# Date 2008-01-16 Time 03:38:46 PST -0800 (1200483526.19 s)
#phil __OFF__

Command line arguments: "../1324.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30852
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1324

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 48.1033, 85.9581, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2429 1.99139
Completeness in resolution range: 0.931523
Completeness with d_max=infinity: 0.928741

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2429
                             d_min =   1.9914

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2429 1.99139
Completeness in resolution range: 0.931523
Completeness with d_max=infinity: 0.928741

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2433 -  4.2620 [2212/2241]  1992   220   9.9%
  bin  2:  4.2620 -  3.3952 [2109/2132]  1900   209   9.9%
  bin  3:  3.3952 -  2.9696 [2091/2116]  1875   216  10.3%
  bin  4:  2.9696 -  2.6997 [2081/2097]  1882   199   9.6%
  bin  5:  2.6997 -  2.5071 [2051/2088]  1839   212  10.3%
  bin  6:  2.5071 -  2.3599 [2050/2084]  1852   198   9.7%
  bin  7:  2.3599 -  2.2421 [2028/2065]  1822   206  10.2%
  bin  8:  2.2421 -  2.1448 [2030/2072]  1828   202  10.0%
  bin  9:  2.1448 -  2.0624 [2028/2064]  1824   204  10.1%
  bin 10:  2.0624 -  1.9914 [ 909/2070]   816    93  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1324/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:
        1.06 -     1.83: 5
        1.83 -     2.59: 42
        2.59 -     3.36: 4031
        3.36 -     4.13: 9237
        4.13 -     4.90: 14492
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.058 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.494 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.673 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.726 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27802 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_1324/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1324/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 72.00625 48.10325 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5121   r_free= 0.4937   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.310585                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.7540 0.99   1428  162 0.4268 0.4370      6.6551      6.6474|
|  2:  4.7540 -  3.7926 0.99   1380  144 0.4530 0.4796      6.8903       6.903|
|  3:  3.7926 -  3.3188 0.99   1353  158 0.4965 0.4194      6.7311      6.6984|
|  4:  3.3188 -  3.0179 0.99   1347  149 0.5159 0.4683       6.558      6.5377|
|  5:  3.0179 -  2.8030 0.98   1322  148 0.5438 0.5600      6.3906      6.3865|
|  6:  2.8030 -  2.6387 0.99   1338  146 0.5452 0.4830      6.2951      6.2193|
|  7:  2.6387 -  2.5071 0.99   1320  149 0.5258 0.5115      6.2668      6.2006|
|  8:  2.5071 -  2.3984 0.99   1315  144 0.5430 0.5424      6.1619      6.1965|
|  9:  2.3984 -  2.3064 0.99   1314  149 0.5443 0.5356      6.1344      6.1357|
| 10:  2.3064 -  2.2271 0.98   1322  144 0.5395 0.5311       6.102      6.1144|
| 11:  2.2271 -  2.1576 0.98   1290  141 0.5455 0.5258      6.0376       6.024|
| 12:  2.1576 -  2.0961 1.00   1310  146 0.5463 0.5014      5.9532      5.9771|
| 13:  2.0961 -  2.0411 0.92   1232  144 0.5427 0.5298      5.8792      5.8348|
| 14:  2.0411 -  1.9914 0.27    359   35 0.5748 0.4578       5.846      5.7626|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.7540  1428   162  0.63  39.95   0.77     0.67      94882.71|
|  2:  4.7540 -  3.7926  1380   144  0.63  41.15   0.84     0.69     131724.47|
|  3:  3.7926 -  3.3188  1353   158  0.51  50.81   0.77     0.62     140269.46|
|  4:  3.3188 -  3.0179  1347   149  0.41  59.09   0.75     0.51     121925.83|
|  5:  3.0179 -  2.8030  1322   148  0.33  65.03   0.69     0.41      96424.48|
|  6:  2.8030 -  2.6387  1338   146  0.32  65.92   0.70     0.38      77280.67|
|  7:  2.6387 -  2.5071  1320   149  0.32  65.85   0.73     0.35      68705.11|
|  8:  2.5071 -  2.3984  1315   144  0.25  71.18   0.68     0.30      66612.20|
|  9:  2.3984 -  2.3064  1314   149  0.20  75.31   0.70     0.24      64754.78|
| 10:  2.3064 -  2.2271  1322   144  0.19  75.51   0.72     0.23      59562.64|
| 11:  2.2271 -  2.1576  1290   141  0.22  73.53   0.72     0.27      51832.77|
| 12:  2.1576 -  2.0961  1310   146  0.27  70.17   0.72     0.34      45293.33|
| 13:  2.0961 -  2.0411  1232   144  0.29  68.28   0.70     0.36      37812.03|
| 14:  2.0411 -  1.9914   359    35  0.29  68.51   0.71     0.35      31191.51|
|alpha:            min =        0.23 max =            0.69 mean =         0.42|
|beta:             min =    31191.51 max =       140269.46 mean =     81013.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.03|
|phase err.(test): min =        0.00 max =           89.99 mean =        62.87|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.598431             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.451   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.857204              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.365   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1483 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2579 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3846 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4988 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6425 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7599 |
|-----------------------------------------------------------------------------|
|-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 |       54.552 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.980 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    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 = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5160   r_free= 0.5016   ksol= 0.00   Bsol= 0.00   scale= 0.729    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.310880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5067   r_free= 0.4875   ksol= 0.30   Bsol= 50.00   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,10.42,5.58,0.00,0.00,0.00); trace/3= 7.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.308492                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.226652             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.820   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.594355              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.129   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5067      final r-factor (work) = 0.4481          |
| start r-factor (free) = 0.4875      final r-factor (free) = 0.4598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 121.4818 = 21.23 * 0.50 * 6.3062 + 1.00 * 54.5520                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.5739 = 21.23 * 0.50 * 6.2566 + 1.00 * 0.1702                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4481      final r-factor (work) = 0.4096          |
| start r-factor (free) = 0.4598      final r-factor (free) = 0.4453          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9901 = 1.59 * 1.00 * 6.2566 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9263 = 1.59 * 1.00 * 6.2140 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.46  15.65    None  None   None       |
|    all(noH): 2823   0      0.00    126.46  15.65    None  None   None       |
|    Sol.    : 438    0      0.00    126.46  26.21    None  None   None       |
|    Mac.    : 2385   0      0.00    75.32   13.71    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:     0.000 -  12.646: 1457   |   5:    63.228 -  75.874:   21        |
|      1:    12.646 -  25.291:  855   |   6:    75.874 -  88.519:    6        |
|      2:    25.291 -  37.937:  310   |   7:    88.519 - 101.165:    4        |
|      3:    37.937 -  50.583:  115   |   8:   101.165 - 113.811:    2        |
