# Date 2008-01-16 Time 02:33:36 PST -0800 (1200479616.34 s)
#phil __OFF__

Command line arguments: "../882.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9518
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 882

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.4607, 85.0941, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97103
Completeness in resolution range: 0.9586
Completeness with d_max=infinity: 0.955701

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9710

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97103
Completeness in resolution range: 0.9586
Completeness with d_max=infinity: 0.955701

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2182 [2143/2169]  1932   211   9.8%
  bin  2:  4.2182 -  3.3604 [2063/2082]  1855   208  10.1%
  bin  3:  3.3604 -  2.9392 [2032/2051]  1827   205  10.1%
  bin  4:  2.9392 -  2.6721 [2014/2044]  1813   201  10.0%
  bin  5:  2.6721 -  2.4815 [2017/2036]  1820   197   9.8%
  bin  6:  2.4815 -  2.3357 [1987/2012]  1781   206  10.4%
  bin  7:  2.3357 -  2.2192 [1990/2018]  1790   200  10.1%
  bin  8:  2.2192 -  2.1228 [1968/2004]  1778   190   9.7%
  bin  9:  2.1228 -  2.0413 [1974/2016]  1773   201  10.2%
  bin 10:  2.0413 -  1.9710 [1401/2003]  1261   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_882/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 29
        2.42 -     3.04: 2207
        3.04 -     3.66: 4753
        3.66 -     4.28: 9098
        4.28 -     4.90: 12409
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.006 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.069 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.076 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.107 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28491 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_882/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_882/model_refine_001.geo

