# Date 2008-01-16 Time 02:45:44 PST -0800 (1200480344.40 s)
#phil __OFF__

Command line arguments: "../967.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12077
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 967

-------------------------------------------------------------------------------
  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: (70.9525, 48.1033, 88.5498, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (70.9525, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02066
Completeness in resolution range: 0.959211
Completeness with d_max=infinity: 0.956214

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0207

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: (70.9525, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02066
Completeness in resolution range: 0.959211
Completeness with d_max=infinity: 0.956214

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3232 [2156/2183]  1939   217  10.1%
  bin  2:  4.3232 -  3.4445 [2047/2063]  1844   203   9.9%
  bin  3:  3.4445 -  3.0130 [2043/2062]  1839   204  10.0%
  bin  4:  3.0130 -  2.7393 [2010/2040]  1810   200  10.0%
  bin  5:  2.7393 -  2.5439 [1993/2012]  1788   205  10.3%
  bin  6:  2.5439 -  2.3945 [2005/2041]  1810   195   9.7%
  bin  7:  2.3945 -  2.2750 [1983/2016]  1784   199  10.0%
  bin  8:  2.2750 -  2.1763 [1978/2012]  1777   201  10.2%
  bin  9:  2.1763 -  2.0927 [1950/1978]  1752   198  10.2%
  bin 10:  2.0927 -  2.0207 [1424/2015]  1287   137   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_967/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: 0.13 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:
        1.76 -     2.39: 15
        2.39 -     3.02: 1975
        3.02 -     3.64: 4476
        3.64 -     4.27: 8837
        4.27 -     4.90: 12228
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.762 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.842 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.873 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.873 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27526 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_967/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_967/model_refine_001.geo

CPU time processing inputs: 8.93


============================ 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 = 70.9525 48.10325 88.54975 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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5266   r_free= 0.5190   ksol= 0.00   Bsol= 0.00   scale= 0.738    |
|                                                                             |
| 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:   1.03 A                  |
| x-ray target function (ml) for work reflections: 6.314965                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1395  154 0.4391 0.4356      6.6697      6.6591|
|  2:  4.8215 -  3.8474 0.99   1338  151 0.4794 0.5190      6.9121      6.9917|
|  3:  3.8474 -  3.3671 0.99   1321  148 0.5166 0.4820      6.7557      6.7192|
|  4:  3.3671 -  3.0620 0.99   1297  135 0.5248 0.4710      6.5862      6.5157|
|  5:  3.0620 -  2.8440 0.99   1298  148 0.5514 0.4961       6.405       6.432|
|  6:  2.8440 -  2.6773 0.99   1302  147 0.5527 0.5809      6.3014      6.2257|
|  7:  2.6773 -  2.5439 0.99   1269  146 0.5489 0.4933      6.2675      6.1701|
|  8:  2.5439 -  2.4336 0.98   1306  138 0.5412 0.5106      6.2009      6.2077|
|  9:  2.4336 -  2.3403 0.98   1272  145 0.5505 0.6673      6.1193      6.1709|
| 10:  2.3403 -  2.2598 0.98   1257  136 0.5809 0.5500      6.1306      6.1478|
| 11:  2.2598 -  2.1893 1.00   1278  147 0.5505 0.5600      6.0445       6.092|
| 12:  2.1893 -  2.1269 0.97   1279  136 0.5562 0.5384      5.9758       6.033|
| 13:  2.1269 -  2.0711 0.98   1252  142 0.5563 0.5120      5.9047      5.8393|
| 14:  2.0711 -  2.0207 0.60    766   86 0.5543 0.5757      5.8655      5.7666|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1395   154  0.61  41.96   0.76     0.64      99306.54|
|  2:  4.8215 -  3.8474  1338   151  0.60  43.69   0.82     0.64     147917.43|
|  3:  3.8474 -  3.3671  1321   148  0.48  53.67   0.75     0.59     153104.53|
|  4:  3.3671 -  3.0620  1297   135  0.37  62.08   0.74     0.45     132402.10|
|  5:  3.0620 -  2.8440  1298   148  0.30  67.47   0.69     0.36      98301.61|
|  6:  2.8440 -  2.6773  1302   147  0.27  69.46   0.67     0.32      83511.42|
|  7:  2.6773 -  2.5439  1269   146  0.28  68.68   0.69     0.32      72419.42|
|  8:  2.5439 -  2.4336  1306   138  0.24  72.20   0.71     0.28      68048.37|
|  9:  2.4336 -  2.3403  1272   145  0.15  78.84   0.67     0.18      65870.73|
| 10:  2.3403 -  2.2598  1257   136  0.08  84.28   0.68     0.09      61585.72|
| 11:  2.2598 -  2.1893  1278   147  0.07  84.48   0.71     0.09      57686.51|
| 12:  2.1893 -  2.1269  1279   136  0.10  82.29   0.70     0.13      51626.65|
| 13:  2.1269 -  2.0711  1252   142  0.09  83.17   0.68     0.11      44255.00|
| 14:  2.0711 -  2.0207   766    86  0.10  82.38   0.70     0.11      35490.62|
|alpha:            min =        0.09 max =            0.64 mean =         0.32|
|beta:             min =    35490.62 max =       153104.53 mean =     85710.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.28|
|phase err.(work): min =        0.00 max =           90.00 mean =        68.89|
|phase err.(test): min =        0.00 max =           89.98 mean =        69.22|
|-----------------------------------------------------------------------------|

