# Date 2008-01-16 Time 03:09:12 PST -0800 (1200481752.36 s)
#phil __OFF__

Command line arguments: "../1126.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28011
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1126

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 85.9581, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (71.655, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.98157
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.9518

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9816

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: (71.655, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.98157
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.9518

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2411 [2148/2174]  1937   211   9.8%
  bin  2:  4.2411 -  3.3785 [2078/2098]  1866   212  10.2%
  bin  3:  3.3785 -  2.9550 [2043/2062]  1838   205  10.0%
  bin  4:  2.9550 -  2.6864 [2016/2046]  1818   198   9.8%
  bin  5:  2.6864 -  2.4948 [2029/2048]  1829   200   9.9%
  bin  6:  2.4948 -  2.3483 [2002/2027]  1791   211  10.5%
  bin  7:  2.3483 -  2.2310 [1987/2015]  1794   193   9.7%
  bin  8:  2.2310 -  2.1342 [1978/2014]  1779   199  10.1%
  bin  9:  2.1342 -  2.0522 [1980/2022]  1783   197   9.9%
  bin 10:  2.0522 -  1.9816 [1328/2014]  1195   133  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1126/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: 0.15 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:
        1.81 -     2.42: 19
        2.42 -     3.04: 2187
        3.04 -     3.66: 4698
        3.66 -     4.28: 9049
        4.28 -     4.90: 12285
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.042 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.059 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.165 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.200 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28233 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_1126/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1126/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 71.655 46.4607 85.95805 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: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4630   r_free= 0.4500   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.262762                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7308 0.99   1401  159 0.3885 0.3893      6.5648      6.5623|
|  2:  4.7308 -  3.7739 0.99   1344  144 0.3690 0.3849      6.7503      6.7086|
|  3:  3.7739 -  3.3025 0.99   1322  144 0.4149 0.3723       6.617      6.6656|
|  4:  3.3025 -  3.0031 0.99   1311  156 0.4425 0.4130      6.5074      6.4547|
|  5:  3.0031 -  2.7892 0.99   1300  143 0.4894 0.5011      6.3513      6.3717|
|  6:  2.7892 -  2.6257 0.99   1305  141 0.4842 0.4747      6.2613      6.2252|
|  7:  2.6257 -  2.4948 0.99   1305  139 0.5197 0.4898      6.2511      6.2133|
|  8:  2.4948 -  2.3866 0.98   1256  147 0.5120 0.4533      6.1622      6.1431|
|  9:  2.3866 -  2.2951 0.98   1296  151 0.4906 0.5010      6.1094      6.1168|
| 10:  2.2951 -  2.2161 1.00   1288  136 0.5151 0.4519      6.0943      6.0743|
| 11:  2.2161 -  2.1470 0.98   1271  138 0.5141 0.4941      6.0388      6.0087|
| 12:  2.1470 -  2.0858 0.98   1266  143 0.4975 0.5779      5.9621       6.037|
| 13:  2.0858 -  2.0310 0.98   1271  143 0.5503 0.5028       5.888      5.7963|
| 14:  2.0310 -  1.9816 0.53    694   75 0.5362 0.4608      5.8566      5.8112|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7308  1401   159  0.70  34.47   0.79     0.75      71852.84|
|  2:  4.7308 -  3.7739  1344   144  0.74  32.08   0.89     0.80      93083.21|
|  3:  3.7739 -  3.3025  1322   144  0.65  40.06   0.86     0.76      97380.57|
|  4:  3.3025 -  3.0031  1311   156  0.58  45.66   0.81     0.68      87778.27|
|  5:  3.0031 -  2.7892  1300   143  0.47  54.40   0.74     0.56      75086.10|
|  6:  2.7892 -  2.6257  1305   141  0.43  57.17   0.74     0.50      68128.17|
|  7:  2.6257 -  2.4948  1305   139  0.42  58.70   0.74     0.47      61075.65|
|  8:  2.4948 -  2.3866  1256   147  0.42  58.61   0.72     0.49      54262.58|
|  9:  2.3866 -  2.2951  1296   151  0.46  55.52   0.74     0.51      45959.62|
| 10:  2.2951 -  2.2161  1288   136  0.44  57.10   0.76     0.51      42933.81|
| 11:  2.2161 -  2.1470  1271   138  0.40  60.19   0.77     0.47      42541.78|
| 12:  2.1470 -  2.0858  1266   143  0.36  63.24   0.77     0.43      41803.87|
| 13:  2.0858 -  2.0310  1271   143  0.33  65.37   0.72     0.42      36254.79|
| 14:  2.0310 -  1.9816   694    75  0.41  59.34   0.71     0.45      27375.12|
|alpha:            min =        0.42 max =            0.80 mean =         0.56|
|beta:             min =    27375.12 max =        97380.57 mean =     61877.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.53|
|phase err.(test): min =        0.00 max =           89.87 mean =        52.62|
|-----------------------------------------------------------------------------|

============================== 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 = 11.605320             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.598   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.947523              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.510   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      689 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1498 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2644 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3922 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5046 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6547 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7714 |
|-----------------------------------------------------------------------------|
|-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 |       53.826 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.699 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    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 = 11.967)------------------------------------------|
|    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: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4687   r_free= 0.4550   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.265363                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4546   r_free= 0.4398   ksol= 0.30   Bsol= 20.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.11,8.23,7.02,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.257070                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.443435             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.162   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.896166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.620   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4546      final r-factor (work) = 0.3612          |
| start r-factor (free) = 0.4398      final r-factor (free) = 0.3838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.5285 = 10.44 * 0.50 * 6.2629 + 1.00 * 53.8257                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.2396 = 10.44 * 0.50 * 6.1484 + 1.00 * 0.1343                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3612      final r-factor (work) = 0.3086          |
| start r-factor (free) = 0.3838      final r-factor (free) = 0.3536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5244 = 0.90 * 1.00 * 6.1484 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4189 = 0.90 * 1.00 * 6.0310 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.14   12.12    None  None   None       |
|    all(noH): 2823   0      0.00    77.14   12.12    None  None   None       |
|    Sol.    : 438    0      0.00    77.14   28.25    None  None   None       |
|    Mac.    : 2385   0      0.00    76.53   9.16     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 -   7.714: 1332   |   5:    38.570 -  46.284:   68        |
|      1:     7.714 -  15.428:  737   |   6:    46.284 -  53.998:   34        |
|      2:    15.428 -  23.142:  332   |   7:    53.998 -  61.711:   24        |
|      3:    23.142 -  30.856:  183   |   8:    61.711 -  69.425:    7        |
