# Date 2008-01-16 Time 02:08:02 PST -0800 (1200478082.33 s)
#phil __OFF__

Command line arguments: "../703.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28201
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 703

-------------------------------------------------------------------------------
  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: (70.25, 47.6339, 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: 3.38, per 1000 atoms: 1.20


================================== 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: (70.25, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00075
Completeness in resolution range: 0.949493
Completeness with d_max=infinity: 0.946557

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   2.0008

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: (70.25, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00075
Completeness in resolution range: 0.949493
Completeness with d_max=infinity: 0.946557

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2808 [2173/2200]  1953   220  10.1%
  bin  2:  4.2808 -  3.4107 [2072/2088]  1866   206   9.9%
  bin  3:  3.4107 -  2.9833 [2064/2083]  1858   206  10.0%
  bin  4:  2.9833 -  2.7123 [2035/2065]  1830   205  10.1%
  bin  5:  2.7123 -  2.5188 [2009/2028]  1812   197   9.8%
  bin  6:  2.5188 -  2.3709 [2021/2057]  1814   207  10.2%
  bin  7:  2.3709 -  2.2526 [2009/2042]  1814   195   9.7%
  bin  8:  2.2526 -  2.1548 [1987/2022]  1779   208  10.5%
  bin  9:  2.1548 -  2.0721 [1985/2012]  1795   190   9.6%
  bin 10:  2.0721 -  2.0008 [1234/2034]  1109   125  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_703/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 7
        2.11 -     2.81: 765
        2.81 -     3.51: 4365
        3.51 -     4.20: 9117
        4.20 -     4.90: 13506
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.414 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.675 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.675 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.767 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.803 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27755 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_703/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_703/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 = 70.25 47.63395 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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4971   r_free= 0.4856   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.296486                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1407  156 0.4036 0.3870      6.6201      6.5759|
|  2:  4.7744 -  3.8096 0.99   1359  153 0.4260 0.4939      6.8248      6.9857|
|  3:  3.8096 -  3.3340 0.99   1324  146 0.4715 0.4371      6.7178      6.6658|
|  4:  3.3340 -  3.0319 0.99   1315  139 0.4892 0.4331      6.5415      6.4877|
|  5:  3.0319 -  2.8160 0.99   1312  150 0.5300 0.4752      6.3912      6.4092|
|  6:  2.8160 -  2.6510 0.99   1313  145 0.5262 0.5783      6.2864      6.2238|
|  7:  2.6510 -  2.5188 0.99   1289  145 0.5143 0.4447       6.239      6.1252|
|  8:  2.5188 -  2.4096 0.98   1291  145 0.5414 0.4700      6.2082      6.1604|
|  9:  2.4096 -  2.3172 0.98   1300  145 0.5307 0.5921      6.1164      6.1979|
| 10:  2.3172 -  2.2375 0.98   1276  136 0.5602 0.4743      6.1259      6.0825|
| 11:  2.2375 -  2.1678 1.00   1301  148 0.5259 0.5433      6.0339      6.0813|
| 12:  2.1678 -  2.1060 0.97   1268  138 0.5418 0.5491      5.9657      6.0158|
| 13:  2.1060 -  2.0507 0.98   1269  140 0.5501 0.5399      5.8933       5.832|
| 14:  2.0507 -  2.0008 0.47    606   73 0.5488 0.5247      5.8809      5.7882|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1407   156  0.68  35.60   0.79     0.70      75122.73|
|  2:  4.7744 -  3.8096  1359   153  0.67  37.99   0.85     0.71     120186.84|
|  3:  3.8096 -  3.3340  1324   146  0.56  47.12   0.79     0.66     126341.95|
|  4:  3.3340 -  3.0319  1315   139  0.47  54.51   0.77     0.55     109428.69|
|  5:  3.0319 -  2.8160  1312   150  0.39  60.31   0.72     0.46      85001.24|
|  6:  2.8160 -  2.6510  1313   145  0.36  63.07   0.70     0.42      74750.65|
|  7:  2.6510 -  2.5188  1289   145  0.38  61.15   0.72     0.43      64163.97|
|  8:  2.5188 -  2.4096  1291   145  0.40  60.15   0.71     0.45      55834.45|
|  9:  2.4096 -  2.3172  1300   145  0.36  62.65   0.69     0.43      53986.04|
| 10:  2.3172 -  2.2375  1276   136  0.31  66.97   0.71     0.37      52360.12|
| 11:  2.2375 -  2.1678  1301   148  0.26  70.33   0.72     0.32      51672.80|
| 12:  2.1678 -  2.1060  1268   138  0.24  71.89   0.73     0.31      46995.18|
| 13:  2.1060 -  2.0507  1269   140  0.23  73.16   0.70     0.28      40710.53|
| 14:  2.0507 -  2.0008   606    73  0.21  74.51   0.71     0.22      32614.91|
|alpha:            min =        0.22 max =            0.71 mean =         0.46|
|beta:             min =    32614.91 max =       126341.95 mean =     72597.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.98 mean =        59.09|
|phase err.(test): min =        0.00 max =           89.84 mean =        59.25|
|-----------------------------------------------------------------------------|

