# Date 2008-01-16 Time 00:57:56 PST -0800 (1200473876.86 s)
#phil __OFF__

Command line arguments: "../237.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8899
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 237

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 48.1033, 86.822, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0412 1.96084
Completeness in resolution range: 0.921055
Completeness with d_max=infinity: 0.918335

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0412
                             d_min =   1.9608

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0412 1.96084
Completeness in resolution range: 0.921055
Completeness with d_max=infinity: 0.918335

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0416 -  4.1968 [2229/2258]  2001   228  10.2%
  bin  2:  4.1968 -  3.3431 [2140/2163]  1927   213  10.0%
  bin  3:  3.3431 -  2.9241 [2119/2144]  1914   205   9.7%
  bin  4:  2.9241 -  2.6583 [2090/2117]  1877   213  10.2%
  bin  5:  2.6583 -  2.4687 [2061/2094]  1856   205   9.9%
  bin  6:  2.4687 -  2.3237 [2087/2115]  1876   211  10.1%
  bin  7:  2.3237 -  2.2077 [2064/2100]  1862   202   9.8%
  bin  8:  2.2077 -  2.1119 [2046/2088]  1842   204  10.0%
  bin  9:  2.1119 -  2.0308 [1993/2086]  1795   198   9.9%
  bin 10:  2.0308 -  1.9608 [ 760/2103]   680    80  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_237/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 9
        1.93 -     2.67: 105
        2.67 -     3.41: 4446
        3.41 -     4.16: 9330
        4.16 -     4.90: 14341
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.187 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.278 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.308 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.568 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28226 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_237/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_237/model_refine_001.geo

CPU time processing inputs: 10.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 48.10325 86.82195 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: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5129   r_free= 0.4995   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.311036                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.6814 0.99   1457  160 0.4267 0.4437      6.6607      6.7106|
|  2:  4.6814 -  3.7345 0.99   1390  155 0.4521 0.4623      6.8709      6.8839|
|  3:  3.7345 -  3.2679 0.99   1359  152 0.4932 0.4750      6.7221      6.7198|
|  4:  3.2679 -  2.9717 0.98   1359  146 0.5100 0.4628      6.5428      6.5086|
|  5:  2.9717 -  2.7601 0.99   1343  155 0.5565 0.5389      6.3884      6.3961|
|  6:  2.7601 -  2.5982 0.99   1361  148 0.5434 0.4952      6.2975      6.1832|
|  7:  2.5982 -  2.4687 0.98   1306  148 0.5269 0.5197      6.2408      6.1926|
|  8:  2.4687 -  2.3616 0.98   1339  144 0.5399 0.4844      6.1822      6.1856|
|  9:  2.3616 -  2.2710 0.99   1336  144 0.5538 0.5730      6.1209      6.1757|
| 10:  2.2710 -  2.1929 0.99   1341  146 0.5472 0.5464      6.0967      6.1038|
| 11:  2.1929 -  2.1245 0.97   1304  148 0.5726 0.5382      6.0379      6.0481|
| 12:  2.1245 -  2.0640 0.98   1311  155 0.5387 0.5130      5.9517      5.9581|
| 13:  2.0640 -  2.0098 0.84   1119  121 0.5391 0.5766       5.865      5.8292|
| 14:  2.0098 -  1.9608 0.23    305   37 0.6037 0.4745      5.9346      5.7352|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0416 -  4.6814  1457   160  0.61  42.39   0.78     0.62     100077.22|
|  2:  4.6814 -  3.7345  1390   155  0.62  42.47   0.85     0.67     139033.40|
|  3:  3.7345 -  3.2679  1359   152  0.51  51.33   0.80     0.63     141365.58|
|  4:  3.2679 -  2.9717  1359   146  0.44  56.75   0.76     0.54     114149.27|
|  5:  2.9717 -  2.7601  1343   155  0.34  64.25   0.70     0.43      92198.67|
|  6:  2.7601 -  2.5982  1361   148  0.32  66.10   0.69     0.37      78070.33|
|  7:  2.5982 -  2.4687  1306   148  0.27  70.04   0.72     0.32      73567.15|
|  8:  2.4687 -  2.3616  1339   144  0.27  69.99   0.71     0.31      64375.39|
|  9:  2.3616 -  2.2710  1336   144  0.25  71.21   0.69     0.32      62337.77|
| 10:  2.2710 -  2.1929  1341   146  0.27  70.15   0.73     0.33      54449.95|
| 11:  2.1929 -  2.1245  1304   148  0.26  71.01   0.72     0.35      52635.01|
| 12:  2.1245 -  2.0640  1311   155  0.26  70.86   0.73     0.35      46872.62|
| 13:  2.0640 -  2.0098  1119   121  0.25  71.21   0.72     0.34      40035.13|
| 14:  2.0098 -  1.9608   305    37  0.28  68.86   0.70     0.30      29863.57|
|alpha:            min =        0.30 max =            0.67 mean =         0.43|
|beta:             min =    29863.57 max =       141365.58 mean =     81620.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.65|
|phase err.(test): min =        0.00 max =           89.97 mean =        62.71|
|-----------------------------------------------------------------------------|

