# Date 2008-01-16 Time 03:29:15 PST -0800 (1200482955.97 s)
#phil __OFF__

Command line arguments: "../1259.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 = 21771
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1259

-------------------------------------------------------------------------------
  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: (72.0062, 46.6953, 86.39, 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: (72.0062, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.99157
Completeness in resolution range: 0.954723
Completeness with d_max=infinity: 0.951893

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   1.9916

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: (72.0062, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.99157
Completeness in resolution range: 0.954723
Completeness with d_max=infinity: 0.951893

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.2625 [2148/2174]  1937   211   9.8%
  bin  2:  4.2625 -  3.3955 [2078/2098]  1866   212  10.2%
  bin  3:  3.3955 -  2.9699 [2041/2060]  1836   205  10.0%
  bin  4:  2.9699 -  2.7000 [2015/2045]  1817   198   9.8%
  bin  5:  2.7000 -  2.5074 [2030/2049]  1830   200   9.9%
  bin  6:  2.5074 -  2.3601 [2003/2028]  1792   211  10.5%
  bin  7:  2.3601 -  2.2423 [1988/2016]  1795   193   9.7%
  bin  8:  2.2423 -  2.1450 [1973/2009]  1774   199  10.1%
  bin  9:  2.1450 -  2.0626 [1982/2024]  1785   197   9.9%
  bin 10:  2.0626 -  1.9916 [1331/2015]  1198   133  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1259/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:
        1.81 -     2.42: 12
        2.42 -     3.04: 2181
        3.04 -     3.66: 4637
        3.66 -     4.28: 8994
        4.28 -     4.90: 12259
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 341 " - " O   HOH Z 207 "  1.921 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.921 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.924 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.013 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28078 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_1259/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1259/model_refine_001.geo

CPU time processing inputs: 9.75


============================ 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 = 72.00625 46.69535 86.39 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: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4584   r_free= 0.4482   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.259495                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7547 0.99   1401  159 0.3841 0.3726      6.5642      6.5378|
|  2:  4.7547 -  3.7930 0.99   1343  144 0.3622 0.3839      6.7412      6.7167|
|  3:  3.7930 -  3.3191 0.99   1323  144 0.4095 0.3682      6.6123      6.6577|
|  4:  3.3191 -  3.0182 0.99   1311  156 0.4337 0.4205      6.4966      6.4452|
|  5:  3.0182 -  2.8033 0.99   1299  143 0.4835 0.4986      6.3454      6.3764|
|  6:  2.8033 -  2.6389 0.99   1303  141 0.4772 0.4756      6.2586      6.2261|
|  7:  2.6389 -  2.5074 0.99   1306  139 0.5186 0.5004       6.248      6.2272|
|  8:  2.5074 -  2.3987 0.98   1257  147 0.5073 0.4697      6.1588      6.1454|
|  9:  2.3987 -  2.3066 0.98   1297  151 0.4889 0.5242      6.1058      6.1418|
| 10:  2.3066 -  2.2273 1.00   1287  135 0.5191 0.4225      6.0927      6.0527|
| 11:  2.2273 -  2.1578 0.98   1271  139 0.5211 0.4679      6.0445      6.0002|
| 12:  2.1578 -  2.0963 0.98   1266  143 0.4940 0.5797      5.9611       6.042|
| 13:  2.0963 -  2.0413 0.98   1269  143 0.5365 0.4948      5.8886      5.7954|
| 14:  2.0413 -  1.9916 0.54    697   75 0.5147 0.4508      5.8511      5.7736|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.7547  1401   159  0.71  33.42   0.79     0.75      68162.46|
|  2:  4.7547 -  3.7930  1343   144  0.74  31.90   0.89     0.79      90716.31|
|  3:  3.7930 -  3.3191  1323   144  0.65  39.73   0.85     0.75      95876.46|
|  4:  3.3191 -  3.0182  1311   156  0.58  45.27   0.81     0.68      87001.44|
|  5:  3.0182 -  2.8033  1299   143  0.48  53.80   0.74     0.56      74155.63|
|  6:  2.8033 -  2.6389  1303   141  0.43  57.42   0.75     0.50      68099.31|
|  7:  2.6389 -  2.5074  1306   139  0.40  59.94   0.73     0.44      62307.21|
|  8:  2.5074 -  2.3987  1257   147  0.39  60.62   0.72     0.46      56492.07|
|  9:  2.3987 -  2.3066  1297   151  0.44  57.22   0.74     0.48      47610.22|
| 10:  2.3066 -  2.2273  1287   135  0.43  57.40   0.75     0.50      43141.93|
| 11:  2.2273 -  2.1578  1271   139  0.41  59.29   0.76     0.48      41537.19|
| 12:  2.1578 -  2.0963  1266   143  0.38  61.66   0.76     0.45      40449.49|
| 13:  2.0963 -  2.0413  1269   143  0.37  62.25   0.71     0.46      34543.44|
| 14:  2.0413 -  1.9916   697    75  0.47  54.41   0.72     0.52      24711.81|
|alpha:            min =        0.44 max =            0.79 mean =         0.56|
|beta:             min =    24711.81 max =        95876.46 mean =     61146.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.14|
|phase err.(test): min =        0.00 max =           89.90 mean =        52.10|
|-----------------------------------------------------------------------------|