CPU time processing inputs: 9.23


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.4607 85.09415 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: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4628   r_free= 0.4457   ksol= 0.00   Bsol= 0.00   scale= 0.809    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.260095                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7050 0.99   1392  155 0.3882 0.3957      6.5606      6.5564|
|  2:  4.7050 -  3.7536 0.99   1343  146 0.3723 0.3655      6.7375      6.7215|
|  3:  3.7536 -  3.2848 0.99   1313  147 0.4153 0.3778      6.6252      6.6799|
|  4:  3.2848 -  2.9870 0.99   1315  153 0.4422 0.3966      6.5092       6.441|
|  5:  2.9870 -  2.7743 0.99   1297  139 0.4890 0.4857      6.3502      6.3388|
|  6:  2.7743 -  2.6117 0.99   1287  143 0.4849 0.5007      6.2581      6.2462|
|  7:  2.6117 -  2.4815 0.99   1300  139 0.5076 0.4583      6.2523      6.2049|
|  8:  2.4815 -  2.3739 0.98   1261  151 0.5201 0.4551      6.1615      6.1457|
|  9:  2.3739 -  2.2828 0.98   1280  145 0.4898 0.4813      6.1119      6.1151|
| 10:  2.2828 -  2.2043 0.99   1280  138 0.5103 0.5134      6.1052      6.0961|
| 11:  2.2043 -  2.1356 0.98   1286  138 0.5121 0.4861      6.0359      6.0202|
| 12:  2.1356 -  2.0747 0.97   1241  139 0.4976 0.5233      5.9641      6.0161|
| 13:  2.0747 -  2.0202 1.00   1265  140 0.5368 0.5229      5.8807      5.8215|
| 14:  2.0202 -  1.9710 0.59    770   86 0.5448 0.5398      5.8411      5.7818|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7050  1392   155  0.69  35.22   0.80     0.74      73026.54|
|  2:  4.7050 -  3.7536  1343   146  0.73  32.26   0.89     0.81      93807.28|
|  3:  3.7536 -  3.2848  1313   147  0.64  40.06   0.86     0.78      97465.56|
|  4:  3.2848 -  2.9870  1315   153  0.58  45.20   0.82     0.69      86604.50|
|  5:  2.9870 -  2.7743  1297   139  0.48  53.77   0.75     0.57      74193.94|
|  6:  2.7743 -  2.6117  1287   143  0.46  55.48   0.74     0.53      65979.26|
|  7:  2.6117 -  2.4815  1300   139  0.45  56.35   0.75     0.51      59030.77|
|  8:  2.4815 -  2.3739  1261   151  0.44  56.81   0.72     0.53      52391.95|
|  9:  2.3739 -  2.2828  1280   145  0.46  55.11   0.75     0.52      46179.80|
| 10:  2.2828 -  2.2043  1280   138  0.44  57.13   0.77     0.51      43131.27|
| 11:  2.2043 -  2.1356  1286   138  0.40  59.96   0.78     0.48      42069.47|
| 12:  2.1356 -  2.0747  1241   139  0.37  62.61   0.77     0.44      41370.09|
| 13:  2.0747 -  2.0202  1265   140  0.30  67.96   0.74     0.38      37812.24|
| 14:  2.0202 -  1.9710   770    86  0.27  70.32   0.71     0.30      32091.05|
|alpha:            min =        0.30 max =            0.81 mean =         0.57|
|beta:             min =    32091.05 max =        97465.56 mean =     61585.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.70|
|phase err.(test): min =        0.00 max =           89.93 mean =        52.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.156497             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.132   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.967103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.277   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      704 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1518 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2665 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3959 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5083 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6629 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7766 |
|-----------------------------------------------------------------------------|
|-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 |       53.426 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.767 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    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 = 11.754)------------------------------------------|
|    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: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4686   r_free= 0.4510   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.263578                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4536   r_free= 0.4356   ksol= 0.34   Bsol= 1.42   scale= 1.018    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.10,9.09,8.86,0.00,0.00,0.00); trace/3= 8.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.253832                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.665751              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.720   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.373   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4536      final r-factor (work) = 0.3615          |
| start r-factor (free) = 0.4356      final r-factor (free) = 0.3865          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.6905 = 9.67 * 0.50 * 6.2623 + 1.00 * 53.4256                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8413 = 9.67 * 0.50 * 6.1474 + 1.00 * 0.1318                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3615      final r-factor (work) = 0.3147          |
| start r-factor (free) = 0.3865      final r-factor (free) = 0.3661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5691 = 0.90 * 1.00 * 6.1474 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4653 = 0.90 * 1.00 * 6.0328 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.83   12.12    None  None   None       |
|    all(noH): 2823   0      0.00    88.83   12.12    None  None   None       |
|    Sol.    : 438    0      0.00    75.53   27.12    None  None   None       |
|    Mac.    : 2385   0      0.00    88.83   9.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.883: 1437   |   5:    44.416 -  53.300:   43        |
|      1:     8.883 -  17.767:  783   |   6:    53.300 -  62.183:   12        |
|      2:    17.767 -  26.650:  279   |   7:    62.183 -  71.066:    4        |
|      3:    26.650 -  35.533:  165   |   8:    71.066 -  79.949:    2        |
|      4:    35.533 -  44.416:   96   |   9:    79.949 -  88.833:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3147 r_free = 0.3661             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3141 r_free = 0.3669             target_work(ml) = 6.007         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3141   r_free= 0.3669   ksol= 0.34   Bsol= 1.42   scale= 1.112    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.10,9.09,8.86,0.00,0.00,0.00); trace/3= 8.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.006911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3093   r_free= 0.3599   ksol= 0.33   Bsol= 32.47   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,4.43,5.32,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.003578                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.739101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.423   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386472              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.610  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3093      final r-factor (work) = 0.2208          |
| start r-factor (free) = 0.3599      final r-factor (free) = 0.2741          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4104 = 3.74 * 0.50 * 6.0328 + 1.00 * 0.1318                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0215 = 3.74 * 0.50 * 5.8608 + 1.00 * 0.0644                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2208      final r-factor (work) = 0.2008          |
| start r-factor (free) = 0.2741      final r-factor (free) = 0.2556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2792 = 0.39 * 1.00 * 5.8608 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2054 = 0.39 * 1.00 * 5.6799 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.03   12.13    None  None   None       |
|    all(noH): 2823   0      0.00    85.03   12.13    None  None   None       |
|    Sol.    : 438    0      1.36    73.72   31.79    None  None   None       |
|    Mac.    : 2385   0      0.00    85.03   8.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.503: 1592   |   5:    42.513 -  51.016:   65        |
|      1:     8.503 -  17.005:  617   |   6:    51.016 -  59.519:   20        |
|      2:    17.005 -  25.508:  204   |   7:    59.519 -  68.021:    4        |
|      3:    25.508 -  34.011:  161   |   8:    68.021 -  76.524:    2        |
|      4:    34.011 -  42.513:  155   |   9:    76.524 -  85.027:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2008 r_free = 0.2556             target_work(ml) = 5.647         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2005 r_free = 0.2552             target_work(ml) = 5.646         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2005   r_free= 0.2552   ksol= 0.33   Bsol= 32.47   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.12,4.43,5.32,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.646132                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1998   r_free= 0.2529   ksol= 0.33   Bsol= 42.90   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,2.65,3.66,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.645362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.363484              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.830  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.743243              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.816  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1998      final r-factor (work) = 0.1444          |
| start r-factor (free) = 0.2529      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6285 = 3.36 * 0.50 * 5.6870 + 1.00 * 0.0644                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3349 = 3.36 * 0.50 * 5.5133 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1444      final r-factor (work) = 0.1313          |
| start r-factor (free) = 0.1902      final r-factor (free) = 0.1788          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6212 = 1.74 * 1.00 * 5.5133 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2701 = 1.74 * 1.00 * 5.3098 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.76   13.16    None  None   None       |
|    all(noH): 2823   0      0.00    92.76   13.16    None  None   None       |
|    Sol.    : 438    0      2.21    81.41   38.12    None  None   None       |
|    Mac.    : 2385   0      0.00    92.76   8.58     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.276: 1713   |   5:    46.378 -  55.653:  101        |
|      1:     9.276 -  18.551:  553   |   6:    55.653 -  64.929:   57        |
|      2:    18.551 -  27.827:  148   |   7:    64.929 -  74.205:   21        |
