# Date 2008-01-16 Time 00:39:27 PST -0800 (1200472767.44 s)
#phil __OFF__

Command line arguments: "../97.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3609
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 97

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 47.6339, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.951
Completeness in resolution range: 0.907781
Completeness with d_max=infinity: 0.905096

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9376
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.951
Completeness in resolution range: 0.907781
Completeness with d_max=infinity: 0.905096

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9380 -  4.1756 [2261/2289]  2029   232  10.3%
  bin  2:  4.1756 -  3.3263 [2182/2205]  1965   217   9.9%
  bin  3:  3.3263 -  2.9094 [2151/2176]  1941   210   9.8%
  bin  4:  2.9094 -  2.6450 [2114/2132]  1902   212  10.0%
  bin  5:  2.6450 -  2.4563 [2104/2146]  1883   221  10.5%
  bin  6:  2.4563 -  2.3120 [2122/2150]  1919   203   9.6%
  bin  7:  2.3120 -  2.1966 [2075/2111]  1871   204   9.8%
  bin  8:  2.1966 -  2.1013 [2091/2133]  1885   206   9.9%
  bin  9:  2.1013 -  2.0206 [1947/2117]  1755   192   9.9%
  bin 10:  2.0206 -  1.9510 [ 542/2120]   480    62  11.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.04 -     1.81: 12
        1.81 -     2.59: 71
        2.59 -     3.36: 4096
        3.36 -     4.13: 9361
        4.13 -     4.90: 14776
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.044 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.110 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.315 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.319 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.366 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28311 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_001.geo

CPU time processing inputs: 9.23


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 47.63395 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5160   r_free= 0.5105   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.309061                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.6576 0.99   1468  162 0.4151 0.4188      6.6465      6.6844|
|  2:  4.6576 -  3.7156 0.99   1421  155 0.4502 0.5034      6.8432      6.9295|
|  3:  3.7156 -  3.2515 0.99   1384  160 0.4998 0.4740      6.7134      6.7233|
|  4:  3.2515 -  2.9567 0.99   1376  145 0.5158 0.4945       6.537      6.5102|
|  5:  2.9567 -  2.7462 0.99   1371  154 0.5506 0.5192      6.3779      6.4021|
|  6:  2.7462 -  2.5852 0.99   1371  156 0.5447 0.5689      6.2889      6.2113|
|  7:  2.5852 -  2.4563 0.98   1329  160 0.5441 0.4558      6.2281      6.1551|
|  8:  2.4563 -  2.3498 0.98   1365  142 0.5592 0.5452      6.1873      6.1944|
|  9:  2.3498 -  2.2596 0.99   1361  142 0.5602 0.5390      6.1255      6.1657|
| 10:  2.2596 -  2.1819 0.98   1351  148 0.5559 0.5979      6.0947      6.1178|
| 11:  2.1819 -  2.1139 0.97   1333  161 0.5524 0.5514      5.9988      6.0314|
| 12:  2.1139 -  2.0536 0.98   1321  150 0.5593 0.5678       5.954      5.9247|
| 13:  2.0536 -  1.9997 0.70    961   97 0.5558 0.5359      5.8754      5.8214|
| 14:  1.9997 -  1.9510 0.16    218   27 0.5805 0.5097      5.9336      5.7129|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9380 -  4.6576  1468   162  0.64  39.44   0.78     0.65      89023.87|
|  2:  4.6576 -  3.7156  1421   155  0.61  43.15   0.86     0.67     144474.37|
|  3:  3.7156 -  3.2515  1384   160  0.48  53.82   0.79     0.60     151410.10|
|  4:  3.2515 -  2.9567  1376   145  0.36  62.70   0.76     0.46     129369.89|
|  5:  2.9567 -  2.7462  1371   154  0.28  69.35   0.70     0.35      99821.49|
|  6:  2.7462 -  2.5852  1371   156  0.24  72.23   0.70     0.30      86486.98|
|  7:  2.5852 -  2.4563  1329   160  0.26  70.87   0.71     0.31      74949.44|
|  8:  2.4563 -  2.3498  1365   142  0.29  68.11   0.70     0.36      63499.79|
|  9:  2.3498 -  2.2596  1361   142  0.30  67.97   0.69     0.37      59895.95|
| 10:  2.2596 -  2.1819  1351   148  0.25  71.10   0.73     0.31      53374.73|
| 11:  2.1819 -  2.1139  1333   161  0.16  78.29   0.71     0.21      55171.32|
| 12:  2.1139 -  2.0536  1321   150  0.13  80.35   0.72     0.18      50800.06|
| 13:  2.0536 -  1.9997   961    97  0.13  80.19   0.72     0.19      44978.76|
| 14:  1.9997 -  1.9510   218    27  0.23  72.72   0.75     0.24      32272.45|
|alpha:            min =        0.18 max =            0.67 mean =         0.39|
|beta:             min =    32272.45 max =       151410.10 mean =     85638.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.41|
|phase err.(test): min =        0.00 max =           89.98 mean =        65.89|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.351338             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.534   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.494963              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.089   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.738 -  1.154:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.154 -  1.570:       11 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.570 -  1.987:       45 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.987 -  2.403:      287 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.403 -  2.819:     1033 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.819 -  3.235:     2249 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.235 -  3.651:     3792 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.651 -  4.068:     5324 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.068 -  4.484:     7073 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.484 -  4.900:     8564 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.733 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.738 |       3.162 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5208   r_free= 0.5132   ksol= 0.00   Bsol= 0.00   scale= 0.737    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.309194                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5086   r_free= 0.5070   ksol= 0.32   Bsol= 1.31   scale= 0.973    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.51,9.65,10.47,0.00,0.00,0.00); trace/3= 9.21                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.303740                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 22.407242             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.796   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.091101              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.937   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5086      final r-factor (work) = 0.4452          |
| start r-factor (free) = 0.5070      final r-factor (free) = 0.4723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 124.3938 = 22.41 * 0.50 * 6.3070 + 1.00 * 53.7328                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 70.2740 = 22.41 * 0.50 * 6.2573 + 1.00 * 0.1698                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4452      final r-factor (work) = 0.4040          |
| start r-factor (free) = 0.4723      final r-factor (free) = 0.4695          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0991 = 2.09 * 1.00 * 6.2573 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9991 = 2.09 * 1.00 * 6.2054 + 1.00 * 0.0230                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.87   16.51    None  None   None       |
|    all(noH): 2823   0      0.00    91.87   16.51    None  None   None       |
|    Sol.    : 438    0      0.00    91.87   26.51    None  None   None       |
|    Mac.    : 2385   0      0.00    84.30   14.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.187: 1029   |   5:    45.936 -  55.123:   63        |
|      1:     9.187 -  18.374:  792   |   6:    55.123 -  64.310:   29        |
|      2:    18.374 -  27.562:  481   |   7:    64.310 -  73.497:   16        |
|      3:    27.562 -  36.749:  275   |   8:    73.497 -  82.685:    7        |