============================== 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 = 17.322606             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.054   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.701941              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.950   (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:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      672 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2574 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3828 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4966 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6469 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7613 |
|-----------------------------------------------------------------------------|
|-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 |       54.535 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.843 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    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 = 12.302)------------------------------------------|
|    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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5026   r_free= 0.4886   ksol= 0.00   Bsol= 0.00   scale= 0.740    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.297913                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4897   r_free= 0.4769   ksol= 0.30   Bsol= 20.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.79,9.29,11.29,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.290325                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.234438             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.864   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.445398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.653   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4897      final r-factor (work) = 0.4151          |
| start r-factor (free) = 0.4769      final r-factor (free) = 0.4379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.4808 = 15.23 * 0.50 * 6.2944 + 1.00 * 54.5347                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.5337 = 15.23 * 0.50 * 6.2204 + 1.00 * 0.1516                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4151      final r-factor (work) = 0.3732          |
| start r-factor (free) = 0.4379      final r-factor (free) = 0.4272          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0054 = 1.45 * 1.00 * 6.2204 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9114 = 1.45 * 1.00 * 6.1507 + 1.00 * 0.0212                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.49   15.11    None  None   None       |
|    all(noH): 2823   0      0.00    91.49   15.11    None  None   None       |
|    Sol.    : 438    0      0.00    91.49   27.11    None  None   None       |
|    Mac.    : 2385   0      0.00    72.03   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.149: 1138   |   5:    45.747 -  54.896:   67        |
|      1:     9.149 -  18.299:  815   |   6:    54.896 -  64.045:   28        |
|      2:    18.299 -  27.448:  432   |   7:    64.045 -  73.195:   15        |
|      3:    27.448 -  36.597:  226   |   8:    73.195 -  82.344:    5        |
|      4:    36.597 -  45.747:   94   |   9:    82.344 -  91.493:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3732 r_free = 0.4272             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3725 r_free = 0.4270             target_work(ml) = 6.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3725   r_free= 0.4270   ksol= 0.30   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.79,9.29,11.29,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.135230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3710   r_free= 0.4224   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.82,5.75,7.46,0.00,0.00,0.00); trace/3= 5.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.137372                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.510569              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.775  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554255              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.306  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3710      final r-factor (work) = 0.2937          |
| start r-factor (free) = 0.4224      final r-factor (free) = 0.3564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.3772 = 9.51 * 0.50 * 6.1459 + 1.00 * 0.1516                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8051 = 9.51 * 0.50 * 6.0369 + 1.00 * 0.0980                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2937      final r-factor (work) = 0.2737          |
| start r-factor (free) = 0.3564      final r-factor (free) = 0.3343          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3685 = 0.55 * 1.00 * 6.0369 + 1.00 * 0.0225                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3325 = 0.55 * 1.00 * 5.9268 + 1.00 * 0.0475                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    234.54  14.67    None  None   None       |
|    all(noH): 2823   0      0.00    234.54  14.67    None  None   None       |
|    Sol.    : 438    0      0.00    88.98   30.61    None  None   None       |
|    Mac.    : 2385   0      0.00    234.54  11.74    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 -  23.454: 2275   |   5:   117.272 - 140.726:    0        |
|      1:    23.454 -  46.909:  459   |   6:   140.726 - 164.180:    0        |
|      2:    46.909 -  70.363:   79   |   7:   164.180 - 187.635:    0        |
|      3:    70.363 -  93.817:    9   |   8:   187.635 - 211.089:    0        |
|      4:    93.817 - 117.272:    0   |   9:   211.089 - 234.543:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2737 r_free = 0.3343             target_work(ml) = 5.902         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2735 r_free = 0.3345             target_work(ml) = 5.901         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2735   r_free= 0.3345   ksol= 0.32   Bsol= 50.00   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.82,5.75,7.46,0.00,0.00,0.00); trace/3= 5.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.901224                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2721   r_free= 0.3337   ksol= 0.31   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,3.39,4.82,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.902220                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.016357              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.536  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.351528              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.174   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2721      final r-factor (work) = 0.2154          |
| start r-factor (free) = 0.3337      final r-factor (free) = 0.2620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0007 = 4.02 * 0.50 * 5.9271 + 1.00 * 0.0980                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7434 = 4.02 * 0.50 * 5.8094 + 1.00 * 0.0771                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2154      final r-factor (work) = 0.1886          |
| start r-factor (free) = 0.2620      final r-factor (free) = 0.2423          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8786 = 1.35 * 1.00 * 5.8094 + 1.00 * 0.0271                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6528 = 1.35 * 1.00 * 5.6313 + 1.00 * 0.0419                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    134.54  15.53    None  None   None       |
|    all(noH): 2823   0      0.00    134.54  15.53    None  None   None       |
|    Sol.    : 438    0      1.34    110.35  41.42    None  None   None       |
|    Mac.    : 2385   0      0.00    134.54  10.78    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 -  13.454: 1834   |   5:    67.272 -  80.726:   45        |
|      1:    13.454 -  26.909:  520   |   6:    80.726 -  94.180:   15        |
|      2:    26.909 -  40.363:  183   |   7:    94.180 - 107.635:    0        |
|      3:    40.363 -  53.817:  122   |   8:   107.635 - 121.089:    1        |
|      4:    53.817 -  67.272:  101   |   9:   121.089 - 134.543:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1886 r_free = 0.2423             target_work(ml) = 5.596         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1885 r_free = 0.2425             target_work(ml) = 5.596         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1885   r_free= 0.2425   ksol= 0.31   Bsol= 50.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,3.39,4.82,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.596139                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1881   r_free= 0.2421   ksol= 0.31   Bsol= 76.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.82,1.99,3.51,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.593842                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.879313              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.188   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.799605              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.112   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1881      final r-factor (work) = 0.1474          |
| start r-factor (free) = 0.2421      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8266 = 4.88 * 0.50 * 5.6358 + 1.00 * 0.0771                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4912 = 4.88 * 0.50 * 5.4965 + 1.00 * 0.0815                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1474      final r-factor (work) = 0.1385          |
