# Date 2008-01-16 Time 00:39:30 PST -0800 (1200472770.59 s)
#phil __OFF__

Command line arguments: "../99.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 = 15491
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 99

-------------------------------------------------------------------------------
  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: (68.4938, 47.8686, 84.2302, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (68.4938, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95056
Completeness in resolution range: 0.943593
Completeness with d_max=infinity: 0.940739

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9212
                             d_min =   1.9506

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: (68.4938, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95056
Completeness in resolution range: 0.943593
Completeness with d_max=infinity: 0.940739

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9216 -  4.1746 [2179/2208]  1958   221  10.1%
  bin  2:  4.1746 -  3.3255 [2091/2114]  1885   206   9.9%
  bin  3:  3.3255 -  2.9087 [2060/2085]  1851   209  10.1%
  bin  4:  2.9087 -  2.6444 [2029/2056]  1834   195   9.6%
  bin  5:  2.6444 -  2.4557 [2036/2069]  1825   211  10.4%
  bin  6:  2.4557 -  2.3115 [2025/2053]  1835   190   9.4%
  bin  7:  2.3115 -  2.1961 [2005/2041]  1798   207  10.3%
  bin  8:  2.1961 -  2.1008 [2003/2045]  1801   202  10.1%
  bin  9:  2.1008 -  2.0201 [1954/2029]  1760   194   9.9%
  bin 10:  2.0201 -  1.9506 [1207/2060]  1083   124  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_99/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:
        1.12 -     1.88: 21
        1.88 -     2.63: 143
        2.63 -     3.39: 4377
        3.39 -     4.14: 9529
        4.14 -     4.90: 14828
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.125 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.171 3.040 -x+1/2,-y+1,z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.319 3.270 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.359 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.375 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28893 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_99/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_99/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 68.49375 47.8686 84.23025 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: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5282   r_free= 0.5214   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.06 A                  |
| x-ray target function (ml) for work reflections: 6.316943                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6565 0.99   1416  159 0.4505 0.4456      6.6831      6.7224|
|  2:  4.6565 -  3.7148 0.99   1356  148 0.4793 0.4615      6.8921      6.8924|
|  3:  3.7148 -  3.2507 0.99   1341  149 0.5084 0.4887       6.747      6.7894|
|  4:  3.2507 -  2.9560 0.98   1317  141 0.5099 0.5112       6.564      6.5506|
|  5:  2.9560 -  2.7456 0.99   1320  152 0.5691 0.5714      6.4073      6.3954|
|  6:  2.7456 -  2.5846 0.99   1318  145 0.5432 0.5327      6.2982      6.2103|
|  7:  2.5846 -  2.4557 0.98   1285  148 0.5659 0.5417      6.2721      6.2005|
|  8:  2.4557 -  2.3493 0.98   1317  136 0.5557 0.5447       6.185      6.2303|
|  9:  2.3493 -  2.2591 0.99   1289  143 0.5697 0.5725      6.1325      6.1562|
| 10:  2.2591 -  2.1814 0.99   1292  148 0.5604 0.5703      6.1235      6.1356|
| 11:  2.1814 -  2.1134 0.97   1283  140 0.5596 0.5830      6.0366      6.0408|
| 12:  2.1134 -  2.0532 0.98   1281  148 0.5474 0.5533      5.9708      6.0075|
| 13:  2.0532 -  1.9992 0.90   1168  130 0.5632 0.5722      5.8969      5.8912|
| 14:  1.9992 -  1.9506 0.49    647   72 0.5759 0.4331      5.8808      5.6608|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6565  1416   159  0.59  43.91   0.77     0.61     104393.76|
|  2:  4.6565 -  3.7148  1356   148  0.58  45.21   0.83     0.65     155212.62|
|  3:  3.7148 -  3.2507  1341   149  0.46  55.33   0.81     0.59     163325.05|
|  4:  3.2507 -  2.9560  1317   141  0.36  62.94   0.79     0.46     136251.86|
|  5:  2.9560 -  2.7456  1320   152  0.25  70.90   0.70     0.34     106764.60|
|  6:  2.7456 -  2.5846  1318   145  0.24  72.28   0.70     0.28      85812.87|
|  7:  2.5846 -  2.4557  1285   148  0.21  74.42   0.71     0.24      75615.17|
|  8:  2.4557 -  2.3493  1317   136  0.19  75.70   0.71     0.24      70005.31|
|  9:  2.3493 -  2.2591  1289   143  0.14  79.91   0.70     0.18      67251.54|
| 10:  2.2591 -  2.1814  1292   148  0.10  82.46   0.77     0.13      61490.92|
| 11:  2.1814 -  2.1134  1283   140  0.07  85.03   0.74     0.09      57200.66|
| 12:  2.1134 -  2.0532  1281   148  0.10  82.34   0.74     0.14      52400.29|