|      4:    30.856 -  38.570:  103   |   9:    69.425 -  77.139:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3086 r_free = 0.3536             target_work(ml) = 5.998         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3081 r_free = 0.3539             target_work(ml) = 5.998         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3081   r_free= 0.3539   ksol= 0.30   Bsol= 20.00   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.11,8.23,7.02,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.997528                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3049   r_free= 0.3491   ksol= 0.34   Bsol= 45.43   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.80,4.55,4.68,0.00,0.00,0.00); trace/3= 5.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.997070                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.959782              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.581   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.408412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.639  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3049      final r-factor (work) = 0.2195          |
| start r-factor (free) = 0.3491      final r-factor (free) = 0.2706          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0684 = 3.96 * 0.50 * 6.0277 + 1.00 * 0.1343                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6681 = 3.96 * 0.50 * 5.8584 + 1.00 * 0.0692                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2195      final r-factor (work) = 0.2033          |
| start r-factor (free) = 0.2706      final r-factor (free) = 0.2587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4070 = 0.41 * 1.00 * 5.8584 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3548 = 0.41 * 1.00 * 5.6807 + 1.00 * 0.0348                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.22   12.14    None  None   None       |
|    all(noH): 2823   0      0.00    77.22   12.14    None  None   None       |
|    Sol.    : 438    0      0.00    77.22   30.51    None  None   None       |
|    Mac.    : 2385   0      0.00    76.17   8.76     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:     0.000 -   7.722: 1357   |   5:    38.609 -  46.331:   76        |
|      1:     7.722 -  15.444:  755   |   6:    46.331 -  54.053:   37        |
|      2:    15.444 -  23.166:  259   |   7:    54.053 -  61.775:   21        |
|      3:    23.166 -  30.888:  199   |   8:    61.775 -  69.497:    7        |
|      4:    30.888 -  38.609:  109   |   9:    69.497 -  77.219:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2033 r_free = 0.2587             target_work(ml) = 5.660         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2031 r_free = 0.2586             target_work(ml) = 5.660         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2031   r_free= 0.2586   ksol= 0.34   Bsol= 45.43   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.80,4.55,4.68,0.00,0.00,0.00); trace/3= 5.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.659590                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2021   r_free= 0.2576   ksol= 0.34   Bsol= 45.44   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.82,2.86,3.89,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.660599                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.910933              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.036  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.423859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.020   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2021      final r-factor (work) = 0.1478          |
| start r-factor (free) = 0.2576      final r-factor (free) = 0.1978          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8728 = 5.91 * 0.50 * 5.6856 + 1.00 * 0.0692                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4358 = 5.91 * 0.50 * 5.5343 + 1.00 * 0.0795                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1478      final r-factor (work) = 0.1314          |
| start r-factor (free) = 0.1978      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3590 = 0.42 * 1.00 * 5.5343 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2711 = 0.42 * 1.00 * 5.3325 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.94   12.46    None  None   None       |
|    all(noH): 2823   0      0.00    79.94   12.46    None  None   None       |
|    Sol.    : 438    0      1.37    77.76   34.61    None  None   None       |
|    Mac.    : 2385   0      0.00    79.94   8.39     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 -   7.994: 1542   |   5:    39.971 -  47.965:   97        |
|      1:     7.994 -  15.988:  667   |   6:    47.965 -  55.959:   65        |
|      2:    15.988 -  23.982:  184   |   7:    55.959 -  63.953:   27        |
|      3:    23.982 -  31.977:  118   |   8:    63.953 -  71.947:    6        |
|      4:    31.977 -  39.971:  113   |   9:    71.947 -  79.941:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1314 r_free = 0.1792             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1314 r_free = 0.1790             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1790   ksol= 0.34   Bsol= 45.44   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.82,2.86,3.89,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.276148                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1312   r_free= 0.1781   ksol= 0.33   Bsol= 45.44   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,2.08,3.28,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.274520                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.311682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.172  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.167278              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.594  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1312      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1781      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9173 = 3.31 * 0.50 * 5.3373 + 1.00 * 0.0795                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7431 = 3.31 * 0.50 * 5.2340 + 1.00 * 0.0764                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8863 = 0.17 * 1.00 * 5.2340 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8795 = 0.17 * 1.00 * 5.1958 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.00   12.15    None  None   None       |
|    all(noH): 2823   0      0.00    79.00   12.15    None  None   None       |
|    Sol.    : 438    0      2.15    76.90   33.23    None  None   None       |
|    Mac.    : 2385   0      0.00    79.00   8.27     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 -   7.900: 1548   |   5:    39.498 -  47.397:   98        |
|      1:     7.900 -  15.799:  681   |   6:    47.397 -  55.297:   62        |
|      2:    15.799 -  23.699:  174   |   7:    55.297 -  63.196:   18        |
|      3:    23.699 -  31.598:  122   |   8:    63.196 -  71.096:    8        |
|      4:    31.598 -  39.498:  109   |   9:    71.096 -  78.996:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1175 r_free = 0.1637             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1174 r_free = 0.1633             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1174   r_free= 0.1633   ksol= 0.33   Bsol= 45.44   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.83,2.08,3.28,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184670                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1632   ksol= 0.32   Bsol= 45.44   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,1.92,3.12,0.00,0.00,0.00); trace/3= 2.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184337                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.493232              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.576  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.154486              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1173      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9551 = 1.49 * 0.50 * 5.1952 + 1.00 * 0.0764                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9353 = 1.49 * 0.50 * 5.1954 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8146 = 0.15 * 1.00 * 5.1954 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8197 = 0.15 * 1.00 * 5.1983 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.89   11.95    None  None   None       |
|    all(noH): 2823   0      0.00    76.89   11.95    None  None   None       |
|    Sol.    : 438    0      2.25    73.80   32.04    None  None   None       |