============================== 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 = 28.670938             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.418   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.097497              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.044   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      157 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      670 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1469 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2545 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3814 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4919 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6393 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7549 |
|-----------------------------------------------------------------------------|
|-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 |       54.914 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.804 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    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 = 12.551)------------------------------------------|
|    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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5307   r_free= 0.5225   ksol= 0.00   Bsol= 0.00   scale= 0.713    |
|                                                                             |
| 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:   1.04 A                  |
| x-ray target function (ml) for work reflections: 6.315540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5212   r_free= 0.5143   ksol= 0.28   Bsol= 20.00   scale= 0.919   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.43,10.11,10.03,0.00,0.00,0.00); trace/3= 8.53                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.05 A                  |
| x-ray target function (ml) for work reflections: 6.312048                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 24.121680             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.978   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.546319              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.595   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5212      final r-factor (work) = 0.4723          |
| start r-factor (free) = 0.5143      final r-factor (free) = 0.4875          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 131.0630 = 24.12 * 0.50 * 6.3137 + 1.00 * 54.9144                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.8633 = 24.12 * 0.50 * 6.2771 + 1.00 * 0.1562                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4723      final r-factor (work) = 0.4307          |
| start r-factor (free) = 0.4875      final r-factor (free) = 0.4789          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9983 = 2.55 * 1.00 * 6.2771 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9127 = 2.55 * 1.00 * 6.2363 + 1.00 * 0.0331                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    145.75  20.57    None  None   None       |
|    all(noH): 2823   0      0.00    145.75  20.57    None  None   None       |
|    Sol.    : 438    0      0.00    145.75  30.62    None  None   None       |
|    Mac.    : 2385   0      0.00    109.79  18.72    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 -  14.575: 1317   |   5:    72.874 -  87.448:   37        |
|      1:    14.575 -  29.150:  828   |   6:    87.448 - 102.023:   11        |
|      2:    29.150 -  43.724:  359   |   7:   102.023 - 116.598:    6        |
|      3:    43.724 -  58.299:  185   |   8:   116.598 - 131.173:    1        |
|      4:    58.299 -  72.874:   77   |   9:   131.173 - 145.747:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4307 r_free = 0.4789             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4296 r_free = 0.4797             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4296   r_free= 0.4797   ksol= 0.28   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.43,10.11,10.03,0.00,0.00,0.00); trace/3= 8.53                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 5.975201                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4284   r_free= 0.4744   ksol= 0.33   Bsol= 80.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.85,5.91,6.42,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 5.976918                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.926764             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.587  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.738350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.350  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4284      final r-factor (work) = 0.3778          |
| start r-factor (free) = 0.4744      final r-factor (free) = 0.4536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.7867 = 15.93 * 0.50 * 6.2324 + 1.00 * 0.1557                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.3259 = 15.93 * 0.50 * 5.9289 + 1.00 * 0.1119                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3778      final r-factor (work) = 0.3743          |
| start r-factor (free) = 0.4536      final r-factor (free) = 0.4414          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4105 = 0.74 * 1.00 * 5.9289 + 1.00 * 0.0329                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5581 = 0.74 * 1.00 * 6.1583 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    143.37  16.85    None  None   None       |
|    all(noH): 2823   0      0.00    143.37  16.85    None  None   None       |
|    Sol.    : 438    0      0.00    143.37  27.42    None  None   None       |
|    Mac.    : 2385   0      0.00    74.14   14.91    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 -  14.337: 1515   |   5:    71.685 -  86.022:   11        |
|      1:    14.337 -  28.674:  873   |   6:    86.022 - 100.359:    4        |
|      2:    28.674 -  43.011:  305   |   7:   100.359 - 114.696:    2        |
|      3:    43.011 -  57.348:   86   |   8:   114.696 - 129.033:    0        |
|      4:    57.348 -  71.685:   26   |   9:   129.033 - 143.370:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3743 r_free = 0.4414             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3741 r_free = 0.4413             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3741   r_free= 0.4413   ksol= 0.33   Bsol= 80.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.85,5.91,6.42,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.148103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3741   r_free= 0.4405   ksol= 0.33   Bsol= 91.40   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,4.30,4.17,0.00,0.00,0.00); trace/3= 3.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.149536                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.938230             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.139  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561521              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.091  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3741      final r-factor (work) = 0.3080          |
| start r-factor (free) = 0.4405      final r-factor (free) = 0.3680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.1071 = 14.94 * 0.50 * 6.1581 + 1.00 * 0.1119                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.5553 = 14.94 * 0.50 * 6.0813 + 1.00 * 0.1333                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3080      final r-factor (work) = 0.2869          |
| start r-factor (free) = 0.3680      final r-factor (free) = 0.3532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4261 = 0.56 * 1.00 * 6.0813 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3700 = 0.56 * 1.00 * 5.9623 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    150.81  16.71    None  None   None       |
|    all(noH): 2823   0      0.00    150.81  16.71    None  None   None       |
|    Sol.    : 438    0      0.00    141.82  31.89    None  None   None       |
|    Mac.    : 2385   0      0.00    150.81  13.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  15.082: 1582   |   5:    75.407 -  90.489:    7        |
|      1:    15.082 -  30.163:  856   |   6:    90.489 - 105.570:    2        |
|      2:    30.163 -  45.244:  281   |   7:   105.570 - 120.652:    0        |
|      3:    45.244 -  60.326:   67   |   8:   120.652 - 135.733:    0        |
|      4:    60.326 -  75.407:   26   |   9:   135.733 - 150.815:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2869 r_free = 0.3532             target_work(ml) = 5.945         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2866 r_free = 0.3538             target_work(ml) = 5.945         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2866   r_free= 0.3538   ksol= 0.33   Bsol= 91.40   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,4.30,4.17,0.00,0.00,0.00); trace/3= 3.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.945294                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2854   r_free= 0.3526   ksol= 0.33   Bsol= 81.19   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.55,2.40,2.28,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.944092                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.111307              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.686961              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.111  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2854      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.3526      final r-factor (free) = 0.2972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3290 = 7.11 * 0.50 * 5.9611 + 1.00 * 0.1333                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.9653 = 7.11 * 0.50 * 5.8721 + 1.00 * 0.0860                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.2125          |
| start r-factor (free) = 0.2972      final r-factor (free) = 0.2683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0551 = 0.69 * 1.00 * 5.8721 + 1.00 * 0.0212                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9554 = 0.69 * 1.00 * 5.7356 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.04  16.82    None  None   None       |