| 13:  2.0532 -  1.9992  1168   130  0.20  75.48   0.74     0.26      41745.68|
| 14:  1.9992 -  1.9506   647    72  0.39  60.44   0.70     0.45      26172.49|
|alpha:            min =        0.09 max =            0.65 mean =         0.33|
|beta:             min =    26172.49 max =       163325.05 mean =     89193.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.28|
|phase err.(work): min =        0.00 max =           89.99 mean =        68.98|
|phase err.(test): min =        0.00 max =           89.98 mean =        69.19|
|-----------------------------------------------------------------------------|

============================== 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 = 34.845014             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.072   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.628565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.450   (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 |  0.993 -  1.384:       10 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.384 -  1.775:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.775 -  2.165:      115 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.165 -  2.556:      534 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.556 -  2.947:     1341 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.947 -  3.337:     2487 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.337 -  3.728:     4013 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.728 -  4.119:     5243 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.119 -  4.509:     6933 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.509 -  4.900:     8250 |
|-----------------------------------------------------------------------------|
|-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 |       52.935 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.993 |       3.706 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5311   r_free= 0.5248   ksol= 0.00   Bsol= 0.00   scale= 0.739    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.06 A                  |
| x-ray target function (ml) for work reflections: 6.316833                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5220   r_free= 0.5157   ksol= 0.34   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.73,9.89,7.85,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.20 A                  |
| x-ray target function (ml) for work reflections: 6.315055                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 29.009499             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.356   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.266552              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.157   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5220      final r-factor (work) = 0.4681          |
| start r-factor (free) = 0.5157      final r-factor (free) = 0.4910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 144.5320 = 29.01 * 0.50 * 6.3149 + 1.00 * 52.9352                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.1615 = 29.01 * 0.50 * 6.2703 + 1.00 * 0.2118                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4681      final r-factor (work) = 0.4375          |
| start r-factor (free) = 0.4910      final r-factor (free) = 0.4922          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.2264 = 2.27 * 1.00 * 6.2703 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1787 = 2.27 * 1.00 * 6.2453 + 1.00 * 0.0234                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.26   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    99.26   17.24    None  None   None       |
|    Sol.    : 438    0      0.00    99.26   22.88    None  None   None       |
|    Mac.    : 2385   0      0.00    86.91   16.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.926:  917   |   5:    49.628 -  59.554:   37        |
|      1:     9.926 -  19.851:  948   |   6:    59.554 -  69.479:   16        |
|      2:    19.851 -  29.777:  529   |   7:    69.479 -  79.405:    8        |
|      3:    29.777 -  39.703:  241   |   8:    79.405 -  89.331:    5        |
|      4:    39.703 -  49.628:  119   |   9:    89.331 -  99.256:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4375 r_free = 0.4922             target_work(ml) = 6.238         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4370 r_free = 0.4909             target_work(ml) = 6.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4370   r_free= 0.4909   ksol= 0.34   Bsol= 0.00   scale= 1.111    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.73,9.89,7.85,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.237199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4365   r_free= 0.4830   ksol= 0.38   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,6.25,5.21,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.238348                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.321430             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.649  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.102810              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.165  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4365      final r-factor (work) = 0.3851          |
