# Date 2008-01-16 Time 02:10:05 PST -0800 (1200478205.58 s)
#phil __OFF__

Command line arguments: "../723.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23601
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 723

-------------------------------------------------------------------------------
  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, 48.1033, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0589 2.00069
Completeness in resolution range: 0.950184
Completeness with d_max=infinity: 0.947244

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0589
                             d_min =   2.0007

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, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0589 2.00069
Completeness in resolution range: 0.950184
Completeness with d_max=infinity: 0.947244

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0593 -  4.2805 [2178/2206]  1957   221  10.1%
  bin  2:  4.2805 -  3.4105 [2061/2084]  1857   204   9.9%
  bin  3:  3.4105 -  2.9832 [2061/2083]  1855   206  10.0%
  bin  4:  2.9832 -  2.7122 [2031/2050]  1831   200   9.8%
  bin  5:  2.7122 -  2.5187 [2021/2050]  1808   213  10.5%
  bin  6:  2.5187 -  2.3708 [2007/2048]  1814   193   9.6%
  bin  7:  2.3708 -  2.2525 [1999/2035]  1804   195   9.8%
  bin  8:  2.2525 -  2.1548 [2000/2037]  1795   205  10.2%
  bin  9:  2.1548 -  2.0720 [1981/2013]  1785   196   9.9%
  bin 10:  2.0720 -  2.0007 [1250/2010]  1124   126  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_723/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 20
        2.42 -     3.04: 2152
        3.04 -     3.66: 4593
        3.66 -     4.28: 8828
        4.28 -     4.90: 12200
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.865 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.904 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.974 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.137 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27788 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_723/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_723/model_refine_001.geo

CPU time processing inputs: 9.34


============================ 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 48.10325 87.68585 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 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5080   r_free= 0.4947   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.304982                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7739 0.99   1402  157 0.4147 0.4202      6.6351      6.6443|
|  2:  4.7739 -  3.8094 0.99   1362  151 0.4516 0.4818      6.8709      6.9469|
|  3:  3.8094 -  3.3338 0.99   1326  149 0.4760 0.4380      6.7282      6.6751|
|  4:  3.3338 -  3.0317 0.99   1315  136 0.5082 0.4641      6.5668      6.4922|
|  5:  3.0317 -  2.8159 0.99   1305  149 0.5419 0.5170      6.3965      6.4327|
|  6:  2.8159 -  2.6509 0.98   1305  149 0.5385 0.5052      6.2953      6.1893|
|  7:  2.6509 -  2.5187 0.99   1293  153 0.5226 0.4740      6.2595      6.1732|
|  8:  2.5187 -  2.4096 0.99   1309  131 0.5264 0.4865      6.1868      6.1634|
|  9:  2.4096 -  2.3171 0.98   1291  147 0.5437 0.6196      6.1144      6.1845|
| 10:  2.3171 -  2.2375 0.98   1276  142 0.5793 0.5276      6.1283       6.145|
| 11:  2.2375 -  2.1677 0.98   1285  148 0.5447 0.5647      6.0316      6.0591|
| 12:  2.1677 -  2.1059 0.99   1287  136 0.5397 0.5306      5.9713      6.0038|
| 13:  2.1059 -  2.0506 0.97   1265  138 0.5454 0.5060      5.8967      5.8361|
| 14:  2.0506 -  2.0007 0.48    609   73 0.5668 0.5205      5.8724      5.7613|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0593 -  4.7739  1402   157  0.64  39.46   0.78     0.66      89630.15|
|  2:  4.7739 -  3.8094  1362   151  0.64  40.52   0.84     0.69     129856.39|
|  3:  3.8094 -  3.3338  1326   149  0.54  49.08   0.78     0.64     134857.64|
|  4:  3.3338 -  3.0317  1315   136  0.45  56.11   0.76     0.53     113815.98|
|  5:  3.0317 -  2.8159  1305   149  0.38  60.99   0.70     0.46      87419.07|
|  6:  2.8159 -  2.6509  1305   149  0.38  61.26   0.68     0.44      72091.93|
|  7:  2.6509 -  2.5187  1293   153  0.37  62.18   0.73     0.41      64928.54|
|  8:  2.5187 -  2.4096  1309   131  0.33  65.06   0.72     0.38      61786.64|
|  9:  2.4096 -  2.3171  1291   147  0.25  71.05   0.68     0.31      61865.87|
| 10:  2.3171 -  2.2375  1276   142  0.22  73.28   0.70     0.28      57130.79|
| 11:  2.2375 -  2.1677  1285   148  0.22  73.49   0.71     0.27      53344.80|
| 12:  2.1677 -  2.1059  1287   136  0.24  71.98   0.74     0.31      47787.50|
| 13:  2.1059 -  2.0506  1265   138  0.25  71.48   0.70     0.31      40367.71|
| 14:  2.0506 -  2.0007   609    73  0.26  70.71   0.70     0.28      30199.67|
|alpha:            min =        0.27 max =            0.69 mean =         0.43|
|beta:             min =    30199.67 max =       134857.64 mean =     76930.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.27|
|phase err.(test): min =        0.00 max =           89.92 mean =        61.65|
|-----------------------------------------------------------------------------|