|      3:    27.827 -  37.102:  121   |   8:    74.205 -  83.480:    5        |
|      4:    37.102 -  46.378:  101   |   9:    83.480 -  92.756:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1313 r_free = 0.1788             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1312 r_free = 0.1787             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1312   r_free= 0.1787   ksol= 0.33   Bsol= 42.90   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,2.65,3.66,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275973                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1788   ksol= 0.32   Bsol= 42.90   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,2.24,3.15,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.276218                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.253553              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.271  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.217624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.882  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1314      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1788      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0479 = 2.25 * 0.50 * 5.3115 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9612 = 2.25 * 0.50 * 5.2378 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1536 = 0.22 * 1.00 * 5.2378 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1417 = 0.22 * 1.00 * 5.2005 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.08   12.49    None  None   None       |
|    all(noH): 2823   0      0.00    91.08   12.49    None  None   None       |
|    Sol.    : 438    0      2.11    78.35   34.97    None  None   None       |
|    Mac.    : 2385   0      0.00    91.08   8.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.108: 1733   |   5:    45.540 -  54.648:   82        |
|      1:     9.108 -  18.216:  560   |   6:    54.648 -  63.756:   43        |
|      2:    18.216 -  27.324:  152   |   7:    63.756 -  72.864:    9        |
|      3:    27.324 -  36.432:  140   |   8:    72.864 -  81.972:    6        |
|      4:    36.432 -  45.540:   96   |   9:    81.972 -  91.080:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1621             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1618             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1618   ksol= 0.32   Bsol= 42.90   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,2.24,3.15,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184334                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1616   ksol= 0.32   Bsol= 42.90   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.08,2.96,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184323                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.569510              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.246  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.157344              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.203  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1402 = 1.57 * 0.50 * 5.2001 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1153 = 1.57 * 0.50 * 5.1737 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8240 = 0.16 * 1.00 * 5.1737 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8222 = 0.16 * 1.00 * 5.1695 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.64   12.20    None  None   None       |
|    all(noH): 2823   0      0.00    89.64   12.20    None  None   None       |
|    Sol.    : 438    0      2.13    76.62   33.55    None  None   None       |
|    Mac.    : 2385   0      0.00    89.64   8.28     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.964: 1735   |   5:    44.818 -  53.781:   73        |
|      1:     8.964 -  17.927:  577   |   6:    53.781 -  62.745:   33        |
|      2:    17.927 -  26.891:  140   |   7:    62.745 -  71.709:    8        |
|      3:    26.891 -  35.854:  146   |   8:    71.709 -  80.672:    6        |
|      4:    35.854 -  44.818:  103   |   9:    80.672 -  89.636:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1588             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1585             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1585   ksol= 0.32   Bsol= 42.90   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.08,2.96,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167048                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7050 0.99   1392  155 0.1023 0.1271      5.3941      5.5145|
|  2:  4.7050 -  3.7536 0.99   1343  146 0.0915 0.1184      5.4753      5.6654|
|  3:  3.7536 -  3.2848 0.99   1313  147 0.1105 0.1544      5.5078      5.8564|
|  4:  3.2848 -  2.9870 0.99   1315  153 0.1244 0.1589      5.4765      5.6019|
|  5:  2.9870 -  2.7743 0.99   1297  139 0.1381 0.1767      5.3498      5.5451|
|  6:  2.7743 -  2.6117 0.99   1287  143 0.1243 0.1802      5.2185       5.474|
|  7:  2.6117 -  2.4815 0.99   1300  139 0.1310 0.1609      5.2063      5.3585|
|  8:  2.4815 -  2.3739 0.98   1261  151 0.1214 0.1848      5.0723      5.3834|
|  9:  2.3739 -  2.2828 0.98   1280  145 0.1205 0.1719      5.0533      5.3206|
| 10:  2.2828 -  2.2043 0.99   1280  138 0.1158 0.1736      4.9625      5.1907|
| 11:  2.2043 -  2.1356 0.98   1286  138 0.1206 0.1780      4.9706      5.3041|
| 12:  2.1356 -  2.0747 0.97   1241  139 0.1127 0.1552      4.8896      5.0892|
| 13:  2.0747 -  2.0202 1.00   1265  140 0.1246 0.1798      4.8186      5.1096|
| 14:  2.0202 -  1.9710 0.59    770   86 0.1095 0.1580      4.6812      4.8862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7050  1392   155  0.94   8.68   0.98     0.96       6917.78|
|  2:  4.7050 -  3.7536  1343   146  0.95   7.98   1.02     1.00       9096.18|
|  3:  3.7536 -  3.2848  1313   147  0.93  11.63   1.03     1.02      10868.19|
|  4:  3.2848 -  2.9870  1315   153  0.92  13.63   1.01     0.98      10408.44|
|  5:  2.9870 -  2.7743  1297   139  0.90  16.04   0.99     0.96       8247.82|
|  6:  2.7743 -  2.6117  1287   143  0.90  15.74   0.98     0.96       7005.55|
|  7:  2.6117 -  2.4815  1300   139  0.90  15.78   1.00     0.97       6531.48|
|  8:  2.4815 -  2.3739  1261   151  0.91  15.53   0.99     0.96       5215.95|
|  9:  2.3739 -  2.2828  1280   145  0.91  15.24   1.01     1.00       5080.32|
| 10:  2.2828 -  2.2043  1280   138  0.91  15.07   1.01     0.97       4179.37|
| 11:  2.2043 -  2.1356  1286   138  0.90  16.17   1.01     0.96       4376.13|
| 12:  2.1356 -  2.0747  1241   139  0.92  14.83   1.02     1.02       3988.09|
| 13:  2.0747 -  2.0202  1265   140  0.90  16.63   1.01     1.01       3415.26|
| 14:  2.0202 -  1.9710   770    86  0.92  14.29   1.00     0.97       2511.54|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2511.54 max =        10868.19 mean =      6424.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.02|
|phase err.(test): min =        0.00 max =           88.34 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1585   ksol= 0.32   Bsol= 45.25   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,-0.37,0.52,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167000                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1585   ksol= 0.32   Bsol= 45.25   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,-0.37,0.52,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167000                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7050 0.99   1392  155 0.1023 0.1270      5.3936      5.5137|
|  2:  4.7050 -  3.7536 0.99   1343  146 0.0915 0.1184       5.475      5.6655|
|  3:  3.7536 -  3.2848 0.99   1313  147 0.1105 0.1544      5.5078      5.8563|
|  4:  3.2848 -  2.9870 0.99   1315  153 0.1244 0.1589      5.4765      5.6019|
|  5:  2.9870 -  2.7743 0.99   1297  139 0.1381 0.1767      5.3499      5.5453|
|  6:  2.7743 -  2.6117 0.99   1287  143 0.1243 0.1802      5.2185      5.4739|
|  7:  2.6117 -  2.4815 0.99   1300  139 0.1310 0.1609      5.2062      5.3584|
|  8:  2.4815 -  2.3739 0.98   1261  151 0.1214 0.1849      5.0722      5.3834|
|  9:  2.3739 -  2.2828 0.98   1280  145 0.1205 0.1719      5.0533      5.3205|
| 10:  2.2828 -  2.2043 0.99   1280  138 0.1158 0.1736      4.9625      5.1908|
| 11:  2.2043 -  2.1356 0.98   1286  138 0.1206 0.1780      4.9706      5.3041|
| 12:  2.1356 -  2.0747 0.97   1241  139 0.1127 0.1551      4.8898      5.0893|
| 13:  2.0747 -  2.0202 1.00   1265  140 0.1246 0.1798      4.8187        5.11|
| 14:  2.0202 -  1.9710 0.59    770   86 0.1095 0.1581      4.6812      4.8862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7050  1392   155  0.94   8.67   0.98     0.96       6908.16|
|  2:  4.7050 -  3.7536  1343   146  0.95   7.97   1.02     1.00       9088.66|
|  3:  3.7536 -  3.2848  1313   147  0.93  11.62   1.02     1.02      10865.81|
|  4:  3.2848 -  2.9870  1315   153  0.92  13.63   1.00     0.98      10409.56|
|  5:  2.9870 -  2.7743  1297   139  0.90  16.04   0.99     0.96       8249.00|
|  6:  2.7743 -  2.6117  1287   143  0.90  15.74   0.98     0.96       7006.11|
|  7:  2.6117 -  2.4815  1300   139  0.90  15.78   0.99     0.97       6530.41|
|  8:  2.4815 -  2.3739  1261   151  0.91  15.52   0.98     0.96       5215.78|
|  9:  2.3739 -  2.2828  1280   145  0.91  15.24   1.01     0.99       5079.50|
| 10:  2.2828 -  2.2043  1280   138  0.91  15.07   1.01     0.97       4178.92|
| 11:  2.2043 -  2.1356  1286   138  0.90  16.17   1.00     0.96       4375.84|
| 12:  2.1356 -  2.0747  1241   139  0.92  14.83   1.02     1.01       3989.60|
| 13:  2.0747 -  2.0202  1265   140  0.90  16.63   1.01     1.00       3416.35|
| 14:  2.0202 -  1.9710   770    86  0.92  14.29   0.99     0.96       2512.07|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2512.07 max =        10865.81 mean =      6423.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.02|
|phase err.(test): min =        0.00 max =           88.34 mean =        13.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.35    91.99   14.55    None  None   None       |
|    all(noH): 2823   0      2.35    91.99   14.55    None  None   None       |
|    Sol.    : 438    0      4.48    78.97   35.90    None  None   None       |
|    Mac.    : 2385   0      2.35    91.99   10.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.350 -  11.313: 1735   |   5:    47.168 -  56.131:   73        |
|      1:    11.313 -  20.277:  577   |   6:    56.131 -  65.095:   33        |
|      2:    20.277 -  29.240:  140   |   7:    65.095 -  74.058:    8        |
|      3:    29.240 -  38.204:  146   |   8:    74.058 -  83.022:    6        |
|      4:    38.204 -  47.168:  103   |   9:    83.022 -  91.985:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.401 - 5.575
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 321
   mapped sites are within: 0.728 - 5.575