| start r-factor (free) = 0.4830      final r-factor (free) = 0.4456          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.6661 = 20.32 * 0.50 * 6.2451 + 1.00 * 0.2118                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.0878 = 20.32 * 0.50 * 6.1957 + 1.00 * 0.1346                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3851      final r-factor (work) = 0.3658          |
| start r-factor (free) = 0.4456      final r-factor (free) = 0.4368          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8702 = 1.10 * 1.00 * 6.1957 + 1.00 * 0.0374                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7866 = 1.10 * 1.00 * 6.1398 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.81  17.67    None  None   None       |
|    all(noH): 2823   0      0.00    104.81  17.67    None  None   None       |
|    Sol.    : 438    0      0.00    102.89  27.04    None  None   None       |
|    Mac.    : 2385   0      0.00    104.81  15.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.481:  991   |   5:    52.403 -  62.884:   33        |
|      1:    10.481 -  20.961:  894   |   6:    62.884 -  73.365:   16        |
|      2:    20.961 -  31.442:  540   |   7:    73.365 -  83.845:    5        |
|      3:    31.442 -  41.923:  255   |   8:    83.845 -  94.326:    1        |
|      4:    41.923 -  52.403:   84   |   9:    94.326 - 104.807:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3658 r_free = 0.4368             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3657 r_free = 0.4367             target_work(ml) = 6.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3657   r_free= 0.4367   ksol= 0.38   Bsol= 50.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,6.25,5.21,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.128778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3628   r_free= 0.4325   ksol= 0.34   Bsol= 51.65   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.13,3.42,2.77,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.126511                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.254494             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.542  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.761514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.781  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3628      final r-factor (work) = 0.3011          |
| start r-factor (free) = 0.4325      final r-factor (free) = 0.3754          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.8125 = 13.25 * 0.50 * 6.1380 + 1.00 * 0.1346                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.3125 = 13.25 * 0.50 * 6.0662 + 1.00 * 0.1104                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3011      final r-factor (work) = 0.2669          |
| start r-factor (free) = 0.3754      final r-factor (free) = 0.3541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.8335 = 3.76 * 1.00 * 6.0662 + 1.00 * 0.0154                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.3857 = 3.76 * 1.00 * 5.9439 + 1.00 * 0.0275                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.24  19.43    None  None   None       |
|    all(noH): 2823   0      0.00    114.24  19.43    None  None   None       |
|    Sol.    : 438    0      0.00    114.24  41.16    None  None   None       |
|    Mac.    : 2385   0      0.00    106.31  15.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.424: 1254   |   5:    57.120 -  68.544:   86        |
|      1:    11.424 -  22.848:  724   |   6:    68.544 -  79.968:   38        |
|      2:    22.848 -  34.272:  348   |   7:    79.968 -  91.392:   29        |
|      3:    34.272 -  45.696:  213   |   8:    91.392 - 102.816:   14        |
|      4:    45.696 -  57.120:  110   |   9:   102.816 - 114.240:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2669 r_free = 0.3541             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2667 r_free = 0.3537             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2667   r_free= 0.3537   ksol= 0.34   Bsol= 51.65   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.13,3.42,2.77,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.919559                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2666   r_free= 0.3521   ksol= 0.33   Bsol= 51.65   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.62,2.45,1.92,0.00,0.00,0.00); trace/3= 1.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.915766                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.135592              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.916  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.469417              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.310  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2666      final r-factor (work) = 0.2255          |
