Starting phenix.real_space_refine
on Fri Jul  3 11:42:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u3y_41867/07_2026/8u3y_41867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u3y_41867/07_2026/8u3y_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u3y_41867/07_2026/8u3y_41867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u3y_41867/07_2026/8u3y_41867.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u3y_41867/07_2026/8u3y_41867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u3y_41867/07_2026/8u3y_41867.map"
  }
  resolution = 3.1
  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=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.94, per 1000 atoms: 0.35
  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: 1.45
  Conformation dependent library (CDL) restraints added in 758.7 milliseconds
  

  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: 2.12
  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: 3.99

  Time building geometry restraints manager: 1.87 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=" C3'  DC D  44 "
       pdb=" C2'  DC D  44 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.33e+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=" C3'  DG C  12 "
       pdb=" C2'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.81e+00
  ... (remaining 14555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 19858
        2.21 -     4.42: 380
        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=" O4'  DC c  36 "
        pdb=" C4'  DC c  36 "
        pdb=" C3'  DC c  36 "
      ideal   model   delta    sigma   weight residual
     106.00  102.79    3.21 6.00e-01 2.78e+00 2.86e+01
  angle pdb=" O4'  DC c  26 "
        pdb=" C4'  DC c  26 "
        pdb=" C3'  DC c  26 "
      ideal   model   delta    sigma   weight residual
     106.00  102.82    3.18 6.00e-01 2.78e+00 2.81e+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=" O4'  DC C  21 "
        pdb=" C4'  DC C  21 "
        pdb=" C3'  DC C  21 "
      ideal   model   delta    sigma   weight residual
     106.00  102.99    3.01 6.00e-01 2.78e+00 2.52e+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 -    0.091: 2178
       0.091 -    0.183: 136
       0.183 -    0.274: 6
       0.274 -    0.366: 1
       0.366 -    0.457: 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       2.34   -2.79   -0.46 2.00e-01 2.50e+01 5.22e+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:                  0.000
  Normalize map: mean=0, sd=1:             11.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     19.720
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
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= 0.403
  Angle     :  0.739  11.053  20271  Z= 0.516
  Chirality :  0.046   0.457   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 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: -0.24 (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
 ARG   0.014   0.001   ARG A 832 
 TYR   0.020   0.002   TYR A 362 
 PHE   0.024   0.002   PHE A1324 
 TRP   0.013   0.002   TRP A  18 
 HIS   0.006   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00644 /  0.40 (14560)
  covalent geometry    : angle       0.73855 /  0.52 (20271)
  hydrogen bonds       : bond        0.16489 / 11.09 (  620)
  hydrogen bonds       : angle       7.14356 /  5.06 ( 1705)

*********************** 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  : 0.485 
Fit side-chains
REVERT: A  534 MET cc_start: 0.7192 (mmm) cc_final: 0.6989 (mmm)
REVERT: A 1256 GLN cc_start: 0.7432 (mt0) cc_final: 0.7180 (tt0)
  outliers start: 3
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1548
  time to fit residues: 17.2502
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  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3732 r_free = 0.3732 target = 0.125167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.086793 restraints weight = 41707.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 3.32
r_work: 0.2902 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.0911

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= 0.159
  Angle     :  0.592  13.298  20271  Z= 0.337
  Chirality :  0.044   0.367   2322
  Planarity :  0.004   0.058   2066
  Dihedral  : 19.691 176.576   3430
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.82 %
    Favored  : 96.10 %
  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:  0.14 (0.23), residues: 1331
  helix:  0.67 (0.20), residues: 650
  sheet:  0.22 (0.58), residues: 84
  loop : -0.48 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 967 
 TYR   0.016   0.001   TYR A1242 
 PHE   0.016   0.001   PHE A 539 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.009   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.16 (14560)
  covalent geometry    : angle       0.59247 /  0.34 (20271)
  hydrogen bonds       : bond        0.06595 /  4.44 (  620)
  hydrogen bonds       : angle       5.03048 /  3.64 ( 1705)