============================== 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 = 19.104870             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.654   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.887762              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.065   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      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:     1474 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2568 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3852 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4970 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6453 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7603 |
|-----------------------------------------------------------------------------|
|-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 |       54.544 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.779 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    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 = 12.311)------------------------------------------|
|    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 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5129   r_free= 0.4966   ksol= 0.00   Bsol= 0.00   scale= 0.732    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.306311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5016   r_free= 0.4885   ksol= 0.30   Bsol= 20.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.46,11.55,9.07,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.300053                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.388806             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.649   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.649166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.230   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5016      final r-factor (work) = 0.4374          |
| start r-factor (free) = 0.4885      final r-factor (free) = 0.4476          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 109.3497 = 17.39 * 0.50 * 6.3035 + 1.00 * 54.5443                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.4696 = 17.39 * 0.50 * 6.2482 + 1.00 * 0.1456                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4374      final r-factor (work) = 0.3964          |
| start r-factor (free) = 0.4476      final r-factor (free) = 0.4437          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3190 = 1.65 * 1.00 * 6.2482 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2350 = 1.65 * 1.00 * 6.1910 + 1.00 * 0.0249                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.03  16.73    None  None   None       |
|    all(noH): 2823   0      0.00    122.03  16.73    None  None   None       |
|    Sol.    : 438    0      0.00    122.03  27.90    None  None   None       |
|    Mac.    : 2385   0      0.00    85.31   14.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.203: 1333   |   5:    61.014 -  73.217:   27        |
|      1:    12.203 -  24.406:  828   |   6:    73.217 -  85.420:   14        |
|      2:    24.406 -  36.608:  391   |   7:    85.420 -  97.622:    1        |
|      3:    36.608 -  48.811:  169   |   8:    97.622 - 109.825:    1        |
|      4:    48.811 -  61.014:   57   |   9:   109.825 - 122.028:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3964 r_free = 0.4437             target_work(ml) = 6.182         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3955 r_free = 0.4430             target_work(ml) = 6.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3955   r_free= 0.4430   ksol= 0.30   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.46,11.55,9.07,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.181864                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3932   r_free= 0.4373   ksol= 0.30   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.03,6.94,5.09,0.00,0.00,0.00); trace/3= 4.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.182883                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.946465              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.263  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.542321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.119  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3932      final r-factor (work) = 0.3381          |
| start r-factor (free) = 0.4373      final r-factor (free) = 0.4106          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.8113 = 8.95 * 0.50 * 6.1848 + 1.00 * 0.1451                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.4495 = 8.95 * 0.50 * 6.1148 + 1.00 * 0.0965                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3381      final r-factor (work) = 0.3312          |
| start r-factor (free) = 0.4106      final r-factor (free) = 0.3959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3408 = 0.54 * 1.00 * 6.1148 + 1.00 * 0.0246                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3101 = 0.54 * 1.00 * 6.0844 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.12  14.56    None  None   None       |
|    all(noH): 2823   0      0.00    117.12  14.56    None  None   None       |
|    Sol.    : 438    0      0.83    117.12  27.01    None  None   None       |
|    Mac.    : 2385   0      0.00    67.44   12.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.712: 1466   |   5:    58.559 -  70.271:   21        |
|      1:    11.712 -  23.424:  847   |   6:    70.271 -  81.983:    6        |
|      2:    23.424 -  35.136:  336   |   7:    81.983 -  93.695:    0        |
|      3:    35.136 -  46.847:  109   |   8:    93.695 - 105.406:    1        |
|      4:    46.847 -  58.559:   36   |   9:   105.406 - 117.118:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3312 r_free = 0.3959             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3312 r_free = 0.3962             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3312   r_free= 0.3962   ksol= 0.30   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.03,6.94,5.09,0.00,0.00,0.00); trace/3= 4.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.074207                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3313   r_free= 0.3949   ksol= 0.30   Bsol= 50.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.65,5.26,3.44,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.075015                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.617656              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428922              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.198  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3313      final r-factor (work) = 0.2799          |
| start r-factor (free) = 0.3949      final r-factor (free) = 0.3346          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2295 = 6.62 * 0.50 * 6.0846 + 1.00 * 0.0965                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9556 = 6.62 * 0.50 * 6.0061 + 1.00 * 0.0826                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2799      final r-factor (work) = 0.2662          |
| start r-factor (free) = 0.3346      final r-factor (free) = 0.3222          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5867 = 0.43 * 1.00 * 6.0061 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5578 = 0.43 * 1.00 * 5.9083 + 1.00 * 0.0236                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.36  14.35    None  None   None       |
|    all(noH): 2823   0      0.00    103.36  14.35    None  None   None       |
|    Sol.    : 438    0      1.33    103.36  30.41    None  None   None       |
|    Mac.    : 2385   0      0.00    71.37   11.40    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 -  10.336: 1425   |   5:    51.679 -  62.014:   43        |
|      1:    10.336 -  20.672:  774   |   6:    62.014 -  72.350:    8        |
|      2:    20.672 -  31.007:  322   |   7:    72.350 -  82.686:    5        |
|      3:    31.007 -  41.343:  166   |   8:    82.686 -  93.022:    0        |
|      4:    41.343 -  51.679:   79   |   9:    93.022 - 103.357:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2662 r_free = 0.3222             target_work(ml) = 5.897         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2660 r_free = 0.3224             target_work(ml) = 5.897         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2660   r_free= 0.3224   ksol= 0.30   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.65,5.26,3.44,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.897044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2658   r_free= 0.3225   ksol= 0.31   Bsol= 50.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,4.09,2.73,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.897352                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.323727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.041  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.685860              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.990   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2658      final r-factor (work) = 0.1987          |
| start r-factor (free) = 0.3225      final r-factor (free) = 0.2467          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6709 = 8.32 * 0.50 * 5.9079 + 1.00 * 0.0831                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1614 = 8.32 * 0.50 * 5.7824 + 1.00 * 0.0957                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1987      final r-factor (work) = 0.1847          |
| start r-factor (free) = 0.2467      final r-factor (free) = 0.2375          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7641 = 1.69 * 1.00 * 5.7824 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4722 = 1.69 * 1.00 * 5.5910 + 1.00 * 0.0466                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.76  14.19    None  None   None       |
