Starting phenix.real_space_refine
on Fri Jul  3 05:35:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w7q_65730/07_2026/9w7q_65730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w7q_65730/07_2026/9w7q_65730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w7q_65730/07_2026/9w7q_65730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w7q_65730/07_2026/9w7q_65730.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w7q_65730/07_2026/9w7q_65730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w7q_65730/07_2026/9w7q_65730.map"
  }
  resolution = 3.79
  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=   0.006 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     135      5.49       5
     S      19      5.16       5
     C    7195      2.51       5
     N    2128      2.21       5
     O    2628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 12105
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1129, 9201
          Classifications: {'peptide': 1129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 1098}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 618
          Classifications: {'DNA': 30}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 29}
    Chain: "C"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 305
          Classifications: {'DNA': 15}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 1981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 1981
          Classifications: {'RNA': 93}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 37}
          Link IDs: {'rna2p': 11, 'rna3p': 81}
  Time building chain proxies: 2.59, per 1000 atoms: 0.21
  Number of scatterers: 12105
  At special positions: 0
  Unit cell: (134.75, 104.566, 144.452, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     135     15.00
     O    2628      8.00
     N    2128      7.00
     C    7195      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: 1.00
  Conformation dependent library (CDL) restraints added in 547.2 milliseconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      56.2% alpha, 8.0% beta
      52 base pairs and 75 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.769A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.859A  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 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.781A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.546A  pdb=" N   PHE A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
      removed outlier: 4.037A  pdb=" N   LEU A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 214
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.528A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 283
      removed outlier: 4.369A  pdb=" N   ASP A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLN A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 307
      removed outlier: 3.649A  pdb=" N   PHE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG A 307 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.725A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    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 382
      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
    Processing helix  chain 'A' and resid 411 through 426
      removed outlier: 4.223A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 4.063A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASP A 435 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 474 through 476
      No H-bonds generated for 'chain 'A' and resid 474 through 476'
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.580A  pdb=" N   GLN A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.120A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.538A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
      removed outlier: 3.627A  pdb=" N   ILE A 632 " --> pdb=" O   ASP A 628 " (cutoff:3.500A)
    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 668
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 699
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.665A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 940
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.071A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 997
      removed outlier: 4.437A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.517A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    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 1241
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.596A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
    Processing helix  chain 'A' and resid 1314 through 1317
      removed outlier: 3.604A  pdb=" N   ASN A1317 " --> pdb=" O   THR A1314 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1314 through 1317'
    Processing helix  chain 'A' and resid 1339 through 1344
      removed outlier: 3.768A  pdb=" N   VAL A1342 " --> pdb=" O   THR A1339 " (cutoff:3.500A)
      removed outlier: 3.665A  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 957