============================== 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 = 22.199124             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.586   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.841447              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.160   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.878 -  1.281:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.281 -  1.683:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.683 -  2.085:       57 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.085 -  2.487:      397 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.487 -  2.889:     1173 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.889 -  3.291:     2342 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.291 -  3.693:     3886 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.693 -  4.096:     5227 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.096 -  4.498:     6902 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.498 -  4.900:     8297 |
|-----------------------------------------------------------------------------|
|-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 |       53.825 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.878 |       2.569 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    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 = 11.871)------------------------------------------|
|    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: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5182   r_free= 0.5033   ksol= 0.00   Bsol= 0.00   scale= 0.737    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.311181                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5078   r_free= 0.4959   ksol= 0.32   Bsol= 5.97   scale= 0.961    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,11.99,7.64,0.00,0.00,0.00); trace/3= 8.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.304791                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.456190             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.338   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.898422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.723   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5078      final r-factor (work) = 0.4482          |
| start r-factor (free) = 0.4959      final r-factor (free) = 0.4590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 121.4969 = 21.46 * 0.50 * 6.3079 + 1.00 * 53.8248                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 67.3369 = 21.46 * 0.50 * 6.2623 + 1.00 * 0.1549                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4482      final r-factor (work) = 0.4071          |
| start r-factor (free) = 0.4590      final r-factor (free) = 0.4633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.9031 = 1.90 * 1.00 * 6.2623 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8163 = 1.90 * 1.00 * 6.2117 + 1.00 * 0.0238                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.29  17.34    None  None   None       |
|    all(noH): 2823   0      0.00    110.29  17.34    None  None   None       |
|    Sol.    : 438    0      0.00    110.29  27.51    None  None   None       |
|    Mac.    : 2385   0      0.00    77.39   15.47    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 -  11.029: 1157   |   5:    55.147 -  66.177:   49        |
|      1:    11.029 -  22.059:  851   |   6:    66.177 -  77.206:   16        |
|      2:    22.059 -  33.088:  424   |   7:    77.206 -  88.235:    6        |
|      3:    33.088 -  44.118:  225   |   8:    88.235 -  99.265:    4        |
|      4:    44.118 -  55.147:   89   |   9:    99.265 - 110.294:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4071 r_free = 0.4633             target_work(ml) = 6.203         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4067 r_free = 0.4627             target_work(ml) = 6.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4067   r_free= 0.4627   ksol= 0.32   Bsol= 5.97   scale= 1.118    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,11.99,7.64,0.00,0.00,0.00); trace/3= 8.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.202164                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4039   r_free= 0.4560   ksol= 0.29   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,6.71,4.00,0.00,0.00,0.00); trace/3= 4.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.202813                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.722728             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.381  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.643145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.190  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4039      final r-factor (work) = 0.3495          |
| start r-factor (free) = 0.4560      final r-factor (free) = 0.4167          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.4371 = 10.72 * 0.50 * 6.2079 + 1.00 * 0.1544                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.0373 = 10.72 * 0.50 * 6.1433 + 1.00 * 0.1009                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3495      final r-factor (work) = 0.3397          |
| start r-factor (free) = 0.4167      final r-factor (free) = 0.4044          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9751 = 0.64 * 1.00 * 6.1433 + 1.00 * 0.0241                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9351 = 0.64 * 1.00 * 6.1005 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.93   16.30    None  None   None       |
|    all(noH): 2823   0      0.00    98.93   16.30    None  None   None       |
|    Sol.    : 438    0      0.00    98.93   27.67    None  None   None       |
|    Mac.    : 2385   0      0.00    75.18   14.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.893: 1060   |   5:    49.466 -  59.359:   30        |
|      1:     9.893 -  19.786:  904   |   6:    59.359 -  69.252:   13        |
|      2:    19.786 -  29.680:  471   |   7:    69.252 -  79.146:    8        |
|      3:    29.680 -  39.573:  233   |   8:    79.146 -  89.039:    0        |
|      4:    39.573 -  49.466:  100   |   9:    89.039 -  98.932:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3397 r_free = 0.4044             target_work(ml) = 6.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3395 r_free = 0.4047             target_work(ml) = 6.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3395   r_free= 0.4047   ksol= 0.29   Bsol= 20.00   scale= 1.059   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,6.71,4.00,0.00,0.00,0.00); trace/3= 4.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.090589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3389   r_free= 0.4027   ksol= 0.31   Bsol= 48.22   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.02,4.59,2.39,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.090123                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.829092             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.136  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441089              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.863  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3389      final r-factor (work) = 0.2647          |
| start r-factor (free) = 0.4027      final r-factor (free) = 0.3218          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.2841 = 13.83 * 0.50 * 6.1007 + 1.00 * 0.1009                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.6051 = 13.83 * 0.50 * 6.0001 + 1.00 * 0.1172                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2647      final r-factor (work) = 0.2539          |
| start r-factor (free) = 0.3218      final r-factor (free) = 0.3125          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6639 = 0.44 * 1.00 * 6.0001 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6490 = 0.44 * 1.00 * 5.8543 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.42   16.25    None  None   None       |
|    all(noH): 2823   0      0.00    98.42   16.25    None  None   None       |
|    Sol.    : 438    0      1.62    98.42   28.90    None  None   None       |
|    Mac.    : 2385   0      0.00    75.91   13.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.842: 1076   |   5:    49.210 -  59.052:   31        |
|      1:     9.842 -  19.684:  912   |   6:    59.052 -  68.894:   13        |
|      2:    19.684 -  29.526:  450   |   7:    68.894 -  78.736:   10        |
|      3:    29.526 -  39.368:  231   |   8:    78.736 -  88.577:    0        |
|      4:    39.368 -  49.210:   96   |   9:    88.577 -  98.419:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2539 r_free = 0.3125             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2537 r_free = 0.3125             target_work(ml) = 5.843         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2537   r_free= 0.3125   ksol= 0.31   Bsol= 48.22   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.02,4.59,2.39,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.843309                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2520   r_free= 0.3108   ksol= 0.32   Bsol= 44.30   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,2.22,1.39,0.00,0.00,0.00); trace/3= 1.04                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.842356                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.476260              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.510  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.070954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.326   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2520      final r-factor (work) = 0.2076          |
| start r-factor (free) = 0.3108      final r-factor (free) = 0.2637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0767 = 6.48 * 0.50 * 5.8551 + 1.00 * 0.1172                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7584 = 6.48 * 0.50 * 5.7691 + 1.00 * 0.0774                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2076      final r-factor (work) = 0.1829          |
| start r-factor (free) = 0.2637      final r-factor (free) = 0.2379          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2154 = 1.07 * 1.00 * 5.7691 + 1.00 * 0.0370                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0905 = 1.07 * 1.00 * 5.6210 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.60   16.20    None  None   None       |