|      4:    50.583 -  63.228:   52   |   9:   113.811 - 126.456:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4096 r_free = 0.4453             target_work(ml) = 6.203         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4089 r_free = 0.4448             target_work(ml) = 6.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4089   r_free= 0.4448   ksol= 0.30   Bsol= 50.00   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,10.42,5.58,0.00,0.00,0.00); trace/3= 7.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.201770                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4078   r_free= 0.4408   ksol= 0.29   Bsol= 50.00   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.37,6.31,3.47,0.00,0.00,0.00); trace/3= 4.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.203477                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.192415             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.873  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.790811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.653  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4078      final r-factor (work) = 0.3511          |
| start r-factor (free) = 0.4408      final r-factor (free) = 0.4202          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.0354 = 12.19 * 0.50 * 6.2114 + 1.00 * 0.1697                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.5390 = 12.19 * 0.50 * 6.1395 + 1.00 * 0.1116                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3511      final r-factor (work) = 0.3418          |
| start r-factor (free) = 0.4202      final r-factor (free) = 0.4121          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8740 = 0.79 * 1.00 * 6.1395 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8380 = 0.79 * 1.00 * 6.1016 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.63  15.20    None  None   None       |
|    all(noH): 2823   0      0.00    125.63  15.20    None  None   None       |
|    Sol.    : 438    0      0.00    125.63  27.66    None  None   None       |
|    Mac.    : 2385   0      0.00    77.42   12.92    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 -  12.563: 1490   |   5:    62.816 -  75.379:   18        |
|      1:    12.563 -  25.126:  850   |   6:    75.379 -  87.942:    3        |
|      2:    25.126 -  37.689:  310   |   7:    87.942 - 100.505:    4        |
|      3:    37.689 -  50.252:  109   |   8:   100.505 - 113.068:    1        |
|      4:    50.252 -  62.816:   37   |   9:   113.068 - 125.631:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3418 r_free = 0.4121             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3415 r_free = 0.4134             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3415   r_free= 0.4134   ksol= 0.29   Bsol= 50.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.37,6.31,3.47,0.00,0.00,0.00); trace/3= 4.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.094322                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3416   r_free= 0.4112   ksol= 0.31   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.13,4.75,3.06,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.093938                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.705136              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.854  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.607750              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.243  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3416      final r-factor (work) = 0.2838          |
| start r-factor (free) = 0.4112      final r-factor (free) = 0.3434          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.7186 = 9.71 * 0.50 * 6.1013 + 1.00 * 0.1116                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.3498 = 9.71 * 0.50 * 6.0274 + 1.00 * 0.1013                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2838      final r-factor (work) = 0.2585          |
| start r-factor (free) = 0.3434      final r-factor (free) = 0.3308          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7034 = 1.61 * 1.00 * 6.0274 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5046 = 1.61 * 1.00 * 5.8980 + 1.00 * 0.0221                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.37  16.68    None  None   None       |
|    all(noH): 2823   0      0.00    130.37  16.68    None  None   None       |
|    Sol.    : 438    0      0.00    130.37  38.13    None  None   None       |
|    Mac.    : 2385   0      0.00    93.64   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.037: 1578   |   5:    65.184 -  78.220:   46        |
|      1:    13.037 -  26.073:  663   |   6:    78.220 -  91.257:   20        |
|      2:    26.073 -  39.110:  292   |   7:    91.257 - 104.294:    5        |
|      3:    39.110 -  52.147:  147   |   8:   104.294 - 117.330:    1        |
|      4:    52.147 -  65.184:   70   |   9:   117.330 - 130.367:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2585 r_free = 0.3308             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2584 r_free = 0.3306             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2584   r_free= 0.3306   ksol= 0.31   Bsol= 50.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.13,4.75,3.06,0.00,0.00,0.00); trace/3= 3.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.880793                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2582   r_free= 0.3299   ksol= 0.30   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,3.51,2.15,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.879900                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.727674              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.596   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.439010              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.355  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2582      final r-factor (work) = 0.2064          |
| start r-factor (free) = 0.3299      final r-factor (free) = 0.2740          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8367 = 8.73 * 0.50 * 5.8974 + 1.00 * 0.1013                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.3821 = 8.73 * 0.50 * 5.7940 + 1.00 * 0.0981                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2064      final r-factor (work) = 0.1927          |
| start r-factor (free) = 0.2740      final r-factor (free) = 0.2544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5658 = 0.44 * 1.00 * 5.7940 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5046 = 0.44 * 1.00 * 5.6558 + 1.00 * 0.0216                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.23  16.11    None  None   None       |
|    all(noH): 2823   0      0.00    130.23  16.11    None  None   None       |
|    Sol.    : 438    0      0.00    130.23  38.98    None  None   None       |
|    Mac.    : 2385   0      0.00    119.58  11.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.023: 1708   |   5:    65.117 -  78.141:   45        |
|      1:    13.023 -  26.047:  569   |   6:    78.141 -  91.164:   18        |
|      2:    26.047 -  39.070:  276   |   7:    91.164 - 104.187:    5        |
|      3:    39.070 -  52.094:  132   |   8:   104.187 - 117.211:    1        |
|      4:    52.094 -  65.117:   67   |   9:   117.211 - 130.234:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1927 r_free = 0.2544             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1925 r_free = 0.2538             target_work(ml) = 5.619         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1925   r_free= 0.2538   ksol= 0.30   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,3.51,2.15,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.619130                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1924   r_free= 0.2536   ksol= 0.33   Bsol= 63.61   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.64,2.02,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.619829                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.261158              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.694  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.565005              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.214  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1924      final r-factor (work) = 0.1682          |
| start r-factor (free) = 0.2536      final r-factor (free) = 0.2269          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1484 = 4.26 * 0.50 * 5.6559 + 1.00 * 0.0981                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9400 = 4.26 * 0.50 * 5.5669 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1682      final r-factor (work) = 0.1659          |