|      4:    36.749 -  45.936:  126   |   9:    82.685 -  91.872:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4040 r_free = 0.4695             target_work(ml) = 6.194         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4037 r_free = 0.4698             target_work(ml) = 6.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4037   r_free= 0.4698   ksol= 0.32   Bsol= 1.31   scale= 1.121    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.51,9.65,10.47,0.00,0.00,0.00); trace/3= 9.21                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.193874                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4014   r_free= 0.4646   ksol= 0.34   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,5.57,6.50,0.00,0.00,0.00); trace/3= 5.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.194682                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.735922             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.818  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.785860              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.453  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4014      final r-factor (work) = 0.3288          |
| start r-factor (free) = 0.4646      final r-factor (free) = 0.3905          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.4662 = 10.74 * 0.50 * 6.2028 + 1.00 * 0.1698                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9752 = 10.74 * 0.50 * 6.1235 + 1.00 * 0.1042                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3288      final r-factor (work) = 0.3078          |
| start r-factor (free) = 0.3905      final r-factor (free) = 0.3720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8355 = 0.79 * 1.00 * 6.1235 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7461 = 0.79 * 1.00 * 6.0204 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.10   15.87    None  None   None       |
|    all(noH): 2823   0      0.00    99.10   15.87    None  None   None       |
|    Sol.    : 438    0      0.00    99.10   31.43    None  None   None       |
|    Mac.    : 2385   0      0.00    85.53   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.910: 1189   |   5:    49.548 -  59.457:   44        |
|      1:     9.910 -  19.819:  825   |   6:    59.457 -  69.367:   19        |
|      2:    19.819 -  29.729:  415   |   7:    69.367 -  79.276:    9        |
|      3:    29.729 -  39.638:  212   |   8:    79.276 -  89.186:    6        |
|      4:    39.638 -  49.548:  103   |   9:    89.186 -  99.095:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3078 r_free = 0.3720             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3077 r_free = 0.3721             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3077   r_free= 0.3721   ksol= 0.34   Bsol= 50.00   scale= 1.076   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,5.57,6.50,0.00,0.00,0.00); trace/3= 5.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.000520                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3049   r_free= 0.3702   ksol= 0.33   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.17,3.09,3.84,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.000354                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.687599              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.384  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.953  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3049      final r-factor (work) = 0.2217          |
| start r-factor (free) = 0.3702      final r-factor (free) = 0.2756          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.2697 = 9.69 * 0.50 * 6.0212 + 1.00 * 0.1042                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6527 = 9.69 * 0.50 * 5.8953 + 1.00 * 0.0973                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2217      final r-factor (work) = 0.1964          |
| start r-factor (free) = 0.2756      final r-factor (free) = 0.2512          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8550 = 0.31 * 1.00 * 5.8953 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7814 = 0.31 * 1.00 * 5.6732 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.51   15.09    None  None   None       |
|    all(noH): 2823   0      0.00    87.51   15.09    None  None   None       |
|    Sol.    : 438    0      2.86    87.51   36.13    None  None   None       |
|    Mac.    : 2385   0      0.00    80.87   11.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.751: 1196   |   5:    43.753 -  52.503:  109        |
|      1:     8.751 -  17.501:  895   |   6:    52.503 -  61.254:   38        |
|      2:    17.501 -  26.252:  271   |   7:    61.254 -  70.004:   12        |
|      3:    26.252 -  35.002:  153   |   8:    70.004 -  78.755:    9        |
|      4:    35.002 -  43.753:  137   |   9:    78.755 -  87.505:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1964 r_free = 0.2512             target_work(ml) = 5.622         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1962 r_free = 0.2514             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1962   r_free= 0.2514   ksol= 0.33   Bsol= 50.00   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.17,3.09,3.84,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.620265                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1942   r_free= 0.2499   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,1.21,2.16,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.618846                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.421439              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.064  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.600116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.657   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1942      final r-factor (work) = 0.1540          |
| start r-factor (free) = 0.2499      final r-factor (free) = 0.1983          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8178 = 3.42 * 0.50 * 5.6821 + 1.00 * 0.0973                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5314 = 3.42 * 0.50 * 5.5314 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.1983      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3293 = 0.60 * 1.00 * 5.5314 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2399 = 0.60 * 1.00 * 5.3741 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.70   15.75    None  None   None       |
|    all(noH): 2823   0      0.00    90.70   15.75    None  None   None       |
|    Sol.    : 438    0      3.11    85.15   41.74    None  None   None       |
|    Mac.    : 2385   0      0.00    90.70   10.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.070: 1297   |   5:    45.352 -  54.422:  106        |
|      1:     9.070 -  18.141:  871   |   6:    54.422 -  63.493:   70        |
|      2:    18.141 -  27.211:  202   |   7:    63.493 -  72.563:   39        |
|      3:    27.211 -  36.282:  116   |   8:    72.563 -  81.634:   17        |
|      4:    36.282 -  45.352:   98   |   9:    81.634 -  90.704:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1422 r_free = 0.1908             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1420 r_free = 0.1910             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1910   ksol= 0.33   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,1.21,2.16,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.354810                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1915   ksol= 0.33   Bsol= 59.02   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.64,1.79,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.354424                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.111478              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.921  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.233615              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.720  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1915      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4317 = 3.11 * 0.50 * 5.3755 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3332 = 3.11 * 0.50 * 5.3087 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1712          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2612 = 0.23 * 1.00 * 5.3087 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2399 = 0.23 * 1.00 * 5.2644 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.69    89.70   15.22    None  None   None       |
|    all(noH): 2823   0      0.69    89.70   15.22    None  None   None       |
|    Sol.    : 438    0      3.75    86.45   39.54    None  None   None       |
|    Mac.    : 2385   0      0.69    89.70   10.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.688 -   9.589: 1398   |   5:    45.193 -  54.094:   96        |
|      1:     9.589 -  18.490:  817   |   6:    54.094 -  62.995:   64        |
|      2:    18.490 -  27.391:  184   |   7:    62.995 -  71.896:   22        |
|      3:    27.391 -  36.292:  116   |   8:    71.896 -  80.797:   19        |