============================== 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 = 10.869082             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.075   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.915382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.942   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1492 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2627 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3873 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5061 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6478 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7670 |
|-----------------------------------------------------------------------------|
|-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 |       54.099 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.639 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    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 = 12.137)------------------------------------------|
|    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: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4646   r_free= 0.4542   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.261716                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4507   r_free= 0.4369   ksol= 0.32   Bsol= 20.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.54,7.51,7.38,0.00,0.00,0.00); trace/3= 8.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.253048                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.148955             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.635   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.878893              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.277   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4507      final r-factor (work) = 0.3563          |
| start r-factor (free) = 0.4369      final r-factor (free) = 0.3771          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.8727 = 10.15 * 0.50 * 6.2614 + 1.00 * 54.0993                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.3022 = 10.15 * 0.50 * 6.1431 + 1.00 * 0.1294                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3563      final r-factor (work) = 0.3032          |
| start r-factor (free) = 0.3771      final r-factor (free) = 0.3426          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4139 = 0.88 * 1.00 * 6.1431 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3109 = 0.88 * 1.00 * 6.0261 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    52.35   11.11    None  None   None       |
|    all(noH): 2823   0      0.00    52.35   11.11    None  None   None       |
|    Sol.    : 438    0      0.00    52.35   25.06    None  None   None       |
|    Mac.    : 2385   0      0.00    47.46   8.54     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 -   5.235:  967   |   5:    26.174 -  31.409:  114        |
|      1:     5.235 -  10.470:  732   |   6:    31.409 -  36.644:   77        |
|      2:    10.470 -  15.705:  425   |   7:    36.644 -  41.879:   51        |
|      3:    15.705 -  20.940:  263   |   8:    41.879 -  47.114:   27        |
|      4:    20.940 -  26.174:  154   |   9:    47.114 -  52.349:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3032 r_free = 0.3426             target_work(ml) = 5.993         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3026 r_free = 0.3437             target_work(ml) = 5.992         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3026   r_free= 0.3437   ksol= 0.32   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.54,7.51,7.38,0.00,0.00,0.00); trace/3= 8.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.992398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2997   r_free= 0.3392   ksol= 0.34   Bsol= 47.54   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.92,4.04,4.74,0.00,0.00,0.00); trace/3= 5.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.991676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.254874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.043   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.473525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.393  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2997      final r-factor (work) = 0.2019          |
| start r-factor (free) = 0.3392      final r-factor (free) = 0.2571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.9960 = 8.25 * 0.50 * 6.0247 + 1.00 * 0.1292                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1567 = 8.25 * 0.50 * 5.8317 + 1.00 * 0.0868                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2019      final r-factor (work) = 0.1768          |
| start r-factor (free) = 0.2571      final r-factor (free) = 0.2292          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8005 = 0.47 * 1.00 * 5.8317 + 1.00 * 0.0391                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6584 = 0.47 * 1.00 * 5.5909 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.22   11.54    None  None   None       |
|    all(noH): 2823   0      0.00    64.22   11.54    None  None   None       |
|    Sol.    : 438    0      0.00    64.22   31.77    None  None   None       |
|    Mac.    : 2385   0      0.00    58.47   7.83     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 -   6.422: 1311   |   5:    32.111 -  38.533:  119        |
|      1:     6.422 -  12.844:  737   |   6:    38.533 -  44.955:   89        |
|      2:    12.844 -  19.266:  269   |   7:    44.955 -  51.377:   49        |
|      3:    19.266 -  25.689:  120   |   8:    51.377 -  57.799:   26        |
|      4:    25.689 -  32.111:  100   |   9:    57.799 -  64.221:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1768 r_free = 0.2292             target_work(ml) = 5.532         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1766 r_free = 0.2289             target_work(ml) = 5.531         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1766   r_free= 0.2289   ksol= 0.34   Bsol= 47.54   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.92,4.04,4.74,0.00,0.00,0.00); trace/3= 5.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.531204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1746   r_free= 0.2258   ksol= 0.33   Bsol= 47.54   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,2.78,3.90,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.528123                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.649063              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.753  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.590287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.303  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1746      final r-factor (work) = 0.1425          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5016 = 2.65 * 0.50 * 5.5978 + 1.00 * 0.0872                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2734 = 2.65 * 0.50 * 5.4434 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1425      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6675 = 1.59 * 1.00 * 5.4434 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4703 = 1.59 * 1.00 * 5.3167 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.22   12.66    None  None   None       |
|    all(noH): 2823   0      0.00    82.22   12.66    None  None   None       |
|    Sol.    : 438    0      0.98    82.22   37.31    None  None   None       |
|    Mac.    : 2385   0      0.00    75.31   8.14     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 -   8.222: 1599   |   5:    41.109 -  49.330:   90        |
|      1:     8.222 -  16.443:  608   |   6:    49.330 -  57.552:   65        |
|      2:    16.443 -  24.665:  181   |   7:    57.552 -  65.774:   46        |
|      3:    24.665 -  32.887:  106   |   8:    65.774 -  73.995:   21        |
|      4:    32.887 -  41.109:  100   |   9:    73.995 -  82.217:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1832             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1330 r_free = 0.1831             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1831   ksol= 0.33   Bsol= 47.54   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,2.78,3.90,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.301503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1829   ksol= 0.32   Bsol= 57.69   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,2.47,3.65,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299995                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.761646              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.288  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321920              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.052  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1829      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4064 = 2.76 * 0.50 * 5.3178 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3349 = 2.76 * 0.50 * 5.2604 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1210      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7084 = 0.32 * 1.00 * 5.2604 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7057 = 0.32 * 1.00 * 5.2238 + 1.00 * 0.0240                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.21   12.24    None  None   None       |
|    all(noH): 2823   0      0.00    82.21   12.24    None  None   None       |
|    Sol.    : 438    0      1.53    82.21   35.54    None  None   None       |
|    Mac.    : 2385   0      0.00    77.25   7.97     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 -   8.221: 1646   |   5:    41.105 -  49.325:   85        |
|      1:     8.221 -  16.442:  598   |   6:    49.325 -  57.546:   67        |
|      2:    16.442 -  24.663:  165   |   7:    57.546 -  65.767:   30        |
|      3:    24.663 -  32.884:  108   |   8:    65.767 -  73.988:   12        |
|      4:    32.884 -  41.105:  105   |   9:    73.988 -  82.209:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1684             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1683             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1683   ksol= 0.32   Bsol= 57.69   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,2.47,3.65,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1682   ksol= 0.33   Bsol= 56.65   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,2.50,3.66,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209524                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.144836              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.891  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.968908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1682      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6729 = 2.14 * 0.50 * 5.2234 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6466 = 2.14 * 0.50 * 5.2036 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0540 = 0.97 * 1.00 * 5.2036 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0441 = 0.97 * 1.00 * 5.1921 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.91   12.32    None  None   None       |
|    all(noH): 2823   0      0.00    87.91   12.32    None  None   None       |
|    Sol.    : 438    0      1.19    87.91   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    82.84   7.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.791: 1716   |   5:    43.955 -  52.746:   90        |
|      1:     8.791 -  17.582:  553   |   6:    52.746 -  61.537:   53        |
|      2:    17.582 -  26.373:  159   |   7:    61.537 -  70.328:   22        |
|      3:    26.373 -  35.164:  116   |   8:    70.328 -  79.120:    8        |
|      4:    35.164 -  43.955:   99   |   9:    79.120 -  87.911:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1675             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1674             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1674   ksol= 0.33   Bsol= 56.65   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,2.50,3.66,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195423                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7547 0.99   1401  159 0.1010 0.1397      5.4031      5.5938|
|  2:  4.7547 -  3.7930 0.99   1343  144 0.0892 0.1133      5.4714      5.6165|
|  3:  3.7930 -  3.3191 0.99   1323  144 0.1081 0.1579      5.4997      5.8889|
|  4:  3.3191 -  3.0182 0.99   1311  156 0.1255 0.1754      5.4945       5.673|
|  5:  3.0182 -  2.8033 0.99   1299  143 0.1413 0.1857      5.3749      5.5958|
|  6:  2.8033 -  2.6389 0.99   1303  141 0.1275 0.1910      5.2625      5.5239|
|  7:  2.6389 -  2.5074 0.99   1306  139 0.1321 0.1683      5.2234      5.3734|
|  8:  2.5074 -  2.3987 0.98   1257  147 0.1226 0.1925      5.1161      5.4231|
|  9:  2.3987 -  2.3066 0.98   1297  151 0.1263 0.1955      5.1083      5.4053|
| 10:  2.3066 -  2.2273 1.00   1287  135 0.1193 0.1653       5.005      5.2008|
| 11:  2.2273 -  2.1578 0.98   1271  139 0.1194 0.1901      4.9996      5.3428|
| 12:  2.1578 -  2.0963 0.98   1266  143 0.1137 0.1767      4.9071       5.186|
| 13:  2.0963 -  2.0413 0.98   1269  143 0.1247 0.1869      4.8659      5.1278|
| 14:  2.0413 -  1.9916 0.54    697   75 0.1095 0.1749      4.7314      4.9719|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.7547  1401   159  0.94   9.27   0.97     0.95       7580.54|
|  2:  4.7547 -  3.7930  1343   144  0.95   8.42   1.00     0.99       9709.28|
|  3:  3.7930 -  3.3191  1323   144  0.93  11.83   1.02     1.02      11074.64|
|  4:  3.3191 -  3.0182  1311   156  0.92  14.27   1.00     0.98      11266.19|
|  5:  3.0182 -  2.8033  1299   143  0.89  16.88   0.99     0.97       9174.96|
|  6:  2.8033 -  2.6389  1303   141  0.89  17.01   0.98     0.95       8009.17|
|  7:  2.6389 -  2.5074  1306   139  0.90  16.50   0.99     0.96       7003.15|
|  8:  2.5074 -  2.3987  1257   147  0.89  16.96   0.98     0.95       5987.55|
|  9:  2.3987 -  2.3066  1297   151  0.90  16.73   0.99     0.96       5868.30|
| 10:  2.3066 -  2.2273  1287   135  0.90  16.33   0.99     0.96       4784.15|
| 11:  2.2273 -  2.1578  1271   139  0.89  17.00   0.98     0.93       4767.62|
| 12:  2.1578 -  2.0963  1266   143  0.91  15.90   1.00     1.00       4283.01|
| 13:  2.0963 -  2.0413  1269   143  0.89  17.78   0.99     0.97       3945.70|
| 14:  2.0413 -  1.9916   697    75  0.90  16.77   0.97     0.93       3094.36|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3094.36 max =        11266.19 mean =      7063.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.99|
|phase err.(test): min =        0.00 max =           88.31 mean =        14.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1674   ksol= 0.32   Bsol= 59.30   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.02,-0.56,0.58,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195418                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1674   ksol= 0.32   Bsol= 59.30   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.02,-0.56,0.58,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195418                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7547 0.99   1401  159 0.1010 0.1395       5.402      5.5937|
|  2:  4.7547 -  3.7930 0.99   1343  144 0.0892 0.1132      5.4713      5.6164|
|  3:  3.7930 -  3.3191 0.99   1323  144 0.1081 0.1579      5.4995      5.8887|
|  4:  3.3191 -  3.0182 0.99   1311  156 0.1255 0.1754      5.4945      5.6731|
|  5:  3.0182 -  2.8033 0.99   1299  143 0.1413 0.1858      5.3751       5.596|
|  6:  2.8033 -  2.6389 0.99   1303  141 0.1275 0.1910      5.2627      5.5239|
|  7:  2.6389 -  2.5074 0.99   1306  139 0.1321 0.1682      5.2234      5.3732|
|  8:  2.5074 -  2.3987 0.98   1257  147 0.1225 0.1925      5.1161      5.4233|
|  9:  2.3987 -  2.3066 0.98   1297  151 0.1263 0.1955      5.1086      5.4056|
| 10:  2.3066 -  2.2273 1.00   1287  135 0.1193 0.1653       5.005      5.2004|
| 11:  2.2273 -  2.1578 0.98   1271  139 0.1195 0.1902      4.9997      5.3433|
| 12:  2.1578 -  2.0963 0.98   1266  143 0.1138 0.1767      4.9074      5.1858|
| 13:  2.0963 -  2.0413 0.98   1269  143 0.1247 0.1870      4.8661       5.128|
| 14:  2.0413 -  1.9916 0.54    697   75 0.1095 0.1751      4.7318      4.9727|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.7547  1401   159  0.94   9.26   0.97     0.95       7564.44|
|  2:  4.7547 -  3.7930  1343   144  0.95   8.42   1.00     0.99       9701.21|
|  3:  3.7930 -  3.3191  1323   144  0.93  11.82   1.02     1.02      11070.25|
|  4:  3.3191 -  3.0182  1311   156  0.92  14.27   1.00     0.98      11268.48|
|  5:  3.0182 -  2.8033  1299   143  0.89  16.88   0.99     0.97       9178.70|
|  6:  2.8033 -  2.6389  1303   141  0.89  17.02   0.98     0.95       8010.78|
|  7:  2.6389 -  2.5074  1306   139  0.90  16.50   0.99     0.96       7003.74|
|  8:  2.5074 -  2.3987  1257   147  0.89  16.96   0.98     0.95       5988.42|
|  9:  2.3987 -  2.3066  1297   151  0.90  16.73   1.00     0.96       5869.24|
| 10:  2.3066 -  2.2273  1287   135  0.90  16.33   1.00     0.96       4783.57|
| 11:  2.2273 -  2.1578  1271   139  0.89  17.00   0.99     0.93       4766.75|
| 12:  2.1578 -  2.0963  1266   143  0.91  15.90   1.01     1.00       4285.06|
| 13:  2.0963 -  2.0413  1269   143  0.89  17.79   0.99     0.97       3947.97|
| 14:  2.0413 -  1.9916   697    75  0.90  16.79   0.97     0.93       3097.93|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3097.93 max =        11268.48 mean =      7061.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.99|
|phase err.(test): min =        0.00 max =           88.32 mean =        14.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.137)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.14    91.05   15.46    None  None   None       |
|    all(noH): 2823   0      3.14    91.05   15.46    None  None   None       |
|    Sol.    : 438    0      4.33    91.05   39.06    None  None   None       |
|    Mac.    : 2385   0      3.14    85.98   11.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.141 -  11.932: 1716   |   5:    47.097 -  55.888:   90        |
|      1:    11.932 -  20.723:  553   |   6:    55.888 -  64.679:   53        |
|      2:    20.723 -  29.514:  159   |   7:    64.679 -  73.470:   22        |
|      3:    29.514 -  38.306:  116   |   8:    73.470 -  82.261:    8        |
|      4:    38.306 -  47.097:   99   |   9:    82.261 -  91.052:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.378 - 5.774
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 340
   mapped sites are within: 0.704 - 5.774