|    Mac.    : 2385   0      0.00    76.89   8.26     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 -   7.689: 1500   |   5:    38.443 -  46.131:   96        |
|      1:     7.689 -  15.377:  709   |   6:    46.131 -  53.820:   56        |
|      2:    15.377 -  23.066:  190   |   7:    53.820 -  61.508:   15        |
|      3:    23.066 -  30.754:  130   |   8:    61.508 -  69.197:    6        |
|      4:    30.754 -  38.443:  116   |   9:    69.197 -  76.885:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1201 r_free = 0.1637             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1200 r_free = 0.1636             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1636   ksol= 0.32   Bsol= 45.44   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,1.92,3.12,0.00,0.00,0.00); trace/3= 2.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199539                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7308 0.99   1401  159 0.1041 0.1337      5.4103       5.579|
|  2:  4.7308 -  3.7739 0.99   1344  144 0.0930 0.1158      5.4935      5.6422|
|  3:  3.7739 -  3.3025 0.99   1322  144 0.1116 0.1528      5.5146        5.86|
|  4:  3.3025 -  3.0031 0.99   1311  156 0.1267 0.1687      5.4944      5.6384|
|  5:  3.0031 -  2.7892 0.99   1300  143 0.1443 0.1833      5.3818      5.5933|
|  6:  2.7892 -  2.6257 0.99   1305  141 0.1301 0.1905      5.2584      5.5176|
|  7:  2.6257 -  2.4948 0.99   1305  139 0.1370 0.1625      5.2445      5.3775|
|  8:  2.4948 -  2.3866 0.98   1256  147 0.1267 0.1954      5.1215      5.4385|
|  9:  2.3866 -  2.2951 0.98   1296  151 0.1295 0.1928      5.1122       5.379|
| 10:  2.2951 -  2.2161 1.00   1288  136 0.1245 0.1686      5.0079      5.1958|
| 11:  2.2161 -  2.1470 0.98   1271  138 0.1234 0.1887       5.001      5.3296|
| 12:  2.1470 -  2.0858 0.98   1266  143 0.1158 0.1657       4.902      5.1439|
| 13:  2.0858 -  2.0310 0.98   1271  143 0.1285 0.1828      4.8566      5.1133|
| 14:  2.0310 -  1.9816 0.53    694   75 0.1099 0.1596      4.7052      4.9036|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7308  1401   159  0.94   9.00   0.98     0.96       7240.21|
|  2:  4.7308 -  3.7739  1344   144  0.95   8.39   1.01     1.00       9573.78|
|  3:  3.7739 -  3.3025  1322   144  0.93  11.85   1.02     1.02      11076.46|
|  4:  3.3025 -  3.0031  1311   156  0.92  14.02   1.00     0.97      10821.19|
|  5:  3.0031 -  2.7892  1300   143  0.89  16.74   0.99     0.97       8917.34|
|  6:  2.7892 -  2.6257  1305   141  0.90  16.61   0.98     0.95       7620.23|
|  7:  2.6257 -  2.4948  1305   139  0.90  16.51   0.99     0.97       7054.86|
|  8:  2.4948 -  2.3866  1256   147  0.90  16.70   0.98     0.95       5826.14|
|  9:  2.3866 -  2.2951  1296   151  0.90  16.47   1.00     0.98       5755.64|
| 10:  2.2951 -  2.2161  1288   136  0.90  15.93   1.01     0.97       4613.87|
| 11:  2.2161 -  2.1470  1271   138  0.90  16.69   1.00     0.95       4657.33|
| 12:  2.1470 -  2.0858  1266   143  0.91  15.53   1.02     1.02       4128.14|
| 13:  2.0858 -  2.0310  1271   143  0.90  16.92   1.01     1.00       3663.63|
| 14:  2.0310 -  1.9816   694    75  0.91  15.64   0.99     0.96       2798.03|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2798.03 max =        11076.46 mean =      6865.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.69|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1636   ksol= 0.32   Bsol= 47.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.06,-0.57,0.63,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199512                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1636   ksol= 0.32   Bsol= 47.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.06,-0.57,0.63,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.199512                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7308 0.99   1401  159 0.1040 0.1337      5.4099      5.5782|
|  2:  4.7308 -  3.7739 0.99   1344  144 0.0930 0.1158      5.4932      5.6421|
|  3:  3.7739 -  3.3025 0.99   1322  144 0.1116 0.1528      5.5145      5.8597|
|  4:  3.3025 -  3.0031 0.99   1311  156 0.1267 0.1686      5.4943      5.6385|
|  5:  3.0031 -  2.7892 0.99   1300  143 0.1443 0.1834       5.382      5.5937|
|  6:  2.7892 -  2.6257 0.99   1305  141 0.1301 0.1905      5.2585      5.5173|
|  7:  2.6257 -  2.4948 0.99   1305  139 0.1369 0.1624      5.2443      5.3771|
|  8:  2.4948 -  2.3866 0.98   1256  147 0.1267 0.1953      5.1213      5.4385|
|  9:  2.3866 -  2.2951 0.98   1296  151 0.1295 0.1929      5.1124      5.3792|
| 10:  2.2951 -  2.2161 1.00   1288  136 0.1245 0.1684      5.0077      5.1954|
| 11:  2.2161 -  2.1470 0.98   1271  138 0.1234 0.1887      5.0009      5.3299|
| 12:  2.1470 -  2.0858 0.98   1266  143 0.1158 0.1658      4.9025      5.1438|
| 13:  2.0858 -  2.0310 0.98   1271  143 0.1286 0.1829      4.8568      5.1138|
| 14:  2.0310 -  1.9816 0.53    694   75 0.1099 0.1597      4.7055      4.9042|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7308  1401   159  0.94   8.99   0.98     0.96       7231.16|
|  2:  4.7308 -  3.7739  1344   144  0.95   8.37   1.01     0.99       9563.29|
|  3:  3.7739 -  3.3025  1322   144  0.93  11.85   1.02     1.01      11069.69|
|  4:  3.3025 -  3.0031  1311   156  0.92  14.02   1.00     0.97      10822.77|
|  5:  3.0031 -  2.7892  1300   143  0.89  16.75   0.98     0.97       8920.32|
|  6:  2.7892 -  2.6257  1305   141  0.90  16.61   0.97     0.95       7619.96|
|  7:  2.6257 -  2.4948  1305   139  0.90  16.50   0.99     0.96       7052.28|
|  8:  2.4948 -  2.3866  1256   147  0.90  16.69   0.98     0.95       5826.35|
|  9:  2.3866 -  2.2951  1296   151  0.90  16.47   1.00     0.97       5755.47|
| 10:  2.2951 -  2.2161  1288   136  0.90  15.93   1.00     0.97       4611.89|
| 11:  2.2161 -  2.1470  1271   138  0.90  16.68   0.99     0.94       4654.79|
| 12:  2.1470 -  2.0858  1266   143  0.91  15.53   1.01     1.01       4130.50|
| 13:  2.0858 -  2.0310  1271   143  0.90  16.93   1.00     0.99       3666.45|
| 14:  2.0310 -  1.9816   694    75  0.91  15.65   0.98     0.95       2800.85|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2800.85 max =        11069.69 mean =      6864.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.69|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.967)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.41    79.30   14.37    None  None   None       |
|    all(noH): 2823   0      2.41    79.30   14.37    None  None   None       |
|    Sol.    : 438    0      4.67    76.21   34.45    None  None   None       |
|    Mac.    : 2385   0      2.41    79.30   10.68    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:     2.413 -  10.102: 1500   |   5:    40.856 -  48.544:   96        |
|      1:    10.102 -  17.790:  709   |   6:    48.544 -  56.233:   56        |
|      2:    17.790 -  25.479:  190   |   7:    56.233 -  63.921:   15        |
|      3:    25.479 -  33.167:  130   |   8:    63.921 -  71.610:    6        |
|      4:    33.167 -  40.856:  116   |   9:    71.610 -  79.298:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.458 - 4.737
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 320
   mapped sites are within: 0.707 - 4.737

peak=   10.629 closest distance to " CB  VAL A 230 " =    1.477
peak=    7.204 closest distance to " CG2 VAL A 296 " =    1.126
peak=    5.971 closest distance to " CD2 LEU A   5 " =    1.316
peak=    5.854 closest distance to " NH2 ARG A  56 " =    2.221
peak=    5.851 closest distance to " NH1 ARG A 138 " =    1.025
peak=    5.806 closest distance to " CG  LEU A   5 " =    1.276
peak=    5.428 closest distance to " CG  ARG A 138 " =    1.042
peak=    5.381 closest distance to " O   HOH Z 232 " =    2.242
peak=    5.233 closest distance to " CG  LEU A 228 " =    1.220
peak=    5.142 closest distance to " CB  GLN A 223 " =    1.399
peak=    5.054 closest distance to " CG  PRO A 198 " =    1.329
peak=    4.945 closest distance to " NE2 GLN A  11 " =    1.164
peak=    4.804 closest distance to " CD  ARG A 138 " =    1.109
peak=    4.799 closest distance to " O   HOH Z 144 " =    1.851
peak=    4.778 closest distance to " CB  SER A  63 " =    1.288
peak=    4.762 closest distance to " CB  ASN A 148 " =    1.368
peak=    4.759 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.752 closest distance to " CD2 LEU A 228 " =    1.190
peak=    4.732 closest distance to " CG  PRO A 243 " =    1.149
peak=    4.731 closest distance to " C   PRO A 198 " =    1.589