|    all(noH): 2823   0      0.00    96.60   16.20    None  None   None       |
|    Sol.    : 438    0      4.10    96.60   34.39    None  None   None       |
|    Mac.    : 2385   0      0.00    83.39   12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.660: 1153   |   5:    48.298 -  57.958:   48        |
|      1:     9.660 -  19.319:  847   |   6:    57.958 -  67.618:   13        |
|      2:    19.319 -  28.979:  357   |   7:    67.618 -  77.277:    9        |
|      3:    28.979 -  38.639:  248   |   8:    77.277 -  86.937:    4        |
|      4:    38.639 -  48.298:  140   |   9:    86.937 -  96.597:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1829 r_free = 0.2379             target_work(ml) = 5.572         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1828 r_free = 0.2380             target_work(ml) = 5.572         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1828   r_free= 0.2380   ksol= 0.32   Bsol= 44.30   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,2.22,1.39,0.00,0.00,0.00); trace/3= 1.04                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.572277                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1830   r_free= 0.2383   ksol= 0.32   Bsol= 44.30   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,1.05,0.85,0.00,0.00,0.00); trace/3= 0.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.573613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.252697              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.433  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.564758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.111   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1830      final r-factor (work) = 0.1538          |
| start r-factor (free) = 0.2383      final r-factor (free) = 0.2111          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0362 = 4.25 * 0.50 * 5.6241 + 1.00 * 0.0774                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7827 = 4.25 * 0.50 * 5.5039 + 1.00 * 0.0795                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1538      final r-factor (work) = 0.1382          |
| start r-factor (free) = 0.2111      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1212 = 0.56 * 1.00 * 5.5039 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0580 = 0.56 * 1.00 * 5.3953 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.59   16.05    None  None   None       |
|    all(noH): 2823   0      0.00    88.59   16.05    None  None   None       |
|    Sol.    : 438    0      4.45    88.59   39.34    None  None   None       |
|    Mac.    : 2385   0      0.00    82.26   11.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.859: 1070   |   5:    44.296 -  53.155:  113        |
|      1:     8.859 -  17.718: 1035   |   6:    53.155 -  62.014:   69        |
|      2:    17.718 -  26.577:  255   |   7:    62.014 -  70.873:   30        |
|      3:    26.577 -  35.437:  119   |   8:    70.873 -  79.732:    8        |
|      4:    35.437 -  44.296:  118   |   9:    79.732 -  88.591:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1382 r_free = 0.1883             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1381 r_free = 0.1884             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1381   r_free= 0.1884   ksol= 0.32   Bsol= 44.30   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,1.05,0.85,0.00,0.00,0.00); trace/3= 0.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.331419                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.6814 0.99   1457  160 0.0977 0.1438      5.4013      5.6427|
|  2:  4.6814 -  3.7345 0.99   1390  155 0.0932 0.1207      5.5269      5.7653|
|  3:  3.7345 -  3.2679 0.99   1359  152 0.1310 0.1925      5.6477      6.0252|
|  4:  3.2679 -  2.9717 0.98   1359  146 0.1549 0.1950      5.6401      5.8049|
|  5:  2.9717 -  2.7601 0.99   1343  155 0.1708 0.2005      5.5365      5.6806|
|  6:  2.7601 -  2.5982 0.99   1361  148 0.1554 0.2325      5.4029      5.5905|
|  7:  2.5982 -  2.4687 0.98   1306  148 0.1567 0.2024      5.3312      5.5246|
|  8:  2.4687 -  2.3616 0.98   1339  144 0.1524 0.1992      5.2716      5.4779|
|  9:  2.3616 -  2.2710 0.99   1336  144 0.1536 0.2253      5.2163      5.5191|
| 10:  2.2710 -  2.1929 0.99   1341  146 0.1493 0.2213      5.1837      5.3844|
| 11:  2.1929 -  2.1245 0.97   1304  148 0.1468 0.2070      5.1161       5.387|
| 12:  2.1245 -  2.0640 0.98   1311  155 0.1512 0.2137      5.0796      5.3565|
| 13:  2.0640 -  2.0098 0.84   1119  121 0.1484 0.2079       4.971      5.1848|
| 14:  2.0098 -  1.9608 0.23    305   37 0.1263 0.1833      4.8422      5.0041|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0416 -  4.6814  1457   160  0.93  10.11   0.97     0.96       8216.57|
|  2:  4.6814 -  3.7345  1390   155  0.94   9.88   1.03     1.02      11673.35|
|  3:  3.7345 -  3.2679  1359   152  0.91  14.63   1.03     1.02      14860.12|
|  4:  3.2679 -  2.9717  1359   146  0.88  18.23   1.02     1.01      15511.25|
|  5:  2.9717 -  2.7601  1343   155  0.86  20.48   1.01     0.99      12881.01|
|  6:  2.7601 -  2.5982  1361   148  0.86  20.77   0.99     0.95      10514.99|
|  7:  2.5982 -  2.4687  1306   148  0.87  19.14   1.00     0.95       8359.95|
|  8:  2.4687 -  2.3616  1339   144  0.86  20.14   1.02     0.98       8129.44|
|  9:  2.3616 -  2.2710  1336   144  0.86  20.22   1.01     0.96       7213.79|
| 10:  2.2710 -  2.1929  1341   146  0.85  21.16   1.01     0.97       7231.43|
| 11:  2.1929 -  2.1245  1304   148  0.86  20.80   1.02     0.96       6362.43|
| 12:  2.1245 -  2.0640  1311   155  0.85  21.28   1.01     1.01       6062.07|
| 13:  2.0640 -  2.0098  1119   121  0.86  20.52   1.00     0.98       4794.01|
| 14:  2.0098 -  1.9608   305    37  0.88  17.98   0.98     0.92       3445.16|
|alpha:            min =        0.92 max =            1.02 mean =         0.98|
|beta:             min =     3445.16 max =        15511.25 mean =      9352.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.86 mean =        18.13|
|phase err.(test): min =        0.00 max =           89.75 mean =        17.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1892   ksol= 0.32   Bsol= 53.46   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.48,0.71,0.00,0.00,0.00); trace/3= -0.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333691                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1383   r_free= 0.1892   ksol= 0.32   Bsol= 53.46   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.48,0.71,0.00,0.00,0.00); trace/3= -0.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333691                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0416 -  4.6814 0.99   1457  160 0.1002 0.1518      5.4276      5.6724|
|  2:  4.6814 -  3.7345 0.99   1390  155 0.0951 0.1205      5.5458      5.7663|
|  3:  3.7345 -  3.2679 0.99   1359  152 0.1318 0.1935      5.6509      6.0248|
|  4:  3.2679 -  2.9717 0.98   1359  146 0.1547 0.1952       5.639      5.8045|
|  5:  2.9717 -  2.7601 0.99   1343  155 0.1704 0.1994      5.5336      5.6782|
|  6:  2.7601 -  2.5982 0.99   1361  148 0.1549 0.2309      5.3993      5.5849|
|  7:  2.5982 -  2.4687 0.98   1306  148 0.1561 0.2025      5.3273      5.5248|
|  8:  2.4687 -  2.3616 0.98   1339  144 0.1514 0.1988      5.2694      5.4785|
|  9:  2.3616 -  2.2710 0.99   1336  144 0.1529 0.2256      5.2139      5.5154|
| 10:  2.2710 -  2.1929 0.99   1341  146 0.1486 0.2217      5.1814      5.3861|
| 11:  2.1929 -  2.1245 0.97   1304  148 0.1464 0.2066       5.115      5.3868|
| 12:  2.1245 -  2.0640 0.98   1311  155 0.1510 0.2138      5.0796      5.3563|
| 13:  2.0640 -  2.0098 0.84   1119  121 0.1482 0.2071      4.9691      5.1813|
| 14:  2.0098 -  1.9608 0.23    305   37 0.1263 0.1827      4.8399      5.0018|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0416 -  4.6814  1457   160  0.93  10.53   0.97     0.95       8794.89|
|  2:  4.6814 -  3.7345  1390   155  0.94  10.17   1.03     1.01      12112.75|
|  3:  3.7345 -  3.2679  1359   152  0.91  14.73   1.02     1.01      15006.52|
|  4:  3.2679 -  2.9717  1359   146  0.88  18.24   1.01     1.00      15490.02|
|  5:  2.9717 -  2.7601  1343   155  0.86  20.40   1.01     0.98      12783.23|
|  6:  2.7601 -  2.5982  1361   148  0.86  20.67   0.98     0.94      10443.39|
|  7:  2.5982 -  2.4687  1306   148  0.87  19.07   0.99     0.94       8311.12|
|  8:  2.4687 -  2.3616  1339   144  0.86  20.07   1.01     0.97       8114.62|
|  9:  2.3616 -  2.2710  1336   144  0.86  20.20   1.00     0.95       7203.96|
| 10:  2.2710 -  2.1929  1341   146  0.85  21.13   1.00     0.95       7217.39|
| 11:  2.1929 -  2.1245  1304   148  0.86  20.81   1.00     0.95       6365.19|
| 12:  2.1245 -  2.0640  1311   155  0.86  21.24   1.00     0.99       6054.92|
| 13:  2.0640 -  2.0098  1119   121  0.86  20.44   0.99     0.97       4763.33|
| 14:  2.0098 -  1.9608   305    37  0.88  17.91   0.97     0.91       3404.99|
|alpha:            min =        0.91 max =            1.01 mean =         0.97|
|beta:             min =     3404.99 max =        15490.02 mean =      9421.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.97 mean =        18.16|
|phase err.(test): min =        0.00 max =           89.27 mean =        17.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.871)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.59   16.05    None  None   None       |
|    all(noH): 2823   0      0.00    88.59   16.05    None  None   None       |
|    Sol.    : 438    0      4.46    88.59   39.34    None  None   None       |
|    Mac.    : 2385   0      0.00    82.27   11.77    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:     0.003 -   8.862: 1070   |   5:    44.299 -  53.158:  113        |
|      1:     8.862 -  17.721: 1035   |   6:    53.158 -  62.017:   69        |
|      2:    17.721 -  26.580:  255   |   7:    62.017 -  70.876:   30        |
|      3:    26.580 -  35.440:  119   |   8:    70.876 -  79.735:    8        |
|      4:    35.440 -  44.299:  118   |   9:    79.735 -  88.594:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 349         
Filter by distance & map next to the model:
   mapped sites are within: 0.367 - 5.786
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 349
   mapped sites are within: 0.730 - 5.786