peak=   10.409 closest distance to " CB  VAL A 230 " =    1.451
peak=    7.441 closest distance to " CG2 VAL A 296 " =    1.134
peak=    7.044 closest distance to " CG  ARG A 138 " =    1.143
peak=    6.039 closest distance to " CG  LEU A   5 " =    1.182
peak=    5.727 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.644 closest distance to " CD2 LEU A   5 " =    1.126
peak=    5.501 closest distance to " O   HOH Z 111 " =    1.981
peak=    5.342 closest distance to " CG  LEU A 228 " =    1.177
peak=    5.186 closest distance to " NH1 ARG A 138 " =    0.994
peak=    5.066 closest distance to " CB  GLN A 183 " =    1.239
peak=    5.058 closest distance to " O   HOH Z 232 " =    2.236
peak=    5.055 closest distance to " NE2 GLN A  11 " =    1.148
peak=    4.876 closest distance to " CG  PRO A 198 " =    1.214
peak=    4.779 closest distance to " CB  ASN A 148 " =    1.343
peak=    4.774 closest distance to " NH1AARG A 145 " =    1.237
peak=    4.761 closest distance to " CG  PRO A 213 " =    1.287
peak=    4.744 closest distance to " CG  PRO A 243 " =    1.134
peak=    4.738 closest distance to " O   HOH Z 298 " =    2.024
peak=    4.676 closest distance to " CB  VAL A 230 " =    1.243
peak=    4.674 closest distance to " CB  SER A  63 " =    1.291
peak=    4.631 closest distance to " O   PRO A 198 " =    1.565
peak=    4.620 closest distance to " O   HOH Z 369 " =    2.025
peak=    4.593 closest distance to " CD  ARG A 138 " =    1.181
peak=    4.504 closest distance to " CG  PRO A 280 " =    0.866
peak=    4.444 closest distance to " O   HOH Z 303 " =    2.220
peak=    4.421 closest distance to " O   HOH Z 427 " =    3.193
peak=    4.403 closest distance to " CD  ARG A 159 " =    0.814
peak=    4.396 closest distance to " CD2 LEU A 228 " =    1.182
peak=    4.394 closest distance to " O   HOH Z 144 " =    1.680
peak=    4.358 closest distance to " CB  ASP A 124 " =    0.754
peak=    4.297 closest distance to " CB  TRP A 266 " =    0.992
peak=    4.274 closest distance to " CB  VAL A 296 " =    1.057
peak=    4.262 closest distance to " O   HOH Z 368 " =    2.124
peak=    4.251 closest distance to " CZ  PHE A 218 " =    1.057
peak=    4.230 closest distance to " O   HOH Z 425 " =    1.478
peak=    4.228 closest distance to " O   HOH Z 236 " =    2.101
peak=    4.206 closest distance to " CB  LEU A 228 " =    1.257
peak=    4.190 closest distance to " CB  ASN A 187 " =    2.028
peak=    4.184 closest distance to " O   HOH Z 102 " =    1.175
peak=    4.164 closest distance to " O   HOH Z 158 " =    2.941
peak=    4.145 closest distance to " O   HOH Z 316 " =    3.004
peak=    4.122 closest distance to " O   HOH Z 183 " =    1.403
peak=    4.111 closest distance to " CB  ARG A 275 " =    0.914
peak=    4.106 closest distance to " CB  GLU A 152 " =    1.328
peak=    4.089 closest distance to " CB  VAL A 265 " =    1.265
peak=    4.086 closest distance to " O   HOH Z 272 " =    1.927
peak=    4.083 closest distance to " CD1 LEU A 300 " =    1.240
peak=    4.076 closest distance to " O   HOH Z 411 " =    3.555
peak=    4.069 closest distance to " CB  GLU A 128 " =    1.070
peak=    4.063 closest distance to " O   HOH Z   9 " =    2.154
peak=    4.061 closest distance to " O   HOH Z  54 " =    2.430
peak=    4.061 closest distance to " CB  SER A 216 " =    0.972
peak=    4.037 closest distance to " CB  ASP A 140 " =    0.903
peak=    4.027 closest distance to " CD ALYS A 290 " =    1.017
peak=    4.019 closest distance to " O   HOH Z 112 " =    1.643
peak=    3.987 closest distance to " CZ  PHE A 192 " =    0.957
peak=    3.982 closest distance to " O   HOH Z  88 " =    3.168
peak=    3.980 closest distance to " CA  MET A  40 " =    1.090
peak=    3.980 closest distance to " O   HOH Z 346 " =    1.644
peak=    3.968 closest distance to " ND2 ASN A 187 " =    1.453
peak=    3.967 closest distance to " O   HOH Z 234 " =    3.910
peak=    3.947 closest distance to " O   HOH Z 132 " =    2.600
peak=    3.935 closest distance to " NH1 ARG A  56 " =    0.968
peak=    3.920 closest distance to " O   HOH Z 410 " =    1.488
peak=    3.894 closest distance to " CB  SER A 212 " =    1.191
peak=    3.884 closest distance to " CG2 THR A 221 " =    1.064
peak=    3.880 closest distance to " CB  ASN A  39 " =    0.906
peak=    3.873 closest distance to " O   HOH Z 286 " =    2.299
peak=    3.869 closest distance to " O   HOH Z 193 " =    1.757
peak=    3.868 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.864 closest distance to " CA  TYR A  30 " =    0.964
peak=    3.863 closest distance to " CB  LEU A 237 " =    0.833
peak=    3.860 closest distance to " OD2 ASP A 286 " =    2.871
peak=    3.858 closest distance to " CG  GLN A  88 " =    1.065
peak=    3.834 closest distance to " CB  SER A   3 " =    1.488
peak=    3.818 closest distance to " CB  ARG A  79 " =    1.502
peak=    3.816 closest distance to " O   HOH Z 437 " =    1.692
peak=    3.811 closest distance to " O   HOH Z 403 " =    1.750
peak=    3.808 closest distance to " O   HOH Z 261 " =    2.156
peak=    3.805 closest distance to " O   HOH Z 188 " =    3.079
peak=    3.805 closest distance to " CB  THR A  82 " =    1.353
peak=    3.796 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.792 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.780 closest distance to " O   HOH Z 126 " =    1.532
peak=    3.777 closest distance to " O   SER A  87 " =    2.352
peak=    3.751 closest distance to " O   HOH Z 222 " =    2.402
peak=    3.750 closest distance to " CB  VAL A 202 " =    1.586
peak=    3.746 closest distance to " CG1 ILE A 151 " =    1.164
peak=    3.742 closest distance to " CA  ALA A  21 " =    1.195
peak=    3.738 closest distance to " CB  MET A  40 " =    0.827
peak=    3.736 closest distance to " NH1 ARG A  14 " =    0.953
peak=    3.734 closest distance to " O   HOH Z 171 " =    3.932
peak=    3.732 closest distance to " NZ  LYS A 117 " =    3.254
peak=    3.729 closest distance to " O   HOH Z 214 " =    1.927
peak=    3.723 closest distance to " CG BARG A 275 " =    1.544
peak=    3.722 closest distance to " O   HOH Z  80 " =    1.691
peak=    3.718 closest distance to " O   HOH Z   2 " =    1.571
peak=    3.713 closest distance to " CB  SER A 210 " =    0.853
peak=    3.711 closest distance to " CB  ALA A 104 " =    0.835
peak=    3.708 closest distance to " CB  LEU A 143 " =    1.182
peak=    3.706 closest distance to " O   MET A 105 " =    1.768
peak=    3.697 closest distance to " O   HOH Z 193 " =    2.112
peak=    3.696 closest distance to " O   HOH Z 247 " =    1.382
peak=    3.692 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.674 closest distance to " O   HOH Z  57 " =    1.371
peak=    3.668 closest distance to " O   HOH Z  78 " =    1.602
peak=    3.665 closest distance to " CG  LEU A   5 " =    0.752
peak=    3.664 closest distance to " CA  ASP A 124 " =    0.704
peak=    3.660 closest distance to " CA  SER A  87 " =    0.926
peak=    3.659 closest distance to " CB  PRO A  54 " =    0.790
peak=    3.652 closest distance to " CA  GLY A 267 " =    0.939