peak=   11.171 closest distance to " CB  VAL A 230 " =    1.485
peak=    8.468 closest distance to " CG2 VAL A 296 " =    1.257
peak=    6.304 closest distance to " CG  ARG A 138 " =    1.083
peak=    6.151 closest distance to " CG  LEU A   5 " =    1.267
peak=    5.893 closest distance to " NH2 ARG A  56 " =    2.160
peak=    5.886 closest distance to " CD2 LEU A   5 " =    1.283
peak=    5.630 closest distance to " NE2 GLN A  11 " =    1.170
peak=    5.604 closest distance to " CD1AILE A 234 " =    1.083
peak=    5.233 closest distance to " O   HOH Z 144 " =    1.826
peak=    5.183 closest distance to " CG  LEU A 228 " =    1.193
peak=    5.096 closest distance to " NH1 ARG A 138 " =    1.010
peak=    5.076 closest distance to " CG  PRO A 198 " =    1.300
peak=    5.030 closest distance to " O   HOH Z 232 " =    2.268
peak=    4.910 closest distance to " O   HOH Z 126 " =    1.920
peak=    4.866 closest distance to " CB  GLN A 223 " =    1.342
peak=    4.750 closest distance to " CB  GLN A 183 " =    1.172
peak=    4.722 closest distance to " CB  ARG A 275 " =    0.860
peak=    4.695 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.688 closest distance to " C   PRO A 198 " =    1.564
peak=    4.619 closest distance to " CD2 LEU A 228 " =    1.240
peak=    4.550 closest distance to " CB  SER A  63 " =    1.293
peak=    4.497 closest distance to " CB  SER A   3 " =    1.421
peak=    4.494 closest distance to " O   HOH Z 316 " =    2.936
peak=    4.492 closest distance to " O   HOH Z 124 " =    1.406
peak=    4.489 closest distance to " O   HOH Z 236 " =    1.932
peak=    4.468 closest distance to " CB  ASN A 148 " =    1.380
peak=    4.447 closest distance to " O   HOH Z 193 " =    1.917
peak=    4.446 closest distance to " CB  GLU A 152 " =    1.265
peak=    4.443 closest distance to " O   HOH Z 278 " =    0.915
peak=    4.441 closest distance to " O   HOH Z 263 " =    1.636
peak=    4.430 closest distance to " O   HOH Z 427 " =    2.792
peak=    4.370 closest distance to " CB  VAL A 296 " =    1.157
peak=    4.342 closest distance to " O   HOH Z 298 " =    1.788
peak=    4.332 closest distance to " CB  GLU A 128 " =    1.017
peak=    4.328 closest distance to " CD  ARG A 138 " =    1.139
peak=    4.296 closest distance to " CB  VAL A 230 " =    1.193
peak=    4.275 closest distance to " O   HOH Z 425 " =    1.445
peak=    4.260 closest distance to " O   HOH Z 272 " =    1.879
peak=    4.237 closest distance to " OD1 ASN A  69 " =    2.663
peak=    4.232 closest distance to " CG  PRO A 243 " =    1.141
peak=    4.229 closest distance to " CB  TYR A 169 " =    0.728
peak=    4.206 closest distance to " OD2 ASP A 286 " =    2.782
peak=    4.174 closest distance to " ND2 ASN A 187 " =    1.603
peak=    4.164 closest distance to " CB  SER A 216 " =    0.753
peak=    4.134 closest distance to " CB  VAL A 265 " =    1.286
peak=    4.133 closest distance to " N   PHE A 130 " =    1.294
peak=    4.125 closest distance to " CD  ARG A  66 " =    2.576
peak=    4.100 closest distance to " CA  ALA A  21 " =    1.166
peak=    4.099 closest distance to " O   HOH Z 369 " =    1.996
peak=    4.095 closest distance to " O   HOH Z 193 " =    1.794
peak=    4.092 closest distance to " O   HOH Z 303 " =    2.120
peak=    4.083 closest distance to " O   HOH Z 368 " =    1.985
peak=    4.056 closest distance to " CG  PRO A 280 " =    0.834
peak=    4.012 closest distance to " O   HOH Z 234 " =    3.598
peak=    4.007 closest distance to " O   HOH Z   9 " =    2.004
peak=    3.999 closest distance to " O   SER A  87 " =    2.381
peak=    3.993 closest distance to " O   HOH Z   7 " =    1.205
peak=    3.990 closest distance to " O   HOH Z 411 " =    3.726
peak=    3.979 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.950 closest distance to " O   HOH Z 108 " =    1.275
peak=    3.938 closest distance to " CG2 VAL A 257 " =    0.975
peak=    3.934 closest distance to " CA  SER A  87 " =    0.922
peak=    3.933 closest distance to " CB  MET A  40 " =    0.822
peak=    3.913 closest distance to " O   HOH Z   2 " =    1.662
peak=    3.908 closest distance to " CB  TRP A 266 " =    0.976
peak=    3.907 closest distance to " O   HOH Z 203 " =    1.773
peak=    3.891 closest distance to " CA  THR A 264 " =    0.809
peak=    3.887 closest distance to " O   HOH Z 128 " =    1.939
peak=    3.885 closest distance to " O   HOH Z 346 " =    1.590
peak=    3.879 closest distance to " CG  LEU A 167 " =    1.165
peak=    3.872 closest distance to " O   HOH Z 344 " =    2.823
peak=    3.867 closest distance to " CG  GLN A  88 " =    1.072
peak=    3.860 closest distance to " CE3 TRP A 274 " =    2.538
peak=    3.849 closest distance to " O   HOH Z 130 " =    2.169
peak=    3.837 closest distance to " O   HOH Z  55 " =    2.238
peak=    3.831 closest distance to " O   HOH Z  88 " =    3.255
peak=    3.831 closest distance to " NH1AARG A 145 " =    1.041
peak=    3.822 closest distance to " O   HOH Z 158 " =    2.918
peak=    3.808 closest distance to " O   HOH Z  78 " =    1.837
peak=    3.791 closest distance to " O   HOH Z 193 " =    1.800
peak=    3.777 closest distance to " O   HOH Z 132 " =    2.536
peak=    3.772 closest distance to " CB  LEU A 143 " =    1.128
peak=    3.771 closest distance to " O   HOH Z  68 " =    2.061
peak=    3.753 closest distance to " CA  ALA A  51 " =    1.041
peak=    3.745 closest distance to " O   HOH Z 389 " =    1.917
peak=    3.741 closest distance to " O   HOH Z   3 " =    1.972
peak=    3.741 closest distance to " O   HOH Z  61 " =    1.603
peak=    3.739 closest distance to " C   ALA A 299 " =    0.982
peak=    3.734 closest distance to " CB  ASN A 148 " =    1.936
peak=    3.732 closest distance to " CA  VAL A  41 " =    0.827
peak=    3.727 closest distance to " CB  ARG A  79 " =    1.399
peak=    3.726 closest distance to " CB  PRO A 198 " =    0.916
peak=    3.722 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.716 closest distance to " CA  ASN A 215 " =    1.087
peak=    3.715 closest distance to " O   HOH Z 273 " =    2.669
peak=    3.712 closest distance to " O   HOH Z  58 " =    1.614
peak=    3.696 closest distance to " O   HOH Z 117 " =    2.020
peak=    3.694 closest distance to " O   HOH Z  30 " =    1.449
peak=    3.687 closest distance to " CB  ASN A 187 " =    1.166
peak=    3.681 closest distance to " O   HOH Z 222 " =    2.365
peak=    3.679 closest distance to " O   HOH Z 371 " =    2.796
peak=    3.676 closest distance to " CB  TRP A 179 " =    1.369
peak=    3.674 closest distance to " CD  ARG A 159 " =    0.729
peak=    3.664 closest distance to " O   HOH Z 248 " =    1.821
peak=    3.658 closest distance to " O   HOH Z 227 " =    2.122
peak=    3.654 closest distance to " O   HOH Z 133 " =    1.694
peak=    3.653 closest distance to " CB  ARG A 139 " =    1.015
peak=    3.645 closest distance to " CA  LEU A 282 " =    1.110
peak=    3.645 closest distance to " O   HOH Z 175 " =    2.163
peak=    3.641 closest distance to " CG1BVAL A  72 " =    1.601
peak=    3.639 closest distance to " CG BARG A 102 " =    1.839
peak=    3.634 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.633 closest distance to " CE  LYS A  76 " =    0.953
peak=    3.631 closest distance to " CB  LEU A 228 " =    1.278
peak=    3.625 closest distance to " CB  ILE A 234 " =    0.893
peak=    3.624 closest distance to " O   HOH Z 189 " =    2.713
peak=    3.620 closest distance to " CA  TYR A  30 " =    0.955
peak=    3.619 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.618 closest distance to " O   HOH Z 260 " =    1.339
peak=    3.612 closest distance to " O   HOH Z 197 " =    3.290
peak=    3.601 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.593 closest distance to " O   HOH Z  43 " =    2.151
peak=    3.590 closest distance to " O   HOH Z   1 " =    1.773
peak=    3.589 closest distance to " CB  GLN A  88 " =    1.256
peak=    3.586 closest distance to " OG BSER A 164 " =    2.275
peak=    3.584 closest distance to " CD BLYS A 290 " =    1.087
peak=    3.584 closest distance to " CG2 THR A 221 " =    1.109
peak=    3.569 closest distance to " O   HOH Z 403 " =    1.656
peak=    3.565 closest distance to " O   HOH Z 108 " =    2.048
peak=    3.557 closest distance to " N   ARG A 156 " =    1.313
peak=    3.557 closest distance to " CA  ALA A 158 " =    1.116
peak=    3.557 closest distance to " CB  ASN A 142 " =    0.943
peak=    3.550 closest distance to " O   HOH Z 250 " =    1.345
peak=    3.547 closest distance to " O   HOH Z 350 " =    1.538
peak=    3.544 closest distance to " CB  THR A 157 " =    1.056
peak=    3.533 closest distance to " CA  THR A 221 " =    0.845
peak=    3.531 closest distance to " CB  PRO A  54 " =    0.770
peak=    3.528 closest distance to " CB  GLU A 277 " =    3.509
peak=    3.519 closest distance to " CA  LYS A 290 " =    1.230
peak=    3.518 closest distance to " NE AARG A 275 " =    1.367
peak=    3.511 closest distance to " O   HOH Z  44 " =    1.776
peak=    3.510 closest distance to " O   TRP A 274 " =    1.890
peak=    3.509 closest distance to " CD1 ILE A  33 " =    1.654
peak=    3.508 closest distance to " CG1 ILE A  33 " =    1.369
peak=    3.507 closest distance to " CD2 LEU A 167 " =    0.752
peak=    3.505 closest distance to " O   HOH Z 247 " =    1.314
peak=    3.503 closest distance to " NH1 ARG A  14 " =    0.943
peak=    3.497 closest distance to " O   HOH Z 207 " =    1.669
peak=    3.496 closest distance to " O   HOH Z  40 " =    2.070
peak=    3.494 closest distance to " O   HOH Z  48 " =    1.467
peak=    3.492 closest distance to " OD1BASN A 224 " =    2.247
peak=    3.487 closest distance to " CE  MET A  93 " =    1.496
peak=    3.479 closest distance to " O   HOH Z  10 " =    1.775
peak=    3.473 closest distance to " O   HOH Z 437 " =    2.207
peak=    3.470 closest distance to " CA  ILE A 234 " =    0.915
peak=    3.468 closest distance to " O   HOH Z  50 " =    1.515
peak=    3.455 closest distance to " ND1 HIS A  86 " =    1.720
peak=    3.455 closest distance to " O   HOH Z  63 " =    1.278