| start r-factor (free) = 0.2269      final r-factor (free) = 0.2246          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2122 = 0.57 * 1.00 * 5.5669 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1877 = 0.57 * 1.00 * 5.5047 + 1.00 * 0.0775                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.19  16.13    None  None   None       |
|    all(noH): 2823   0      0.00    130.19  16.13    None  None   None       |
|    Sol.    : 438    0      1.66    130.19  39.14    None  None   None       |
|    Mac.    : 2385   0      0.00    112.78  11.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.019: 1732   |   5:    65.093 -  78.112:   43        |
|      1:    13.019 -  26.037:  545   |   6:    78.112 -  91.131:   20        |
|      2:    26.037 -  39.056:  276   |   7:    91.131 - 104.149:    5        |
|      3:    39.056 -  52.075:  132   |   8:   104.149 - 117.168:    2        |
|      4:    52.075 -  65.093:   67   |   9:   117.168 - 130.187:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1659 r_free = 0.2246             target_work(ml) = 5.499         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1657 r_free = 0.2243             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1657   r_free= 0.2243   ksol= 0.33   Bsol= 63.61   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.64,2.02,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.498304                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.7540 0.99   1428  162 0.1093 0.1592      5.5183      5.7513|
|  2:  4.7540 -  3.7926 0.99   1380  144 0.1094 0.1456      5.6632      5.9155|
|  3:  3.7926 -  3.3188 0.99   1353  158 0.1470 0.2016      5.7812      6.0613|
|  4:  3.3188 -  3.0179 0.99   1347  149 0.1796 0.2284      5.7744      5.9519|
|  5:  3.0179 -  2.8030 0.98   1322  148 0.1979 0.2528      5.6741       5.851|
|  6:  2.8030 -  2.6387 0.99   1338  146 0.1952 0.2760      5.5655      5.7498|
|  7:  2.6387 -  2.5071 0.99   1320  149 0.1799 0.2415      5.4983      5.7014|
|  8:  2.5071 -  2.3984 0.99   1315  144 0.1973 0.2601      5.4551      5.6998|
|  9:  2.3984 -  2.3064 0.99   1314  149 0.1975 0.2684      5.4395      5.6388|
| 10:  2.3064 -  2.2271 0.98   1322  144 0.1882 0.2572      5.3944      5.5869|
| 11:  2.2271 -  2.1576 0.98   1290  141 0.1905 0.2666      5.3379       5.612|
| 12:  2.1576 -  2.0961 1.00   1310  146 0.1848 0.2492      5.2562      5.4222|
| 13:  2.0961 -  2.0411 0.92   1232  144 0.1931 0.2567      5.1893       5.365|
| 14:  2.0411 -  1.9914 0.27    359   35 0.1556 0.2814      5.0605      5.3744|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.7540  1428   162  0.92  11.92   0.97     0.95      10805.81|
|  2:  4.7540 -  3.7926  1380   144  0.92  12.24   1.03     1.01      15116.95|
|  3:  3.7926 -  3.3188  1353   158  0.88  17.51   1.04     1.04      20154.38|
|  4:  3.3188 -  3.0179  1347   149  0.85  21.43   1.02     0.99      20658.52|
|  5:  3.0179 -  2.8030  1322   148  0.81  25.09   1.02     1.00      18191.49|
|  6:  2.8030 -  2.6387  1338   146  0.83  23.84   1.00     0.94      13883.75|
|  7:  2.6387 -  2.5071  1320   149  0.84  23.17   1.01     0.96      12618.70|
|  8:  2.5071 -  2.3984  1315   144  0.81  25.37   1.02     0.94      11747.54|
|  9:  2.3984 -  2.3064  1314   149  0.81  25.91   1.03     0.97      11756.96|
| 10:  2.3064 -  2.2271  1322   144  0.82  24.95   1.02     0.93      10527.54|
| 11:  2.2271 -  2.1576  1290   141  0.81  25.94   1.02     0.95       9834.39|
| 12:  2.1576 -  2.0961  1310   146  0.82  25.17   1.01     0.96       8707.92|
| 13:  2.0961 -  2.0411  1232   144  0.80  26.87   1.01     0.97       7715.62|
| 14:  2.0411 -  1.9914   359    35  0.80  26.56   1.01     0.94       6502.61|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     6502.61 max =        20658.52 mean =     13126.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.84 mean =        22.21|
|phase err.(test): min =        0.00 max =           89.53 mean =        21.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2247   ksol= 0.33   Bsol= 63.66   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,0.29,0.04,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.498430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2247   ksol= 0.33   Bsol= 63.66   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,0.29,0.04,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.498430                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.7540 0.99   1428  162 0.1102 0.1574      5.5112      5.7403|
|  2:  4.7540 -  3.7926 0.99   1380  144 0.1104 0.1492      5.6645      5.9328|
|  3:  3.7926 -  3.3188 0.99   1353  158 0.1469 0.2023      5.7862      6.0647|
|  4:  3.3188 -  3.0179 0.99   1347  149 0.1794 0.2287      5.7754      5.9522|
|  5:  3.0179 -  2.8030 0.98   1322  148 0.1981 0.2527      5.6752      5.8517|
|  6:  2.8030 -  2.6387 0.99   1338  146 0.1951 0.2752      5.5657      5.7486|
|  7:  2.6387 -  2.5071 0.99   1320  149 0.1797 0.2425      5.4987      5.7041|
|  8:  2.5071 -  2.3984 0.99   1315  144 0.1969 0.2599      5.4552      5.6994|
|  9:  2.3984 -  2.3064 0.99   1314  149 0.1971 0.2686      5.4391       5.639|
| 10:  2.3064 -  2.2271 0.98   1322  144 0.1879 0.2574      5.3938      5.5883|
| 11:  2.2271 -  2.1576 0.98   1290  141 0.1905 0.2669      5.3382      5.6116|
| 12:  2.1576 -  2.0961 1.00   1310  146 0.1847 0.2495      5.2568      5.4237|
| 13:  2.0961 -  2.0411 0.92   1232  144 0.1930 0.2569      5.1897      5.3666|
| 14:  2.0411 -  1.9914 0.27    359   35 0.1553 0.2799      5.0605      5.3693|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.7540  1428   162  0.92  11.67   0.96     0.94      10316.63|
|  2:  4.7540 -  3.7926  1380   144  0.92  12.20   1.02     1.01      15007.54|
|  3:  3.7926 -  3.3188  1353   158  0.88  17.64   1.03     1.03      20504.33|
|  4:  3.3188 -  3.0179  1347   149  0.85  21.43   1.01     0.98      20711.45|
|  5:  3.0179 -  2.8030  1322   148  0.81  25.08   1.00     0.98      18206.08|
|  6:  2.8030 -  2.6387  1338   146  0.83  23.84   0.98     0.93      13917.55|
|  7:  2.6387 -  2.5071  1320   149  0.83  23.20   0.99     0.95      12654.45|
|  8:  2.5071 -  2.3984  1315   144  0.81  25.39   0.99     0.92      11772.93|
|  9:  2.3984 -  2.3064  1314   149  0.81  25.89   1.01     0.95      11769.25|
| 10:  2.3064 -  2.2271  1322   144  0.82  24.95   0.99     0.91      10531.30|
| 11:  2.2271 -  2.1576  1290   141  0.81  25.94   0.99     0.93       9840.01|
| 12:  2.1576 -  2.0961  1310   146  0.82  25.20   0.98     0.93       8730.54|
| 13:  2.0961 -  2.0411  1232   144  0.80  26.86   0.98     0.94       7719.96|
| 14:  2.0411 -  1.9914   359    35  0.80  26.59   0.98     0.92       6498.00|
|alpha:            min =        0.91 max =            1.03 mean =         0.95|
|beta:             min =     6498.00 max =        20711.45 mean =     13120.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.84|
|phase err.(work): min =        0.00 max =           89.97 mean =        22.20|
|phase err.(test): min =        0.00 max =           88.44 mean =        21.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    131.83  17.77    None  None   None       |
|    all(noH): 2823   0      1.65    131.83  17.77    None  None   None       |
|    Sol.    : 438    0      3.31    131.83  40.79    None  None   None       |
|    Mac.    : 2385   0      1.65    114.42  13.55    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:     1.647 -  14.666: 1732   |   5:    66.740 -  79.759:   43        |
|      1:    14.666 -  27.684:  545   |   6:    79.759 -  92.778:   20        |
|      2:    27.684 -  40.703:  276   |   7:    92.778 - 105.796:    5        |
|      3:    40.703 -  53.722:  132   |   8:   105.796 - 118.815:    2        |
|      4:    53.722 -  66.740:   67   |   9:   118.815 - 131.834:    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)= 352         
Filter by distance & map next to the model:
   mapped sites are within: 0.107 - 5.642
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 352
   mapped sites are within: 0.707 - 5.642

peak=    7.145 closest distance to " O   HOH Z  84 " =    1.311
peak=    6.128 closest distance to " O   HOH Z  41 " =    1.037
peak=    6.085 closest distance to " O   HOH Z 120 " =    1.597
peak=    6.031 closest distance to " O   HOH Z 426 " =    1.201
peak=    5.897 closest distance to " N   ASP A 298 " =    0.821
peak=    5.849 closest distance to " O   HOH Z 335 " =    0.879
peak=    5.767 closest distance to " O   HOH Z 103 " =    1.041