peak=    4.724 closest distance to " CB  GLN A 183 " =    1.171
peak=    4.656 closest distance to " CA  VAL A 296 " =    1.196
peak=    4.624 closest distance to " CB  VAL A 230 " =    1.244
peak=    4.494 closest distance to " CB  SER A   3 " =    1.447
peak=    4.486 closest distance to " O   HOH Z 126 " =    1.922
peak=    4.479 closest distance to " CB  ASP A 124 " =    0.739
peak=    4.478 closest distance to " O   HOH Z 236 " =    1.909
peak=    4.469 closest distance to " O   HOH Z 425 " =    1.498
peak=    4.468 closest distance to " O   HOH Z 298 " =    1.817
peak=    4.447 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.406 closest distance to " CB  ASN A  39 " =    0.880
peak=    4.364 closest distance to " CB  SER A 216 " =    0.875
peak=    4.347 closest distance to " O   HOH Z 427 " =    2.917
peak=    4.328 closest distance to " O   HOH Z 369 " =    1.990
peak=    4.327 closest distance to " ND2 ASN A 187 " =    1.490
peak=    4.324 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.307 closest distance to " NH1AARG A 145 " =    1.207
peak=    4.252 closest distance to " CA  SER A  87 " =    0.906
peak=    4.222 closest distance to " CB  GLU A 152 " =    1.216
peak=    4.200 closest distance to " CB  VAL A 265 " =    1.298
peak=    4.187 closest distance to " O   HOH Z  55 " =    2.307
peak=    4.177 closest distance to " OD2 ASP A 286 " =    2.854
peak=    4.171 closest distance to " CD  ARG A 159 " =    0.823
peak=    4.156 closest distance to " CB  TRP A 266 " =    0.925
peak=    4.139 closest distance to " O   HOH Z 368 " =    1.992
peak=    4.078 closest distance to " CG  GLN A  88 " =    1.071
peak=    4.075 closest distance to " CB  GLU A 128 " =    0.982
peak=    4.073 closest distance to " O   HOH Z 234 " =    3.777
peak=    4.059 closest distance to " O   HOH Z 316 " =    3.036
peak=    4.032 closest distance to " CB  LEU A 143 " =    1.126
peak=    4.027 closest distance to " CG  LEU A 167 " =    1.200
peak=    4.022 closest distance to " O   HOH Z 303 " =    2.211
peak=    4.018 closest distance to " CB  LEU A 228 " =    1.219
peak=    4.009 closest distance to " O   HOH Z 411 " =    3.576
peak=    4.001 closest distance to " O   HOH Z 437 " =    2.029
peak=    3.996 closest distance to " CD1 LEU A 300 " =    1.266
peak=    3.984 closest distance to " O   SER A  87 " =    2.320
peak=    3.982 closest distance to " CZ  PHE A 218 " =    1.044
peak=    3.954 closest distance to " O   HOH Z   7 " =    1.297
peak=    3.942 closest distance to " O   HOH Z 410 " =    1.550
peak=    3.935 closest distance to " N   PHE A 130 " =    1.276
peak=    3.930 closest distance to " CB  ARG A  79 " =    1.442
peak=    3.927 closest distance to " CD  ARG A  66 " =    2.316
peak=    3.898 closest distance to " O   HOH Z 403 " =    1.685
peak=    3.897 closest distance to " O   HOH Z   9 " =    2.052
peak=    3.890 closest distance to " O   HOH Z  88 " =    3.242
peak=    3.889 closest distance to " NH1 ARG A  56 " =    0.962
peak=    3.886 closest distance to " O   HOH Z 346 " =    1.673
peak=    3.884 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.874 closest distance to " CB  ASN A 187 " =    0.995
peak=    3.863 closest distance to " O   HOH Z 158 " =    3.002
peak=    3.862 closest distance to " O   HOH Z 193 " =    1.784
peak=    3.856 closest distance to " CG1 ILE A 151 " =    1.198
peak=    3.847 closest distance to " O   HOH Z   2 " =    1.798
peak=    3.847 closest distance to " CB  ASN A 142 " =    0.957
peak=    3.834 closest distance to " CA  ALA A  51 " =    1.057
peak=    3.832 closest distance to " O   HOH Z 209 " =    2.395
peak=    3.831 closest distance to " O   HOH Z 222 " =    2.355
peak=    3.831 closest distance to " CD BLYS A 290 " =    1.048
peak=    3.808 closest distance to " ND2 ASN A 249 " =    1.875
peak=    3.797 closest distance to " CB  PRO A 198 " =    0.854
peak=    3.777 closest distance to " CA  ASN A 215 " =    1.212
peak=    3.764 closest distance to " CB  SER A 212 " =    1.242
peak=    3.753 closest distance to " CZ  PHE A 192 " =    0.925
peak=    3.746 closest distance to " O   HOH Z 193 " =    1.957
peak=    3.740 closest distance to " CG1BVAL A  72 " =    1.645
peak=    3.728 closest distance to " OD1 ASN A  69 " =    2.663
peak=    3.727 closest distance to " CB  SER A 210 " =    0.826
peak=    3.717 closest distance to " CG2 THR A 221 " =    0.966
peak=    3.711 closest distance to " CB  MET A  40 " =    0.827
peak=    3.702 closest distance to " O   HOH Z 171 " =    3.901
peak=    3.682 closest distance to " O   HOH Z 132 " =    2.541
peak=    3.682 closest distance to " CA  TYR A  30 " =    0.959
peak=    3.672 closest distance to " NE AARG A 275 " =    1.344
peak=    3.670 closest distance to " O   HOH Z 193 " =    1.958
peak=    3.670 closest distance to " O   HOH Z 263 " =    1.546
peak=    3.666 closest distance to " O   HOH Z  61 " =    1.619
peak=    3.663 closest distance to " CB  VAL A 202 " =    1.565
peak=    3.661 closest distance to " O   HOH Z   1 " =    2.060
peak=    3.660 closest distance to " O   HOH Z 248 " =    1.821
peak=    3.646 closest distance to " CB  THR A 157 " =    1.160
peak=    3.627 closest distance to " CA  ILE A 234 " =    1.076
peak=    3.625 closest distance to " CB  GLU A 236 " =    1.126
peak=    3.624 closest distance to " O   HOH Z 371 " =    2.744
peak=    3.612 closest distance to " CB  THR A  82 " =    1.352
peak=    3.608 closest distance to " CB  GLN A  88 " =    1.272
peak=    3.607 closest distance to " CA  THR A 264 " =    0.788
peak=    3.604 closest distance to " CB  ALA A 104 " =    0.765
peak=    3.604 closest distance to " O   HOH Z 273 " =    2.618
peak=    3.601 closest distance to " O   HOH Z  21 " =    1.716
peak=    3.599 closest distance to " C   ALA A 299 " =    0.959
peak=    3.594 closest distance to " ND1 HIS A  86 " =    1.706
peak=    3.594 closest distance to " CB  ASP A 140 " =    0.806
peak=    3.593 closest distance to " CA  ALA A  21 " =    1.207
peak=    3.591 closest distance to " CB  HIS A 108 " =    0.821
peak=    3.585 closest distance to " CB  ALA A 291 " =    1.301
peak=    3.584 closest distance to " CE3 TRP A 274 " =    2.434
peak=    3.583 closest distance to " O   HOH Z 344 " =    2.962
peak=    3.573 closest distance to " O   HOH Z 350 " =    1.578
peak=    3.573 closest distance to " CA  ALA A 154 " =    1.068
peak=    3.562 closest distance to " N   ARG A 156 " =    1.352
peak=    3.559 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.556 closest distance to " CE1 TYR A 186 " =    1.391
peak=    3.550 closest distance to " CG2 VAL A 257 " =    0.985
peak=    3.545 closest distance to " CB  VAL A 250 " =    1.123
peak=    3.544 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.539 closest distance to " O   HOH Z 189 " =    2.909
peak=    3.537 closest distance to " O   HOH Z 133 " =    1.754
peak=    3.528 closest distance to " O   HOH Z 261 " =    2.261
peak=    3.527 closest distance to " OH  TYR A 186 " =    1.032
peak=    3.527 closest distance to " CB  ILE A 120 " =    1.270
peak=    3.524 closest distance to " N   ASN A  39 " =    1.070
peak=    3.515 closest distance to " O   HOH Z 368 " =    3.654
peak=    3.508 closest distance to " O   HOH Z  58 " =    1.733
peak=    3.496 closest distance to " O   HOH Z  30 " =    1.594
peak=    3.495 closest distance to " CG1 VAL A 296 " =    1.202
peak=    3.493 closest distance to " NH1 ARG A  14 " =    0.918
peak=    3.493 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.490 closest distance to " CZ3 TRP A 123 " =    1.382
peak=    3.485 closest distance to " CB  ASN A 110 " =    1.059
peak=    3.485 closest distance to " NH2AARG A 190 " =    1.664
peak=    3.479 closest distance to " CB  PRO A  54 " =    0.861
peak=    3.478 closest distance to " CA  ALA A 295 " =    1.025
peak=    3.477 closest distance to " CB  ALA A 161 " =    0.917
peak=    3.475 closest distance to " CB  GLN A 103 " =    1.105
peak=    3.472 closest distance to " O   HOH Z 423 " =    1.570
peak=    3.470 closest distance to " CB  ALA A   1 " =    4.737
peak=    3.467 closest distance to " O   HOH Z 271 " =    2.069
peak=    3.465 closest distance to " O   HOH Z   1 " =    1.820
peak=    3.464 closest distance to " CA  MET A  40 " =    1.071
peak=    3.463 closest distance to " CA  ASP A 124 " =    0.707
peak=    3.463 closest distance to " O   HOH Z 185 " =    1.823
peak=    3.463 closest distance to " O   HOH Z 135 " =    1.855