peak=    3.649 closest distance to " CB  ASN A 110 " =    1.206
peak=    3.639 closest distance to " CD  LYS A 166 " =    1.312
peak=    3.638 closest distance to " CA  ALA A  51 " =    1.043
peak=    3.637 closest distance to " CB  ARG A 190 " =    1.620
peak=    3.628 closest distance to " N   PHE A 130 " =    1.299
peak=    3.627 closest distance to " OD1 ASN A  69 " =    2.628
peak=    3.625 closest distance to " O   HOH Z 184 " =    1.567
peak=    3.618 closest distance to " CB  GLN A  88 " =    1.273
peak=    3.617 closest distance to " O   HOH Z 290 " =    1.249
peak=    3.610 closest distance to " CB  GLU A 277 " =    3.648
peak=    3.606 closest distance to " CA  ASN A 215 " =    1.189
peak=    3.603 closest distance to " ND2 ASN A 249 " =    1.884
peak=    3.602 closest distance to " CB  ASN A 142 " =    0.977
peak=    3.602 closest distance to " CB  GLN A 103 " =    1.105
peak=    3.601 closest distance to " CA  ALA A 295 " =    1.106
peak=    3.590 closest distance to " ND1 HIS A  86 " =    1.713
peak=    3.590 closest distance to " CD2 LEU A 255 " =    1.637
peak=    3.579 closest distance to " CA  LYS A 117 " =    1.205
peak=    3.579 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.578 closest distance to " O   HOH Z  20 " =    1.962
peak=    3.573 closest distance to " CD  ARG A  66 " =    2.300
peak=    3.573 closest distance to " CA  ILE A  33 " =    1.729
peak=    3.569 closest distance to " O   HOH Z  10 " =    1.853
peak=    3.567 closest distance to " OH  TYR A 214 " =    1.269
peak=    3.564 closest distance to " CA  ALA A 291 " =    0.997
peak=    3.560 closest distance to " O   HOH Z 352 " =    1.739
peak=    3.556 closest distance to " O   HOH Z 147 " =    1.682
peak=    3.553 closest distance to " CB  ALA A 291 " =    1.324
peak=    3.537 closest distance to " OG  SER A  62 " =    3.036
peak=    3.535 closest distance to " CB AVAL A  41 " =    1.352
peak=    3.529 closest distance to " CA  ALA A 154 " =    1.077
peak=    3.522 closest distance to " O   HOH Z 185 " =    1.927
peak=    3.519 closest distance to " O   HOH Z 345 " =    3.520
peak=    3.519 closest distance to " O   HOH Z 371 " =    3.192
peak=    3.516 closest distance to " O   HOH Z 109 " =    2.667
peak=    3.507 closest distance to " CA  ALA A 299 " =    0.966
peak=    3.505 closest distance to " CA  ILE A 234 " =    1.095
peak=    3.503 closest distance to " O   HOH Z   3 " =    1.875
peak=    3.500 closest distance to " CB  GLU A 152 " =    0.971
peak=    3.499 closest distance to " O   HOH Z 280 " =    3.039
peak=    3.498 closest distance to " CG  MET A 185 " =    1.221
peak=    3.487 closest distance to " CA  THR A 264 " =    0.728
peak=    3.485 closest distance to " O   HOH Z 108 " =    2.773
peak=    3.481 closest distance to " OG BSER A 134 " =    2.945
peak=    3.480 closest distance to " CA  ALA A 158 " =    1.198
peak=    3.479 closest distance to " O   HOH Z 282 " =    1.790
peak=    3.470 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.468 closest distance to " CD  ARG A 269 " =    0.921
peak=    3.464 closest distance to " O   HOH Z  44 " =    2.258
peak=    3.460 closest distance to " O   HOH Z 197 " =    3.061
peak=    3.459 closest distance to " CG  ARG A 159 " =    1.108
peak=    3.457 closest distance to " O   HOH Z 313 " =    1.729
peak=    3.455 closest distance to " CB  ALA A 248 " =    1.023
peak=    3.453 closest distance to " CE1 TYR A 186 " =    1.367
peak=    3.452 closest distance to " CA  TYR A 116 " =    1.506
peak=    3.448 closest distance to " NH2 ARG A 219 " =    1.781
peak=    3.446 closest distance to " CA  ARG A 195 " =    1.310
peak=    3.443 closest distance to " O   HOH Z 209 " =    2.521
peak=    3.438 closest distance to " CB  ASN A 187 " =    1.033
peak=    3.437 closest distance to " CG1 VAL A 153 " =    0.933
peak=    3.429 closest distance to " CG2 VAL A 257 " =    0.927
peak=    3.429 closest distance to " NH2 ARG A 156 " =    1.104
peak=    3.428 closest distance to " CG2 ILE A 234 " =    0.925
peak=    3.426 closest distance to " O   HOH Z 133 " =    1.776
peak=    3.424 closest distance to " O   TRP A 274 " =    1.773
peak=    3.422 closest distance to " CB  THR A 157 " =    1.108
peak=    3.421 closest distance to " O   HOH Z   1 " =    1.896
peak=    3.420 closest distance to " CB  ALA A 248 " =    1.344
peak=    3.416 closest distance to " NE AARG A 275 " =    1.310
peak=    3.412 closest distance to " CA  THR A 221 " =    0.918
peak=    3.411 closest distance to " O   HOH Z 135 " =    2.035
peak=    3.411 closest distance to " O   HOH Z 180 " =    2.092
peak=    3.410 closest distance to " CG1 VAL A 174 " =    1.142
peak=    3.408 closest distance to " O   TYR A 116 " =    1.201
peak=    3.404 closest distance to " CA  ARG A  36 " =    1.208
peak=    3.404 closest distance to " CD  ARG A 219 " =    1.078
peak=    3.403 closest distance to " CB  ILE A 120 " =    1.304
peak=    3.402 closest distance to " O   HOH Z  88 " =    2.631
peak=    3.400 closest distance to " O   HOH Z 116 " =    1.813
peak=    3.392 closest distance to " CB  ALA A 227 " =    0.920
peak=    3.392 closest distance to " O   HOH Z 435 " =    1.955
peak=    3.391 closest distance to " CB  TRP A 150 " =    1.434
peak=    3.390 closest distance to " CB  VAL A 250 " =    1.089
peak=    3.384 closest distance to " O   HOH Z 313 " =    1.805
peak=    3.381 closest distance to " O   HOH Z 409 " =    2.826
peak=    3.375 closest distance to " O   HOH Z 353 " =    2.684
peak=    3.371 closest distance to " O   ALA A 291 " =    1.533
peak=    3.371 closest distance to " O   HOH Z 273 " =    2.608
peak=    3.365 closest distance to " CE2 TYR A 186 " =    0.917
peak=    3.363 closest distance to " CB  ALA A 161 " =    0.980
peak=    3.360 closest distance to " O   HOH Z   7 " =    1.192
peak=    3.360 closest distance to " ND1 HIS A  81 " =    1.779
peak=    3.358 closest distance to " O   HOH Z 302 " =    1.847
peak=    3.349 closest distance to " O   HOH Z  59 " =    2.131
peak=    3.347 closest distance to " O   HOH Z 340 " =    2.288
peak=    3.344 closest distance to " OG  SER A  22 " =    2.954
peak=    3.343 closest distance to " N   SER A 135 " =    1.366
peak=    3.341 closest distance to " O   HOH Z   1 " =    1.822
peak=    3.338 closest distance to " CB  TRP A 179 " =    1.482
peak=    3.332 closest distance to " CB  PHE A  16 " =    1.166
peak=    3.331 closest distance to " OD1 ASN A 217 " =    1.597
peak=    3.329 closest distance to " CG1BVAL A  72 " =    1.636
peak=    3.328 closest distance to " CB  GLU A  46 " =    0.998
peak=    3.328 closest distance to " CG1 VAL A 296 " =    1.276
peak=    3.326 closest distance to " O   HOH Z 281 " =    4.714
peak=    3.326 closest distance to " CD1 LEU A   5 " =    1.316
peak=    3.324 closest distance to " NE2 HIS A 207 " =    1.402
peak=    3.323 closest distance to " O   HOH Z  63 " =    1.560
peak=    3.322 closest distance to " CD  ARG A  14 " =    1.248
peak=    3.321 closest distance to " CB  ALA A  34 " =    0.977