peak=    8.850 closest distance to " CB  VAL A 230 " =    1.375
peak=    6.868 closest distance to " O   HOH Z 400 " =    1.145
peak=    6.800 closest distance to " CG1 ILE A 234 " =    1.429
peak=    6.504 closest distance to " O   HOH Z 120 " =    1.370
peak=    6.257 closest distance to " OD1 ASN A 301 " =    1.069
peak=    6.142 closest distance to " O   HOH Z 210 " =    1.684
peak=    5.962 closest distance to " O   HOH Z  46 " =    1.440
peak=    5.564 closest distance to " NZ  LYS A  76 " =    1.075
peak=    5.308 closest distance to " O   HOH Z 404 " =    1.582
peak=    5.110 closest distance to " O   HOH Z 124 " =    1.447
peak=    5.078 closest distance to " O   HOH Z 117 " =    1.145
peak=    5.006 closest distance to " O   HOH Z 126 " =    1.643
peak=    4.968 closest distance to " O   HOH Z 146 " =    1.697
peak=    4.927 closest distance to " CG  LEU A   5 " =    1.353
peak=    4.890 closest distance to " O   HOH Z 415 " =    1.299
peak=    4.849 closest distance to " CB  VAL A 296 " =    1.450
peak=    4.842 closest distance to " O   GLN A  11 " =    0.933
peak=    4.806 closest distance to " CB  SER A  63 " =    1.261
peak=    4.799 closest distance to " O   HOH Z 403 " =    2.012
peak=    4.758 closest distance to " O   ASN A 285 " =    0.899
peak=    4.669 closest distance to " O   HOH Z 193 " =    1.687
peak=    4.649 closest distance to " O   HOH Z  80 " =    2.413
peak=    4.590 closest distance to " O   HOH Z  49 " =    1.495
peak=    4.587 closest distance to " OD2 ASP A 298 " =    0.925
peak=    4.571 closest distance to " O   HOH Z 142 " =    2.430
peak=    4.561 closest distance to " O   HOH Z 154 " =    2.088
peak=    4.528 closest distance to " O   HOH Z 128 " =    1.803
peak=    4.527 closest distance to " ND2 ASN A 249 " =    2.166
peak=    4.521 closest distance to " CB  ARG A 275 " =    0.962
peak=    4.511 closest distance to " CB  ASN A 285 " =    1.037
peak=    4.507 closest distance to " O   HOH Z 248 " =    1.618
peak=    4.505 closest distance to " O   HOH Z 412 " =    3.451
peak=    4.502 closest distance to " O   HOH Z  44 " =    1.572
peak=    4.447 closest distance to " CB  VAL A 230 " =    1.210
peak=    4.446 closest distance to " CG AARG A 275 " =    1.226
peak=    4.445 closest distance to " O   HOH Z 130 " =    2.353
peak=    4.427 closest distance to " O   HOH Z 146 " =    1.743
peak=    4.416 closest distance to " CG1 VAL A 296 " =    1.234
peak=    4.412 closest distance to " O   HOH Z 102 " =    1.678
peak=    4.324 closest distance to " O   HOH Z 425 " =    1.667
peak=    4.319 closest distance to " CD  ARG A  36 " =    1.246
peak=    4.309 closest distance to " OE1 GLN A  55 " =    1.551
peak=    4.276 closest distance to " CA  SER A  12 " =    1.310
peak=    4.276 closest distance to " CB  GLU A 175 " =    1.299
peak=    4.258 closest distance to " O   HOH Z 144 " =    2.011
peak=    4.252 closest distance to " NE2 GLN A  11 " =    0.952
peak=    4.249 closest distance to " CG  ARG A  66 " =    0.996
peak=    4.247 closest distance to " O   HOH Z 130 " =    1.241
peak=    4.246 closest distance to " NH2 ARG A 156 " =    1.156
peak=    4.240 closest distance to " CB  ASN A 187 " =    1.301
peak=    4.238 closest distance to " CA  TYR A  30 " =    0.925
peak=    4.219 closest distance to " CG  PRO A 280 " =    0.818
peak=    4.193 closest distance to " CD  LYS A 166 " =    1.642
peak=    4.154 closest distance to " O   HOH Z 361 " =    3.155
peak=    4.132 closest distance to " N   ASP A 286 " =    0.988
peak=    4.129 closest distance to " O   HOH Z 435 " =    1.951
peak=    4.114 closest distance to " OE1 GLU A   2 " =    1.460
peak=    4.110 closest distance to " O   HOH Z 279 " =    1.062
peak=    4.110 closest distance to " CB  THR A  31 " =    1.568
peak=    4.108 closest distance to " OE1 GLN A  11 " =    1.967
peak=    4.091 closest distance to " O   HOH Z 394 " =    1.882
peak=    4.088 closest distance to " O   HOH Z 427 " =    2.572
peak=    4.052 closest distance to " CD2 TRP A 179 " =    1.274
peak=    4.048 closest distance to " O   HOH Z 236 " =    1.649
peak=    4.048 closest distance to " O   HOH Z  68 " =    2.192
peak=    4.044 closest distance to " O   HOH Z 158 " =    1.406
peak=    4.038 closest distance to " CE  LYS A 119 " =    1.327
peak=    4.035 closest distance to " NE1 TRP A  92 " =    1.408
peak=    4.027 closest distance to " O   HOH Z 134 " =    2.310
peak=    4.013 closest distance to " CG  PRO A 243 " =    1.123
peak=    4.012 closest distance to " O   HOH Z 431 " =    1.694
peak=    3.992 closest distance to " CG  PRO A  54 " =    1.284
peak=    3.989 closest distance to " OG  SER A  62 " =    2.627
peak=    3.961 closest distance to " CD2 LEU A 228 " =    1.276
peak=    3.958 closest distance to " CA  TRP A  85 " =    1.131
peak=    3.954 closest distance to " O   HOH Z  76 " =    1.190
peak=    3.949 closest distance to " O   HOH Z 113 " =    2.383
peak=    3.938 closest distance to " O   HOH Z 327 " =    1.617
peak=    3.936 closest distance to " C   ALA A 299 " =    0.819
peak=    3.925 closest distance to " CA  ALA A 100 " =    1.202
peak=    3.923 closest distance to " CG1 ILE A  33 " =    1.261
peak=    3.915 closest distance to " CD2 LEU A   5 " =    1.228
peak=    3.909 closest distance to " CB  PRO A  54 " =    0.983
peak=    3.904 closest distance to " N   GLU A  44 " =    1.373
peak=    3.899 closest distance to " O   HOH Z  40 " =    1.876
peak=    3.870 closest distance to " ND2 ASN A 110 " =    1.326
peak=    3.856 closest distance to " CB  ASN A 148 " =    1.172
peak=    3.851 closest distance to " NH1AARG A 275 " =    1.112
peak=    3.847 closest distance to " O   HOH Z 209 " =    2.498
peak=    3.841 closest distance to " CA  VAL A  41 " =    0.947
peak=    3.824 closest distance to " O   HOH Z 249 " =    1.279
peak=    3.822 closest distance to " O   HOH Z 433 " =    1.855
peak=    3.817 closest distance to " O   HOH Z  48 " =    1.609
peak=    3.816 closest distance to " CG2 THR A  31 " =    1.112
peak=    3.811 closest distance to " CB  VAL A 202 " =    1.285
peak=    3.809 closest distance to " O   HOH Z 234 " =    3.376
peak=    3.807 closest distance to " O   HOH Z 406 " =    1.463
peak=    3.801 closest distance to " CB  ALA A 299 " =    1.272
peak=    3.800 closest distance to " CB  TRP A 179 " =    1.247
peak=    3.799 closest distance to " O   HOH Z 357 " =    1.991
peak=    3.783 closest distance to " O   HOH Z 402 " =    1.464
peak=    3.782 closest distance to " O   HOH Z 238 " =    1.831
peak=    3.780 closest distance to " O   HOH Z  43 " =    2.721
peak=    3.775 closest distance to " O   HOH Z 126 " =    2.256
peak=    3.767 closest distance to " CE1 HIS A 108 " =    1.192
peak=    3.766 closest distance to " O   HOH Z 414 " =    2.857
peak=    3.763 closest distance to " O   SER A  87 " =    2.252
peak=    3.762 closest distance to " O   HOH Z  63 " =    2.184
peak=    3.759 closest distance to " CG  GLN A  77 " =    0.812
peak=    3.753 closest distance to " O   HOH Z  54 " =    1.122
peak=    3.751 closest distance to " CD  GLN A 194 " =    1.572
peak=    3.750 closest distance to " O   GLU A   2 " =    1.555
peak=    3.747 closest distance to " O   HOH Z 423 " =    1.987
peak=    3.744 closest distance to " O   ALA A 165 " =    1.339
peak=    3.731 closest distance to " CG  PRO A 198 " =    1.476