peak=    3.462 closest distance to " CA  LEU A 282 " =    0.996
peak=    3.462 closest distance to " CB  ALA A   9 " =    1.562
peak=    3.460 closest distance to " CD  ARG A 269 " =    0.991
peak=    3.451 closest distance to " CB  ALA A  34 " =    0.977
peak=    3.449 closest distance to " CD  ARG A 219 " =    1.050
peak=    3.449 closest distance to " N   VAL A 126 " =    1.079
peak=    3.441 closest distance to " CA  LYS A 117 " =    1.179
peak=    3.435 closest distance to " O   HOH Z 313 " =    1.801
peak=    3.434 closest distance to " O   HOH Z 217 " =    3.179
peak=    3.433 closest distance to " O   HOH Z   3 " =    1.874
peak=    3.432 closest distance to " CZ  PHE A 208 " =    1.220
peak=    3.430 closest distance to " CG  ARG A 159 " =    1.041
peak=    3.430 closest distance to " O   HOH Z 334 " =    1.547
peak=    3.427 closest distance to " O   HOH Z 282 " =    1.890
peak=    3.426 closest distance to " O   HOH Z 184 " =    1.501
peak=    3.424 closest distance to " CA  TYR A 186 " =    1.558
peak=    3.422 closest distance to " CD1 LEU A   5 " =    1.328
peak=    3.421 closest distance to " CA  THR A 221 " =    0.856
peak=    3.421 closest distance to " O   ASN A 209 " =    1.391
peak=    3.420 closest distance to " O   HOH Z  78 " =    1.630
peak=    3.417 closest distance to " CD2 LEU A 255 " =    1.568
peak=    3.415 closest distance to " OG  SER A 206 " =    1.176
peak=    3.412 closest distance to " O   HOH Z 183 " =    1.422
peak=    3.407 closest distance to " O   HOH Z  68 " =    1.960
peak=    3.405 closest distance to " CA  GLN A 223 " =    0.869
peak=    3.400 closest distance to " O   HOH Z 112 " =    1.577
peak=    3.400 closest distance to " NH2 ARG A 156 " =    1.124
peak=    3.398 closest distance to " O   HOH Z 371 " =    1.743
peak=    3.398 closest distance to " O   HOH Z 402 " =    1.451
peak=    3.391 closest distance to " O   HOH Z 352 " =    1.830
peak=    3.390 closest distance to " O   HOH Z 216 " =    2.696
peak=    3.389 closest distance to " O   HOH Z 214 " =    1.892
peak=    3.386 closest distance to " CB  LEU A 237 " =    0.779
peak=    3.382 closest distance to " CB  PHE A  16 " =    1.223
peak=    3.380 closest distance to " OG  SER A  62 " =    2.946
peak=    3.380 closest distance to " O   HOH Z 180 " =    2.119
peak=    3.379 closest distance to " CE  LYS A  76 " =    0.910
peak=    3.377 closest distance to " O   HOH Z 227 " =    2.005
peak=    3.373 closest distance to " O   HOH Z 280 " =    3.095
peak=    3.371 closest distance to " O   HOH Z 435 " =    2.050
peak=    3.370 closest distance to " CG BARG A 275 " =    1.549
peak=    3.368 closest distance to " CA  GLY A 267 " =    1.157
peak=    3.366 closest distance to " O   TYR A 116 " =    1.222
peak=    3.364 closest distance to " NH2BARG A 145 " =    1.946
peak=    3.359 closest distance to " O   HOH Z 126 " =    1.504
peak=    3.356 closest distance to " O   HOH Z 302 " =    1.854
peak=    3.355 closest distance to " CB  GLU A 277 " =    3.583
peak=    3.348 closest distance to " OG BSER A 134 " =    2.954
peak=    3.348 closest distance to " ND1 HIS A  81 " =    1.801
peak=    3.346 closest distance to " CB  TRP A 179 " =    1.421
peak=    3.341 closest distance to " NZ ALYS A 290 " =    1.166
peak=    3.341 closest distance to " CD1 ILE A 106 " =    0.874
peak=    3.336 closest distance to " CA  ARG A 195 " =    1.254
peak=    3.335 closest distance to " CB  ARG A 190 " =    1.744
peak=    3.330 closest distance to " CG1 VAL A 174 " =    0.969
peak=    3.325 closest distance to " O   HOH Z 128 " =    1.998
peak=    3.322 closest distance to " CE  MET A  93 " =    1.556
peak=    3.316 closest distance to " O   HOH Z 175 " =    2.171
peak=    3.315 closest distance to " CA  ILE A  33 " =    1.627
peak=    3.314 closest distance to " CB  LYS A 117 " =    1.244
peak=    3.312 closest distance to " CD  ARG A  66 " =    2.645
peak=    3.307 closest distance to " CD1 ILE A  33 " =    1.721
peak=    3.301 closest distance to " O   HOH Z 209 " =    2.450
peak=    3.298 closest distance to " OG BSER A 212 " =    2.739
peak=    3.297 closest distance to " CB  ALA A  10 " =    0.879
peak=    3.291 closest distance to " O   HOH Z 419 " =    1.788
peak=    3.288 closest distance to " CB  ALA A 184 " =    0.976
peak=    3.282 closest distance to " O   HOH Z 197 " =    3.249
peak=    3.281 closest distance to " CB  ALA A 248 " =    1.053
peak=    3.275 closest distance to " CB BVAL A  41 " =    1.113
peak=    3.273 closest distance to " CA  PHE A 283 " =    1.046
peak=    3.273 closest distance to " O   GLN A 278 " =    1.371
peak=    3.271 closest distance to " CB  ALA A 137 " =    0.986
peak=    3.266 closest distance to " CG  GLN A 278 " =    1.260
peak=    3.262 closest distance to " OG  SER A  22 " =    2.927
peak=    3.262 closest distance to " O   HOH Z 148 " =    3.429
peak=    3.261 closest distance to " OH  TYR A 214 " =    1.214
peak=    3.261 closest distance to " O   HOH Z 147 " =    1.696
peak=    3.261 closest distance to " CB  TRP A 150 " =    1.518
peak=    3.259 closest distance to " O   HOH Z 271 " =    2.587
peak=    3.258 closest distance to " CB  ALA A 248 " =    1.316
peak=    3.257 closest distance to " CH2 TRP A 150 " =    0.930
peak=    3.256 closest distance to " NE2 HIS A 207 " =    1.306
peak=    3.255 closest distance to " O   HOH Z  97 " =    1.940
peak=    3.255 closest distance to " O   HOH Z 303 " =    1.870
peak=    3.251 closest distance to " CB  MET A  47 " =    1.031
peak=    3.248 closest distance to " N   TYR A  15 " =    0.804
peak=    3.245 closest distance to " CD2 TYR A 186 " =    1.048
peak=    3.244 closest distance to " O   HOH Z 247 " =    1.443
peak=    3.243 closest distance to " O   TRP A 274 " =    1.765
peak=    3.241 closest distance to " CE2 TYR A 186 " =    0.932
peak=    3.240 closest distance to " O   HOH Z 109 " =    2.620
peak=    3.239 closest distance to " O   HOH Z 305 " =    3.527
peak=    3.235 closest distance to " CB  ASN A 224 " =    1.007
peak=    3.235 closest distance to " O   HOH Z 366 " =    2.851
peak=    3.233 closest distance to " CA  ILE A 106 " =    0.795
peak=    3.220 closest distance to " CG  MET A 185 " =    1.172
peak=    3.218 closest distance to " O   HOH Z  57 " =    1.168
peak=    3.217 closest distance to " CG2 ILE A 109 " =    0.899
peak=    3.217 closest distance to " O   HOH Z 280 " =    1.798
peak=    3.214 closest distance to " CG1 ILE A  49 " =    1.305
peak=    3.213 closest distance to " O   HOH Z  61 " =    1.549
peak=    3.208 closest distance to " O   HOH Z 294 " =    1.594
peak=    3.205 closest distance to " N   SER A 135 " =    1.328
peak=    3.203 closest distance to " N   SER A 271 " =    0.996
peak=    3.202 closest distance to " O   HOH Z 145 " =    1.581
peak=    3.202 closest distance to " O   HOH Z 213 " =    2.810
peak=    3.201 closest distance to " O   HOH Z 345 " =    1.889
peak=    3.198 closest distance to " N   GLN A 278 " =    0.901
peak=    3.191 closest distance to " C   GLN A  88 " =    1.519
peak=    3.191 closest distance to " CG  MET A 185 " =    0.969
peak=    3.188 closest distance to " O   HOH Z 145 " =    3.494
peak=    3.187 closest distance to " CB  ALA A 114 " =    1.295
peak=    3.187 closest distance to " OG  SER A 135 " =    1.358
peak=    3.187 closest distance to " CB  ILE A 234 " =    1.085
peak=    3.179 closest distance to " CD  ARG A  14 " =    1.212
peak=    3.178 closest distance to " CG BARG A 102 " =    1.849
peak=    3.178 closest distance to " OD1BASN A 224 " =    2.351
peak=    3.176 closest distance to " CB  TYR A 247 " =    0.964
peak=    3.174 closest distance to " CA  ALA A 158 " =    1.108
peak=    3.173 closest distance to " O   HOH Z 185 " =    2.152
peak=    3.172 closest distance to " O   HOH Z 285 " =    2.888
peak=    3.171 closest distance to " O   HOH Z 409 " =    2.803
peak=    3.163 closest distance to " CB  ASN A 173 " =    1.009
peak=    3.163 closest distance to " O   HOH Z 105 " =    1.534
peak=    3.162 closest distance to " O   MET A 105 " =    1.687
peak=    3.158 closest distance to " CD  PRO A 243 " =    1.455
peak=    3.158 closest distance to " CG  GLN A 144 " =    0.914
peak=    3.157 closest distance to " O   PRO A 213 " =    1.538
peak=    3.157 closest distance to " CG  MET A 113 " =    1.392
peak=    3.154 closest distance to " CA  LYS A  48 " =    1.326
peak=    3.153 closest distance to " CB  SER A  28 " =    0.978