peak=    3.320 closest distance to " O   HOH Z 124 " =    1.849
peak=    3.318 closest distance to " O   HOH Z 248 " =    1.842
peak=    3.317 closest distance to " O   HOH Z 332 " =    1.639
peak=    3.314 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.313 closest distance to " O   HOH Z 291 " =    1.659
peak=    3.303 closest distance to " O   HOH Z 402 " =    1.433
peak=    3.303 closest distance to " CG1 ILE A  49 " =    1.497
peak=    3.300 closest distance to " CG2 THR A 220 " =    1.079
peak=    3.299 closest distance to " O   HOH Z  29 " =    2.517
peak=    3.299 closest distance to " O   HOH Z 166 " =    3.579
peak=    3.299 closest distance to " OG  SER A 135 " =    1.264
peak=    3.296 closest distance to " O   HOH Z 271 " =    2.133
peak=    3.296 closest distance to " CA  ASP A 162 " =    1.067
peak=    3.291 closest distance to " CB  ALA A 242 " =    0.819
peak=    3.287 closest distance to " CB  GLU A 236 " =    1.340
peak=    3.286 closest distance to " O   HOH Z 423 " =    2.770
peak=    3.282 closest distance to " O   HOH Z 305 " =    3.531
peak=    3.281 closest distance to " O   HOH Z 156 " =    2.838
peak=    3.276 closest distance to " O   HOH Z 407 " =    2.092
peak=    3.272 closest distance to " O   HOH Z 368 " =    3.641
peak=    3.268 closest distance to " O   HOH Z 235 " =    1.634
peak=    3.267 closest distance to " N   SER A 134 " =    1.424
peak=    3.267 closest distance to " N   TYR A  15 " =    0.824
peak=    3.265 closest distance to " O   HOH Z 148 " =    2.155
peak=    3.264 closest distance to " CG  GLU A  37 " =    0.799
peak=    3.263 closest distance to " O   GLN A 278 " =    1.562
peak=    3.261 closest distance to " O   HOH Z 193 " =    1.860
peak=    3.261 closest distance to " O   HOH Z  88 " =    3.466
peak=    3.259 closest distance to " OG  SER A 206 " =    1.173
peak=    3.257 closest distance to " O   HOH Z 133 " =    2.496
peak=    3.255 closest distance to " O   ARG A  56 " =    2.808
peak=    3.249 closest distance to " C   GLN A  88 " =    1.576
peak=    3.248 closest distance to " O  BHOH Z  74 " =    1.332
peak=    3.247 closest distance to " O   HOH Z  21 " =    1.729
peak=    3.247 closest distance to " O   THR A 220 " =    1.316
peak=    3.246 closest distance to " O   HOH Z 128 " =    2.107
peak=    3.245 closest distance to " O   HOH Z 213 " =    1.993
peak=    3.245 closest distance to " O   HOH Z 392 " =    1.870
peak=    3.241 closest distance to " O   HOH Z 175 " =    2.211
peak=    3.240 closest distance to " CB  ALA A 137 " =    0.983
peak=    3.239 closest distance to " CB  ALA A 114 " =    1.090
peak=    3.233 closest distance to " O   HOH Z 213 " =    3.185
peak=    3.233 closest distance to " O   HOH Z 285 " =    2.826
peak=    3.230 closest distance to " O   HOH Z 134 " =    2.646
peak=    3.229 closest distance to " CA  ASP A 140 " =    1.304
peak=    3.228 closest distance to " OH  TYR A 186 " =    0.989
peak=    3.228 closest distance to " CG BARG A 102 " =    1.872
peak=    3.225 closest distance to " O   HOH Z 344 " =    3.064
peak=    3.225 closest distance to " N   ASN A  39 " =    1.227
peak=    3.225 closest distance to " CB  TYR A 116 " =    0.854
peak=    3.224 closest distance to " CA  TYR A 186 " =    1.563
peak=    3.223 closest distance to " CA  LEU A 282 " =    0.984
peak=    3.219 closest distance to " CA  GLY A 211 " =    1.349
peak=    3.219 closest distance to " CE2 TYR A 293 " =    0.993
peak=    3.218 closest distance to " O   HOH Z 250 " =    1.249
peak=    3.214 closest distance to " O   HOH Z 392 " =    1.389
peak=    3.212 closest distance to " O   HOH Z  58 " =    1.575
peak=    3.210 closest distance to " CB  ARG A 138 " =    1.643
peak=    3.209 closest distance to " O   HOH Z 295 " =    1.484
peak=    3.208 closest distance to " NH2BARG A 145 " =    2.038
peak=    3.208 closest distance to " O   ALA A  10 " =    1.650
peak=    3.207 closest distance to " O   HOH Z 175 " =    3.611
peak=    3.205 closest distance to " CG  GLN A 278 " =    1.263
peak=    3.202 closest distance to " O   HOH Z 216 " =    2.800
peak=    3.202 closest distance to " CA  ALA A 160 " =    0.922
peak=    3.200 closest distance to " CA  VAL A  41 " =    0.918
peak=    3.199 closest distance to " O   HOH Z 174 " =    1.114
peak=    3.197 closest distance to " CD1 ILE A 106 " =    0.848
peak=    3.197 closest distance to " O   HOH Z 263 " =    1.562
peak=    3.194 closest distance to " CA  LEU A 101 " =    1.607
peak=    3.193 closest distance to " CA  PHE A 283 " =    1.128
peak=    3.191 closest distance to " CB  TYR A  30 " =    1.134
peak=    3.191 closest distance to " CG  ARG A 269 " =    1.736
peak=    3.191 closest distance to " CB  SER A  62 " =    1.240
peak=    3.190 closest distance to " O   HOH Z 334 " =    1.557
peak=    3.185 closest distance to " O   HOH Z 227 " =    1.977
peak=    3.184 closest distance to " CB  VAL A 268 " =    0.848
peak=    3.179 closest distance to " OG  SER A  28 " =    1.563
peak=    3.178 closest distance to " CD2 TRP A 179 " =    1.319
peak=    3.170 closest distance to " OG BSER A 164 " =    2.173
peak=    3.165 closest distance to " O   HOH Z 128 " =    1.614
peak=    3.163 closest distance to " CB  ALA A 100 " =    1.425
peak=    3.161 closest distance to " OG  SER A  62 " =    3.145
peak=    3.158 closest distance to " CG  MET A 113 " =    1.675
peak=    3.154 closest distance to " NE2 GLN A  58 " =    5.774
peak=    3.154 closest distance to " CA  ARG A 102 " =    1.170
peak=    3.151 closest distance to " O   HOH Z 423 " =    1.528
peak=    3.150 closest distance to " O   HOH Z 122 " =    1.570
peak=    3.149 closest distance to " CG  MET A 188 " =    0.973
peak=    3.142 closest distance to " O   HOH Z 273 " =    1.572
peak=    3.139 closest distance to " CB  PHE A 283 " =    0.917
peak=    3.135 closest distance to " O   HOH Z 425 " =    1.950
peak=    3.132 closest distance to " O   HOH Z  97 " =    2.115
peak=    3.130 closest distance to " O   HOH Z  68 " =    1.513
peak=    3.127 closest distance to " CG2 ILE A 106 " =    0.858
peak=    3.126 closest distance to " CB  LEU A  83 " =    0.873
peak=    3.125 closest distance to " CG  MET A 185 " =    1.046
peak=    3.116 closest distance to " CB  ALA A 184 " =    0.940
peak=    3.106 closest distance to " O   HOH Z 294 " =    1.581
peak=    3.101 closest distance to " O   HOH Z 327 " =    1.990
peak=    3.096 closest distance to " O   HOH Z 152 " =    1.696
peak=    3.095 closest distance to " O   HOH Z 380 " =    1.847
peak=    3.091 closest distance to " CB  ARG A 139 " =    0.912
peak=    3.090 closest distance to " O   HOH Z 130 " =    3.924
peak=    3.084 closest distance to " CG  LEU A  25 " =    1.922
peak=    3.083 closest distance to " O   ALA A 158 " =    1.416
peak=    3.076 closest distance to " O   HOH Z 329 " =    3.899
peak=    3.060 closest distance to " CA  ILE A 106 " =    0.825
peak=    3.040 closest distance to " CB  ASN A 224 " =    0.964
peak=    3.039 closest distance to " CB  PRO A 243 " =    1.208
peak=    3.033 closest distance to " N   ARG A 156 " =    1.389