      removed outlier: 4.250A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE A   7 " --> pdb=" O   ASN A 758 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 760 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A 762 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 4.475A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (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 942 through 943
      removed outlier: 4.706A  pdb=" N   LYS A 942 " --> pdb=" O   ILE A 950 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.625A  pdb=" N   ALA A1147 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.709A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      132 hydrogen bonds
      260 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      75 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2639
        1.33 -     1.45: 3274
        1.45 -     1.57: 6400
        1.57 -     1.69: 270
        1.69 -     1.81: 36
  Bond restraints: 12619
  Sorted by residual:
  bond pdb=" C3'  DT B  10 "
       pdb=" C2'  DT B  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.38e+01
  bond pdb=" C3'  DA B  27 "
       pdb=" C2'  DA B  27 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.24e+01
  bond pdb=" C3'  DG B  12 "
       pdb=" C2'  DG B  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.10e+01
  bond pdb=" C3'  DA C  13 "
       pdb=" C2'  DA C  13 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" C4'  DA B  24 "
       pdb=" C3'  DA B  24 "
    ideal  model  delta    sigma   weight residual
    1.529  1.501  0.028 1.00e-02 1.00e+04 7.61e+00
  ... (remaining 12614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 16805
        1.40 -     2.79: 745
        2.79 -     4.19: 76
        4.19 -     5.58: 13
        5.58 -     6.98: 1
  Bond angle restraints: 17640
  Sorted by residual:
  angle pdb=" O4'  DG B  18 "
        pdb=" C4'  DG B  18 "
        pdb=" C3'  DG B  18 "
      ideal   model   delta    sigma   weight residual
     106.00  102.61    3.39 6.00e-01 2.78e+00 3.20e+01
  angle pdb=" O4'  DG B  23 "
        pdb=" C4'  DG B  23 "
        pdb=" C3'  DG B  23 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.20e+01
  angle pdb=" O4'  DA B  22 "
        pdb=" C4'  DA B  22 "
        pdb=" C3'  DA B  22 "
      ideal   model   delta    sigma   weight residual
     106.00  103.20    2.80 6.00e-01 2.78e+00 2.18e+01
  angle pdb=" N3   DT B   4 "
        pdb=" C4   DT B   4 "
        pdb=" O4   DT B   4 "
      ideal   model   delta    sigma   weight residual
     119.90  122.47   -2.57 6.00e-01 2.78e+00 1.83e+01
  angle pdb=" N3   DT B  19 "
        pdb=" C4   DT B  19 "
        pdb=" O4   DT B  19 "
      ideal   model   delta    sigma   weight residual
     119.90  122.44   -2.54 6.00e-01 2.78e+00 1.79e+01
  ... (remaining 17635 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 6750
       17.25 -    34.50: 538
       34.50 -    51.75: 192
       51.75 -    69.00: 141
       69.00 -    86.25: 25
  Dihedral angle restraints: 7646
    sinusoidal: 4329
      harmonic: 3317
  Sorted by residual:
  dihedral pdb=" CA  PHE A  86 "
           pdb=" C   PHE A  86 "
           pdb=" N   SER A  87 "
           pdb=" CA  SER A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.78  -18.22     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  TYR A1201 "
           pdb=" C   TYR A1201 "
           pdb=" N   SER A1202 "
           pdb=" CA  SER A1202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.79   18.21     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  VAL A 181 "
           pdb=" C   VAL A 181 "
           pdb=" N   ASP A 182 "
           pdb=" CA  ASP A 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.87  -17.13     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 7643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1278
       0.029 -    0.057: 478
       0.057 -    0.086: 173
       0.086 -    0.115: 90
       0.115 -    0.143: 16
  Chirality restraints: 2035
  Sorted by residual:
  chirality pdb=" C1'   A D  42 "
            pdb=" O4'   A D  42 "
            pdb=" C2'   A D  42 "
            pdb=" N9    A D  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  VAL A  27 "
            pdb=" N   VAL A  27 "
            pdb=" C   VAL A  27 "
            pdb=" CB  VAL A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.71e-01
  chirality pdb=" C3'  DG C   4 "
            pdb=" C4'  DG C   4 "
            pdb=" O3'  DG C   4 "
            pdb=" C2'  DG C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 2032 not shown)

  Planarity restraints: 1751
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  42 "   -0.022 2.00e-02 2.50e+03   1.01e-02 2.81e+00
        pdb=" N9    A D  42 "    0.022 2.00e-02 2.50e+03
        pdb=" C8    A D  42 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    A D  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    A D  42 "   -0.009 2.00e-02 2.50e+03
        pdb=" N6    A D  42 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  42 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    A D  42 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A D  42 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  54 "    0.020 2.00e-02 2.50e+03   8.80e-03 2.32e+00