|      4:    36.292 -  45.193:  101   |   9:    80.797 -  89.698:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1262 r_free = 0.1712             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1260 r_free = 0.1710             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1710   ksol= 0.33   Bsol= 59.02   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.64,1.79,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.247025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.6576 0.99   1468  162 0.1016 0.1422      5.4348      5.6393|
|  2:  4.6576 -  3.7156 0.99   1421  155 0.0906 0.1141       5.494      5.7072|
|  3:  3.7156 -  3.2515 0.99   1384  160 0.1216 0.1609      5.5798      5.8604|
|  4:  3.2515 -  2.9567 0.99   1376  145 0.1389 0.1821      5.5253      5.7297|
|  5:  2.9567 -  2.7462 0.99   1371  154 0.1543 0.1789      5.4527      5.5971|
|  6:  2.7462 -  2.5852 0.99   1371  156 0.1399 0.2289      5.3099      5.5798|
|  7:  2.5852 -  2.4563 0.98   1329  160 0.1449 0.1696       5.255      5.3824|
|  8:  2.4563 -  2.3498 0.98   1365  142 0.1353 0.1875      5.1673       5.367|
|  9:  2.3498 -  2.2596 0.99   1361  142 0.1341 0.1995      5.1029      5.3874|
| 10:  2.2596 -  2.1819 0.98   1351  148 0.1298 0.1881      5.0479      5.2436|
| 11:  2.1819 -  2.1139 0.97   1333  161 0.1308 0.1939      4.9818       5.316|
| 12:  2.1139 -  2.0536 0.98   1321  150 0.1295 0.1650      4.9361      5.1161|
| 13:  2.0536 -  1.9997 0.70    961   97 0.1206 0.1923      4.8215      5.0195|
| 14:  1.9997 -  1.9510 0.16    218   27 0.1134 0.1906      4.7812      5.0081|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9380 -  4.6576  1468   162  0.93  10.15   0.97     0.95       8472.61|
|  2:  4.6576 -  3.7156  1421   155  0.94   9.20   1.01     1.00      10525.33|
|  3:  3.7156 -  3.2515  1384   160  0.92  12.95   1.02     1.02      12572.31|
|  4:  3.2515 -  2.9567  1376   145  0.90  15.99   1.01     1.00      12025.42|
|  5:  2.9567 -  2.7462  1371   154  0.88  18.71   1.00     0.98      11002.05|
|  6:  2.7462 -  2.5852  1371   156  0.88  18.49   0.97     0.94       8555.34|
|  7:  2.5852 -  2.4563  1329   160  0.89  17.69   0.99     0.95       7262.90|
|  8:  2.4563 -  2.3498  1365   142  0.89  17.53   1.01     0.97       6388.69|
|  9:  2.3498 -  2.2596  1361   142  0.89  17.46   1.00     0.97       5723.56|
| 10:  2.2596 -  2.1819  1351   148  0.88  17.87   1.00     0.98       5365.34|
| 11:  2.1819 -  2.1139  1333   161  0.88  18.28   1.00     0.96       4901.22|
| 12:  2.1139 -  2.0536  1321   150  0.89  17.43   1.00     1.00       4332.96|
| 13:  2.0536 -  1.9997   961    97  0.89  17.66   0.99     0.97       3644.36|
| 14:  1.9997 -  1.9510   218    27  0.91  15.02   0.97     0.93       3013.77|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     3013.77 max =        12572.31 mean =      7826.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.99|
|phase err.(test): min =        0.00 max =           89.73 mean =        15.48|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1710   ksol= 0.32   Bsol= 53.78   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,0.08,1.31,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.246965                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1710   ksol= 0.32   Bsol= 53.78   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,0.08,1.31,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.246965                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.6576 0.99   1468  162 0.1014 0.1418      5.4324      5.6348|
|  2:  4.6576 -  3.7156 0.99   1421  155 0.0901 0.1137      5.4902      5.7034|
|  3:  3.7156 -  3.2515 0.99   1384  160 0.1216 0.1608      5.5786      5.8604|
|  4:  3.2515 -  2.9567 0.99   1376  145 0.1390 0.1826      5.5258       5.731|
|  5:  2.9567 -  2.7462 0.99   1371  154 0.1545 0.1791      5.4542       5.598|
|  6:  2.7462 -  2.5852 0.99   1371  156 0.1400 0.2291      5.3108      5.5807|
|  7:  2.5852 -  2.4563 0.98   1329  160 0.1451 0.1698       5.256      5.3832|
|  8:  2.4563 -  2.3498 0.98   1365  142 0.1354 0.1871      5.1678      5.3665|
|  9:  2.3498 -  2.2596 0.99   1361  142 0.1342 0.1997      5.1034      5.3896|
| 10:  2.2596 -  2.1819 0.98   1351  148 0.1298 0.1880      5.0482      5.2441|
| 11:  2.1819 -  2.1139 0.97   1333  161 0.1308 0.1940      4.9824      5.3162|
| 12:  2.1139 -  2.0536 0.98   1321  150 0.1296 0.1650      4.9367      5.1169|
| 13:  2.0536 -  1.9997 0.70    961   97 0.1207 0.1924      4.8221      5.0193|
| 14:  1.9997 -  1.9510 0.16    218   27 0.1133 0.1908      4.7817      5.0098|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9380 -  4.6576  1468   162  0.93  10.11   0.97     0.95       8424.03|
|  2:  4.6576 -  3.7156  1421   155  0.94   9.15   1.01     1.00      10457.48|
|  3:  3.7156 -  3.2515  1384   160  0.92  12.92   1.02     1.02      12516.14|
|  4:  3.2515 -  2.9567  1376   145  0.90  16.00   1.01     1.00      12028.01|
|  5:  2.9567 -  2.7462  1371   154  0.88  18.72   1.00     0.98      11032.40|
|  6:  2.7462 -  2.5852  1371   156  0.88  18.51   0.97     0.93       8579.60|
|  7:  2.5852 -  2.4563  1329   160  0.89  17.70   0.99     0.95       7276.80|
|  8:  2.4563 -  2.3498  1365   142  0.89  17.54   1.00     0.96       6397.26|
|  9:  2.3498 -  2.2596  1361   142  0.89  17.47   1.00     0.96       5733.37|
| 10:  2.2596 -  2.1819  1351   148  0.88  17.88   1.00     0.97       5372.13|
| 11:  2.1819 -  2.1139  1333   161  0.88  18.29   0.99     0.96       4909.18|
| 12:  2.1139 -  2.0536  1321   150  0.89  17.43   1.00     1.00       4337.69|
| 13:  2.0536 -  1.9997   961    97  0.89  17.66   0.98     0.96       3646.84|
| 14:  1.9997 -  1.9510   218    27  0.91  15.04   0.97     0.92       3016.04|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3016.04 max =        12516.14 mean =      7821.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.99|
|phase err.(test): min =        0.00 max =           89.98 mean =        15.48|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.820)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.05    90.06   15.59    None  None   None       |
|    all(noH): 2823   0      1.05    90.06   15.59    None  None   None       |
|    Sol.    : 438    0      4.12    86.81   39.90    None  None   None       |
|    Mac.    : 2385   0      1.05    90.06   11.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.054 -   9.955: 1398   |   5:    45.558 -  54.459:   96        |
|      1:     9.955 -  18.856:  817   |   6:    54.459 -  63.360:   64        |
|      2:    18.856 -  27.757:  184   |   7:    63.360 -  72.261:   22        |
|      3:    27.757 -  36.658:  116   |   8:    72.261 -  81.162:   19        |
|      4:    36.658 -  45.558:  101   |   9:    81.162 -  90.063:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.498 - 4.249
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 339
   mapped sites are within: 0.716 - 4.249

peak=   10.312 closest distance to " CB  VAL A 230 " =    1.453
peak=    7.958 closest distance to " O   HOH Z 255 " =    1.378
peak=    7.004 closest distance to " O   HOH Z 169 " =    1.221
peak=    6.872 closest distance to " CD1AILE A 234 " =    1.314
peak=    6.586 closest distance to " CG1 VAL A 296 " =    1.216
peak=    5.915 closest distance to " O   HOH Z 248 " =    1.630
peak=    5.885 closest distance to " O   HOH Z 117 " =    1.396
peak=    5.652 closest distance to " O   HOH Z 258 " =    1.410
peak=    5.631 closest distance to " O   HOH Z 403 " =    1.872
peak=    5.597 closest distance to " O   HOH Z 404 " =    1.315
peak=    5.411 closest distance to " CD2 LEU A   5 " =    1.230
peak=    5.410 closest distance to " O   HOH Z 210 " =    1.272
peak=    5.263 closest distance to " O   HOH Z 124 " =    1.395
peak=    5.193 closest distance to " O   HOH Z 203 " =    1.036
peak=    5.101 closest distance to " CG  LEU A   5 " =    1.382
peak=    5.082 closest distance to " O   HOH Z  43 " =    1.992
peak=    5.002 closest distance to " CB  ARG A 275 " =    0.931
peak=    4.928 closest distance to " O   HOH Z 126 " =    1.585
peak=    4.913 closest distance to " CG  PRO A  54 " =    1.409
peak=    4.858 closest distance to " O   HOH Z  76 " =    1.353
peak=    4.820 closest distance to " NE2 GLN A  11 " =    1.131
peak=    4.762 closest distance to " NH2 ARG A  56 " =    2.063
peak=    4.704 closest distance to " O   HOH Z 406 " =    1.812
peak=    4.678 closest distance to " CB  SER A  26 " =    1.861
peak=    4.631 closest distance to " CD2 LEU A 228 " =    1.229
peak=    4.608 closest distance to " CB  VAL A 296 " =    1.405
peak=    4.560 closest distance to " O   HOH Z  97 " =    1.474
peak=    4.549 closest distance to " O   HOH Z 188 " =    1.336
