER A1216 "    0.030 2.00e-02 2.50e+03
        pdb=" O   SER A1216 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A1217 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 2063 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 115
        2.55 -     3.14: 10973
        3.14 -     3.73: 22606
        3.73 -     4.31: 32982
        4.31 -     4.90: 52413
  Nonbonded interactions: 119089
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  10 "
            pdb="MG    MG A1401 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" OE2 GLU A 762 "
            pdb="MG    MG A1401 "
     model   vdw
     2.080 2.170
  nonbonded pdb=" ND1 HIS A 983 "
            pdb="MG    MG A1402 "
     model   vdw
     2.093 2.250
  nonbonded pdb=" OP2   A B  65 "
            pdb="MG    MG B 101 "
     model   vdw
     2.106 2.170
  nonbonded pdb=" OG1 THR A1167 "
            pdb=" OE1 GLU A1170 "
     model   vdw
     2.139 3.040
  ... (remaining 119084 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             96.870
  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:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     49.510
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.080
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  150.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  14560  Z= 0.294
  Angle     :  0.718  11.053  20271  Z= 0.431
  Chirality :  0.045   0.447   2322
  Planarity :  0.003   0.047   2066
  Dihedral  : 18.578 171.176   6288
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.50 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.23), residues: 1331
  helix:  0.41 (0.20), residues: 652
  sheet: -0.39 (0.49), residues: 115
  loop : -0.66 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  18 
 HIS   0.006   0.001   HIS A 412 
 PHE   0.024   0.002   PHE A1324 
 TYR   0.020   0.002   TYR A 362 
 ARG   0.014   0.001   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16489 (  620)
  hydrogen bonds       : angle       7.14356 ( 1705)
  covalent geometry    : bond        0.00634 (14560)
  covalent geometry    : angle       0.71831 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 1.384 
Fit side-chains
REVERT: A  534 MET cc_start: 0.7192 (mmm) cc_final: 0.6989 (mmm)
REVERT: A 1256 GLN cc_start: 0.7433 (mt0) cc_final: 0.7180 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 78
  average time/residue: 0.3203
  time to fit residues: 36.0579
Evaluate side-chains
  62 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 122 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   chunk 131 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A1364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.123506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.085212 restraints weight = 40949.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 3.10
r_work: 0.2888 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14560  Z= 0.158
  Angle     :  0.593  13.553  20271  Z= 0.313
  Chirality :  0.040   0.239   2322
  Planarity :  0.004   0.055   2066
  Dihedral  : 19.567 173.493   3430
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.90 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.23), residues: 1331
  helix:  0.75 (0.20), residues: 650
  sheet:  0.28 (0.59), residues: 84
  loop : -0.47 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 464 
 HIS   0.009   0.001   HIS A  41 
 PHE   0.014   0.001   PHE A 970 
 TYR   0.016   0.001   TYR A1242 
 ARG   0.006   0.001   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05201 (  620)
  hydrogen bonds       : angle       4.86970 ( 1705)
  covalent geometry    : bond        0.00348 (14560)
  covalent geometry    : angle       0.59271 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 1.478 
Fit side-chains
REVERT: A  402 GLN cc_start: 0.9058 (mp10) cc_final: 0.8843 (mp10)
REVERT: A  781 MET cc_start: 0.8216 (tpt) cc_final: 0.7817 (tpt)
REVERT: A  943 TYR cc_start: 0.8542 (m-80) cc_final: 0.8266 (m-80)
REVERT: A 1148 LYS cc_start: 0.8103 (mttp) cc_final: 0.7879 (mtmm)
REVERT: A 1149 VAL cc_start: 0.8324 (m) cc_final: 0.8112 (p)
REVERT: A 1256 GLN cc_start: 0.7823 (mt0) cc_final: 0.7576 (tt0)
REVERT: A 1268 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7820 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.2846
  time to fit residues: 32.9541
Evaluate side-chains
  68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 140 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9442

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A1364 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.122186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085280 restraints weight = 37068.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.69
r_work: 0.2893 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14560  Z= 0.179
  Angle     :  0.556   8.554  20271  Z= 0.295
  Chirality :  0.040   0.224   2322
  Planarity :  0.004   0.044   2066
  Dihedral  : 19.498 169.821   3430
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.90 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.23), residues: 1331
  helix:  0.94 (0.20), residues: 649
  sheet: -0.53 (0.49), residues: 123
  loop : -0.32 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  18 
 HIS   0.010   0.001   HIS A  41 
 PHE   0.014   0.001   PHE A 970 
 TYR   0.014   0.001   TYR A 362 