peak=    3.727 closest distance to " O   HOH Z  78 " =    1.738
peak=    3.724 closest distance to " O   HOH Z  85 " =    1.830
peak=    3.715 closest distance to " O   HOH Z 111 " =    1.677
peak=    3.715 closest distance to " CB  GLN A 223 " =    1.509
peak=    3.711 closest distance to " CG2 VAL A 197 " =    1.257
peak=    3.705 closest distance to " O   VAL A  72 " =    1.405
peak=    3.691 closest distance to " N   ASP A 298 " =    0.952
peak=    3.682 closest distance to " CB  SER A  62 " =    1.182
peak=    3.680 closest distance to " O   HOH Z 131 " =    2.331
peak=    3.677 closest distance to " O   HOH Z  80 " =    3.196
peak=    3.660 closest distance to " CZ3 TRP A 266 " =    1.037
peak=    3.655 closest distance to " CB  GLN A 183 " =    1.249
peak=    3.643 closest distance to " O   HOH Z 132 " =    2.280
peak=    3.640 closest distance to " CB  SER A 141 " =    0.942
peak=    3.636 closest distance to " O   HOH Z 271 " =    1.670
peak=    3.635 closest distance to " O   HOH Z 426 " =    1.242
peak=    3.619 closest distance to " O   HOH Z 183 " =    1.809
peak=    3.616 closest distance to " CG  MET A 185 " =    1.214
peak=    3.616 closest distance to " O   HOH Z  39 " =    1.837
peak=    3.611 closest distance to " N   THR A  42 " =    1.569
peak=    3.609 closest distance to " CG2 VAL A 296 " =    1.054
peak=    3.607 closest distance to " N   CYS A 260 " =    1.206
peak=    3.603 closest distance to " O   ASP A 124 " =    1.523
peak=    3.602 closest distance to " O   HOH Z 291 " =    1.438
peak=    3.596 closest distance to " CB  GLN A  73 " =    1.283
peak=    3.591 closest distance to " CB  ARG A  79 " =    0.928
peak=    3.588 closest distance to " CZ  PHE A  38 " =    1.116
peak=    3.583 closest distance to " N   SER A 164 " =    1.032
peak=    3.583 closest distance to " O   HOH Z 245 " =    1.371
peak=    3.575 closest distance to " O   HOH Z 227 " =    2.017
peak=    3.574 closest distance to " CB  GLU A 277 " =    0.955
peak=    3.574 closest distance to " O   HOH Z  66 " =    1.562
peak=    3.569 closest distance to " O   HOH Z 418 " =    3.060
peak=    3.565 closest distance to " O   HOH Z 139 " =    4.466
peak=    3.561 closest distance to " CB  THR A 235 " =    1.277
peak=    3.560 closest distance to " CA  ALA A  51 " =    1.016
peak=    3.556 closest distance to " O   HOH Z 132 " =    2.717
peak=    3.555 closest distance to " O   HOH Z  29 " =    1.347
peak=    3.554 closest distance to " O   HOH Z 369 " =    1.806
peak=    3.548 closest distance to " O   HOH Z  53 " =    1.296
peak=    3.540 closest distance to " CD  GLN A  73 " =    1.281
peak=    3.531 closest distance to " CD1 TRP A 274 " =    1.133
peak=    3.518 closest distance to " CG2 THR A 294 " =    1.368
peak=    3.514 closest distance to " CE1 TYR A 186 " =    1.439
peak=    3.507 closest distance to " CG2 THR A 221 " =    1.286
peak=    3.502 closest distance to " O   HOH Z 273 " =    3.082
peak=    3.502 closest distance to " O   ASP A 191 " =    1.580
peak=    3.500 closest distance to " CA  ARG A 195 " =    1.215
peak=    3.497 closest distance to " CB  GLN A  58 " =    1.165
peak=    3.496 closest distance to " O   HOH Z 155 " =    3.164
peak=    3.495 closest distance to " O   HOH Z 258 " =    2.210
peak=    3.484 closest distance to " CG  LEU A 228 " =    1.260
peak=    3.484 closest distance to " O   HOH Z 299 " =    3.945
peak=    3.469 closest distance to " N   GLY A  75 " =    1.221
peak=    3.467 closest distance to " CD  ARG A 269 " =    1.025
peak=    3.465 closest distance to " O   HOH Z 152 " =    1.769
peak=    3.464 closest distance to " CD  ARG A 159 " =    0.851
peak=    3.460 closest distance to " CZ  PHE A 218 " =    1.277
peak=    3.459 closest distance to " OD1 ASN A  60 " =    1.108
peak=    3.455 closest distance to " O   HOH Z 246 " =    1.292
peak=    3.454 closest distance to " CB  ARG A 269 " =    1.948
peak=    3.454 closest distance to " CB  GLN A  73 " =    1.185
peak=    3.451 closest distance to " CG  ARG A  36 " =    1.076
peak=    3.450 closest distance to " O   HOH Z 365 " =    2.266
peak=    3.450 closest distance to " O   HOH Z 214 " =    1.510
peak=    3.447 closest distance to " OG  SER A 245 " =    1.393
peak=    3.443 closest distance to " CG2 ILE A  20 " =    1.349
peak=    3.441 closest distance to " O   HOH Z 298 " =    5.179
peak=    3.438 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.435 closest distance to " CG2 ILE A 234 " =    1.179
peak=    3.431 closest distance to " O   HOH Z 366 " =    2.401
peak=    3.431 closest distance to " O   HOH Z  88 " =    3.396
peak=    3.430 closest distance to " CB  SER A   3 " =    1.206
peak=    3.426 closest distance to " CE3 TRP A 150 " =    1.111
peak=    3.426 closest distance to " NH1 ARG A  14 " =    1.274
peak=    3.424 closest distance to " O   HOH Z 379 " =    2.829
peak=    3.424 closest distance to " NE  ARG A 219 " =    1.452
peak=    3.422 closest distance to " O   HOH Z 232 " =    2.362
peak=    3.417 closest distance to " O   ASP A 200 " =    1.566
peak=    3.417 closest distance to " CA  ILE A 120 " =    1.281
peak=    3.416 closest distance to " O   HOH Z 364 " =    2.156
peak=    3.409 closest distance to " CB  LEU A 237 " =    0.789
peak=    3.408 closest distance to " O   HOH Z 185 " =    1.792
peak=    3.403 closest distance to " O   THR A 220 " =    1.008
peak=    3.402 closest distance to " CG2 THR A 220 " =    0.833
peak=    3.399 closest distance to " CD  ARG A  36 " =    1.045
peak=    3.393 closest distance to " CD2 LEU A  25 " =    1.079
peak=    3.391 closest distance to " O   LYS A 289 " =    1.038
peak=    3.390 closest distance to " CD  ARG A  24 " =    1.344
peak=    3.387 closest distance to " O   HOH Z 332 " =    1.646
peak=    3.384 closest distance to " O   HOH Z 422 " =    2.812
peak=    3.381 closest distance to " O   HOH Z 255 " =    1.570
peak=    3.375 closest distance to " CB  SER A  62 " =    3.593
peak=    3.371 closest distance to " NH1AARG A 145 " =    1.058
peak=    3.370 closest distance to " O   HOH Z 340 " =    1.793
peak=    3.368 closest distance to " CG1 ILE A  20 " =    1.414
peak=    3.368 closest distance to " CA  ASP A 191 " =    1.121
peak=    3.364 closest distance to " O   PRO A 198 " =    1.501
peak=    3.364 closest distance to " O   HOH Z 280 " =    3.239
peak=    3.363 closest distance to " CA  ILE A  33 " =    1.501
peak=    3.363 closest distance to " O   HOH Z 156 " =    3.334
peak=    3.361 closest distance to " O   HOH Z 371 " =    2.575
peak=    3.360 closest distance to " CG  PRO A 163 " =    4.049
peak=    3.360 closest distance to " ND2 ASN A 301 " =    1.023
peak=    3.352 closest distance to " O   HOH Z 383 " =    2.125
peak=    3.351 closest distance to " CB  MET A  40 " =    0.863
peak=    3.350 closest distance to " NZ  LYS A 117 " =    2.696
peak=    3.350 closest distance to " O   HOH Z  44 " =    2.644
peak=    3.349 closest distance to " CD  LYS A 289 " =    1.113
peak=    3.345 closest distance to " O   HOH Z 350 " =    1.302
peak=    3.344 closest distance to " O   HOH Z   4 " =    1.561
peak=    3.340 closest distance to " O   HOH Z 298 " =    2.438
peak=    3.334 closest distance to " CG1 VAL A 153 " =    1.054
peak=    3.334 closest distance to " CB  TYR A  30 " =    0.981
peak=    3.333 closest distance to " CA  ALA A 248 " =    1.235
peak=    3.327 closest distance to " OG  SER A  62 " =    3.306