peak=    4.548 closest distance to " O   HOH Z 128 " =    1.710
peak=    4.521 closest distance to " CD2 TRP A 179 " =    1.334
peak=    4.503 closest distance to " CB  GLN A 223 " =    1.520
peak=    4.472 closest distance to " O   HOH Z 238 " =    2.110
peak=    4.460 closest distance to " CA  ALA A  51 " =    1.072
peak=    4.432 closest distance to " CZ  PHE A 218 " =    1.163
peak=    4.401 closest distance to " O   HOH Z 193 " =    2.405
peak=    4.377 closest distance to " O   HOH Z 411 " =    3.812
peak=    4.369 closest distance to " CA  TYR A  30 " =    1.003
peak=    4.357 closest distance to " O   HOH Z 394 " =    1.683
peak=    4.352 closest distance to " O   HOH Z 368 " =    2.298
peak=    4.347 closest distance to " O   HOH Z 425 " =    1.546
peak=    4.335 closest distance to " O   HOH Z 251 " =    1.724
peak=    4.322 closest distance to " O   HOH Z 375 " =    1.305
peak=    4.303 closest distance to " O   HOH Z 154 " =    1.806
peak=    4.298 closest distance to " CB  PRO A  54 " =    0.987
peak=    4.294 closest distance to " CB  GLU A 152 " =    1.203
peak=    4.260 closest distance to " O   HOH Z 375 " =    1.003
peak=    4.243 closest distance to " CB  VAL A 230 " =    1.220
peak=    4.235 closest distance to " CB  SER A  63 " =    1.122
peak=    4.233 closest distance to " O   HOH Z 272 " =    1.892
peak=    4.227 closest distance to " O   HOH Z 130 " =    2.602
peak=    4.209 closest distance to " O   HOH Z 359 " =    1.882
peak=    4.208 closest distance to " CG  LEU A 228 " =    1.170
peak=    4.202 closest distance to " CZ3 TRP A 266 " =    1.023
peak=    4.184 closest distance to " CD  LYS A 166 " =    1.515
peak=    4.181 closest distance to " O   HOH Z 142 " =    2.530
peak=    4.147 closest distance to " CB  ASN A 148 " =    1.307
peak=    4.145 closest distance to " O   HOH Z 209 " =    2.290
peak=    4.133 closest distance to " O   HOH Z 414 " =    1.827
peak=    4.113 closest distance to " O   HOH Z 402 " =    1.423
peak=    4.112 closest distance to " O   HOH Z 188 " =    2.666
peak=    4.106 closest distance to " O   HOH Z 346 " =    1.490
peak=    4.103 closest distance to " O   HOH Z  63 " =    2.025
peak=    4.089 closest distance to " O   HOH Z  49 " =    1.373
peak=    4.078 closest distance to " CD  LYS A  76 " =    1.867
peak=    4.066 closest distance to " O   HOH Z 232 " =    2.329
peak=    4.038 closest distance to " O   HOH Z 236 " =    1.648
peak=    4.029 closest distance to " CB  GLN A  55 " =    0.880
peak=    4.023 closest distance to " CB  GLN A 183 " =    1.280
peak=    4.018 closest distance to " CB  GLU A 277 " =    3.712
peak=    4.015 closest distance to " O   HOH Z 102 " =    1.407
peak=    3.995 closest distance to " O   HOH Z   4 " =    1.733
peak=    3.993 closest distance to " O   HOH Z 234 " =    3.555
peak=    3.981 closest distance to " O   HOH Z 286 " =    2.079
peak=    3.979 closest distance to " O   HOH Z 327 " =    1.708
peak=    3.951 closest distance to " O   HOH Z 190 " =    1.174
peak=    3.941 closest distance to " NH1AARG A 275 " =    1.044
peak=    3.920 closest distance to " O   HOH Z  85 " =    1.765
peak=    3.915 closest distance to " CA  ASP A 162 " =    0.994
peak=    3.907 closest distance to " O   HOH Z 372 " =    1.129
peak=    3.901 closest distance to " CD  PRO A  54 " =    0.968
peak=    3.899 closest distance to " O   HOH Z 246 " =    1.195
peak=    3.890 closest distance to " CG  PRO A 243 " =    1.110
peak=    3.890 closest distance to " O   HOH Z 316 " =    3.127
peak=    3.878 closest distance to " CG2 VAL A 296 " =    1.026
peak=    3.865 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.850 closest distance to " CB AVAL A  41 " =    1.291
peak=    3.841 closest distance to " O   HOH Z 116 " =    1.341
peak=    3.840 closest distance to " CG1 ILE A  20 " =    1.312
peak=    3.837 closest distance to " O   PRO A 198 " =    1.586
peak=    3.836 closest distance to " CG2 ILE A 234 " =    1.252
peak=    3.786 closest distance to " O   HOH Z  80 " =    2.085
peak=    3.783 closest distance to " O   HOH Z 419 " =    1.980
peak=    3.775 closest distance to " CB  ARG A  79 " =    1.248
peak=    3.773 closest distance to " O   HOH Z 389 " =    1.950
peak=    3.771 closest distance to " O   HOH Z 423 " =    1.802
peak=    3.766 closest distance to " O   HOH Z 247 " =    1.627
peak=    3.762 closest distance to " O   HOH Z 132 " =    2.792
peak=    3.755 closest distance to " O  BHOH Z 338 " =    1.161
peak=    3.752 closest distance to " CA  ARG A  36 " =    1.065
peak=    3.751 closest distance to " O   HOH Z  40 " =    1.963
peak=    3.747 closest distance to " CG AARG A 102 " =    1.052
peak=    3.741 closest distance to " O   SER A  87 " =    2.194
peak=    3.729 closest distance to " O   HOH Z 423 " =    2.166
peak=    3.726 closest distance to " O   HOH Z 214 " =    3.236
peak=    3.725 closest distance to " CB  ASN A 142 " =    1.129
peak=    3.724 closest distance to " O   HOH Z 380 " =    1.824
peak=    3.723 closest distance to " O   HOH Z  30 " =    1.378
peak=    3.712 closest distance to " O   HOH Z 433 " =    1.420
peak=    3.706 closest distance to " CG  GLN A  58 " =    1.069
peak=    3.705 closest distance to " O   HOH Z 134 " =    1.513
peak=    3.701 closest distance to " O   HOH Z 146 " =    1.488
peak=    3.699 closest distance to " O   HOH Z 214 " =    1.269
peak=    3.697 closest distance to " CE  LYS A  76 " =    0.862
peak=    3.696 closest distance to " CG AARG A 275 " =    1.238
peak=    3.678 closest distance to " O   ASP A 124 " =    1.663
peak=    3.674 closest distance to " NZ  LYS A 117 " =    2.711
peak=    3.671 closest distance to " O   HOH Z 298 " =    4.249
peak=    3.664 closest distance to " CG  MET A 185 " =    1.271
peak=    3.663 closest distance to " O   ALA A 165 " =    1.368
peak=    3.657 closest distance to " O   HOH Z 422 " =    2.595
peak=    3.657 closest distance to " O   HOH Z 137 " =    1.633
peak=    3.653 closest distance to " O   HOH Z 287 " =    1.754
peak=    3.638 closest distance to " CB  SER A   3 " =    1.345
peak=    3.634 closest distance to " O   HOH Z 328 " =    1.547
peak=    3.633 closest distance to " O   HOH Z 142 " =    1.600
peak=    3.632 closest distance to " O   HOH Z 107 " =    0.931
peak=    3.609 closest distance to " CD  ARG A 195 " =    0.960
peak=    3.607 closest distance to " NH2 ARG A  56 " =    1.193
peak=    3.597 closest distance to " O   HOH Z 369 " =    2.083
peak=    3.597 closest distance to " O   HOH Z 344 " =    1.773
peak=    3.597 closest distance to " CB  PHE A 204 " =    0.875
peak=    3.589 closest distance to " CD2 LEU A 297 " =    1.025
peak=    3.583 closest distance to " O   HOH Z 193 " =    2.071
peak=    3.580 closest distance to " O   HOH Z 403 " =    1.497
peak=    3.578 closest distance to " CD  LYS A 119 " =    1.889
peak=    3.569 closest distance to " NH2BARG A 145 " =    2.402
peak=    3.569 closest distance to " CG  PRO A 198 " =    1.238
peak=    3.566 closest distance to " O   HOH Z 213 " =    1.636
peak=    3.565 closest distance to " O   HOH Z  95 " =    1.369
peak=    3.562 closest distance to " CB  THR A  31 " =    1.532
peak=    3.560 closest distance to " O   HOH Z 415 " =    3.543
peak=    3.559 closest distance to " O   HOH Z 130 " =    1.225
peak=    3.557 closest distance to " NH1AARG A 145 " =    1.370
peak=    3.549 closest distance to " O   HOH Z 431 " =    1.298
peak=    3.549 closest distance to " O   THR A 182 " =    1.550
peak=    3.541 closest distance to " CB  TRP A 179 " =    1.275
peak=    3.540 closest distance to " O   HOH Z 313 " =    1.663
peak=    3.538 closest distance to " O   HOH Z 303 " =    2.235
peak=    3.524 closest distance to " CB  SER A  62 " =    0.878
peak=    3.523 closest distance to " CA  ALA A 160 " =    1.048
peak=    3.522 closest distance to " CA  ALA A 295 " =    0.937
peak=    3.520 closest distance to " OG BSER A 212 " =    2.563
peak=    3.519 closest distance to " CE1 HIS A 108 " =    1.290
peak=    3.507 closest distance to " CD1 ILE A 199 " =    1.220
peak=    3.506 closest distance to " O   HOH Z 265 " =    1.994
peak=    3.504 closest distance to " O   HOH Z 357 " =    2.068
peak=    3.498 closest distance to " CB  PRO A 198 " =    1.159
peak=    3.494 closest distance to " CA  SER A  32 " =    1.794
peak=    3.494 closest distance to " CB  ALA A  71 " =    1.340
peak=    3.485 closest distance to " O   GLU A   2 " =    1.799
peak=    3.485 closest distance to " N   ASN A  39 " =    1.450
peak=    3.480 closest distance to " NH2 ARG A 156 " =    1.051
peak=    3.477 closest distance to " O   ASN A 284 " =    1.847
peak=    3.477 closest distance to " O   HOH Z  35 " =    2.074