|    all(noH): 2823   0      0.00    102.76  14.19    None  None   None       |
|    Sol.    : 438    0      0.00    102.76  32.65    None  None   None       |
|    Mac.    : 2385   0      0.00    93.41   10.80    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 -  10.276: 1469   |   5:    51.379 -  61.654:   51        |
|      1:    10.276 -  20.551:  733   |   6:    61.654 -  71.930:    9        |
|      2:    20.551 -  30.827:  288   |   7:    71.930 -  82.206:    5        |
|      3:    30.827 -  41.103:  174   |   8:    82.206 -  92.481:    1        |
|      4:    41.103 -  51.379:   91   |   9:    92.481 - 102.757:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1847 r_free = 0.2375             target_work(ml) = 5.575         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1846 r_free = 0.2379             target_work(ml) = 5.575         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1846   r_free= 0.2379   ksol= 0.31   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,4.09,2.73,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.574899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1845   r_free= 0.2372   ksol= 0.33   Bsol= 58.60   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.94,2.77,2.77,0.00,0.00,0.00); trace/3= 2.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.574484                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.565138              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.570  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.596223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.437   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1845      final r-factor (work) = 0.1538          |
| start r-factor (free) = 0.2372      final r-factor (free) = 0.2065          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6547 = 5.57 * 0.50 * 5.5916 + 1.00 * 0.0957                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4008 = 5.57 * 0.50 * 5.5018 + 1.00 * 0.0918                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1538      final r-factor (work) = 0.1377          |
| start r-factor (free) = 0.2065      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3499 = 0.60 * 1.00 * 5.5018 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2202 = 0.60 * 1.00 * 5.3798 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.59   14.17    None  None   None       |
|    all(noH): 2823   0      0.00    93.59   14.17    None  None   None       |
|    Sol.    : 438    0      1.85    93.59   38.08    None  None   None       |
|    Mac.    : 2385   0      0.00    75.50   9.78     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 -   9.359: 1500   |   5:    46.794 -  56.152:  100        |
|      1:     9.359 -  18.717:  731   |   6:    56.152 -  65.511:   58        |
|      2:    18.717 -  28.076:  189   |   7:    65.511 -  74.870:   20        |
|      3:    28.076 -  37.435:  112   |   8:    74.870 -  84.228:    6        |
|      4:    37.435 -  46.794:  106   |   9:    84.228 -  93.587:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1377 r_free = 0.1875             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1376 r_free = 0.1875             target_work(ml) = 5.326         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1875   ksol= 0.33   Bsol= 58.60   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.94,2.77,2.77,0.00,0.00,0.00); trace/3= 2.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.325613                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7739 0.99   1402  157 0.1024 0.1414      5.4478       5.648|
|  2:  4.7739 -  3.8094 0.99   1362  151 0.0960 0.1214      5.5388      5.7368|
|  3:  3.8094 -  3.3338 0.99   1326  149 0.1276 0.1842      5.6517      6.0421|
|  4:  3.3338 -  3.0317 0.99   1315  136 0.1470 0.1870      5.6183      5.7618|
|  5:  3.0317 -  2.8159 0.99   1305  149 0.1690 0.1942      5.5289      5.6628|
|  6:  2.8159 -  2.6509 0.98   1305  149 0.1547 0.2441       5.399      5.6635|
|  7:  2.6509 -  2.5187 0.99   1293  153 0.1537 0.2028      5.3558      5.5507|
|  8:  2.5187 -  2.4096 0.99   1309  131 0.1530 0.2037      5.2905      5.5117|
|  9:  2.4096 -  2.3171 0.98   1291  147 0.1568 0.2154      5.2191      5.4728|
| 10:  2.3171 -  2.2375 0.98   1276  142 0.1502 0.2065       5.176      5.3901|
| 11:  2.2375 -  2.1677 0.98   1285  148 0.1450 0.2271      5.1182      5.4325|
| 12:  2.1677 -  2.1059 0.99   1287  136 0.1424 0.1999      5.0582      5.3212|
| 13:  2.1059 -  2.0506 0.97   1265  138 0.1514 0.2041      4.9921      5.1759|
| 14:  2.0506 -  2.0007 0.48    609   73 0.1430 0.2094      4.8787      5.0906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0593 -  4.7739  1402   157  0.93  10.37   0.96     0.93       8608.77|
|  2:  4.7739 -  3.8094  1362   151  0.94  10.06   1.01     1.00      11614.98|
|  3:  3.8094 -  3.3338  1326   149  0.91  14.21   1.02     1.02      14663.00|
|  4:  3.3338 -  3.0317  1315   136  0.89  17.15   1.01     0.99      14558.58|
|  5:  3.0317 -  2.8159  1305   149  0.86  20.05   1.01     0.99      12324.98|
|  6:  2.8159 -  2.6509  1305   149  0.86  20.61   0.98     0.93      10273.22|
|  7:  2.6509 -  2.5187  1293   153  0.87  19.42   0.99     0.96       9062.12|
|  8:  2.5187 -  2.4096  1309   131  0.87  19.83   1.00     0.95       8296.02|
|  9:  2.4096 -  2.3171  1291   147  0.86  20.43   1.01     0.97       7361.43|
| 10:  2.3171 -  2.2375  1276   142  0.86  20.56   1.00     0.94       6691.16|
| 11:  2.2375 -  2.1677  1285   148  0.86  20.25   1.00     0.94       6298.06|
| 12:  2.1677 -  2.1059  1287   136  0.87  19.88   1.01     0.99       5750.19|
| 13:  2.1059 -  2.0506  1265   138  0.87  20.00   0.99     0.97       4819.51|
| 14:  2.0506 -  2.0007   609    73  0.87  19.13   0.96     0.91       3785.06|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3785.06 max =        14663.00 mean =      9102.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.86|
|phase err.(test): min =        0.00 max =           89.40 mean =        16.88|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1379   r_free= 0.1878   ksol= 0.33   Bsol= 67.08   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.08,0.28,0.80,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.325208                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1379   r_free= 0.1878   ksol= 0.33   Bsol= 67.08   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.08,0.28,0.80,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.325208                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0593 -  4.7739 0.99   1402  157 0.1049 0.1406      5.4472        5.63|
|  2:  4.7739 -  3.8094 0.99   1362  151 0.0968 0.1224      5.5417      5.7446|
|  3:  3.8094 -  3.3338 0.99   1326  149 0.1284 0.1842      5.6549       6.043|
|  4:  3.3338 -  3.0317 0.99   1315  136 0.1472 0.1872      5.6185      5.7629|
|  5:  3.0317 -  2.8159 0.99   1305  149 0.1687 0.1936       5.528      5.6611|
|  6:  2.8159 -  2.6509 0.98   1305  149 0.1540 0.2432      5.3967      5.6619|
|  7:  2.6509 -  2.5187 0.99   1293  153 0.1533 0.2032      5.3542      5.5496|
|  8:  2.5187 -  2.4096 0.99   1309  131 0.1522 0.2035      5.2888      5.5127|
|  9:  2.4096 -  2.3171 0.98   1291  147 0.1565 0.2157      5.2178      5.4721|
| 10:  2.3171 -  2.2375 0.98   1276  142 0.1502 0.2074      5.1756      5.3923|
| 11:  2.2375 -  2.1677 0.98   1285  148 0.1444 0.2270      5.1168      5.4309|
| 12:  2.1677 -  2.1059 0.99   1287  136 0.1424 0.2008      5.0581      5.3236|
| 13:  2.1059 -  2.0506 0.97   1265  138 0.1513 0.2027      4.9913      5.1725|
| 14:  2.0506 -  2.0007 0.48    609   73 0.1426 0.2073       4.877      5.0865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0593 -  4.7739  1402   157  0.93  10.24   0.96     0.93       8186.36|
|  2:  4.7739 -  3.8094  1362   151  0.94   9.97   1.01     1.00      11451.76|
|  3:  3.8094 -  3.3338  1326   149  0.91  14.28   1.02     1.02      14801.01|
|  4:  3.3338 -  3.0317  1315   136  0.89  17.18   1.00     0.98      14570.88|
|  5:  3.0317 -  2.8159  1305   149  0.86  20.04   1.00     0.99      12307.54|
|  6:  2.8159 -  2.6509  1305   149  0.86  20.57   0.97     0.93      10253.98|
|  7:  2.6509 -  2.5187  1293   153  0.87  19.41   0.99     0.95       9062.91|
|  8:  2.5187 -  2.4096  1309   131  0.87  19.81   0.99     0.94       8281.98|
|  9:  2.4096 -  2.3171  1291   147  0.86  20.42   1.00     0.96       7361.45|
| 10:  2.3171 -  2.2375  1276   142  0.86  20.55   0.99     0.93       6685.73|
| 11:  2.2375 -  2.1677  1285   148  0.86  20.24   0.99     0.94       6305.01|
| 12:  2.1677 -  2.1059  1287   136  0.87  19.87   0.99     0.98       5750.01|
| 13:  2.1059 -  2.0506  1265   138  0.87  19.96   0.97     0.95       4802.23|
| 14:  2.0506 -  2.0007   609    73  0.87  19.05   0.95     0.90       3754.01|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3754.01 max =        14801.01 mean =      9061.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.84|
|phase err.(test): min =        0.00 max =           89.70 mean =        16.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.311)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    95.52   16.10    None  None   None       |
|    all(noH): 2823   0      1.93    95.52   16.10    None  None   None       |
|    Sol.    : 438    0      3.78    95.52   40.01    None  None   None       |
|    Mac.    : 2385   0      1.93    77.43   11.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.929 -  11.288: 1500   |   5:    48.723 -  58.082:  100        |
|      1:    11.288 -  20.647:  731   |   6:    58.082 -  67.440:   58        |
|      2:    20.647 -  30.005:  189   |   7:    67.440 -  76.799:   20        |
|      3:    30.005 -  39.364:  112   |   8:    76.799 -  86.158:    6        |
|      4:    39.364 -  48.723:  106   |   9:    86.158 -  95.516:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.198 - 4.929
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 322
   mapped sites are within: 0.709 - 4.929