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.672 - 5.562
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 201
   mapped sites are within: 0.767 - 5.562

peak=   -4.954 closest distance to " CG2 VAL A 230 " =    0.888
peak=   -4.382 closest distance to " O   HOH Z 231 " =    1.625
peak=   -4.331 closest distance to " CD  ARG A 138 " =    1.181
peak=   -4.282 closest distance to " CD  ARG A  14 " =    3.233
peak=   -4.260 closest distance to " OE1 GLN A 223 " =    2.221
peak=   -4.236 closest distance to " O   HOH Z 102 " =    1.370
peak=   -4.236 closest distance to " CG  ARG A 138 " =    0.914
peak=   -4.201 closest distance to " CD  ARG A 156 " =    2.091
peak=   -4.051 closest distance to " OG BSER A 134 " =    1.265
peak=   -4.045 closest distance to " CG1 VAL A 296 " =    1.324
peak=   -4.001 closest distance to " O   HOH Z  52 " =    1.549
peak=   -3.988 closest distance to " CD1 TYR A 247 " =    2.793
peak=   -3.976 closest distance to " O   HOH Z  38 " =    1.437
peak=   -3.973 closest distance to " CA  ASP A  27 " =    2.485
peak=   -3.948 closest distance to " N   THR A 157 " =    1.478
peak=   -3.901 closest distance to " O   HOH Z 179 " =    2.309
peak=   -3.900 closest distance to " O   HOH Z 377 " =    1.752
peak=   -3.885 closest distance to " CB  PRO A 243 " =    2.626
peak=   -3.876 closest distance to " O   HOH Z 266 " =    5.232
peak=   -3.872 closest distance to " OG  SER A  87 " =    1.464
peak=   -3.852 closest distance to " O   HOH Z 389 " =    1.991
peak=   -3.833 closest distance to " O   HOH Z  43 " =    1.632
peak=   -3.825 closest distance to " O   HOH Z 198 " =    2.432
peak=   -3.819 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.806 closest distance to " O   HOH Z 231 " =    0.866
peak=   -3.794 closest distance to " O   HOH Z  73 " =    2.015
peak=   -3.782 closest distance to " CD1 LEU A   5 " =    2.624
peak=   -3.774 closest distance to " O   GLY A  80 " =    2.510
peak=   -3.771 closest distance to " CG  TRP A 266 " =    1.788
peak=   -3.771 closest distance to " CD2 LEU A 167 " =    1.851
peak=   -3.771 closest distance to " CG1 VAL A 250 " =    2.692
peak=   -3.770 closest distance to " CE2 TYR A  30 " =    2.704
peak=   -3.767 closest distance to " CG2 VAL A 296 " =    1.403
peak=   -3.766 closest distance to " OE1 GLN A  88 " =    1.085
peak=   -3.761 closest distance to " CZ3 TRP A 179 " =    1.144
peak=   -3.729 closest distance to " O   HOH Z 275 " =    1.534
peak=   -3.727 closest distance to " CA  GLY A 241 " =    3.024
peak=   -3.722 closest distance to " CB  VAL A 230 " =    1.029
peak=   -3.719 closest distance to " O   PRO A 163 " =    1.990
peak=   -3.713 closest distance to " CB  ALA A  43 " =    2.559
peak=   -3.696 closest distance to " CG  MET A 105 " =    1.003
peak=   -3.684 closest distance to " CG2 ILE A  49 " =    2.817
peak=   -3.665 closest distance to " O   ILE A 109 " =    2.686
peak=   -3.663 closest distance to " O   HOH Z 290 " =    1.343
peak=   -3.655 closest distance to " CA  GLY A 241 " =    2.296
peak=   -3.651 closest distance to " CD2 PHE A  61 " =    1.869
peak=   -3.631 closest distance to " CE3 TRP A 150 " =    2.253
peak=   -3.630 closest distance to " O   GLY A 203 " =    2.375
peak=   -3.625 closest distance to " CD  LYS A 289 " =    2.473
peak=   -3.625 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.618 closest distance to " O   HOH Z 211 " =    1.456
peak=   -3.618 closest distance to " O   HOH Z 350 " =    1.762
peak=   -3.616 closest distance to " O   VAL A 189 " =    2.516
peak=   -3.611 closest distance to " OXT GLY A 302 " =    3.130
peak=   -3.610 closest distance to " CG  ASP A 231 " =    0.767
peak=   -3.609 closest distance to " C   LEU A 222 " =    0.826
peak=   -3.606 closest distance to " O   HOH Z 394 " =    1.531
peak=   -3.595 closest distance to " NH2AARG A 275 " =    5.562
peak=   -3.587 closest distance to " O   HOH Z 435 " =    2.741
peak=   -3.575 closest distance to " CG1 VAL A 112 " =    2.575
peak=   -3.567 closest distance to " O   HOH Z  60 " =    2.284
peak=   -3.565 closest distance to " OH  TYR A 214 " =    1.161
peak=   -3.564 closest distance to " N   ALA A  43 " =    2.244
peak=   -3.563 closest distance to " ND2 ASN A  45 " =    1.103
peak=   -3.559 closest distance to " O   GLY A 211 " =    1.361
peak=   -3.559 closest distance to " CE BMET A  47 " =    1.537
peak=   -3.555 closest distance to " CB  TRP A  85 " =    2.484
peak=   -3.554 closest distance to " CB  PRO A 163 " =    2.541
peak=   -3.551 closest distance to " O   HOH Z 351 " =    1.453
peak=   -3.540 closest distance to " CE1 TYR A 169 " =    2.473
peak=   -3.539 closest distance to " OG  SER A 206 " =    1.744
peak=   -3.535 closest distance to " CB  PHE A 130 " =    1.279
peak=   -3.534 closest distance to " CD1 LEU A 101 " =    2.486
peak=   -3.529 closest distance to " CD2 TYR A 293 " =    2.047
peak=   -3.517 closest distance to " CG2 THR A   4 " =    1.966
peak=   -3.516 closest distance to " CD1 ILE A 239 " =    2.154
peak=   -3.507 closest distance to " CG1 VAL A 112 " =    3.032
peak=   -3.504 closest distance to " CD1 LEU A 228 " =    2.421
peak=   -3.488 closest distance to " C   ASN A 285 " =    2.507
peak=   -3.483 closest distance to " CA  GLY A 203 " =    2.491
peak=   -3.474 closest distance to " CB  ALA A   9 " =    2.616
peak=   -3.474 closest distance to " CA  ALA A   8 " =    1.536
peak=   -3.470 closest distance to " O   HOH Z  10 " =    1.631
peak=   -3.469 closest distance to " O   HOH Z 426 " =    1.619
peak=   -3.464 closest distance to " C   HIS A 108 " =    1.154
peak=   -3.463 closest distance to " CG2BVAL A  41 " =    2.546
peak=   -3.453 closest distance to " C   ALA A 158 " =    1.266
peak=   -3.440 closest distance to " OD1 ASN A 187 " =    1.402
peak=   -3.438 closest distance to " ND2 ASN A  60 " =    1.478
peak=   -3.437 closest distance to " O   HOH Z 353 " =    2.153
peak=   -3.433 closest distance to " O   HOH Z 118 " =    3.103
peak=   -3.432 closest distance to " CA  ASN A 127 " =    1.142
peak=   -3.430 closest distance to " N   ASN A  60 " =    1.252
peak=   -3.416 closest distance to " N   ALA A 226 " =    2.190
peak=   -3.414 closest distance to " O   HOH Z  44 " =    2.128
peak=   -3.412 closest distance to " O   HOH Z 196 " =    2.336
peak=   -3.411 closest distance to " CG  PRO A 163 " =    2.442
peak=   -3.407 closest distance to " O   HOH Z 407 " =    3.325