| start r-factor (free) = 0.2016      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4344 = 0.80 * 1.00 * 5.4965 + 1.00 * 0.0393                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3056 = 0.80 * 1.00 * 5.3645 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.71  15.01    None  None   None       |
|    all(noH): 2823   0      0.00    116.71  15.01    None  None   None       |
|    Sol.    : 438    0      1.64    111.93  42.33    None  None   None       |
|    Mac.    : 2385   0      0.00    116.71  9.99     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 -  11.671: 1779   |   5:    58.354 -  70.024:   66        |
|      1:    11.671 -  23.342:  551   |   6:    70.024 -  81.695:   34        |
|      2:    23.342 -  35.012:  148   |   7:    81.695 -  93.366:   17        |
|      3:    35.012 -  46.683:  115   |   8:    93.366 - 105.037:    1        |
|      4:    46.683 -  58.354:  109   |   9:   105.037 - 116.707:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1385 r_free = 0.1891             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1384 r_free = 0.1890             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1890   ksol= 0.31   Bsol= 76.56   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.82,1.99,3.51,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.333128                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1888   ksol= 0.33   Bsol= 77.43   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,1.93,3.40,0.00,0.00,0.00); trace/3= 2.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.332935                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.970502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.449  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.925577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.809  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1384      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1888      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7326 = 3.97 * 0.50 * 5.3649 + 1.00 * 0.0819                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5951 = 3.97 * 0.50 * 5.2938 + 1.00 * 0.0857                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1749      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9157 = 0.93 * 1.00 * 5.2938 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8682 = 0.93 * 1.00 * 5.2426 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.72  14.60    None  None   None       |
|    all(noH): 2823   0      0.00    112.72  14.60    None  None   None       |
|    Sol.    : 438    0      1.83    112.72  41.61    None  None   None       |
|    Mac.    : 2385   0      0.00    107.07  9.64     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 -  11.272: 1807   |   5:    56.359 -  67.631:   73        |
|      1:    11.272 -  22.544:  521   |   6:    67.631 -  78.902:   37        |
|      2:    22.544 -  33.815:  142   |   7:    78.902 -  90.174:   18        |
|      3:    33.815 -  45.087:  119   |   8:    90.174 - 101.446:    6        |
|      4:    45.087 -  56.359:   97   |   9:   101.446 - 112.718:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1724             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1223 r_free = 0.1724             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1724   ksol= 0.33   Bsol= 77.43   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.03,1.93,3.40,0.00,0.00,0.00); trace/3= 2.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.234792                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1407  156 0.0996 0.1336      5.4123      5.5665|
|  2:  4.7744 -  3.8096 0.99   1359  153 0.0857 0.1079      5.4555      5.6755|
|  3:  3.8096 -  3.3340 0.99   1324  146 0.1123 0.1637      5.5279      5.9113|
|  4:  3.3340 -  3.0319 0.99   1315  139 0.1306 0.1812      5.5202      5.6977|
|  5:  3.0319 -  2.8160 0.99   1312  150 0.1494 0.1764      5.4397      5.5919|
|  6:  2.8160 -  2.6510 0.99   1313  145 0.1406 0.2344      5.3188      5.6375|
|  7:  2.6510 -  2.5188 0.99   1289  145 0.1442 0.1819      5.2902      5.4297|
|  8:  2.5188 -  2.4096 0.98   1291  145 0.1312 0.1814      5.1902      5.4261|
|  9:  2.4096 -  2.3172 0.98   1300  145 0.1346 0.2180      5.1294      5.4408|
| 10:  2.3172 -  2.2375 0.98   1276  136 0.1309 0.1699       5.077      5.2276|
| 11:  2.2375 -  2.1678 1.00   1301  148 0.1277 0.2048      5.0384      5.3742|
| 12:  2.1678 -  2.1060 0.97   1268  138 0.1263 0.1894      4.9746       5.277|
| 13:  2.1060 -  2.0507 0.98   1269  140 0.1202 0.1833      4.8573      5.0777|
| 14:  2.0507 -  2.0008 0.47    606   73 0.1106 0.1973      4.7344      5.0722|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1407   156  0.94   9.70   0.96     0.94       8089.84|
|  2:  4.7744 -  3.8096  1359   153  0.95   8.66   1.00     0.98       9789.51|
|  3:  3.8096 -  3.3340  1324   146  0.93  12.16   1.02     1.02      11497.35|
|  4:  3.3340 -  3.0319  1315   139  0.91  14.90   1.01     0.99      11907.13|
|  5:  3.0319 -  2.8160  1312   150  0.88  18.06   1.01     0.97      10373.08|
|  6:  2.8160 -  2.6510  1313   145  0.87  19.02   0.98     0.95       9049.08|
|  7:  2.6510 -  2.5188  1289   145  0.89  17.93   0.99     0.95       7985.08|
|  8:  2.5188 -  2.4096  1291   145  0.89  17.49   0.99     0.96       6877.32|
|  9:  2.4096 -  2.3172  1300   145  0.89  17.89   1.00     0.95       6101.46|
| 10:  2.3172 -  2.2375  1276   136  0.88  18.44   0.99     0.94       5575.57|
| 11:  2.2375 -  2.1678  1301   148  0.88  18.71   0.98     0.93       5444.45|
| 12:  2.1678 -  2.1060  1268   138  0.89  17.93   1.00     0.98       4945.17|
| 13:  2.1060 -  2.0507  1269   140  0.89  17.88   0.98     0.96       3954.59|
| 14:  2.0507 -  2.0008   606    73  0.90  15.82   0.95     0.91       2916.22|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2916.22 max =        11907.13 mean =      7680.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.97|
|phase err.(test): min =        0.00 max =           89.93 mean =        15.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1723   ksol= 0.33   Bsol= 71.97   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.25,1.22,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.234777                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1723   ksol= 0.33   Bsol= 71.97   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.25,1.22,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.234777                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1407  156 0.0992 0.1334        5.41      5.5652|
|  2:  4.7744 -  3.8096 0.99   1359  153 0.0853 0.1074      5.4527      5.6696|
|  3:  3.8096 -  3.3340 0.99   1324  146 0.1123 0.1640       5.527      5.9137|
|  4:  3.3340 -  3.0319 0.99   1315  139 0.1308 0.1814      5.5217      5.6988|
|  5:  3.0319 -  2.8160 0.99   1312  150 0.1495 0.1765      5.4411       5.593|
|  6:  2.8160 -  2.6510 0.99   1313  145 0.1407 0.2347      5.3197      5.6385|
|  7:  2.6510 -  2.5188 0.99   1289  145 0.1443 0.1823      5.2912      5.4311|
|  8:  2.5188 -  2.4096 0.98   1291  145 0.1314 0.1813       5.191      5.4268|
|  9:  2.4096 -  2.3172 0.98   1300  145 0.1345 0.2180      5.1298      5.4416|
| 10:  2.3172 -  2.2375 0.98   1276  136 0.1309 0.1700      5.0773      5.2286|
| 11:  2.2375 -  2.1678 1.00   1301  148 0.1277 0.2042      5.0383      5.3733|
| 12:  2.1678 -  2.1060 0.97   1268  138 0.1263 0.1891      4.9744      5.2758|
| 13:  2.1060 -  2.0507 0.98   1269  140 0.1202 0.1835      4.8571      5.0782|
| 14:  2.0507 -  2.0008 0.47    606   73 0.1107 0.1965      4.7351      5.0707|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1407   156  0.94   9.68   0.96     0.94       8064.51|
|  2:  4.7744 -  3.8096  1359   153  0.95   8.61   1.01     0.98       9729.51|
|  3:  3.8096 -  3.3340  1324   146  0.93  12.12   1.03     1.02      11448.70|
|  4:  3.3340 -  3.0319  1315   139  0.91  14.91   1.01     1.00      11930.84|
|  5:  3.0319 -  2.8160  1312   150  0.88  18.08   1.01     0.98      10408.86|
|  6:  2.8160 -  2.6510  1313   145  0.87  19.04   0.98     0.95       9063.24|
|  7:  2.6510 -  2.5188  1289   145  0.89  17.95   0.99     0.95       8004.16|
|  8:  2.5188 -  2.4096  1291   145  0.89  17.51   0.99     0.96       6888.89|
|  9:  2.4096 -  2.3172  1300   145  0.89  17.91   1.00     0.95       6116.00|
| 10:  2.3172 -  2.2375  1276   136  0.88  18.45   1.00     0.95       5576.47|
| 11:  2.2375 -  2.1678  1301   148  0.88  18.71   0.99     0.93       5444.01|
| 12:  2.1678 -  2.1060  1268   138  0.89  17.93   1.01     0.99       4943.07|
| 13:  2.1060 -  2.0507  1269   140  0.89  17.86   0.99     0.96       3950.92|
| 14:  2.0507 -  2.0008   606    73  0.90  15.81   0.96     0.92       2912.65|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2912.65 max =        11930.84 mean =      7678.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.97|
|phase err.(test): min =        0.00 max =           89.99 mean =        15.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.302)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.25    114.96  16.84    None  None   None       |
|    all(noH): 2823   0      2.25    114.96  16.84    None  None   None       |
|    Sol.    : 438    0      4.08    114.96  43.85    None  None   None       |
|    Mac.    : 2385   0      2.25    109.31  11.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.245 -  13.517: 1807   |   5:    58.604 -  69.876:   73        |
|      1:    13.517 -  24.789:  521   |   6:    69.876 -  81.148:   37        |
|      2:    24.789 -  36.061:  142   |   7:    81.148 -  92.420:   18        |
|      3:    36.061 -  47.332:  119   |   8:    92.420 - 103.691:    6        |
|      4:    47.332 -  58.604:   97   |   9:   103.691 - 114.963:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.166 - 5.402
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 333
   mapped sites are within: 0.726 - 5.402