 ARG   0.007   0.001   ARG A1303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04872 (  620)
  hydrogen bonds       : angle       4.63901 ( 1705)
  covalent geometry    : bond        0.00403 (14560)
  covalent geometry    : angle       0.55594 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 1.592 
Fit side-chains
REVERT: A   24 GLU cc_start: 0.7882 (mp0) cc_final: 0.7681 (mp0)
REVERT: A  402 GLN cc_start: 0.9093 (mp10) cc_final: 0.8801 (mp10)
REVERT: A  781 MET cc_start: 0.8305 (tpt) cc_final: 0.7932 (tpt)
REVERT: A  804 THR cc_start: 0.9366 (m) cc_final: 0.9102 (p)
REVERT: A 1256 GLN cc_start: 0.7866 (mt0) cc_final: 0.7635 (tt0)
REVERT: A 1268 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7800 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 76
  average time/residue: 0.3301
  time to fit residues: 37.2485
Evaluate side-chains
  69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1158 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 140 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0020
   chunk 37 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 134 optimal weight:    2.9990
   overall best weight:    1.0392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.122463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.084123 restraints weight = 42494.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.17
r_work: 0.2866 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14560  Z= 0.187
  Angle     :  0.563  13.864  20271  Z= 0.295
  Chirality :  0.040   0.217   2322
  Planarity :  0.004   0.043   2066
  Dihedral  : 19.434 169.513   3430
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  5.98 %
    Favored  : 93.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.23), residues: 1331
  helix:  1.05 (0.20), residues: 650
  sheet: -0.55 (0.50), residues: 120
  loop : -0.31 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  18 
 HIS   0.004   0.001   HIS A 412 
 PHE   0.013   0.001   PHE A 970 
 TYR   0.014   0.001   TYR A 362 
 ARG   0.004   0.001   ARG A 629 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04702 (  620)
  hydrogen bonds       : angle       4.57025 ( 1705)
  covalent geometry    : bond        0.00421 (14560)
  covalent geometry    : angle       0.56310 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 1.547 
Fit side-chains
REVERT: A  402 GLN cc_start: 0.9128 (mp10) cc_final: 0.8821 (mp10)
REVERT: A  781 MET cc_start: 0.8334 (tpt) cc_final: 0.7980 (tpt)
REVERT: A  786 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7145 (mp0)
REVERT: A  804 THR cc_start: 0.9355 (m) cc_final: 0.9104 (p)
REVERT: A 1256 GLN cc_start: 0.7897 (mt0) cc_final: 0.7692 (tt0)
REVERT: A 1268 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7829 (mt-10)
  outliers start: 5
  outliers final: 1
  residues processed: 72
  average time/residue: 0.3561
  time to fit residues: 38.3087
Evaluate side-chains
  66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  786 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 119 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.123481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086736 restraints weight = 29623.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.41
r_work: 0.2928 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14560  Z= 0.158
  Angle     :  0.523   8.035  20271  Z= 0.278
  Chirality :  0.038   0.205   2322
  Planarity :  0.003   0.043   2066
  Dihedral  : 19.370 168.813   3430
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  6.40 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.23), residues: 1331
  helix:  1.16 (0.21), residues: 650
  sheet: -0.60 (0.51), residues: 115
  loop : -0.27 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 723 
 PHE   0.013   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A 362 
 ARG   0.003   0.000   ARG A 859 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04432 (  620)
  hydrogen bonds       : angle       4.47554 ( 1705)
  covalent geometry    : bond        0.00352 (14560)
  covalent geometry    : angle       0.52342 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 2.301 
Fit side-chains
REVERT: A  781 MET cc_start: 0.8318 (tpt) cc_final: 0.7964 (tpt)
REVERT: A  786 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7113 (mp0)
REVERT: A  804 THR cc_start: 0.9336 (m) cc_final: 0.9078 (p)
REVERT: A 1170 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8110 (pm20)
REVERT: A 1268 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7794 (mt-10)
  outliers start: 5
  outliers final: 2
  residues processed: 69
  average time/residue: 0.4301
  time to fit residues: 44.9934
Evaluate side-chains
  65 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue 1158 LYS
Chi-restraints excluded: chain A residue 1170 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0870
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 139 optimal weight:    3.9990
   chunk 121 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.0962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.122571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.083718 restraints weight = 25423.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.25
r_work: 0.2942 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14560  Z= 0.193
  Angle     :  0.563  17.556  20271  Z= 0.292
  Chirality :  0.039   0.212   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.346 169.037   3430