peak=    3.454 closest distance to " CA  ALA A 154 " =    1.072
peak=    3.445 closest distance to " CE1 TYR A 186 " =    1.353
peak=    3.439 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.430 closest distance to " CD  ARG A 269 " =    1.044
peak=    3.429 closest distance to " O   HOH Z 261 " =    2.219
peak=    3.429 closest distance to " O   HOH Z 344 " =    1.116
peak=    3.429 closest distance to " O   HOH Z 322 " =    1.935
peak=    3.424 closest distance to " CB  ALA A 291 " =    1.348
peak=    3.419 closest distance to " O   HOH Z 209 " =    2.335
peak=    3.416 closest distance to " NH2BARG A 145 " =    1.982
peak=    3.414 closest distance to " O   HOH Z 359 " =    3.870
peak=    3.410 closest distance to " O   HOH Z 244 " =    1.583
peak=    3.410 closest distance to " O   HOH Z 334 " =    1.556
peak=    3.409 closest distance to " CZ  PHE A 218 " =    1.066
peak=    3.408 closest distance to " CA  VAL A 126 " =    0.950
peak=    3.408 closest distance to " O   HOH Z 126 " =    1.566
peak=    3.407 closest distance to " O   HOH Z 134 " =    1.457
peak=    3.402 closest distance to " CB BVAL A  41 " =    1.280
peak=    3.401 closest distance to " O   THR A  31 " =    1.486
peak=    3.401 closest distance to " O   HOH Z 271 " =    1.904
peak=    3.399 closest distance to " O   HOH Z 202 " =    1.164
peak=    3.398 closest distance to " O   HOH Z 216 " =    2.463
peak=    3.397 closest distance to " NH2 ARG A 156 " =    1.073
peak=    3.396 closest distance to " CD2 LEU A 255 " =    1.419
peak=    3.387 closest distance to " CB  ALA A 248 " =    1.360
peak=    3.385 closest distance to " O   HOH Z  59 " =    1.863
peak=    3.383 closest distance to " O   HOH Z 329 " =    3.768
peak=    3.382 closest distance to " O   HOH Z 251 " =    1.674
peak=    3.381 closest distance to " O   HOH Z 303 " =    1.783
peak=    3.379 closest distance to " O   MET A 105 " =    1.727
peak=    3.370 closest distance to " O   HOH Z   1 " =    1.781
peak=    3.369 closest distance to " CZ  PHE A 192 " =    0.983
peak=    3.365 closest distance to " NZ  LYS A  48 " =    2.149
peak=    3.365 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.365 closest distance to " O   HOH Z 209 " =    2.376
peak=    3.363 closest distance to " O   HOH Z 213 " =    2.448
peak=    3.359 closest distance to " N   ASN A  39 " =    1.030
peak=    3.353 closest distance to " CB  GLU A 236 " =    1.157
peak=    3.349 closest distance to " ND1 HIS A  81 " =    1.643
peak=    3.348 closest distance to " O   HOH Z 145 " =    1.693
peak=    3.347 closest distance to " CG1 ILE A 151 " =    1.149
peak=    3.344 closest distance to " N   VAL A 126 " =    1.238
peak=    3.340 closest distance to " OG  SER A  22 " =    2.864
peak=    3.334 closest distance to " CB  VAL A 250 " =    1.074
peak=    3.333 closest distance to " O   HOH Z 180 " =    2.057
peak=    3.329 closest distance to " O   HOH Z 280 " =    1.717
peak=    3.322 closest distance to " O   HOH Z 368 " =    3.600
peak=    3.321 closest distance to " O   HOH Z 148 " =    3.345
peak=    3.312 closest distance to " CB  LYS A 117 " =    1.193
peak=    3.309 closest distance to " O   HOH Z 214 " =    1.942
peak=    3.309 closest distance to " CB  TYR A  30 " =    1.495
peak=    3.307 closest distance to " OG  SER A  62 " =    2.869
peak=    3.306 closest distance to " CG2 ILE A 106 " =    0.956
peak=    3.303 closest distance to " O   HOH Z  21 " =    1.757
peak=    3.303 closest distance to " OG  SER A 206 " =    1.164
peak=    3.299 closest distance to " O   HOH Z 327 " =    1.928
peak=    3.299 closest distance to " CE2 TYR A 186 " =    0.987
peak=    3.297 closest distance to " O   HOH Z 435 " =    2.118
peak=    3.297 closest distance to " O   HOH Z 313 " =    1.751
peak=    3.296 closest distance to " CB  HIS A 108 " =    0.843
peak=    3.295 closest distance to " O   HOH Z 236 " =    1.534
peak=    3.294 closest distance to " O   ALA A 158 " =    1.367
peak=    3.292 closest distance to " O   HOH Z 371 " =    1.805
peak=    3.291 closest distance to " NE2 GLN A  58 " =    5.575
peak=    3.291 closest distance to " CZ3 TRP A 123 " =    1.334
peak=    3.288 closest distance to " O   HOH Z 135 " =    1.924
peak=    3.281 closest distance to " O   HOH Z 109 " =    2.603
peak=    3.279 closest distance to " CG  MET A 185 " =    1.182
peak=    3.276 closest distance to " O   HOH Z  71 " =    1.270
peak=    3.276 closest distance to " O   HOH Z 276 " =    1.274
peak=    3.273 closest distance to " CD2 TYR A 186 " =    1.066
peak=    3.271 closest distance to " CB  ALA A 161 " =    0.829
peak=    3.271 closest distance to " NH2AARG A 190 " =    1.571
peak=    3.268 closest distance to " O   HOH Z 409 " =    2.902
peak=    3.264 closest distance to " O   HOH Z 426 " =    1.563
peak=    3.263 closest distance to " CB  LEU A 255 " =    0.893
peak=    3.262 closest distance to " O   HOH Z 172 " =    3.419
peak=    3.261 closest distance to " CG1 VAL A 153 " =    0.923
peak=    3.260 closest distance to " O   HOH Z 423 " =    2.655
peak=    3.259 closest distance to " O   HOH Z 419 " =    1.816
peak=    3.259 closest distance to " O   HOH Z 425 " =    2.007
peak=    3.257 closest distance to " CB  ALA A  34 " =    0.948
peak=    3.252 closest distance to " CG  ARG A 159 " =    0.916
peak=    3.250 closest distance to " CB  SER A  62 " =    1.242
peak=    3.249 closest distance to " CD1 ILE A 106 " =    0.971
peak=    3.245 closest distance to " NZ BLYS A 290 " =    1.111
peak=    3.242 closest distance to " O  BHOH Z 338 " =    2.579
peak=    3.238 closest distance to " O   HOH Z 345 " =    3.434
peak=    3.236 closest distance to " CD1 LEU A  96 " =    0.773
peak=    3.234 closest distance to " CB  SER A 212 " =    1.296
peak=    3.233 closest distance to " O   HOH Z 423 " =    1.610
peak=    3.233 closest distance to " CA  GLY A 267 " =    1.010
peak=    3.232 closest distance to " O   GLN A  58 " =    1.577
peak=    3.230 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.228 closest distance to " CB  ALA A 114 " =    1.245
peak=    3.228 closest distance to " CB  SER A 210 " =    0.790
peak=    3.223 closest distance to " O   HOH Z  54 " =    1.543
peak=    3.222 closest distance to " O   HOH Z 116 " =    1.634
peak=    3.218 closest distance to " OG BSER A 134 " =    2.901
peak=    3.215 closest distance to " CB  ALA A 248 " =    1.009
peak=    3.215 closest distance to " O   HOH Z 145 " =    3.461
peak=    3.203 closest distance to " O   HOH Z 285 " =    1.949
peak=    3.202 closest distance to " CG  MET A 185 " =    1.008
peak=    3.201 closest distance to " O   HOH Z 255 " =    1.729
peak=    3.200 closest distance to " O   HOH Z 355 " =    1.679
peak=    3.198 closest distance to " O   HOH Z 388 " =    2.075
peak=    3.194 closest distance to " O   HOH Z   9 " =    1.990
peak=    3.193 closest distance to " O   HOH Z 407 " =    2.245
peak=    3.192 closest distance to " O   HOH Z 380 " =    1.896
peak=    3.184 closest distance to " O   HOH Z 422 " =    2.626
peak=    3.182 closest distance to " O   HOH Z  37 " =    1.203
peak=    3.172 closest distance to " O   HOH Z 339 " =    2.217
peak=    3.170 closest distance to " O   PRO A 198 " =    1.320
peak=    3.168 closest distance to " CB  ASN A 110 " =    1.148
peak=    3.165 closest distance to " CA  ASP A 140 " =    1.297
peak=    3.165 closest distance to " O   HOH Z 410 " =    1.609
peak=    3.164 closest distance to " OE2 GLU A   2 " =    1.746
peak=    3.162 closest distance to " O   HOH Z 196 " =    3.206
peak=    3.162 closest distance to " N   GLN A 278 " =    0.942
peak=    3.159 closest distance to " CA  TYR A 186 " =    1.525
peak=    3.154 closest distance to " CG BARG A 275 " =    1.471
peak=    3.152 closest distance to " CB  SER A  28 " =    0.877
peak=    3.146 closest distance to " CG1BVAL A 121 " =    1.049
peak=    3.144 closest distance to " CB  TRP A 150 " =    1.559
peak=    3.143 closest distance to " N   ASN A 127 " =    1.281
peak=    3.142 closest distance to " CD  LYS A 166 " =    1.281
peak=    3.141 closest distance to " CB  SER A  26 " =    1.630
peak=    3.138 closest distance to " O   HOH Z 171 " =    2.204
peak=    3.135 closest distance to " NH1 ARG A  56 " =    0.940
peak=    3.134 closest distance to " CB  LEU A 237 " =    0.864
peak=    3.132 closest distance to " O   HOH Z 128 " =    2.026
peak=    3.132 closest distance to " N   SER A 135 " =    1.264
peak=    3.131 closest distance to " CA  LYS A  48 " =    1.284
peak=    3.123 closest distance to " O   HOH Z 353 " =    2.551
peak=    3.122 closest distance to " O   HOH Z  49 " =    2.370
peak=    3.118 closest distance to " CB  ALA A   1 " =    4.619
peak=    3.117 closest distance to " CA  GLN A 194 " =    1.212
peak=    3.114 closest distance to " O   HOH Z 380 " =    1.593
peak=    3.112 closest distance to " O   HOH Z  88 " =    2.632
peak=    3.111 closest distance to " C   VAL A 265 " =    1.422
peak=    3.108 closest distance to " CB  PRO A 243 " =    1.349
peak=    3.097 closest distance to " CA  ARG A  36 " =    1.111
peak=    3.094 closest distance to " O   HOH Z 291 " =    1.846
peak=    3.093 closest distance to " N   TYR A  15 " =    0.800
peak=    3.090 closest distance to " CB  ILE A 120 " =    1.296
peak=    3.089 closest distance to " CB  ARG A 190 " =    1.796
peak=    3.086 closest distance to " O   HOH Z 433 " =    1.822
peak=    3.074 closest distance to " CD1 LEU A 261 " =    1.221
peak=    3.072 closest distance to " CG2 ILE A 120 " =    1.319
peak=    3.056 closest distance to " CG2 ILE A  20 " =    1.571
peak=    3.052 closest distance to " O   HOH Z  88 " =    2.654
peak=    3.047 closest distance to " CG  MET A 188 " =    0.996
peak=    3.045 closest distance to " O   HOH Z 213 " =    1.895
peak=    3.040 closest distance to " CZ AARG A 145 " =    1.226
peak=    3.037 closest distance to " OH  TYR A 214 " =    1.172
peak=    3.036 closest distance to " CG1 VAL A 174 " =    1.035
peak=    3.025 closest distance to " NH2AARG A 190 " =    1.072
peak=    3.022 closest distance to " CB  GLN A 278 " =    0.801