peak=   -3.405 closest distance to " CG1 VAL A 197 " =    2.403
peak=   -3.400 closest distance to " O   HOH Z  13 " =    1.434
peak=   -3.398 closest distance to " O   HOH Z 166 " =    1.576
peak=   -3.393 closest distance to " N   THR A  18 " =    1.318
peak=   -3.389 closest distance to " O   HOH Z 166 " =    1.888
peak=   -3.383 closest distance to " CD1 PHE A  59 " =    1.840
peak=   -3.377 closest distance to " O   TRP A  70 " =    1.458
peak=   -3.376 closest distance to " OG ASER A 134 " =    1.324
peak=   -3.376 closest distance to " CB  ASN A  39 " =    2.198
peak=   -3.372 closest distance to " CD  GLN A  58 " =    0.973
peak=   -3.365 closest distance to " O   HOH Z 128 " =    2.614
peak=   -3.361 closest distance to " N   LYS A 166 " =    2.002
peak=   -3.359 closest distance to " CB  ALA A 248 " =    2.501
peak=   -3.358 closest distance to " O   HOH Z 281 " =    2.671
peak=   -3.352 closest distance to " CG  GLN A  88 " =    0.861
peak=   -3.340 closest distance to " CB  ALA A 227 " =    2.388
peak=   -3.339 closest distance to " C   MET A 188 " =    1.471
peak=   -3.337 closest distance to " CD  ARG A 139 " =    1.636
peak=   -3.334 closest distance to " O   HOH Z 417 " =    2.840
peak=   -3.329 closest distance to " O   HOH Z 295 " =    1.504
peak=   -3.327 closest distance to " O   HOH Z   2 " =    1.933
peak=   -3.327 closest distance to " CB  PHE A 192 " =    1.714
peak=   -3.321 closest distance to " CB  ALA A 291 " =    2.119
peak=   -3.318 closest distance to " O   HOH Z 292 " =    1.690
peak=   -3.318 closest distance to " CB  SER A  63 " =    3.405
peak=   -3.317 closest distance to " CH2 TRP A 177 " =    2.282
peak=   -3.316 closest distance to " NH2 ARG A  66 " =    2.303
peak=   -3.314 closest distance to " CD2 LEU A 300 " =    2.753
peak=   -3.310 closest distance to " CE2 PHE A 218 " =    2.555
peak=   -3.308 closest distance to " N   SER A 276 " =    1.377
peak=   -3.304 closest distance to " CB  ALA A 291 " =    2.243
peak=   -3.304 closest distance to " O   HOH Z 371 " =    2.189
peak=   -3.302 closest distance to " OD2 ASP A 171 " =    1.856
peak=   -3.298 closest distance to " CD1 ILE A  33 " =    2.488
peak=   -3.297 closest distance to " N   SER A 212 " =    1.854
peak=   -3.294 closest distance to " CA  SER A 135 " =    1.362
peak=   -3.292 closest distance to " CD1 LEU A 101 " =    2.847
peak=   -3.290 closest distance to " C   GLN A 240 " =    2.393
peak=   -3.290 closest distance to " CG  PHE A 283 " =    2.723
peak=   -3.284 closest distance to " O   HOH Z 184 " =    1.828
peak=   -3.280 closest distance to " CG1 VAL A 265 " =    2.462
peak=   -3.279 closest distance to " NE2 GLN A  88 " =    2.244
peak=   -3.278 closest distance to " CA  ASP A 298 " =    1.037
peak=   -3.275 closest distance to " O   HOH Z 437 " =    1.779
peak=   -3.274 closest distance to " OG BSER A 134 " =    1.840
peak=   -3.273 closest distance to " O   HOH Z 198 " =    1.564
peak=   -3.264 closest distance to " CD  PRO A 213 " =    2.168
peak=   -3.263 closest distance to " O   HOH Z 103 " =    1.859
peak=   -3.258 closest distance to " CG2 VAL A 112 " =    2.574
peak=   -3.254 closest distance to " O   HOH Z 282 " =    5.063
peak=   -3.253 closest distance to " OG1 THR A 246 " =    1.382
peak=   -3.251 closest distance to " C   ASN A 187 " =    1.582
peak=   -3.249 closest distance to " CG  GLU A 152 " =    1.967
peak=   -3.245 closest distance to " CE  MET A 105 " =    2.194
peak=   -3.243 closest distance to " O   HOH Z 250 " =    1.528
peak=   -3.242 closest distance to " OD1 ASN A 148 " =    1.434
peak=   -3.239 closest distance to " CB  ASN A 252 " =    1.499
peak=   -3.237 closest distance to " O   HOH Z 111 " =    2.214
peak=   -3.236 closest distance to " CG  LEU A 228 " =    0.967
peak=   -3.230 closest distance to " O   HOH Z 108 " =    1.633
peak=   -3.224 closest distance to " O   HOH Z 359 " =    3.286
peak=   -3.221 closest distance to " CZ  PHE A 130 " =    1.139
peak=   -3.214 closest distance to " O   HOH Z 390 " =    2.246
peak=   -3.214 closest distance to " NH2 ARG A  79 " =    1.898
peak=   -3.210 closest distance to " C   LEU A 143 " =    1.251
peak=   -3.201 closest distance to " OG1 THR A 178 " =    1.323
peak=   -3.199 closest distance to " CG  ARG A 269 " =    2.437
peak=   -3.185 closest distance to " O   HOH Z 241 " =    1.287
peak=   -3.182 closest distance to " N   ALA A 248 " =    1.670
peak=   -3.179 closest distance to " N   THR A  52 " =    1.731
peak=   -3.177 closest distance to " O   ASN A 301 " =    1.572
peak=   -3.173 closest distance to " CG  HIS A  86 " =    1.012
peak=   -3.173 closest distance to " O   HOH Z 222 " =    1.563
peak=   -3.170 closest distance to " CA  VAL A 296 " =    1.062
peak=   -3.169 closest distance to " SD BMET A  47 " =    1.009
peak=   -3.167 closest distance to " CB  PRO A  54 " =    2.475
peak=   -3.163 closest distance to " ND2 ASN A  45 " =    1.971
peak=   -3.162 closest distance to " O   SER A  22 " =    2.243
peak=   -3.158 closest distance to " O   HOH Z 436 " =    1.529
peak=   -3.156 closest distance to " CD2 LEU A   5 " =    1.247
peak=   -3.150 closest distance to " CG1 VAL A  78 " =    2.380
peak=   -3.149 closest distance to " O   VAL A 197 " =    1.459
peak=   -3.144 closest distance to " O   HOH Z  51 " =    1.279
peak=   -3.144 closest distance to " O   HOH Z 359 " =    1.618
peak=   -3.142 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.142 closest distance to " SG BCYS A 201 " =    2.260
peak=   -3.137 closest distance to " CD  GLN A 223 " =    1.664
peak=   -3.135 closest distance to " O   THR A  18 " =    1.560
peak=   -3.134 closest distance to " NE2 GLN A 278 " =    1.263
peak=   -3.128 closest distance to " O   HOH Z 174 " =    2.710
peak=   -3.127 closest distance to " ND2 ASN A  60 " =    1.773
peak=   -3.127 closest distance to " CG  ARG A 259 " =    2.760
peak=   -3.127 closest distance to " O   THR A  31 " =    1.372
peak=   -3.123 closest distance to " CE3 TRP A  70 " =    1.716
peak=   -3.123 closest distance to " CB  CYS A 254 " =    2.005
peak=   -3.089 closest distance to " CD1 LEU A 297 " =    2.562
peak=   -3.079 closest distance to " C   SER A  22 " =    2.222
peak=   -3.067 closest distance to " O   HOH Z 113 " =    2.404
peak=   -3.056 closest distance to " N   ALA A 248 " =    2.485
peak=   -3.030 closest distance to " OG BSER A 164 " =    1.061
peak=   -3.029 closest distance to " O   HOH Z 177 " =    1.690