        pdb=" N9    G D  54 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    G D  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G D  54 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G D  54 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G D  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G D  54 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G D  54 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G D  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G D  54 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    G D  54 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G D  54 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  49 "    0.019 2.00e-02 2.50e+03   8.88e-03 2.17e+00
        pdb=" N9    A D  49 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    A D  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  49 "    0.004 2.00e-02 2.50e+03
        pdb=" C5    A D  49 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    A D  49 "    0.000 2.00e-02 2.50e+03
        pdb=" N6    A D  49 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  49 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A D  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A D  49 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1748 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 4
        2.02 -     2.74: 1168
        2.74 -     3.46: 17088
        3.46 -     4.18: 30430
        4.18 -     4.90: 48617
  Nonbonded interactions: 97307
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 510 "
            pdb=" O5'   A D   5 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" ND2 ASN A  77 "
            pdb=" O2    U D  59 "
     model   vdw
     1.299 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C5    C D  18 "
     model   vdw
     1.433 3.420
  nonbonded pdb=" SD  MET A 495 "
            pdb=" C1'  DA B  24 "
     model   vdw
     1.771 3.830
  nonbonded pdb=" OG  SER A 719 "
            pdb=" OE1 GLU A 722 "
     model   vdw
     2.132 3.040
  ... (remaining 97302 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:             0.020
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     13.370
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12619  Z= 0.322
  Angle     :  0.640   6.978  17640  Z= 0.485
  Chirality :  0.039   0.143   2035
  Planarity :  0.004   0.034   1751
  Dihedral  : 16.621  86.247   5498
  Min Nonbonded Distance : 1.298

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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:  0.77 (0.25), residues: 1123
  helix:  1.10 (0.22), residues: 561
  sheet:  0.64 (0.54), residues: 83
  loop : -0.10 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  69 
 TYR   0.016   0.001   TYR A1141 
 PHE   0.018   0.002   PHE A 164 
 TRP   0.020   0.002   TRP A1126 
 HIS   0.005   0.001   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.32 (12619)
  covalent geometry    : angle       0.63966 /  0.48 (17640)
  hydrogen bonds       : bond        0.16616 / 11.38 (  572)
  hydrogen bonds       : angle       5.71791 /  3.95 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 MET cc_start: 0.5602 (mtt) cc_final: 0.5283 (ttm)
REVERT: A  621 LEU cc_start: 0.9561 (tp) cc_final: 0.9336 (tp)
REVERT: A  648 MET cc_start: 0.9387 (mmm) cc_final: 0.8929 (mmm)
REVERT: A  930 HIS cc_start: 0.8104 (m-70) cc_final: 0.7868 (m-70)
REVERT: A 1172 SER cc_start: 0.9493 (m) cc_final: 0.8922 (p)
REVERT: A 1238 LEU cc_start: 0.9563 (mt) cc_final: 0.9292 (pp)
REVERT: A 1357 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7872 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1183
  time to fit residues: 33.6355
Evaluate side-chains
  111 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:   40.0000
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 123 optimal weight:   40.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  99 HIS
A 224 ASN
A 265 GLN
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 698 HIS
A1286 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.054737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.037508 restraints weight = 80668.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.039124 restraints weight = 41121.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.040188 restraints weight = 27137.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.040802 restraints weight = 20900.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.041303 restraints weight = 17820.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12619  Z= 0.190
  Angle     :  0.681  11.701  17640  Z= 0.377
  Chirality :  0.043   0.249   2035
  Planarity :  0.005   0.056   1751
  Dihedral  : 19.052  85.870   3122
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  8.62 %
    Favored  : 89.69 %
  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:  0.57 (0.25), residues: 1123