|    all(noH): 2823   0      0.00    130.04  16.82    None  None   None       |
|    Sol.    : 438    0      0.00    130.04  41.92    None  None   None       |
|    Mac.    : 2385   0      0.00    94.34   12.21    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 -  13.004: 1638   |   5:    65.018 -  78.022:   55        |
|      1:    13.004 -  26.007:  648   |   6:    78.022 -  91.026:   21        |
|      2:    26.007 -  39.011:  244   |   7:    91.026 - 104.030:    5        |
|      3:    39.011 -  52.015:  129   |   8:   104.030 - 117.033:    0        |
|      4:    52.015 -  65.018:   82   |   9:   117.033 - 130.037:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2125 r_free = 0.2683             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2123 r_free = 0.2693             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2123   r_free= 0.2693   ksol= 0.33   Bsol= 81.19   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.55,2.40,2.28,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.694964                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2121   r_free= 0.2693   ksol= 0.33   Bsol= 80.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,1.37,1.85,0.00,0.00,0.00); trace/3= 1.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.694249                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.102900              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.491360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.398  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2121      final r-factor (work) = 0.1804          |
| start r-factor (free) = 0.2693      final r-factor (free) = 0.2293          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9845 = 3.10 * 0.50 * 5.7355 + 1.00 * 0.0862                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7982 = 3.10 * 0.50 * 5.6259 + 1.00 * 0.0698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1804      final r-factor (work) = 0.1709          |
| start r-factor (free) = 0.2293      final r-factor (free) = 0.2226          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7796 = 0.49 * 1.00 * 5.6259 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7291 = 0.49 * 1.00 * 5.5243 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.74  16.41    None  None   None       |
|    all(noH): 2823   0      0.00    119.74  16.41    None  None   None       |
|    Sol.    : 438    0      1.14    119.74  43.93    None  None   None       |
|    Mac.    : 2385   0      0.00    97.36   11.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.974: 1643   |   5:    59.871 -  71.845:   69        |
|      1:    11.974 -  23.948:  656   |   6:    71.845 -  83.819:   40        |
|      2:    23.948 -  35.923:  179   |   7:    83.819 -  95.794:   12        |
|      3:    35.923 -  47.897:  126   |   8:    95.794 - 107.768:    3        |
|      4:    47.897 -  59.871:   94   |   9:   107.768 - 119.742:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1709 r_free = 0.2226             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1707 r_free = 0.2228             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1707   r_free= 0.2228   ksol= 0.33   Bsol= 80.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,1.37,1.85,0.00,0.00,0.00); trace/3= 1.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.509175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1395  154 0.1190 0.1606      5.5717      5.7431|
|  2:  4.8215 -  3.8474 0.99   1338  151 0.1164 0.1479      5.7191      5.9318|
|  3:  3.8474 -  3.3671 0.99   1321  148 0.1562 0.2062      5.8325      6.1496|
|  4:  3.3671 -  3.0620 0.99   1297  135 0.1872 0.2296      5.8174      5.9529|
|  5:  3.0620 -  2.8440 0.99   1298  148 0.2068 0.2374      5.7181      5.8336|
|  6:  2.8440 -  2.6773 0.99   1302  147 0.1896 0.2916      5.5795      5.8006|
|  7:  2.6773 -  2.5439 0.99   1269  146 0.1889 0.2361      5.5369      5.6967|
|  8:  2.5439 -  2.4336 0.98   1306  138 0.1979 0.2395      5.5065      5.6929|
|  9:  2.4336 -  2.3403 0.98   1272  145 0.1969 0.2725      5.4287      5.6617|
| 10:  2.3403 -  2.2598 0.98   1257  136 0.1846 0.2347      5.3575        5.49|
| 11:  2.2598 -  2.1893 1.00   1278  147 0.1897 0.2634      5.3241       5.611|
| 12:  2.1893 -  2.1269 0.97   1279  136 0.1773 0.2378      5.2234      5.5111|
| 13:  2.1269 -  2.0711 0.98   1252  142 0.1883 0.2509       5.196      5.3472|
| 14:  2.0711 -  2.0207 0.60    766   86 0.1762 0.2600      5.1146       5.329|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1395   154  0.91  12.93   0.95     0.92      11691.72|
|  2:  4.8215 -  3.8474  1338   151  0.92  12.49   1.00     0.98      16170.85|
|  3:  3.8474 -  3.3671  1321   148  0.89  17.47   1.02     1.00      20871.40|
|  4:  3.3671 -  3.0620  1297   135  0.86  20.72   1.00     0.95      20785.88|
|  5:  3.0620 -  2.8440  1298   148  0.82  24.65   1.00     0.99      18337.54|
|  6:  2.8440 -  2.6773  1302   147  0.83  24.13   0.96     0.90      14422.86|
|  7:  2.6773 -  2.5439  1269   146  0.83  23.45   0.99     0.94      13124.32|
|  8:  2.5439 -  2.4336  1306   138  0.82  24.62   0.98     0.92      12404.53|
|  9:  2.4336 -  2.3403  1272   145  0.81  25.43   1.00     0.92      11084.71|
| 10:  2.3403 -  2.2598  1257   136  0.82  24.26   1.00     0.93       9379.16|
| 11:  2.2598 -  2.1893  1278   147  0.83  23.68   0.98     0.90       8606.51|
| 12:  2.1893 -  2.1269  1279   136  0.84  22.84   0.99     0.96       7746.83|
| 13:  2.1269 -  2.0711  1252   142  0.82  24.97   0.97     0.92       7445.94|
| 14:  2.0711 -  2.0207   766    86  0.82  24.81   0.93     0.86       6356.00|
|alpha:            min =        0.86 max =            1.00 mean =         0.94|
|beta:             min =     6356.00 max =        20871.40 mean =     12983.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.96 mean =        21.70|
|phase err.(test): min =        0.00 max =           89.38 mean =        20.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1709   r_free= 0.2230   ksol= 0.34   Bsol= 83.94   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.10,0.92,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.510671                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1709   r_free= 0.2230   ksol= 0.34   Bsol= 83.94   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,0.10,0.92,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.510671                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1395  154 0.1201 0.1625      5.5833      5.7602|
|  2:  4.8215 -  3.8474 0.99   1338  151 0.1175 0.1478       5.727      5.9331|
|  3:  3.8474 -  3.3671 0.99   1321  148 0.1564 0.2064      5.8336      6.1492|
|  4:  3.3671 -  3.0620 0.99   1297  135 0.1871 0.2300      5.8174      5.9542|
|  5:  3.0620 -  2.8440 0.99   1298  148 0.2071 0.2376      5.7184      5.8335|
|  6:  2.8440 -  2.6773 0.99   1302  147 0.1895 0.2911      5.5788      5.7983|
|  7:  2.6773 -  2.5439 0.99   1269  146 0.1888 0.2362      5.5366       5.697|
|  8:  2.5439 -  2.4336 0.98   1306  138 0.1976 0.2398      5.5061      5.6932|
|  9:  2.4336 -  2.3403 0.98   1272  145 0.1968 0.2724      5.4289      5.6613|
| 10:  2.3403 -  2.2598 0.98   1257  136 0.1846 0.2354      5.3579      5.4917|
| 11:  2.2598 -  2.1893 1.00   1278  147 0.1894 0.2633      5.3239      5.6102|
| 12:  2.1893 -  2.1269 0.97   1279  136 0.1771 0.2385      5.2237      5.5129|
| 13:  2.1269 -  2.0711 0.98   1252  142 0.1884 0.2509      5.1956      5.3468|
| 14:  2.0711 -  2.0207 0.60    766   86 0.1761 0.2595      5.1138      5.3279|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1395   154  0.91  13.21   0.95     0.91      11992.65|
|  2:  4.8215 -  3.8474  1338   151  0.92  12.62   1.00     0.98      16410.60|
|  3:  3.8474 -  3.3671  1321   148  0.89  17.49   1.02     1.00      20976.74|
|  4:  3.3671 -  3.0620  1297   135  0.86  20.72   1.00     0.95      20793.24|
|  5:  3.0620 -  2.8440  1298   148  0.82  24.64   1.00     0.99      18324.28|
|  6:  2.8440 -  2.6773  1302   147  0.83  24.10   0.96     0.90      14405.21|
|  7:  2.6773 -  2.5439  1269   146  0.83  23.43   0.99     0.94      13108.56|
|  8:  2.5439 -  2.4336  1306   138  0.82  24.62   0.98     0.92      12407.87|
|  9:  2.4336 -  2.3403  1272   145  0.81  25.43   1.00     0.92      11092.91|
| 10:  2.3403 -  2.2598  1257   136  0.82  24.28   1.00     0.93       9390.64|
| 11:  2.2598 -  2.1893  1278   147  0.83  23.70   0.98     0.90       8623.13|
| 12:  2.1893 -  2.1269  1279   136  0.84  22.86   0.99     0.96       7759.97|
| 13:  2.1269 -  2.0711  1252   142  0.82  24.97   0.97     0.92       7444.77|
| 14:  2.0711 -  2.0207   766    86  0.82  24.78   0.93     0.86       6338.69|
|alpha:            min =        0.86 max =            1.00 mean =         0.94|
|beta:             min =     6338.69 max =        20976.74 mean =     13033.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.97 mean =        21.73|
|phase err.(test): min =        0.00 max =           89.25 mean =        20.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    120.83  17.49    None  None   None       |
|    all(noH): 2823   0      1.08    120.83  17.49    None  None   None       |
|    Sol.    : 438    0      2.22    120.83  45.01    None  None   None       |
|    Mac.    : 2385   0      1.08    98.45   12.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.085 -  13.059: 1643   |   5:    60.956 -  72.930:   69        |
|      1:    13.059 -  25.033:  656   |   6:    72.930 -  84.904:   40        |
|      2:    25.033 -  37.007:  179   |   7:    84.904 -  96.878:   12        |
|      3:    37.007 -  48.981:  126   |   8:    96.878 - 108.852:    3        |
|      4:    48.981 -  60.956:   94   |   9:   108.852 - 120.827:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 347         
Filter by distance & map next to the model:
   mapped sites are within: 0.730 - 4.768
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 347 from: 347
   mapped sites are within: 0.730 - 4.768