peak=    6.610 closest distance to " O   HOH Z 120 " =    1.549
peak=    6.607 closest distance to " O   HOH Z  57 " =    1.122
peak=    6.507 closest distance to " OD1 ASN A 301 " =    1.122
peak=    6.295 closest distance to " CG2 VAL A 230 " =    1.221
peak=    6.272 closest distance to " CG1 ILE A 234 " =    1.448
peak=    6.058 closest distance to " O   HOH Z 210 " =    1.995
peak=    5.801 closest distance to " O   GLN A  11 " =    0.999
peak=    5.426 closest distance to " O   HOH Z 117 " =    1.436
peak=    5.344 closest distance to " CG  PRO A 280 " =    0.977
peak=    5.174 closest distance to " O   HOH Z 128 " =    1.947
peak=    5.087 closest distance to " CG  LEU A   5 " =    1.253
peak=    5.009 closest distance to " CB  SER A  63 " =    1.292
peak=    4.979 closest distance to " CB  VAL A 296 " =    1.254
peak=    4.864 closest distance to " NH2 ARG A  56 " =    2.334
peak=    4.860 closest distance to " CB  VAL A 230 " =    1.232
peak=    4.825 closest distance to " O   HOH Z 412 " =    3.299
peak=    4.783 closest distance to " O   HOH Z 425 " =    1.849
peak=    4.730 closest distance to " NH2 ARG A 156 " =    1.208
peak=    4.689 closest distance to " CA  TYR A  30 " =    0.976
peak=    4.630 closest distance to " O   HOH Z 404 " =    1.398
peak=    4.597 closest distance to " O   HOH Z 139 " =    1.505
peak=    4.587 closest distance to " CG AARG A 275 " =    1.244
peak=    4.579 closest distance to " O   HOH Z 403 " =    2.204
peak=    4.545 closest distance to " CD2 LEU A 228 " =    1.326
peak=    4.496 closest distance to " CB  GLN A 183 " =    1.201
peak=    4.483 closest distance to " O   HOH Z 431 " =    1.767
peak=    4.480 closest distance to " CD  LYS A 166 " =    1.697
peak=    4.473 closest distance to " OE1 GLN A  55 " =    1.417
peak=    4.464 closest distance to " CE1 HIS A 115 " =    1.220
peak=    4.462 closest distance to " O   ASP A 124 " =    1.310
peak=    4.456 closest distance to " CB  ALA A 299 " =    1.180
peak=    4.430 closest distance to " O   HOH Z 248 " =    1.758
peak=    4.392 closest distance to " N   SER A 164 " =    0.975
peak=    4.376 closest distance to " O   HOH Z 146 " =    1.873
peak=    4.354 closest distance to " O   HOH Z 124 " =    1.329
peak=    4.353 closest distance to " CG  GLN A  77 " =    0.862
peak=    4.261 closest distance to " O   HOH Z  49 " =    1.485
peak=    4.240 closest distance to " CG  LEU A 228 " =    1.263
peak=    4.212 closest distance to " O   HOH Z  53 " =    1.298
peak=    4.201 closest distance to " CD  ARG A  36 " =    1.073
peak=    4.185 closest distance to " OD2 ASP A 298 " =    0.879
peak=    4.171 closest distance to " O   HOH Z 422 " =    1.220
peak=    4.163 closest distance to " O   HOH Z  48 " =    2.086
peak=    4.109 closest distance to " O   HOH Z 234 " =    3.477
peak=    4.106 closest distance to " CB  SER A  62 " =    1.055
peak=    4.100 closest distance to " CE  LYS A 119 " =    1.471
peak=    4.096 closest distance to " O   HOH Z 139 " =    1.803
peak=    4.068 closest distance to " O   HOH Z 193 " =    2.185
peak=    4.063 closest distance to " NH1AARG A 145 " =    1.323
peak=    4.058 closest distance to " NE2 GLN A  11 " =    0.990
peak=    4.055 closest distance to " CG1 ILE A 120 " =    1.098
peak=    4.053 closest distance to " O   HOH Z 130 " =    2.565
peak=    4.048 closest distance to " OE1 GLN A  11 " =    2.182
peak=    4.020 closest distance to " CG1 VAL A 296 " =    1.207
peak=    4.016 closest distance to " O   HOH Z 357 " =    2.303
peak=    3.993 closest distance to " O   SER A  87 " =    2.328
peak=    3.988 closest distance to " O   HOH Z 343 " =    2.751
peak=    3.981 closest distance to " CA  ARG A 195 " =    1.202
peak=    3.971 closest distance to " CZ  PHE A 218 " =    1.290
peak=    3.949 closest distance to " CB  TRP A 179 " =    1.415
peak=    3.916 closest distance to " CB  ALA A 100 " =    1.408
peak=    3.915 closest distance to " CB  VAL A 202 " =    1.350
peak=    3.907 closest distance to " CB  ASN A 285 " =    0.915
peak=    3.896 closest distance to " CE1 HIS A 108 " =    1.054
peak=    3.894 closest distance to " NH2AARG A 145 " =    1.100
peak=    3.887 closest distance to " O   HOH Z 388 " =    1.256
peak=    3.880 closest distance to " O   HOH Z 394 " =    1.891
peak=    3.874 closest distance to " NH2 ARG A  79 " =    1.423
peak=    3.872 closest distance to " O   ALA A 165 " =    1.300
peak=    3.863 closest distance to " ND2 ASN A 301 " =    0.983
peak=    3.808 closest distance to " O   HOH Z 126 " =    1.658
peak=    3.794 closest distance to " O   HOH Z 199 " =    1.490
peak=    3.792 closest distance to " CB  GLN A 223 " =    1.480
peak=    3.789 closest distance to " CB  GLU A 152 " =    1.117
peak=    3.785 closest distance to " CG  MET A 185 " =    1.190
peak=    3.784 closest distance to " CB  ARG A 275 " =    0.821
peak=    3.780 closest distance to " CB  MET A  40 " =    0.879
peak=    3.777 closest distance to " O   HOH Z 427 " =    2.590
peak=    3.776 closest distance to " CB  TRP A 179 " =    1.569
peak=    3.773 closest distance to " CG2 ILE A 234 " =    1.317
peak=    3.765 closest distance to " O   HOH Z 261 " =    2.515
peak=    3.764 closest distance to " CG2BVAL A  41 " =    1.274
peak=    3.763 closest distance to " O   HOH Z 130 " =    1.078
peak=    3.760 closest distance to " O   HOH Z 273 " =    3.091
peak=    3.749 closest distance to " O   HOH Z 426 " =    1.190
peak=    3.744 closest distance to " CD2 TRP A 179 " =    1.200
peak=    3.741 closest distance to " O   HOH Z  80 " =    2.010
peak=    3.729 closest distance to " O   HOH Z 214 " =    1.521
peak=    3.719 closest distance to " O   HOH Z  35 " =    1.941
peak=    3.710 closest distance to " CB  PRO A  54 " =    0.869
peak=    3.700 closest distance to " OE1 GLU A   2 " =    1.432
peak=    3.699 closest distance to " CD ALYS A 290 " =    1.293
peak=    3.697 closest distance to " O   GLU A   2 " =    1.731
peak=    3.694 closest distance to " CB  THR A  31 " =    1.309
peak=    3.692 closest distance to " O   HOH Z 423 " =    1.835
peak=    3.687 closest distance to " CB  THR A 235 " =    1.329
peak=    3.671 closest distance to " CG  PRO A 243 " =    1.270
peak=    3.671 closest distance to " CA  SER A  12 " =    1.364
peak=    3.647 closest distance to " O   HOH Z  57 " =    2.439
peak=    3.641 closest distance to " O   HOH Z  40 " =    2.131
peak=    3.637 closest distance to " O   HOH Z 401 " =    1.222
peak=    3.620 closest distance to " CB  GLN A  73 " =    1.444
peak=    3.620 closest distance to " O   HOH Z 435 " =    1.767
peak=    3.607 closest distance to " O   HOH Z 417 " =    3.049
peak=    3.604 closest distance to " O   HOH Z 395 " =    1.515
peak=    3.603 closest distance to " CA  ARG A  66 " =    0.877
peak=    3.598 closest distance to " O   HOH Z  48 " =    1.777
peak=    3.595 closest distance to " CG  MET A 188 " =    0.938
peak=    3.594 closest distance to " O   HOH Z 176 " =    1.667
peak=    3.591 closest distance to " O   HOH Z 134 " =    2.427
peak=    3.590 closest distance to " NZ  LYS A  48 " =    1.317
peak=    3.589 closest distance to " CG1 VAL A 153 " =    1.071
peak=    3.587 closest distance to " NZ  LYS A  76 " =    1.106
peak=    3.576 closest distance to " CG  PRO A  54 " =    1.192
peak=    3.574 closest distance to " O   ASP A 200 " =    1.625
peak=    3.573 closest distance to " O   HOH Z 368 " =    4.189
peak=    3.571 closest distance to " CG2 ILE A  33 " =    1.416
peak=    3.570 closest distance to " CD1 LEU A 228 " =    1.577
peak=    3.565 closest distance to " ND2 ASN A 249 " =    2.188
peak=    3.564 closest distance to " CG  ARG A 138 " =    1.505
peak=    3.562 closest distance to " O   HOH Z 369 " =    1.517
peak=    3.561 closest distance to " O   HOH Z 359 " =    1.641
peak=    3.559 closest distance to " CZ3 TRP A  92 " =    1.299
peak=    3.555 closest distance to " O   HOH Z 150 " =    1.910
peak=    3.552 closest distance to " O   HOH Z 232 " =    2.247
peak=    3.545 closest distance to " CG2 VAL A 197 " =    1.165
peak=    3.544 closest distance to " N   ASN A  39 " =    1.216
peak=    3.543 closest distance to " O   HOH Z 246 " =    1.455
peak=    3.535 closest distance to " CB  ARG A 269 " =    1.943
peak=    3.534 closest distance to " CD  PRO A  54 " =    1.029
peak=    3.530 closest distance to " N   TYR A 247 " =    1.257
peak=    3.525 closest distance to " O   HOH Z 418 " =    1.770
peak=    3.522 closest distance to " O   HOH Z  59 " =    1.883
peak=    3.517 closest distance to " O   HOH Z 126 " =    2.689
peak=    3.516 closest distance to " CB  LEU A 281 " =    0.829
peak=    3.504 closest distance to " CB  ASN A 148 " =    1.411
peak=    3.499 closest distance to " O   ASP A 298 " =    0.921
peak=    3.499 closest distance to " CB  ALA A 242 " =    1.020
peak=    3.498 closest distance to " O   HOH Z  44 " =    1.793
peak=    3.493 closest distance to " O   HOH Z  26 " =    1.212
peak=    3.492 closest distance to " CE1 TYR A 186 " =    1.232
peak=    3.489 closest distance to " CA  ASN A 215 " =    1.151
peak=    3.489 closest distance to " O   HOH Z 251 " =    1.530
peak=    3.487 closest distance to " CA  GLN A  11 " =    0.876
peak=    3.484 closest distance to " O   HOH Z 415 " =    1.248
peak=    3.484 closest distance to " O   HOH Z 301 " =    2.155
peak=    3.481 closest distance to " NE1 TRP A  92 " =    1.370
peak=    3.481 closest distance to " O   GLY A  91 " =    1.172
peak=    3.480 closest distance to " O   HOH Z  63 " =    2.070
peak=    3.476 closest distance to " CB  GLU A 277 " =    3.885
peak=    3.472 closest distance to " CB  THR A 294 " =    1.531
peak=    3.471 closest distance to " O   HOH Z 197 " =    4.900
peak=    3.467 closest distance to " O   HOH Z 227 " =    1.660
peak=    3.466 closest distance to " CB  ARG A  79 " =    1.095
peak=    3.462 closest distance to " O   HOH Z  44 " =    2.111
peak=    3.460 closest distance to " O   PRO A  90 " =    1.472
peak=    3.456 closest distance to " CG1 ILE A  33 " =    1.139
peak=    3.453 closest distance to " O   HOH Z 102 " =    1.464