  helix:  0.87 (0.22), residues: 567
  sheet:  0.77 (0.56), residues: 92
  loop : -0.18 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  71 
 TYR   0.017   0.002   TYR A1141 
 PHE   0.016   0.002   PHE A 351 
 TRP   0.009   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 595 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.19 (12619)
  covalent geometry    : angle       0.68105 /  0.38 (17640)
  hydrogen bonds       : bond        0.05801 /  3.93 (  572)
  hydrogen bonds       : angle       4.95824 /  3.43 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9671 (mtmt) cc_final: 0.9260 (ttpt)
REVERT: A   71 ARG cc_start: 0.9590 (mtm180) cc_final: 0.9104 (ttm-80)
REVERT: A  321 MET cc_start: 0.9465 (mmp) cc_final: 0.9208 (mmm)
REVERT: A  398 LEU cc_start: 0.9162 (mt) cc_final: 0.8728 (mt)
REVERT: A  492 ILE cc_start: 0.9842 (mm) cc_final: 0.9582 (tt)
REVERT: A  510 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9352 (ptmm)
REVERT: A  534 MET cc_start: 0.6717 (mtt) cc_final: 0.6039 (ttm)
REVERT: A  564 LEU cc_start: 0.9618 (tt) cc_final: 0.9353 (pp)
REVERT: A  623 LEU cc_start: 0.9632 (tt) cc_final: 0.9418 (tt)
REVERT: A  648 MET cc_start: 0.9711 (mmm) cc_final: 0.9072 (mmm)
REVERT: A  652 LYS cc_start: 0.9446 (mttt) cc_final: 0.8849 (mmmm)
REVERT: A  751 MET cc_start: 0.9386 (tpp) cc_final: 0.9141 (ttt)
REVERT: A 1213 MET cc_start: 0.9410 (ttp) cc_final: 0.9015 (ttm)
REVERT: A 1324 PHE cc_start: 0.8645 (p90) cc_final: 0.8108 (p90)
REVERT: A 1357 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8499 (mp0)
  outliers start: 17
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1043
  time to fit residues: 18.8934
Evaluate side-chains
  107 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  510 LYS
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  758 ASN
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1259 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 103 optimal weight:   10.0000
   chunk 100 optimal weight:   40.0000
   chunk 94 optimal weight:    0.9990
   chunk 119 optimal weight:   30.0000
   chunk 71 optimal weight:   40.0000
   chunk 97 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   overall best weight:    5.5994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 GLN
A1261 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.053760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.036733 restraints weight = 81469.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.038316 restraints weight = 41428.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.039344 restraints weight = 27333.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.040010 restraints weight = 21019.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.040394 restraints weight = 17758.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12619  Z= 0.211
  Angle     :  0.643  12.851  17640  Z= 0.356
  Chirality :  0.041   0.238   2035
  Planarity :  0.004   0.064   1751
  Dihedral  : 19.086  85.673   3122
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.65 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  8.72 %
    Favored  : 89.10 %
  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:  0.51 (0.25), residues: 1123
  helix:  0.82 (0.21), residues: 563
  sheet:  1.13 (0.59), residues: 81
  loop : -0.28 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.018   0.002   TYR A 973 
 PHE   0.027   0.002   PHE A 539 
 TRP   0.014   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.21 (12619)
  covalent geometry    : angle       0.64303 /  0.36 (17640)
  hydrogen bonds       : bond        0.05364 /  3.64 (  572)
  hydrogen bonds       : angle       4.85146 /  3.35 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9709 (mtmt) cc_final: 0.9180 (ttpt)
REVERT: A  442 LYS cc_start: 0.9725 (tttt) cc_final: 0.9416 (ttpp)
REVERT: A  495 MET cc_start: 0.9560 (mpp) cc_final: 0.9185 (mpp)
REVERT: A  534 MET cc_start: 0.6828 (mtt) cc_final: 0.5803 (ttm)
REVERT: A  648 MET cc_start: 0.9691 (mmm) cc_final: 0.9140 (mmm)
REVERT: A  751 MET cc_start: 0.9325 (tpp) cc_final: 0.9008 (ttt)
REVERT: A 1169 MET cc_start: 0.9179 (ttp) cc_final: 0.7675 (tmm)
REVERT: A 1219 GLU cc_start: 0.9083 (tp30) cc_final: 0.8594 (tp30)
REVERT: A 1357 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8636 (tp30)
  outliers start: 22
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0953
  time to fit residues: 14.8085
Evaluate side-chains
  93 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  758 ASN
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 101 optimal weight:    7.9990
   chunk 121 optimal weight:   20.0000
   chunk 46 optimal weight:    6.9990
   chunk 112 optimal weight:   50.0000
   overall best weight:    4.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1305 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.053601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.036652 restraints weight = 80789.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.038177 restraints weight = 41204.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.039196 restraints weight = 27214.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.039788 restraints weight = 20956.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.040265 restraints weight = 17860.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12619  Z= 0.168