peak=    5.662 closest distance to " OD1 ASN A 301 " =    0.851
peak=    5.600 closest distance to " N   GLU A 277 " =    0.760
peak=    5.366 closest distance to " O   HOH Z  54 " =    1.543
peak=    5.321 closest distance to " NE  ARG A  36 " =    0.856
peak=    5.284 closest distance to " CB  SER A  26 " =    0.756
peak=    5.133 closest distance to " O   HOH Z 102 " =    1.506
peak=    5.088 closest distance to " O   HOH Z 117 " =    1.674
peak=    5.047 closest distance to " CB  SER A  63 " =    1.413
peak=    4.976 closest distance to " CG  LEU A   5 " =    1.333
peak=    4.868 closest distance to " CG  GLN A  77 " =    0.956
peak=    4.814 closest distance to " O   HOH Z 422 " =    1.231
peak=    4.814 closest distance to " CG1 ILE A 234 " =    1.458
peak=    4.811 closest distance to " O   HOH Z 410 " =    0.984
peak=    4.670 closest distance to " CG  PRO A 280 " =    1.213
peak=    4.655 closest distance to " NH1AARG A 145 " =    1.120
peak=    4.633 closest distance to " O   HOH Z 178 " =    1.102
peak=    4.625 closest distance to " CG2 VAL A 296 " =    1.155
peak=    4.470 closest distance to " O   HOH Z 111 " =    1.797
peak=    4.451 closest distance to " NH1 ARG A 269 " =    0.893
peak=    4.440 closest distance to " OG  SER A   3 " =    0.818
peak=    4.403 closest distance to " CD  LYS A 166 " =    1.892
peak=    4.402 closest distance to " CB  VAL A 230 " =    1.167
peak=    4.392 closest distance to " O   HOH Z 181 " =    0.961
peak=    4.392 closest distance to " O   HOH Z  57 " =    0.979
peak=    4.390 closest distance to " O   HOH Z 272 " =    1.897
peak=    4.337 closest distance to " CG1 VAL A 153 " =    1.640
peak=    4.299 closest distance to " CD2 LEU A 228 " =    1.445
peak=    4.295 closest distance to " O   HOH Z 411 " =    2.794
peak=    4.289 closest distance to " NH1BARG A 275 " =    1.027
peak=    4.267 closest distance to " NH1 ARG A  56 " =    1.161
peak=    4.260 closest distance to " ND2 ASN A 301 " =    1.003
peak=    4.232 closest distance to " CG AARG A 275 " =    1.084
peak=    4.225 closest distance to " CG  PRO A  54 " =    1.286
peak=    4.210 closest distance to " CD  ARG A 269 " =    0.843
peak=    4.208 closest distance to " O   HOH Z 210 " =    1.680
peak=    4.207 closest distance to " CA  GLY A 196 " =    0.901
peak=    4.206 closest distance to " CB  GLN A  73 " =    0.755
peak=    4.146 closest distance to " O   HOH Z  37 " =    1.468
peak=    4.119 closest distance to " NH1 ARG A 138 " =    0.972
peak=    4.116 closest distance to " CB  TRP A 266 " =    0.977
peak=    4.104 closest distance to " O   HOH Z 209 " =    1.183
peak=    4.094 closest distance to " O   HOH Z  67 " =    1.814
peak=    4.089 closest distance to " CB  ASN A 285 " =    1.056
peak=    4.082 closest distance to " CD  ARG A  36 " =    1.066
peak=    4.069 closest distance to " O   HOH Z 344 " =    0.840
peak=    4.069 closest distance to " CB  GLN A  88 " =    1.359
peak=    4.062 closest distance to " O   HOH Z 209 " =    1.963
peak=    4.035 closest distance to " OE1 GLN A 278 " =    1.998
peak=    4.023 closest distance to " O   HOH Z 404 " =    1.716
peak=    4.020 closest distance to " N   ALA A 256 " =    1.248
peak=    3.984 closest distance to " O   HOH Z 396 " =    1.034
peak=    3.961 closest distance to " O   HOH Z   9 " =    2.272
peak=    3.949 closest distance to " O   HOH Z 134 " =    2.241
peak=    3.948 closest distance to " CB  PRO A  54 " =    0.880
peak=    3.947 closest distance to " CD2 LEU A   5 " =    1.151
peak=    3.944 closest distance to " ND2 ASN A  45 " =    1.360
peak=    3.934 closest distance to " O   HOH Z 184 " =    1.968
peak=    3.932 closest distance to " O   HOH Z 133 " =    2.159
peak=    3.931 closest distance to " O   GLN A  11 " =    0.818
peak=    3.927 closest distance to " O   HOH Z   1 " =    2.890
peak=    3.924 closest distance to " OE1 GLN A  73 " =    1.573
peak=    3.923 closest distance to " CB  GLN A 183 " =    1.153
peak=    3.919 closest distance to " O   HOH Z  61 " =    0.898
peak=    3.912 closest distance to " O   HOH Z  47 " =    1.768
peak=    3.909 closest distance to " O   HOH Z 387 " =    2.651
peak=    3.906 closest distance to " O   LYS A 117 " =    1.041
peak=    3.905 closest distance to " CG1 ILE A 120 " =    1.295
peak=    3.893 closest distance to " OD1 ASN A  69 " =    0.758
peak=    3.887 closest distance to " O   HOH Z  97 " =    2.056
peak=    3.880 closest distance to " CA  ILE A  33 " =    1.201
peak=    3.879 closest distance to " CD ALYS A 290 " =    1.228
peak=    3.871 closest distance to " CB  PRO A 198 " =    1.312
peak=    3.845 closest distance to " CD  GLN A  88 " =    0.953
peak=    3.845 closest distance to " O   HOH Z 336 " =    2.553
peak=    3.839 closest distance to " O   HOH Z 182 " =    1.566
peak=    3.834 closest distance to " O   HOH Z  89 " =    3.796
peak=    3.833 closest distance to " O   HOH Z 411 " =    1.753
peak=    3.833 closest distance to " CB  LYS A 193 " =    1.012
peak=    3.829 closest distance to " CB  GLN A 223 " =    1.355
peak=    3.828 closest distance to " CB  THR A 235 " =    1.402
peak=    3.824 closest distance to " O   HOH Z 244 " =    1.825
peak=    3.823 closest distance to " O   HOH Z  48 " =    2.095
peak=    3.818 closest distance to " ND2 ASN A 285 " =    1.108
peak=    3.815 closest distance to " O   HOH Z 368 " =    3.128
peak=    3.794 closest distance to " CA  THR A 246 " =    1.040
peak=    3.779 closest distance to " O   HOH Z 339 " =    1.463
peak=    3.772 closest distance to " O   HOH Z 359 " =    1.826
peak=    3.770 closest distance to " CB  ALA A 137 " =    1.218
peak=    3.767 closest distance to " O   HOH Z 388 " =    1.189
peak=    3.767 closest distance to " CB  TRP A 179 " =    1.334
peak=    3.764 closest distance to " O   HOH Z 395 " =    1.637
peak=    3.750 closest distance to " O   HOH Z 126 " =    1.941
peak=    3.749 closest distance to " CE  LYS A 119 " =    1.501
peak=    3.717 closest distance to " O   HOH Z 416 " =    1.745
peak=    3.709 closest distance to " CZ  PHE A 218 " =    1.144
peak=    3.702 closest distance to " NE2 GLN A  89 " =    0.828
peak=    3.701 closest distance to " O   HOH Z 431 " =    2.101
peak=    3.691 closest distance to " O   HOH Z 419 " =    2.458
peak=    3.691 closest distance to " O   HOH Z 124 " =    1.352
peak=    3.686 closest distance to " O   HOH Z  63 " =    1.878
peak=    3.679 closest distance to " CB  MET A  47 " =    1.160
peak=    3.675 closest distance to " CA  ARG A 195 " =    1.242
peak=    3.668 closest distance to " O   GLU A   2 " =    1.841
peak=    3.658 closest distance to " NH2AARG A 102 " =    1.123
peak=    3.656 closest distance to " CB  VAL A 202 " =    1.389
peak=    3.651 closest distance to " O   ARG A 275 " =    0.713
peak=    3.649 closest distance to " O   LEU A  25 " =    0.726
peak=    3.645 closest distance to " O   HOH Z 420 " =    5.642
peak=    3.642 closest distance to " OE2 GLU A  37 " =    1.156
peak=    3.636 closest distance to " O   HOH Z 146 " =    1.957
peak=    3.632 closest distance to " CB  PHE A 283 " =    0.881
peak=    3.625 closest distance to " CA  PRO A  54 " =    0.787
peak=    3.615 closest distance to " O   HOH Z 427 " =    3.291
peak=    3.603 closest distance to " CB  TRP A 123 " =    1.249
peak=    3.600 closest distance to " O   HOH Z  64 " =    2.002
peak=    3.600 closest distance to " O   HOH Z 149 " =    1.622
peak=    3.592 closest distance to " O   HOH Z 379 " =    2.574
peak=    3.586 closest distance to " NH2AARG A 190 " =    1.030
peak=    3.586 closest distance to " CA  LEU A   5 " =    0.835
peak=    3.586 closest distance to " CA  ALA A  21 " =    1.648
peak=    3.567 closest distance to " O   HOH Z 158 " =    1.485
peak=    3.563 closest distance to " CB  LEU A  83 " =    0.707
peak=    3.561 closest distance to " CG  ARG A 269 " =    0.734
peak=    3.559 closest distance to " CB  TYR A  30 " =    0.804
peak=    3.559 closest distance to " CB  GLN A  58 " =    1.121
peak=    3.556 closest distance to " O   HOH Z  99 " =    2.250
peak=    3.548 closest distance to " O   HOH Z 234 " =    3.343
peak=    3.545 closest distance to " N   GLU A  44 " =    1.073
peak=    3.545 closest distance to " CG  GLN A 278 " =    1.285
peak=    3.543 closest distance to " O   HOH Z 329 " =    2.983
peak=    3.540 closest distance to " O   HOH Z 426 " =    1.975
peak=    3.539 closest distance to " CG2 THR A 220 " =    1.411