peak=   10.361 closest distance to " CB  VAL A 230 " =    1.435
peak=    6.036 closest distance to " O   HOH Z 210 " =    1.358
peak=    5.663 closest distance to " CD1AILE A 234 " =    1.143
peak=    5.493 closest distance to " CG1 VAL A 296 " =    1.184
peak=    5.399 closest distance to " NH2 ARG A  56 " =    2.155
peak=    5.367 closest distance to " CB  GLN A 223 " =    1.512
peak=    5.209 closest distance to " CG  LEU A   5 " =    1.184
peak=    5.088 closest distance to " NE2 GLN A  11 " =    1.108
peak=    4.852 closest distance to " CA  TYR A  30 " =    0.986
peak=    4.787 closest distance to " CG  LEU A 228 " =    1.278
peak=    4.780 closest distance to " O   HOH Z 248 " =    1.274
peak=    4.712 closest distance to " O   HOH Z 126 " =    1.658
peak=    4.697 closest distance to " CB  SER A  63 " =    1.179
peak=    4.691 closest distance to " CB  VAL A 296 " =    1.094
peak=    4.620 closest distance to " O   HOH Z 251 " =    1.814
peak=    4.611 closest distance to " O   HOH Z 128 " =    1.497
peak=    4.585 closest distance to " O   HOH Z 142 " =    1.741
peak=    4.575 closest distance to " O   HOH Z 425 " =    1.607
peak=    4.526 closest distance to " O   HOH Z 431 " =    1.191
peak=    4.493 closest distance to " CD2 LEU A   5 " =    1.095
peak=    4.476 closest distance to " O   HOH Z  49 " =    1.502
peak=    4.469 closest distance to " CZ  PHE A 218 " =    1.175
peak=    4.453 closest distance to " O   PRO A 198 " =    1.588
peak=    4.440 closest distance to " O   HOH Z 232 " =    2.195
peak=    4.436 closest distance to " CG  PRO A  54 " =    1.300
peak=    4.434 closest distance to " O   HOH Z 154 " =    1.717
peak=    4.422 closest distance to " CB  GLN A 183 " =    1.249
peak=    4.401 closest distance to " CA  ALA A 295 " =    0.962
peak=    4.394 closest distance to " CG  ARG A  66 " =    2.577
peak=    4.380 closest distance to " O   HOH Z 403 " =    1.788
peak=    4.350 closest distance to " CZ3 TRP A 266 " =    1.095
peak=    4.342 closest distance to " CD2 TRP A 179 " =    1.279
peak=    4.324 closest distance to " CB  ARG A 275 " =    0.940
peak=    4.311 closest distance to " O   HOH Z 214 " =    1.538
peak=    4.298 closest distance to " CA  ALA A  51 " =    1.000
peak=    4.286 closest distance to " CB  ASN A 142 " =    1.197
peak=    4.272 closest distance to " O   HOH Z 411 " =    3.931
peak=    4.266 closest distance to " CG  PRO A 280 " =    0.924
peak=    4.252 closest distance to " O   HOH Z 359 " =    1.980
peak=    4.223 closest distance to " O   HOH Z  76 " =    1.256
peak=    4.171 closest distance to " O   HOH Z 365 " =    2.366
peak=    4.158 closest distance to " CB  ARG A 190 " =    1.667
peak=    4.113 closest distance to " O   HOH Z 369 " =    2.136
peak=    4.100 closest distance to " CG2 VAL A 296 " =    1.004
peak=    4.094 closest distance to " CD2 LEU A 228 " =    1.277
peak=    4.075 closest distance to " CB  GLU A 277 " =    3.787
peak=    4.036 closest distance to " O   HOH Z 346 " =    1.446
peak=    4.030 closest distance to " CB  TRP A 179 " =    1.380
peak=    4.010 closest distance to " O   SER A  87 " =    2.353
peak=    4.008 closest distance to " O   HOH Z  63 " =    1.892
peak=    3.988 closest distance to " CA  TYR A 116 " =    1.368
peak=    3.976 closest distance to " CA  ALA A 160 " =    0.973
peak=    3.966 closest distance to " O   HOH Z 238 " =    1.071
peak=    3.959 closest distance to " O   HOH Z 433 " =    1.576
peak=    3.946 closest distance to " O   HOH Z  30 " =    1.042
peak=    3.940 closest distance to " CG  PRO A 198 " =    1.422
peak=    3.919 closest distance to " O   HOH Z 265 " =    2.027
peak=    3.907 closest distance to " O   HOH Z 130 " =    1.109
peak=    3.903 closest distance to " O   HOH Z 406 " =    1.535
peak=    3.883 closest distance to " O   HOH Z 422 " =    2.608
peak=    3.883 closest distance to " CG2AVAL A 121 " =    2.154
peak=    3.869 closest distance to " O   ASP A 124 " =    1.220
peak=    3.864 closest distance to " O   HOH Z 313 " =    1.720
peak=    3.859 closest distance to " O   HOH Z 280 " =    2.928
peak=    3.855 closest distance to " OG  SER A 245 " =    1.607
peak=    3.836 closest distance to " CD1 LEU A  96 " =    0.838
peak=    3.829 closest distance to " O   HOH Z 423 " =    1.828
peak=    3.821 closest distance to " CB  VAL A 202 " =    1.483
peak=    3.819 closest distance to " CG  PRO A 243 " =    1.134
peak=    3.813 closest distance to " CB  GLU A 128 " =    1.155
peak=    3.813 closest distance to " CG AARG A 275 " =    1.218
peak=    3.810 closest distance to " OE1 GLN A  88 " =    0.875
peak=    3.808 closest distance to " CB  VAL A 265 " =    1.184
peak=    3.803 closest distance to " O   HOH Z 303 " =    2.345
peak=    3.803 closest distance to " O   HOH Z 402 " =    1.437
peak=    3.774 closest distance to " O   HOH Z 142 " =    2.350
peak=    3.770 closest distance to " CA  GLY A 267 " =    0.992
peak=    3.767 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.763 closest distance to " CG2 ILE A 234 " =    1.099
peak=    3.760 closest distance to " O   HOH Z 234 " =    3.620
peak=    3.757 closest distance to " CB  GLU A 152 " =    1.148
peak=    3.751 closest distance to " CA  ARG A  36 " =    1.041
peak=    3.737 closest distance to " O  BHOH Z 338 " =    2.262
peak=    3.737 closest distance to " O   HOH Z 174 " =    2.392
peak=    3.733 closest distance to " O   HOH Z  43 " =    2.019
peak=    3.732 closest distance to " O   HOH Z 427 " =    2.967
peak=    3.730 closest distance to " NH1AARG A 145 " =    1.293
peak=    3.726 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.724 closest distance to " O   HOH Z 214 " =    2.735
peak=    3.724 closest distance to " O   HOH Z 199 " =    1.616
peak=    3.720 closest distance to " CB AVAL A  41 " =    1.275
peak=    3.715 closest distance to " NE2 GLN A  77 " =    3.306
peak=    3.709 closest distance to " CD  LYS A 166 " =    1.372
peak=    3.700 closest distance to " CB  THR A  52 " =    0.912
peak=    3.683 closest distance to " CA  ILE A 106 " =    0.823
peak=    3.680 closest distance to " CB  ASN A 148 " =    1.447
peak=    3.675 closest distance to " CG  MET A 185 " =    1.233
peak=    3.673 closest distance to " CB  ASP A 124 " =    0.767
peak=    3.671 closest distance to " O   HOH Z 417 " =    3.066
peak=    3.670 closest distance to " OG BSER A 164 " =    2.262
peak=    3.668 closest distance to " O   HOH Z 361 " =    3.421
peak=    3.661 closest distance to " CB  VAL A 230 " =    1.226
peak=    3.659 closest distance to " CG  PRO A 213 " =    1.211
peak=    3.659 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.658 closest distance to " CB  PRO A  54 " =    0.887
peak=    3.657 closest distance to " CG2 VAL A 197 " =    1.070
peak=    3.647 closest distance to " O   HOH Z   5 " =    1.655
peak=    3.647 closest distance to " CB  TRP A 266 " =    1.050
peak=    3.644 closest distance to " O   HOH Z 188 " =    3.015
peak=    3.643 closest distance to " CG2 THR A 221 " =    1.180
peak=    3.642 closest distance to " O   HOH Z  56 " =    1.699
peak=    3.633 closest distance to " O   HOH Z 287 " =    1.733
peak=    3.628 closest distance to " CA  SER A  87 " =    0.973
peak=    3.627 closest distance to " CB  ARG A  79 " =    1.405
peak=    3.625 closest distance to " O   HOH Z 247 " =    1.342
peak=    3.624 closest distance to " O   HOH Z   4 " =    1.611
peak=    3.623 closest distance to " CA  ARG A 195 " =    1.153
peak=    3.613 closest distance to " CA  LYS A 117 " =    1.255
peak=    3.608 closest distance to " CD  LYS A 119 " =    1.833
peak=    3.604 closest distance to " NZ  LYS A  48 " =    1.343
peak=    3.602 closest distance to " CG  GLN A  58 " =    0.941
peak=    3.598 closest distance to " CG1 ILE A  49 " =    1.764
peak=    3.592 closest distance to " CG  GLU A  37 " =    0.968
peak=    3.591 closest distance to " O   HOH Z 203 " =    1.815
peak=    3.587 closest distance to " O   HOH Z 193 " =    1.657
peak=    3.580 closest distance to " O   ASP A 200 " =    1.659
peak=    3.576 closest distance to " CA  VAL A 125 " =    1.185
peak=    3.572 closest distance to " ND2 ASN A 187 " =    1.701
peak=    3.562 closest distance to " O   HOH Z 394 " =    1.512
peak=    3.562 closest distance to " OG BSER A 134 " =    2.871
peak=    3.561 closest distance to " CD  PRO A  54 " =    1.002
peak=    3.557 closest distance to " O   ALA A 165 " =    1.300
peak=    3.538 closest distance to " CB  ALA A   9 " =    1.670
peak=    3.535 closest distance to " CB  PRO A  90 " =    1.255
peak=    3.532 closest distance to " O   HOH Z  78 " =    1.703
peak=    3.530 closest distance to " CB  ASN A 215 " =    1.287
peak=    3.530 closest distance to " CG1 ILE A  20 " =    1.276
peak=    3.528 closest distance to " O   HOH Z  48 " =    1.693
peak=    3.526 closest distance to " CB  TYR A 169 " =    0.789
peak=    3.521 closest distance to " CB  GLU A  46 " =    0.937
peak=    3.520 closest distance to " O   HOH Z 193 " =    2.024
peak=    3.517 closest distance to " CA  ALA A  21 " =    1.225
peak=    3.516 closest distance to " NH2AARG A 275 " =    3.233
peak=    3.516 closest distance to " CA  ALA A 291 " =    0.915
peak=    3.514 closest distance to " O   HOH Z 133 " =    1.503
peak=    3.513 closest distance to " O   HOH Z 420 " =    5.402
peak=    3.511 closest distance to " O   HOH Z 391 " =    2.877
peak=    3.503 closest distance to " CD1 ILE A 199 " =    1.150
peak=    3.498 closest distance to " O   HOH Z 393 " =    3.713
peak=    3.496 closest distance to " O   HOH Z 393 " =    3.220
peak=    3.496 closest distance to " CB  GLN A  89 " =    1.174
peak=    3.491 closest distance to " NH2AARG A 145 " =    1.105
peak=    3.487 closest distance to " CA  VAL A  41 " =    0.814
peak=    3.487 closest distance to " CA  LEU A 282 " =    1.117
peak=    3.485 closest distance to " O   HOH Z 107 " =    0.953
peak=    3.485 closest distance to " O   HOH Z 316 " =    3.161
peak=    3.483 closest distance to " OD1 ASN A  69 " =    2.536
peak=    3.478 closest distance to " CB  ASP A 298 " =    1.198
peak=    3.476 closest distance to " OD2 ASP A 298 " =    3.809
peak=    3.468 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.466 closest distance to " O   HOH Z   9 " =    1.079
peak=    3.463 closest distance to " O   HOH Z 368 " =    4.092
peak=    3.462 closest distance to " O   HOH Z  83 " =    1.530
peak=    3.457 closest distance to " O   HOH Z 368 " =    2.025