  Angle     :  0.602  10.380  17640  Z= 0.333
  Chirality :  0.040   0.324   2035
  Planarity :  0.004   0.061   1751
  Dihedral  : 19.063  86.912   3122
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.47 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  9.22 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.25), residues: 1123
  helix:  0.92 (0.22), residues: 563
  sheet:  1.01 (0.57), residues: 81
  loop : -0.26 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 437 
 TYR   0.018   0.001   TYR A1187 
 PHE   0.019   0.002   PHE A1204 
 TRP   0.014   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.17 (12619)
  covalent geometry    : angle       0.60231 /  0.33 (17640)
  hydrogen bonds       : bond        0.04664 /  3.13 (  572)
  hydrogen bonds       : angle       4.70675 /  3.25 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9685 (mtmt) cc_final: 0.9138 (ttpt)
REVERT: A  101 LEU cc_start: 0.9572 (tt) cc_final: 0.9264 (pp)
REVERT: A  321 MET cc_start: 0.9424 (mmp) cc_final: 0.9079 (mmm)
REVERT: A  398 LEU cc_start: 0.9333 (mt) cc_final: 0.8857 (mt)
REVERT: A  441 GLU cc_start: 0.9568 (pt0) cc_final: 0.9177 (pp20)
REVERT: A  442 LYS cc_start: 0.9710 (tttt) cc_final: 0.9340 (ttpp)
REVERT: A  492 ILE cc_start: 0.9801 (mm) cc_final: 0.9565 (tt)
REVERT: A  510 LYS cc_start: 0.9643 (ptmm) cc_final: 0.9296 (ptmm)
REVERT: A  534 MET cc_start: 0.6928 (mtt) cc_final: 0.5913 (ttm)
REVERT: A  564 LEU cc_start: 0.9603 (tt) cc_final: 0.9356 (pp)
REVERT: A  648 MET cc_start: 0.9737 (mmm) cc_final: 0.9162 (mmm)
REVERT: A 1124 LYS cc_start: 0.9730 (tttt) cc_final: 0.9514 (mtmm)
REVERT: A 1219 GLU cc_start: 0.9085 (tp30) cc_final: 0.8457 (tp30)
REVERT: A 1357 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8202 (mp0)
  outliers start: 21
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0935
  time to fit residues: 13.7138
Evaluate side-chains
  95 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  758 ASN
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 109 optimal weight:   30.0000
   chunk 108 optimal weight:    5.9990
   chunk 4 optimal weight:   30.0000
   chunk 94 optimal weight:   10.0000
   chunk 122 optimal weight:   30.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 22 optimal weight:   30.0000
   chunk 76 optimal weight:   30.0000
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.051967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.035271 restraints weight = 85157.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.036734 restraints weight = 43553.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.037747 restraints weight = 28875.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.038295 restraints weight = 22223.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.038762 restraints weight = 19090.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12619  Z= 0.242
  Angle     :  0.640   9.896  17640  Z= 0.358
  Chirality :  0.040   0.212   2035
  Planarity :  0.005   0.063   1751
  Dihedral  : 19.120  87.923   3122
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 10.90 %
    Favored  : 86.92 %
  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:  0.40 (0.24), residues: 1123
  helix:  0.82 (0.21), residues: 568
  sheet:  0.87 (0.58), residues: 81
  loop : -0.42 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 967 
 TYR   0.016   0.002   TYR A 973 
 PHE   0.018   0.002   PHE A 966 
 TRP   0.016   0.002   TRP A 659 
 HIS   0.008   0.002   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00457 /  0.24 (12619)
  covalent geometry    : angle       0.64033 /  0.36 (17640)
  hydrogen bonds       : bond        0.05343 /  3.61 (  572)
  hydrogen bonds       : angle       4.85245 /  3.35 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9704 (mtmt) cc_final: 0.9199 (ttpt)
REVERT: A  442 LYS cc_start: 0.9756 (tttt) cc_final: 0.9463 (ttpp)
REVERT: A  492 ILE cc_start: 0.9819 (mm) cc_final: 0.9605 (tt)
REVERT: A  495 MET cc_start: 0.9517 (mpp) cc_final: 0.9136 (mpp)
REVERT: A  516 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8925 (mt-10)
REVERT: A  534 MET cc_start: 0.7109 (mtt) cc_final: 0.6074 (ttm)
REVERT: A  648 MET cc_start: 0.9714 (mmm) cc_final: 0.9084 (mmm)
REVERT: A 1169 MET cc_start: 0.9289 (ttp) cc_final: 0.8020 (tmm)
REVERT: A 1219 GLU cc_start: 0.9147 (tp30) cc_final: 0.8654 (tp30)
REVERT: A 1357 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8652 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0902
  time to fit residues: 12.4016
Evaluate side-chains
  87 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 124 optimal weight:   40.0000
   chunk 80 optimal weight:    9.9990
   chunk 52 optimal weight:   30.0000