peak=    3.471 closest distance to " O   HOH Z   1 " =    2.524
peak=    3.466 closest distance to " ND2 ASN A 249 " =    0.875
peak=    3.463 closest distance to " O  BHOH Z  74 " =    1.240
peak=    3.462 closest distance to " CD  ARG A 269 " =    1.136
peak=    3.461 closest distance to " CB  GLU A 277 " =    0.942
peak=    3.459 closest distance to " O   HOH Z 263 " =    1.834
peak=    3.454 closest distance to " OE1 GLU A   2 " =    1.962
peak=    3.454 closest distance to " O   HOH Z  83 " =    1.580
peak=    3.454 closest distance to " CA  VAL A  41 " =    0.743
peak=    3.448 closest distance to " CD1 LEU A   5 " =    1.692
peak=    3.448 closest distance to " CB  THR A  52 " =    0.909
peak=    3.446 closest distance to " O   HOH Z 193 " =    1.805
peak=    3.445 closest distance to " CA  ARG A 195 " =    1.199
peak=    3.445 closest distance to " O   HOH Z 126 " =    1.784
peak=    3.439 closest distance to " O   HOH Z  67 " =    1.989
peak=    3.436 closest distance to " O   HOH Z 207 " =    1.235
peak=    3.436 closest distance to " NE1 TRP A  92 " =    1.418
peak=    3.434 closest distance to " O   HOH Z 173 " =    2.366
peak=    3.433 closest distance to " CB  SER A 141 " =    1.066
peak=    3.432 closest distance to " O   HOH Z  78 " =    1.666
peak=    3.429 closest distance to " O   HOH Z 371 " =    1.347
peak=    3.426 closest distance to " NH2AARG A 145 " =    0.898
peak=    3.424 closest distance to " CB  ARG A 190 " =    1.854
peak=    3.424 closest distance to " CA  ASN A 217 " =    1.143
peak=    3.424 closest distance to " CA  TYR A 116 " =    1.437
peak=    3.419 closest distance to " O   HOH Z 189 " =    2.424
peak=    3.417 closest distance to " CB  TYR A  30 " =    1.093
peak=    3.417 closest distance to " NE2 GLN A  77 " =    3.330
peak=    3.416 closest distance to " CB  ASP A 191 " =    1.155
peak=    3.416 closest distance to " ND2 ASN A 187 " =    1.583
peak=    3.414 closest distance to " O   HOH Z   9 " =    2.375
peak=    3.411 closest distance to " O   HOH Z 199 " =    1.574
peak=    3.411 closest distance to " O   HOH Z 322 " =    2.209
peak=    3.408 closest distance to " CA  ALA A 158 " =    1.537
peak=    3.403 closest distance to " O   HOH Z 298 " =    2.421
peak=    3.403 closest distance to " CG  PHE A 204 " =    0.952
peak=    3.401 closest distance to " OE1 GLN A  11 " =    1.902
peak=    3.400 closest distance to " OG BSER A 212 " =    2.114
peak=    3.400 closest distance to " OG  SER A 135 " =    1.404
peak=    3.397 closest distance to " CD1 LEU A  96 " =    1.043
peak=    3.393 closest distance to " CG  ARG A  66 " =    1.065
peak=    3.392 closest distance to " O   HOH Z 313 " =    1.839
peak=    3.391 closest distance to " CA  ILE A 234 " =    0.969
peak=    3.390 closest distance to " CB  ALA A 248 " =    1.427
peak=    3.381 closest distance to " O  BHOH Z 338 " =    2.023
peak=    3.377 closest distance to " O   HOH Z 120 " =    2.626
peak=    3.376 closest distance to " CG2 THR A 221 " =    1.102
peak=    3.375 closest distance to " O   HOH Z  32 " =    2.291
peak=    3.369 closest distance to " O   HOH Z 132 " =    2.491
peak=    3.368 closest distance to " O   HOH Z   4 " =    1.830
peak=    3.364 closest distance to " CE1 TYR A 186 " =    1.204
peak=    3.362 closest distance to " O   HOH Z 427 " =    2.564
peak=    3.359 closest distance to " O   HOH Z 438 " =    2.100
peak=    3.349 closest distance to " CB  ALA A   9 " =    1.742
peak=    3.336 closest distance to " O   ASP A 200 " =    1.667
peak=    3.329 closest distance to " CG2 VAL A 197 " =    1.095
peak=    3.329 closest distance to " O   HOH Z 371 " =    2.637
peak=    3.326 closest distance to " O   HOH Z 162 " =    1.962
peak=    3.325 closest distance to " NH1 ARG A  14 " =    1.047
peak=    3.319 closest distance to " O   HOH Z 383 " =    1.898
peak=    3.318 closest distance to " CG  PRO A 213 " =    1.289
peak=    3.316 closest distance to " CB  ALA A 114 " =    0.750
peak=    3.310 closest distance to " CG2 ILE A 120 " =    1.596
peak=    3.310 closest distance to " CB  TYR A 169 " =    0.875
peak=    3.308 closest distance to " CB  SER A  99 " =    1.236
peak=    3.307 closest distance to " CB  THR A 235 " =    1.363
peak=    3.305 closest distance to " CD2 LEU A  83 " =    1.541
peak=    3.297 closest distance to " OG BSER A 164 " =    2.282
peak=    3.296 closest distance to " O   HOH Z 339 " =    1.363
peak=    3.294 closest distance to " CB  SER A  62 " =    1.085
peak=    3.291 closest distance to " O   HOH Z 365 " =    2.547
peak=    3.290 closest distance to " O   HOH Z 250 " =    1.282
peak=    3.286 closest distance to " ND2 ASN A 252 " =    1.696
peak=    3.285 closest distance to " O   HOH Z 387 " =    2.003
peak=    3.281 closest distance to " CB  ARG A  79 " =    0.883
peak=    3.280 closest distance to " CA  ASP A 149 " =    1.147
peak=    3.280 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.274 closest distance to " CA  THR A 246 " =    1.036
peak=    3.273 closest distance to " O   HOH Z 345 " =    1.722
peak=    3.271 closest distance to " O   LEU A 228 " =    1.569
peak=    3.269 closest distance to " CB  ASN A 215 " =    1.110
peak=    3.259 closest distance to " O   HOH Z 285 " =    2.007
peak=    3.255 closest distance to " O   HOH Z 209 " =    2.776
peak=    3.254 closest distance to " CB  ARG A 156 " =    1.091
peak=    3.251 closest distance to " O   HOH Z 366 " =    2.384
peak=    3.251 closest distance to " O   HOH Z 385 " =    3.750
peak=    3.250 closest distance to " SD  MET A 185 " =    1.422
peak=    3.250 closest distance to " CA  ALA A 100 " =    0.937
peak=    3.247 closest distance to " CB  VAL A 265 " =    1.241
peak=    3.247 closest distance to " CB  ASP A 140 " =    1.025
peak=    3.245 closest distance to " CA  THR A  82 " =    1.562
peak=    3.245 closest distance to " O   HOH Z  46 " =    1.422
peak=    3.243 closest distance to " O   HOH Z 428 " =    3.749
peak=    3.242 closest distance to " O   HOH Z 412 " =    3.536
peak=    3.242 closest distance to " CD2 TYR A 186 " =    1.067
peak=    3.241 closest distance to " CB  ASN A 187 " =    1.359
peak=    3.241 closest distance to " O   HOH Z  40 " =    2.366
peak=    3.240 closest distance to " O   HOH Z 350 " =    1.518
peak=    3.239 closest distance to " CB  VAL A 202 " =    1.384
peak=    3.237 closest distance to " CB  ASN A 110 " =    1.098
peak=    3.233 closest distance to " O   HOH Z   9 " =    2.283
peak=    3.232 closest distance to " CB  LEU A   5 " =    1.359
peak=    3.227 closest distance to " CG1 ILE A  49 " =    1.520
peak=    3.227 closest distance to " O   HOH Z  21 " =    1.907
peak=    3.226 closest distance to " CB  ASP A 124 " =    0.777
peak=    3.224 closest distance to " O   HOH Z 111 " =    1.472
peak=    3.223 closest distance to " O   HOH Z 279 " =    2.136
peak=    3.223 closest distance to " O   HOH Z 154 " =    2.227
peak=    3.221 closest distance to " OD1 ASP A 231 " =    1.973
peak=    3.219 closest distance to " CB  SER A 288 " =    1.487
peak=    3.218 closest distance to " CA  SER A  87 " =    0.950
peak=    3.215 closest distance to " OG  SER A  62 " =    2.674
peak=    3.214 closest distance to " O   HOH Z 298 " =    1.772
peak=    3.212 closest distance to " CB  PRO A 243 " =    1.075
peak=    3.211 closest distance to " NH2 ARG A  36 " =    1.861
peak=    3.209 closest distance to " CZ  PHE A  38 " =    1.078
peak=    3.208 closest distance to " CE2 TYR A 169 " =    1.353
peak=    3.205 closest distance to " CE  LYS A 119 " =    1.032
peak=    3.201 closest distance to " O   HOH Z 197 " =    1.979
peak=    3.197 closest distance to " O   HOH Z 148 " =    3.360
peak=    3.196 closest distance to " O   HOH Z 325 " =    2.152
peak=    3.185 closest distance to " CB  ASP A 107 " =    1.244
peak=    3.184 closest distance to " O   ALA A 292 " =    1.158
peak=    3.184 closest distance to " CG  LEU A 167 " =    1.146
peak=    3.184 closest distance to " CB  GLU A  46 " =    1.026
peak=    3.182 closest distance to " CB  GLN A  89 " =    1.312
peak=    3.181 closest distance to " O   HOH Z 388 " =    2.342
peak=    3.180 closest distance to " O   HOH Z  54 " =    1.636
peak=    3.180 closest distance to " O   HOH Z 245 " =    1.471
peak=    3.179 closest distance to " O   HOH Z 175 " =    3.703
peak=    3.178 closest distance to " CB  ASN A  39 " =    0.716
peak=    3.175 closest distance to " CB  ARG A 219 " =    1.162
peak=    3.169 closest distance to " O   HOH Z 129 " =    1.176
peak=    3.168 closest distance to " CZ2 TRP A 150 " =    1.069
peak=    3.165 closest distance to " CE1 TYR A  30 " =    1.149