peak=    3.321 closest distance to " O   HOH Z 265 " =    1.706
peak=    3.320 closest distance to " O   HOH Z 234 " =    2.041
peak=    3.319 closest distance to " NH2 ARG A  36 " =    1.783
peak=    3.317 closest distance to " O  BHOH Z 338 " =    2.436
peak=    3.312 closest distance to " CB  ALA A  71 " =    1.348
peak=    3.312 closest distance to " CA  THR A 294 " =    2.093
peak=    3.308 closest distance to " O   HOH Z   6 " =    2.307
peak=    3.308 closest distance to " OH  TYR A 293 " =    1.329
peak=    3.305 closest distance to " O   HOH Z 272 " =    2.031
peak=    3.304 closest distance to " CG2AVAL A 121 " =    1.873
peak=    3.302 closest distance to " O   HOH Z 250 " =    1.309
peak=    3.299 closest distance to " O   HOH Z 344 " =    2.745
peak=    3.296 closest distance to " CA  LEU A  83 " =    1.393
peak=    3.292 closest distance to " O   HOH Z 123 " =    2.329
peak=    3.289 closest distance to " O   HOH Z 423 " =    2.114
peak=    3.285 closest distance to " CB  ARG A 190 " =    1.848
peak=    3.281 closest distance to " O   HOH Z 339 " =    1.556
peak=    3.280 closest distance to " CB  GLN A  88 " =    1.352
peak=    3.280 closest distance to " O   HOH Z 336 " =    1.827
peak=    3.279 closest distance to " O   HOH Z 226 " =    1.497
peak=    3.278 closest distance to " CB  PHE A  16 " =    1.185
peak=    3.278 closest distance to " O   HOH Z 342 " =    0.771
peak=    3.277 closest distance to " CA  ALA A 295 " =    0.878
peak=    3.276 closest distance to " O   HOH Z 170 " =    2.772
peak=    3.275 closest distance to " O   PRO A 213 " =    1.346
peak=    3.272 closest distance to " CB  THR A  52 " =    0.824
peak=    3.271 closest distance to " CB  GLN A 194 " =    1.084
peak=    3.271 closest distance to " CZ3 TRP A  92 " =    1.195
peak=    3.269 closest distance to " O   HOH Z  52 " =    1.413
peak=    3.263 closest distance to " O   HOH Z 280 " =    3.652
peak=    3.261 closest distance to " O   HOH Z  97 " =    1.215
peak=    3.260 closest distance to " O   HOH Z  85 " =    1.598
peak=    3.257 closest distance to " O   HOH Z 370 " =    1.147
peak=    3.257 closest distance to " O   HOH Z 341 " =    1.766
peak=    3.256 closest distance to " CA  THR A 246 " =    0.999
peak=    3.256 closest distance to " CG2AVAL A  72 " =    1.959
peak=    3.255 closest distance to " CB  SER A  62 " =    0.808
peak=    3.254 closest distance to " CA  ASP A 298 " =    0.882
peak=    3.250 closest distance to " CA  ALA A 129 " =    0.810
peak=    3.244 closest distance to " N   ASN A  39 " =    1.368
peak=    3.241 closest distance to " O   HOH Z 409 " =    3.393
peak=    3.241 closest distance to " O   HOH Z 331 " =    1.171
peak=    3.240 closest distance to " CG  LYS A  76 " =    1.103
peak=    3.238 closest distance to " O   HOH Z 256 " =    2.349
peak=    3.233 closest distance to " CB  TRP A 266 " =    1.028
peak=    3.232 closest distance to " NE  ARG A  14 " =    1.242
peak=    3.231 closest distance to " O   HOH Z 130 " =    2.894
peak=    3.229 closest distance to " CB  GLU A   2 " =    1.132
peak=    3.227 closest distance to " CB  ALA A 226 " =    1.146
peak=    3.219 closest distance to " CG  LYS A 119 " =    1.155
peak=    3.218 closest distance to " O   HOH Z 151 " =    1.771
peak=    3.212 closest distance to " CB BVAL A  41 " =    1.078
peak=    3.207 closest distance to " CB  SER A  97 " =    1.164
peak=    3.206 closest distance to " CB  GLU A 236 " =    1.324
peak=    3.203 closest distance to " N   TYR A  15 " =    0.889
peak=    3.202 closest distance to " CE AMET A  47 " =    1.069
peak=    3.198 closest distance to " CB  SER A  28 " =    0.852
peak=    3.195 closest distance to " CE3 TRP A  85 " =    1.325
peak=    3.193 closest distance to " CZ2 TRP A 274 " =    1.185
peak=    3.191 closest distance to " CG1BVAL A  72 " =    2.707
peak=    3.190 closest distance to " NH1 ARG A  36 " =    1.265
peak=    3.189 closest distance to " O   HOH Z 428 " =    1.297
peak=    3.188 closest distance to " O   HOH Z  57 " =    2.196
peak=    3.188 closest distance to " O   HOH Z 301 " =    1.722
peak=    3.187 closest distance to " CA  ASP A 140 " =    1.256
peak=    3.183 closest distance to " CB  GLU A 152 " =    1.189
peak=    3.183 closest distance to " CA  SER A  32 " =    1.665
peak=    3.182 closest distance to " O   HOH Z 315 " =    1.765
peak=    3.180 closest distance to " O   HOH Z 143 " =    1.472
peak=    3.174 closest distance to " CB  SER A  26 " =    1.611
peak=    3.171 closest distance to " O   HOH Z 328 " =    2.089
peak=    3.171 closest distance to " NH2 ARG A  79 " =    1.379
peak=    3.167 closest distance to " CB  PRO A 243 " =    1.039
peak=    3.166 closest distance to " O   HOH Z 381 " =    1.379
peak=    3.163 closest distance to " O   HOH Z 158 " =    3.014
peak=    3.162 closest distance to " CD1 LEU A 101 " =    1.264
peak=    3.160 closest distance to " O   HOH Z 289 " =    1.608
peak=    3.151 closest distance to " O   HOH Z   7 " =    1.100
peak=    3.150 closest distance to " CG1 ILE A 120 " =    1.034
peak=    3.149 closest distance to " O   HOH Z 200 " =    3.270
peak=    3.141 closest distance to " O   HOH Z 109 " =    2.533
peak=    3.139 closest distance to " O   HOH Z 217 " =    2.863
peak=    3.139 closest distance to " O   HOH Z 217 " =    2.679
peak=    3.139 closest distance to " O   HOH Z 299 " =    1.577
peak=    3.137 closest distance to " O   HOH Z 337 " =    1.721
peak=    3.124 closest distance to " O   HOH Z 380 " =    2.033
peak=    3.123 closest distance to " O   HOH Z  77 " =    1.473
peak=    3.110 closest distance to " O   HOH Z  90 " =    5.786
peak=    3.104 closest distance to " CA  SER A  62 " =    0.888
peak=    3.102 closest distance to " CA  MET A  40 " =    1.161
peak=    3.098 closest distance to " O   HOH Z 298 " =    4.303
peak=    3.096 closest distance to " CG2 THR A  42 " =    0.836
peak=    3.094 closest distance to " NE2 HIS A 108 " =    0.730
peak=    3.092 closest distance to " CG1 ILE A 106 " =    0.857
peak=    3.092 closest distance to " CB  LEU A  25 " =    0.889
peak=    3.091 closest distance to " NH2AARG A 145 " =    1.143
peak=    3.087 closest distance to " CA  ASN A 249 " =    1.416
peak=    3.083 closest distance to " CG2 THR A  29 " =    1.184
peak=    3.081 closest distance to " O   HOH Z 424 " =    3.973
peak=    3.080 closest distance to " N   ASP A 162 " =    2.237
peak=    3.079 closest distance to " CG  TRP A 179 " =    2.492
peak=    3.077 closest distance to " O   HOH Z 287 " =    1.692
peak=    3.076 closest distance to " O   HOH Z 277 " =    2.892
peak=    3.075 closest distance to " O   HOH Z  42 " =    2.334
peak=    3.068 closest distance to " O   HOH Z   5 " =    1.790
peak=    3.063 closest distance to " NH2BARG A 190 " =    1.662
peak=    3.063 closest distance to " O   HOH Z 159 " =    1.248
peak=    3.061 closest distance to " OXT GLY A 302 " =    1.788
peak=    3.054 closest distance to " O   HOH Z 423 " =    2.626
peak=    3.047 closest distance to " CA  PHE A 130 " =    1.222
peak=    3.045 closest distance to " N   LYS A 166 " =    0.983
peak=    3.044 closest distance to " O   HOH Z 250 " =    1.554
peak=    3.042 closest distance to " O   HOH Z 214 " =    2.335
peak=    3.034 closest distance to " CA  ARG A  66 " =    1.128
peak=    3.010 closest distance to " O   VAL A  72 " =    0.889