peak=    3.536 closest distance to " O   SER A 276 " =    1.168
peak=    3.534 closest distance to " O   HOH Z 269 " =    3.117
peak=    3.529 closest distance to " CG  GLN A 183 " =    1.320
peak=    3.521 closest distance to " O   THR A 251 " =    1.468
peak=    3.516 closest distance to " O   HOH Z  85 " =    2.138
peak=    3.515 closest distance to " CG  GLU A 277 " =    2.918
peak=    3.511 closest distance to " O   HOH Z  19 " =    2.102
peak=    3.508 closest distance to " CA  VAL A 112 " =    1.310
peak=    3.506 closest distance to " OG ASER A 134 " =    1.179
peak=    3.497 closest distance to " CB  ILE A 199 " =    0.964
peak=    3.495 closest distance to " CB  PRO A  54 " =    1.118
peak=    3.494 closest distance to " CG2 ILE A 106 " =    0.986
peak=    3.492 closest distance to " OD1 ASP A 140 " =    0.850
peak=    3.490 closest distance to " O   HOH Z 174 " =    1.880
peak=    3.489 closest distance to " NZ  LYS A 117 " =    0.740
peak=    3.486 closest distance to " O   HOH Z 368 " =    1.507
peak=    3.476 closest distance to " O   HOH Z 159 " =    1.050
peak=    3.476 closest distance to " OH  TYR A 116 " =    1.545
peak=    3.471 closest distance to " O   HOH Z 402 " =    1.726
peak=    3.471 closest distance to " NZ  LYS A 117 " =    3.040
peak=    3.469 closest distance to " N   SER A 164 " =    1.045
peak=    3.467 closest distance to " CA  GLY A 267 " =    1.608
peak=    3.463 closest distance to " CA  GLY A 267 " =    1.516
peak=    3.462 closest distance to " O   ALA A 291 " =    1.620
peak=    3.461 closest distance to " O   HOH Z 211 " =    2.457
peak=    3.458 closest distance to " CD1 LEU A 222 " =    1.188
peak=    3.458 closest distance to " CD1 TRP A 266 " =    1.040
peak=    3.458 closest distance to " O   HOH Z  89 " =    2.096
peak=    3.450 closest distance to " CB  VAL A 296 " =    0.950
peak=    3.448 closest distance to " O   HOH Z 271 " =    2.165
peak=    3.444 closest distance to " O   HOH Z 365 " =    2.852
peak=    3.444 closest distance to " O   HOH Z 117 " =    1.924
peak=    3.440 closest distance to " CG  PRO A 198 " =    1.423
peak=    3.439 closest distance to " O   HOH Z 119 " =    1.860
peak=    3.438 closest distance to " CB  ALA A 100 " =    1.688
peak=    3.436 closest distance to " CA  LYS A  48 " =    1.371
peak=    3.431 closest distance to " O   HOH Z 203 " =    1.852
peak=    3.430 closest distance to " O   HOH Z  35 " =    1.565
peak=    3.429 closest distance to " O   HOH Z 298 " =    2.624
peak=    3.428 closest distance to " O   HOH Z  83 " =    1.059
peak=    3.426 closest distance to " CA  SER A  87 " =    0.942
peak=    3.425 closest distance to " O   HOH Z  51 " =    2.678
peak=    3.423 closest distance to " O   HOH Z 193 " =    2.054
peak=    3.422 closest distance to " OH  TYR A 247 " =    1.088
peak=    3.417 closest distance to " O   HOH Z  48 " =    2.107
peak=    3.410 closest distance to " O   HOH Z 276 " =    0.772
peak=    3.409 closest distance to " CG  GLU A  37 " =    0.957
peak=    3.407 closest distance to " O   HOH Z 214 " =    1.414
peak=    3.403 closest distance to " O   HOH Z 118 " =    1.689
peak=    3.402 closest distance to " CA  ARG A  36 " =    1.143
peak=    3.395 closest distance to " CD  ARG A 138 " =    1.183
peak=    3.387 closest distance to " CA  ALA A 100 " =    1.320
peak=    3.385 closest distance to " O   HOH Z 394 " =    2.122
peak=    3.383 closest distance to " N   TYR A 116 " =    1.696
peak=    3.377 closest distance to " CB  SER A  62 " =    1.160
peak=    3.376 closest distance to " O   HOH Z 311 " =    4.475
peak=    3.375 closest distance to " O   HOH Z 232 " =    0.955
peak=    3.372 closest distance to " O   HOH Z 125 " =    2.225
peak=    3.371 closest distance to " O   HOH Z 119 " =    2.392
peak=    3.370 closest distance to " CB  SER A  62 " =    1.401
peak=    3.370 closest distance to " CB  ALA A  64 " =    0.800
peak=    3.365 closest distance to " N   VAL A  67 " =    0.983
peak=    3.359 closest distance to " CB  TRP A 150 " =    1.444
peak=    3.354 closest distance to " N   TYR A 169 " =    1.275
peak=    3.349 closest distance to " NZ  LYS A  76 " =    1.131
peak=    3.348 closest distance to " O   HOH Z 417 " =    1.527
peak=    3.344 closest distance to " OG ASER A 258 " =    0.870
peak=    3.344 closest distance to " O   LYS A 289 " =    1.174
peak=    3.339 closest distance to " CB  GLN A 103 " =    1.014
peak=    3.337 closest distance to " CD1 LEU A   5 " =    1.141
peak=    3.335 closest distance to " O   HOH Z 344 " =    2.686
peak=    3.330 closest distance to " O   HOH Z 216 " =    1.631
peak=    3.329 closest distance to " O   HOH Z 185 " =    2.265
peak=    3.323 closest distance to " O   HOH Z 189 " =    3.268
peak=    3.316 closest distance to " CA  GLU A 152 " =    0.966
peak=    3.314 closest distance to " CG1BVAL A 121 " =    1.385
peak=    3.314 closest distance to " CA  ARG A  66 " =    1.104
peak=    3.309 closest distance to " CE3 TRP A 274 " =    0.853
peak=    3.309 closest distance to " CD2 HIS A  86 " =    1.338
peak=    3.307 closest distance to " OD2 ASP A 286 " =    3.226
peak=    3.305 closest distance to " O   HOH Z 185 " =    2.051
peak=    3.304 closest distance to " O   HOH Z  22 " =    2.446
peak=    3.304 closest distance to " CA  ALA A 295 " =    0.822
peak=    3.304 closest distance to " CB  GLU A 128 " =    1.192
peak=    3.302 closest distance to " NE2 HIS A  86 " =    1.581
peak=    3.300 closest distance to " CB  TRP A 150 " =    1.104
peak=    3.300 closest distance to " O   GLY A  91 " =    1.218
peak=    3.298 closest distance to " O   HOH Z  88 " =    2.846
peak=    3.296 closest distance to " O   HOH Z 183 " =    0.875
peak=    3.295 closest distance to " CG2 THR A  42 " =    1.123
peak=    3.292 closest distance to " O   HOH Z  58 " =    1.838
peak=    3.288 closest distance to " O   HOH Z 167 " =    1.442
peak=    3.288 closest distance to " O   GLN A 278 " =    0.951
peak=    3.285 closest distance to " O   HOH Z 406 " =    1.649
peak=    3.285 closest distance to " CB  GLU A 152 " =    1.174
peak=    3.279 closest distance to " O   HOH Z  90 " =    3.228
peak=    3.275 closest distance to " CZ3 TRP A 274 " =    4.834
peak=    3.275 closest distance to " NH2AARG A 275 " =    3.471
peak=    3.274 closest distance to " O   SER A 271 " =    1.133
peak=    3.263 closest distance to " O   HOH Z  28 " =    1.538
peak=    3.258 closest distance to " N   ASN A 127 " =    1.242
peak=    3.258 closest distance to " OD2 ASP A 298 " =    3.732
peak=    3.254 closest distance to " O   HOH Z 324 " =    1.633
peak=    3.251 closest distance to " O   HOH Z 248 " =    0.761
peak=    3.242 closest distance to " OD2 ASP A  65 " =    0.876
peak=    3.241 closest distance to " CD  LYS A 289 " =    1.071
peak=    3.241 closest distance to " CB  ALA A 256 " =    1.205
peak=    3.237 closest distance to " O   HOH Z 425 " =    1.861
peak=    3.236 closest distance to " O   HOH Z  50 " =    3.852
peak=    3.227 closest distance to " CB  SER A 141 " =    1.137
peak=    3.227 closest distance to " OD2 ASP A 171 " =    1.422
peak=    3.214 closest distance to " O   HOH Z 389 " =    1.981
peak=    3.205 closest distance to " CB  ALA A   1 " =    0.947
peak=    3.200 closest distance to " CG2 THR A  18 " =    0.984
peak=    3.199 closest distance to " O   HOH Z 369 " =    1.894
peak=    3.198 closest distance to " OG  SER A 276 " =    0.742
peak=    3.194 closest distance to " CB  PHE A  16 " =    1.164
peak=    3.193 closest distance to " NH2 ARG A 156 " =    1.129
peak=    3.191 closest distance to " OD1 ASN A 217 " =    1.463
peak=    3.188 closest distance to " O   LEU A 282 " =    1.058
peak=    3.186 closest distance to " O   PRO A  90 " =    1.469
peak=    3.186 closest distance to " CG2 ILE A  20 " =    1.175
peak=    3.183 closest distance to " O   HOH Z 162 " =    2.046
peak=    3.179 closest distance to " O   HOH Z 219 " =    5.244
peak=    3.178 closest distance to " CG2 ILE A 109 " =    1.340
peak=    3.177 closest distance to " O   HOH Z 336 " =    1.590
peak=    3.167 closest distance to " OG  SER A 271 " =    2.060
peak=    3.162 closest distance to " O   HOH Z 130 " =    3.275
peak=    3.154 closest distance to " CG  ASP A 231 " =    0.844
peak=    3.150 closest distance to " O   HOH Z 393 " =    2.500
peak=    3.146 closest distance to " CB  PRO A 243 " =    1.356
peak=    3.146 closest distance to " CA  ARG A 102 " =    1.390