peak=    3.449 closest distance to " O   HOH Z 396 " =    1.160
peak=    3.448 closest distance to " CA  ASN A 249 " =    1.308
peak=    3.447 closest distance to " CD1 LEU A 222 " =    0.778
peak=    3.446 closest distance to " CG2 THR A 221 " =    1.227
peak=    3.445 closest distance to " OG  SER A 245 " =    1.614
peak=    3.444 closest distance to " CB  THR A  52 " =    0.905
peak=    3.444 closest distance to " CB  TRP A 150 " =    1.547
peak=    3.443 closest distance to " O   HOH Z  54 " =    1.004
peak=    3.436 closest distance to " OH  TYR A 293 " =    1.355
peak=    3.434 closest distance to " OD1 ASP A 191 " =    1.734
peak=    3.430 closest distance to " CD  LYS A 119 " =    1.923
peak=    3.430 closest distance to " O   HOH Z 183 " =    1.854
peak=    3.427 closest distance to " CD  ARG A 159 " =    0.847
peak=    3.421 closest distance to " O  BHOH Z 338 " =    0.957
peak=    3.420 closest distance to " O   HOH Z 299 " =    2.662
peak=    3.413 closest distance to " CB  MET A 105 " =    1.462
peak=    3.412 closest distance to " CG  GLN A  11 " =    0.926
peak=    3.411 closest distance to " CA  ALA A 295 " =    0.964
peak=    3.411 closest distance to " CB  ASN A 187 " =    1.211
peak=    3.409 closest distance to " CG2 ILE A  20 " =    1.465
peak=    3.409 closest distance to " O   HOH Z 421 " =    1.717
peak=    3.407 closest distance to " O   HOH Z 419 " =    1.994
peak=    3.407 closest distance to " O   HOH Z 291 " =    1.561
peak=    3.404 closest distance to " CB  TRP A 266 " =    1.045
peak=    3.402 closest distance to " OG  SER A  62 " =    2.789
peak=    3.395 closest distance to " O   HOH Z 368 " =    3.027
peak=    3.395 closest distance to " O   ARG A  14 " =    1.484
peak=    3.387 closest distance to " C   ALA A 299 " =    0.848
peak=    3.385 closest distance to " O   HOH Z 196 " =    1.530
peak=    3.378 closest distance to " CG1 ILE A  20 " =    1.271
peak=    3.367 closest distance to " O   VAL A  72 " =    1.376
peak=    3.366 closest distance to " CB  SER A 141 " =    1.013
peak=    3.364 closest distance to " O   HOH Z  88 " =    2.684
peak=    3.364 closest distance to " O   HOH Z   4 " =    1.705
peak=    3.363 closest distance to " N   ASP A 162 " =    1.228
peak=    3.360 closest distance to " O   HOH Z  30 " =    1.275
peak=    3.359 closest distance to " CA  VAL A  41 " =    0.915
peak=    3.355 closest distance to " CB  GLU A 175 " =    1.308
peak=    3.354 closest distance to " O   HOH Z 433 " =    1.944
peak=    3.350 closest distance to " CG2 VAL A  78 " =    1.063
peak=    3.349 closest distance to " O   HOH Z 265 " =    1.995
peak=    3.349 closest distance to " OE2 GLU A   2 " =    2.081
peak=    3.348 closest distance to " O   HOH Z 415 " =    1.555
peak=    3.343 closest distance to " O   HOH Z 150 " =    2.029
peak=    3.342 closest distance to " NH2BARG A 190 " =    1.926
peak=    3.339 closest distance to " CB  ARG A 219 " =    1.363
peak=    3.338 closest distance to " CD1 LEU A   5 " =    1.315
peak=    3.330 closest distance to " CA  ASP A 191 " =    1.229
peak=    3.329 closest distance to " O   HOH Z 156 " =    4.929
peak=    3.323 closest distance to " O   PHE A  16 " =    1.563
peak=    3.323 closest distance to " O   HOH Z 163 " =    2.039
peak=    3.322 closest distance to " CB  SER A  26 " =    1.652
peak=    3.321 closest distance to " CB  PRO A  90 " =    1.213
peak=    3.320 closest distance to " CA  GLY A 196 " =    0.822
peak=    3.317 closest distance to " OG  SER A  62 " =    2.946
peak=    3.311 closest distance to " CZ  PHE A  38 " =    1.083
peak=    3.308 closest distance to " O   HOH Z 430 " =    2.140
peak=    3.307 closest distance to " NH1 ARG A 269 " =    0.831
peak=    3.305 closest distance to " O   HOH Z 280 " =    3.037
peak=    3.305 closest distance to " O   THR A 220 " =    1.062
peak=    3.304 closest distance to " O   HOH Z 142 " =    1.748
peak=    3.301 closest distance to " CA  ASP A 140 " =    1.323
peak=    3.298 closest distance to " O   HOH Z 365 " =    2.296
peak=    3.296 closest distance to " ND1 HIS A  81 " =    1.646
peak=    3.295 closest distance to " CB  ALA A 248 " =    1.441
peak=    3.294 closest distance to " O   HOH Z 279 " =    1.113
peak=    3.294 closest distance to " O   HOH Z  47 " =    2.787
peak=    3.293 closest distance to " N   ASP A 298 " =    1.221
peak=    3.291 closest distance to " O   HOH Z  42 " =    2.431
peak=    3.289 closest distance to " O   HOH Z 368 " =    4.285
peak=    3.289 closest distance to " CG  ARG A  36 " =    1.101
peak=    3.287 closest distance to " O   HOH Z 345 " =    1.873
peak=    3.285 closest distance to " OD2 ASP A  27 " =    1.355
peak=    3.285 closest distance to " CG  ASN A 252 " =    1.260
peak=    3.278 closest distance to " CB  LEU A  83 " =    0.736
peak=    3.276 closest distance to " O  BHOH Z 338 " =    2.384
peak=    3.272 closest distance to " CA  LEU A  83 " =    1.231
peak=    3.269 closest distance to " O   HOH Z  68 " =    2.467
peak=    3.269 closest distance to " CA  ALA A  51 " =    1.029
peak=    3.269 closest distance to " CA  TYR A 116 " =    1.466
peak=    3.266 closest distance to " NE2 GLN A 194 " =    1.551
peak=    3.265 closest distance to " O   HOH Z 155 " =    2.985
peak=    3.259 closest distance to " N   ILE A  33 " =    0.986
peak=    3.255 closest distance to " CA  ASP A 149 " =    1.262
peak=    3.250 closest distance to " CZ3 TRP A 266 " =    1.172
peak=    3.249 closest distance to " O   HOH Z 132 " =    2.818
peak=    3.245 closest distance to " CG  PRO A 198 " =    1.430
peak=    3.241 closest distance to " O   HOH Z 217 " =    2.964
peak=    3.241 closest distance to " CA  ILE A 106 " =    0.771
peak=    3.234 closest distance to " O   HOH Z  85 " =    2.035
peak=    3.231 closest distance to " OD2 ASP A 298 " =    3.514
peak=    3.231 closest distance to " CG ALYS A 290 " =    1.093
peak=    3.231 closest distance to " O   HOH Z  64 " =    2.655
peak=    3.230 closest distance to " O   PRO A 198 " =    1.508
peak=    3.230 closest distance to " CB  ASN A 142 " =    1.364
peak=    3.230 closest distance to " CB  SER A 288 " =    1.769
peak=    3.228 closest distance to " O   HOH Z 153 " =    2.271
peak=    3.223 closest distance to " CB  PHE A 283 " =    0.924
peak=    3.220 closest distance to " C   VAL A 265 " =    1.158
peak=    3.218 closest distance to " O   HOH Z 131 " =    2.299
peak=    3.215 closest distance to " ND2 ASN A 110 " =    1.279
peak=    3.214 closest distance to " CB  ASN A  39 " =    0.709
peak=    3.214 closest distance to " CA  THR A 246 " =    0.896
peak=    3.211 closest distance to " O   HOH Z 344 " =    2.956
peak=    3.209 closest distance to " CA  SER A  87 " =    0.996
peak=    3.205 closest distance to " CA  SER A  62 " =    0.830
peak=    3.199 closest distance to " O   HOH Z 327 " =    1.673
peak=    3.196 closest distance to " O   HOH Z 128 " =    1.989
peak=    3.193 closest distance to " O   HOH Z 316 " =    3.148
peak=    3.191 closest distance to " CB  GLU A  46 " =    0.944
peak=    3.190 closest distance to " CB  SER A  97 " =    1.488
peak=    3.186 closest distance to " O   HOH Z 328 " =    2.183
peak=    3.184 closest distance to " CB  ALA A 256 " =    1.363
peak=    3.181 closest distance to " O   HOH Z 285 " =    1.903
peak=    3.180 closest distance to " O   HOH Z 285 " =    2.535
peak=    3.178 closest distance to " O   HOH Z 109 " =    2.963
peak=    3.177 closest distance to " CB  SER A   3 " =    1.064
peak=    3.176 closest distance to " O   HOH Z 189 " =    3.094
peak=    3.174 closest distance to " O   HOH Z 185 " =    1.719
peak=    3.172 closest distance to " O   HOH Z  38 " =    1.501
peak=    3.172 closest distance to " O   LYS A 289 " =    1.138
peak=    3.170 closest distance to " CB  ALA A  71 " =    1.301
peak=    3.169 closest distance to " CD  ARG A 269 " =    0.925
peak=    3.168 closest distance to " O   HOH Z  20 " =    2.896
peak=    3.167 closest distance to " CB  ARG A 190 " =    1.869
peak=    3.161 closest distance to " O   HOH Z 380 " =    1.901
peak=    3.159 closest distance to " CG2 THR A  29 " =    1.613
peak=    3.156 closest distance to " O   HOH Z 337 " =    1.563
peak=    3.151 closest distance to " CB  ALA A 226 " =    1.143
peak=    3.151 closest distance to " O   HOH Z 406 " =    1.600
peak=    3.146 closest distance to " O   HOH Z 223 " =    1.277
peak=    3.142 closest distance to " CB  TYR A  30 " =    0.993
peak=    3.142 closest distance to " O   HOH Z  56 " =    1.710
peak=    3.136 closest distance to " NH1 ARG A  14 " =    1.046
peak=    3.133 closest distance to " NE  ARG A  36 " =    1.158
peak=    3.128 closest distance to " O   HOH Z 417 " =    1.173
peak=    3.127 closest distance to " CB  LEU A 143 " =    1.137
peak=    3.125 closest distance to " OD1 ASN A 217 " =    1.668
peak=    3.123 closest distance to " CB  SER A 146 " =    1.198
peak=    3.117 closest distance to " O   HOH Z 189 " =    3.489
peak=    3.109 closest distance to " CA  VAL A 125 " =    0.993
peak=    3.108 closest distance to " CA  ALA A 100 " =    1.018
peak=    3.105 closest distance to " CA  ASN A 217 " =    1.250
peak=    3.105 closest distance to " CB  ARG A 259 " =    1.972
peak=    3.100 closest distance to " CG2 THR A  42 " =    0.853
peak=    3.087 closest distance to " O   HOH Z  90 " =    3.780
peak=    3.086 closest distance to " CA  CYS A 168 " =    1.199
peak=    3.080 closest distance to " CG  PRO A 213 " =    1.188
peak=    3.080 closest distance to " O   HOH Z 394 " =    3.998
peak=    3.078 closest distance to " O   HOH Z 250 " =    1.373
peak=    3.077 closest distance to " O   HOH Z  78 " =    1.644
peak=    3.068 closest distance to " O   HOH Z  46 " =    1.279
peak=    3.067 closest distance to " O   MET A 113 " =    1.251
peak=    3.041 closest distance to " CG  ARG A  66 " =    1.022
peak=    3.032 closest distance to " CZ3 TRP A  85 " =    0.897
peak=    3.010 closest distance to " C   ILE A 106 " =    1.755
peak=    3.005 closest distance to " O   THR A 220 " =    1.406