peak=    3.152 closest distance to " O   HOH Z 332 " =    1.518
peak=    3.146 closest distance to " CB  GLU A  46 " =    1.038
peak=    3.145 closest distance to " O   HOH Z  49 " =    2.443
peak=    3.135 closest distance to " O   HOH Z 345 " =    3.441
peak=    3.131 closest distance to " O   HOH Z  59 " =    1.966
peak=    3.119 closest distance to " O   HOH Z 124 " =    2.176
peak=    3.119 closest distance to " CG2 ILE A 106 " =    0.803
peak=    3.118 closest distance to " OG1 THR A 294 " =    3.547
peak=    3.109 closest distance to " CB  ARG A 139 " =    0.951
peak=    3.109 closest distance to " O   HOH Z 353 " =    2.585
peak=    3.107 closest distance to " O   THR A 294 " =    1.060
peak=    3.105 closest distance to " OG  SER A  28 " =    1.566
peak=    3.102 closest distance to " CA  ARG A  36 " =    1.176
peak=    3.100 closest distance to " CD1 ILE A 263 " =    1.269
peak=    3.100 closest distance to " CA  GLY A 211 " =    1.247
peak=    3.100 closest distance to " CB  PRO A 243 " =    1.279
peak=    3.098 closest distance to " O   HOH Z 152 " =    1.871
peak=    3.097 closest distance to " CB  SER A  62 " =    1.185
peak=    3.088 closest distance to " O   HOH Z 426 " =    1.846
peak=    3.086 closest distance to " O   HOH Z 329 " =    3.819
peak=    3.082 closest distance to " O   HOH Z 217 " =    1.604
peak=    3.073 closest distance to " O   HOH Z 252 " =    1.769
peak=    3.072 closest distance to " O   HOH Z 213 " =    2.197
peak=    3.066 closest distance to " O   HOH Z 407 " =    2.096
peak=    3.065 closest distance to " CD1AILE A 234 " =    0.982
peak=    3.062 closest distance to " O   PHE A  61 " =    1.402
peak=    3.025 closest distance to " O   HOH Z  43 " =    2.134

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.304 - 5.427
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 209
   mapped sites are within: 0.712 - 5.427

peak=   -5.957 closest distance to " CG2 VAL A 230 " =    0.758
peak=   -4.844 closest distance to " O   HOH Z 231 " =    0.800
peak=   -4.822 closest distance to " O   HOH Z 290 " =    0.994
peak=   -4.356 closest distance to " O   HOH Z 231 " =    1.348
peak=   -4.253 closest distance to " CG  ARG A 138 " =    1.035
peak=   -4.200 closest distance to " CG1 VAL A 296 " =    1.335
peak=   -4.158 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.153 closest distance to " CD1 TYR A 247 " =    2.755
peak=   -4.128 closest distance to " O   PRO A 198 " =    1.178
peak=   -4.111 closest distance to " CD  ARG A 156 " =    2.004
peak=   -4.069 closest distance to " CD  ARG A  14 " =    3.067
peak=   -4.034 closest distance to " CA  GLY A 241 " =    2.319
peak=   -4.013 closest distance to " N   THR A 157 " =    1.471
peak=   -4.011 closest distance to " O   HOH Z 351 " =    1.326
peak=   -3.982 closest distance to " CD  ARG A 138 " =    1.134
peak=   -3.943 closest distance to " CZ3 TRP A 179 " =    1.147
peak=   -3.941 closest distance to " CB  PRO A 163 " =    2.599
peak=   -3.916 closest distance to " CG2 VAL A 296 " =    1.002
peak=   -3.907 closest distance to " O   HOH Z  52 " =    1.497
peak=   -3.892 closest distance to " C   LEU A 222 " =    0.814
peak=   -3.879 closest distance to " OE1 GLN A  88 " =    1.078
peak=   -3.855 closest distance to " CA  ASP A  27 " =    2.433
peak=   -3.850 closest distance to " CG  LEU A 101 " =    2.563
peak=   -3.847 closest distance to " O   HOH Z 435 " =    2.873
peak=   -3.824 closest distance to " O   GLY A 203 " =    2.445
peak=   -3.792 closest distance to " CD  GLN A 223 " =    1.996
peak=   -3.779 closest distance to " O   HOH Z 211 " =    1.496
peak=   -3.768 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.743 closest distance to " CG  MET A 105 " =    0.971
peak=   -3.742 closest distance to " O   PRO A 163 " =    1.897
peak=   -3.713 closest distance to " C   ALA A 158 " =    1.310
peak=   -3.702 closest distance to " N   ALA A  43 " =    2.323
peak=   -3.700 closest distance to " CB  ALA A 248 " =    2.570
peak=   -3.684 closest distance to " O   HOH Z 389 " =    1.904
peak=   -3.684 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -3.683 closest distance to " CG  TRP A 266 " =    1.738
peak=   -3.667 closest distance to " O   VAL A  67 " =    2.505
peak=   -3.663 closest distance to " NH2 ARG A  79 " =    1.891
peak=   -3.661 closest distance to " CD  GLN A  58 " =    0.836
peak=   -3.652 closest distance to " O   HOH Z  38 " =    1.680
peak=   -3.640 closest distance to " CG1 VAL A 197 " =    2.404
peak=   -3.639 closest distance to " CD2 TYR A 293 " =    2.081
peak=   -3.639 closest distance to " CE2 TYR A  30 " =    2.863
peak=   -3.629 closest distance to " CE BMET A  47 " =    1.665
peak=   -3.628 closest distance to " O   HOH Z 417 " =    2.876
peak=   -3.627 closest distance to " OG  SER A 206 " =    1.780
peak=   -3.622 closest distance to " O   HOH Z 179 " =    2.331
peak=   -3.607 closest distance to " CB  ALA A  43 " =    2.487
peak=   -3.604 closest distance to " OG BSER A 134 " =    1.324
peak=   -3.602 closest distance to " O   HOH Z 266 " =    5.021
peak=   -3.586 closest distance to " CG  PHE A 283 " =    2.626
peak=   -3.584 closest distance to " CD1 ILE A 239 " =    2.126
peak=   -3.578 closest distance to " O   HOH Z 166 " =    1.401
peak=   -3.578 closest distance to " CB  VAL A 230 " =    1.007
peak=   -3.569 closest distance to " O   ILE A 109 " =    2.650
peak=   -3.566 closest distance to " O   GLY A 211 " =    1.266
peak=   -3.564 closest distance to " O   HOH Z 275 " =    1.521
peak=   -3.553 closest distance to " CD1 LEU A 101 " =    2.450
peak=   -3.549 closest distance to " CD  LYS A 289 " =    2.632
peak=   -3.542 closest distance to " OG  SER A  87 " =    1.442
peak=   -3.541 closest distance to " O   HOH Z 388 " =    2.145
peak=   -3.538 closest distance to " CB  ALA A   9 " =    2.538
peak=   -3.528 closest distance to " O   HOH Z  60 " =    2.246
peak=   -3.522 closest distance to " CB  VAL A 296 " =    1.092
peak=   -3.521 closest distance to " CD1 LEU A 228 " =    2.381
peak=   -3.518 closest distance to " N   GLN A  58 " =    1.955
peak=   -3.510 closest distance to " O   HOH Z 368 " =    1.432
peak=   -3.508 closest distance to " NH2AARG A 275 " =    5.427
peak=   -3.497 closest distance to " CD  GLN A  88 " =    0.801
peak=   -3.492 closest distance to " O   HOH Z 359 " =    1.623
peak=   -3.489 closest distance to " OG  SER A  97 " =    2.187
peak=   -3.489 closest distance to " O   HOH Z  51 " =    1.011
peak=   -3.484 closest distance to " O   HOH Z 281 " =    2.687
peak=   -3.480 closest distance to " CB  ALA A 248 " =    2.030
peak=   -3.476 closest distance to " O   GLY A  80 " =    2.502
peak=   -3.476 closest distance to " O   HOH Z 140 " =    1.277
peak=   -3.474 closest distance to " CA  GLY A 241 " =    2.995
peak=   -3.466 closest distance to " C   ASN A 285 " =    2.483
peak=   -3.460 closest distance to " CG1 VAL A 112 " =    3.069
peak=   -3.457 closest distance to " O   HOH Z 185 " =    2.272
peak=   -3.455 closest distance to " OG BSER A 134 " =    1.772
peak=   -3.448 closest distance to " O   HOH Z 394 " =    1.486
peak=   -3.447 closest distance to " O   VAL A 189 " =    2.518
peak=   -3.447 closest distance to " O   SER A  62 " =    2.326
peak=   -3.445 closest distance to " O   HOH Z 407 " =    3.191
peak=   -3.443 closest distance to " CB  TRP A  85 " =    2.519
peak=   -3.440 closest distance to " CD1 TYR A 169 " =    2.467
peak=   -3.438 closest distance to " CA  THR A  18 " =    1.373
peak=   -3.424 closest distance to " O   HOH Z 241 " =    1.277
peak=   -3.421 closest distance to " O   HOH Z  56 " =    0.774
peak=   -3.416 closest distance to " O   HOH Z  43 " =    1.764
peak=   -3.406 closest distance to " O   GLY A 196 " =    1.275
peak=   -3.401 closest distance to " O   HOH Z 309 " =    2.347
peak=   -3.400 closest distance to " ND2 ASN A  45 " =    1.117
peak=   -3.396 closest distance to " N   THR A  52 " =    1.797
peak=   -3.395 closest distance to " C   MET A 188 " =    1.576
peak=   -3.381 closest distance to " O   HOH Z 423 " =    1.120
peak=   -3.372 closest distance to " O   HOH Z 345 " =    2.084
peak=   -3.364 closest distance to " CD2 PHE A  61 " =    1.880
peak=   -3.360 closest distance to " SG BCYS A 201 " =    2.249
peak=   -3.356 closest distance to " CG  PRO A 163 " =    2.452
peak=   -3.347 closest distance to " C   ASP A 231 " =    2.583
peak=   -3.338 closest distance to " CD  GLN A 223 " =    0.805