peak=    3.145 closest distance to " O   HOH Z  44 " =    2.448
peak=    3.144 closest distance to " CA  GLY A  23 " =    0.765
peak=    3.142 closest distance to " OE1 GLN A  11 " =    2.032
peak=    3.138 closest distance to " O   HOH Z 207 " =    2.500
peak=    3.138 closest distance to " CD2 LEU A 255 " =    1.461
peak=    3.136 closest distance to " CB  ALA A 248 " =    1.351
peak=    3.135 closest distance to " CB  MET A  40 " =    0.841
peak=    3.131 closest distance to " O   HOH Z 112 " =    1.595
peak=    3.128 closest distance to " CB  ALA A 114 " =    1.560
peak=    3.123 closest distance to " O   HOH Z 340 " =    1.468
peak=    3.123 closest distance to " C   ASN A 209 " =    1.320
peak=    3.120 closest distance to " CB  ARG A 259 " =    1.744
peak=    3.119 closest distance to " O   HOH Z   3 " =    1.606
peak=    3.115 closest distance to " CZ  TYR A  68 " =    0.855
peak=    3.107 closest distance to " O   HOH Z  32 " =    2.194
peak=    3.091 closest distance to " CB  ARG A  56 " =    1.075
peak=    3.090 closest distance to " O   HOH Z 189 " =    4.213
peak=    3.086 closest distance to " CA  GLY A 287 " =    1.209
peak=    3.080 closest distance to " CD2 TYR A  68 " =    1.380
peak=    3.072 closest distance to " C   SER A  32 " =    0.865
peak=    3.068 closest distance to " CB  ILE A 120 " =    1.404
peak=    3.066 closest distance to " CA  ILE A 120 " =    1.273
peak=    3.064 closest distance to " O   HOH Z   4 " =    1.773
peak=    3.060 closest distance to " O   HOH Z 188 " =    1.732
peak=    3.049 closest distance to " CG2 ILE A 234 " =    1.023
peak=    3.040 closest distance to " O   HOH Z 380 " =    2.944
peak=    3.039 closest distance to " NE2 HIS A  81 " =    1.228
peak=    3.019 closest distance to " CE BMET A  47 " =    1.190

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.144 - 5.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 221
   mapped sites are within: 0.733 - 5.746

peak=   -4.751 closest distance to " N   GLN A  58 " =    1.535
peak=   -4.530 closest distance to " CG1 VAL A 112 " =    2.329
peak=   -4.389 closest distance to " N   ARG A 275 " =    1.079
peak=   -4.338 closest distance to " NH2 ARG A  66 " =    0.923
peak=   -4.316 closest distance to " CG2BVAL A  41 " =    2.469
peak=   -4.188 closest distance to " CD  GLN A 223 " =    1.148
peak=   -4.174 closest distance to " CD1 PHE A  59 " =    1.902
peak=   -4.163 closest distance to " CD  GLN A  77 " =    0.789
peak=   -4.150 closest distance to " SG  CYS A 168 " =    1.024
peak=   -4.129 closest distance to " CD  ARG A 269 " =    2.445
peak=   -4.077 closest distance to " O   HOH Z 400 " =    0.735
peak=   -4.074 closest distance to " CA  ARG A  24 " =    1.457
peak=   -4.072 closest distance to " C   SER A 271 " =    1.447
peak=   -4.068 closest distance to " O   HOH Z  52 " =    2.330
peak=   -4.040 closest distance to " OG  SER A  63 " =    1.595
peak=   -4.038 closest distance to " CA  ASN A 127 " =    1.039
peak=   -4.034 closest distance to " O   HOH Z 186 " =    1.229
peak=   -4.010 closest distance to " CE  MET A 105 " =    2.488
peak=   -4.008 closest distance to " O   HOH Z  55 " =    2.669
peak=   -3.969 closest distance to " O   GLN A  94 " =    2.286
peak=   -3.907 closest distance to " C   ASN A 285 " =    2.358
peak=   -3.896 closest distance to " O   HOH Z 151 " =    1.319
peak=   -3.880 closest distance to " NE2 GLN A  58 " =    3.757
peak=   -3.870 closest distance to " O   HOH Z 103 " =    2.249
peak=   -3.869 closest distance to " C   TRP A 274 " =    0.899
peak=   -3.859 closest distance to " C   GLY A  91 " =    1.691
peak=   -3.849 closest distance to " NE2 HIS A  86 " =    0.879
peak=   -3.836 closest distance to " O   HOH Z 210 " =    1.080
peak=   -3.834 closest distance to " CA  SER A 164 " =    1.747
peak=   -3.814 closest distance to " OE2 GLU A  53 " =    1.101
peak=   -3.803 closest distance to " CA  THR A  29 " =    1.370
peak=   -3.795 closest distance to " O   HOH Z 231 " =    0.965
peak=   -3.789 closest distance to " OG  SER A  32 " =    1.666
peak=   -3.783 closest distance to " O   HOH Z 400 " =    1.013
peak=   -3.782 closest distance to " CG  GLU A   2 " =    1.745
peak=   -3.771 closest distance to " O   HOH Z 396 " =    1.814
peak=   -3.750 closest distance to " O   LEU A 297 " =    1.668
peak=   -3.748 closest distance to " CD2 PHE A  59 " =    2.279
peak=   -3.732 closest distance to " CB  ALA A 291 " =    2.375
peak=   -3.726 closest distance to " NH2 ARG A  36 " =    1.403
peak=   -3.720 closest distance to " N   ARG A 275 " =    0.961
peak=   -3.705 closest distance to " CB  SER A  63 " =    3.370
peak=   -3.704 closest distance to " O   HOH Z 166 " =    1.525
peak=   -3.703 closest distance to " CZ  PHE A 218 " =    1.117
peak=   -3.680 closest distance to " CA  GLY A 229 " =    2.421
peak=   -3.678 closest distance to " OG  SER A  97 " =    2.319
peak=   -3.677 closest distance to " O   HOH Z  13 " =    0.733
peak=   -3.675 closest distance to " CG  TRP A 266 " =    1.899
peak=   -3.673 closest distance to " CD2 LEU A 143 " =    2.390
peak=   -3.672 closest distance to " N   TYR A  68 " =    2.844
peak=   -3.669 closest distance to " C   SER A  63 " =    1.673
peak=   -3.660 closest distance to " O  BHOH Z  74 " =    1.493
peak=   -3.659 closest distance to " CB  PHE A 130 " =    1.288
peak=   -3.655 closest distance to " O   HOH Z 388 " =    1.771
peak=   -3.653 closest distance to " C   TYR A  30 " =    1.251
peak=   -3.647 closest distance to " O   ASN A  60 " =    1.285
peak=   -3.638 closest distance to " CZ  ARG A  66 " =    0.820
peak=   -3.632 closest distance to " CA  ASP A 298 " =    1.271
peak=   -3.630 closest distance to " CD2 LEU A 237 " =    2.420
peak=   -3.628 closest distance to " CG2 ILE A 263 " =    2.245
peak=   -3.622 closest distance to " C   SER A  32 " =    1.654
peak=   -3.618 closest distance to " CG2AVAL A 121 " =    2.279
peak=   -3.615 closest distance to " OD1 ASP A  27 " =    1.177
peak=   -3.614 closest distance to " CG2 VAL A 296 " =    0.814
peak=   -3.613 closest distance to " O   HOH Z  92 " =    1.244
peak=   -3.607 closest distance to " CA  SER A 271 " =    2.267
peak=   -3.603 closest distance to " N   SER A 212 " =    1.381
peak=   -3.599 closest distance to " CG  MET A 105 " =    0.906
peak=   -3.598 closest distance to " O   HOH Z 272 " =    0.885
peak=   -3.592 closest distance to " O   HOH Z 351 " =    1.654
peak=   -3.577 closest distance to " CA  GLU A 277 " =    1.373
peak=   -3.573 closest distance to " CD2 TYR A 293 " =    1.626
peak=   -3.563 closest distance to " OD2 ASP A  50 " =    2.148
peak=   -3.543 closest distance to " O   ILE A  33 " =    1.192
peak=   -3.534 closest distance to " O   HOH Z 311 " =    3.110
peak=   -3.519 closest distance to " O   THR A  31 " =    1.683
peak=   -3.512 closest distance to " CZ  ARG A  36 " =    1.839
peak=   -3.510 closest distance to " C   ALA A  10 " =    1.303
peak=   -3.510 closest distance to " CA  THR A   4 " =    1.859
peak=   -3.500 closest distance to " CD  LYS A 289 " =    2.326
peak=   -3.490 closest distance to " CD1 LEU A   5 " =    1.628
peak=   -3.490 closest distance to " O   HOH Z 274 " =    2.589
peak=   -3.479 closest distance to " CG1 VAL A 296 " =    1.326
peak=   -3.473 closest distance to " CB  ALA A 291 " =    2.143
peak=   -3.469 closest distance to " N   GLY A 262 " =    1.621
peak=   -3.465 closest distance to " O   GLN A 240 " =    3.373
peak=   -3.463 closest distance to " ND2 ASN A 301 " =    1.804
peak=   -3.462 closest distance to " O   HOH Z 111 " =    0.780
peak=   -3.457 closest distance to " O   HOH Z 118 " =    1.460
peak=   -3.456 closest distance to " N   SER A 134 " =    1.260
peak=   -3.455 closest distance to " O   GLY A  80 " =    1.447
peak=   -3.453 closest distance to " CD1 LEU A  25 " =    2.519
peak=   -3.453 closest distance to " OE1 GLN A 122 " =    0.786
peak=   -3.446 closest distance to " O   SER A 276 " =    1.804
peak=   -3.443 closest distance to " O   HOH Z 282 " =    4.762
peak=   -3.440 closest distance to " O   HOH Z 237 " =    2.113
peak=   -3.438 closest distance to " OE2 GLU A  37 " =    0.885
peak=   -3.432 closest distance to " C   VAL A 121 " =    1.153
peak=   -3.431 closest distance to " CA  ASP A  27 " =    1.516
peak=   -3.424 closest distance to " N   GLY A 287 " =    1.637
peak=   -3.420 closest distance to " NZ  LYS A 119 " =    1.842
peak=   -3.416 closest distance to " O   HOH Z  56 " =    2.017