peak=    6.790 closest distance to " O   HOH Z 342 " =    1.351
peak=    6.634 closest distance to " O   GLN A  11 " =    1.233
peak=    5.840 closest distance to " O   HOH Z  57 " =    1.142
peak=    5.751 closest distance to " O   GLN A  73 " =    1.171
peak=    5.576 closest distance to " CA  VAL A 230 " =    1.330
peak=    5.563 closest distance to " OD1 ASN A 301 " =    1.162
peak=    5.552 closest distance to " O  BHOH Z 338 " =    1.394
peak=    5.519 closest distance to " CG1 ILE A 234 " =    1.583
peak=    5.467 closest distance to " O   HOH Z 248 " =    1.785
peak=    5.455 closest distance to " O   HOH Z 120 " =    1.809
peak=    5.385 closest distance to " O   HOH Z 117 " =    2.030
peak=    5.371 closest distance to " O  BHOH Z  74 " =    1.219
peak=    5.257 closest distance to " CG1 ILE A 120 " =    1.134
peak=    5.220 closest distance to " N   SER A 164 " =    0.987
peak=    5.188 closest distance to " CG  GLN A  77 " =    1.035
peak=    5.124 closest distance to " CB  VAL A 230 " =    1.305
peak=    5.072 closest distance to " O   HOH Z 426 " =    1.385
peak=    5.064 closest distance to " O   HOH Z 139 " =    1.748
peak=    5.058 closest distance to " CG BARG A 275 " =    1.310
peak=    4.999 closest distance to " CD  ARG A  36 " =    1.256
peak=    4.971 closest distance to " CB  SER A  26 " =    0.958
peak=    4.935 closest distance to " CG  ASN A  69 " =    1.146
peak=    4.901 closest distance to " NH1 ARG A 269 " =    1.118
peak=    4.867 closest distance to " O   LEU A  25 " =    0.955
peak=    4.859 closest distance to " O   HOH Z 159 " =    1.277
peak=    4.828 closest distance to " O   HOH Z  84 " =    1.057
peak=    4.774 closest distance to " O   HOH Z 422 " =    1.379
peak=    4.770 closest distance to " O   HOH Z 425 " =    2.130
peak=    4.725 closest distance to " CB  SER A  63 " =    1.213
peak=    4.723 closest distance to " O   HOH Z  70 " =    1.146
peak=    4.703 closest distance to " O   HOH Z  54 " =    1.709
peak=    4.703 closest distance to " O   SER A   3 " =    1.092
peak=    4.669 closest distance to " CZ  PHE A 218 " =    1.118
peak=    4.657 closest distance to " ND2 ASN A 110 " =    0.980
peak=    4.630 closest distance to " CG1BVAL A 121 " =    1.314
peak=    4.564 closest distance to " O   THR A  29 " =    1.024
peak=    4.557 closest distance to " OH  TYR A  68 " =    1.108
peak=    4.506 closest distance to " CG  LEU A   5 " =    1.397
peak=    4.497 closest distance to " O   HOH Z 102 " =    1.676
peak=    4.475 closest distance to " CZ3 TRP A 266 " =    1.076
peak=    4.468 closest distance to " O   HOH Z 107 " =    1.615
peak=    4.456 closest distance to " O   HOH Z  67 " =    1.504
peak=    4.416 closest distance to " O   HOH Z  41 " =    1.074
peak=    4.402 closest distance to " N   PHE A  59 " =    1.168
peak=    4.382 closest distance to " CE1 HIS A 115 " =    1.178
peak=    4.357 closest distance to " CG  ARG A  36 " =    1.257
peak=    4.352 closest distance to " CG2 THR A  31 " =    1.249
peak=    4.323 closest distance to " CG1 VAL A 296 " =    1.302
peak=    4.315 closest distance to " CG  GLN A  11 " =    1.150
peak=    4.313 closest distance to " O   HOH Z 246 " =    1.786
peak=    4.307 closest distance to " CD  ARG A 269 " =    0.802
peak=    4.267 closest distance to " O   HOH Z 431 " =    2.030
peak=    4.259 closest distance to " O   HOH Z  91 " =    1.118
peak=    4.238 closest distance to " O   HOH Z  32 " =    1.144
peak=    4.213 closest distance to " O   HOH Z 279 " =    1.128
peak=    4.201 closest distance to " O   HOH Z 223 " =    1.525
peak=    4.191 closest distance to " N   GLN A  11 " =    0.833
peak=    4.182 closest distance to " O   HOH Z 128 " =    2.098
peak=    4.182 closest distance to " CD2 LEU A 228 " =    1.276
peak=    4.160 closest distance to " ND2 ASN A 301 " =    1.072
peak=    4.156 closest distance to " O   HOH Z 277 " =    1.289
peak=    4.108 closest distance to " CB  SER A 288 " =    1.326
peak=    4.105 closest distance to " O   ASP A 298 " =    0.970
peak=    4.097 closest distance to " O   HOH Z 411 " =    3.370
peak=    4.074 closest distance to " CB  GLN A  88 " =    1.271
peak=    4.064 closest distance to " O   HOH Z 174 " =    1.836
peak=    4.053 closest distance to " O   ASN A 301 " =    1.469
peak=    4.046 closest distance to " CB  LEU A  25 " =    0.879
peak=    4.040 closest distance to " NH2AARG A 145 " =    1.214
peak=    4.034 closest distance to " O   HOH Z 296 " =    1.887
peak=    4.027 closest distance to " C   ALA A 299 " =    0.934
peak=    4.003 closest distance to " OE1 GLN A  55 " =    1.426
peak=    4.001 closest distance to " O   HOH Z 104 " =    2.599
peak=    3.981 closest distance to " OD2 ASP A 298 " =    1.010
peak=    3.977 closest distance to " CB  TYR A  30 " =    0.960
peak=    3.960 closest distance to " OG ASER A  12 " =    1.090
peak=    3.956 closest distance to " CB  LEU A  83 " =    0.753
peak=    3.937 closest distance to " O   HOH Z 251 " =    1.990
peak=    3.934 closest distance to " N   GLY A  75 " =    0.941
peak=    3.933 closest distance to " NH1BARG A 102 " =    1.151
peak=    3.928 closest distance to " CB  ASN A  39 " =    0.738
peak=    3.920 closest distance to " O   PRO A 198 " =    1.693
peak=    3.907 closest distance to " O   GLU A   2 " =    1.777
peak=    3.905 closest distance to " N   ASP A 298 " =    0.896
peak=    3.890 closest distance to " CA  ARG A  66 " =    0.958
peak=    3.882 closest distance to " NH2 ARG A 156 " =    1.170
peak=    3.867 closest distance to " O   HOH Z 272 " =    1.538
peak=    3.863 closest distance to " CD2 TRP A 179 " =    1.126
peak=    3.861 closest distance to " CG  GLU A  37 " =    1.136
peak=    3.849 closest distance to " O   HOH Z 158 " =    1.732
peak=    3.841 closest distance to " O   HOH Z 124 " =    1.591
peak=    3.834 closest distance to " CA  CYS A 260 " =    0.975
peak=    3.823 closest distance to " CD2 TYR A  68 " =    1.117
peak=    3.816 closest distance to " CD BLYS A 290 " =    1.145
peak=    3.813 closest distance to " O   ALA A 242 " =    1.167
peak=    3.805 closest distance to " CB  ASN A 285 " =    1.008
peak=    3.797 closest distance to " O   HOH Z 343 " =    2.532
peak=    3.797 closest distance to " CB  LEU A  25 " =    1.080
peak=    3.788 closest distance to " CB  GLN A  73 " =    1.052
peak=    3.785 closest distance to " O   HOH Z  85 " =    2.062
peak=    3.780 closest distance to " N   LYS A 119 " =    0.920
peak=    3.778 closest distance to " O   HOH Z  27 " =    1.251
peak=    3.770 closest distance to " CB  ALA A 114 " =    0.875
peak=    3.758 closest distance to " CG  LYS A  76 " =    1.145
peak=    3.755 closest distance to " O   HOH Z 146 " =    2.042
peak=    3.753 closest distance to " O   ASP A 200 " =    1.484
peak=    3.753 closest distance to " CB  GLU A   2 " =    0.931
peak=    3.750 closest distance to " ND2BASN A 224 " =    0.932
peak=    3.744 closest distance to " O   HOH Z  38 " =    1.893
peak=    3.741 closest distance to " CB  ALA A  34 " =    1.062
peak=    3.740 closest distance to " CB  SER A  62 " =    1.096
peak=    3.738 closest distance to " O   HOH Z 193 " =    2.368
peak=    3.730 closest distance to " CG  PRO A 280 " =    0.956
peak=    3.729 closest distance to " O   HOH Z 147 " =    1.509
peak=    3.727 closest distance to " CE1 TYR A 186 " =    1.129
peak=    3.725 closest distance to " CB  SER A   3 " =    1.120