| start r-factor (free) = 0.3521      final r-factor (free) = 0.3005          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3708 = 5.14 * 0.50 * 5.9430 + 1.00 * 0.1104                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1165 = 5.14 * 0.50 * 5.8610 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2255      final r-factor (work) = 0.2128          |
| start r-factor (free) = 0.3005      final r-factor (free) = 0.2720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7790 = 0.47 * 1.00 * 5.8610 + 1.00 * 0.0278                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7194 = 0.47 * 1.00 * 5.7560 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.92  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    113.92  17.45    None  None   None       |
|    Sol.    : 438    0      2.73    113.92  41.35    None  None   None       |
|    Mac.    : 2385   0      0.00    101.92  13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.392: 1473   |   5:    56.959 -  68.351:   56        |
|      1:    11.392 -  22.784:  686   |   6:    68.351 -  79.743:   42        |
|      2:    22.784 -  34.175:  247   |   7:    79.743 -  91.134:   15        |
|      3:    34.175 -  45.567:  175   |   8:    91.134 - 102.526:    7        |
|      4:    45.567 -  56.959:  117   |   9:   102.526 - 113.918:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2128 r_free = 0.2720             target_work(ml) = 5.700         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2125 r_free = 0.2717             target_work(ml) = 5.699         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2125   r_free= 0.2717   ksol= 0.33   Bsol= 51.65   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.62,2.45,1.92,0.00,0.00,0.00); trace/3= 1.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.699451                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2120   r_free= 0.2710   ksol= 0.33   Bsol= 43.93   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,1.47,0.97,0.00,0.00,0.00); trace/3= 0.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.699592                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.679332              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.029  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719775              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.837   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2120      final r-factor (work) = 0.1662          |
| start r-factor (free) = 0.2710      final r-factor (free) = 0.2219          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4139 = 5.68 * 0.50 * 5.7567 + 1.00 * 0.0667                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9939 = 5.68 * 0.50 * 5.6027 + 1.00 * 0.0840                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1662      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2219      final r-factor (free) = 0.2043          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0467 = 0.72 * 1.00 * 5.6027 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9330 = 0.72 * 1.00 * 5.4466 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.37  16.80    None  None   None       |
|    all(noH): 2823   0      0.00    110.37  16.80    None  None   None       |
|    Sol.    : 438    0      0.00    110.37  44.58    None  None   None       |
|    Mac.    : 2385   0      0.00    102.22  11.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.037: 1543   |   5:    55.183 -  66.219:   87        |
|      1:    11.037 -  22.073:  706   |   6:    66.219 -  77.256:   51        |
|      2:    22.073 -  33.110:  171   |   7:    77.256 -  88.292:   15        |
|      3:    33.110 -  44.146:  112   |   8:    88.292 -  99.329:    8        |
|      4:    44.146 -  55.183:  125   |   9:    99.329 - 110.365:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1493 r_free = 0.2043             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1490 r_free = 0.2043             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.2043   ksol= 0.33   Bsol= 43.93   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,1.47,0.97,0.00,0.00,0.00); trace/3= 0.65                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.394550                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6565 0.99   1416  159 0.1119 0.1482      5.5173      5.7071|