peak=    3.163 closest distance to " CA  ALA A 129 " =    1.337
peak=    3.160 closest distance to " O   HOH Z  63 " =    1.974
peak=    3.158 closest distance to " CA  SER A  12 " =    1.378
peak=    3.155 closest distance to " CA  ARG A 139 " =    1.223
peak=    3.155 closest distance to " O   HOH Z  44 " =    2.791
peak=    3.153 closest distance to " OG  SER A  62 " =    3.770
peak=    3.152 closest distance to " O   HOH Z 172 " =    3.659
peak=    3.151 closest distance to " O   HOH Z  13 " =    1.634
peak=    3.150 closest distance to " O   HOH Z 368 " =    3.427
peak=    3.150 closest distance to " CB  PRO A  90 " =    1.187
peak=    3.140 closest distance to " O   HOH Z  99 " =    1.793
peak=    3.139 closest distance to " CG1 VAL A 153 " =    0.988
peak=    3.139 closest distance to " N   ASP A 162 " =    1.313
peak=    3.138 closest distance to " CG2 ILE A  20 " =    1.325
peak=    3.138 closest distance to " N   CYS A 260 " =    0.732
peak=    3.133 closest distance to " CD  ARG A 139 " =    1.341
peak=    3.129 closest distance to " CB  ASN A 209 " =    0.925
peak=    3.128 closest distance to " O   HOH Z 256 " =    2.400
peak=    3.125 closest distance to " O   HOH Z 390 " =    2.498
peak=    3.120 closest distance to " O   HOH Z  59 " =    1.893
peak=    3.114 closest distance to " O   HOH Z  28 " =    1.695
peak=    3.113 closest distance to " O   HOH Z 200 " =    2.827
peak=    3.110 closest distance to " N   GLN A 194 " =    1.535
peak=    3.109 closest distance to " O   HOH Z 423 " =    3.085
peak=    3.107 closest distance to " O   HOH Z  88 " =    3.328
peak=    3.102 closest distance to " O   HOH Z 213 " =    2.255
peak=    3.096 closest distance to " O   HOH Z 132 " =    1.025
peak=    3.094 closest distance to " O   GLN A  88 " =    1.454
peak=    3.087 closest distance to " O   HOH Z  11 " =    1.370
peak=    3.078 closest distance to " CB  ALA A 295 " =    1.287
peak=    3.078 closest distance to " CE2 TYR A 169 " =    2.014
peak=    3.075 closest distance to " NE AARG A 145 " =    0.747
peak=    3.061 closest distance to " CA  GLU A 152 " =    0.876
peak=    3.060 closest distance to " O   HOH Z   1 " =    3.229
peak=    3.057 closest distance to " CB  SER A  32 " =    1.264

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.561 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 213
   mapped sites are within: 0.704 - 5.939

peak=   -4.714 closest distance to " O   HOH Z 203 " =    0.795
peak=   -4.648 closest distance to " O   HOH Z 193 " =    0.878
peak=   -4.366 closest distance to " CG2BVAL A  41 " =    2.632
peak=   -4.353 closest distance to " CD2 LEU A 237 " =    2.746
peak=   -4.310 closest distance to " CG  GLN A  58 " =    0.855
peak=   -4.294 closest distance to " CD  ARG A 156 " =    1.976
peak=   -4.195 closest distance to " CD2 TYR A 293 " =    1.942
peak=   -4.171 closest distance to " O   GLY A 241 " =    2.390
peak=   -4.169 closest distance to " O   HOH Z 423 " =    2.593
peak=   -4.101 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -4.054 closest distance to " OG BSER A 134 " =    1.352
peak=   -4.029 closest distance to " CG1 VAL A 296 " =    1.028
peak=   -4.024 closest distance to " O   PRO A 198 " =    1.287
peak=   -4.021 closest distance to " CD  ARG A  14 " =    3.148
peak=   -3.932 closest distance to " CB  ALA A 248 " =    2.222
peak=   -3.916 closest distance to " O   HOH Z 210 " =    0.862
peak=   -3.914 closest distance to " CG  MET A  93 " =    2.451
peak=   -3.913 closest distance to " O   HOH Z 116 " =    1.053
peak=   -3.905 closest distance to " O   HOH Z 351 " =    1.707
peak=   -3.877 closest distance to " O   HOH Z 411 " =    5.711
peak=   -3.859 closest distance to " O   HOH Z 166 " =    1.578
peak=   -3.845 closest distance to " CD1 PHE A  59 " =    2.079
peak=   -3.817 closest distance to " O   HOH Z 216 " =    1.234
peak=   -3.810 closest distance to " O   PRO A 163 " =    2.121
peak=   -3.772 closest distance to " O   HOH Z 221 " =    1.046
peak=   -3.764 closest distance to " O   HOH Z 286 " =    1.924
peak=   -3.752 closest distance to " O   HOH Z 119 " =    2.007
peak=   -3.740 closest distance to " OG  SER A  97 " =    2.416
peak=   -3.726 closest distance to " O   GLY A  80 " =    2.643
peak=   -3.710 closest distance to " CH2 TRP A 179 " =    1.244
peak=   -3.710 closest distance to " O   HOH Z 131 " =    4.207
peak=   -3.708 closest distance to " O   TRP A  92 " =    2.135
peak=   -3.701 closest distance to " CB  PHE A 208 " =    2.301
peak=   -3.697 closest distance to " CG  GLN A 103 " =    2.459
peak=   -3.681 closest distance to " OXT GLY A 302 " =    2.925
peak=   -3.678 closest distance to " CA  VAL A  67 " =    2.899
peak=   -3.676 closest distance to " O   HOH Z 166 " =    1.688
peak=   -3.669 closest distance to " OH  TYR A 172 " =    1.831
peak=   -3.666 closest distance to " NE2 GLN A  88 " =    1.079
peak=   -3.665 closest distance to " O   HOH Z 109 " =    0.714
peak=   -3.649 closest distance to " C   HIS A 108 " =    1.128
peak=   -3.648 closest distance to " O   HOH Z 266 " =    1.505
peak=   -3.638 closest distance to " O   HOH Z 111 " =    1.651
peak=   -3.628 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.620 closest distance to " C   THR A 279 " =    1.098
peak=   -3.619 closest distance to " O   HOH Z 179 " =    2.229
peak=   -3.614 closest distance to " CB  ALA A 129 " =    2.389
peak=   -3.612 closest distance to " O   HOH Z 345 " =    2.857
peak=   -3.608 closest distance to " CB  ALA A  51 " =    1.895
peak=   -3.607 closest distance to " CB  ALA A  43 " =    2.521
peak=   -3.604 closest distance to " CZ  PHE A  38 " =    2.366
peak=   -3.586 closest distance to " O  BHOH Z 338 " =    1.156
peak=   -3.580 closest distance to " O   HOH Z  28 " =    2.428
peak=   -3.562 closest distance to " O   HOH Z 340 " =    1.817
peak=   -3.560 closest distance to " CG1 VAL A 112 " =    2.547
peak=   -3.556 closest distance to " O   HOH Z 312 " =    1.661
peak=   -3.547 closest distance to " NE2 GLN A  11 " =    1.594
peak=   -3.541 closest distance to " O   HOH Z 423 " =    3.973
peak=   -3.538 closest distance to " ND2 ASN A  69 " =    1.984
peak=   -3.531 closest distance to " CE3 TRP A 150 " =    2.285
peak=   -3.527 closest distance to " CE BMET A  47 " =    1.285
peak=   -3.523 closest distance to " O   HOH Z 372 " =    0.882
peak=   -3.522 closest distance to " SG  CYS A 260 " =    2.090
peak=   -3.522 closest distance to " O   HOH Z 151 " =    0.973
peak=   -3.515 closest distance to " O   ALA A 256 " =    1.794
peak=   -3.514 closest distance to " O   HOH Z 285 " =    1.878
peak=   -3.513 closest distance to " O   HOH Z 246 " =    0.895
peak=   -3.510 closest distance to " CH2 TRP A 150 " =    1.068
peak=   -3.506 closest distance to " CD1 PHE A  59 " =    2.073
peak=   -3.502 closest distance to " O   HOH Z 250 " =    1.977
peak=   -3.500 closest distance to " O   HOH Z 407 " =    2.700
peak=   -3.492 closest distance to " O   HOH Z 174 " =    3.623
peak=   -3.492 closest distance to " O   HOH Z 165 " =    1.918
peak=   -3.486 closest distance to " O   ALA A 227 " =    1.291
peak=   -3.486 closest distance to " CG  MET A 105 " =    0.937
peak=   -3.473 closest distance to " O   HOH Z 269 " =    1.177
peak=   -3.473 closest distance to " CZ2 TRP A  92 " =    2.786
peak=   -3.472 closest distance to " O   HOH Z 388 " =    2.110
peak=   -3.465 closest distance to " O   VAL A 174 " =    2.161
peak=   -3.462 closest distance to " N   SER A 276 " =    1.443
peak=   -3.458 closest distance to " O   HOH Z 150 " =    1.987
peak=   -3.451 closest distance to " ND2BASN A 224 " =    1.873
peak=   -3.451 closest distance to " C   ILE A 239 " =    2.144
peak=   -3.449 closest distance to " OE1 GLN A 223 " =    2.394
peak=   -3.448 closest distance to " OG1 THR A  52 " =    2.544
peak=   -3.447 closest distance to " CB  SER A 210 " =    1.180
peak=   -3.444 closest distance to " O   HOH Z 433 " =    0.874
peak=   -3.444 closest distance to " CE1 TYR A 247 " =    2.584
peak=   -3.440 closest distance to " CD2 LEU A 167 " =    1.731
peak=   -3.431 closest distance to " O   HOH Z 214 " =    2.586
peak=   -3.428 closest distance to " O   HOH Z 290 " =    0.818
peak=   -3.426 closest distance to " CB  ALA A   9 " =    2.408
peak=   -3.426 closest distance to " O   HOH Z 387 " =    2.737
peak=   -3.423 closest distance to " O   HOH Z   6 " =    1.941
peak=   -3.422 closest distance to " O   HOH Z 297 " =    2.747
peak=   -3.422 closest distance to " O   HOH Z 214 " =    0.948
peak=   -3.419 closest distance to " O   SER A 273 " =    1.099
peak=   -3.406 closest distance to " CG  PRO A 243 " =    1.670