*********************** 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  : 0.480 
Fit side-chains
REVERT: A  402 GLN cc_start: 0.9054 (mp10) cc_final: 0.8831 (mp10)
REVERT: A  534 MET cc_start: 0.7200 (mmm) cc_final: 0.6995 (mmm)
REVERT: A  943 TYR cc_start: 0.8549 (m-80) cc_final: 0.8276 (m-80)
REVERT: A 1149 VAL cc_start: 0.8363 (m) cc_final: 0.8161 (p)
REVERT: A 1256 GLN cc_start: 0.7782 (mt0) cc_final: 0.7559 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1286
  time to fit residues: 14.8818
Evaluate side-chains
  63 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 114 optimal weight:    0.0970
   chunk 116 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 140 optimal weight:    9.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3695 r_free = 0.3695 target = 0.123094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.084888 restraints weight = 40594.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 3.09
r_work: 0.2881 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    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 = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.2887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14560  Z= 0.172
  Angle     :  0.548   8.518  20271  Z= 0.314
  Chirality :  0.042   0.337   2322
  Planarity :  0.004   0.046   2066
  Dihedral  : 19.677 173.979   3430
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.15 %
    Favored  : 94.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.26 (0.23), residues: 1331
  helix:  0.85 (0.20), residues: 650
  sheet: -0.56 (0.49), residues: 123
  loop : -0.33 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 778 
 TYR   0.016   0.001   TYR A1242 
 PHE   0.014   0.001   PHE A 970 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.010   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.17 (14560)
  covalent geometry    : angle       0.54849 /  0.31 (20271)
  hydrogen bonds       : bond        0.05781 /  3.88 (  620)
  hydrogen bonds       : angle       4.77291 /  3.45 ( 1705)

*********************** 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
  71 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A   24 GLU cc_start: 0.7907 (mp0) cc_final: 0.7671 (mp0)
REVERT: A  402 GLN cc_start: 0.9074 (mp10) cc_final: 0.8780 (mp10)
REVERT: A  781 MET cc_start: 0.8255 (tpt) cc_final: 0.7870 (tpt)
REVERT: A 1242 TYR cc_start: 0.7868 (t80) cc_final: 0.7606 (t80)
REVERT: A 1256 GLN cc_start: 0.7849 (mt0) cc_final: 0.7569 (tt0)
  outliers start: 3
  outliers final: 2
  residues processed: 70
  average time/residue: 0.1363
  time to fit residues: 14.2258
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  : 0.490 
-------------------------------------------------------------------------------
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 77 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0270
   chunk 123 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 135 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 126 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6038

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.123443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.084265 restraints weight = 37582.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.56
r_work: 0.2960 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    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 = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14560  Z= 0.134
  Angle     :  0.501   8.327  20271  Z= 0.290
  Chirality :  0.041   0.361   2322
  Planarity :  0.004   0.043   2066
  Dihedral  : 19.666 170.663   3430
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.65 %
    Favored  : 94.02 %
  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:  0.46 (0.23), residues: 1331
  helix:  1.06 (0.20), residues: 650
  sheet: -0.54 (0.50), residues: 118
  loop : -0.28 (0.26), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 629 
 TYR   0.011   0.001   TYR A1242 
 PHE   0.012   0.001   PHE A1235 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.003   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.13 (14560)
  covalent geometry    : angle       0.50082 /  0.29 (20271)
  hydrogen bonds       : bond        0.05120 /  3.42 (  620)
  hydrogen bonds       : angle       4.61557 /  3.34 ( 1705)

*********************** 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
  75 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A   24 GLU cc_start: 0.7842 (mp0) cc_final: 0.7630 (mp0)
REVERT: A  402 GLN cc_start: 0.9051 (mp10) cc_final: 0.8763 (mp10)
REVERT: A  643 PHE cc_start: 0.9180 (m-80) cc_final: 0.8976 (m-80)
REVERT: A  781 MET cc_start: 0.8284 (tpt) cc_final: 0.7932 (tpt)
REVERT: A  786 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7186 (mp0)
REVERT: A 1242 TYR cc_start: 0.7871 (t80) cc_final: 0.7660 (t80)
REVERT: A 1256 GLN cc_start: 0.7895 (mt0) cc_final: 0.7605 (tt0)
  outliers start: 4
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1359
  time to fit residues: 15.0135
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 125 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 863 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.121973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085532 restraints weight = 31793.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.41
r_work: 0.2912 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2915
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14560  Z= 0.188
  Angle     :  0.532   9.511  20271  Z= 0.303
  Chirality :  0.042   0.345   2322
  Planarity :  0.004   0.043   2066
  Dihedral  : 19.604 170.820   3430
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  6.23 %
    Favored  : 93.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.46 (0.23), residues: 1331
  helix:  1.08 (0.20), residues: 650
  sheet: -0.61 (0.50), residues: 120
  loop : -0.29 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1303 
 TYR   0.016   0.001   TYR A 362 
 PHE   0.014   0.001   PHE A 970 
 TRP   0.007   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A 723 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.19 (14560)
  covalent geometry    : angle       0.53200 /  0.30 (20271)
  hydrogen bonds       : bond        0.05243 /  3.53 (  620)
  hydrogen bonds       : angle       4.61324 /  3.34 ( 1705)