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 5.786
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 213
   mapped sites are within: 0.727 - 5.786

peak=   -5.798 closest distance to " CG2 VAL A 230 " =    0.795
peak=   -4.956 closest distance to " CD  ARG A  14 " =    3.051
peak=   -4.791 closest distance to " OD1 ASN A 301 " =    0.727
peak=   -4.480 closest distance to " O   PRO A 198 " =    1.267
peak=   -4.337 closest distance to " O   HOH Z 400 " =    0.788
peak=   -4.299 closest distance to " O   HOH Z 422 " =    1.101
peak=   -4.279 closest distance to " O   HOH Z 155 " =    1.688
peak=   -4.221 closest distance to " O   HOH Z 411 " =    5.171
peak=   -4.218 closest distance to " CD1 PHE A  59 " =    1.833
peak=   -4.211 closest distance to " CG  GLN A  58 " =    1.092
peak=   -4.187 closest distance to " CD  GLN A 223 " =    1.654
peak=   -4.169 closest distance to " O   HOH Z 411 " =    1.468
peak=   -4.149 closest distance to " O   GLN A  11 " =    1.062
peak=   -4.119 closest distance to " CD2 TYR A  30 " =    2.664
peak=   -4.111 closest distance to " CD2 LEU A 237 " =    2.389
peak=   -4.081 closest distance to " O   HOH Z 109 " =    2.884
peak=   -4.041 closest distance to " NH2 ARG A  36 " =    1.239
peak=   -3.992 closest distance to " CB  ALA A 248 " =    2.166
peak=   -3.981 closest distance to " O   HOH Z  37 " =    1.313
peak=   -3.939 closest distance to " O   HOH Z   7 " =    1.176
peak=   -3.924 closest distance to " O   HOH Z 384 " =    1.645
peak=   -3.918 closest distance to " O   HOH Z 151 " =    0.954
peak=   -3.896 closest distance to " O   HOH Z 166 " =    1.563
peak=   -3.879 closest distance to " CD1 TRP A 179 " =    1.242
peak=   -3.862 closest distance to " O   HOH Z 164 " =    5.786
peak=   -3.861 closest distance to " O  BHOH Z 338 " =    1.308
peak=   -3.858 closest distance to " O   ASN A 285 " =    1.228
peak=   -3.855 closest distance to " CD  ARG A  36 " =    0.938
peak=   -3.845 closest distance to " O   HOH Z 205 " =    0.814
peak=   -3.831 closest distance to " O   HOH Z 166 " =    1.208
peak=   -3.825 closest distance to " CG  PRO A 243 " =    1.839
peak=   -3.824 closest distance to " CG2 ILE A  49 " =    2.660
peak=   -3.806 closest distance to " O   ALA A  34 " =    2.450
peak=   -3.787 closest distance to " CZ3 TRP A  70 " =    1.285
peak=   -3.787 closest distance to " O   HOH Z 221 " =    1.124
peak=   -3.780 closest distance to " O   LEU A 300 " =    2.531
peak=   -3.776 closest distance to " O   VAL A  67 " =    2.889
peak=   -3.775 closest distance to " O   HOH Z 425 " =    1.128
peak=   -3.763 closest distance to " ND2 ASN A  39 " =    1.243
peak=   -3.755 closest distance to " OD2 ASP A 298 " =    0.869
peak=   -3.737 closest distance to " O   HOH Z 137 " =    1.548
peak=   -3.734 closest distance to " CG2BVAL A  41 " =    2.319
peak=   -3.730 closest distance to " SD  MET A 105 " =    0.951
peak=   -3.703 closest distance to " CA  SER A 276 " =    1.420
peak=   -3.698 closest distance to " O   SER A 273 " =    1.005
peak=   -3.681 closest distance to " O   HOH Z 285 " =    1.203
peak=   -3.671 closest distance to " CA  SER A 164 " =    1.947
peak=   -3.671 closest distance to " NE  ARG A 156 " =    2.022
peak=   -3.658 closest distance to " OG  SER A  97 " =    2.299
peak=   -3.657 closest distance to " O   HOH Z  52 " =    2.218
peak=   -3.654 closest distance to " O   HOH Z 362 " =    4.299
peak=   -3.644 closest distance to " O   HOH Z 250 " =    1.746
peak=   -3.636 closest distance to " O   GLY A 241 " =    2.333
peak=   -3.629 closest distance to " CG2 VAL A 189 " =    2.077
peak=   -3.624 closest distance to " N   VAL A  72 " =    1.197
peak=   -3.619 closest distance to " O   HOH Z  92 " =    1.257
peak=   -3.618 closest distance to " O   HOH Z 174 " =    1.707
peak=   -3.585 closest distance to " CG2 ILE A  20 " =    2.848
peak=   -3.580 closest distance to " N   ALA A   1 " =    2.189
peak=   -3.572 closest distance to " O   HOH Z 231 " =    1.962
peak=   -3.554 closest distance to " C   TRP A 274 " =    1.158
peak=   -3.549 closest distance to " O   HOH Z   6 " =    2.229
peak=   -3.534 closest distance to " C   THR A 279 " =    1.394
peak=   -3.526 closest distance to " O   HOH Z 120 " =    1.195
peak=   -3.514 closest distance to " C   HIS A 108 " =    1.212
peak=   -3.513 closest distance to " CG  LEU A   5 " =    0.889
peak=   -3.513 closest distance to " O   HOH Z 432 " =    0.871
peak=   -3.507 closest distance to " OD1 ASP A 298 " =    2.256
peak=   -3.505 closest distance to " CA  ASP A 298 " =    1.108
peak=   -3.504 closest distance to " O   HOH Z  35 " =    1.095
peak=   -3.501 closest distance to " CB  LEU A 167 " =    1.999
peak=   -3.480 closest distance to " O   HOH Z 101 " =    1.539
peak=   -3.474 closest distance to " O   HOH Z 259 " =    1.137
peak=   -3.469 closest distance to " O   HOH Z 222 " =    1.140
peak=   -3.464 closest distance to " CG2 THR A 279 " =    1.564
peak=   -3.454 closest distance to " C   VAL A 265 " =    1.058
peak=   -3.452 closest distance to " CD2 TYR A 293 " =    1.218
peak=   -3.451 closest distance to " CG  GLN A  73 " =    0.784
peak=   -3.447 closest distance to " OXT GLY A 302 " =    2.918
peak=   -3.444 closest distance to " O   HOH Z 340 " =    1.082
peak=   -3.443 closest distance to " O   HOH Z  46 " =    1.282
peak=   -3.443 closest distance to " CG1 VAL A 112 " =    2.415
peak=   -3.435 closest distance to " O   HOH Z 420 " =    5.482
peak=   -3.432 closest distance to " C   LYS A  76 " =    1.740
peak=   -3.422 closest distance to " CB  HIS A  86 " =    2.451
peak=   -3.416 closest distance to " O   SER A  95 " =    1.677
peak=   -3.412 closest distance to " CA  ALA A 114 " =    0.974
peak=   -3.409 closest distance to " C   ASP A 286 " =    1.221
peak=   -3.406 closest distance to " O   HOH Z 210 " =    1.226
peak=   -3.399 closest distance to " O   ILE A 109 " =    2.524
peak=   -3.399 closest distance to " O   HOH Z 369 " =    2.441
peak=   -3.398 closest distance to " O   HOH Z 418 " =    1.316
peak=   -3.395 closest distance to " CA  ASN A 110 " =    1.101
peak=   -3.392 closest distance to " O   HOH Z 119 " =    1.965
peak=   -3.389 closest distance to " SD  MET A 105 " =    2.483
peak=   -3.389 closest distance to " CE  MET A 105 " =    2.234
peak=   -3.389 closest distance to " CA  GLU A 277 " =    1.148
peak=   -3.388 closest distance to " O   HOH Z 234 " =    3.854
peak=   -3.378 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.376 closest distance to " O   HOH Z 196 " =    1.509
peak=   -3.375 closest distance to " CD2 LEU A 300 " =    2.636
peak=   -3.372 closest distance to " ND2 ASN A 249 " =    2.040
peak=   -3.371 closest distance to " CZ  TYR A 172 " =    1.834
peak=   -3.369 closest distance to " CG  ASP A 286 " =    1.093
peak=   -3.364 closest distance to " O   HOH Z  71 " =    2.018
peak=   -3.362 closest distance to " OG  SER A 271 " =    1.443
peak=   -3.356 closest distance to " O   VAL A 174 " =    2.099
peak=   -3.351 closest distance to " OE2 GLU A 128 " =    1.895
peak=   -3.348 closest distance to " O   HOH Z 219 " =    4.199
peak=   -3.347 closest distance to " O   HOH Z  56 " =    1.584
peak=   -3.341 closest distance to " CA  GLY A 133 " =    2.026
peak=   -3.339 closest distance to " N   ALA A  43 " =    2.820
peak=   -3.339 closest distance to " CG2 THR A  18 " =    2.861
peak=   -3.336 closest distance to " O   HOH Z 377 " =    2.151
peak=   -3.332 closest distance to " O   HOH Z  24 " =    1.854
peak=   -3.329 closest distance to " O   HOH Z 198 " =    1.176
peak=   -3.322 closest distance to " O   HOH Z 388 " =    2.307
peak=   -3.320 closest distance to " O   HOH Z 388 " =    1.482
peak=   -3.318 closest distance to " OD1 ASN A 301 " =    0.999
peak=   -3.317 closest distance to " CG1 VAL A 296 " =    1.072
peak=   -3.317 closest distance to " OE2 GLU A 152 " =    1.722
peak=   -3.314 closest distance to " CG  GLN A 103 " =    2.182
peak=   -3.310 closest distance to " CD2 LEU A 237 " =    2.739
peak=   -3.310 closest distance to " O   HOH Z 176 " =    1.733
peak=   -3.310 closest distance to " O   LYS A 117 " =    1.618
peak=   -3.303 closest distance to " O   HOH Z 368 " =    1.889
peak=   -3.300 closest distance to " OD2 ASP A 270 " =    1.277
peak=   -3.298 closest distance to " O   HOH Z 417 " =    1.019
peak=   -3.295 closest distance to " O   HOH Z 131 " =    4.253
peak=   -3.288 closest distance to " CD1 TYR A 247 " =    2.470
peak=   -3.288 closest distance to " O   HOH Z 378 " =    0.858
peak=   -3.287 closest distance to " CG1 VAL A 197 " =    2.421
peak=   -3.277 closest distance to " CA  GLY A 203 " =    2.014
peak=   -3.254 closest distance to " O   HOH Z 145 " =    2.686
peak=   -3.254 closest distance to " O   HOH Z 311 " =    2.980
peak=   -3.253 closest distance to " O   HOH Z 275 " =    1.561
peak=   -3.251 closest distance to " O   HOH Z  10 " =    1.853
peak=   -3.247 closest distance to " OG  SER A  87 " =    1.788
peak=   -3.244 closest distance to " CG2 VAL A 202 " =    2.588
peak=   -3.243 closest distance to " O   HOH Z   1 " =    1.725
peak=   -3.239 closest distance to " CA  VAL A 197 " =    0.991
peak=   -3.237 closest distance to " O   SER A 206 " =    1.232
peak=   -3.231 closest distance to " CE1 PHE A 283 " =    2.302
peak=   -3.223 closest distance to " O   HOH Z 423 " =    2.715
peak=   -3.223 closest distance to " OG  SER A  32 " =    1.373
peak=   -3.220 closest distance to " O   TYR A  15 " =    1.837
peak=   -3.218 closest distance to " O   HOH Z 233 " =    2.277
peak=   -3.216 closest distance to " O   HOH Z  56 " =    2.234
peak=   -3.212 closest distance to " O   HOH Z 146 " =    1.046
peak=   -3.211 closest distance to " CG  ARG A  24 " =    2.129
peak=   -3.210 closest distance to " OG BSER A 212 " =    1.532
peak=   -3.209 closest distance to " O   HOH Z 171 " =    2.355
peak=   -3.204 closest distance to " O   HOH Z 405 " =    1.428
peak=   -3.202 closest distance to " O   HOH Z 165 " =    2.030
peak=   -3.198 closest distance to " ND2 ASN A  60 " =    1.860
peak=   -3.197 closest distance to " C   GLN A 144 " =    0.963
peak=   -3.197 closest distance to " O   HOH Z  29 " =    1.458
peak=   -3.194 closest distance to " O   HOH Z 126 " =    1.845
peak=   -3.193 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.192 closest distance to " CG  LEU A  83 " =    1.819
peak=   -3.188 closest distance to " O   HOH Z 269 " =    3.708
peak=   -3.187 closest distance to " O   HOH Z 422 " =    0.997
peak=   -3.184 closest distance to " O   HOH Z 152 " =    1.364
peak=   -3.183 closest distance to " OH  TYR A 169 " =    0.865
peak=   -3.180 closest distance to " N   LYS A 289 " =    1.048
peak=   -3.172 closest distance to " O   PHE A 218 " =    1.316
peak=   -3.171 closest distance to " CE1 TYR A 169 " =    2.320
peak=   -3.165 closest distance to " O   HOH Z 219 " =    2.456
peak=   -3.164 closest distance to " O   HOH Z 134 " =    1.860
peak=   -3.163 closest distance to " SG  CYS A 260 " =    1.987
peak=   -3.162 closest distance to " O   HOH Z 124 " =    1.267
peak=   -3.161 closest distance to " CB  ALA A  43 " =    2.726
peak=   -3.157 closest distance to " O   HOH Z 301 " =    2.486
peak=   -3.155 closest distance to " O   HOH Z 424 " =    2.269
peak=   -3.149 closest distance to " CD  LYS A 289 " =    2.307
peak=   -3.147 closest distance to " OD1 ASN A 148 " =    1.241
peak=   -3.139 closest distance to " O   HOH Z 329 " =    1.024
peak=   -3.136 closest distance to " OD1 ASP A 149 " =    1.348
peak=   -3.134 closest distance to " CD1 LEU A  96 " =    2.086
peak=   -3.134 closest distance to " O   THR A  18 " =    1.435
peak=   -3.129 closest distance to " O   HOH Z 135 " =    2.133
peak=   -3.126 closest distance to " O   HOH Z  60 " =    1.962
peak=   -3.122 closest distance to " C   ASN A 285 " =    2.198
peak=   -3.119 closest distance to " CD  GLN A 223 " =    0.951
peak=   -3.116 closest distance to " O   HOH Z 393 " =    1.186
peak=   -3.113 closest distance to " NE2 GLN A 278 " =    1.938
peak=   -3.111 closest distance to " O   TRP A  92 " =    2.140
peak=   -3.104 closest distance to " O   HOH Z  78 " =    2.068
peak=   -3.104 closest distance to " O   ALA A 227 " =    1.185
peak=   -3.103 closest distance to " OE2 GLU A 277 " =    4.009
peak=   -3.102 closest distance to " OG  SER A  26 " =    1.414
peak=   -3.101 closest distance to " NE  ARG A 139 " =    1.223
peak=   -3.100 closest distance to " NZ  LYS A 289 " =    1.530
peak=   -3.095 closest distance to " O   HOH Z 108 " =    2.023
peak=   -3.092 closest distance to " O   ASP A 298 " =    1.492
peak=   -3.086 closest distance to " O   HOH Z 185 " =    1.799
peak=   -3.079 closest distance to " O   SER A   3 " =    0.924
peak=   -3.079 closest distance to " O   HOH Z 215 " =    3.841
peak=   -3.076 closest distance to " CE2 TRP A 179 " =    1.038
peak=   -3.076 closest distance to " CD  ARG A 138 " =    2.822
peak=   -3.074 closest distance to " O   HOH Z  57 " =    0.877
peak=   -3.067 closest distance to " O   VAL A  67 " =    2.589
peak=   -3.063 closest distance to " CG  MET A  93 " =    2.395
peak=   -3.058 closest distance to " O   HOH Z 351 " =    1.275
peak=   -3.053 closest distance to " OD2 ASP A 132 " =    2.292
peak=   -3.053 closest distance to " CG  ARG A 259 " =    2.448
peak=   -3.051 closest distance to " CG1BVAL A  72 " =    1.788
peak=   -3.050 closest distance to " ND2 ASN A  60 " =    1.459
peak=   -3.044 closest distance to " C   MET A 188 " =    1.106