peak=    3.455 closest distance to " O   HOH Z 213 " =    1.763
peak=    3.455 closest distance to " CD  ARG A 269 " =    0.953
peak=    3.452 closest distance to " O   HOH Z  19 " =    1.954
peak=    3.444 closest distance to " CZ  PHE A  38 " =    1.186
peak=    3.442 closest distance to " CB  SER A   3 " =    1.528
peak=    3.436 closest distance to " CB  ASP A 140 " =    1.022
peak=    3.436 closest distance to " O   HOH Z 154 " =    2.250
peak=    3.435 closest distance to " CG AARG A 102 " =    1.270
peak=    3.431 closest distance to " O   HOH Z 299 " =    4.363
peak=    3.428 closest distance to " CZ3 TRP A  85 " =    0.951
peak=    3.428 closest distance to " O  BHOH Z  74 " =    1.236
peak=    3.426 closest distance to " O   HOH Z  63 " =    1.432
peak=    3.421 closest distance to " CB  PRO A 280 " =    1.221
peak=    3.418 closest distance to " CB  SER A  26 " =    1.832
peak=    3.414 closest distance to " CA  MET A 105 " =    1.054
peak=    3.413 closest distance to " OG  SER A 276 " =    1.388
peak=    3.410 closest distance to " O   ASN A  74 " =    1.415
peak=    3.407 closest distance to " O   HOH Z 365 " =    2.670
peak=    3.394 closest distance to " CG  ARG A 138 " =    1.284
peak=    3.393 closest distance to " CB  ASN A 110 " =    1.179
peak=    3.391 closest distance to " O   HOH Z  80 " =    1.901
peak=    3.391 closest distance to " CA  GLY A 211 " =    1.375
peak=    3.388 closest distance to " CA  GLU A 152 " =    0.938
peak=    3.386 closest distance to " O   HOH Z  44 " =    2.074
peak=    3.382 closest distance to " CA  ALA A 100 " =    0.974
peak=    3.381 closest distance to " O   HOH Z 146 " =    1.582
peak=    3.380 closest distance to " OG  SER A 135 " =    1.308
peak=    3.378 closest distance to " O   HOH Z 130 " =    2.203
peak=    3.378 closest distance to " CB  THR A 235 " =    1.309
peak=    3.378 closest distance to " CD  ARG A 195 " =    0.987
peak=    3.378 closest distance to " CG  PHE A 204 " =    0.909
peak=    3.377 closest distance to " O   HOH Z 117 " =    1.153
peak=    3.377 closest distance to " CB  SER A 288 " =    1.545
peak=    3.375 closest distance to " O   HOH Z 189 " =    2.931
peak=    3.367 closest distance to " O   HOH Z 193 " =    1.341
peak=    3.363 closest distance to " CB  GLN A  88 " =    1.232
peak=    3.355 closest distance to " CD2 TYR A 186 " =    1.010
peak=    3.354 closest distance to " O   HOH Z 158 " =    3.207
peak=    3.352 closest distance to " CB  ALA A 248 " =    1.034
peak=    3.350 closest distance to " O   HOH Z 258 " =    1.875
peak=    3.347 closest distance to " O   HOH Z   3 " =    1.979
peak=    3.340 closest distance to " O   HOH Z 176 " =    1.548
peak=    3.338 closest distance to " O   HOH Z  44 " =    2.578
peak=    3.338 closest distance to " O   HOH Z 126 " =    1.874
peak=    3.336 closest distance to " CB  ALA A  10 " =    1.255
peak=    3.335 closest distance to " ND2 ASN A 249 " =    1.948
peak=    3.334 closest distance to " O   ASP A 124 " =    1.792
peak=    3.330 closest distance to " N   ASN A  39 " =    1.249
peak=    3.327 closest distance to " CG  LEU A 167 " =    1.128
peak=    3.327 closest distance to " O   HOH Z  88 " =    3.294
peak=    3.321 closest distance to " CB  ALA A 291 " =    1.188
peak=    3.320 closest distance to " CG  MET A 188 " =    0.867
peak=    3.317 closest distance to " O   THR A 182 " =    1.468
peak=    3.315 closest distance to " O   HOH Z 407 " =    2.461
peak=    3.313 closest distance to " O   HOH Z 327 " =    2.320
peak=    3.312 closest distance to " CE3 TRP A  85 " =    1.084
peak=    3.309 closest distance to " O   GLU A   2 " =    1.526
peak=    3.308 closest distance to " CB  SER A 216 " =    0.951
peak=    3.308 closest distance to " CB  PHE A 204 " =    1.030
peak=    3.308 closest distance to " CB  TYR A 247 " =    1.059
peak=    3.304 closest distance to " CZ3 TRP A 274 " =    4.482
peak=    3.303 closest distance to " CD1 ILE A  33 " =    1.691
peak=    3.301 closest distance to " CD1 LEU A 300 " =    1.072
peak=    3.299 closest distance to " O   HOH Z 285 " =    2.133
peak=    3.295 closest distance to " O   HOH Z 383 " =    1.859
peak=    3.295 closest distance to " O   HOH Z 371 " =    2.448
peak=    3.293 closest distance to " CB  ASP A 107 " =    1.146
peak=    3.292 closest distance to " O   HOH Z 437 " =    1.543
peak=    3.291 closest distance to " CA  ASP A 162 " =    0.981
peak=    3.290 closest distance to " CA  ASN A 217 " =    1.150
peak=    3.287 closest distance to " O   HOH Z 408 " =    3.157
peak=    3.277 closest distance to " O   HOH Z 124 " =    1.131
peak=    3.276 closest distance to " N   VAL A 126 " =    1.465
peak=    3.276 closest distance to " CE3 TRP A 150 " =    1.160
peak=    3.275 closest distance to " CD  GLN A  73 " =    1.188
peak=    3.273 closest distance to " CA  ARG A 156 " =    1.140
peak=    3.271 closest distance to " O   HOH Z 361 " =    2.673
peak=    3.271 closest distance to " CD  LYS A  76 " =    2.086
peak=    3.269 closest distance to " CG1 ILE A  33 " =    1.198
peak=    3.269 closest distance to " CA  ARG A 102 " =    1.174
peak=    3.265 closest distance to " O   HOH Z 298 " =    1.858
peak=    3.263 closest distance to " O   HOH Z 336 " =    1.830
peak=    3.259 closest distance to " O   HOH Z 279 " =    2.307
peak=    3.258 closest distance to " O   HOH Z  63 " =    0.992
peak=    3.256 closest distance to " O   HOH Z 345 " =    1.769
peak=    3.256 closest distance to " CB  TRP A 179 " =    1.549
peak=    3.255 closest distance to " CD2 LEU A 255 " =    1.685
peak=    3.251 closest distance to " CD1 LEU A   5 " =    1.346
peak=    3.248 closest distance to " CG1 VAL A 153 " =    0.996
peak=    3.247 closest distance to " O   HOH Z 134 " =    1.181
peak=    3.246 closest distance to " O   HOH Z 298 " =    2.392
peak=    3.242 closest distance to " O   HOH Z 293 " =    2.006
peak=    3.241 closest distance to " CA  GLN A  94 " =    0.759
peak=    3.241 closest distance to " CG1 VAL A 174 " =    1.294
peak=    3.235 closest distance to " O   HOH Z 353 " =    2.702
peak=    3.235 closest distance to " O   HOH Z 180 " =    2.215
peak=    3.234 closest distance to " O   HOH Z  47 " =    2.698
peak=    3.233 closest distance to " O   PRO A 213 " =    1.397
peak=    3.230 closest distance to " O   HOH Z 285 " =    2.222
peak=    3.230 closest distance to " N   PHE A 130 " =    1.346
peak=    3.228 closest distance to " CB  MET A  40 " =    0.922
peak=    3.228 closest distance to " NH2 ARG A  36 " =    1.657
peak=    3.225 closest distance to " CB  MET A 105 " =    1.135
peak=    3.224 closest distance to " CA  ASN A 127 " =    1.193
peak=    3.223 closest distance to " O   HOH Z 250 " =    1.335
peak=    3.222 closest distance to " CA  ARG A 139 " =    1.279
peak=    3.220 closest distance to " ND2AASN A 224 " =    0.849
peak=    3.211 closest distance to " OG BSER A 258 " =    3.376
peak=    3.209 closest distance to " O   HOH Z   1 " =    2.489
peak=    3.208 closest distance to " CA  SER A  12 " =    1.400
peak=    3.207 closest distance to " O   HOH Z 207 " =    1.207
peak=    3.196 closest distance to " O   HOH Z 116 " =    1.836
peak=    3.196 closest distance to " NH1 ARG A  14 " =    1.100
peak=    3.196 closest distance to " O   HOH Z 133 " =    2.557
peak=    3.196 closest distance to " CA  ALA A 154 " =    1.048
peak=    3.195 closest distance to " O   HOH Z 272 " =    1.838
peak=    3.194 closest distance to " O   HOH Z 357 " =    2.199
peak=    3.192 closest distance to " O   HOH Z 211 " =    0.977
peak=    3.189 closest distance to " CA  ASP A 140 " =    1.335
peak=    3.186 closest distance to " NZ  LYS A 117 " =    1.246
peak=    3.184 closest distance to " CD1 LEU A 101 " =    1.135
peak=    3.182 closest distance to " CG2 VAL A 126 " =    0.846
peak=    3.179 closest distance to " CB  SER A  62 " =    0.926
peak=    3.178 closest distance to " O   HOH Z 291 " =    1.373
peak=    3.176 closest distance to " CA  CYS A 260 " =    1.530
peak=    3.175 closest distance to " O   ALA A 158 " =    1.206
peak=    3.173 closest distance to " CB  TYR A  30 " =    1.124
peak=    3.163 closest distance to " O   ASN A 209 " =    1.265
peak=    3.163 closest distance to " O   HOH Z 151 " =    1.719
peak=    3.157 closest distance to " CB  ALA A 100 " =    1.393
peak=    3.155 closest distance to " O   HOH Z 394 " =    3.796
peak=    3.148 closest distance to " O   THR A 251 " =    1.079
peak=    3.145 closest distance to " O   HOH Z 147 " =    1.728
peak=    3.141 closest distance to " CG1AVAL A 121 " =    0.801
peak=    3.140 closest distance to " CD1 LEU A 228 " =    1.482
peak=    3.135 closest distance to " O   HOH Z 419 " =    1.708
peak=    3.132 closest distance to " O   HOH Z 125 " =    3.919
peak=    3.130 closest distance to " CB  LEU A  83 " =    0.726
peak=    3.129 closest distance to " CB  ALA A 248 " =    1.307
peak=    3.127 closest distance to " O   HOH Z  40 " =    1.763
peak=    3.127 closest distance to " CB  SER A  97 " =    0.989
peak=    3.127 closest distance to " O   HOH Z 148 " =    3.230
peak=    3.127 closest distance to " CB  ALA A  43 " =    0.906
peak=    3.105 closest distance to " CZ3 TRP A  92 " =    1.252
peak=    3.104 closest distance to " O   HOH Z 163 " =    1.455
peak=    3.104 closest distance to " NE2 GLN A  58 " =    4.644
peak=    3.102 closest distance to " O   HOH Z 162 " =    1.304
peak=    3.101 closest distance to " CB  PRO A 243 " =    1.358
peak=    3.099 closest distance to " CG  GLN A  77 " =    0.817
peak=    3.095 closest distance to " OG  SER A  62 " =    2.898
peak=    3.094 closest distance to " O   HOH Z 117 " =    1.783
peak=    3.091 closest distance to " NE2 HIS A 115 " =    1.011
peak=    3.079 closest distance to " CA  ALA A 104 " =    0.918
peak=    3.078 closest distance to " CA  GLY A 133 " =    3.686
peak=    3.078 closest distance to " CB  ALA A 242 " =    0.880
peak=    3.077 closest distance to " O   HOH Z 102 " =    1.288
peak=    3.077 closest distance to " CB  PHE A 283 " =    0.839
peak=    3.063 closest distance to " O   HOH Z 329 " =    4.185
peak=    3.054 closest distance to " CB  ALA A  34 " =    0.857
peak=    3.048 closest distance to " O   HOH Z 109 " =    2.546
peak=    3.047 closest distance to " O   HOH Z 156 " =    2.632
peak=    3.045 closest distance to " CG  GLN A  58 " =    3.083
peak=    3.025 closest distance to " CB  ASN A 148 " =    2.026