*********************** 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
  71 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  402 GLN cc_start: 0.9075 (mp10) cc_final: 0.8746 (mp10)
REVERT: A  643 PHE cc_start: 0.9195 (m-80) cc_final: 0.8967 (m-80)
REVERT: A  781 MET cc_start: 0.8310 (tpt) cc_final: 0.7954 (tpt)
REVERT: A  786 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7131 (mp0)
  outliers start: 3
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1325
  time to fit residues: 13.9164
Evaluate side-chains
  66 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  786 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 142 optimal weight:   10.0000
   chunk 110 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 129 optimal weight:    3.9990
   overall best weight:    1.0182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.122271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.085114 restraints weight = 35530.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.55
r_work: 0.2911 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.1476

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= 0.173
  Angle     :  0.520  10.869  20271  Z= 0.297
  Chirality :  0.041   0.332   2322
  Planarity :  0.004   0.042   2066
  Dihedral  : 19.562 170.133   3430
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  6.89 %
    Favored  : 92.69 %
  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:  0.48 (0.23), residues: 1331
  helix:  1.11 (0.20), residues: 650
  sheet: -0.62 (0.50), residues: 120
  loop : -0.29 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 832 
 TYR   0.017   0.001   TYR A1242 
 PHE   0.013   0.001   PHE A 970 
 TRP   0.006   0.001   TRP A  18 
 HIS   0.004   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00376 /  0.17 (14560)
  covalent geometry    : angle       0.52041 /  0.30 (20271)
  hydrogen bonds       : bond        0.05069 /  3.42 (  620)
  hydrogen bonds       : angle       4.58134 /  3.32 ( 1705)

*********************** 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
  70 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A  643 PHE cc_start: 0.9211 (m-80) cc_final: 0.8991 (m-80)
REVERT: A  781 MET cc_start: 0.8327 (tpt) cc_final: 0.7974 (tpt)
REVERT: A  786 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7152 (mp0)
REVERT: A 1170 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8112 (pm20)
REVERT: A 1242 TYR cc_start: 0.8059 (t80) cc_final: 0.7809 (t80)
  outliers start: 5
  outliers final: 2
  residues processed: 69
  average time/residue: 0.1289
  time to fit residues: 13.1890
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  : 0.548 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 142 optimal weight:   20.0000
   chunk 95 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0980
   chunk 124 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0470
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.5078

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.125093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.085442 restraints weight = 33368.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.56
r_work: 0.2967 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
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      :  0.002   0.027  14560  Z= 0.122
  Angle     :  0.482  10.105  20271  Z= 0.279
  Chirality :  0.039   0.311   2322
  Planarity :  0.003   0.042   2066
  Dihedral  : 19.491 168.223   3430
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  6.81 %
    Favored  : 92.86 %
  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:  0.72 (0.23), residues: 1331
  helix:  1.28 (0.21), residues: 650
  sheet:  0.57 (0.64), residues: 75
  loop : -0.36 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 832 
 TYR   0.012   0.001   TYR A1242 
 PHE   0.011   0.001   PHE A1235 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.003   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.12 (14560)
  covalent geometry    : angle       0.48169 /  0.28 (20271)
  hydrogen bonds       : bond        0.04683 /  3.16 (  620)
  hydrogen bonds       : angle       4.48053 /  3.25 ( 1705)

*********************** 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
  74 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A  643 PHE cc_start: 0.9192 (m-80) cc_final: 0.8977 (m-80)
REVERT: A  781 MET cc_start: 0.8247 (tpt) cc_final: 0.7897 (tpt)
REVERT: A  786 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7045 (mp0)
REVERT: A 1170 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8018 (pm20)
  outliers start: 4
  outliers final: 2
  residues processed: 73
  average time/residue: 0.1210
  time to fit residues: 13.4684
Evaluate side-chains
  72 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 139 optimal weight:    5.9990
   chunk 140 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0370
   overall best weight:    1.4064

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.122459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.083100 restraints weight = 27496.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.33
r_work: 0.2931 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14560  Z= 0.224
  Angle     :  0.562  12.426  20271  Z= 0.314
  Chirality :  0.043   0.293   2322
  Planarity :  0.004   0.043   2066
  Dihedral  : 19.468 169.757   3430
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.23 %
    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 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:  0.48 (0.23), residues: 1331
  helix:  1.11 (0.21), residues: 650
  sheet: -0.60 (0.50), residues: 120
  loop : -0.30 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 832 
 TYR   0.019   0.001   TYR A 362 
 PHE   0.015   0.001   PHE A 970 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.22 (14560)
  covalent geometry    : angle       0.56241 /  0.31 (20271)
  hydrogen bonds       : bond        0.05158 /  3.51 (  620)
  hydrogen bonds       : angle       4.59364 /  3.33 ( 1705)