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 239         
Filter by distance & map next to the model:
   mapped sites are within: 0.640 - 5.942
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 236 from: 239
   mapped sites are within: 0.746 - 5.942

peak=   -5.225 closest distance to " CG2 VAL A 230 " =    0.972
peak=   -4.629 closest distance to " O   HOH Z 400 " =    0.977
peak=   -4.592 closest distance to " OD1 ASN A 301 " =    0.746
peak=   -4.469 closest distance to " CD  ARG A  14 " =    3.155
peak=   -4.461 closest distance to " CD  GLN A  58 " =    0.910
peak=   -4.454 closest distance to " O   HOH Z 166 " =    1.361
peak=   -4.408 closest distance to " O   HOH Z 411 " =    5.423
peak=   -4.315 closest distance to " CD  GLN A 223 " =    1.262
peak=   -4.260 closest distance to " CG  PRO A 243 " =    1.720
peak=   -4.212 closest distance to " O   HOH Z  52 " =    2.199
peak=   -4.200 closest distance to " OD1 ASN A 148 " =    1.310
peak=   -4.162 closest distance to " CA  ASP A 298 " =    1.115
peak=   -4.123 closest distance to " CA  SER A 276 " =    1.432
peak=   -4.111 closest distance to " O   HOH Z  13 " =    1.679
peak=   -4.079 closest distance to " CG1 VAL A 112 " =    2.582
peak=   -4.072 closest distance to " CD1 PHE A  59 " =    1.956
peak=   -4.070 closest distance to " O   HOH Z   5 " =    1.807
peak=   -4.058 closest distance to " CG2 ILE A  49 " =    2.641
peak=   -4.016 closest distance to " O   GLN A  11 " =    0.919
peak=   -3.957 closest distance to " CA  VAL A 197 " =    0.975
peak=   -3.952 closest distance to " O   HOH Z 174 " =    1.641
peak=   -3.930 closest distance to " CG1 VAL A 296 " =    0.977
peak=   -3.881 closest distance to " CG  ARG A 269 " =    2.560
peak=   -3.880 closest distance to " CD  ARG A  36 " =    0.918
peak=   -3.878 closest distance to " CA  TYR A  68 " =    2.936
peak=   -3.874 closest distance to " OXT GLY A 302 " =    2.920
peak=   -3.870 closest distance to " O   HOH Z  37 " =    1.351
peak=   -3.868 closest distance to " O   HOH Z 351 " =    1.799
peak=   -3.842 closest distance to " CB  ALA A 291 " =    2.513
peak=   -3.815 closest distance to " CG1 VAL A 197 " =    2.426
peak=   -3.811 closest distance to " CB  ALA A 161 " =    2.563
peak=   -3.796 closest distance to " CB  ALA A 248 " =    2.354
peak=   -3.790 closest distance to " CD1 LEU A 167 " =    2.060
peak=   -3.756 closest distance to " O   HOH Z 250 " =    1.721
peak=   -3.723 closest distance to " N   ALA A   1 " =    2.582
peak=   -3.713 closest distance to " OD1 ASP A 298 " =    2.325
peak=   -3.694 closest distance to " CZ3 TRP A  70 " =    1.438
peak=   -3.693 closest distance to " O   HOH Z  35 " =    1.237
peak=   -3.675 closest distance to " C   VAL A 265 " =    0.980
peak=   -3.673 closest distance to " N   ALA A 226 " =    2.294
peak=   -3.670 closest distance to " CE  MET A 105 " =    2.320
peak=   -3.667 closest distance to " OG  SER A  63 " =    1.088
peak=   -3.665 closest distance to " O   HOH Z 103 " =    2.312
peak=   -3.662 closest distance to " N   SER A 134 " =    1.203
peak=   -3.662 closest distance to " O   HOH Z  60 " =    1.783
peak=   -3.657 closest distance to " CG1 VAL A 250 " =    2.446
peak=   -3.657 closest distance to " CA  SER A 164 " =    1.954
peak=   -3.649 closest distance to " O   HOH Z 150 " =    1.036
peak=   -3.646 closest distance to " O   HOH Z 231 " =    1.670
peak=   -3.641 closest distance to " O   HOH Z 151 " =    0.938
peak=   -3.636 closest distance to " O   HOH Z 222 " =    1.351
peak=   -3.626 closest distance to " O   HOH Z  30 " =    1.273
peak=   -3.621 closest distance to " O   HOH Z 361 " =    4.461
peak=   -3.621 closest distance to " O   SER A  95 " =    2.031
peak=   -3.620 closest distance to " O   PRO A 198 " =    1.294
peak=   -3.618 closest distance to " CD2 PHE A  61 " =    2.122
peak=   -3.618 closest distance to " CG  GLN A 103 " =    2.345
peak=   -3.615 closest distance to " O   HOH Z   7 " =    1.550
peak=   -3.611 closest distance to " O   HOH Z 109 " =    3.354
peak=   -3.608 closest distance to " NH1 ARG A 195 " =    1.023
peak=   -3.606 closest distance to " CE2 PHE A 218 " =    2.455
peak=   -3.595 closest distance to " O   SER A 276 " =    1.555
peak=   -3.591 closest distance to " O   HOH Z 401 " =    1.275
peak=   -3.590 closest distance to " CG2 VAL A 189 " =    2.232
peak=   -3.579 closest distance to " CG2 THR A 279 " =    1.987
peak=   -3.573 closest distance to " CG  MET A  93 " =    2.385
peak=   -3.562 closest distance to " O   HOH Z 407 " =    3.339
peak=   -3.557 closest distance to " CE  LYS A 119 " =    2.235
peak=   -3.553 closest distance to " N   ALA A  43 " =    2.696
peak=   -3.552 closest distance to " OG  SER A  97 " =    2.406
peak=   -3.548 closest distance to " O   HOH Z 171 " =    2.309
peak=   -3.547 closest distance to " CE2 PHE A  61 " =    2.620
peak=   -3.546 closest distance to " CG1AVAL A 121 " =    1.288
peak=   -3.546 closest distance to " O   HOH Z 368 " =    1.943
peak=   -3.544 closest distance to " O   HOH Z  57 " =    0.861
peak=   -3.539 closest distance to " OE2 GLU A 152 " =    1.504
peak=   -3.538 closest distance to " OD2 ASP A 298 " =    0.899
peak=   -3.528 closest distance to " O   TYR A  15 " =    1.794
peak=   -3.526 closest distance to " CD  GLN A 223 " =    0.848
peak=   -3.523 closest distance to " O   HOH Z 216 " =    1.165
peak=   -3.520 closest distance to " O   HOH Z 369 " =    2.554
peak=   -3.515 closest distance to " O   HOH Z 275 " =    1.694
peak=   -3.506 closest distance to " O   HOH Z 394 " =    1.651
peak=   -3.506 closest distance to " NH2 ARG A  66 " =    1.641
peak=   -3.497 closest distance to " C   ASN A 285 " =    2.362
peak=   -3.495 closest distance to " CB  ALA A 291 " =    2.483
peak=   -3.490 closest distance to " CA  TRP A 274 " =    1.015
peak=   -3.489 closest distance to " CB  HIS A  86 " =    2.356
peak=   -3.485 closest distance to " N   VAL A 230 " =    1.073
peak=   -3.483 closest distance to " O   HOH Z  15 " =    1.396
peak=   -3.479 closest distance to " O   HOH Z 285 " =    1.628
peak=   -3.470 closest distance to " O   HOH Z  56 " =    1.800
peak=   -3.464 closest distance to " CG2 THR A 182 " =    2.372
peak=   -3.460 closest distance to " OG BSER A 210 " =    1.193
peak=   -3.451 closest distance to " O   HOH Z 313 " =    1.287
peak=   -3.449 closest distance to " O   HOH Z 423 " =    2.938
peak=   -3.444 closest distance to " CG  LEU A  83 " =    2.223
peak=   -3.444 closest distance to " CB  PRO A 243 " =    2.940
peak=   -3.441 closest distance to " O   HOH Z  54 " =    1.345
peak=   -3.438 closest distance to " O   SER A 206 " =    1.206
peak=   -3.435 closest distance to " OG  SER A 141 " =    1.340
peak=   -3.433 closest distance to " O   HOH Z 121 " =    2.790
peak=   -3.431 closest distance to " CD2 LEU A 228 " =    2.691
peak=   -3.421 closest distance to " O   HOH Z 137 " =    1.504
peak=   -3.420 closest distance to " CB  ALA A  10 " =    2.036
peak=   -3.413 closest distance to " O   HOH Z 101 " =    1.403
peak=   -3.411 closest distance to " O   HOH Z 414 " =    2.068
peak=   -3.410 closest distance to " C   THR A 264 " =    1.301
peak=   -3.409 closest distance to " CD2 TYR A 293 " =    1.741
peak=   -3.406 closest distance to " CD2 PHE A 225 " =    0.995
peak=   -3.400 closest distance to " N   SER A   3 " =    2.474
peak=   -3.397 closest distance to " N   ILE A 120 " =    1.288
peak=   -3.389 closest distance to " O   HOH Z 198 " =    1.231
peak=   -3.389 closest distance to " O   HOH Z 412 " =    2.279
peak=   -3.388 closest distance to " CD2 PHE A 192 " =    2.151
peak=   -3.386 closest distance to " O   HOH Z  90 " =    3.122