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.777 - 5.785
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 219
   mapped sites are within: 0.777 - 5.785

peak=   -4.929 closest distance to " CG2 VAL A 230 " =    0.777
peak=   -4.486 closest distance to " CG1 VAL A 296 " =    1.106
peak=   -4.448 closest distance to " CB  PRO A 243 " =    2.808
peak=   -4.420 closest distance to " SG  CYS A 254 " =    3.352
peak=   -4.396 closest distance to " O   HOH Z 193 " =    0.843
peak=   -4.377 closest distance to " CG2 ILE A  49 " =    2.871
peak=   -4.347 closest distance to " CG1 VAL A 250 " =    2.742
peak=   -4.313 closest distance to " CA  ASP A 298 " =    1.063
peak=   -4.309 closest distance to " O   HOH Z 196 " =    2.350
peak=   -4.215 closest distance to " O   VAL A  67 " =    2.754
peak=   -4.196 closest distance to " O   HOH Z 211 " =    1.002
peak=   -4.157 closest distance to " CD  GLN A  58 " =    1.056
peak=   -4.107 closest distance to " CE2 PHE A  61 " =    2.644
peak=   -4.080 closest distance to " O   HOH Z  10 " =    1.696
peak=   -4.039 closest distance to " O   HOH Z 283 " =    2.609
peak=   -4.033 closest distance to " O   PRO A 198 " =    1.304
peak=   -4.031 closest distance to " O   HOH Z  37 " =    1.941
peak=   -4.024 closest distance to " CE2 TYR A  30 " =    2.650
peak=   -4.020 closest distance to " O   HOH Z 411 " =    5.591
peak=   -3.981 closest distance to " OG BSER A 134 " =    1.464
peak=   -3.970 closest distance to " O   HOH Z 166 " =    1.692
peak=   -3.959 closest distance to " C   HIS A 108 " =    1.243
peak=   -3.957 closest distance to " ND2BASN A 224 " =    1.914
peak=   -3.950 closest distance to " CD  ARG A 156 " =    2.131
peak=   -3.914 closest distance to " CG2 VAL A 189 " =    2.048
peak=   -3.885 closest distance to " O   HOH Z 166 " =    1.584
peak=   -3.883 closest distance to " CE2 TRP A  70 " =    2.263
peak=   -3.882 closest distance to " CG  ARG A 269 " =    2.329
peak=   -3.880 closest distance to " CE3 TRP A 150 " =    2.313
peak=   -3.875 closest distance to " OXT GLY A 302 " =    3.004
peak=   -3.868 closest distance to " CD1 PHE A  59 " =    2.118
peak=   -3.866 closest distance to " CD  PRO A 243 " =    1.972
peak=   -3.859 closest distance to " CD2 TYR A 293 " =    1.955
peak=   -3.854 closest distance to " CD1 LEU A 101 " =    2.379
peak=   -3.850 closest distance to " O   HOH Z 340 " =    1.585
peak=   -3.850 closest distance to " CH2 TRP A 179 " =    1.192
peak=   -3.847 closest distance to " O   PRO A 163 " =    2.137
peak=   -3.806 closest distance to " O   HOH Z 285 " =    2.085
peak=   -3.780 closest distance to " CG  GLN A 103 " =    2.501
peak=   -3.777 closest distance to " CD2 PHE A  61 " =    2.136
peak=   -3.765 closest distance to " CG  PRO A 243 " =    1.667
peak=   -3.761 closest distance to " O   HOH Z 431 " =    2.227
peak=   -3.754 closest distance to " CG1 VAL A 112 " =    2.727
peak=   -3.737 closest distance to " O   HOH Z 351 " =    1.660
peak=   -3.736 closest distance to " OG  SER A  97 " =    2.354
peak=   -3.734 closest distance to " O   HOH Z 231 " =    2.332
peak=   -3.728 closest distance to " O   HOH Z  68 " =    1.629
peak=   -3.726 closest distance to " O   SER A 271 " =    2.026
peak=   -3.698 closest distance to " N   ALA A  43 " =    2.717
peak=   -3.666 closest distance to " CZ  TYR A 169 " =    1.846
peak=   -3.662 closest distance to " O   HOH Z  19 " =    2.418
peak=   -3.651 closest distance to " O   HOH Z 216 " =    1.028
peak=   -3.641 closest distance to " O   HOH Z 200 " =    1.620
peak=   -3.624 closest distance to " O   HOH Z 154 " =    1.340
peak=   -3.624 closest distance to " O   HOH Z 128 " =    2.651
peak=   -3.613 closest distance to " N   SER A 276 " =    1.535
peak=   -3.603 closest distance to " OD1 ASN A 148 " =    1.440
peak=   -3.603 closest distance to " CG2BVAL A  41 " =    1.768
peak=   -3.588 closest distance to " OE1 GLN A 223 " =    2.213
peak=   -3.579 closest distance to " O   ALA A  34 " =    2.564
peak=   -3.577 closest distance to " O   HOH Z 177 " =    1.940
peak=   -3.570 closest distance to " CB  ALA A  10 " =    2.299
peak=   -3.569 closest distance to " OD1 ASN A 173 " =    1.401
peak=   -3.564 closest distance to " O   TYR A 186 " =    1.850
peak=   -3.562 closest distance to " O   HOH Z 348 " =    2.225
peak=   -3.559 closest distance to " CA  GLY A 203 " =    2.398
peak=   -3.554 closest distance to " CE3 TRP A  70 " =    1.886
peak=   -3.546 closest distance to " O   HOH Z 102 " =    1.684
peak=   -3.545 closest distance to " O   HOH Z 394 " =    1.699
peak=   -3.539 closest distance to " O   HOH Z  78 " =    1.927
peak=   -3.537 closest distance to " O   HOH Z  52 " =    1.751
peak=   -3.530 closest distance to " CG1 VAL A 112 " =    2.700
peak=   -3.524 closest distance to " CB  ALA A 161 " =    2.577
peak=   -3.521 closest distance to " O   HOH Z 149 " =    2.021
peak=   -3.518 closest distance to " O   HOH Z 131 " =    4.035
peak=   -3.518 closest distance to " CG  GLU A 277 " =    1.261
peak=   -3.516 closest distance to " O   HOH Z 275 " =    1.645
peak=   -3.516 closest distance to " CB  VAL A 230 " =    1.095
peak=   -3.515 closest distance to " CD  GLN A  88 " =    0.892
peak=   -3.514 closest distance to " NH2 ARG A  79 " =    2.212
peak=   -3.509 closest distance to " O   HOH Z 174 " =    2.057
peak=   -3.496 closest distance to " NH1 ARG A 195 " =    1.045
peak=   -3.494 closest distance to " CG2 THR A 182 " =    2.325
peak=   -3.487 closest distance to " C   LEU A 143 " =    1.125
peak=   -3.485 closest distance to " O   HOH Z 171 " =    2.398
peak=   -3.483 closest distance to " O   HOH Z 136 " =    2.672
peak=   -3.480 closest distance to " CG1BVAL A  72 " =    2.599
peak=   -3.478 closest distance to " O   HOH Z 423 " =    2.367
peak=   -3.470 closest distance to " O   HOH Z 407 " =    2.902
peak=   -3.461 closest distance to " O   HOH Z 377 " =    2.039
peak=   -3.459 closest distance to " O   HOH Z 156 " =    3.493
peak=   -3.458 closest distance to " O   VAL A 189 " =    1.900
peak=   -3.455 closest distance to " CZ  PHE A  38 " =    2.415
peak=   -3.447 closest distance to " O   HOH Z  13 " =    1.952
peak=   -3.442 closest distance to " O   HOH Z 378 " =    1.612
peak=   -3.439 closest distance to " CG2 THR A 178 " =    2.356
peak=   -3.434 closest distance to " O   HOH Z 198 " =    1.772
peak=   -3.433 closest distance to " CD1 ILE A 151 " =    2.490
peak=   -3.429 closest distance to " O   HOH Z 107 " =    0.970
peak=   -3.418 closest distance to " NH2 ARG A 159 " =    2.374
peak=   -3.417 closest distance to " NE2 GLN A  11 " =    1.630
peak=   -3.409 closest distance to " O   ARG A  56 " =    3.947
peak=   -3.405 closest distance to " CB  ALA A 248 " =    2.318
peak=   -3.397 closest distance to " CG  MET A 105 " =    1.006
peak=   -3.393 closest distance to " CG  GLU A  53 " =    1.577
peak=   -3.392 closest distance to " O   GLY A  17 " =    1.194
peak=   -3.390 closest distance to " O   HOH Z 384 " =    2.161
peak=   -3.388 closest distance to " O   HOH Z 236 " =    1.582