peak=    3.704 closest distance to " NE2 HIS A 108 " =    0.745
peak=    3.704 closest distance to " O   HOH Z 210 " =    1.810
peak=    3.702 closest distance to " ND2 ASN A  74 " =    0.906
peak=    3.697 closest distance to " NH2 ARG A  56 " =    1.431
peak=    3.695 closest distance to " CB  ARG A 275 " =    0.817
peak=    3.688 closest distance to " O   HOH Z 261 " =    1.523
peak=    3.686 closest distance to " O   HOH Z 207 " =    1.566
peak=    3.681 closest distance to " O   HOH Z  40 " =    2.316
peak=    3.680 closest distance to " CA  ASP A 124 " =    0.929
peak=    3.680 closest distance to " OG  SER A  62 " =    2.825
peak=    3.679 closest distance to " OE1 GLN A  88 " =    1.112
peak=    3.679 closest distance to " CB  ALA A  10 " =    1.327
peak=    3.679 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.677 closest distance to " O   HOH Z  61 " =    1.199
peak=    3.674 closest distance to " NH1AARG A 145 " =    1.298
peak=    3.669 closest distance to " N   TYR A  15 " =    0.974
peak=    3.666 closest distance to " O   HOH Z 234 " =    3.741
peak=    3.666 closest distance to " CB  LEU A 281 " =    0.944
peak=    3.665 closest distance to " OD2 ASP A  65 " =    1.064
peak=    3.657 closest distance to " O   HOH Z 407 " =    2.276
peak=    3.655 closest distance to " O   HOH Z  54 " =    1.982
peak=    3.653 closest distance to " CA  ARG A 102 " =    1.363
peak=    3.633 closest distance to " OE2 GLU A   2 " =    2.280
peak=    3.632 closest distance to " NH1 ARG A  36 " =    1.441
peak=    3.632 closest distance to " O   VAL A 121 " =    0.897
peak=    3.630 closest distance to " O   HOH Z  47 " =    1.567
peak=    3.626 closest distance to " O   HOH Z 377 " =    1.822
peak=    3.625 closest distance to " NZ  LYS A  76 " =    0.919
peak=    3.622 closest distance to " CG2 THR A 157 " =    1.006
peak=    3.620 closest distance to " NE2 GLN A  58 " =    3.651
peak=    3.610 closest distance to " CB  VAL A 296 " =    1.199
peak=    3.602 closest distance to " N   SER A 271 " =    1.125
peak=    3.588 closest distance to " O   HOH Z 221 " =    1.464
peak=    3.580 closest distance to " CG2BVAL A  41 " =    1.251
peak=    3.574 closest distance to " O   HOH Z  53 " =    1.009
peak=    3.563 closest distance to " O   HOH Z  65 " =    1.120
peak=    3.561 closest distance to " CA  PRO A 198 " =    1.181
peak=    3.561 closest distance to " O   HOH Z 394 " =    1.925
peak=    3.558 closest distance to " O   HOH Z 131 " =    1.008
peak=    3.558 closest distance to " CA  HIS A 115 " =    1.165
peak=    3.555 closest distance to " CG  PRO A 198 " =    1.495
peak=    3.551 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.550 closest distance to " O   LYS A 117 " =    0.925
peak=    3.547 closest distance to " CB  TRP A 179 " =    1.450
peak=    3.547 closest distance to " CD1 LEU A 297 " =    1.222
peak=    3.546 closest distance to " O   HOH Z  91 " =    2.405
peak=    3.542 closest distance to " CB  GLN A 183 " =    1.138
peak=    3.538 closest distance to " O   GLN A  77 " =    0.861
peak=    3.533 closest distance to " CA  VAL A 112 " =    1.122
peak=    3.532 closest distance to " O   HOH Z   9 " =    2.188
peak=    3.528 closest distance to " CB  SER A  62 " =    4.063
peak=    3.521 closest distance to " CB  ALA A 137 " =    1.374
peak=    3.517 closest distance to " CA  ALA A 100 " =    1.240
peak=    3.517 closest distance to " O   HOH Z 126 " =    1.855
peak=    3.516 closest distance to " N   LYS A 193 " =    1.596
peak=    3.513 closest distance to " N   ALA A 256 " =    1.179
peak=    3.512 closest distance to " CB  PHE A  59 " =    1.124
peak=    3.511 closest distance to " CG2 ILE A 120 " =    1.256
peak=    3.507 closest distance to " CB  SER A 273 " =    0.954
peak=    3.505 closest distance to " OH  TYR A 293 " =    0.889
peak=    3.504 closest distance to " N   ALA A   1 " =    2.327
peak=    3.499 closest distance to " O   HOH Z 401 " =    1.601
peak=    3.491 closest distance to " O   HOH Z 141 " =    1.547
peak=    3.491 closest distance to " CD  LYS A 289 " =    1.236
peak=    3.483 closest distance to " O   HOH Z 388 " =    1.340
peak=    3.482 closest distance to " CB  ALA A 292 " =    0.833
peak=    3.480 closest distance to " CD2 LEU A   5 " =    1.227
peak=    3.475 closest distance to " O   HOH Z 134 " =    2.067
peak=    3.471 closest distance to " NE2 GLN A 278 " =    2.304
peak=    3.468 closest distance to " O   HOH Z  14 " =    1.738
peak=    3.464 closest distance to " CB  TRP A 150 " =    1.443
peak=    3.463 closest distance to " O   HOH Z  76 " =    1.704
peak=    3.461 closest distance to " N   ASN A 187 " =    0.837
peak=    3.440 closest distance to " CA  ASN A  74 " =    0.865
peak=    3.438 closest distance to " CG  PRO A  54 " =    1.197
peak=    3.434 closest distance to " O   HOH Z 417 " =    1.590
peak=    3.431 closest distance to " O   HOH Z  26 " =    1.521
peak=    3.427 closest distance to " O   HOH Z 261 " =    2.176
peak=    3.426 closest distance to " CB  VAL A 202 " =    1.517
peak=    3.423 closest distance to " O   HOH Z 303 " =    2.396
peak=    3.421 closest distance to " N   TYR A 186 " =    1.609
peak=    3.418 closest distance to " CG2 ILE A  20 " =    1.416
peak=    3.418 closest distance to " CB  MET A  47 " =    1.052
peak=    3.414 closest distance to " ND2 ASN A  45 " =    2.556
peak=    3.414 closest distance to " CA  ALA A  21 " =    1.570
peak=    3.410 closest distance to " CD2 LEU A 297 " =    0.749
peak=    3.401 closest distance to " CA  GLY A 118 " =    0.735
peak=    3.399 closest distance to " O   VAL A  72 " =    1.014
peak=    3.398 closest distance to " CA  TRP A 274 " =    0.938
peak=    3.392 closest distance to " N   LEU A   5 " =    1.126
peak=    3.385 closest distance to " O   ARG A 275 " =    0.829
peak=    3.384 closest distance to " O   HOH Z 337 " =    2.115
peak=    3.379 closest distance to " CB  ASN A 148 " =    1.590
peak=    3.378 closest distance to " O   GLN A 103 " =    1.192
peak=    3.376 closest distance to " CB  LYS A 119 " =    1.351
peak=    3.373 closest distance to " O   MET A 185 " =    1.018
peak=    3.373 closest distance to " O   HOH Z 272 " =    1.740
peak=    3.371 closest distance to " CD1 ILE A 263 " =    1.244
peak=    3.369 closest distance to " CG2 THR A 279 " =    3.639
peak=    3.363 closest distance to " O   HOH Z 215 " =    1.336
peak=    3.361 closest distance to " O   HOH Z 359 " =    1.888
peak=    3.359 closest distance to " O   HOH Z 291 " =    1.285
peak=    3.359 closest distance to " O   HOH Z 153 " =    2.478
peak=    3.358 closest distance to " CB ASER A 164 " =    1.203
peak=    3.357 closest distance to " CA  TRP A  85 " =    1.107
peak=    3.351 closest distance to " O   HOH Z 361 " =    3.740
peak=    3.351 closest distance to " CA  THR A 246 " =    1.082
peak=    3.346 closest distance to " O   HOH Z 285 " =    2.584
peak=    3.344 closest distance to " OE1 GLN A  58 " =    1.091
peak=    3.343 closest distance to " O   HOH Z   5 " =    2.349
peak=    3.338 closest distance to " CD1 ILE A 199 " =    1.727
peak=    3.336 closest distance to " CE3 TRP A  85 " =    1.157
peak=    3.335 closest distance to " O   HOH Z  44 " =    2.106
peak=    3.335 closest distance to " N   ALA A 292 " =    1.051
peak=    3.334 closest distance to " O   HOH Z  18 " =    2.225