peak=   -3.385 closest distance to " CB  PRO A  54 " =    2.577
peak=   -3.379 closest distance to " O   ASP A 298 " =    1.821
peak=   -3.378 closest distance to " OG1 THR A  82 " =    1.310
peak=   -3.378 closest distance to " O   ALA A  34 " =    2.509
peak=   -3.375 closest distance to " O   HOH Z 418 " =    1.544
peak=   -3.375 closest distance to " OE2 GLU A 277 " =    2.968
peak=   -3.365 closest distance to " O   HOH Z 265 " =    1.359
peak=   -3.365 closest distance to " OE1 GLN A  88 " =    1.160
peak=   -3.361 closest distance to " CG  PRO A 280 " =    1.903
peak=   -3.361 closest distance to " O   HOH Z 221 " =    1.090
peak=   -3.358 closest distance to " O   HOH Z 189 " =    2.193
peak=   -3.357 closest distance to " O   HOH Z 108 " =    2.039
peak=   -3.357 closest distance to " CZ  ARG A 259 " =    0.924
peak=   -3.356 closest distance to " CH2 TRP A 179 " =    1.145
peak=   -3.352 closest distance to " O   HOH Z 283 " =    2.226
peak=   -3.348 closest distance to " O   HOH Z 127 " =    1.732
peak=   -3.344 closest distance to " O   HOH Z 252 " =    3.839
peak=   -3.342 closest distance to " OH  TYR A 172 " =    1.848
peak=   -3.342 closest distance to " NH2 ARG A  36 " =    1.303
peak=   -3.342 closest distance to " ND2 ASN A  45 " =    1.306
peak=   -3.341 closest distance to " N   ALA A 295 " =    0.969
peak=   -3.340 closest distance to " O   HOH Z 422 " =    0.995
peak=   -3.331 closest distance to " O   HOH Z 231 " =    2.123
peak=   -3.330 closest distance to " O   HOH Z 134 " =    2.090
peak=   -3.326 closest distance to " CB  SER A 146 " =    2.071
peak=   -3.323 closest distance to " CZ  TYR A 169 " =    1.678
peak=   -3.320 closest distance to " O  BHOH Z 338 " =    1.216
peak=   -3.315 closest distance to " CD  GLN A  77 " =    0.953
peak=   -3.314 closest distance to " CG  ASP A  50 " =    2.370
peak=   -3.313 closest distance to " ND2 ASN A  60 " =    1.767
peak=   -3.303 closest distance to " O   HOH Z 114 " =    3.373
peak=   -3.303 closest distance to " CD  ARG A 156 " =    2.110
peak=   -3.302 closest distance to " ND2 ASN A  60 " =    1.652
peak=   -3.297 closest distance to " CZ2 TRP A 179 " =    2.198
peak=   -3.292 closest distance to " O   HOH Z 166 " =    1.415
peak=   -3.290 closest distance to " O   HOH Z 210 " =    0.868
peak=   -3.288 closest distance to " O   HOH Z 422 " =    1.363
peak=   -3.286 closest distance to " OD2 ASP A 171 " =    2.022
peak=   -3.284 closest distance to " O   SER A 271 " =    1.966
peak=   -3.278 closest distance to " O   HOH Z 114 " =    1.610
peak=   -3.277 closest distance to " CD1 ILE A 263 " =    2.449
peak=   -3.275 closest distance to " CG  GLN A  11 " =    1.223
peak=   -3.273 closest distance to " CD1 ILE A 151 " =    2.446
peak=   -3.271 closest distance to " O   HOH Z  64 " =    1.566
peak=   -3.266 closest distance to " CD1 LEU A  25 " =    2.686
peak=   -3.266 closest distance to " O   HOH Z  81 " =    1.366
peak=   -3.265 closest distance to " CG1 VAL A 189 " =    2.397
peak=   -3.255 closest distance to " O   HOH Z 165 " =    1.498
peak=   -3.252 closest distance to " CE3 TRP A 150 " =    2.345
peak=   -3.252 closest distance to " CD1 TYR A 247 " =    2.440
peak=   -3.250 closest distance to " O   HOH Z 340 " =    1.386
peak=   -3.250 closest distance to " O   HOH Z  40 " =    2.783
peak=   -3.249 closest distance to " O   HOH Z 290 " =    1.172
peak=   -3.239 closest distance to " CA  GLY A  98 " =    2.048
peak=   -3.239 closest distance to " O   HOH Z 269 " =    4.613
peak=   -3.237 closest distance to " O   HOH Z 301 " =    2.542
peak=   -3.236 closest distance to " O   HOH Z 200 " =    1.393
peak=   -3.235 closest distance to " CG2 ILE A 263 " =    2.151
peak=   -3.234 closest distance to " O   HOH Z  88 " =    4.292
peak=   -3.234 closest distance to " CG  ARG A 259 " =    2.491
peak=   -3.232 closest distance to " CB  ALA A  43 " =    2.692
peak=   -3.229 closest distance to " CA  GLY A 241 " =    3.283
peak=   -3.226 closest distance to " O   HOH Z 124 " =    1.577
peak=   -3.225 closest distance to " C   ALA A 158 " =    1.394
peak=   -3.224 closest distance to " O   HOH Z  58 " =    0.927
peak=   -3.222 closest distance to " O   HOH Z 388 " =    1.893
peak=   -3.221 closest distance to " O   HOH Z 378 " =    1.193
peak=   -3.217 closest distance to " CA  GLY A 203 " =    2.344
peak=   -3.217 closest distance to " CZ  PHE A  38 " =    2.498
peak=   -3.214 closest distance to " OG  SER A  62 " =    1.023
peak=   -3.209 closest distance to " O   HOH Z 131 " =    0.793
peak=   -3.209 closest distance to " O   HOH Z 107 " =    1.012
peak=   -3.201 closest distance to " O   HOH Z 184 " =    1.337
peak=   -3.194 closest distance to " CG2 THR A 235 " =    2.646
peak=   -3.190 closest distance to " CG  LEU A   5 " =    0.896
peak=   -3.190 closest distance to " O   HOH Z   6 " =    2.004
peak=   -3.190 closest distance to " CD2 TYR A  30 " =    2.611
peak=   -3.188 closest distance to " O   SER A 135 " =    2.145
peak=   -3.185 closest distance to " O   HOH Z 244 " =    1.750
peak=   -3.183 closest distance to " O   HOH Z 234 " =    4.161
peak=   -3.182 closest distance to " CG  PRO A 163 " =    1.685
peak=   -3.175 closest distance to " O   HOH Z 156 " =    3.572
peak=   -3.175 closest distance to " OG  SER A  87 " =    1.850
peak=   -3.168 closest distance to " OD1 ASN A 173 " =    1.493
peak=   -3.167 closest distance to " NE  ARG A  66 " =    4.740
peak=   -3.157 closest distance to " NE2 HIS A 115 " =    1.113
peak=   -3.157 closest distance to " O   HOH Z  55 " =    1.501
peak=   -3.153 closest distance to " O   HOH Z 150 " =    1.653
peak=   -3.150 closest distance to " ND2 ASN A  45 " =    2.550
peak=   -3.141 closest distance to " CG1BVAL A  72 " =    5.564
peak=   -3.138 closest distance to " SD  MET A 105 " =    2.441
peak=   -3.136 closest distance to " O   HOH Z 196 " =    1.622
peak=   -3.136 closest distance to " CD1 ILE A 109 " =    2.188
peak=   -3.135 closest distance to " NH2 ARG A  79 " =    1.935
peak=   -3.135 closest distance to " CB  SER A  62 " =    5.942
peak=   -3.134 closest distance to " O   CYS A 201 " =    1.016
peak=   -3.133 closest distance to " O   HOH Z 310 " =    4.132
peak=   -3.132 closest distance to " O   HOH Z 392 " =    3.527
peak=   -3.130 closest distance to " O   HOH Z 109 " =    1.190
peak=   -3.126 closest distance to " CZ  ARG A  79 " =    1.823
peak=   -3.120 closest distance to " OH  TYR A 247 " =    1.884
peak=   -3.119 closest distance to " O   HOH Z 368 " =    1.306
peak=   -3.116 closest distance to " NE  ARG A  79 " =    1.278
peak=   -3.110 closest distance to " N   THR A  52 " =    1.676
peak=   -3.110 closest distance to " CB  ASP A 162 " =    2.642
peak=   -3.109 closest distance to " O   HOH Z 259 " =    1.543
peak=   -3.107 closest distance to " CB  MET A 188 " =    1.625
peak=   -3.106 closest distance to " C   LEU A 222 " =    0.917
peak=   -3.097 closest distance to " C   MET A 188 " =    1.260
peak=   -3.094 closest distance to " O   HOH Z  29 " =    1.279
peak=   -3.093 closest distance to " CG1BVAL A  72 " =    2.656
peak=   -3.069 closest distance to " O   HOH Z 265 " =    1.969
peak=   -3.068 closest distance to " O   HOH Z 378 " =    1.418
peak=   -3.061 closest distance to " O   HOH Z 411 " =    1.732
peak=   -3.060 closest distance to " CA  ASN A 127 " =    1.033
peak=   -3.060 closest distance to " CD  PRO A 213 " =    2.196
peak=   -3.053 closest distance to " O   HOH Z 417 " =    1.234
peak=   -3.052 closest distance to " O   HOH Z 137 " =    1.026
peak=   -3.045 closest distance to " O   VAL A 174 " =    2.252
peak=   -3.036 closest distance to " O   HOH Z 109 " =    1.180