peak=   -3.335 closest distance to " CD  GLU A 277 " =    0.905
peak=   -3.333 closest distance to " O   HOH Z 295 " =    1.475
peak=   -3.332 closest distance to " O   HOH Z 377 " =    1.863
peak=   -3.330 closest distance to " CG  LEU A 228 " =    0.898
peak=   -3.330 closest distance to " ND2 ASN A  60 " =    1.873
peak=   -3.329 closest distance to " CD  GLU A 152 " =    0.774
peak=   -3.328 closest distance to " C   HIS A 108 " =    1.126
peak=   -3.328 closest distance to " CD1 PHE A  59 " =    1.875
peak=   -3.325 closest distance to " O   HOH Z 322 " =    0.849
peak=   -3.324 closest distance to " CG2 THR A   4 " =    1.941
peak=   -3.324 closest distance to " O   SER A  22 " =    2.294
peak=   -3.322 closest distance to " O   VAL A 121 " =    1.161
peak=   -3.319 closest distance to " CB  ASN A  39 " =    2.157
peak=   -3.313 closest distance to " CG2 THR A 178 " =    2.256
peak=   -3.306 closest distance to " CD2 LEU A 237 " =    2.722
peak=   -3.302 closest distance to " O   HOH Z 423 " =    2.211
peak=   -3.296 closest distance to " CB  PHE A 192 " =    1.703
peak=   -3.292 closest distance to " O   ALA A 161 " =    1.515
peak=   -3.290 closest distance to " O   VAL A 197 " =    1.390
peak=   -3.286 closest distance to " O   HOH Z 437 " =    1.790
peak=   -3.286 closest distance to " CA  VAL A 296 " =    1.042
peak=   -3.283 closest distance to " N   SER A 276 " =    1.254
peak=   -3.273 closest distance to " O   HOH Z 102 " =    1.512
peak=   -3.270 closest distance to " NE2 GLN A 278 " =    0.960
peak=   -3.265 closest distance to " O   HOH Z 103 " =    1.885
peak=   -3.264 closest distance to " O   HOH Z  53 " =    1.657
peak=   -3.262 closest distance to " O   HOH Z 275 " =    1.846
peak=   -3.261 closest distance to " OD1 ASN A 148 " =    1.381
peak=   -3.251 closest distance to " O   HOH Z  10 " =    1.581
peak=   -3.250 closest distance to " OG1 THR A 178 " =    1.250
peak=   -3.246 closest distance to " CE3 TRP A 150 " =    2.138
peak=   -3.245 closest distance to " C   PHE A  59 " =    1.239
peak=   -3.245 closest distance to " O   HOH Z 371 " =    1.229
peak=   -3.242 closest distance to " CD1 LEU A   5 " =    2.675
peak=   -3.242 closest distance to " CD2 LEU A   5 " =    0.956
peak=   -3.240 closest distance to " O   HOH Z 353 " =    2.221
peak=   -3.237 closest distance to " O   HOH Z 350 " =    1.955
peak=   -3.237 closest distance to " CD1 LEU A 101 " =    2.690
peak=   -3.236 closest distance to " CD1 LEU A 297 " =    2.579
peak=   -3.232 closest distance to " O   HOH Z 390 " =    2.410
peak=   -3.232 closest distance to " O   HOH Z 108 " =    1.582
peak=   -3.230 closest distance to " O   HOH Z 176 " =    0.712
peak=   -3.228 closest distance to " O   HOH Z  22 " =    2.464
peak=   -3.228 closest distance to " CA  GLY A 203 " =    2.369
peak=   -3.222 closest distance to " O   HOH Z  98 " =    2.238
peak=   -3.221 closest distance to " CD  ARG A 139 " =    1.667
peak=   -3.220 closest distance to " O   HOH Z 377 " =    1.171
peak=   -3.220 closest distance to " N   GLY A  23 " =    2.208
peak=   -3.217 closest distance to " ND2 ASN A  45 " =    1.618
peak=   -3.215 closest distance to " CZ BARG A 275 " =    1.690
peak=   -3.212 closest distance to " CB  PHE A 130 " =    1.278
peak=   -3.204 closest distance to " CB  ALA A 291 " =    2.252
peak=   -3.203 closest distance to " O   HOH Z 359 " =    3.387
peak=   -3.195 closest distance to " O   HOH Z  73 " =    2.130
peak=   -3.195 closest distance to " C   ASP A 270 " =    1.430
peak=   -3.194 closest distance to " CA  ARG A 139 " =    0.996
peak=   -3.188 closest distance to " CG2 VAL A 202 " =    2.795
peak=   -3.188 closest distance to " O   HOH Z  65 " =    1.187
peak=   -3.187 closest distance to " O   HOH Z 166 " =    1.990
peak=   -3.183 closest distance to " NZ  LYS A 119 " =    3.475
peak=   -3.182 closest distance to " CG  LYS A 193 " =    2.376
peak=   -3.182 closest distance to " O   HOH Z  93 " =    0.768
peak=   -3.181 closest distance to " CB  ASP A 132 " =    2.326
peak=   -3.180 closest distance to " CZ3 TRP A 274 " =    0.949
peak=   -3.175 closest distance to " O   HOH Z 111 " =    2.293
peak=   -3.170 closest distance to " N   ALA A 226 " =    2.200
peak=   -3.166 closest distance to " N   SER A 212 " =    1.791
peak=   -3.166 closest distance to " CG  ARG A 259 " =    2.506
peak=   -3.165 closest distance to " CG1 VAL A 265 " =    2.428
peak=   -3.164 closest distance to " OG  SER A   3 " =    1.671
peak=   -3.164 closest distance to " CD2 LEU A 300 " =    3.031
peak=   -3.162 closest distance to " CB  TYR A 172 " =    2.363
peak=   -3.160 closest distance to " CB  ALA A 114 " =    2.445
peak=   -3.158 closest distance to " O   HOH Z 210 " =    0.775
peak=   -3.156 closest distance to " CA  SER A 135 " =    1.383
peak=   -3.152 closest distance to " C   VAL A 174 " =    1.819
peak=   -3.146 closest distance to " CE  MET A 105 " =    2.299
peak=   -3.145 closest distance to " NH2 ARG A 159 " =    2.339
peak=   -3.142 closest distance to " OD2 ASP A 171 " =    1.801
peak=   -3.133 closest distance to " O   HOH Z   2 " =    1.708
peak=   -3.132 closest distance to " O   VAL A  67 " =    2.557
peak=   -3.130 closest distance to " CG2 THR A 279 " =    1.986
peak=   -3.127 closest distance to " OG ASER A 134 " =    1.627
peak=   -3.127 closest distance to " O   ARG A 145 " =    1.580
peak=   -3.121 closest distance to " O   VAL A 197 " =    1.073
peak=   -3.117 closest distance to " CH2 TRP A 177 " =    2.242
peak=   -3.114 closest distance to " O   HOH Z   2 " =    1.688
peak=   -3.113 closest distance to " CD  PRO A 243 " =    2.109
peak=   -3.112 closest distance to " O   PRO A 198 " =    1.341
peak=   -3.109 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.103 closest distance to " ND2 ASN A  60 " =    1.660
peak=   -3.101 closest distance to " O   HOH Z 168 " =    1.946
peak=   -3.097 closest distance to " CG2AVAL A  72 " =    4.360
peak=   -3.095 closest distance to " CB  TYR A  15 " =    2.127
peak=   -3.090 closest distance to " O   HOH Z 222 " =    1.206
peak=   -3.067 closest distance to " O   HOH Z 298 " =    1.201
peak=   -3.062 closest distance to " NH2 ARG A  36 " =    2.310
peak=   -3.058 closest distance to " CG2 THR A  18 " =    2.779
peak=   -3.051 closest distance to " C   ALA A 165 " =    1.966

================= 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    :  0.4630 0.4500   6.262762e+00   6.247446e+00
   1_bss:  0.4546 0.4398   6.257070e+00   6.239605e+00
   1_xyz:  0.3612 0.3838   6.110093e+00   6.152057e+00
   1_adp:  0.3086 0.3536   5.997983e+00   6.097863e+00
   1_occ:  0.3081 0.3539   5.997528e+00   6.099187e+00
   2_bss:  0.3049 0.3491   5.997070e+00   6.097009e+00
   2_xyz:  0.2195 0.2706   5.717828e+00   5.882670e+00
   2_adp:  0.2033 0.2587   5.659926e+00   5.841117e+00
   2_occ:  0.2031 0.2586   5.659590e+00   5.840960e+00
   3_bss:  0.2021 0.2576   5.660599e+00   5.841428e+00
   3_xyz:  0.1478 0.1978   5.382706e+00   5.609268e+00
   3_adp:  0.1314 0.1792   5.277281e+00   5.510358e+00
   3_occ:  0.1314 0.1790   5.276148e+00   5.509060e+00
   4_bss:  0.1312 0.1781   5.274520e+00   5.505271e+00
   4_xyz:  0.1183 0.1666   5.196244e+00   5.441498e+00
   4_adp:  0.1175 0.1637   5.185973e+00   5.425658e+00
   4_occ:  0.1174 0.1633   5.184670e+00   5.423683e+00
   5_bss:  0.1173 0.1632   5.184337e+00   5.423476e+00
   5_xyz:  0.1197 0.1636   5.196887e+00   5.425941e+00
   5_adp:  0.1201 0.1637   5.200107e+00   5.430399e+00
   5_occ:  0.1200 0.1636   5.199539e+00   5.429626e+00
   5_bss:  0.1199 0.1636   5.199512e+00   5.429571e+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:  0.300  20.000   9.109   8.232   7.017   0.000   0.000   0.000
   1_xyz:  0.300  20.000   9.109   8.232   7.017   0.000   0.000   0.000
   1_adp:  0.300  20.000   9.109   8.232   7.017   0.000   0.000   0.000
   1_occ:  0.300  20.000   9.109   8.232   7.017   0.000   0.000   0.000
   2_bss:  0.340  45.426   5.802   4.552   4.679   0.000   0.000   0.000
   2_xyz:  0.340  45.426   5.802   4.552   4.679   0.000   0.000   0.000
   2_adp:  0.340  45.426   5.802   4.552   4.679   0.000   0.000   0.000
   2_occ:  0.340  45.426   5.802   4.552   4.679   0.000   0.000   0.000
   3_bss:  0.341  45.437   3.816   2.860   3.887   0.000   0.000   0.000
   3_xyz:  0.341  45.437   3.816   2.860   3.887   0.000   0.000   0.000
   3_adp:  0.341  45.437   3.816   2.860   3.887   0.000   0.000   0.000
   3_occ:  0.341  45.437   3.816   2.860   3.887   0.000   0.000   0.000