peak=    3.332 closest distance to " O   PHE A 283 " =    1.265
peak=    3.329 closest distance to " OE1 GLN A  73 " =    1.346
peak=    3.327 closest distance to " O   HOH Z 287 " =    1.771
peak=    3.325 closest distance to " O   ALA A  84 " =    1.681
peak=    3.324 closest distance to " C   TYR A  30 " =    0.854
peak=    3.322 closest distance to " CA  ALA A 248 " =    1.397
peak=    3.321 closest distance to " CB  TRP A 179 " =    1.604
peak=    3.319 closest distance to " CE1 HIS A 108 " =    1.224
peak=    3.316 closest distance to " O   HOH Z 404 " =    1.761
peak=    3.312 closest distance to " CB  MET A  40 " =    0.799
peak=    3.309 closest distance to " O   HOH Z 289 " =    1.323
peak=    3.308 closest distance to " O   HOH Z 149 " =    1.374
peak=    3.305 closest distance to " O   HOH Z 286 " =    1.983
peak=    3.304 closest distance to " O   HOH Z  58 " =    1.675
peak=    3.302 closest distance to " CG  LEU A 228 " =    1.455
peak=    3.300 closest distance to " NH2 ARG A  56 " =    2.241
peak=    3.294 closest distance to " O   HOH Z  49 " =    1.739
peak=    3.294 closest distance to " CB  ARG A 156 " =    1.114
peak=    3.294 closest distance to " O   HOH Z 435 " =    2.012
peak=    3.292 closest distance to " CA  TYR A  30 " =    1.108
peak=    3.290 closest distance to " CG2 VAL A 125 " =    1.118
peak=    3.289 closest distance to " CB  PRO A 243 " =    1.334
peak=    3.289 closest distance to " CG2 VAL A 197 " =    1.289
peak=    3.286 closest distance to " NH1 ARG A 159 " =    0.975
peak=    3.282 closest distance to " CG2 THR A  42 " =    0.955
peak=    3.281 closest distance to " CB  GLU A 175 " =    1.153
peak=    3.278 closest distance to " OE1 GLU A  37 " =    0.896
peak=    3.277 closest distance to " O   LYS A 119 " =    0.898
peak=    3.275 closest distance to " CB  VAL A 126 " =    0.885
peak=    3.274 closest distance to " O   HOH Z 166 " =    2.430
peak=    3.270 closest distance to " O   HOH Z 368 " =    3.249
peak=    3.270 closest distance to " CB  THR A  52 " =    0.961
peak=    3.265 closest distance to " O   HOH Z 258 " =    1.659
peak=    3.264 closest distance to " O   ASP A 124 " =    1.351
peak=    3.261 closest distance to " O   VAL A 112 " =    1.639
peak=    3.260 closest distance to " CD1 ILE A  33 " =    1.728
peak=    3.257 closest distance to " CA  GLN A  11 " =    1.510
peak=    3.256 closest distance to " CA  GLU A 152 " =    0.914
peak=    3.254 closest distance to " NE2 HIS A  86 " =    1.116
peak=    3.253 closest distance to " CD  LYS A 119 " =    1.569
peak=    3.253 closest distance to " CB  ALA A 244 " =    1.009
peak=    3.251 closest distance to " CB  VAL A 112 " =    1.702
peak=    3.247 closest distance to " O   HOH Z 411 " =    1.468
peak=    3.246 closest distance to " CB  ALA A 299 " =    1.203
peak=    3.244 closest distance to " NZ  LYS A 181 " =    0.761
peak=    3.244 closest distance to " CA  ALA A 154 " =    1.254
peak=    3.241 closest distance to " O   HOH Z 339 " =    1.311
peak=    3.233 closest distance to " O   HOH Z 174 " =    1.623
peak=    3.231 closest distance to " O   HOH Z 222 " =    1.093
peak=    3.231 closest distance to " CA  GLY A 196 " =    0.800
peak=    3.229 closest distance to " O   HOH Z 424 " =    0.883
peak=    3.228 closest distance to " O   HOH Z  54 " =    2.130
peak=    3.228 closest distance to " O   HOH Z 203 " =    1.175
peak=    3.221 closest distance to " CG  GLU A 236 " =    0.884
peak=    3.221 closest distance to " O   HOH Z  56 " =    2.159
peak=    3.216 closest distance to " CB  TRP A 266 " =    0.962
peak=    3.211 closest distance to " NE2 HIS A  81 " =    1.222
peak=    3.210 closest distance to " CB  SER A  97 " =    1.259
peak=    3.209 closest distance to " CA  SER A  87 " =    0.957
peak=    3.201 closest distance to " CB  GLN A 223 " =    1.385
peak=    3.200 closest distance to " CG2 THR A  52 " =    1.334
peak=    3.200 closest distance to " CB  ASP A 171 " =    0.761
peak=    3.194 closest distance to " O   HOH Z 395 " =    1.653
peak=    3.189 closest distance to " CA  LYS A 117 " =    1.495
peak=    3.183 closest distance to " CA  GLY A 267 " =    0.949
peak=    3.183 closest distance to " CZ3 TRP A 274 " =    4.589
peak=    3.183 closest distance to " O   HOH Z 343 " =    1.591
peak=    3.180 closest distance to " O   HOH Z 364 " =    1.807
peak=    3.179 closest distance to " CA  ARG A  36 " =    1.008
peak=    3.179 closest distance to " CA  ALA A 160 " =    1.159
peak=    3.177 closest distance to " O   HOH Z 106 " =    3.553
peak=    3.175 closest distance to " O   HOH Z 419 " =    2.280
peak=    3.172 closest distance to " CA  GLY A   6 " =    0.843
peak=    3.172 closest distance to " CA  TRP A  92 " =    1.025
peak=    3.165 closest distance to " C   PRO A 163 " =    1.458
peak=    3.161 closest distance to " O   HOH Z 132 " =    3.384
peak=    3.160 closest distance to " NH2AARG A 190 " =    0.931
peak=    3.157 closest distance to " C   ARG A  79 " =    1.350
peak=    3.157 closest distance to " N   ILE A  33 " =    0.972
peak=    3.156 closest distance to " O   HOH Z 358 " =    1.860
peak=    3.156 closest distance to " CB  PHE A 283 " =    0.874
peak=    3.155 closest distance to " O   HOH Z 200 " =    1.447
peak=    3.154 closest distance to " CA  LEU A   5 " =    0.961
peak=    3.149 closest distance to " OD1 ASP A 238 " =    0.840
peak=    3.146 closest distance to " CG  GLN A 278 " =    1.159
peak=    3.143 closest distance to " CG2 ILE A 234 " =    0.868
peak=    3.141 closest distance to " NE2 GLN A  77 " =    3.021
peak=    3.140 closest distance to " O   HOH Z 379 " =    1.782
peak=    3.138 closest distance to " N   TYR A 247 " =    1.168
peak=    3.137 closest distance to " O   HOH Z 156 " =    4.768
peak=    3.137 closest distance to " O   HOH Z  68 " =    2.483
peak=    3.136 closest distance to " CZ  PHE A 204 " =    1.206
peak=    3.136 closest distance to " OG  SER A  22 " =    2.587
peak=    3.133 closest distance to " CA  ASP A 162 " =    1.177
peak=    3.129 closest distance to " O   HOH Z 134 " =    2.191
peak=    3.129 closest distance to " O   HOH Z 325 " =    2.200
peak=    3.124 closest distance to " CB  ASP A 140 " =    1.017
peak=    3.123 closest distance to " O   HOH Z 238 " =    1.725
peak=    3.118 closest distance to " NH1 ARG A  79 " =    0.871
peak=    3.113 closest distance to " CB  SER A 210 " =    0.955
peak=    3.113 closest distance to " O   HOH Z 327 " =    2.752
peak=    3.112 closest distance to " CB  ARG A 219 " =    1.304
peak=    3.110 closest distance to " O   HOH Z 324 " =    1.739
peak=    3.107 closest distance to " O   HOH Z 418 " =    3.495
peak=    3.098 closest distance to " O   HOH Z 189 " =    3.881
peak=    3.091 closest distance to " O   HOH Z 163 " =    1.902
peak=    3.088 closest distance to " O   HOH Z 428 " =    3.952
peak=    3.087 closest distance to " N   SER A   3 " =    0.730
peak=    3.087 closest distance to " CG2 VAL A 268 " =    1.029
peak=    3.084 closest distance to " CB  ASP A 191 " =    1.181
peak=    3.080 closest distance to " O   HOH Z 427 " =    3.077
peak=    3.080 closest distance to " OD1 ASP A 272 " =    1.078
peak=    3.056 closest distance to " NE2 GLN A  11 " =    1.056
peak=    3.055 closest distance to " O   HOH Z 221 " =    1.581
peak=    3.049 closest distance to " CG2 THR A   4 " =    1.341
peak=    3.044 closest distance to " O   HOH Z 130 " =    2.482