   chunk 7 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 79 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    7.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 412 HIS
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.050960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.034489 restraints weight = 86490.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.035977 restraints weight = 44184.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.036942 restraints weight = 29251.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037485 restraints weight = 22681.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.037915 restraints weight = 19490.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12619  Z= 0.263
  Angle     :  0.670   9.772  17640  Z= 0.370
  Chirality :  0.041   0.235   2035
  Planarity :  0.004   0.062   1751
  Dihedral  : 19.193  88.971   3122
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.45 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.69 %
    Favored  : 85.83 %
  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:  0.09 (0.24), residues: 1123
  helix:  0.61 (0.21), residues: 569
  sheet:  0.21 (0.62), residues: 73
  loop : -0.52 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 557 
 TYR   0.012   0.002   TYR A 132 
 PHE   0.015   0.002   PHE A 352 
 TRP   0.016   0.002   TRP A 659 
 HIS   0.006   0.002   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.26 (12619)
  covalent geometry    : angle       0.67027 /  0.37 (17640)
  hydrogen bonds       : bond        0.05310 /  3.55 (  572)
  hydrogen bonds       : angle       4.94155 /  3.39 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9683 (mtmt) cc_final: 0.9206 (ttpt)
REVERT: A  321 MET cc_start: 0.9406 (mmp) cc_final: 0.8977 (mmm)
REVERT: A  442 LYS cc_start: 0.9768 (tttt) cc_final: 0.9501 (mmmm)
REVERT: A  534 MET cc_start: 0.7095 (mtt) cc_final: 0.6077 (ttm)
REVERT: A  564 LEU cc_start: 0.9653 (tt) cc_final: 0.9405 (pp)
REVERT: A  648 MET cc_start: 0.9690 (mmm) cc_final: 0.9074 (mmm)
REVERT: A  751 MET cc_start: 0.9268 (ttm) cc_final: 0.8955 (ttm)
REVERT: A 1169 MET cc_start: 0.9334 (ttp) cc_final: 0.7959 (tmm)
REVERT: A 1219 GLU cc_start: 0.9141 (tp30) cc_final: 0.8762 (tp30)
REVERT: A 1357 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8600 (tp30)
  outliers start: 15
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0814
  time to fit residues: 11.1401
Evaluate side-chains
  90 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  758 ASN
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1144 LEU
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 80 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 123 optimal weight:   40.0000
   chunk 74 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.051263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.034891 restraints weight = 85425.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.036405 restraints weight = 43330.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.037395 restraints weight = 28518.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.037955 restraints weight = 21919.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.038427 restraints weight = 18728.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12619  Z= 0.164
  Angle     :  0.590  11.276  17640  Z= 0.328
  Chirality :  0.039   0.286   2035
  Planarity :  0.004   0.058   1751
  Dihedral  : 19.133  89.860   3122
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.83 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.48 %
    Favored  : 85.53 %
  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:  0.42 (0.24), residues: 1123
  helix:  0.93 (0.21), residues: 570
  sheet:  0.49 (0.64), residues: 71
  loop : -0.46 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.010   0.001   TYR A1187 
 PHE   0.012   0.001   PHE A1204 
 TRP   0.009   0.001   TRP A 659 
 HIS   0.006   0.001   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.16 (12619)
  covalent geometry    : angle       0.59025 /  0.33 (17640)
  hydrogen bonds       : bond        0.04460 /  2.95 (  572)
  hydrogen bonds       : angle       4.63919 /  3.19 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9652 (mtmt) cc_final: 0.9170 (ttpt)
REVERT: A  321 MET cc_start: 0.9406 (mmp) cc_final: 0.8989 (mmm)
REVERT: A  332 LEU cc_start: 0.9410 (tp) cc_final: 0.9009 (pp)
REVERT: A  335 LEU cc_start: 0.9816 (tp) cc_final: 0.9446 (pp)
REVERT: A  442 LYS cc_start: 0.9730 (tttt) cc_final: 0.9484 (mmmm)
REVERT: A  495 MET cc_start: 0.9583 (mpp) cc_final: 0.9203 (mpp)
REVERT: A  510 LYS cc_start: 0.9649 (ptmm) cc_final: 0.9404 (ptmt)
REVERT: A  534 MET cc_start: 0.7070 (mtt) cc_final: 0.6054 (ttm)
REVERT: A  564 LEU cc_start: 0.9623 (tt) cc_final: 0.9374 (pp)
REVERT: A  648 MET cc_start: 0.9696 (mmm) cc_final: 0.9078 (mmm)
REVERT: A  751 MET cc_start: 0.9256 (ttm) cc_final: 0.8765 (ppp)
REVERT: A 1089 MET cc_start: 0.8582 (mmp) cc_final: 0.7835 (mmt)
REVERT: A 1219 GLU cc_start: 0.9222 (tp30) cc_final: 0.8769 (tp30)
REVERT: A 1357 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8576 (tp30)
  outliers start: 10