================= 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    :  0.5129 0.4995   6.311036e+00   6.300525e+00
   1_bss:  0.5078 0.4959   6.304791e+00   6.301283e+00
   1_xyz:  0.4482 0.4590   6.251208e+00   6.268526e+00
   1_adp:  0.4071 0.4633   6.203012e+00   6.264011e+00
   1_occ:  0.4067 0.4627   6.202164e+00   6.264178e+00
   2_bss:  0.4039 0.4560   6.202813e+00   6.263534e+00
   2_xyz:  0.3495 0.4167   6.107312e+00   6.213189e+00
   2_adp:  0.3397 0.4044   6.090852e+00   6.197570e+00
   2_occ:  0.3395 0.4047   6.090589e+00   6.197547e+00
   3_bss:  0.3389 0.4027   6.090123e+00   6.196608e+00
   3_xyz:  0.2647 0.3218   5.874203e+00   6.031840e+00
   3_adp:  0.2539 0.3125   5.844274e+00   6.013058e+00
   3_occ:  0.2537 0.3125   5.843309e+00   6.012513e+00
   4_bss:  0.2520 0.3108   5.842356e+00   6.009916e+00
   4_xyz:  0.2076 0.2637   5.676827e+00   5.871037e+00
   4_adp:  0.1829 0.2379   5.572494e+00   5.781049e+00
   4_occ:  0.1828 0.2380   5.572277e+00   5.781195e+00
   5_bss:  0.1830 0.2383   5.573613e+00   5.780176e+00
   5_xyz:  0.1538 0.2111   5.437327e+00   5.671952e+00
   5_adp:  0.1382 0.1883   5.331778e+00   5.561638e+00
   5_occ:  0.1381 0.1884   5.331419e+00   5.561547e+00
   5_bss:  0.1383 0.1892   5.333691e+00   5.562992e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.316   5.970   6.842  11.985   7.643   0.000   0.000   0.000
   1_xyz:  0.316   5.970   6.842  11.985   7.643   0.000   0.000   0.000
   1_adp:  0.316   5.970   6.842  11.985   7.643   0.000   0.000   0.000
   1_occ:  0.316   5.970   6.842  11.985   7.643   0.000   0.000   0.000
   2_bss:  0.295  20.001   2.902   6.713   4.001   0.000   0.000   0.000
   2_xyz:  0.295  20.001   2.902   6.713   4.001   0.000   0.000   0.000
   2_adp:  0.295  20.001   2.902   6.713   4.001   0.000   0.000   0.000
   2_occ:  0.295  20.001   2.902   6.713   4.001   0.000   0.000   0.000
   3_bss:  0.314  48.221   1.016   4.594   2.387   0.000   0.000   0.000
   3_xyz:  0.314  48.221   1.016   4.594   2.387   0.000   0.000   0.000
   3_adp:  0.314  48.221   1.016   4.594   2.387   0.000   0.000   0.000
   3_occ:  0.314  48.221   1.016   4.594   2.387   0.000   0.000   0.000
   4_bss:  0.322  44.296  -0.481   2.221   1.392   0.000   0.000   0.000
   4_xyz:  0.322  44.296  -0.481   2.221   1.392   0.000   0.000   0.000
   4_adp:  0.322  44.296  -0.481   2.221   1.392   0.000   0.000   0.000
   4_occ:  0.322  44.296  -0.481   2.221   1.392   0.000   0.000   0.000
   5_bss:  0.317  44.296  -1.247   1.047   0.851   0.000   0.000   0.000
   5_xyz:  0.317  44.296  -1.247   1.047   0.851   0.000   0.000   0.000
   5_adp:  0.317  44.296  -1.247   1.047   0.851   0.000   0.000   0.000
   5_occ:  0.317  44.296  -1.247   1.047   0.851   0.000   0.000   0.000
   5_bss:  0.324  53.463  -1.445   0.484   0.711   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.656 0.3603  0.4308    81607.625
   1_bss:  65.050 0.3275  0.5002    82863.401
   1_xyz:  56.997 0.4308  0.6462    67572.032
   1_adp:  55.432 0.4505  0.7548    65339.898
   1_occ:  55.356 0.4515  0.7555    65266.355
   2_bss:  54.759 0.4592  0.6710    64397.507
   2_xyz:  48.280 0.5410  0.7937    52846.243
   2_adp:  46.403 0.5649  0.8383    50285.289
   2_occ:  46.433 0.5644  0.8369    50237.682
   3_bss:  46.114 0.5684  0.7908    49750.055
   3_xyz:  34.983 0.7003  0.9397    29323.909
   3_adp:  33.900 0.7130  0.9575    27878.293
   3_occ:  33.880 0.7132  0.9576    27835.558
   4_bss:  33.721 0.7150  0.9070    27610.345
   4_xyz:  27.131 0.7878  0.9663    18624.072
   4_adp:  24.067 0.8205  0.9841    15214.772
   4_occ:  24.064 0.8206  0.9844    15227.859
   5_bss:  23.991 0.8212  0.9561    15154.879
   5_xyz:  20.818 0.8529  0.9750    11630.527
   5_adp:  18.065 0.8795  0.9796     9348.423
   5_occ:  18.057 0.8796  0.9798     9350.727
   5_bss:  18.087 0.8795  0.9698     9420.261
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3825e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3825e+01
   1_xyz:   1.752  0.014  0.110 18.387  0.007  4.120   1.5488e-01
   1_adp:   1.752  0.014  0.110 18.387  0.007  4.120   1.5488e-01
   1_occ:   1.752  0.014  0.110 18.387  0.007  4.120   1.5488e-01
   2_bss:   1.752  0.014  0.110 18.387  0.007  4.120   1.5488e-01
   2_xyz:   1.310  0.009  0.084 16.860  0.005  4.103   1.0090e-01
   2_adp:   1.310  0.009  0.084 16.860  0.005  4.103   1.0090e-01
   2_occ:   1.310  0.009  0.084 16.860  0.005  4.103   1.0090e-01
   3_bss:   1.310  0.009  0.084 16.860  0.005  4.103   1.0090e-01
   3_xyz:   1.437  0.011  0.099 16.583  0.005  4.103   1.1720e-01
   3_adp:   1.437  0.011  0.099 16.583  0.005  4.103   1.1720e-01
   3_occ:   1.437  0.011  0.099 16.583  0.005  4.103   1.1720e-01
   4_bss:   1.437  0.011  0.099 16.583  0.005  4.103   1.1720e-01
   4_xyz:   1.121  0.008  0.077 15.587  0.004  4.119   7.7410e-02
   4_adp:   1.121  0.008  0.077 15.587  0.004  4.119   7.7410e-02
   4_occ:   1.121  0.008  0.077 15.587  0.004  4.119   7.7410e-02
   5_bss:   1.121  0.008  0.077 15.587  0.004  4.119   7.7410e-02
   5_xyz:   1.158  0.009  0.085 15.464  0.004  4.124   7.9539e-02
   5_adp:   1.158  0.009  0.085 15.464  0.004  4.124   7.9539e-02
   5_occ:   1.158  0.009  0.085 15.464  0.004  4.124   7.9539e-02
   5_bss:   1.158  0.009  0.085 15.464  0.004  4.124   7.9539e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.878   6.9719e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.878   6.9719e+00
   1_xyz:  15.996  0.161  0.521 87.197  0.042  2.191   1.0681e-01
   1_adp:  15.996  0.161  0.521 87.197  0.042  2.191   1.0681e-01
   1_occ:  15.996  0.161  0.521 87.197  0.042  2.191   1.0681e-01
   2_bss:  15.996  0.161  0.521 87.197  0.042  2.191   1.0681e-01
   2_xyz:   7.011  0.113  0.289 85.379  0.044  2.087   7.2583e-02
   2_adp:   7.011  0.113  0.289 85.379  0.044  2.087   7.2583e-02
   2_occ:   7.011  0.113  0.289 85.379  0.044  2.087   7.2583e-02
   3_bss:   7.011  0.113  0.289 85.379  0.044  2.087   7.2583e-02
   3_xyz:   9.669  0.068  0.340 84.336  0.031  2.142   1.0156e-01
   3_adp:   9.669  0.068  0.340 84.336  0.031  2.142   1.0156e-01
   3_occ:   9.669  0.068  0.340 84.336  0.031  2.142   1.0156e-01
   4_bss:   9.669  0.068  0.340 84.336  0.031  2.142   1.0156e-01
   4_xyz:   6.688  0.051  0.217 81.957  0.033  2.128   6.2913e-02
   4_adp:   6.688  0.051  0.217 81.957  0.033  2.128   6.2913e-02
   4_occ:   6.688  0.051  0.217 81.957  0.033  2.128   6.2913e-02
   5_bss:   6.688  0.051  0.217 81.957  0.033  2.128   6.2913e-02
   5_xyz:   7.922  0.048  0.429 82.042  0.038  2.162   7.9518e-02
   5_adp:   7.922  0.048  0.429 82.042  0.038  2.162   7.9518e-02
   5_occ:   7.922  0.048  0.429 82.042  0.038  2.162   7.9518e-02
   5_bss:   7.922  0.048  0.429 82.042  0.038  2.162   7.9518e-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: 110.29   0.00  17.34  77.39   0.00  15.47 110.29   0.00  27.51
   1_occ: 110.29   0.00  17.34  77.39   0.00  15.47 110.29   0.00  27.51
   2_bss: 110.29   0.00  17.34  77.39   0.00  15.47 110.29   0.00  27.51
   2_xyz: 110.29   0.00  17.34  77.39   0.00  15.47 110.29   0.00  27.51
   2_adp:  98.93   0.00  16.30  75.18   0.00  14.22  98.93   0.00  27.67
   2_occ:  98.93   0.00  16.30  75.18   0.00  14.22  98.93   0.00  27.67
   3_bss:  98.93   0.00  16.30  75.18   0.00  14.22  98.93   0.00  27.67
   3_xyz:  98.93   0.00  16.30  75.18   0.00  14.22  98.93   0.00  27.67
   3_adp:  98.42   0.00  16.25  75.91   0.00  13.93  98.42   1.62  28.90
   3_occ:  98.42   0.00  16.25  75.91   0.00  13.93  98.42   1.62  28.90
   4_bss:  98.42   0.00  16.25  75.91   0.00  13.93  98.42   1.62  28.90
   4_xyz:  98.42   0.00  16.25  75.91   0.00  13.93  98.42   1.62  28.90
   4_adp:  96.60   0.00  16.20  83.39   0.00  12.86  96.60   4.10  34.39
   4_occ:  96.60   0.00  16.20  83.39   0.00  12.86  96.60   4.10  34.39
   5_bss:  96.60   0.00  16.20  83.39   0.00  12.86  96.60   4.10  34.39
   5_xyz:  96.60   0.00  16.20  83.39   0.00  12.86  96.60   4.10  34.39
   5_adp:  88.59   0.00  16.05  82.26   0.00  11.77  88.59   4.45  39.34
   5_occ:  88.59   0.00  16.05  82.26   0.00  11.77  88.59   4.45  39.34
   5_bss:  88.59   0.00  16.05  82.27   0.00  11.77  88.59   4.46  39.34
------------------------------------------------------------------------
 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:    1.178    0.004    0.414
   1_adp:    1.178    0.004    0.414
   1_occ:    1.178    0.004    0.414
   2_bss:    1.178    0.004    0.414
   2_xyz:    1.640    0.037    0.575
   2_adp:    1.640    0.037    0.575
   2_occ:    1.640    0.037    0.575
   3_bss:    1.640    0.037    0.575
   3_xyz:    1.741    0.029    0.776
   3_adp:    1.741    0.029    0.776
   3_occ:    1.741    0.029    0.776
   4_bss:    1.741    0.029    0.776
   4_xyz:    2.111    0.070    0.854
   4_adp:    2.111    0.070    0.854
   4_occ:    2.111    0.070    0.854
   5_bss:    2.111    0.070    0.854
   5_xyz:    2.182    0.082    0.926
   5_adp:    2.182    0.082    0.926
   5_occ:    2.182    0.082    0.926
   5_bss:    2.182    0.082    0.926
------------------------------------------------------------------------

CPU time actual refinement: 349.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_237/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_237/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_237/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_237/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_237/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.74 
  Macro-tasks:
    bulk solvent and scale       = 47.59  
    individual site refinement   = 140.86 
    weights calculation          = 33.37  
    collect and process          = 6.38   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.31 
  Micro-tasks:
    mask                            = 3.09   
    f_calc                          = 108.40 
    alpha_beta                      = 8.60   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 116.83 
    fmodel                         = 7.96   
    r_factors                      = 0.32   
    phase_errors                   = 9.60   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 256.24 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.976 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    623 calls, 108.11 s
gradients_fft:          567 calls, 104.31 s

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

# Date 2008-01-16 Time 01:03:59 PST -0800 (1200474239.81 s)
Start R-work = 0.5129, R-free = 0.4995 (no bulk solvent and anisotropic scale)
Final R-work = 0.1564, R-free = 0.2040 (no bulk solvent and anisotropic scale)

Start R-work = 0.5078, R-free = 0.4959
Final R-work = 0.1383, R-free = 0.1892