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.452 - 5.299
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 211
   mapped sites are within: 0.722 - 5.299

peak=   -4.495 closest distance to " O   HOH Z  44 " =    2.010
peak=   -4.227 closest distance to " CG2BVAL A  41 " =    2.336
peak=   -4.187 closest distance to " O   HOH Z 400 " =    0.961
peak=   -4.170 closest distance to " CG1 VAL A 112 " =    2.690
peak=   -4.081 closest distance to " CD  ARG A 269 " =    2.631
peak=   -4.043 closest distance to " O   HOH Z  53 " =    0.963
peak=   -3.979 closest distance to " O   HOH Z 422 " =    2.343
peak=   -3.960 closest distance to " CB  ALA A 291 " =    2.401
peak=   -3.954 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.937 closest distance to " O   HOH Z 411 " =    5.009
peak=   -3.925 closest distance to " CD  GLN A 223 " =    1.143
peak=   -3.914 closest distance to " O   SER A   3 " =    1.042
peak=   -3.910 closest distance to " CG2 VAL A 230 " =    0.929
peak=   -3.907 closest distance to " CA  TRP A 274 " =    0.969
peak=   -3.901 closest distance to " OG  SER A 288 " =    1.105
peak=   -3.889 closest distance to " O   HOH Z  65 " =    1.447
peak=   -3.889 closest distance to " CG  LEU A   5 " =    0.999
peak=   -3.883 closest distance to " O   HOH Z 265 " =    2.038
peak=   -3.865 closest distance to " CD  ARG A  14 " =    3.054
peak=   -3.864 closest distance to " O   HOH Z 407 " =    1.470
peak=   -3.857 closest distance to " O   HOH Z 141 " =    1.404
peak=   -3.836 closest distance to " OD1 ASN A 301 " =    0.774
peak=   -3.831 closest distance to " O   HOH Z 153 " =    2.026
peak=   -3.785 closest distance to " O   HOH Z 250 " =    1.461
peak=   -3.781 closest distance to " ND2 ASN A  60 " =    1.599
peak=   -3.774 closest distance to " O   HOH Z 155 " =    1.718
peak=   -3.766 closest distance to " O   HOH Z   2 " =    2.666
peak=   -3.759 closest distance to " O   HOH Z  54 " =    1.493
peak=   -3.753 closest distance to " CA  GLY A 241 " =    2.342
peak=   -3.738 closest distance to " CA  VAL A 197 " =    1.105
peak=   -3.736 closest distance to " N   THR A  52 " =    1.593
peak=   -3.732 closest distance to " N   SER A 134 " =    1.119
peak=   -3.731 closest distance to " CA  SER A 164 " =    1.913
peak=   -3.728 closest distance to " CZ  ARG A  36 " =    1.300
peak=   -3.726 closest distance to " CD  GLU A 236 " =    1.138
peak=   -3.723 closest distance to " O   HOH Z  41 " =    2.363
peak=   -3.707 closest distance to " CA  GLU A 277 " =    0.918
peak=   -3.697 closest distance to " CG2 ILE A 120 " =    1.168
peak=   -3.685 closest distance to " OG  SER A  87 " =    1.826
peak=   -3.673 closest distance to " NE2 GLN A 194 " =    2.286
peak=   -3.654 closest distance to " CD  GLN A  77 " =    0.935
peak=   -3.651 closest distance to " CD2 TYR A  15 " =    2.264
peak=   -3.648 closest distance to " O   VAL A 121 " =    0.876
peak=   -3.644 closest distance to " N   VAL A 230 " =    0.869
peak=   -3.643 closest distance to " N   ARG A 275 " =    0.981
peak=   -3.640 closest distance to " CG  PRO A 243 " =    1.662
peak=   -3.638 closest distance to " O   HOH Z 205 " =    1.595
peak=   -3.636 closest distance to " CG  LEU A   5 " =    1.532
peak=   -3.633 closest distance to " OD2 ASP A 171 " =    1.928
peak=   -3.622 closest distance to " O   HOH Z 122 " =    1.114
peak=   -3.619 closest distance to " O   HOH Z 257 " =    1.317
peak=   -3.607 closest distance to " O   HOH Z 216 " =    0.981
peak=   -3.605 closest distance to " O   GLN A  73 " =    1.075
peak=   -3.602 closest distance to " O   HOH Z 114 " =    1.318
peak=   -3.596 closest distance to " CG  ASP A 286 " =    1.467
peak=   -3.594 closest distance to " CG1 VAL A 153 " =    2.387
peak=   -3.592 closest distance to " O   HOH Z 156 " =    2.912
peak=   -3.591 closest distance to " O   HOH Z 231 " =    0.805
peak=   -3.589 closest distance to " ND2 ASN A 249 " =    1.029
peak=   -3.574 closest distance to " O   ASP A  27 " =    1.342
peak=   -3.570 closest distance to " CG  ASP A  50 " =    2.242
peak=   -3.568 closest distance to " CE3 TRP A  70 " =    1.236
peak=   -3.566 closest distance to " ND2 ASN A 110 " =    1.051
peak=   -3.558 closest distance to " SG  CYS A 254 " =    3.306
peak=   -3.555 closest distance to " OG  SER A 276 " =    0.945
peak=   -3.553 closest distance to " O   TYR A  15 " =    2.177
peak=   -3.550 closest distance to " SG  CYS A 254 " =    2.858
peak=   -3.550 closest distance to " CG  GLN A 103 " =    2.118
peak=   -3.546 closest distance to " O   HOH Z  52 " =    2.050
peak=   -3.545 closest distance to " CE  LYS A  76 " =    0.996
peak=   -3.541 closest distance to " O   ALA A  43 " =    1.904
peak=   -3.538 closest distance to " O   HOH Z 192 " =    2.008
peak=   -3.526 closest distance to " O   HOH Z 361 " =    3.961
peak=   -3.519 closest distance to " O   HOH Z 109 " =    3.977
peak=   -3.511 closest distance to " O   HOH Z 384 " =    1.718
peak=   -3.510 closest distance to " O   THR A  82 " =    1.428
peak=   -3.510 closest distance to " NH1 ARG A  56 " =    1.188
peak=   -3.507 closest distance to " O   HOH Z 251 " =    4.304
peak=   -3.504 closest distance to " CZ  TYR A  68 " =    1.079
peak=   -3.503 closest distance to " CG2 VAL A 202 " =    2.347
peak=   -3.502 closest distance to " C   SER A  28 " =    1.108
peak=   -3.500 closest distance to " OG  SER A  32 " =    1.331
peak=   -3.496 closest distance to " CE2 PHE A 283 " =    2.616
peak=   -3.493 closest distance to " O   ASP A 298 " =    1.674
peak=   -3.490 closest distance to " O   HOH Z 151 " =    1.093
peak=   -3.489 closest distance to " CG  PRO A 198 " =    2.182
peak=   -3.479 closest distance to " O   HOH Z  40 " =    2.992
peak=   -3.476 closest distance to " CA  SER A 271 " =    2.237
peak=   -3.470 closest distance to " CG  LEU A 167 " =    1.109
peak=   -3.467 closest distance to " OE1 GLU A  44 " =    0.960
peak=   -3.456 closest distance to " O   HOH Z 150 " =    0.968
peak=   -3.440 closest distance to " C   ILE A 120 " =    1.272
peak=   -3.435 closest distance to " CA  GLY A 229 " =    2.569
peak=   -3.434 closest distance to " OD1 ASN A  69 " =    1.009
peak=   -3.431 closest distance to " CB  SER A  26 " =    1.270
peak=   -3.430 closest distance to " O   TRP A 150 " =    0.971
peak=   -3.426 closest distance to " O   SER A  95 " =    2.201
peak=   -3.425 closest distance to " O   HOH Z 127 " =    1.694
peak=   -3.424 closest distance to " O   GLN A  11 " =    0.787
peak=   -3.419 closest distance to " OG  SER A  87 " =    1.651
peak=   -3.415 closest distance to " OG  SER A   3 " =    1.065
peak=   -3.404 closest distance to " OD1 ASP A 272 " =    1.415
peak=   -3.401 closest distance to " NE2 GLN A  55 " =    2.303
peak=   -3.400 closest distance to " O  BHOH Z  74 " =    1.344
peak=   -3.390 closest distance to " O   HOH Z 352 " =    1.905
peak=   -3.389 closest distance to " CG  ASP A  65 " =    1.102
peak=   -3.385 closest distance to " O   HOH Z 222 " =    1.249
peak=   -3.377 closest distance to " N   LEU A  25 " =    0.990
peak=   -3.366 closest distance to " O   HOH Z 295 " =    1.729
peak=   -3.365 closest distance to " CE2 PHE A 218 " =    2.279
peak=   -3.364 closest distance to " NH2 ARG A  66 " =    1.527
peak=   -3.363 closest distance to " O   HOH Z 405 " =    2.393
peak=   -3.363 closest distance to " N   PHE A  59 " =    1.257
peak=   -3.353 closest distance to " NE2 GLN A  58 " =    2.536
peak=   -3.349 closest distance to " O   HOH Z 198 " =    1.998
peak=   -3.346 closest distance to " CZ  ARG A 259 " =    0.854
peak=   -3.345 closest distance to " O   HOH Z 166 " =    1.487
peak=   -3.340 closest distance to " O   HOH Z  10 " =    1.680
peak=   -3.340 closest distance to " CG1AVAL A 121 " =    1.134
peak=   -3.334 closest distance to " CD1 LEU A  25 " =    0.904
peak=   -3.330 closest distance to " C   LEU A 101 " =    1.061
peak=   -3.324 closest distance to " O   HOH Z 192 " =    1.440
peak=   -3.322 closest distance to " CA  ASP A  65 " =    1.146
peak=   -3.321 closest distance to " OD2 ASP A 286 " =    2.947
peak=   -3.309 closest distance to " O   HOH Z 423 " =    0.962
peak=   -3.297 closest distance to " O   HOH Z 260 " =    2.025
peak=   -3.297 closest distance to " CG1 VAL A 296 " =    1.040
peak=   -3.291 closest distance to " CA  LEU A  25 " =    1.180
peak=   -3.283 closest distance to " CD  GLN A  55 " =    0.863
peak=   -3.283 closest distance to " OD1 ASP A 107 " =    1.230
peak=   -3.280 closest distance to " O   HOH Z  70 " =    2.055
peak=   -3.279 closest distance to " CG  GLN A  58 " =    1.578
peak=   -3.276 closest distance to " OD1 ASP A 171 " =    1.703
peak=   -3.275 closest distance to " CG1 VAL A 197 " =    2.500
peak=   -3.272 closest distance to " OE1 GLU A  37 " =    1.225
peak=   -3.270 closest distance to " O   HOH Z 345 " =    2.459
peak=   -3.270 closest distance to " CG2 ILE A  33 " =    2.684
peak=   -3.267 closest distance to " O   HOH Z 132 " =    3.320
peak=   -3.265 closest distance to " C   TYR A  30 " =    1.016
peak=   -3.265 closest distance to " O   HOH Z 221 " =    0.722
peak=   -3.264 closest distance to " CG2 VAL A 202 " =    2.753
peak=   -3.264 closest distance to " O   HOH Z 256 " =    2.467
peak=   -3.263 closest distance to " O   HOH Z  57 " =    0.930
peak=   -3.258 closest distance to " NZ  LYS A 289 " =    1.360
peak=   -3.243 closest distance to " CA  THR A 264 " =    1.362
peak=   -3.243 closest distance to " O   HOH Z  35 " =    2.400
peak=   -3.240 closest distance to " O   HOH Z 259 " =    0.992
peak=   -3.239 closest distance to " O   HOH Z 196 " =    1.406
peak=   -3.238 closest distance to " CA  LEU A 143 " =    1.023
peak=   -3.238 closest distance to " CG2 THR A 264 " =    2.239
peak=   -3.234 closest distance to " N   ALA A 184 " =    1.055
peak=   -3.231 closest distance to " CA  ALA A   8 " =    1.462
peak=   -3.231 closest distance to " CD2 LEU A 237 " =    2.767
peak=   -3.229 closest distance to " O   HOH Z  81 " =    1.517
peak=   -3.228 closest distance to " CD2 LEU A 228 " =    0.999
peak=   -3.227 closest distance to " N   PHE A  59 " =    1.811
peak=   -3.224 closest distance to " O   HOH Z 394 " =    1.767
peak=   -3.221 closest distance to " CD  GLN A 223 " =    0.771
peak=   -3.218 closest distance to " CA  ASP A 298 " =    1.208
peak=   -3.217 closest distance to " CD2 PHE A  61 " =    2.263
peak=   -3.216 closest distance to " O   HOH Z 426 " =    0.918
peak=   -3.208 closest distance to " O   GLN A  94 " =    2.194
peak=   -3.204 closest distance to " OE1 GLN A  88 " =    0.876
peak=   -3.196 closest distance to " C   LEU A 222 " =    1.056
peak=   -3.196 closest distance to " CB  VAL A 230 " =    0.950
peak=   -3.195 closest distance to " O   HOH Z 329 " =    1.318
peak=   -3.195 closest distance to " N   SER A 212 " =    1.766
peak=   -3.180 closest distance to " O   MET A  47 " =    2.136
peak=   -3.179 closest distance to " O   HOH Z 431 " =    1.863
peak=   -3.174 closest distance to " O   HOH Z  19 " =    2.370
peak=   -3.168 closest distance to " O   HOH Z 269 " =    1.323
peak=   -3.165 closest distance to " O   HOH Z 378 " =    1.541
peak=   -3.165 closest distance to " CD2 TYR A 293 " =    1.737
peak=   -3.164 closest distance to " O   HOH Z 171 " =    5.299
peak=   -3.162 closest distance to " CG2 ILE A  49 " =    2.871
peak=   -3.161 closest distance to " O   HOH Z 401 " =    1.318
peak=   -3.159 closest distance to " CE3 TRP A 150 " =    2.152
peak=   -3.158 closest distance to " CG  LEU A  83 " =    2.356
peak=   -3.152 closest distance to " O   ASN A 148 " =    2.040
peak=   -3.148 closest distance to " CD2 LEU A 237 " =    2.405
peak=   -3.143 closest distance to " O   HOH Z 195 " =    1.593
peak=   -3.133 closest distance to " O   HOH Z 119 " =    4.814
peak=   -3.129 closest distance to " N   ASP A 272 " =    1.162
peak=   -3.125 closest distance to " CD1 ILE A 109 " =    2.124
peak=   -3.124 closest distance to " O   HOH Z 279 " =    1.232
peak=   -3.124 closest distance to " O   HOH Z  39 " =    0.925
peak=   -3.121 closest distance to " OD1 ASP A 231 " =    0.830
peak=   -3.117 closest distance to " C   MET A 188 " =    1.190
peak=   -3.111 closest distance to " O   HOH Z 203 " =    1.140
peak=   -3.106 closest distance to " O   HOH Z  50 " =    1.209
peak=   -3.105 closest distance to " N   ALA A  34 " =    2.560
peak=   -3.097 closest distance to " ND2 ASN A  60 " =    2.465
peak=   -3.097 closest distance to " O   HOH Z 174 " =    1.287
peak=   -3.088 closest distance to " O   HOH Z 287 " =    1.363
peak=   -3.088 closest distance to " C   LYS A 119 " =    1.116
peak=   -3.087 closest distance to " CD  GLN A  58 " =    0.768
peak=   -3.086 closest distance to " CD1 ILE A 151 " =    2.640
peak=   -3.085 closest distance to " O   GLN A  73 " =    0.754
peak=   -3.084 closest distance to " NH1 ARG A 195 " =    1.033
peak=   -3.083 closest distance to " O   HOH Z 273 " =    0.994
peak=   -3.080 closest distance to " O   TYR A  15 " =    2.507
peak=   -3.078 closest distance to " CB  ASN A  69 " =    1.414
peak=   -3.077 closest distance to " O   ASP A 298 " =    0.774
peak=   -3.060 closest distance to " CB  ALA A   9 " =    2.525
peak=   -3.025 closest distance to " O   HOH Z 174 " =    1.365
peak=   -3.023 closest distance to " O   HOH Z 112 " =    0.884
peak=   -3.017 closest distance to " CG  GLN A  58 " =    0.862