  outliers final: 10
  residues processed: 87
  average time/residue: 0.0928
  time to fit residues: 12.4734
Evaluate side-chains
  86 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 101 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.051798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.035266 restraints weight = 84323.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.036755 restraints weight = 42615.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.037759 restraints weight = 28113.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.038332 restraints weight = 21593.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.038772 restraints weight = 18472.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12619  Z= 0.157
  Angle     :  0.597  16.484  17640  Z= 0.323
  Chirality :  0.039   0.280   2035
  Planarity :  0.004   0.055   1751
  Dihedral  : 19.100  90.395   3122
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.92 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.08 %
    Favored  : 85.73 %
  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:  0.54 (0.25), residues: 1123
  helix:  1.05 (0.21), residues: 571
  sheet:  0.20 (0.61), residues: 79
  loop : -0.37 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 557 
 TYR   0.010   0.001   TYR A1187 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.009   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.16 (12619)
  covalent geometry    : angle       0.59658 /  0.32 (17640)
  hydrogen bonds       : bond        0.04413 /  2.93 (  572)
  hydrogen bonds       : angle       4.56753 /  3.14 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9645 (mtmt) cc_final: 0.9176 (ttpt)
REVERT: A  335 LEU cc_start: 0.9812 (tp) cc_final: 0.9429 (pp)
REVERT: A  442 LYS cc_start: 0.9725 (tttt) cc_final: 0.9480 (mmmm)
REVERT: A  495 MET cc_start: 0.9598 (mpp) cc_final: 0.9261 (mpp)
REVERT: A  510 LYS cc_start: 0.9642 (ptmm) cc_final: 0.9410 (ptmt)
REVERT: A  534 MET cc_start: 0.7139 (mtt) cc_final: 0.6116 (ttm)
REVERT: A  564 LEU cc_start: 0.9626 (tt) cc_final: 0.9397 (pp)
REVERT: A  648 MET cc_start: 0.9696 (mmm) cc_final: 0.9100 (mmm)
REVERT: A  751 MET cc_start: 0.9211 (ttm) cc_final: 0.8769 (ppp)
REVERT: A  763 MET cc_start: 0.1664 (ttt) cc_final: 0.1382 (ttp)
REVERT: A 1089 MET cc_start: 0.8590 (mmp) cc_final: 0.8194 (mmm)
REVERT: A 1219 GLU cc_start: 0.9249 (tp30) cc_final: 0.8790 (tp30)
REVERT: A 1357 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8058 (mp0)
  outliers start: 12
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0944
  time to fit residues: 13.0061
Evaluate side-chains
  88 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 68 optimal weight:   20.0000
   chunk 71 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 96 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 116 optimal weight:   30.0000
   chunk 80 optimal weight:    6.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.050659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.034344 restraints weight = 86397.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.035799 restraints weight = 44148.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.036769 restraints weight = 29202.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.037332 restraints weight = 22502.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.037775 restraints weight = 19216.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12619  Z= 0.189
  Angle     :  0.611  12.526  17640  Z= 0.333
  Chirality :  0.039   0.284   2035
  Planarity :  0.004   0.056   1751
  Dihedral  : 19.091  90.631   3122
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.19 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.38 %
    Favored  : 85.13 %
  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:  0.47 (0.24), residues: 1123
  helix:  0.98 (0.21), residues: 571
  sheet:  0.22 (0.61), residues: 79
  loop : -0.40 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 557 
 TYR   0.010   0.001   TYR A1187 
 PHE   0.013   0.001   PHE A 970 
 TRP   0.011   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.19 (12619)
  covalent geometry    : angle       0.61058 /  0.33 (17640)
  hydrogen bonds       : bond        0.04673 /  3.10 (  572)
  hydrogen bonds       : angle       4.65931 /  3.20 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9650 (mtmt) cc_final: 0.9158 (ttpt)
REVERT: A  332 LEU cc_start: 0.9425 (tp) cc_final: 0.9067 (pp)
REVERT: A  335 LEU cc_start: 0.9818 (tp) cc_final: 0.9462 (pp)
REVERT: A  442 LYS cc_start: 0.9734 (tttt) cc_final: 0.9453 (mmmm)
REVERT: A  510 LYS cc_start: 0.9663 (ptmm) cc_final: 0.9410 (ptmt)
REVERT: A  534 MET cc_start: 0.7238 (mtt) cc_final: 0.6147 (ttm)
REVERT: A  564 LEU cc_start: 0.9626 (tt) cc_final: 0.9394 (pp)
REVERT: A  648 MET cc_start: 0.9697 (mmm) cc_final: 0.9099 (mmm)
REVERT: A 1169 MET cc_start: 0.9347 (ttp) cc_final: 0.8039 (tmm)
REVERT: A 1326 TYR cc_start: 0.9114 (t80) cc_final: 0.8112 (t80)
REVERT: A 1350 GLN cc_start: 0.9136 (mp10) cc_final: 0.8931 (mp10)