peak=   -3.403 closest distance to " CG2 VAL A 296 " =    1.172
peak=   -3.384 closest distance to " O   HOH Z  92 " =    1.652
peak=   -3.380 closest distance to " O   ARG A 219 " =    1.782
peak=   -3.373 closest distance to " CG  LEU A   5 " =    0.918
peak=   -3.359 closest distance to " O   HOH Z 329 " =    0.704
peak=   -3.349 closest distance to " CG1 VAL A  78 " =    2.412
peak=   -3.347 closest distance to " CG2 VAL A 189 " =    1.959
peak=   -3.341 closest distance to " CE  LYS A  76 " =    2.527
peak=   -3.341 closest distance to " O   GLY A  80 " =    2.622
peak=   -3.338 closest distance to " O   HOH Z 219 " =    2.253
peak=   -3.334 closest distance to " CD  ARG A 139 " =    0.976
peak=   -3.329 closest distance to " O   HOH Z  63 " =    1.172
peak=   -3.319 closest distance to " O   HOH Z  30 " =    1.760
peak=   -3.312 closest distance to " O   ASP A 107 " =    2.044
peak=   -3.307 closest distance to " O   HOH Z 205 " =    0.874
peak=   -3.304 closest distance to " CB  ALA A 161 " =    2.393
peak=   -3.303 closest distance to " O   HOH Z 191 " =    5.731
peak=   -3.296 closest distance to " O   SER A  95 " =    1.639
peak=   -3.292 closest distance to " CG  ARG A 269 " =    2.185
peak=   -3.285 closest distance to " O   HOH Z 177 " =    1.438
peak=   -3.284 closest distance to " O   HOH Z  10 " =    1.456
peak=   -3.283 closest distance to " CE1 PHE A 218 " =    1.461
peak=   -3.282 closest distance to " O   HOH Z  65 " =    0.788
peak=   -3.276 closest distance to " CB  ASP A 132 " =    2.347
peak=   -3.272 closest distance to " OG  SER A  63 " =    1.195
peak=   -3.272 closest distance to " CG2AVAL A  72 " =    2.554
peak=   -3.271 closest distance to " CD  LYS A 289 " =    2.379
peak=   -3.267 closest distance to " ND2 ASN A 209 " =    2.528
peak=   -3.267 closest distance to " CA  ALA A 114 " =    0.962
peak=   -3.265 closest distance to " O   HOH Z 136 " =    1.535
peak=   -3.265 closest distance to " O   HOH Z 164 " =    5.939
peak=   -3.263 closest distance to " NH2 ARG A  79 " =    1.608
peak=   -3.258 closest distance to " CZ  PHE A  38 " =    2.058
peak=   -3.258 closest distance to " O   GLY A  75 " =    2.003
peak=   -3.255 closest distance to " CG2 THR A 221 " =    2.334
peak=   -3.254 closest distance to " N   ALA A 226 " =    1.892
peak=   -3.253 closest distance to " NE1 TRP A 266 " =    2.491
peak=   -3.250 closest distance to " O   HOH Z 145 " =    2.795
peak=   -3.246 closest distance to " O   HOH Z 154 " =    1.306
peak=   -3.244 closest distance to " CG  HIS A 115 " =    1.078
peak=   -3.238 closest distance to " O   HOH Z 359 " =    2.750
peak=   -3.233 closest distance to " CZ  ARG A  66 " =    1.089
peak=   -3.229 closest distance to " O   HOH Z 403 " =    1.208
peak=   -3.225 closest distance to " CB  ALA A 248 " =    2.109
peak=   -3.224 closest distance to " CA  GLY A  57 " =    2.033
peak=   -3.211 closest distance to " OH  TYR A 169 " =    0.868
peak=   -3.211 closest distance to " O   HOH Z 180 " =    2.360
peak=   -3.210 closest distance to " O   HOH Z 431 " =    2.247
peak=   -3.209 closest distance to " ND2 ASN A 249 " =    2.220
peak=   -3.208 closest distance to " O   HOH Z 313 " =    1.079
peak=   -3.207 closest distance to " C   VAL A 265 " =    0.882
peak=   -3.203 closest distance to " O   PHE A 218 " =    1.407
peak=   -3.201 closest distance to " CG  LEU A  83 " =    2.089
peak=   -3.200 closest distance to " O   HOH Z  58 " =    0.978
peak=   -3.199 closest distance to " O   ILE A 106 " =    1.656
peak=   -3.197 closest distance to " CZ  TYR A 169 " =    1.701
peak=   -3.197 closest distance to " CB  ASP A 286 " =    1.696
peak=   -3.196 closest distance to " OD2 ASP A 191 " =    1.658
peak=   -3.196 closest distance to " O   HOH Z 137 " =    1.610
peak=   -3.195 closest distance to " O   HOH Z 110 " =    1.426
peak=   -3.192 closest distance to " O   HOH Z 107 " =    1.038
peak=   -3.182 closest distance to " N   SER A   3 " =    2.266
peak=   -3.182 closest distance to " CD1 TYR A 169 " =    2.118
peak=   -3.178 closest distance to " CD2 TYR A 172 " =    2.136
peak=   -3.175 closest distance to " OD2 ASP A 272 " =    1.303
peak=   -3.173 closest distance to " CB  HIS A  86 " =    1.226
peak=   -3.171 closest distance to " CG  GLU A 277 " =    1.333
peak=   -3.168 closest distance to " O   HOH Z 421 " =    2.687
peak=   -3.166 closest distance to " O   SER A 206 " =    1.460
peak=   -3.164 closest distance to " CE  MET A 105 " =    2.218
peak=   -3.160 closest distance to " CD  PRO A 243 " =    1.748
peak=   -3.159 closest distance to " O   GLY A 196 " =    1.020
peak=   -3.159 closest distance to " NE  ARG A 259 " =    1.391
peak=   -3.154 closest distance to " CZ  PHE A 155 " =    1.014
peak=   -3.154 closest distance to " O   HOH Z 265 " =    1.424
peak=   -3.144 closest distance to " CB  ALA A  10 " =    2.238
peak=   -3.144 closest distance to " NE2 GLN A  88 " =    1.638
peak=   -3.140 closest distance to " OG1 THR A  82 " =    1.331
peak=   -3.137 closest distance to " OD2 ASP A  50 " =    1.513
peak=   -3.132 closest distance to " O   HOH Z 390 " =    1.425
peak=   -3.131 closest distance to " CG  ASP A 298 " =    0.907
peak=   -3.129 closest distance to " O   GLN A  77 " =    1.781
peak=   -3.125 closest distance to " O   HOH Z 196 " =    2.018
peak=   -3.122 closest distance to " O   HOH Z 183 " =    1.739
peak=   -3.116 closest distance to " O   HOH Z 139 " =    5.232
peak=   -3.115 closest distance to " OG1 THR A 246 " =    1.725
peak=   -3.114 closest distance to " O   SER A 210 " =    1.794
peak=   -3.111 closest distance to " CA  TRP A 274 " =    1.123
peak=   -3.110 closest distance to " ND2 ASN A 173 " =    1.226
peak=   -3.108 closest distance to " OD1 ASN A  39 " =    1.288
peak=   -3.101 closest distance to " OD2 ASP A 298 " =    1.958
peak=   -3.100 closest distance to " O   HOH Z 283 " =    2.508
peak=   -3.097 closest distance to " O   HOH Z 392 " =    3.663
peak=   -3.096 closest distance to " O   HOH Z 423 " =    2.351
peak=   -3.096 closest distance to " OH  TYR A 247 " =    2.045
peak=   -3.092 closest distance to " O   HOH Z 252 " =    3.616
peak=   -3.092 closest distance to " O   HOH Z 422 " =    1.524
peak=   -3.086 closest distance to " O   HOH Z 313 " =    2.117
peak=   -3.082 closest distance to " O   HOH Z 435 " =    2.548
peak=   -3.081 closest distance to " O   HOH Z 185 " =    2.469
peak=   -3.070 closest distance to " O   HOH Z  73 " =    0.731
peak=   -3.069 closest distance to " O   HOH Z 171 " =    2.460
peak=   -3.064 closest distance to " O   HOH Z 100 " =    0.899
peak=   -3.054 closest distance to " O   HOH Z 199 " =    2.530
peak=   -3.038 closest distance to " CE3 TRP A  70 " =    1.597
peak=   -3.036 closest distance to " NE2 GLN A 194 " =    1.917
peak=   -3.036 closest distance to " CG  ASN A 252 " =    1.457
peak=   -3.034 closest distance to " CD  GLN A  88 " =    0.893
peak=   -3.033 closest distance to " O   HOH Z  44 " =    2.161
peak=   -3.027 closest distance to " O   HOH Z  78 " =    1.981

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.5160 0.5105   6.309061e+00   6.307096e+00
   1_bss:  0.5086 0.5070   6.303740e+00   6.306717e+00
   1_xyz:  0.4452 0.4723   6.239624e+00   6.273958e+00
   1_adp:  0.4040 0.4695   6.194287e+00   6.264405e+00
   1_occ:  0.4037 0.4698   6.193874e+00   6.265118e+00
   2_bss:  0.4014 0.4646   6.194682e+00   6.264868e+00
   2_xyz:  0.3288 0.3905   6.044981e+00   6.167575e+00
   2_adp:  0.3078 0.3720   6.000876e+00   6.134239e+00
   2_occ:  0.3077 0.3721   6.000520e+00   6.134206e+00
   3_bss:  0.3049 0.3702   6.000354e+00   6.133694e+00
   3_xyz:  0.2217 0.2756   5.725889e+00   5.909808e+00
   3_adp:  0.1964 0.2512   5.621503e+00   5.817289e+00
   3_occ:  0.1962 0.2514   5.620265e+00   5.816244e+00
   4_bss:  0.1942 0.2499   5.618846e+00   5.814330e+00
   4_xyz:  0.1540 0.1983   5.411500e+00   5.609105e+00
   4_adp:  0.1422 0.1908   5.355209e+00   5.569097e+00
   4_occ:  0.1420 0.1910   5.354810e+00   5.569324e+00
   5_bss:  0.1423 0.1915   5.354424e+00   5.568762e+00
   5_xyz:  0.1275 0.1770   5.266554e+00   5.497229e+00
   5_adp:  0.1262 0.1712   5.247973e+00   5.467306e+00
   5_occ:  0.1260 0.1710   5.247025e+00   5.466460e+00
   5_bss:  0.1260 0.1710   5.246965e+00   5.466353e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.316   1.306   7.512   9.651  10.475   0.000   0.000   0.000
   1_xyz:  0.316   1.306   7.512   9.651  10.475   0.000   0.000   0.000
   1_adp:  0.316   1.306   7.512   9.651  10.475   0.000   0.000   0.000
   1_occ:  0.316   1.306   7.512   9.651  10.475   0.000   0.000   0.000
   2_bss:  0.342  50.001   3.625   5.573   6.498   0.000   0.000   0.000