peak=   -3.386 closest distance to " NE2 GLN A 103 " =    1.635
peak=   -3.384 closest distance to " O   HOH Z  40 " =    3.007
peak=   -3.382 closest distance to " O   HOH Z  69 " =    1.633
peak=   -3.382 closest distance to " CG2 ILE A  20 " =    3.020
peak=   -3.379 closest distance to " O   HOH Z 251 " =    4.832
peak=   -3.379 closest distance to " CG2AVAL A  41 " =    2.876
peak=   -3.369 closest distance to " CA  GLY A 133 " =    2.423
peak=   -3.367 closest distance to " CE  MET A  93 " =    1.615
peak=   -3.366 closest distance to " SD  MET A  40 " =    1.911
peak=   -3.357 closest distance to " CG  GLN A  58 " =    1.358
peak=   -3.349 closest distance to " CA  GLY A 241 " =    2.362
peak=   -3.347 closest distance to " CD1 ILE A 109 " =    2.792
peak=   -3.346 closest distance to " CD  LYS A 289 " =    2.389
peak=   -3.344 closest distance to " CZ  ARG A 259 " =    0.997
peak=   -3.340 closest distance to " O   HOH Z 290 " =    1.127
peak=   -3.339 closest distance to " O   HOH Z 191 " =    5.785
peak=   -3.339 closest distance to " CD1 ILE A 199 " =    2.435
peak=   -3.337 closest distance to " NE2 HIS A  86 " =    1.099
peak=   -3.325 closest distance to " CE1 PHE A  59 " =    2.053
peak=   -3.322 closest distance to " O   HOH Z 110 " =    1.510
peak=   -3.322 closest distance to " NE2 GLN A 194 " =    2.014
peak=   -3.319 closest distance to " O   HOH Z 329 " =    1.238
peak=   -3.318 closest distance to " C   VAL A 265 " =    0.921
peak=   -3.310 closest distance to " O   SER A 276 " =    1.613
peak=   -3.309 closest distance to " N   ALA A 226 " =    1.982
peak=   -3.308 closest distance to " OE1 GLN A  88 " =    1.110
peak=   -3.305 closest distance to " O   HOH Z 357 " =    2.076
peak=   -3.299 closest distance to " O   HOH Z 359 " =    2.833
peak=   -3.298 closest distance to " CD2 PHE A 192 " =    2.088
peak=   -3.292 closest distance to " CG2 ILE A 263 " =    2.372
peak=   -3.290 closest distance to " O   SER A 210 " =    1.724
peak=   -3.287 closest distance to " ND2 ASN A  45 " =    1.253
peak=   -3.282 closest distance to " CB  TRP A  85 " =    2.576
peak=   -3.281 closest distance to " CA  GLY A 241 " =    3.235
peak=   -3.276 closest distance to " O   HOH Z 395 " =    1.420
peak=   -3.275 closest distance to " O   PHE A 218 " =    1.527
peak=   -3.268 closest distance to " ND2 ASN A  45 " =    2.188
peak=   -3.266 closest distance to " CG2 VAL A 202 " =    2.699
peak=   -3.258 closest distance to " NE  ARG A  79 " =    1.231
peak=   -3.248 closest distance to " OD1 ASN A  39 " =    2.179
peak=   -3.246 closest distance to " CA  LYS A 166 " =    2.127
peak=   -3.241 closest distance to " CD1 ILE A 263 " =    2.098
peak=   -3.239 closest distance to " OG  SER A  62 " =    4.350
peak=   -3.237 closest distance to " ND2 ASN A 187 " =    1.626
peak=   -3.236 closest distance to " O   HOH Z 208 " =    1.472
peak=   -3.234 closest distance to " CD1 TRP A  70 " =    1.880
peak=   -3.232 closest distance to " CD  GLN A 223 " =    1.342
peak=   -3.227 closest distance to " O   HOH Z  96 " =    1.588
peak=   -3.227 closest distance to " O   HOH Z 301 " =    2.455
peak=   -3.225 closest distance to " CE BMET A  47 " =    1.664
peak=   -3.223 closest distance to " ND2 ASN A 249 " =    2.203
peak=   -3.220 closest distance to " CG  HIS A  86 " =    1.213
peak=   -3.216 closest distance to " CD  ARG A 139 " =    1.074
peak=   -3.213 closest distance to " O   HOH Z 115 " =    1.507
peak=   -3.211 closest distance to " O   HOH Z   6 " =    1.678
peak=   -3.206 closest distance to " CG1 VAL A 125 " =    1.869
peak=   -3.204 closest distance to " O   HOH Z 429 " =    1.688
peak=   -3.204 closest distance to " NE2 GLN A 223 " =    1.569
peak=   -3.203 closest distance to " O   HOH Z 127 " =    1.336
peak=   -3.197 closest distance to " CA  ASN A 110 " =    1.112
peak=   -3.196 closest distance to " O   HOH Z 252 " =    3.594
peak=   -3.194 closest distance to " O   GLN A 240 " =    2.441
peak=   -3.194 closest distance to " CG  ARG A 259 " =    2.509
peak=   -3.194 closest distance to " O   HOH Z 264 " =    1.737
peak=   -3.193 closest distance to " O   VAL A 189 " =    2.731
peak=   -3.191 closest distance to " O   HOH Z  60 " =    1.929
peak=   -3.189 closest distance to " SG  CYS A 260 " =    2.470
peak=   -3.188 closest distance to " OH  TYR A 172 " =    1.834
peak=   -3.186 closest distance to " CA  ASN A 127 " =    1.086
peak=   -3.182 closest distance to " O   HOH Z 259 " =    1.902
peak=   -3.181 closest distance to " ND2 ASN A  69 " =    1.990
peak=   -3.181 closest distance to " O   HOH Z 250 " =    1.767
peak=   -3.179 closest distance to " NH2 ARG A  36 " =    2.629
peak=   -3.178 closest distance to " CE1 TYR A 247 " =    2.654
peak=   -3.172 closest distance to " O   HOH Z 147 " =    2.249
peak=   -3.169 closest distance to " O   HOH Z 411 " =    1.693
peak=   -3.166 closest distance to " O   HOH Z 265 " =    2.533
peak=   -3.165 closest distance to " O   HOH Z 426 " =    1.753
peak=   -3.165 closest distance to " CZ  ARG A 156 " =    2.072
peak=   -3.159 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.158 closest distance to " O   TRP A  92 " =    2.066
peak=   -3.157 closest distance to " CD  GLN A  88 " =    0.972
peak=   -3.157 closest distance to " O   HOH Z  43 " =    1.543
peak=   -3.155 closest distance to " O   HOH Z 210 " =    0.783
peak=   -3.153 closest distance to " CG  LEU A  83 " =    2.129
peak=   -3.148 closest distance to " CE3 TRP A 274 " =    2.457
peak=   -3.146 closest distance to " CH2 TRP A 150 " =    1.135
peak=   -3.144 closest distance to " CD2 PHE A 225 " =    1.118
peak=   -3.143 closest distance to " O   TYR A  15 " =    1.854
peak=   -3.141 closest distance to " O   SER A 141 " =    1.787
peak=   -3.141 closest distance to " O   GLY A  75 " =    2.156
peak=   -3.140 closest distance to " O   HOH Z 196 " =    1.906
peak=   -3.136 closest distance to " O   HOH Z 304 " =    1.456
peak=   -3.134 closest distance to " O   HOH Z 177 " =    1.441
peak=   -3.133 closest distance to " CB  TRP A 177 " =    2.278
peak=   -3.133 closest distance to " CG  LEU A   5 " =    1.641
peak=   -3.131 closest distance to " CG  ARG A  66 " =    2.563
peak=   -3.130 closest distance to " O   HOH Z 100 " =    1.247
peak=   -3.128 closest distance to " O   HOH Z  30 " =    1.582
peak=   -3.120 closest distance to " CG  TRP A 266 " =    1.798
peak=   -3.115 closest distance to " CD2 LEU A 300 " =    2.774
peak=   -3.108 closest distance to " O   HOH Z  64 " =    1.703
peak=   -3.106 closest distance to " O   HOH Z 265 " =    1.862
peak=   -3.090 closest distance to " CD1 LEU A   5 " =    2.555
peak=   -3.081 closest distance to " CA  PRO A 243 " =    2.657
peak=   -3.080 closest distance to " O   HOH Z 106 " =    2.038
peak=   -3.070 closest distance to " O   HOH Z 189 " =    2.322
peak=   -3.070 closest distance to " OG  SER A  63 " =    1.205
peak=   -3.068 closest distance to " O   ASP A  27 " =    2.057
peak=   -3.062 closest distance to " C   ASP A 270 " =    1.282
peak=   -3.050 closest distance to " NH2AARG A 275 " =    5.048