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.14 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.23), residues: 1331
  helix:  1.13 (0.21), residues: 650
  sheet: -0.62 (0.49), residues: 120
  loop : -0.28 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  18 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.013   0.001   PHE A 970 
 TYR   0.017   0.001   TYR A1242 
 ARG   0.008   0.000   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04602 (  620)
  hydrogen bonds       : angle       4.51321 ( 1705)
  covalent geometry    : bond        0.00438 (14560)
  covalent geometry    : angle       0.56308 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.484 
Fit side-chains
REVERT: A  781 MET cc_start: 0.8256 (tpt) cc_final: 0.7881 (tpt)
REVERT: A  786 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7060 (mp0)
REVERT: A  804 THR cc_start: 0.9328 (m) cc_final: 0.9081 (p)
REVERT: A 1170 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7996 (pm20)
REVERT: A 1268 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7702 (mt-10)
  outliers start: 4
  outliers final: 2
  residues processed: 67
  average time/residue: 0.3034
  time to fit residues: 30.8929
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue 1158 LYS
Chi-restraints excluded: chain A residue 1170 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 99 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 141 optimal weight:    6.9990
   chunk 17 optimal weight:    0.1980
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.122486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.082216 restraints weight = 35530.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 2.59
r_work: 0.2915 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14560  Z= 0.198
  Angle     :  0.551   8.467  20271  Z= 0.291
  Chirality :  0.040   0.215   2322
  Planarity :  0.004   0.044   2066
  Dihedral  : 19.343 169.175   3430
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.14 %
    Favored  : 92.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.23), residues: 1331
  helix:  1.14 (0.21), residues: 650
  sheet:  0.37 (0.60), residues: 81
  loop : -0.43 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  18 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.013   0.001   PHE A 970 
 TYR   0.017   0.001   TYR A1242 
 ARG   0.010   0.001   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  620)
  hydrogen bonds       : angle       4.50121 ( 1705)
  covalent geometry    : bond        0.00450 (14560)
  covalent geometry    : angle       0.55118 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 1.336 
Fit side-chains
REVERT: A  653 ARG cc_start: 0.8882 (tpp80) cc_final: 0.8571 (mmm-85)
REVERT: A  781 MET cc_start: 0.8334 (tpt) cc_final: 0.7902 (tpt)
REVERT: A  786 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7092 (mp0)
REVERT: A  804 THR cc_start: 0.9311 (m) cc_final: 0.9066 (p)
REVERT: A 1170 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8044 (pm20)
REVERT: A 1268 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7767 (mt-10)
  outliers start: 4
  outliers final: 2
  residues processed: 71
  average time/residue: 0.3028
  time to fit residues: 32.8643
Evaluate side-chains
  68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue 1158 LYS
Chi-restraints excluded: chain A residue 1170 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 110 optimal weight:    0.5980
   chunk 28 optimal weight:    8.9990
   chunk 141 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.082933 restraints weight = 37319.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.69
r_work: 0.2926 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14560  Z= 0.156
  Angle     :  0.541  16.207  20271  Z= 0.282
  Chirality :  0.038   0.203   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.334 168.817   3430
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.23 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.23), residues: 1331
  helix:  1.21 (0.21), residues: 650
  sheet:  0.35 (0.60), residues: 81
  loop : -0.39 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.012   0.001   TYR A1242 
 ARG   0.009   0.000   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04405 (  620)
  hydrogen bonds       : angle       4.47383 ( 1705)
  covalent geometry    : bond        0.00349 (14560)
  covalent geometry    : angle       0.54092 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 1.486 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.8482 (t0) cc_final: 0.8182 (m-30)
REVERT: A  653 ARG cc_start: 0.8850 (tpp80) cc_final: 0.8534 (mmm-85)
REVERT: A  781 MET cc_start: 0.8308 (tpt) cc_final: 0.7938 (tpt)
REVERT: A  786 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7051 (mp0)
REVERT: A  804 THR cc_start: 0.9335 (m) cc_final: 0.9097 (p)
REVERT: A 1170 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8051 (pm20)
REVERT: A 1268 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7736 (mt-10)
  outliers start: 4
  outliers final: 2
  residues processed: 69
  average time/residue: 0.2966
  time to fit residues: 31.2845
Evaluate side-chains
  69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue 1158 LYS
Chi-restraints excluded: chain A residue 1170 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0870
   chunk 128 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