   4_bss:  0.330  45.437   2.826   2.079   3.278   0.000   0.000   0.000
   4_xyz:  0.330  45.437   2.826   2.079   3.278   0.000   0.000   0.000
   4_adp:  0.330  45.437   2.826   2.079   3.278   0.000   0.000   0.000
   4_occ:  0.330  45.437   2.826   2.079   3.278   0.000   0.000   0.000
   5_bss:  0.325  45.437   2.509   1.917   3.123   0.000   0.000   0.000
   5_xyz:  0.325  45.437   2.509   1.917   3.123   0.000   0.000   0.000
   5_adp:  0.325  45.437   2.509   1.917   3.123   0.000   0.000   0.000
   5_occ:  0.325  45.437   2.509   1.917   3.123   0.000   0.000   0.000
   5_bss:  0.325  47.850  -0.058  -0.568   0.626  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.538 0.4897  0.5637    61877.338
   1_bss:  52.735 0.4856  0.7067    59880.142
   1_xyz:  43.359 0.6014  0.8531    42856.886
   1_adp:  38.062 0.6659  0.9635    35713.969
   1_occ:  38.190 0.6643  0.9602    35867.523
   2_bss:  37.931 0.6672  0.8648    35452.731
   2_xyz:  27.438 0.7852  0.9775    19231.303
   2_adp:  25.627 0.8052  0.9958    17453.935
   2_occ:  25.648 0.8049  0.9953    17442.933
   3_bss:  25.633 0.8052  0.9442    17490.769
   3_xyz:  18.956 0.8711  0.9954    10050.306
   3_adp:  16.666 0.8922  1.0081     8247.259
   3_occ:  16.633 0.8924  1.0083     8220.469
   4_bss:  16.571 0.8928  0.9796     8119.252
   4_xyz:  15.074 0.9060  0.9819     7032.626
   4_adp:  14.648 0.9099  0.9830     6849.891
   4_occ:  14.616 0.9102  0.9830     6818.551
   5_bss:  14.609 0.9103  0.9755     6810.753
   5_xyz:  14.600 0.9105  0.9754     6815.734
   5_adp:  14.652 0.9102  0.9754     6878.176
   5_occ:  14.640 0.9102  0.9754     6866.634
   5_bss:  14.638 0.9103  0.9718     6864.897
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3826e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3826e+01
   1_xyz:   1.636  0.013  0.106 18.240  0.006  4.111   1.3433e-01
   1_adp:   1.636  0.013  0.106 18.240  0.006  4.111   1.3433e-01
   1_occ:   1.636  0.013  0.106 18.240  0.006  4.111   1.3433e-01
   2_bss:   1.636  0.013  0.106 18.240  0.006  4.111   1.3433e-01
   2_xyz:   1.033  0.008  0.070 16.398  0.005  4.124   6.9218e-02
   2_adp:   1.033  0.008  0.070 16.398  0.005  4.124   6.9218e-02
   2_occ:   1.033  0.008  0.070 16.398  0.005  4.124   6.9218e-02
   3_bss:   1.033  0.008  0.070 16.398  0.005  4.124   6.9218e-02
   3_xyz:   1.139  0.009  0.088 16.262  0.004  4.112   7.9549e-02
   3_adp:   1.139  0.009  0.088 16.262  0.004  4.112   7.9549e-02
   3_occ:   1.139  0.009  0.088 16.262  0.004  4.112   7.9549e-02
   4_bss:   1.139  0.009  0.088 16.262  0.004  4.112   7.9549e-02
   4_xyz:   1.115  0.009  0.089 16.305  0.004  4.118   7.6360e-02
   4_adp:   1.115  0.009  0.089 16.305  0.004  4.118   7.6360e-02
   4_occ:   1.115  0.009  0.089 16.305  0.004  4.118   7.6360e-02
   5_bss:   1.115  0.009  0.089 16.305  0.004  4.118   7.6360e-02
   5_xyz:   0.936  0.006  0.073 15.743  0.003  4.119   5.6377e-02
   5_adp:   0.936  0.006  0.073 15.743  0.003  4.119   5.6377e-02
   5_occ:   0.936  0.006  0.073 15.743  0.003  4.119   5.6377e-02
   5_bss:   0.936  0.006  0.073 15.743  0.003  4.119   5.6377e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9789e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9789e+00
   1_xyz:  13.639  0.163  0.445 86.820  0.035  2.254   1.0032e-01
   1_adp:  13.639  0.163  0.445 86.820  0.035  2.254   1.0032e-01
   1_occ:  13.639  0.163  0.445 86.820  0.035  2.254   1.0032e-01
   2_bss:  13.639  0.163  0.445 86.820  0.035  2.254   1.0032e-01
   2_xyz:   6.572  0.076  0.268 87.133  0.047  2.355   6.5043e-02
   2_adp:   6.572  0.076  0.268 87.133  0.047  2.355   6.5043e-02
   2_occ:   6.572  0.076  0.268 87.133  0.047  2.355   6.5043e-02
   3_bss:   6.572  0.076  0.268 87.133  0.047  2.355   6.5043e-02
   3_xyz:   7.938  0.090  0.493 82.768  0.032  2.310   7.3549e-02
   3_adp:   7.938  0.090  0.493 82.768  0.032  2.310   7.3549e-02
   3_occ:   7.938  0.090  0.493 82.768  0.032  2.310   7.3549e-02
   4_bss:   7.938  0.090  0.493 82.768  0.032  2.310   7.3549e-02
   4_xyz:   9.511  0.065  0.605 84.428  0.043  2.314   5.9534e-02
   4_adp:   9.511  0.065  0.605 84.428  0.043  2.314   5.9534e-02
   4_occ:   9.511  0.065  0.605 84.428  0.043  2.314   5.9534e-02
   5_bss:   9.511  0.065  0.605 84.428  0.043  2.314   5.9534e-02
   5_xyz:   7.970  0.043  0.417 83.788  0.036  2.372   3.1089e-02
   5_adp:   7.970  0.043  0.417 83.788  0.036  2.372   3.1089e-02
   5_occ:   7.970  0.043  0.417 83.788  0.036  2.372   3.1089e-02
   5_bss:   7.970  0.043  0.417 83.788  0.036  2.372   3.1089e-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:  77.14   0.00  12.12  76.53   0.00   9.16  77.14   0.00  28.25
   1_occ:  77.14   0.00  12.12  76.53   0.00   9.16  77.14   0.00  28.25
   2_bss:  77.14   0.00  12.12  76.53   0.00   9.16  77.14   0.00  28.25
   2_xyz:  77.14   0.00  12.12  76.53   0.00   9.16  77.14   0.00  28.25
   2_adp:  77.22   0.00  12.14  76.17   0.00   8.76  77.22   0.00  30.51
   2_occ:  77.22   0.00  12.14  76.17   0.00   8.76  77.22   0.00  30.51
   3_bss:  77.22   0.00  12.14  76.17   0.00   8.76  77.22   0.00  30.51
   3_xyz:  77.22   0.00  12.14  76.17   0.00   8.76  77.22   0.00  30.51
   3_adp:  79.94   0.00  12.46  79.94   0.00   8.39  77.76   1.37  34.61
   3_occ:  79.94   0.00  12.46  79.94   0.00   8.39  77.76   1.37  34.61
   4_bss:  79.94   0.00  12.46  79.94   0.00   8.39  77.76   1.37  34.61
   4_xyz:  79.94   0.00  12.46  79.94   0.00   8.39  77.76   1.37  34.61
   4_adp:  79.00   0.00  12.15  79.00   0.00   8.27  76.90   2.15  33.23
   4_occ:  79.00   0.00  12.15  79.00   0.00   8.27  76.90   2.15  33.23
   5_bss:  79.00   0.00  12.15  79.00   0.00   8.27  76.90   2.15  33.23
   5_xyz:  79.00   0.00  12.15  79.00   0.00   8.27  76.90   2.15  33.23
   5_adp:  76.89   0.00  11.95  76.89   0.00   8.26  73.80   2.25  32.04
   5_occ:  76.89   0.00  11.95  76.89   0.00   8.26  73.80   2.25  32.04
   5_bss:  79.30   2.41  14.37  79.30   2.41  10.68  76.21   4.67  34.45
------------------------------------------------------------------------
 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:    1.195    0.025    0.410
   1_adp:    1.195    0.025    0.410
   1_occ:    1.195    0.025    0.410
   2_bss:    1.195    0.025    0.410
   2_xyz:    1.466    0.037    0.541
   2_adp:    1.466    0.037    0.541
   2_occ:    1.466    0.037    0.541
   3_bss:    1.466    0.037    0.541
   3_xyz:    1.542    0.053    0.628
   3_adp:    1.542    0.053    0.628
   3_occ:    1.542    0.053    0.628
   4_bss:    1.542    0.053    0.628
   4_xyz:    1.819    0.033    0.654
   4_adp:    1.819    0.033    0.654
   4_occ:    1.819    0.033    0.654
   5_bss:    1.819    0.033    0.654
   5_xyz:    1.897    0.019    0.661
   5_adp:    1.897    0.019    0.661
   5_occ:    1.897    0.019    0.661
   5_bss:    1.897    0.019    0.661
------------------------------------------------------------------------

CPU time actual refinement: 341.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1126/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_1126/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1126/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1126/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1126/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.39 
  Macro-tasks:
    bulk solvent and scale       = 39.31  
    individual site refinement   = 139.22 
    weights calculation          = 31.73  
    collect and process          = 6.43   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.81 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 109.13 
    alpha_beta                      = 8.17   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 117.99 
    fmodel                         = 7.19   
    r_factors                      = 0.30   
    phase_errors                   = 10.67  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 256.59 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.819 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    659 calls, 108.67 s
gradients_fft:          604 calls, 104.95 s

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

# Date 2008-01-16 Time 03:15:06 PST -0800 (1200482106.26 s)
Start R-work = 0.4630, R-free = 0.4500 (no bulk solvent and anisotropic scale)
Final R-work = 0.1371, R-free = 0.1810 (no bulk solvent and anisotropic scale)

Start R-work = 0.4546, R-free = 0.4398
Final R-work = 0.1199, R-free = 0.1636