peak=   -3.416 closest distance to " O   HOH Z 246 " =    0.743
peak=   -3.415 closest distance to " CG2AVAL A  41 " =    2.452
peak=   -3.404 closest distance to " O   HOH Z 407 " =    0.966
peak=   -3.395 closest distance to " O   HOH Z 335 " =    1.321
peak=   -3.393 closest distance to " O   HOH Z 411 " =    4.580
peak=   -3.392 closest distance to " O   HOH Z  83 " =    1.989
peak=   -3.392 closest distance to " C   LEU A 101 " =    0.967
peak=   -3.390 closest distance to " OG  SER A 273 " =    1.399
peak=   -3.387 closest distance to " O   HOH Z  49 " =    1.493
peak=   -3.379 closest distance to " O   ASP A 298 " =    1.790
peak=   -3.368 closest distance to " O   HOH Z 402 " =    1.092
peak=   -3.367 closest distance to " O   HOH Z 422 " =    1.377
peak=   -3.365 closest distance to " CD  PRO A 213 " =    2.313
peak=   -3.353 closest distance to " CB  ASP A 171 " =    2.218
peak=   -3.349 closest distance to " CG  GLU A  37 " =    1.120
peak=   -3.343 closest distance to " O   HOH Z 265 " =    2.060
peak=   -3.339 closest distance to " O   HOH Z   5 " =    1.809
peak=   -3.339 closest distance to " O   HOH Z 340 " =    1.803
peak=   -3.338 closest distance to " CG  PHE A 130 " =    2.184
peak=   -3.338 closest distance to " O   HOH Z 314 " =    2.366
peak=   -3.332 closest distance to " NH1 ARG A 138 " =    1.387
peak=   -3.331 closest distance to " CD2 TRP A  85 " =    1.183
peak=   -3.327 closest distance to " CB  ALA A 161 " =    2.695
peak=   -3.322 closest distance to " CG  TYR A 214 " =    1.160
peak=   -3.322 closest distance to " OE1 GLN A  88 " =    2.937
peak=   -3.322 closest distance to " O   HOH Z  38 " =    0.922
peak=   -3.322 closest distance to " N   THR A 264 " =    1.404
peak=   -3.321 closest distance to " O   HOH Z 384 " =    1.754
peak=   -3.317 closest distance to " O   HOH Z 362 " =    5.746
peak=   -3.315 closest distance to " O   HOH Z 231 " =    1.649
peak=   -3.314 closest distance to " N   THR A 235 " =    1.175
peak=   -3.305 closest distance to " NH1 ARG A 219 " =    1.931
peak=   -3.301 closest distance to " CD1 ILE A 263 " =    2.496
peak=   -3.300 closest distance to " O   HOH Z  53 " =    2.304
peak=   -3.299 closest distance to " CA  GLU A   2 " =    2.772
peak=   -3.279 closest distance to " CA  THR A   4 " =    1.304
peak=   -3.278 closest distance to " O   HOH Z 435 " =    3.042
peak=   -3.277 closest distance to " OG BSER A  99 " =    1.276
peak=   -3.276 closest distance to " O   HOH Z 186 " =    0.740
peak=   -3.276 closest distance to " CB  ASN A  39 " =    2.113
peak=   -3.273 closest distance to " O   HOH Z 222 " =    1.421
peak=   -3.272 closest distance to " O   HOH Z 326 " =    4.220
peak=   -3.268 closest distance to " O   HOH Z 298 " =    3.397
peak=   -3.267 closest distance to " OG1 THR A 246 " =    1.773
peak=   -3.266 closest distance to " CG2BVAL A  41 " =    1.130
peak=   -3.261 closest distance to " C   SER A   3 " =    2.208
peak=   -3.260 closest distance to " O   HOH Z 244 " =    1.166
peak=   -3.259 closest distance to " O   HOH Z 191 " =    3.952
peak=   -3.258 closest distance to " O   HOH Z 391 " =    1.424
peak=   -3.258 closest distance to " CD  ARG A  14 " =    2.921
peak=   -3.258 closest distance to " O   VAL A 125 " =    1.900
peak=   -3.257 closest distance to " CG1 VAL A  78 " =    1.880
peak=   -3.255 closest distance to " CA  ASP A 286 " =    2.417
peak=   -3.251 closest distance to " CB  LEU A 167 " =    2.048
peak=   -3.249 closest distance to " O   HOH Z 114 " =    2.185
peak=   -3.248 closest distance to " O   HOH Z 124 " =    1.523
peak=   -3.243 closest distance to " CG  PRO A 243 " =    1.709
peak=   -3.239 closest distance to " SG  CYS A 254 " =    3.095
peak=   -3.222 closest distance to " O   HOH Z 290 " =    1.158
peak=   -3.221 closest distance to " O   HOH Z 411 " =    3.864
peak=   -3.221 closest distance to " CG2 THR A   4 " =    1.879
peak=   -3.215 closest distance to " OG1 THR A 157 " =    1.652
peak=   -3.212 closest distance to " CB  ALA A  43 " =    2.798
peak=   -3.211 closest distance to " CB  ASN A  45 " =    0.979
peak=   -3.210 closest distance to " CG  GLN A 103 " =    2.180
peak=   -3.203 closest distance to " CA  ALA A   8 " =    1.498
peak=   -3.203 closest distance to " O   ALA A  34 " =    1.845
peak=   -3.202 closest distance to " CD  ARG A 259 " =    1.643
peak=   -3.201 closest distance to " O   HOH Z 121 " =    3.718
peak=   -3.198 closest distance to " CE2 TYR A 116 " =    1.609
peak=   -3.192 closest distance to " O   THR A  31 " =    2.070
peak=   -3.184 closest distance to " CG2AVAL A  41 " =    2.556
peak=   -3.176 closest distance to " O   LYS A 117 " =    1.724
peak=   -3.174 closest distance to " CA  SER A 276 " =    1.377
peak=   -3.165 closest distance to " OG ASER A 134 " =    1.255
peak=   -3.162 closest distance to " CB  ASN A 224 " =    2.603
peak=   -3.146 closest distance to " O   HOH Z 134 " =    2.019
peak=   -3.145 closest distance to " CB  ALA A 114 " =    2.379
peak=   -3.144 closest distance to " NE1 TRP A 150 " =    1.094
peak=   -3.139 closest distance to " NH1AARG A 102 " =    1.509
peak=   -3.137 closest distance to " OD2 ASP A 171 " =    1.974
peak=   -3.136 closest distance to " CZ  ARG A 156 " =    1.168
peak=   -3.135 closest distance to " O   ALA A  43 " =    2.204
peak=   -3.131 closest distance to " OG  SER A 276 " =    1.120
peak=   -3.129 closest distance to " OE1 GLN A 194 " =    2.519
peak=   -3.128 closest distance to " CA  GLY A 203 " =    2.438
peak=   -3.124 closest distance to " CB  ASP A 286 " =    2.047
peak=   -3.121 closest distance to " CA  HIS A 108 " =    1.348
peak=   -3.121 closest distance to " O   HOH Z  37 " =    1.570
peak=   -3.117 closest distance to " OE2 GLU A  44 " =    1.152
peak=   -3.114 closest distance to " CZ  ARG A  79 " =    1.708
peak=   -3.110 closest distance to " O   ARG A  66 " =    1.179
peak=   -3.099 closest distance to " O   VAL A 250 " =    2.759
peak=   -3.097 closest distance to " CG2 VAL A 230 " =    1.110
peak=   -3.085 closest distance to " O   HOH Z 292 " =    4.256
peak=   -3.076 closest distance to " O   HOH Z 183 " =    1.141
peak=   -3.043 closest distance to " O   TRP A  85 " =    2.215

================= 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    :  0.5121 0.4937   6.310585e+00   6.294759e+00
   1_bss:  0.5067 0.4875   6.308492e+00   6.291751e+00
   1_xyz:  0.4481 0.4598   6.248139e+00   6.266808e+00
   1_adp:  0.4096 0.4453   6.202829e+00   6.255613e+00
   1_occ:  0.4089 0.4448   6.201770e+00   6.254831e+00
   2_bss:  0.4078 0.4408   6.203477e+00   6.254814e+00
   2_xyz:  0.3511 0.4202   6.109608e+00   6.211672e+00
   2_adp:  0.3418 0.4121   6.094013e+00   6.201274e+00
   2_occ:  0.3415 0.4134   6.094322e+00   6.202219e+00
   3_bss:  0.3416 0.4112   6.093938e+00   6.201474e+00
   3_xyz:  0.2838 0.3434   5.938151e+00   6.079063e+00
   3_adp:  0.2585 0.3308   5.881368e+00   6.048122e+00
   3_occ:  0.2584 0.3306   5.880793e+00   6.047670e+00
   4_bss:  0.2582 0.3299   5.879900e+00   6.045542e+00
   4_xyz:  0.2064 0.2740   5.684100e+00   5.881848e+00
   4_adp:  0.1927 0.2544   5.620385e+00   5.821151e+00
   4_occ:  0.1925 0.2538   5.619130e+00   5.819401e+00
   5_bss:  0.1924 0.2536   5.619829e+00   5.819597e+00
   5_xyz:  0.1682 0.2269   5.510019e+00   5.722586e+00
   5_adp:  0.1659 0.2246   5.499078e+00   5.713719e+00
   5_occ:  0.1657 0.2243   5.498304e+00   5.713142e+00
   5_bss:  0.1659 0.2247   5.498430e+00   5.714181e+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  50.000   7.450  10.419   5.580   0.000   0.000   0.000
   1_xyz:  0.300  50.000   7.450  10.419   5.580   0.000   0.000   0.000
   1_adp:  0.300  50.000   7.450  10.419   5.580   0.000   0.000   0.000
   1_occ:  0.300  50.000   7.450  10.419   5.580   0.000   0.000   0.000
   2_bss:  0.293  50.000   4.367   6.314   3.473   0.000   0.000   0.000
   2_xyz:  0.293  50.000   4.367   6.314   3.473   0.000   0.000   0.000
   2_adp:  0.293  50.000   4.367   6.314   3.473   0.000   0.000   0.000
   2_occ:  0.293  50.000   4.367   6.314   3.473   0.000   0.000   0.000
   3_bss:  0.308  50.000   3.133   4.746   3.056   0.000   0.000   0.000
   3_xyz:  0.308  50.000   3.133   4.746   3.056   0.000   0.000   0.000
   3_adp:  0.308  50.000   3.133   4.746   3.056   0.000   0.000   0.000
   3_occ:  0.308  50.000   3.133   4.746   3.056   0.000   0.000   0.000
   4_bss:  0.301  50.000   2.323   3.513   2.151   0.000   0.000   0.000