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.612 - 5.421
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 209
   mapped sites are within: 0.701 - 5.421

peak=   -5.851 closest distance to " CG2 VAL A 230 " =    0.748
peak=   -4.690 closest distance to " CG  ARG A 138 " =    0.958
peak=   -4.687 closest distance to " O   HOH Z 290 " =    1.053
peak=   -4.305 closest distance to " O   HOH Z 231 " =    1.477
peak=   -4.262 closest distance to " CD  ARG A 156 " =    1.997
peak=   -4.245 closest distance to " CD  ARG A  14 " =    3.163
peak=   -4.077 closest distance to " O   HOH Z 388 " =    2.170
peak=   -4.071 closest distance to " CG2 VAL A 296 " =    1.001
peak=   -4.068 closest distance to " CG  ASP A 231 " =    0.748
peak=   -4.035 closest distance to " O   PRO A 198 " =    1.186
peak=   -4.025 closest distance to " N   GLN A  58 " =    1.858
peak=   -4.005 closest distance to " O   HOH Z 435 " =    2.869
peak=   -4.002 closest distance to " O   HOH Z 266 " =    4.685
peak=   -3.985 closest distance to " CD  ARG A 138 " =    1.187
peak=   -3.969 closest distance to " CB  PRO A 163 " =    2.608
peak=   -3.944 closest distance to " CG  GLN A 223 " =    1.935
peak=   -3.934 closest distance to " O   HOH Z  52 " =    1.385
peak=   -3.926 closest distance to " O   HOH Z 351 " =    1.341
peak=   -3.912 closest distance to " C   ASP A 231 " =    2.555
peak=   -3.848 closest distance to " CB  PRO A 243 " =    2.627
peak=   -3.845 closest distance to " CG  PHE A 283 " =    2.675
peak=   -3.803 closest distance to " O   HOH Z 166 " =    1.457
peak=   -3.779 closest distance to " OG  SER A  87 " =    1.347
peak=   -3.759 closest distance to " NH2 ARG A  79 " =    1.866
peak=   -3.758 closest distance to " O   ARG A 145 " =    1.613
peak=   -3.734 closest distance to " CE2 TYR A  30 " =    2.912
peak=   -3.732 closest distance to " C   ALA A 158 " =    1.268
peak=   -3.716 closest distance to " CZ3 TRP A 179 " =    1.217
peak=   -3.699 closest distance to " C   ASN A 285 " =    2.382
peak=   -3.676 closest distance to " C   HIS A 108 " =    1.199
peak=   -3.672 closest distance to " CD1 LEU A 101 " =    2.730
peak=   -3.671 closest distance to " CG1 VAL A 296 " =    1.305
peak=   -3.671 closest distance to " CE2 PHE A 218 " =    2.594
peak=   -3.664 closest distance to " O   HOH Z 211 " =    1.493
peak=   -3.659 closest distance to " CA  GLY A  98 " =    1.929
peak=   -3.646 closest distance to " CG2 THR A   4 " =    1.869
peak=   -3.638 closest distance to " CD  LYS A 289 " =    2.668
peak=   -3.636 closest distance to " O   HOH Z 377 " =    1.974
peak=   -3.633 closest distance to " O   HOH Z  92 " =    1.676
peak=   -3.630 closest distance to " CG  TRP A 266 " =    1.810
peak=   -3.624 closest distance to " O   PRO A 163 " =    1.888
peak=   -3.615 closest distance to " CD1 LEU A 101 " =    2.427
peak=   -3.613 closest distance to " O   HOH Z  43 " =    1.818
peak=   -3.612 closest distance to " O   HOH Z 134 " =    2.669
peak=   -3.611 closest distance to " CE BMET A  47 " =    1.609
peak=   -3.605 closest distance to " N   ALA A  43 " =    2.317
peak=   -3.585 closest distance to " O   GLY A 211 " =    1.304
peak=   -3.584 closest distance to " O   VAL A  67 " =    2.527
peak=   -3.578 closest distance to " ND2 ASN A  45 " =    1.071
peak=   -3.578 closest distance to " CA  GLY A 241 " =    2.271
peak=   -3.578 closest distance to " CG  LEU A 101 " =    2.570
peak=   -3.573 closest distance to " CD1 LEU A 228 " =    2.287
peak=   -3.551 closest distance to " O   ALA A 161 " =    1.491
peak=   -3.550 closest distance to " O   HOH Z 389 " =    1.832
peak=   -3.550 closest distance to " O   HOH Z 185 " =    2.212
peak=   -3.543 closest distance to " CB  ALA A 248 " =    1.958
peak=   -3.542 closest distance to " CG  MET A 105 " =    0.939
peak=   -3.535 closest distance to " O   TYR A 247 " =    2.794
peak=   -3.529 closest distance to " CB  ALA A 244 " =    2.082
peak=   -3.528 closest distance to " CB  PHE A 192 " =    1.771
peak=   -3.519 closest distance to " O   HOH Z 309 " =    2.335
peak=   -3.514 closest distance to " OG BSER A 134 " =    1.174
peak=   -3.513 closest distance to " O   HOH Z 417 " =    2.891
peak=   -3.512 closest distance to " CG1 VAL A 112 " =    2.681
peak=   -3.505 closest distance to " OG BSER A 134 " =    1.701
peak=   -3.498 closest distance to " N   THR A 157 " =    1.434
peak=   -3.495 closest distance to " N   HIS A 115 " =    2.095
peak=   -3.488 closest distance to " O   HOH Z 345 " =    2.058
peak=   -3.485 closest distance to " C   LEU A 222 " =    0.802
peak=   -3.480 closest distance to " C   MET A 188 " =    1.619
peak=   -3.476 closest distance to " CE  MET A 105 " =    2.293
peak=   -3.471 closest distance to " CB  TYR A  15 " =    2.104
peak=   -3.471 closest distance to " OD1 ASN A 187 " =    1.671
peak=   -3.470 closest distance to " O   HOH Z 359 " =    3.344
peak=   -3.462 closest distance to " CB  ALA A 291 " =    2.241
peak=   -3.460 closest distance to " O   HOH Z 407 " =    3.091
peak=   -3.447 closest distance to " CG  PRO A 163 " =    2.551
peak=   -3.429 closest distance to " CB  ASN A  39 " =    2.112
peak=   -3.427 closest distance to " O   HOH Z 111 " =    4.197
peak=   -3.425 closest distance to " O   HOH Z 168 " =    1.994
peak=   -3.425 closest distance to " CB  VAL A 296 " =    1.174
peak=   -3.417 closest distance to " CZ  PHE A  59 " =    1.432
peak=   -3.407 closest distance to " O   HOH Z 241 " =    1.360
peak=   -3.400 closest distance to " O   HOH Z 423 " =    1.136
peak=   -3.400 closest distance to " CG  LEU A 228 " =    0.868
peak=   -3.399 closest distance to " C   ALA A   8 " =    1.528
peak=   -3.394 closest distance to " O   HOH Z 295 " =    1.429
peak=   -3.394 closest distance to " NH2AARG A 275 " =    5.249
peak=   -3.389 closest distance to " O   HOH Z  98 " =    2.301
peak=   -3.388 closest distance to " O   HOH Z 143 " =    2.506
peak=   -3.388 closest distance to " OXT GLY A 302 " =    2.919
peak=   -3.383 closest distance to " O   HOH Z 281 " =    2.832
peak=   -3.383 closest distance to " O   HOH Z 423 " =    2.211
peak=   -3.376 closest distance to " CG2 THR A 178 " =    2.173
peak=   -3.362 closest distance to " O   ILE A 109 " =    2.636
peak=   -3.361 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -3.356 closest distance to " O   GLN A 240 " =    2.108
peak=   -3.352 closest distance to " CA  ASP A  27 " =    2.357
peak=   -3.348 closest distance to " CA  ARG A 139 " =    1.017
peak=   -3.345 closest distance to " N   SER A 276 " =    1.276
peak=   -3.343 closest distance to " O   HOH Z 350 " =    2.283