================= 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    :  0.4584 0.4482   6.259495e+00   6.244950e+00
   1_bss:  0.4507 0.4369   6.253048e+00   6.236129e+00
   1_xyz:  0.3563 0.3771   6.105080e+00   6.148463e+00
   1_adp:  0.3032 0.3426   5.992609e+00   6.093122e+00
   1_occ:  0.3026 0.3437   5.992398e+00   6.094941e+00
   2_bss:  0.2997 0.3392   5.991676e+00   6.092267e+00
   2_xyz:  0.2019 0.2571   5.652445e+00   5.835163e+00
   2_adp:  0.1768 0.2292   5.532367e+00   5.727461e+00
   2_occ:  0.1766 0.2289   5.531204e+00   5.726091e+00
   3_bss:  0.1746 0.2258   5.528123e+00   5.722574e+00
   3_xyz:  0.1425 0.1894   5.346762e+00   5.564053e+00
   3_adp:  0.1331 0.1832   5.301775e+00   5.532966e+00
   3_occ:  0.1330 0.1831   5.301503e+00   5.532691e+00
   4_bss:  0.1331 0.1829   5.299995e+00   5.530540e+00
   4_xyz:  0.1210 0.1723   5.224616e+00   5.471209e+00
   4_adp:  0.1200 0.1684   5.209822e+00   5.449252e+00
   4_occ:  0.1199 0.1683   5.209536e+00   5.448981e+00
   5_bss:  0.1199 0.1682   5.209524e+00   5.448759e+00
   5_xyz:  0.1181 0.1666   5.197259e+00   5.438709e+00
   5_adp:  0.1169 0.1675   5.195755e+00   5.443415e+00
   5_occ:  0.1169 0.1674   5.195423e+00   5.443140e+00
   5_bss:  0.1169 0.1674   5.195418e+00   5.443176e+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:  0.322  20.001  10.540   7.505   7.381   0.000   0.000   0.000
   1_xyz:  0.322  20.001  10.540   7.505   7.381   0.000   0.000   0.000
   1_adp:  0.322  20.001  10.540   7.505   7.381   0.000   0.000   0.000
   1_occ:  0.322  20.001  10.540   7.505   7.381   0.000   0.000   0.000
   2_bss:  0.339  47.535   6.922   4.037   4.745   0.000   0.000   0.000
   2_xyz:  0.339  47.535   6.922   4.037   4.745   0.000   0.000   0.000
   2_adp:  0.339  47.535   6.922   4.037   4.745   0.000   0.000   0.000
   2_occ:  0.339  47.535   6.922   4.037   4.745   0.000   0.000   0.000
   3_bss:  0.332  47.535   4.017   2.781   3.903   0.000   0.000   0.000
   3_xyz:  0.332  47.535   4.017   2.781   3.903   0.000   0.000   0.000
   3_adp:  0.332  47.535   4.017   2.781   3.903   0.000   0.000   0.000
   3_occ:  0.332  47.535   4.017   2.781   3.903   0.000   0.000   0.000
   4_bss:  0.324  57.691   3.282   2.472   3.650   0.000   0.000   0.000
   4_xyz:  0.324  57.691   3.282   2.472   3.650   0.000   0.000   0.000
   4_adp:  0.324  57.691   3.282   2.472   3.650   0.000   0.000   0.000
   4_occ:  0.324  57.691   3.282   2.472   3.650   0.000   0.000   0.000
   5_bss:  0.328  56.654   3.099   2.503   3.661   0.000   0.000   0.000
   5_xyz:  0.328  56.654   3.099   2.503   3.661   0.000   0.000   0.000
   5_adp:  0.328  56.654   3.099   2.503   3.661   0.000   0.000   0.000
   5_occ:  0.328  56.654   3.099   2.503   3.661   0.000   0.000   0.000
   5_bss:  0.325  59.300  -0.024  -0.556   0.581   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.134 0.4948  0.5636    61147.998
   1_bss:  52.132 0.4933  0.7207    59097.897
   1_xyz:  43.038 0.6052  0.8587    42003.394
   1_adp:  37.649 0.6710  0.9585    34862.592
   1_occ:  37.812 0.6689  0.9552    35082.031
   2_bss:  37.516 0.6723  0.8566    34606.030
   2_xyz:  25.858 0.8017  0.9849    17158.882
   2_adp:  22.188 0.8402  1.0136    13403.581
   2_occ:  22.156 0.8405  1.0136    13356.285
   3_bss:  22.052 0.8416  0.9561    13272.617
   3_xyz:  17.812 0.8822  0.9786     9199.433
   3_adp:  17.086 0.8890  0.9795     8592.837
   3_occ:  17.082 0.8890  0.9794     8587.928
   4_bss:  17.022 0.8895  0.9642     8516.075
   4_xyz:  15.684 0.9011  0.9703     7495.339
   4_adp:  15.113 0.9063  0.9722     7201.455
   4_occ:  15.116 0.9062  0.9720     7192.639
   5_bss:  15.116 0.9062  0.9704     7187.669
   5_xyz:  14.862 0.9084  0.9705     7018.091
   5_adp:  14.953 0.9077  0.9665     7070.757
   5_occ:  14.944 0.9078  0.9665     7063.994
   5_bss:  14.945 0.9078  0.9682     7062.859
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4099e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4099e+01
   1_xyz:   1.595  0.012  0.104 18.212  0.006  4.124   1.2937e-01
   1_adp:   1.595  0.012  0.104 18.212  0.006  4.124   1.2937e-01
   1_occ:   1.595  0.012  0.104 18.212  0.006  4.124   1.2937e-01
   2_bss:   1.595  0.012  0.104 18.212  0.006  4.124   1.2937e-01
   2_xyz:   1.196  0.010  0.085 16.677  0.005  4.132   8.6760e-02
   2_adp:   1.196  0.010  0.085 16.677  0.005  4.132   8.6760e-02
   2_occ:   1.196  0.010  0.085 16.677  0.005  4.132   8.6760e-02
   3_bss:   1.196  0.010  0.085 16.677  0.005  4.132   8.6760e-02
   3_xyz:   1.011  0.007  0.077 15.868  0.003  4.126   6.3524e-02
   3_adp:   1.011  0.007  0.077 15.868  0.003  4.126   6.3524e-02
   3_occ:   1.011  0.007  0.077 15.868  0.003  4.126   6.3524e-02
   4_bss:   1.011  0.007  0.077 15.868  0.003  4.126   6.3524e-02
   4_xyz:   1.081  0.009  0.084 15.909  0.004  4.134   7.1264e-02
   4_adp:   1.081  0.009  0.084 15.909  0.004  4.134   7.1264e-02
   4_occ:   1.081  0.009  0.084 15.909  0.004  4.134   7.1264e-02
   5_bss:   1.081  0.009  0.084 15.909  0.004  4.134   7.1264e-02
   5_xyz:   1.047  0.008  0.081 15.664  0.003  4.137   6.6207e-02
   5_adp:   1.047  0.008  0.081 15.664  0.003  4.137   6.6207e-02
   5_occ:   1.047  0.008  0.081 15.664  0.003  4.137   6.6207e-02
   5_bss:   1.047  0.008  0.081 15.664  0.003  4.137   6.6207e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0148e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0148e+00
   1_xyz:  13.053  0.153  0.417 85.802  0.037  2.202   9.6840e-02
   1_adp:  13.053  0.153  0.417 85.802  0.037  2.202   9.6840e-02
   1_occ:  13.053  0.153  0.417 85.802  0.037  2.202   9.6840e-02
   2_bss:  13.053  0.153  0.417 85.802  0.037  2.202   9.6840e-02
   2_xyz:   8.541  0.089  0.266 86.734  0.037  2.237   6.4883e-02
   2_adp:   8.541  0.089  0.266 86.734  0.037  2.237   6.4883e-02
   2_occ:   8.541  0.089  0.266 86.734  0.037  2.237   6.4883e-02
   3_bss:   8.541  0.089  0.266 86.734  0.037  2.237   6.4883e-02
   3_xyz:   8.732  0.057  0.366 81.960  0.031  2.336   3.7218e-02
   3_adp:   8.732  0.057  0.366 81.960  0.031  2.336   3.7218e-02
   3_occ:   8.732  0.057  0.366 81.960  0.031  2.336   3.7218e-02
   4_bss:   8.732  0.057  0.366 81.960  0.031  2.336   3.7218e-02
   4_xyz:   8.719  0.070  0.467 83.987  0.031  2.358   4.7029e-02
   4_adp:   8.719  0.070  0.467 83.987  0.031  2.358   4.7029e-02
   4_occ:   8.719  0.070  0.467 83.987  0.031  2.358   4.7029e-02
   5_bss:   8.719  0.070  0.467 83.987  0.031  2.358   4.7029e-02
   5_xyz:   8.366  0.061  0.469 83.779  0.031  2.360   3.9409e-02
   5_adp:   8.366  0.061  0.469 83.779  0.031  2.360   3.9409e-02
   5_occ:   8.366  0.061  0.469 83.779  0.031  2.360   3.9409e-02
   5_bss:   8.366  0.061  0.469 83.779  0.031  2.360   3.9409e-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:  52.35   0.00  11.11  47.46   0.00   8.54  52.35   0.00  25.06
   1_occ:  52.35   0.00  11.11  47.46   0.00   8.54  52.35   0.00  25.06
   2_bss:  52.35   0.00  11.11  47.46   0.00   8.54  52.35   0.00  25.06
   2_xyz:  52.35   0.00  11.11  47.46   0.00   8.54  52.35   0.00  25.06
   2_adp:  64.22   0.00  11.54  58.47   0.00   7.83  64.22   0.00  31.77
   2_occ:  64.22   0.00  11.54  58.47   0.00   7.83  64.22   0.00  31.77
   3_bss:  64.22   0.00  11.54  58.47   0.00   7.83  64.22   0.00  31.77
   3_xyz:  64.22   0.00  11.54  58.47   0.00   7.83  64.22   0.00  31.77
   3_adp:  82.22   0.00  12.66  75.31   0.00   8.14  82.22   0.98  37.31
   3_occ:  82.22   0.00  12.66  75.31   0.00   8.14  82.22   0.98  37.31
   4_bss:  82.22   0.00  12.66  75.31   0.00   8.14  82.22   0.98  37.31
   4_xyz:  82.22   0.00  12.66  75.31   0.00   8.14  82.22   0.98  37.31
   4_adp:  82.21   0.00  12.24  77.25   0.00   7.97  82.21   1.53  35.54
   4_occ:  82.21   0.00  12.24  77.25   0.00   7.97  82.21   1.53  35.54
   5_bss:  82.21   0.00  12.24  77.25   0.00   7.97  82.21   1.53  35.54
   5_xyz:  82.21   0.00  12.24  77.25   0.00   7.97  82.21   1.53  35.54
   5_adp:  87.91   0.00  12.32  82.84   0.00   7.98  87.91   1.19  35.92
   5_occ:  87.91   0.00  12.32  82.84   0.00   7.98  87.91   1.19  35.92
   5_bss:  91.05   3.14  15.46  85.98   3.14  11.12  91.05   4.33  39.06
------------------------------------------------------------------------
 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:    1.190    0.020    0.406
   1_adp:    1.190    0.020    0.406
   1_occ:    1.190    0.020    0.406
   2_bss:    1.190    0.020    0.406
   2_xyz:    1.525    0.036    0.584
   2_adp:    1.525    0.036    0.584
   2_occ:    1.525    0.036    0.584
   3_bss:    1.525    0.036    0.584
   3_xyz:    1.509    0.035    0.618
   3_adp:    1.509    0.035    0.618
   3_occ:    1.509    0.035    0.618
   4_bss:    1.509    0.035    0.618
   4_xyz:    1.743    0.044    0.647
   4_adp:    1.743    0.044    0.647
   4_occ:    1.743    0.044    0.647
   5_bss:    1.743    0.044    0.647
   5_xyz:    1.843    0.038    0.655
   5_adp:    1.843    0.038    0.655
   5_occ:    1.843    0.038    0.655
   5_bss:    1.843    0.038    0.655
------------------------------------------------------------------------

CPU time actual refinement: 348.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1259/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_1259/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1259/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1259/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1259/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.35 
  Macro-tasks:
    bulk solvent and scale       = 41.63  
    individual site refinement   = 141.54 
    weights calculation          = 32.85  
    collect and process          = 6.40   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 222.55 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 111.01 
    alpha_beta                      = 7.77   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 120.63 
    fmodel                         = 7.24   
    r_factors                      = 0.22   
    phase_errors                   = 10.58  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 260.73 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.910 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    656 calls, 110.62 s
gradients_fft:          600 calls, 107.49 s

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

# Date 2008-01-16 Time 03:35:18 PST -0800 (1200483318.37 s)
Start R-work = 0.4584, R-free = 0.4482 (no bulk solvent and anisotropic scale)
Final R-work = 0.1335, R-free = 0.1830 (no bulk solvent and anisotropic scale)

Start R-work = 0.4507, R-free = 0.4369
Final R-work = 0.1169, R-free = 0.1674