A 863 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.122904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.082843 restraints weight = 33708.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.55
r_work: 0.2928 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14560  Z= 0.176
  Angle     :  0.548  16.853  20271  Z= 0.285
  Chirality :  0.039   0.206   2322
  Planarity :  0.003   0.044   2066
  Dihedral  : 19.306 168.788   3430
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  7.14 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.23), residues: 1331
  helix:  1.22 (0.21), residues: 650
  sheet:  0.31 (0.60), residues: 81
  loop : -0.39 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.012   0.001   PHE A1235 
 TYR   0.013   0.001   TYR A1242 
 ARG   0.009   0.000   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  620)
  hydrogen bonds       : angle       4.46327 ( 1705)
  covalent geometry    : bond        0.00396 (14560)
  covalent geometry    : angle       0.54777 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 1.378 
Fit side-chains
REVERT: A  499 ASP cc_start: 0.8467 (t0) cc_final: 0.8173 (m-30)
REVERT: A  653 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8511 (mmm-85)
REVERT: A  781 MET cc_start: 0.8322 (tpt) cc_final: 0.7938 (tpt)
REVERT: A  786 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7019 (mp0)
REVERT: A  804 THR cc_start: 0.9340 (m) cc_final: 0.9089 (p)
REVERT: A 1170 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8056 (pm20)
  outliers start: 5
  outliers final: 3
  residues processed: 69
  average time/residue: 0.2834
  time to fit residues: 29.7827
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1158 LYS
Chi-restraints excluded: chain A residue 1170 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 123 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0980
   chunk 105 optimal weight:    0.2980
   chunk 35 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 48 optimal weight:    0.4980
   chunk 117 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.125428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.087844 restraints weight = 37759.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.93
r_work: 0.2927 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14560  Z= 0.117
  Angle     :  0.503  12.369  20271  Z= 0.263
  Chirality :  0.036   0.190   2322
  Planarity :  0.003   0.042   2066
  Dihedral  : 19.227 167.624   3430
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  7.39 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.23), residues: 1331
  helix:  1.37 (0.21), residues: 650
  sheet:  0.63 (0.60), residues: 85
  loop : -0.39 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.002   0.001   HIS A 721 
 PHE   0.012   0.001   PHE A1235 
 TYR   0.010   0.001   TYR A 155 
 ARG   0.009   0.000   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03982 (  620)
  hydrogen bonds       : angle       4.34884 ( 1705)
  covalent geometry    : bond        0.00252 (14560)
  covalent geometry    : angle       0.50291 (20271)

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

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

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2662 Ramachandran restraints generated.
    1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
REVERT: A  499 ASP cc_start: 0.8444 (t0) cc_final: 0.8142 (m-30)
REVERT: A  707 ASP cc_start: 0.8299 (m-30) cc_final: 0.8047 (m-30)
REVERT: A  781 MET cc_start: 0.8292 (tpt) cc_final: 0.7950 (tpt)
REVERT: A  786 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7070 (mp0)
REVERT: A  804 THR cc_start: 0.9346 (m) cc_final: 0.9097 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.2601
  time to fit residues: 29.8920
Evaluate side-chains
  69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  786 GLU
Chi-restraints excluded: chain A residue 1158 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 141 optimal weight:    6.9990
   chunk 101 optimal weight:    0.2980
   chunk 100 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 142 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    0.1980
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0770
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
A1364 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.124429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.084241 restraints weight = 35830.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.63
r_work: 0.2951 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14560  Z= 0.142
  Angle     :  0.511   8.090  20271  Z= 0.269
  Chirality :  0.037   0.190   2322
  Planarity :  0.003   0.042   2066
  Dihedral  : 19.213 167.675   3430
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.81 %
    Favored  : 91.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.23), residues: 1331
  helix:  1.38 (0.21), residues: 650
  sheet:  0.43 (0.59), residues: 86
  loop : -0.31 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.012   0.001   PHE A1235 
 TYR   0.011   0.001   TYR A 155 
 ARG   0.010   0.000   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (  620)
  hydrogen bonds       : angle       4.33448 ( 1705)
  covalent geometry    : bond        0.00315 (14560)
  covalent geometry    : angle       0.51102 (20271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8847.29 seconds
wall clock time: 157 minutes 51.30 seconds (9471.30 seconds total)