peak=   -3.343 closest distance to " O   HOH Z  71 " =    0.944
peak=   -3.343 closest distance to " O   HOH Z 437 " =    1.877
peak=   -3.338 closest distance to " O   HOH Z  38 " =    2.006
peak=   -3.337 closest distance to " O   HOH Z 298 " =    1.237
peak=   -3.329 closest distance to " N   GLY A  23 " =    2.132
peak=   -3.327 closest distance to " O   HOH Z 359 " =    1.560
peak=   -3.325 closest distance to " N   SER A 212 " =    1.857
peak=   -3.322 closest distance to " O   HOH Z  13 " =    1.229
peak=   -3.322 closest distance to " OE1 GLN A  88 " =    1.114
peak=   -3.317 closest distance to " CG2 VAL A 112 " =    2.570
peak=   -3.308 closest distance to " N   THR A 235 " =    1.190
peak=   -3.304 closest distance to " O   HOH Z 103 " =    1.946
peak=   -3.303 closest distance to " CD1 ILE A 239 " =    2.126
peak=   -3.302 closest distance to " CD  ARG A 139 " =    1.614
peak=   -3.301 closest distance to " O   HOH Z 385 " =    2.107
peak=   -3.298 closest distance to " O   VAL A  67 " =    2.680
peak=   -3.291 closest distance to " CZ  TYR A 172 " =    1.724
peak=   -3.290 closest distance to " ND2 ASN A  60 " =    1.617
peak=   -3.285 closest distance to " O   HOH Z 371 " =    1.256
peak=   -3.283 closest distance to " O   HOH Z 322 " =    0.965
peak=   -3.282 closest distance to " CD1 TYR A 169 " =    2.565
peak=   -3.281 closest distance to " O   HOH Z 377 " =    1.055
peak=   -3.281 closest distance to " NZ  LYS A 119 " =    3.289
peak=   -3.279 closest distance to " CG  LYS A 193 " =    2.330
peak=   -3.275 closest distance to " O   HOH Z 140 " =    1.573
peak=   -3.274 closest distance to " O   GLY A 203 " =    2.462
peak=   -3.269 closest distance to " O   HOH Z  65 " =    1.120
peak=   -3.269 closest distance to " OG1 THR A 178 " =    1.216
peak=   -3.265 closest distance to " CG1 VAL A 250 " =    2.779
peak=   -3.265 closest distance to " O   HOH Z 222 " =    3.295
peak=   -3.264 closest distance to " O   VAL A 197 " =    1.309
peak=   -3.259 closest distance to " O   HOH Z 210 " =    0.755
peak=   -3.258 closest distance to " CD  GLN A  88 " =    0.748
peak=   -3.251 closest distance to " O   HOH Z 191 " =    5.359
peak=   -3.251 closest distance to " O   SER A  22 " =    2.201
peak=   -3.250 closest distance to " CB  ASP A 132 " =    2.289
peak=   -3.250 closest distance to " ND2 ASN A  60 " =    1.705
peak=   -3.246 closest distance to " O   GLY A 196 " =    1.124
peak=   -3.243 closest distance to " O   VAL A 153 " =    2.174
peak=   -3.237 closest distance to " O   SER A 271 " =    2.244
peak=   -3.236 closest distance to " O   SER A 135 " =    1.462
peak=   -3.230 closest distance to " O   PRO A 198 " =    1.208
peak=   -3.226 closest distance to " CG1 VAL A 197 " =    2.337
peak=   -3.225 closest distance to " NH1AARG A 275 " =    1.857
peak=   -3.221 closest distance to " CG  ASP A  50 " =    2.215
peak=   -3.219 closest distance to " O   ALA A  51 " =    1.495
peak=   -3.216 closest distance to " CB  ILE A  33 " =    2.918
peak=   -3.216 closest distance to " O   HOH Z 275 " =    1.513
peak=   -3.206 closest distance to " CD1 TRP A 179 " =    0.885
peak=   -3.205 closest distance to " CG2 THR A  18 " =    2.710
peak=   -3.203 closest distance to " N   ALA A 226 " =    2.083
peak=   -3.200 closest distance to " CB  ALA A 248 " =    2.419
peak=   -3.199 closest distance to " O   HOH Z 281 " =    4.977
peak=   -3.197 closest distance to " O   HOH Z 327 " =    2.038
peak=   -3.195 closest distance to " CZ  ARG A 259 " =    0.769
peak=   -3.192 closest distance to " CA  GLY A 203 " =    2.215
peak=   -3.190 closest distance to " O   HOH Z 336 " =    5.421
peak=   -3.188 closest distance to " O   HOH Z  60 " =    2.029
peak=   -3.184 closest distance to " CD1 ILE A 199 " =    2.549
peak=   -3.179 closest distance to " CA  ASP A  27 " =    2.438
peak=   -3.175 closest distance to " O   HOH Z  11 " =    2.053
peak=   -3.172 closest distance to " CD2 LEU A   5 " =    0.984
peak=   -3.170 closest distance to " CD2 TYR A 293 " =    2.099
peak=   -3.170 closest distance to " CB  CYS A 254 " =    2.151
peak=   -3.167 closest distance to " CB  TRP A  85 " =    2.506
peak=   -3.159 closest distance to " N   ALA A 248 " =    1.610
peak=   -3.155 closest distance to " CE  LYS A  76 " =    2.800
peak=   -3.152 closest distance to " OG  SER A 206 " =    1.693
peak=   -3.151 closest distance to " C   LEU A 143 " =    1.330
peak=   -3.148 closest distance to " O   HOH Z 148 " =    1.879
peak=   -3.145 closest distance to " N   GLN A 122 " =    1.458
peak=   -3.138 closest distance to " O   HOH Z  90 " =    2.827
peak=   -3.137 closest distance to " CD  GLU A 277 " =    0.912
peak=   -3.136 closest distance to " CG  GLU A 152 " =    0.701
peak=   -3.136 closest distance to " CD  ARG A 259 " =    2.528
peak=   -3.136 closest distance to " O   HOH Z  97 " =    1.638
peak=   -3.134 closest distance to " OXT GLY A 302 " =    3.567
peak=   -3.134 closest distance to " CG  ARG A 269 " =    2.378
peak=   -3.131 closest distance to " O   HOH Z 166 " =    2.141
peak=   -3.125 closest distance to " CG1 VAL A 230 " =    1.839
peak=   -3.123 closest distance to " O   HOH Z 250 " =    1.437
peak=   -3.119 closest distance to " O   HOH Z 369 " =    2.038
peak=   -3.119 closest distance to " CB  TYR A 172 " =    2.238
peak=   -3.118 closest distance to " C   PHE A  59 " =    1.350
peak=   -3.113 closest distance to " O   ASP A 270 " =    1.801
peak=   -3.110 closest distance to " CZ  TYR A 169 " =    1.577
peak=   -3.106 closest distance to " O   HOH Z 174 " =    2.538
peak=   -3.101 closest distance to " NH2 ARG A  66 " =    2.277
peak=   -3.100 closest distance to " O   ILE A  49 " =    1.802
peak=   -3.097 closest distance to " O   TRP A  70 " =    1.490
peak=   -3.095 closest distance to " O   VAL A 189 " =    2.598
peak=   -3.091 closest distance to " O   HOH Z 410 " =    2.064
peak=   -3.090 closest distance to " O   HOH Z   9 " =    1.580
peak=   -3.086 closest distance to " CD2 LEU A 300 " =    2.813
peak=   -3.083 closest distance to " CB  ALA A 291 " =    2.114
peak=   -3.082 closest distance to " OD1 ASN A 301 " =    1.864
peak=   -3.079 closest distance to " OG ASER A 134 " =    1.440
peak=   -3.072 closest distance to " C   ASN A 187 " =    1.825
peak=   -3.063 closest distance to " CG2AVAL A  72 " =    4.356
peak=   -3.059 closest distance to " CD1 TYR A 247 " =    2.691
peak=   -3.056 closest distance to " O   HOH Z 389 " =    1.264
peak=   -3.052 closest distance to " CD  GLN A  58 " =    0.927
peak=   -3.029 closest distance to " O   HOH Z 313 " =    1.712
peak=   -3.006 closest distance to " N   PHE A  59 " =    1.972