   2_xyz:  0.342  50.001   3.625   5.573   6.498   0.000   0.000   0.000
   2_adp:  0.342  50.001   3.625   5.573   6.498   0.000   0.000   0.000
   2_occ:  0.342  50.001   3.625   5.573   6.498   0.000   0.000   0.000
   3_bss:  0.328  50.001   1.174   3.086   3.836   0.000   0.000   0.000
   3_xyz:  0.328  50.001   1.174   3.086   3.836   0.000   0.000   0.000
   3_adp:  0.328  50.001   1.174   3.086   3.836   0.000   0.000   0.000
   3_occ:  0.328  50.001   1.174   3.086   3.836   0.000   0.000   0.000
   4_bss:  0.327  50.001  -0.513   1.207   2.160   0.000   0.000   0.000
   4_xyz:  0.327  50.001  -0.513   1.207   2.160   0.000   0.000   0.000
   4_adp:  0.327  50.001  -0.513   1.207   2.160   0.000   0.000   0.000
   4_occ:  0.327  50.001  -0.513   1.207   2.160   0.000   0.000   0.000
   5_bss:  0.328  59.023  -0.926   0.641   1.790   0.000   0.000   0.000
   5_xyz:  0.328  59.023  -0.926   0.641   1.790   0.000   0.000   0.000
   5_adp:  0.328  59.023  -0.926   0.641   1.790   0.000   0.000   0.000
   5_occ:  0.328  59.023  -0.926   0.641   1.790   0.000   0.000   0.000
   5_bss:  0.325  53.781  -1.386   0.075   1.311   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.460 0.3228  0.3876    85640.719
   1_bss:  66.729 0.3049  0.4681    85902.913
   1_xyz:  58.442 0.4117  0.6304    70248.791
   1_adp:  55.158 0.4544  0.7722    66725.044
   1_occ:  55.210 0.4537  0.7699    66793.173
   2_bss:  54.594 0.4617  0.6917    66257.793
   2_xyz:  43.962 0.5941  0.8738    45186.398
   2_adp:  41.132 0.6289  0.9215    40602.327
   2_occ:  41.107 0.6292  0.9216    40574.451
   3_bss:  40.939 0.6312  0.8453    40421.277
   3_xyz:  28.961 0.7680  0.9830    20779.157
   3_adp:  25.207 0.8092  1.0095    16846.714
   3_occ:  25.144 0.8099  1.0099    16787.744
   4_bss:  25.013 0.8112  0.9504    16660.190
   4_xyz:  19.209 0.8693  0.9811    10396.755
   4_adp:  18.259 0.8784  0.9805     9675.875
   4_occ:  18.267 0.8783  0.9803     9684.029
   5_bss:  18.239 0.8785  0.9653     9677.475
   5_xyz:  16.636 0.8927  0.9741     8251.771
   5_adp:  15.958 0.8989  0.9763     7840.920
   5_occ:  15.938 0.8991  0.9763     7826.862
   5_bss:  15.937 0.8991  0.9717     7821.502
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3733e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3733e+01
   1_xyz:   1.859  0.015  0.113 18.589  0.007  4.107   1.6980e-01
   1_adp:   1.859  0.015  0.113 18.589  0.007  4.107   1.6980e-01
   1_occ:   1.859  0.015  0.113 18.589  0.007  4.107   1.6980e-01
   2_bss:   1.859  0.015  0.113 18.589  0.007  4.107   1.6980e-01
   2_xyz:   1.354  0.010  0.082 16.768  0.006  4.105   1.0422e-01
   2_adp:   1.354  0.010  0.082 16.768  0.006  4.105   1.0422e-01
   2_occ:   1.354  0.010  0.082 16.768  0.006  4.105   1.0422e-01
   3_bss:   1.354  0.010  0.082 16.768  0.006  4.105   1.0422e-01
   3_xyz:   1.303  0.009  0.089 16.453  0.005  4.110   9.7329e-02
   3_adp:   1.303  0.009  0.089 16.453  0.005  4.110   9.7329e-02
   3_occ:   1.303  0.009  0.089 16.453  0.005  4.110   9.7329e-02
   4_bss:   1.303  0.009  0.089 16.453  0.005  4.110   9.7329e-02
   4_xyz:   1.063  0.008  0.077 15.550  0.004  4.127   6.8757e-02
   4_adp:   1.063  0.008  0.077 15.550  0.004  4.127   6.8757e-02
   4_occ:   1.063  0.008  0.077 15.550  0.004  4.127   6.8757e-02
   5_bss:   1.063  0.008  0.077 15.550  0.004  4.127   6.8757e-02
   5_xyz:   1.146  0.009  0.086 15.580  0.004  4.112   7.4289e-02
   5_adp:   1.146  0.009  0.086 15.580  0.004  4.112   7.4289e-02
   5_occ:   1.146  0.009  0.086 15.580  0.004  4.112   7.4289e-02
   5_bss:   1.146  0.009  0.086 15.580  0.004  4.112   7.4289e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.738   6.9548e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.738   6.9548e+00
   1_xyz:  17.001  0.185  0.549 86.630  0.046  2.062   1.1378e-01
   1_adp:  17.001  0.185  0.549 86.630  0.046  2.062   1.1378e-01
   1_occ:  17.001  0.185  0.549 86.630  0.046  2.062   1.1378e-01
   2_bss:  17.001  0.185  0.549 86.630  0.046  2.062   1.1378e-01
   2_xyz:   9.175  0.113  0.259 85.571  0.048  2.072   7.8886e-02
   2_adp:   9.175  0.113  0.259 85.571  0.048  2.072   7.8886e-02
   2_occ:   9.175  0.113  0.259 85.571  0.048  2.072   7.8886e-02
   3_bss:   9.175  0.113  0.259 85.571  0.048  2.072   7.8886e-02
   3_xyz:   7.967  0.066  0.343 87.478  0.044  2.141   7.7710e-02
   3_adp:   7.967  0.066  0.343 87.478  0.044  2.141   7.7710e-02
   3_occ:   7.967  0.066  0.343 87.478  0.044  2.141   7.7710e-02
   4_bss:   7.967  0.066  0.343 87.478  0.044  2.141   7.7710e-02
   4_xyz:   7.483  0.041  0.242 87.951  0.048  2.211   9.2404e-02
   4_adp:   7.483  0.041  0.242 87.951  0.048  2.211   9.2404e-02
   4_occ:   7.483  0.041  0.242 87.951  0.048  2.211   9.2404e-02
   5_bss:   7.483  0.041  0.242 87.951  0.048  2.211   9.2404e-02
   5_xyz:   7.861  0.050  0.425 89.659  0.041  2.226   4.7592e-02
   5_adp:   7.861  0.050  0.425 89.659  0.041  2.226   4.7592e-02
   5_occ:   7.861  0.050  0.425 89.659  0.041  2.226   4.7592e-02
   5_bss:   7.861  0.050  0.425 89.659  0.041  2.226   4.7592e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  91.87   0.00  16.51  84.30   0.00  14.67  91.87   0.00  26.51
   1_occ:  91.87   0.00  16.51  84.30   0.00  14.67  91.87   0.00  26.51
   2_bss:  91.87   0.00  16.51  84.30   0.00  14.67  91.87   0.00  26.51
   2_xyz:  91.87   0.00  16.51  84.30   0.00  14.67  91.87   0.00  26.51
   2_adp:  99.10   0.00  15.87  85.53   0.00  13.01  99.10   0.00  31.43
   2_occ:  99.10   0.00  15.87  85.53   0.00  13.01  99.10   0.00  31.43
   3_bss:  99.10   0.00  15.87  85.53   0.00  13.01  99.10   0.00  31.43
   3_xyz:  99.10   0.00  15.87  85.53   0.00  13.01  99.10   0.00  31.43
   3_adp:  87.51   0.00  15.09  80.87   0.00  11.22  87.51   2.86  36.13
   3_occ:  87.51   0.00  15.09  80.87   0.00  11.22  87.51   2.86  36.13
   4_bss:  87.51   0.00  15.09  80.87   0.00  11.22  87.51   2.86  36.13
   4_xyz:  87.51   0.00  15.09  80.87   0.00  11.22  87.51   2.86  36.13
   4_adp:  90.70   0.00  15.75  90.70   0.00  10.98  85.15   3.11  41.74
   4_occ:  90.70   0.00  15.75  90.70   0.00  10.98  85.15   3.11  41.74
   5_bss:  90.70   0.00  15.75  90.70   0.00  10.98  85.15   3.11  41.74
   5_xyz:  90.70   0.00  15.75  90.70   0.00  10.98  85.15   3.11  41.74
   5_adp:  89.70   0.69  15.22  89.70   0.69  10.76  86.45   3.75  39.54
   5_occ:  89.70   0.69  15.22  89.70   0.69  10.76  86.45   3.75  39.54
   5_bss:  90.06   1.05  15.59  90.06   1.05  11.12  86.81   4.12  39.90
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.327    0.008    0.424
   1_adp:    1.327    0.008    0.424
   1_occ:    1.327    0.008    0.424
   2_bss:    1.327    0.008    0.424
   2_xyz:    2.045    0.039    0.610
   2_adp:    2.045    0.039    0.610
   2_occ:    2.045    0.039    0.610
   3_bss:    2.045    0.039    0.610
   3_xyz:    1.972    0.057    0.782
   3_adp:    1.972    0.057    0.782
   3_occ:    1.972    0.057    0.782
   4_bss:    1.972    0.057    0.782
   4_xyz:    2.146    0.030    0.848
   4_adp:    2.146    0.030    0.848
   4_occ:    2.146    0.030    0.848
   5_bss:    2.146    0.030    0.848
   5_xyz:    2.156    0.034    0.874
   5_adp:    2.156    0.034    0.874
   5_occ:    2.156    0.034    0.874
   5_bss:    2.156    0.034    0.874
------------------------------------------------------------------------

CPU time actual refinement: 344.70


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_97/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 344.54 
  Macro-tasks:
    bulk solvent and scale       = 40.37  
    individual site refinement   = 141.75 
    weights calculation          = 31.83  
    collect and process          = 6.38   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.45 
  Micro-tasks:
    mask                            = 2.51   
    f_calc                          = 108.86 
    alpha_beta                      = 8.31   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 118.08 
    fmodel                         = 7.33   
    r_factors                      = 0.16   
    phase_errors                   = 10.20  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 256.90 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.859 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    651 calls, 108.52 s
gradients_fft:          595 calls, 104.88 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 00:45:26 PST -0800 (1200473126.74 s)
Start R-work = 0.5160, R-free = 0.5105 (no bulk solvent and anisotropic scale)
Final R-work = 0.1443, R-free = 0.1861 (no bulk solvent and anisotropic scale)

Start R-work = 0.5086, R-free = 0.5070
Final R-work = 0.1260, R-free = 0.1710