================= 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    :  0.5080 0.4947   6.304982e+00   6.290560e+00
   1_bss:  0.5016 0.4885   6.300053e+00   6.287170e+00
   1_xyz:  0.4374 0.4476   6.238588e+00   6.245313e+00
   1_adp:  0.3964 0.4437   6.182436e+00   6.238719e+00
   1_occ:  0.3955 0.4430   6.181864e+00   6.239184e+00
   2_bss:  0.3932 0.4373   6.182883e+00   6.238726e+00
   2_xyz:  0.3381 0.4106   6.086784e+00   6.193587e+00
   2_adp:  0.3312 0.3959   6.074571e+00   6.175628e+00
   2_occ:  0.3312 0.3962   6.074207e+00   6.176047e+00
   3_bss:  0.3313 0.3949   6.075015e+00   6.176653e+00
   3_xyz:  0.2799 0.3346   5.928681e+00   6.062914e+00
   3_adp:  0.2662 0.3222   5.897068e+00   6.037711e+00
   3_occ:  0.2660 0.3224   5.897044e+00   6.038435e+00
   4_bss:  0.2658 0.3225   5.897352e+00   6.038838e+00
   4_xyz:  0.1987 0.2467   5.629338e+00   5.812032e+00
   4_adp:  0.1847 0.2375   5.575401e+00   5.776428e+00
   4_occ:  0.1846 0.2379   5.574899e+00   5.776534e+00
   5_bss:  0.1845 0.2372   5.574484e+00   5.773961e+00
   5_xyz:  0.1538 0.2065   5.428355e+00   5.651274e+00
   5_adp:  0.1377 0.1875   5.326078e+00   5.553878e+00
   5_occ:  0.1376 0.1875   5.325613e+00   5.553478e+00
   5_bss:  0.1379 0.1878   5.325208e+00   5.552267e+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   5.457  11.553   9.068   0.000   0.000   0.000
   1_xyz:  0.300  20.000   5.457  11.553   9.068   0.000   0.000   0.000
   1_adp:  0.300  20.000   5.457  11.553   9.068   0.000   0.000   0.000
   1_occ:  0.300  20.000   5.457  11.553   9.068   0.000   0.000   0.000
   2_bss:  0.300  50.000   2.031   6.941   5.093   0.000   0.000   0.000
   2_xyz:  0.300  50.000   2.031   6.941   5.093   0.000   0.000   0.000
   2_adp:  0.300  50.000   2.031   6.941   5.093   0.000   0.000   0.000
   2_occ:  0.300  50.000   2.031   6.941   5.093   0.000   0.000   0.000
   3_bss:  0.298  50.000   1.653   5.259   3.441   0.000   0.000   0.000
   3_xyz:  0.298  50.000   1.653   5.259   3.441   0.000   0.000   0.000
   3_adp:  0.298  50.000   1.653   5.259   3.441   0.000   0.000   0.000
   3_occ:  0.298  50.000   1.653   5.259   3.441   0.000   0.000   0.000
   4_bss:  0.313  50.000   0.933   4.085   2.730   0.000   0.000   0.000
   4_xyz:  0.313  50.000   0.933   4.085   2.730   0.000   0.000   0.000
   4_adp:  0.313  50.000   0.933   4.085   2.730   0.000   0.000   0.000
   4_occ:  0.313  50.000   0.933   4.085   2.730   0.000   0.000   0.000
   5_bss:  0.326  58.600   0.940   2.768   2.771   0.000   0.000   0.000
   5_xyz:  0.326  58.600   0.940   2.768   2.771   0.000   0.000   0.000
   5_adp:  0.326  58.600   0.940   2.768   2.771   0.000   0.000   0.000
   5_occ:  0.326  58.600   0.940   2.768   2.771   0.000   0.000   0.000
   5_bss:  0.331  67.080  -1.078   0.277   0.801   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.312 0.3773  0.4348    76916.021
   1_bss:  61.100 0.3791  0.5602    76068.383
   1_xyz:  52.613 0.4873  0.7052    60148.523
   1_adp:  51.650 0.4991  0.7975    58545.207
   1_occ:  51.709 0.4984  0.7949    58693.232
   2_bss:  51.333 0.5032  0.7047    58187.824
   2_xyz:  46.831 0.5592  0.7845    49661.026
   2_adp:  44.798 0.5849  0.8005    46628.449
   2_occ:  44.791 0.5849  0.8003    46593.135
   3_bss:  44.677 0.5862  0.7693    46372.530
   3_xyz:  36.351 0.6858  0.8854    32342.771
   3_adp:  34.668 0.7056  0.8945    29960.438
   3_occ:  34.710 0.7051  0.8935    30014.731
   4_bss:  34.651 0.7058  0.8680    29954.012
   4_xyz:  24.984 0.8114  0.9565    16145.481
   4_adp:  23.768 0.8242  0.9542    14892.807
   4_occ:  23.766 0.8242  0.9544    14911.526
   5_bss:  23.659 0.8253  0.9421    14796.002
   5_xyz:  20.137 0.8601  0.9637    11055.751
   5_adp:  17.781 0.8822  0.9663     9103.073
   5_occ:  17.765 0.8824  0.9664     9101.000
   5_bss:  17.740 0.8826  0.9591     9060.166
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4544e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4544e+01
   1_xyz:   1.707  0.013  0.108 18.279  0.007  4.124   1.4564e-01
   1_adp:   1.707  0.013  0.108 18.279  0.007  4.124   1.4564e-01
   1_occ:   1.707  0.013  0.108 18.279  0.007  4.124   1.4564e-01
   2_bss:   1.707  0.013  0.108 18.279  0.007  4.124   1.4564e-01
   2_xyz:   1.303  0.009  0.086 16.626  0.004  4.109   9.6525e-02
   2_adp:   1.303  0.009  0.086 16.626  0.004  4.109   9.6525e-02
   2_occ:   1.303  0.009  0.086 16.626  0.004  4.109   9.6525e-02
   3_bss:   1.303  0.009  0.086 16.626  0.004  4.109   9.6525e-02
   3_xyz:   1.220  0.009  0.086 15.771  0.004  4.131   8.2600e-02
   3_adp:   1.220  0.009  0.086 15.771  0.004  4.131   8.2600e-02
   3_occ:   1.220  0.009  0.086 15.771  0.004  4.131   8.2600e-02
   4_bss:   1.220  0.009  0.086 15.771  0.004  4.131   8.2600e-02
   4_xyz:   1.271  0.011  0.088 15.646  0.005  4.113   9.5660e-02
   4_adp:   1.271  0.011  0.088 15.646  0.005  4.113   9.5660e-02
   4_occ:   1.271  0.011  0.088 15.646  0.005  4.113   9.5660e-02
   5_bss:   1.271  0.011  0.088 15.646  0.005  4.113   9.5660e-02
   5_xyz:   1.229  0.011  0.093 15.683  0.004  4.114   9.1834e-02
   5_adp:   1.229  0.011  0.093 15.683  0.004  4.114   9.1834e-02
   5_occ:   1.229  0.011  0.093 15.683  0.004  4.114   9.1834e-02
   5_bss:   1.229  0.011  0.093 15.683  0.004  4.114   9.1834e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0713e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0713e+00
   1_xyz:  14.328  0.123  0.457 88.043  0.055  2.254   1.0344e-01
   1_adp:  14.328  0.123  0.457 88.043  0.055  2.254   1.0344e-01
   1_occ:  14.328  0.123  0.457 88.043  0.055  2.254   1.0344e-01
   2_bss:  14.328  0.123  0.457 88.043  0.055  2.254   1.0344e-01
   2_xyz:   8.417  0.085  0.299 84.737  0.030  2.181   1.1680e-01
   2_adp:   8.417  0.085  0.299 84.737  0.030  2.181   1.1680e-01
   2_occ:   8.417  0.085  0.299 84.737  0.030  2.181   1.1680e-01
   3_bss:   8.417  0.085  0.299 84.737  0.030  2.181   1.1680e-01
   3_xyz:   7.412  0.081  0.314 86.688  0.035  2.238   7.8292e-02
   3_adp:   7.412  0.081  0.314 86.688  0.035  2.238   7.8292e-02
   3_occ:   7.412  0.081  0.314 86.688  0.035  2.238   7.8292e-02
   4_bss:   7.412  0.081  0.314 86.688  0.035  2.238   7.8292e-02
   4_xyz:   7.830  0.073  0.248 86.407  0.045  2.089   8.3687e-02
   4_adp:   7.830  0.073  0.248 86.407  0.045  2.089   8.3687e-02
   4_occ:   7.830  0.073  0.248 86.407  0.045  2.089   8.3687e-02
   5_bss:   7.830  0.073  0.248 86.407  0.045  2.089   8.3687e-02
   5_xyz:   8.375  0.058  0.555 86.481  0.041  2.107   6.6285e-02
   5_adp:   8.375  0.058  0.555 86.481  0.041  2.107   6.6285e-02
   5_occ:   8.375  0.058  0.555 86.481  0.041  2.107   6.6285e-02
   5_bss:   8.375  0.058  0.555 86.481  0.041  2.107   6.6285e-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: 122.03   0.00  16.73  85.31   0.00  14.68 122.03   0.00  27.90
   1_occ: 122.03   0.00  16.73  85.31   0.00  14.68 122.03   0.00  27.90
   2_bss: 122.03   0.00  16.73  85.31   0.00  14.68 122.03   0.00  27.90
   2_xyz: 122.03   0.00  16.73  85.31   0.00  14.68 122.03   0.00  27.90
   2_adp: 117.12   0.00  14.56  67.44   0.00  12.27 117.12   0.83  27.01
   2_occ: 117.12   0.00  14.56  67.44   0.00  12.27 117.12   0.83  27.01
   3_bss: 117.12   0.00  14.56  67.44   0.00  12.27 117.12   0.83  27.01
   3_xyz: 117.12   0.00  14.56  67.44   0.00  12.27 117.12   0.83  27.01
   3_adp: 103.36   0.00  14.35  71.37   0.00  11.40 103.36   1.33  30.41
   3_occ: 103.36   0.00  14.35  71.37   0.00  11.40 103.36   1.33  30.41
   4_bss: 103.36   0.00  14.35  71.37   0.00  11.40 103.36   1.33  30.41
   4_xyz: 103.36   0.00  14.35  71.37   0.00  11.40 103.36   1.33  30.41
   4_adp: 102.76   0.00  14.19  93.41   0.00  10.80 102.76   0.00  32.65
   4_occ: 102.76   0.00  14.19  93.41   0.00  10.80 102.76   0.00  32.65
   5_bss: 102.76   0.00  14.19  93.41   0.00  10.80 102.76   0.00  32.65
   5_xyz: 102.76   0.00  14.19  93.41   0.00  10.80 102.76   0.00  32.65
   5_adp:  93.59   0.00  14.17  75.50   0.00   9.78  93.59   1.85  38.08
   5_occ:  93.59   0.00  14.17  75.50   0.00   9.78  93.59   1.85  38.08
   5_bss:  95.52   1.93  16.10  77.43   1.93  11.71  95.52   3.78  40.01
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.158    0.020    0.408
   1_adp:    1.158    0.020    0.408
   1_occ:    1.158    0.020    0.408
   2_bss:    1.158    0.020    0.408
   2_xyz:    1.604    0.047    0.561
   2_adp:    1.604    0.047    0.561
   2_occ:    1.604    0.047    0.561
   3_bss:    1.604    0.047    0.561
   3_xyz:    1.624    0.041    0.665
   3_adp:    1.624    0.041    0.665
   3_occ:    1.624    0.041    0.665
   4_bss:    1.624    0.041    0.665
   4_xyz:    1.842    0.026    0.828
   4_adp:    1.842    0.026    0.828
   4_occ:    1.842    0.026    0.828
   5_bss:    1.842    0.026    0.828
   5_xyz:    2.074    0.082    0.900
   5_adp:    2.074    0.082    0.900
   5_occ:    2.074    0.082    0.900
   5_bss:    2.074    0.082    0.900
------------------------------------------------------------------------

CPU time actual refinement: 341.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_723/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_723/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_723/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_723/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_723/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.75 
  Macro-tasks:
    bulk solvent and scale       = 41.70  
    individual site refinement   = 142.45 
    weights calculation          = 32.83  
    collect and process          = 6.36   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.47 
  Micro-tasks:
    mask                            = 2.97   
    f_calc                          = 105.64 
    alpha_beta                      = 8.18   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 116.15 
    fmodel                         = 7.48   
    r_factors                      = 0.27   
    phase_errors                   = 10.02  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 252.09 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.828 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    638 calls, 105.26 s
gradients_fft:          583 calls, 103.10 s

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

# Date 2008-01-16 Time 02:16:00 PST -0800 (1200478560.47 s)
Start R-work = 0.5080, R-free = 0.4947 (no bulk solvent and anisotropic scale)
Final R-work = 0.1544, R-free = 0.2035 (no bulk solvent and anisotropic scale)

Start R-work = 0.5016, R-free = 0.4885
Final R-work = 0.1379, R-free = 0.1878