*********************** 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
  64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  643 PHE cc_start: 0.9233 (m-80) cc_final: 0.8995 (m-80)
REVERT: A  781 MET cc_start: 0.8324 (tpt) cc_final: 0.7915 (tpt)
REVERT: A  786 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7065 (mp0)
REVERT: A 1170 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7967 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 64
  average time/residue: 0.1279
  time to fit residues: 12.3760
Evaluate side-chains
  64 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 53 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 117 optimal weight:    0.5980
   chunk 134 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 144 optimal weight:    9.9990
   chunk 61 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 139 optimal weight:    4.9990
   chunk 131 optimal weight:    0.6980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.123821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.083340 restraints weight = 46566.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.99
r_work: 0.2917 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    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 = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1685

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= 0.143
  Angle     :  0.503  10.564  20271  Z= 0.287
  Chirality :  0.040   0.286   2322
  Planarity :  0.003   0.043   2066
  Dihedral  : 19.475 168.277   3430
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.23 %
    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 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:  0.60 (0.23), residues: 1331
  helix:  1.21 (0.21), residues: 650
  sheet: -0.57 (0.52), residues: 115
  loop : -0.25 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 832 
 TYR   0.014   0.001   TYR A1242 
 PHE   0.012   0.001   PHE A 970 
 TRP   0.005   0.001   TRP A 464 
 HIS   0.005   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 (14560)
  covalent geometry    : angle       0.50262 /  0.29 (20271)
  hydrogen bonds       : bond        0.04764 /  3.23 (  620)
  hydrogen bonds       : angle       4.51583 /  3.27 ( 1705)

*********************** 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
  68 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A  190 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7470 (pt0)
REVERT: A  643 PHE cc_start: 0.9217 (m-80) cc_final: 0.8979 (m-80)
REVERT: A  781 MET cc_start: 0.8281 (tpt) cc_final: 0.7935 (tpt)
REVERT: A  786 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7099 (mp0)
REVERT: A 1170 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8034 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 68
  average time/residue: 0.1242
  time to fit residues: 13.0922
Evaluate side-chains
  67 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 124 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0040
   chunk 74 optimal weight:    1.9990
   chunk 57 optimal weight:    0.3980
   chunk 108 optimal weight:    0.0870
   overall best weight:    0.4170

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.125196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.085800 restraints weight = 33893.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.54
r_work: 0.2974 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14560  Z= 0.116
  Angle     :  0.500  18.242  20271  Z= 0.279
  Chirality :  0.039   0.266   2322
  Planarity :  0.003   0.042   2066
  Dihedral  : 19.425 166.372   3430
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  7.23 %
    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 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:  0.74 (0.23), residues: 1331
  helix:  1.32 (0.21), residues: 650
  sheet: -0.46 (0.52), residues: 115
  loop : -0.17 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 832 
 TYR   0.012   0.001   TYR A1242 
 PHE   0.011   0.001   PHE A1235 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.002   0.001   HIS A1262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.12 (14560)
  covalent geometry    : angle       0.49970 /  0.28 (20271)
  hydrogen bonds       : bond        0.04496 /  3.05 (  620)
  hydrogen bonds       : angle       4.43991 /  3.22 ( 1705)

********************** 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: 3
    poor density    : 71
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A  643 PHE cc_start: 0.9207 (m-80) cc_final: 0.8967 (m-80)
REVERT: A  707 ASP cc_start: 0.8263 (m-30) cc_final: 0.7992 (m-30)
REVERT: A  781 MET cc_start: 0.8271 (tpt) cc_final: 0.7939 (tpt)
REVERT: A  786 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7006 (mp0)
REVERT: A 1170 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8040 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1211
  time to fit residues: 13.8002
Evaluate side-chains
  69 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1364 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.122953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.082072 restraints weight = 47753.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 3.07
r_work: 0.2894 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2899
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2899 r_free = 0.2899    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14560  Z= 0.197
  Angle     :  0.533   9.861  20271  Z= 0.299
  Chirality :  0.042   0.257   2322
  Planarity :  0.004   0.043   2066
  Dihedral  : 19.396 167.436   3430
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.48 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.63 (0.23), residues: 1331
  helix:  1.24 (0.21), residues: 650
  sheet: -0.52 (0.50), residues: 120
  loop : -0.24 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 832 
 TYR   0.016   0.001   TYR A 362 
 PHE   0.014   0.001   PHE A1235 
 TRP   0.008   0.001   TRP A  18 
 HIS   0.005   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.20 (14560)
  covalent geometry    : angle       0.53271 /  0.30 (20271)
  hydrogen bonds       : bond        0.04857 /  3.31 (  620)
  hydrogen bonds       : angle       4.50608 /  3.26 ( 1705)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3827.42 seconds
wall clock time: 66 minutes 25.65 seconds (3985.65 seconds total)