REVERT: A 1357 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8526 (tp30)
  outliers start: 15
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0954
  time to fit residues: 12.8674
Evaluate side-chains
  90 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1097 LYS
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 9 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   overall best weight:    5.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.050408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.034191 restraints weight = 86427.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.035625 restraints weight = 43956.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.036595 restraints weight = 29127.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.037145 restraints weight = 22401.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.037601 restraints weight = 19170.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12619  Z= 0.194
  Angle     :  0.623  12.580  17640  Z= 0.337
  Chirality :  0.040   0.292   2035
  Planarity :  0.004   0.056   1751
  Dihedral  : 19.095  91.210   3122
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 13.68 %
    Favored  : 84.94 %
  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:  0.40 (0.24), residues: 1123
  helix:  0.90 (0.21), residues: 571
  sheet:  0.16 (0.62), residues: 79
  loop : -0.40 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 557 
 TYR   0.010   0.001   TYR A1187 
 PHE   0.015   0.001   PHE A 491 
 TRP   0.012   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.19 (12619)
  covalent geometry    : angle       0.62308 /  0.34 (17640)
  hydrogen bonds       : bond        0.04667 /  3.09 (  572)
  hydrogen bonds       : angle       4.72739 /  3.24 ( 1541)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9642 (mtmt) cc_final: 0.9149 (ttpt)
REVERT: A  332 LEU cc_start: 0.9440 (tp) cc_final: 0.9079 (pp)
REVERT: A  335 LEU cc_start: 0.9823 (tp) cc_final: 0.9468 (pp)
REVERT: A  442 LYS cc_start: 0.9742 (tttt) cc_final: 0.9453 (mmmm)
REVERT: A  495 MET cc_start: 0.9626 (mpp) cc_final: 0.9275 (mpp)
REVERT: A  510 LYS cc_start: 0.9667 (ptmm) cc_final: 0.9412 (ptmt)
REVERT: A  534 MET cc_start: 0.7241 (mtt) cc_final: 0.6154 (ttm)
REVERT: A  564 LEU cc_start: 0.9623 (tt) cc_final: 0.9392 (pp)
REVERT: A  648 MET cc_start: 0.9699 (mmm) cc_final: 0.9108 (mmm)
REVERT: A  939 MET cc_start: 0.8630 (mmt) cc_final: 0.7111 (ttt)
REVERT: A 1169 MET cc_start: 0.9356 (ttp) cc_final: 0.8026 (tmm)
REVERT: A 1213 MET cc_start: 0.8886 (tpp) cc_final: 0.8538 (tpp)
REVERT: A 1326 TYR cc_start: 0.9129 (t80) cc_final: 0.8121 (t80)
REVERT: A 1357 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8509 (tp30)
  outliers start: 14
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0924
  time to fit residues: 12.3779
Evaluate side-chains
  91 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  758 ASN
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue 1097 LYS
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1203 LEU
Chi-restraints excluded: chain A residue 1286 ASN
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 102 optimal weight:    7.9990
   chunk 59 optimal weight:    8.9990
   chunk 111 optimal weight:    9.9990
   chunk 95 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 121 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    4.9588

-------------------------------------------------------------------------------
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 = 0.3229 r_free = 0.3229 target = 0.050334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.034170 restraints weight = 87316.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.035708 restraints weight = 43857.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.036612 restraints weight = 28721.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.037327 restraints weight = 22128.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.037660 restraints weight = 18656.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12619  Z= 0.184
  Angle     :  0.625  12.984  17640  Z= 0.335
  Chirality :  0.039   0.270   2035
  Planarity :  0.004   0.054   1751
  Dihedral  : 19.081  91.723   3122
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.10 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 14.27 %
    Favored  : 84.54 %
  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:  0.35 (0.24), residues: 1123
  helix:  0.87 (0.21), residues: 578
  sheet:  0.30 (0.64), residues: 73
  loop : -0.49 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 557 
 TYR   0.010   0.001   TYR A   5 
 PHE   0.012   0.001   PHE A 970 
 TRP   0.011   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.18 (12619)
  covalent geometry    : angle       0.62505 /  0.33 (17640)
  hydrogen bonds       : bond        0.04593 /  3.04 (  572)
  hydrogen bonds       : angle       4.69239 /  3.22 ( 1541)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2061.26 seconds
wall clock time: 36 minutes 26.15 seconds (2186.15 seconds total)