   4_xyz:  0.301  50.000   2.323   3.513   2.151   0.000   0.000   0.000
   4_adp:  0.301  50.000   2.323   3.513   2.151   0.000   0.000   0.000
   4_occ:  0.301  50.000   2.323   3.513   2.151   0.000   0.000   0.000
   5_bss:  0.332  63.615   1.800   2.642   2.019   0.000   0.000   0.000
   5_xyz:  0.332  63.615   1.800   2.642   2.019   0.000   0.000   0.000
   5_adp:  0.332  63.615   1.800   2.642   2.019   0.000   0.000   0.000
   5_occ:  0.332  63.615   1.800   2.642   2.019   0.000   0.000   0.000
   5_bss:  0.326  63.665  -0.330   0.291   0.038   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.009 0.3552  0.4156    81014.702
   1_bss:  63.650 0.3453  0.5009    79616.568
   1_xyz:  57.383 0.4258  0.6082    68326.122
   1_adp:  54.370 0.4645  0.7245    63519.882
   1_occ:  54.268 0.4658  0.7258    63421.534
   2_bss:  54.066 0.4683  0.6603    63123.575
   2_xyz:  49.668 0.5226  0.7351    53619.942
   2_adp:  48.121 0.5422  0.7609    51137.587
   2_occ:  48.192 0.5413  0.7596    51296.123
   3_bss:  47.980 0.5438  0.7364    50756.398
   3_xyz:  37.696 0.6688  0.8831    33322.692
   3_adp:  35.745 0.6916  0.8931    30293.507
   3_occ:  35.707 0.6921  0.8933    30252.456
   4_bss:  35.553 0.6937  0.8654    29999.234
   4_xyz:  28.354 0.7742  0.9398    19602.664
   4_adp:  25.705 0.8032  0.9567    16966.839
   4_occ:  25.658 0.8038  0.9572    16914.543
   5_bss:  25.603 0.8044  0.9413    16886.664
   5_xyz:  22.401 0.8377  0.9634    13373.074
   5_adp:  22.122 0.8406  0.9702    13146.454
   5_occ:  22.100 0.8408  0.9703    13127.962
   5_bss:  22.090 0.8408  0.9537    13122.511
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4552e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4552e+01
   1_xyz:   1.865  0.015  0.115 18.305  0.008  4.125   1.7024e-01
   1_adp:   1.865  0.015  0.115 18.305  0.008  4.125   1.7024e-01
   1_occ:   1.865  0.015  0.115 18.305  0.008  4.125   1.7024e-01
   2_bss:   1.865  0.015  0.115 18.305  0.008  4.125   1.7024e-01
   2_xyz:   1.342  0.009  0.091 17.171  0.005  4.110   1.1162e-01
   2_adp:   1.342  0.009  0.091 17.171  0.005  4.110   1.1162e-01
   2_occ:   1.342  0.009  0.091 17.171  0.005  4.110   1.1162e-01
   3_bss:   1.342  0.009  0.091 17.171  0.005  4.110   1.1162e-01
   3_xyz:   1.289  0.009  0.096 16.127  0.005  4.114   1.0131e-01
   3_adp:   1.289  0.009  0.096 16.127  0.005  4.114   1.0131e-01
   3_occ:   1.289  0.009  0.096 16.127  0.005  4.114   1.0131e-01
   4_bss:   1.289  0.009  0.096 16.127  0.005  4.114   1.0131e-01
   4_xyz:   1.283  0.011  0.088 16.116  0.004  4.117   9.8089e-02
   4_adp:   1.283  0.011  0.088 16.116  0.004  4.117   9.8089e-02
   4_occ:   1.283  0.011  0.088 16.116  0.004  4.117   9.8089e-02
   5_bss:   1.283  0.011  0.088 16.116  0.004  4.117   9.8089e-02
   5_xyz:   1.144  0.009  0.084 15.577  0.004  4.116   7.9365e-02
   5_adp:   1.144  0.009  0.084 15.577  0.004  4.116   7.9365e-02
   5_occ:   1.144  0.009  0.084 15.577  0.004  4.116   7.9365e-02
   5_bss:   1.144  0.009  0.084 15.577  0.004  4.116   7.9365e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0707e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0707e+00
   1_xyz:  16.611  0.135  0.535 88.851  0.056  2.126   1.1465e-01
   1_adp:  16.611  0.135  0.535 88.851  0.056  2.126   1.1465e-01
   1_occ:  16.611  0.135  0.535 88.851  0.056  2.126   1.1465e-01
   2_bss:  16.611  0.135  0.535 88.851  0.056  2.126   1.1465e-01
   2_xyz:   9.985  0.075  0.279 84.887  0.051  1.889   5.9317e-02
   2_adp:   9.985  0.075  0.279 84.887  0.051  1.889   5.9317e-02
   2_occ:   9.985  0.075  0.279 84.887  0.051  1.889   5.9317e-02
   3_bss:   9.985  0.075  0.279 84.887  0.051  1.889   5.9317e-02
   3_xyz:   8.332  0.061  0.360 77.153  0.035  2.065   1.0726e-01
   3_adp:   8.332  0.061  0.360 77.153  0.035  2.065   1.0726e-01
   3_occ:   8.332  0.061  0.360 77.153  0.035  2.065   1.0726e-01
   4_bss:   8.332  0.061  0.360 77.153  0.035  2.065   1.0726e-01
   4_xyz:   9.038  0.067  0.327 80.218  0.031  2.062   9.6601e-02
   4_adp:   9.038  0.067  0.327 80.218  0.031  2.062   9.6601e-02
   4_occ:   9.038  0.067  0.327 80.218  0.031  2.062   9.6601e-02
   5_bss:   9.038  0.067  0.327 80.218  0.031  2.062   9.6601e-02
   5_xyz:   8.330  0.048  0.463 89.937  0.046  2.245   9.4278e-02
   5_adp:   8.330  0.048  0.463 89.937  0.046  2.245   9.4278e-02
   5_occ:   8.330  0.048  0.463 89.937  0.046  2.245   9.4278e-02
   5_bss:   8.330  0.048  0.463 89.937  0.046  2.245   9.4278e-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: 126.46   0.00  15.65  75.32   0.00  13.71 126.46   0.00  26.21
   1_occ: 126.46   0.00  15.65  75.32   0.00  13.71 126.46   0.00  26.21
   2_bss: 126.46   0.00  15.65  75.32   0.00  13.71 126.46   0.00  26.21
   2_xyz: 126.46   0.00  15.65  75.32   0.00  13.71 126.46   0.00  26.21
   2_adp: 125.63   0.00  15.20  77.42   0.00  12.92 125.63   0.00  27.66
   2_occ: 125.63   0.00  15.20  77.42   0.00  12.92 125.63   0.00  27.66
   3_bss: 125.63   0.00  15.20  77.42   0.00  12.92 125.63   0.00  27.66
   3_xyz: 125.63   0.00  15.20  77.42   0.00  12.92 125.63   0.00  27.66
   3_adp: 130.37   0.00  16.68  93.64   0.00  12.74 130.37   0.00  38.13
   3_occ: 130.37   0.00  16.68  93.64   0.00  12.74 130.37   0.00  38.13
   4_bss: 130.37   0.00  16.68  93.64   0.00  12.74 130.37   0.00  38.13
   4_xyz: 130.37   0.00  16.68  93.64   0.00  12.74 130.37   0.00  38.13
   4_adp: 130.23   0.00  16.11 119.58   0.00  11.90 130.23   0.00  38.98
   4_occ: 130.23   0.00  16.11 119.58   0.00  11.90 130.23   0.00  38.98
   5_bss: 130.23   0.00  16.11 119.58   0.00  11.90 130.23   0.00  38.98
   5_xyz: 130.23   0.00  16.11 119.58   0.00  11.90 130.23   0.00  38.98
   5_adp: 130.19   0.00  16.13 112.78   0.00  11.90 130.19   1.66  39.14
   5_occ: 130.19   0.00  16.13 112.78   0.00  11.90 130.19   1.66  39.14
   5_bss: 131.83   1.65  17.77 114.42   1.65  13.55 131.83   3.31  40.79
------------------------------------------------------------------------
 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:    1.145    0.020    0.421
   1_adp:    1.145    0.020    0.421
   1_occ:    1.145    0.020    0.421
   2_bss:    1.145    0.020    0.421
   2_xyz:    1.720    0.028    0.585
   2_adp:    1.720    0.028    0.585
   2_occ:    1.720    0.028    0.585
   3_bss:    1.720    0.028    0.585
   3_xyz:    1.906    0.055    0.760
   3_adp:    1.906    0.055    0.760
   3_occ:    1.906    0.055    0.760
   4_bss:    1.906    0.055    0.760
   4_xyz:    2.375    0.103    0.895
   4_adp:    2.375    0.103    0.895
   4_occ:    2.375    0.103    0.895
   5_bss:    2.375    0.103    0.895
   5_xyz:    2.177    0.046    0.951
   5_adp:    2.177    0.046    0.951
   5_occ:    2.177    0.046    0.951
   5_bss:    2.177    0.046    0.951
------------------------------------------------------------------------

CPU time actual refinement: 345.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1324/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_1324/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1324/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1324/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1324/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.01 
  Macro-tasks:
    bulk solvent and scale       = 36.55  
    individual site refinement   = 152.37 
    weights calculation          = 32.31  
    collect and process          = 6.20   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 227.53 
  Micro-tasks:
    mask                            = 3.05   
    f_calc                          = 111.43 
    alpha_beta                      = 8.41   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 121.56 
    fmodel                         = 6.28   
    r_factors                      = 0.18   
    phase_errors                   = 9.64   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 261.99 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.886 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    616 calls, 111.10 s
gradients_fft:          561 calls, 108.50 s

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

# Date 2008-01-16 Time 03:44:44 PST -0800 (1200483884.65 s)
Start R-work = 0.5121, R-free = 0.4937 (no bulk solvent and anisotropic scale)
Final R-work = 0.1815, R-free = 0.2393 (no bulk solvent and anisotropic scale)

Start R-work = 0.5067, R-free = 0.4875
Final R-work = 0.1659, R-free = 0.2247