================= 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    :  0.4628 0.4457   6.260095e+00   6.246552e+00
   1_bss:  0.4536 0.4356   6.253832e+00   6.237734e+00
   1_xyz:  0.3615 0.3865   6.111407e+00   6.148503e+00
   1_adp:  0.3147 0.3661   6.007677e+00   6.104720e+00
   1_occ:  0.3141 0.3669   6.006911e+00   6.105234e+00
   2_bss:  0.3093 0.3599   6.003578e+00   6.100813e+00
   2_xyz:  0.2208 0.2741   5.723467e+00   5.890666e+00
   2_adp:  0.2008 0.2556   5.647083e+00   5.829290e+00
   2_occ:  0.2005 0.2552   5.646132e+00   5.828975e+00
   3_bss:  0.1998 0.2529   5.645362e+00   5.826688e+00
   3_xyz:  0.1444 0.1902   5.353159e+00   5.574046e+00
   3_adp:  0.1313 0.1788   5.276189e+00   5.508536e+00
   3_occ:  0.1312 0.1787   5.275973e+00   5.508236e+00
   4_bss:  0.1314 0.1788   5.276218e+00   5.508160e+00
   4_xyz:  0.1197 0.1664   5.198677e+00   5.441212e+00
   4_adp:  0.1192 0.1621   5.185153e+00   5.416281e+00
   4_occ:  0.1191 0.1618   5.184334e+00   5.415185e+00
   5_bss:  0.1191 0.1616   5.184323e+00   5.415163e+00
   5_xyz:  0.1158 0.1589   5.166407e+00   5.400495e+00
   5_adp:  0.1163 0.1588   5.167650e+00   5.398366e+00
   5_occ:  0.1162 0.1585   5.167048e+00   5.397593e+00
   5_bss:  0.1162 0.1585   5.167000e+00   5.397567e+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:  0.342   1.418   8.104   9.095   8.857   0.000   0.000   0.000
   1_xyz:  0.342   1.418   8.104   9.095   8.857   0.000   0.000   0.000
   1_adp:  0.342   1.418   8.104   9.095   8.857   0.000   0.000   0.000
   1_occ:  0.342   1.418   8.104   9.095   8.857   0.000   0.000   0.000
   2_bss:  0.332  32.467   4.118   4.434   5.318   0.000   0.000   0.000
   2_xyz:  0.332  32.467   4.118   4.434   5.318   0.000   0.000   0.000
   2_adp:  0.332  32.467   4.118   4.434   5.318   0.000   0.000   0.000
   2_occ:  0.332  32.467   4.118   4.434   5.318   0.000   0.000   0.000
   3_bss:  0.333  42.902   2.799   2.647   3.659   0.000   0.000   0.000
   3_xyz:  0.333  42.902   2.799   2.647   3.659   0.000   0.000   0.000
   3_adp:  0.333  42.902   2.799   2.647   3.659   0.000   0.000   0.000
   3_occ:  0.333  42.902   2.799   2.647   3.659   0.000   0.000   0.000
   4_bss:  0.321  42.902   2.512   2.235   3.149   0.000   0.000   0.000
   4_xyz:  0.321  42.902   2.512   2.235   3.149   0.000   0.000   0.000
   4_adp:  0.321  42.902   2.512   2.235   3.149   0.000   0.000   0.000
   4_occ:  0.321  42.902   2.512   2.235   3.149   0.000   0.000   0.000
   5_bss:  0.325  42.902   2.316   2.077   2.956   0.000   0.000   0.000
   5_xyz:  0.325  42.902   2.316   2.077   2.956   0.000   0.000   0.000
   5_adp:  0.325  42.902   2.316   2.077   2.956   0.000   0.000   0.000
   5_occ:  0.325  42.902   2.316   2.077   2.956   0.000   0.000   0.000
   5_bss:  0.325  45.252  -0.150  -0.366   0.516  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.710 0.4873  0.5661    61588.744
   1_bss:  52.976 0.4818  0.7147    59092.300
   1_xyz:  42.808 0.6080  0.8871    42143.398
   1_adp:  38.386 0.6619  0.9966    36299.838
   1_occ:  38.499 0.6605  0.9938    36405.739
   2_bss:  38.103 0.6648  0.8688    35724.021
   2_xyz:  27.818 0.7809  0.9803    19393.376
   2_adp:  25.140 0.8104  1.0026    16813.616
   2_occ:  25.122 0.8105  1.0026    16773.841
   3_bss:  24.970 0.8117  0.9474    16572.720
   3_xyz:  18.015 0.8802  0.9921     9276.225
   3_adp:  16.492 0.8941  0.9964     8211.473
   3_occ:  16.484 0.8942  0.9963     8199.393
   4_bss:  16.475 0.8943  0.9814     8194.478
   4_xyz:  15.021 0.9065  0.9872     7014.771
   4_adp:  14.400 0.9120  0.9899     6696.634
   4_occ:  14.374 0.9121  0.9899     6675.900
   5_bss:  14.372 0.9122  0.9834     6675.178
   5_xyz:  14.083 0.9146  0.9831     6465.530
   5_adp:  13.982 0.9156  0.9830     6438.640
   5_occ:  13.968 0.9157  0.9829     6425.443
   5_bss:  13.967 0.9157  0.9794     6424.147
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3426e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3426e+01
   1_xyz:   1.624  0.013  0.104 18.288  0.006  4.110   1.3185e-01
   1_adp:   1.624  0.013  0.104 18.288  0.006  4.110   1.3185e-01
   1_occ:   1.624  0.013  0.104 18.288  0.006  4.110   1.3185e-01
   2_bss:   1.624  0.013  0.104 18.288  0.006  4.110   1.3185e-01
   2_xyz:   1.003  0.006  0.068 16.186  0.004  4.121   6.4419e-02
   2_adp:   1.003  0.006  0.068 16.186  0.004  4.121   6.4419e-02
   2_occ:   1.003  0.006  0.068 16.186  0.004  4.121   6.4419e-02
   3_bss:   1.003  0.006  0.068 16.186  0.004  4.121   6.4419e-02
   3_xyz:   1.022  0.007  0.078 15.826  0.003  4.117   6.3036e-02
   3_adp:   1.022  0.007  0.078 15.826  0.003  4.117   6.3036e-02
   3_occ:   1.022  0.007  0.078 15.826  0.003  4.117   6.3036e-02
   4_bss:   1.022  0.007  0.078 15.826  0.003  4.117   6.3036e-02
   4_xyz:   0.972  0.006  0.076 15.820  0.003  4.120   5.9365e-02
   4_adp:   0.972  0.006  0.076 15.820  0.003  4.120   5.9365e-02
   4_occ:   0.972  0.006  0.076 15.820  0.003  4.120   5.9365e-02
   5_bss:   0.972  0.006  0.076 15.820  0.003  4.120   5.9365e-02
   5_xyz:   0.929  0.005  0.073 15.636  0.003  4.121   5.5262e-02
   5_adp:   0.929  0.005  0.073 15.636  0.003  4.121   5.5262e-02
   5_occ:   0.929  0.005  0.073 15.636  0.003  4.121   5.5262e-02
   5_bss:   0.929  0.005  0.073 15.636  0.003  4.121   5.5262e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9265e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9265e+00
   1_xyz:  13.289  0.163  0.443 87.502  0.035  2.274   9.5197e-02
   1_adp:  13.289  0.163  0.443 87.502  0.035  2.274   9.5197e-02
   1_occ:  13.289  0.163  0.443 87.502  0.035  2.274   9.5197e-02
   2_bss:  13.289  0.163  0.443 87.502  0.035  2.274   9.5197e-02
   2_xyz:   6.757  0.056  0.305 89.299  0.044  2.347   4.7080e-02
   2_adp:   6.757  0.056  0.305 89.299  0.044  2.347   4.7080e-02
   2_occ:   6.757  0.056  0.305 89.299  0.044  2.347   4.7080e-02
   3_bss:   6.757  0.056  0.305 89.299  0.044  2.347   4.7080e-02
   3_xyz:   7.716  0.063  0.432 85.722  0.028  2.325   5.1664e-02
   3_adp:   7.716  0.063  0.432 85.722  0.028  2.325   5.1664e-02
   3_occ:   7.716  0.063  0.432 85.722  0.028  2.325   5.1664e-02
   4_bss:   7.716  0.063  0.432 85.722  0.028  2.325   5.1664e-02
   4_xyz:   7.711  0.054  0.449 83.716  0.029  2.324   4.0575e-02
   4_adp:   7.711  0.054  0.449 83.716  0.029  2.324   4.0575e-02
   4_occ:   7.711  0.054  0.449 83.716  0.029  2.324   4.0575e-02
   5_bss:   7.711  0.054  0.449 83.716  0.029  2.324   4.0575e-02
   5_xyz:   7.508  0.045  0.437 84.365  0.025  2.320   3.1032e-02
   5_adp:   7.508  0.045  0.437 84.365  0.025  2.320   3.1032e-02
   5_occ:   7.508  0.045  0.437 84.365  0.025  2.320   3.1032e-02
   5_bss:   7.508  0.045  0.437 84.365  0.025  2.320   3.1032e-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:  88.83   0.00  12.12  88.83   0.00   9.36  75.53   0.00  27.12
   1_occ:  88.83   0.00  12.12  88.83   0.00   9.36  75.53   0.00  27.12
   2_bss:  88.83   0.00  12.12  88.83   0.00   9.36  75.53   0.00  27.12
   2_xyz:  88.83   0.00  12.12  88.83   0.00   9.36  75.53   0.00  27.12
   2_adp:  85.03   0.00  12.13  85.03   0.00   8.52  73.72   1.36  31.79
   2_occ:  85.03   0.00  12.13  85.03   0.00   8.52  73.72   1.36  31.79
   3_bss:  85.03   0.00  12.13  85.03   0.00   8.52  73.72   1.36  31.79
   3_xyz:  85.03   0.00  12.13  85.03   0.00   8.52  73.72   1.36  31.79
   3_adp:  92.76   0.00  13.16  92.76   0.00   8.58  81.41   2.21  38.12
   3_occ:  92.76   0.00  13.16  92.76   0.00   8.58  81.41   2.21  38.12
   4_bss:  92.76   0.00  13.16  92.76   0.00   8.58  81.41   2.21  38.12
   4_xyz:  92.76   0.00  13.16  92.76   0.00   8.58  81.41   2.21  38.12
   4_adp:  91.08   0.00  12.49  91.08   0.00   8.36  78.35   2.11  34.97
   4_occ:  91.08   0.00  12.49  91.08   0.00   8.36  78.35   2.11  34.97
   5_bss:  91.08   0.00  12.49  91.08   0.00   8.36  78.35   2.11  34.97
   5_xyz:  91.08   0.00  12.49  91.08   0.00   8.36  78.35   2.11  34.97
   5_adp:  89.64   0.00  12.20  89.64   0.00   8.28  76.62   2.13  33.55
   5_occ:  89.64   0.00  12.20  89.64   0.00   8.28  76.62   2.13  33.55
   5_bss:  91.99   2.35  14.55  91.99   2.35  10.63  78.97   4.48  35.90
------------------------------------------------------------------------
 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:    1.214    0.010    0.407
   1_adp:    1.214    0.010    0.407
   1_occ:    1.214    0.010    0.407
   2_bss:    1.214    0.010    0.407
   2_xyz:    1.459    0.011    0.541
   2_adp:    1.459    0.011    0.541
   2_occ:    1.459    0.011    0.541
   3_bss:    1.459    0.011    0.541
   3_xyz:    1.542    0.024    0.617
   3_adp:    1.542    0.024    0.617
   3_occ:    1.542    0.024    0.617
   4_bss:    1.542    0.024    0.617
   4_xyz:    1.772    0.028    0.639
   4_adp:    1.772    0.028    0.639
   4_occ:    1.772    0.028    0.639
   5_bss:    1.772    0.028    0.639
   5_xyz:    1.886    0.013    0.655
   5_adp:    1.886    0.013    0.655
   5_occ:    1.886    0.013    0.655
   5_bss:    1.886    0.013    0.655
------------------------------------------------------------------------

CPU time actual refinement: 322.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_882/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_882/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_882/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_882/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_882/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.35 
  Macro-tasks:
    bulk solvent and scale       = 42.33  
    individual site refinement   = 126.95 
    weights calculation          = 32.08  
    collect and process          = 6.54   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 208.03 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 97.62  
    alpha_beta                      = 8.22   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 106.93 
    fmodel                         = 7.13   
    r_factors                      = 0.25   
    phase_errors                   = 10.69  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 234.05 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.601 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    631 calls, 97.25 s
gradients_fft:          576 calls, 94.26 s

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

# Date 2008-01-16 Time 02:39:11 PST -0800 (1200479951.72 s)
Start R-work = 0.4628, R-free = 0.4457 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1754 (no bulk solvent and anisotropic scale)

Start R-work = 0.4536, R-free = 0.4356
Final R-work = 0.1162, R-free = 0.1585