================= 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    :  0.5266 0.5190   6.314965e+00   6.305197e+00
   1_bss:  0.5212 0.5143   6.312048e+00   6.301698e+00
   1_xyz:  0.4723 0.4875   6.271298e+00   6.278609e+00
   1_adp:  0.4307 0.4789   5.974879e+00   6.020948e+00
   1_occ:  0.4296 0.4797   5.975201e+00   6.021721e+00
   2_bss:  0.4284 0.4744   5.976918e+00   6.021798e+00
   2_xyz:  0.3778 0.4536   6.156524e+00   6.244504e+00
   2_adp:  0.3743 0.4414   6.148307e+00   6.232102e+00
   2_occ:  0.3741 0.4413   6.148103e+00   6.231849e+00
   3_bss:  0.3741 0.4405   6.149536e+00   6.231405e+00
   3_xyz:  0.3080 0.3680   5.997106e+00   6.114917e+00
   3_adp:  0.2869 0.3532   5.945422e+00   6.084251e+00
   3_occ:  0.2866 0.3538   5.945294e+00   6.084886e+00
   4_bss:  0.2854 0.3526   5.944092e+00   6.085071e+00
   4_xyz:  0.2371 0.2972   5.785426e+00   5.954381e+00
   4_adp:  0.2125 0.2683   5.694674e+00   5.876187e+00
   4_occ:  0.2123 0.2693   5.694964e+00   5.877105e+00
   5_bss:  0.2121 0.2693   5.694249e+00   5.876543e+00
   5_xyz:  0.1804 0.2293   5.548945e+00   5.742211e+00
   5_adp:  0.1709 0.2226   5.509529e+00   5.710477e+00
   5_occ:  0.1707 0.2228   5.509175e+00   5.710475e+00
   5_bss:  0.1709 0.2230   5.510671e+00   5.711927e+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:  0.281  20.001   5.433  10.115  10.034   0.000   0.000   0.000
   1_xyz:  0.281  20.001   5.433  10.115  10.034   0.000   0.000   0.000
   1_adp:  0.281  20.001   5.433  10.115  10.034   0.000   0.000   0.000
   1_occ:  0.281  20.001   5.433  10.115  10.034   0.000   0.000   0.000
   2_bss:  0.331  80.000   2.852   5.910   6.423   0.000   0.000   0.000
   2_xyz:  0.331  80.000   2.852   5.910   6.423   0.000   0.000   0.000
   2_adp:  0.331  80.000   2.852   5.910   6.423   0.000   0.000   0.000
   2_occ:  0.331  80.000   2.852   5.910   6.423   0.000   0.000   0.000
   3_bss:  0.332  91.403   1.714   4.298   4.168   0.000   0.000   0.000
   3_xyz:  0.332  91.403   1.714   4.298   4.168   0.000   0.000   0.000
   3_adp:  0.332  91.403   1.714   4.298   4.168   0.000   0.000   0.000
   3_occ:  0.332  91.403   1.714   4.298   4.168   0.000   0.000   0.000
   4_bss:  0.333  81.191   0.549   2.399   2.279   0.000   0.000   0.000
   4_xyz:  0.333  81.191   0.549   2.399   2.279   0.000   0.000   0.000
   4_adp:  0.333  81.191   0.549   2.399   2.279   0.000   0.000   0.000
   4_occ:  0.333  81.191   0.549   2.399   2.279   0.000   0.000   0.000
   5_bss:  0.333  80.000   0.067   1.366   1.854   0.000   0.000   0.000
   5_xyz:  0.333  80.000   0.067   1.366   1.854   0.000   0.000   0.000
   5_adp:  0.333  80.000   0.067   1.366   1.854   0.000   0.000   0.000
   5_occ:  0.333  80.000   0.067   1.366   1.854   0.000   0.000   0.000
   5_bss:  0.335  83.945  -1.023   0.105   0.918   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  68.924 0.2770  0.3173    85700.391
   1_bss:  67.194 0.2995  0.4353    84959.566
   1_xyz:  60.007 0.3923  0.5634    72303.057
   1_adp:  59.934 0.3928  0.6431    71640.811
   1_occ:  60.276 0.3884  0.6335    72162.296
   2_bss:  60.160 0.3898  0.5727    71877.360
   2_xyz:  55.228 0.4524  0.6659    62303.294
   2_adp:  51.909 0.4956  0.7201    58298.402
   2_occ:  51.909 0.4956  0.7198    58262.390
   3_bss:  51.862 0.4962  0.6825    58230.339
   3_xyz:  39.997 0.6432  0.8720    38926.645
   3_adp:  37.578 0.6721  0.9022    35259.780
   3_occ:  37.657 0.6711  0.9003    35303.282
   4_bss:  37.555 0.6723  0.8529    35106.367
   4_xyz:  30.636 0.7507  0.9213    23739.024
   4_adp:  27.250 0.7880  0.9299    19246.070
   4_occ:  27.285 0.7876  0.9292    19302.744
   5_bss:  27.246 0.7880  0.9086    19233.002
   5_xyz:  22.713 0.8353  0.9419    13910.987
   5_adp:  21.596 0.8468  0.9370    12976.022
   5_occ:  21.591 0.8469  0.9370    12982.052
   5_bss:  21.618 0.8467  0.9364    13032.063
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4914e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4914e+01
   1_xyz:   1.774  0.014  0.110 18.504  0.007  4.125   1.5617e-01
   1_adp:   1.774  0.014  0.110 18.504  0.007  4.125   1.5617e-01
   1_occ:   1.774  0.014  0.110 18.504  0.007  4.125   1.5617e-01
   2_bss:   1.774  0.014  0.110 18.504  0.007  4.125   1.5617e-01
   2_xyz:   1.381  0.010  0.091 17.528  0.005  4.108   1.1185e-01
   2_adp:   1.381  0.010  0.091 17.528  0.005  4.108   1.1185e-01
   2_occ:   1.381  0.010  0.091 17.528  0.005  4.108   1.1185e-01
   3_bss:   1.381  0.010  0.091 17.528  0.005  4.108   1.1185e-01
   3_xyz:   1.502  0.012  0.109 17.279  0.005  4.111   1.3326e-01
   3_adp:   1.502  0.012  0.109 17.279  0.005  4.111   1.3326e-01
   3_occ:   1.502  0.012  0.109 17.279  0.005  4.111   1.3326e-01
   4_bss:   1.502  0.012  0.109 17.279  0.005  4.111   1.3326e-01
   4_xyz:   1.160  0.010  0.080 15.883  0.005  4.137   8.5951e-02
   4_adp:   1.160  0.010  0.080 15.883  0.005  4.137   8.5951e-02
   4_occ:   1.160  0.010  0.080 15.883  0.005  4.137   8.5951e-02
   5_bss:   1.160  0.010  0.080 15.883  0.005  4.137   8.5951e-02
   5_xyz:   1.078  0.008  0.081 15.309  0.003  4.132   6.9838e-02
   5_adp:   1.078  0.008  0.081 15.309  0.003  4.132   6.9838e-02
   5_occ:   1.078  0.008  0.081 15.309  0.003  4.132   6.9838e-02
   5_bss:   1.078  0.008  0.081 15.309  0.003  4.132   6.9838e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1190e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1190e+00
   1_xyz:  14.602  0.123  0.455 88.226  0.055  2.180   1.0707e-01
   1_adp:  14.602  0.123  0.455 88.226  0.055  2.180   1.0707e-01
   1_occ:  14.602  0.123  0.455 88.226  0.055  2.180   1.0707e-01
   2_bss:  14.602  0.123  0.455 88.226  0.055  2.180   1.0707e-01
   2_xyz:   9.058  0.061  0.296 89.840  0.037  2.053   6.1974e-02
   2_adp:   9.058  0.061  0.296 89.840  0.037  2.053   6.1974e-02
   2_occ:   9.058  0.061  0.296 89.840  0.037  2.053   6.1974e-02
   3_bss:   9.058  0.061  0.296 89.840  0.037  2.053   6.1974e-02
   3_xyz:  10.013  0.093  0.426 87.893  0.031  1.968   9.7386e-02
   3_adp:  10.013  0.093  0.426 87.893  0.031  1.968   9.7386e-02
   3_occ:  10.013  0.093  0.426 87.893  0.031  1.968   9.7386e-02
   4_bss:  10.013  0.093  0.426 87.893  0.031  1.968   9.7386e-02
   4_xyz:   7.802  0.071  0.273 86.926  0.045  2.038   7.4262e-02
   4_adp:   7.802  0.071  0.273 86.926  0.045  2.038   7.4262e-02
   4_occ:   7.802  0.071  0.273 86.926  0.045  2.038   7.4262e-02
   5_bss:   7.802  0.071  0.273 86.926  0.045  2.038   7.4262e-02
   5_xyz:   7.920  0.057  0.309 83.691  0.035  2.293   4.6208e-02
   5_adp:   7.920  0.057  0.309 83.691  0.035  2.293   4.6208e-02
   5_occ:   7.920  0.057  0.309 83.691  0.035  2.293   4.6208e-02
   5_bss:   7.920  0.057  0.309 83.691  0.035  2.293   4.6208e-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: 145.75   0.00  20.57 109.79   0.00  18.72 145.75   0.00  30.62
   1_occ: 145.75   0.00  20.57 109.79   0.00  18.72 145.75   0.00  30.62
   2_bss: 145.75   0.00  20.57 109.79   0.00  18.72 145.75   0.00  30.62
   2_xyz: 145.75   0.00  20.57 109.79   0.00  18.72 145.75   0.00  30.62
   2_adp: 143.37   0.00  16.85  74.14   0.00  14.91 143.37   0.00  27.42
   2_occ: 143.37   0.00  16.85  74.14   0.00  14.91 143.37   0.00  27.42
   3_bss: 143.37   0.00  16.85  74.14   0.00  14.91 143.37   0.00  27.42
   3_xyz: 143.37   0.00  16.85  74.14   0.00  14.91 143.37   0.00  27.42
   3_adp: 150.81   0.00  16.71 150.81   0.00  13.93 141.82   0.00  31.89
   3_occ: 150.81   0.00  16.71 150.81   0.00  13.93 141.82   0.00  31.89
   4_bss: 150.81   0.00  16.71 150.81   0.00  13.93 141.82   0.00  31.89
   4_xyz: 150.81   0.00  16.71 150.81   0.00  13.93 141.82   0.00  31.89
   4_adp: 130.04   0.00  16.82  94.34   0.00  12.21 130.04   0.00  41.92
   4_occ: 130.04   0.00  16.82  94.34   0.00  12.21 130.04   0.00  41.92
   5_bss: 130.04   0.00  16.82  94.34   0.00  12.21 130.04   0.00  41.92
   5_xyz: 130.04   0.00  16.82  94.34   0.00  12.21 130.04   0.00  41.92
   5_adp: 119.74   0.00  16.41  97.36   0.00  11.36 119.74   1.14  43.93
   5_occ: 119.74   0.00  16.41  97.36   0.00  11.36 119.74   1.14  43.93
   5_bss: 120.83   1.08  17.49  98.45   1.08  12.44 120.83   2.22  45.01
------------------------------------------------------------------------
 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:    1.212    0.017    0.409
   1_adp:    1.212    0.017    0.409
   1_occ:    1.212    0.017    0.409
   2_bss:    1.212    0.017    0.409
   2_xyz:    1.567    0.040    0.578
   2_adp:    1.567    0.040    0.578
   2_occ:    1.567    0.040    0.578
   3_bss:    1.567    0.040    0.578
   3_xyz:    1.954    0.033    0.799
   3_adp:    1.954    0.033    0.799
   3_occ:    1.954    0.033    0.799
   4_bss:    1.954    0.033    0.799
   4_xyz:    1.916    0.050    0.895
   4_adp:    1.916    0.050    0.895
   4_occ:    1.916    0.050    0.895
   5_bss:    1.916    0.050    0.895
   5_xyz:    2.066    0.063    0.962
   5_adp:    2.066    0.063    0.962
   5_occ:    2.066    0.063    0.962
   5_bss:    2.066    0.063    0.962
------------------------------------------------------------------------

CPU time actual refinement: 358.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_967/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_967/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_967/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_967/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_967/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.60 
  Macro-tasks:
    bulk solvent and scale       = 65.69  
    individual site refinement   = 140.00 
    weights calculation          = 32.64  
    collect and process          = 6.30   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 244.73 
  Micro-tasks:
    mask                            = 2.72   
    f_calc                          = 106.33 
    alpha_beta                      = 8.53   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 110.48 
    fmodel                         = 10.28  
    r_factors                      = 0.41   
    phase_errors                   = 10.10  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 250.31 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.061 micro seconds
Total CPU time: 6.20 minutes
from_scatterers_fft:    613 calls, 105.94 s
gradients_fft:          558 calls,  99.68 s

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

# Date 2008-01-16 Time 02:51:56 PST -0800 (1200480716.22 s)
Start R-work = 0.5266, R-free = 0.5190 (no bulk solvent and anisotropic scale)
Final R-work = 0.1852, R-free = 0.2373 (no bulk solvent and anisotropic scale)

Start R-work = 0.5212, R-free = 0.5143
Final R-work = 0.1709, R-free = 0.2230