================= 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    :  0.4971 0.4856   6.296486e+00   6.283832e+00
   1_bss:  0.4897 0.4769   6.290325e+00   6.279065e+00
   1_xyz:  0.4151 0.4379   6.202610e+00   6.228255e+00
   1_adp:  0.3732 0.4272   6.135558e+00   6.208159e+00
   1_occ:  0.3725 0.4270   6.135230e+00   6.208850e+00
   2_bss:  0.3710 0.4224   6.137372e+00   6.208595e+00
   2_xyz:  0.2937 0.3564   5.955068e+00   6.091390e+00
   2_adp:  0.2737 0.3343   5.901838e+00   6.048688e+00
   2_occ:  0.2735 0.3345   5.901224e+00   6.049044e+00
   3_bss:  0.2721 0.3337   5.902220e+00   6.049469e+00
   3_xyz:  0.2154 0.2620   5.692299e+00   5.860361e+00
   3_adp:  0.1886 0.2423   5.596036e+00   5.793351e+00
   3_occ:  0.1885 0.2425   5.596139e+00   5.794189e+00
   4_bss:  0.1881 0.2421   5.593842e+00   5.790917e+00
   4_xyz:  0.1474 0.2016   5.390144e+00   5.619008e+00
   4_adp:  0.1385 0.1891   5.333685e+00   5.561045e+00
   4_occ:  0.1384 0.1890   5.333128e+00   5.560545e+00
   5_bss:  0.1384 0.1888   5.332935e+00   5.559709e+00
   5_xyz:  0.1251 0.1749   5.251346e+00   5.490189e+00
   5_adp:  0.1224 0.1724   5.234914e+00   5.475485e+00
   5_occ:  0.1223 0.1724   5.234792e+00   5.475594e+00
   5_bss:  0.1223 0.1723   5.234777e+00   5.475558e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   5.786   9.286  11.293   0.000   0.000   0.000
   1_xyz:  0.300  20.000   5.786   9.286  11.293   0.000   0.000   0.000
   1_adp:  0.300  20.000   5.786   9.286  11.293   0.000   0.000   0.000
   1_occ:  0.300  20.000   5.786   9.286  11.293   0.000   0.000   0.000
   2_bss:  0.319  50.000   2.815   5.745   7.458   0.000   0.000   0.000
   2_xyz:  0.319  50.000   2.815   5.745   7.458   0.000   0.000   0.000
   2_adp:  0.319  50.000   2.815   5.745   7.458   0.000   0.000   0.000
   2_occ:  0.319  50.000   2.815   5.745   7.458   0.000   0.000   0.000
   3_bss:  0.309  50.000   1.703   3.389   4.817   0.000   0.000   0.000
   3_xyz:  0.309  50.000   1.703   3.389   4.817   0.000   0.000   0.000
   3_adp:  0.309  50.000   1.703   3.389   4.817   0.000   0.000   0.000
   3_occ:  0.309  50.000   1.703   3.389   4.817   0.000   0.000   0.000
   4_bss:  0.313  76.557   0.823   1.990   3.511   0.000   0.000   0.000
   4_xyz:  0.313  76.557   0.823   1.990   3.511   0.000   0.000   0.000
   4_adp:  0.313  76.557   0.823   1.990   3.511   0.000   0.000   0.000
   4_occ:  0.313  76.557   0.823   1.990   3.511   0.000   0.000   0.000
   5_bss:  0.334  77.429   1.027   1.934   3.403   0.000   0.000   0.000
   5_xyz:  0.334  77.429   1.027   1.934   3.403   0.000   0.000   0.000
   5_adp:  0.334  77.429   1.027   1.934   3.403   0.000   0.000   0.000
   5_occ:  0.334  77.429   1.027   1.934   3.403   0.000   0.000   0.000
   5_bss:  0.328  71.968  -0.974  -0.251   1.225   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.106 0.4054  0.4639    72582.423
   1_bss:  58.278 0.4154  0.6152    71661.378
   1_xyz:  50.762 0.5098  0.7371    55816.328
   1_adp:  47.922 0.5458  0.8490    51913.621
   1_occ:  47.988 0.5450  0.8467    52021.317
   2_bss:  47.800 0.5474  0.7586    51925.960
   2_xyz:  38.716 0.6572  0.9024    35181.531
   2_adp:  35.426 0.6966  0.9470    30943.635
   2_occ:  35.444 0.6963  0.9463    30939.148
   3_bss:  35.307 0.6980  0.8838    30892.705
   3_xyz:  26.862 0.7915  0.9658    18498.471
   3_adp:  24.258 0.8191  0.9735    15547.290
   3_occ:  24.278 0.8189  0.9731    15559.698
   4_bss:  24.143 0.8202  0.9339    15365.890
   4_xyz:  19.531 0.8655  0.9625    10390.211
   4_adp:  18.018 0.8802  0.9585     9322.519
   4_occ:  18.004 0.8803  0.9587     9315.527
   5_bss:  17.981 0.8805  0.9597     9298.288
   5_xyz:  16.293 0.8957  0.9686     7909.558
   5_adp:  15.898 0.8994  0.9604     7683.177
   5_occ:  15.898 0.8994  0.9604     7679.261
   5_bss:  15.897 0.8994  0.9646     7677.253
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4535e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4535e+01
   1_xyz:   1.759  0.014  0.109 18.302  0.007  4.111   1.5160e-01
   1_adp:   1.759  0.014  0.109 18.302  0.007  4.111   1.5160e-01
   1_occ:   1.759  0.014  0.109 18.302  0.007  4.111   1.5160e-01
   2_bss:   1.759  0.014  0.109 18.302  0.007  4.111   1.5160e-01
   2_xyz:   1.343  0.010  0.085 16.404  0.005  4.112   9.8016e-02
   2_adp:   1.343  0.010  0.085 16.404  0.005  4.112   9.8016e-02
   2_occ:   1.343  0.010  0.085 16.404  0.005  4.112   9.8016e-02
   3_bss:   1.343  0.010  0.085 16.404  0.005  4.112   9.8016e-02
   3_xyz:   1.103  0.008  0.080 15.748  0.005  4.116   7.7122e-02
   3_adp:   1.103  0.008  0.080 15.748  0.005  4.116   7.7122e-02
   3_occ:   1.103  0.008  0.080 15.748  0.005  4.116   7.7122e-02
   4_bss:   1.103  0.008  0.080 15.748  0.005  4.116   7.7122e-02
   4_xyz:   1.183  0.010  0.086 15.597  0.004  4.132   8.1513e-02
   4_adp:   1.183  0.010  0.086 15.597  0.004  4.132   8.1513e-02
   4_occ:   1.183  0.010  0.086 15.597  0.004  4.132   8.1513e-02
   5_bss:   1.183  0.010  0.086 15.597  0.004  4.132   8.1513e-02
   5_xyz:   1.193  0.011  0.092 15.604  0.004  4.132   8.5698e-02
   5_adp:   1.193  0.011  0.092 15.604  0.004  4.132   8.5698e-02
   5_occ:   1.193  0.011  0.092 15.604  0.004  4.132   8.5698e-02
   5_bss:   1.193  0.011  0.092 15.604  0.004  4.132   8.5698e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0694e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0694e+00
   1_xyz:  15.062  0.174  0.465 86.924  0.050  2.185   1.1114e-01
   1_adp:  15.062  0.174  0.465 86.924  0.050  2.185   1.1114e-01
   1_occ:  15.062  0.174  0.465 86.924  0.050  2.185   1.1114e-01
   2_bss:  15.062  0.174  0.465 86.924  0.050  2.185   1.1114e-01
   2_xyz:   9.912  0.086  0.278 86.181  0.028  2.057   6.3343e-02
   2_adp:   9.912  0.086  0.278 86.181  0.028  2.057   6.3343e-02
   2_occ:   9.912  0.086  0.278 86.181  0.028  2.057   6.3343e-02
   3_bss:   9.912  0.086  0.278 86.181  0.028  2.057   6.3343e-02
   3_xyz:   6.846  0.053  0.257 85.982  0.057  2.229   1.3534e-01
   3_adp:   6.846  0.053  0.257 85.982  0.057  2.229   1.3534e-01
   3_occ:   6.846  0.053  0.257 85.982  0.057  2.229   1.3534e-01
   4_bss:   6.846  0.053  0.257 85.982  0.057  2.229   1.3534e-01
   4_xyz:   9.034  0.052  0.381 83.038  0.039  2.254   6.0990e-02
   4_adp:   9.034  0.052  0.381 83.038  0.039  2.254   6.0990e-02
   4_occ:   9.034  0.052  0.381 83.038  0.039  2.254   6.0990e-02
   5_bss:   9.034  0.052  0.381 83.038  0.039  2.254   6.0990e-02
   5_xyz:   8.262  0.056  0.493 83.308  0.037  2.300   6.6201e-02
   5_adp:   8.262  0.056  0.493 83.308  0.037  2.300   6.6201e-02
   5_occ:   8.262  0.056  0.493 83.308  0.037  2.300   6.6201e-02
   5_bss:   8.262  0.056  0.493 83.308  0.037  2.300   6.6201e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  91.49   0.00  15.11  72.03   0.00  12.90  91.49   0.00  27.11
   1_occ:  91.49   0.00  15.11  72.03   0.00  12.90  91.49   0.00  27.11
   2_bss:  91.49   0.00  15.11  72.03   0.00  12.90  91.49   0.00  27.11
   2_xyz:  91.49   0.00  15.11  72.03   0.00  12.90  91.49   0.00  27.11
   2_adp: 234.54   0.00  14.67 234.54   0.00  11.74  88.98   0.00  30.61
   2_occ: 234.54   0.00  14.67 234.54   0.00  11.74  88.98   0.00  30.61
   3_bss: 234.54   0.00  14.67 234.54   0.00  11.74  88.98   0.00  30.61
   3_xyz: 234.54   0.00  14.67 234.54   0.00  11.74  88.98   0.00  30.61
   3_adp: 134.54   0.00  15.53 134.54   0.00  10.78 110.35   1.34  41.42
   3_occ: 134.54   0.00  15.53 134.54   0.00  10.78 110.35   1.34  41.42
   4_bss: 134.54   0.00  15.53 134.54   0.00  10.78 110.35   1.34  41.42
   4_xyz: 134.54   0.00  15.53 134.54   0.00  10.78 110.35   1.34  41.42
   4_adp: 116.71   0.00  15.01 116.71   0.00   9.99 111.93   1.64  42.33
   4_occ: 116.71   0.00  15.01 116.71   0.00   9.99 111.93   1.64  42.33
   5_bss: 116.71   0.00  15.01 116.71   0.00   9.99 111.93   1.64  42.33
   5_xyz: 116.71   0.00  15.01 116.71   0.00   9.99 111.93   1.64  42.33
   5_adp: 112.72   0.00  14.60 107.07   0.00   9.64 112.72   1.83  41.61
   5_occ: 112.72   0.00  14.60 107.07   0.00   9.64 112.72   1.83  41.61
   5_bss: 114.96   2.25  16.84 109.31   2.25  11.88 114.96   4.08  43.85
------------------------------------------------------------------------
 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:    1.278    0.017    0.415
   1_adp:    1.278    0.017    0.415
   1_occ:    1.278    0.017    0.415
   2_bss:    1.278    0.017    0.415
   2_xyz:    2.004    0.056    0.604
   2_adp:    2.004    0.056    0.604
   2_occ:    2.004    0.056    0.604
   3_bss:    2.004    0.056    0.604
   3_xyz:    1.894    0.077    0.706
   3_adp:    1.894    0.077    0.706
   3_occ:    1.894    0.077    0.706
   4_bss:    1.894    0.077    0.706
   4_xyz:    2.149    0.023    0.778
   4_adp:    2.149    0.023    0.778
   4_occ:    2.149    0.023    0.778
   5_bss:    2.149    0.023    0.778
   5_xyz:    2.263    0.061    0.811
   5_adp:    2.263    0.061    0.811
   5_occ:    2.263    0.061    0.811
   5_bss:    2.263    0.061    0.811
------------------------------------------------------------------------

CPU time actual refinement: 350.31


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_703/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_703/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_703/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_703/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_703/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.16 
  Macro-tasks:
    bulk solvent and scale       = 51.95  
    individual site refinement   = 139.63 
    weights calculation          = 31.89  
    collect and process          = 6.38   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 229.95 
  Micro-tasks:
    mask                            = 2.30   
    f_calc                          = 104.90 
    alpha_beta                      = 8.32   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 115.75 
    fmodel                         = 8.81   
    r_factors                      = 0.30   
    phase_errors                   = 10.39  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 252.16 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.869 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    666 calls, 104.50 s
gradients_fft:          612 calls, 102.18 s

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

# Date 2008-01-16 Time 02:14:05 PST -0800 (1200478445.30 s)
Start R-work = 0.4971, R-free = 0.4856 (no bulk solvent and anisotropic scale)
Final R-work = 0.1393, R-free = 0.1869 (no bulk solvent and anisotropic scale)

Start R-work = 0.4897, R-free = 0.4769
Final R-work = 0.1223, R-free = 0.1723