|  2:  4.6565 -  3.7148 0.99   1356  148 0.1049 0.1427      5.6459      5.9395|
|  3:  3.7148 -  3.2507 0.99   1341  149 0.1406 0.1999      5.7351      6.0524|
|  4:  3.2507 -  2.9560 0.98   1317  141 0.1680 0.2099      5.7041      5.8982|
|  5:  2.9560 -  2.7456 0.99   1320  152 0.1776 0.2060      5.5819      5.6933|
|  6:  2.7456 -  2.5846 0.99   1318  145 0.1697 0.2549      5.4767       5.699|
|  7:  2.5846 -  2.4557 0.98   1285  148 0.1624 0.2252      5.3957      5.5927|
|  8:  2.4557 -  2.3493 0.98   1317  136 0.1613 0.2152      5.3347      5.5516|
|  9:  2.3493 -  2.2591 0.99   1289  143 0.1622 0.2458      5.2697      5.5212|
| 10:  2.2591 -  2.1814 0.99   1292  148 0.1612 0.2304      5.2706      5.5031|
| 11:  2.1814 -  2.1134 0.97   1283  140 0.1574 0.2365      5.1792      5.4665|
| 12:  2.1134 -  2.0532 0.98   1281  148 0.1506 0.2131      5.1166      5.3779|
| 13:  2.0532 -  1.9992 0.90   1168  130 0.1505 0.2330      5.0259      5.2981|
| 14:  1.9992 -  1.9506 0.49    647   72 0.1540 0.2277      4.9727      5.1672|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6565  1416   159  0.92  11.95   0.98     0.96      10662.58|
|  2:  4.6565 -  3.7148  1356   148  0.93  11.55   1.05     1.01      14451.52|
|  3:  3.7148 -  3.2507  1341   149  0.89  16.50   1.06     1.04      18579.71|
|  4:  3.2507 -  2.9560  1317   141  0.87  19.31   1.05     1.04      17300.13|
|  5:  2.9560 -  2.7456  1320   152  0.84  21.95   1.03     1.01      14404.47|
|  6:  2.7456 -  2.5846  1318   145  0.85  21.81   1.02     0.96      12106.56|
|  7:  2.5846 -  2.4557  1285   148  0.85  21.54   1.01     0.96      10237.24|
|  8:  2.4557 -  2.3493  1317   136  0.85  21.70   1.05     1.01       9699.34|
|  9:  2.3493 -  2.2591  1289   143  0.85  21.52   1.05     1.01       8283.74|
| 10:  2.2591 -  2.1814  1292   148  0.85  21.35   1.04     0.99       8269.23|
| 11:  2.1814 -  2.1134  1283   140  0.84  22.73   1.04     0.98       7340.94|
| 12:  2.1134 -  2.0532  1281   148  0.85  21.72   1.05     1.01       6632.13|
| 13:  2.0532 -  1.9992  1168   130  0.85  21.94   1.04     1.03       5613.65|
| 14:  1.9992 -  1.9506   647    72  0.84  22.26   1.03     0.97       4883.45|
|alpha:            min =        0.96 max =            1.04 mean =         1.00|
|beta:             min =     4883.45 max =        18579.71 mean =     10906.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.92 mean =        19.65|
|phase err.(test): min =        0.00 max =           89.92 mean =        18.86|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1491   r_free= 0.2041   ksol= 0.33   Bsol= 43.93   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,0.72,0.29,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.395630                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1491   r_free= 0.2041   ksol= 0.33   Bsol= 43.93   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.07,0.72,0.29,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.395630                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6565 0.99   1416  159 0.1125 0.1485      5.5246      5.7028|
|  2:  4.6565 -  3.7148 0.99   1356  148 0.1064 0.1423      5.6558      5.9457|
|  3:  3.7148 -  3.2507 0.99   1341  149 0.1413 0.2000      5.7381      6.0527|
|  4:  3.2507 -  2.9560 0.98   1317  141 0.1681 0.2083      5.7052      5.8979|
|  5:  2.9560 -  2.7456 0.99   1320  152 0.1776 0.2046      5.5811      5.6902|
|  6:  2.7456 -  2.5846 0.99   1318  145 0.1695 0.2555      5.4746      5.7001|
|  7:  2.5846 -  2.4557 0.98   1285  148 0.1621 0.2235      5.3947      5.5908|
|  8:  2.4557 -  2.3493 0.98   1317  136 0.1609 0.2154      5.3333      5.5524|
|  9:  2.3493 -  2.2591 0.99   1289  143 0.1618 0.2452      5.2683      5.5181|
| 10:  2.2591 -  2.1814 0.99   1292  148 0.1612 0.2305      5.2696      5.5041|
| 11:  2.1814 -  2.1134 0.97   1283  140 0.1572 0.2361      5.1783      5.4666|
| 12:  2.1134 -  2.0532 0.98   1281  148 0.1506 0.2124      5.1172      5.3766|
| 13:  2.0532 -  1.9992 0.90   1168  130 0.1506 0.2323       5.026      5.2981|
| 14:  1.9992 -  1.9506 0.49    647   72 0.1541 0.2281      4.9722      5.1682|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6565  1416   159  0.92  12.05   0.97     0.95      10735.18|
|  2:  4.6565 -  3.7148  1356   148  0.93  11.61   1.04     1.00      14538.05|
|  3:  3.7148 -  3.2507  1341   149  0.89  16.51   1.05     1.03      18641.31|
|  4:  3.2507 -  2.9560  1317   141  0.87  19.28   1.03     1.02      17297.47|
|  5:  2.9560 -  2.7456  1320   152  0.84  21.91   1.01     0.99      14362.90|
|  6:  2.7456 -  2.5846  1318   145  0.85  21.76   0.99     0.94      12076.51|
|  7:  2.5846 -  2.4557  1285   148  0.85  21.54   0.99     0.93      10222.48|
|  8:  2.4557 -  2.3493  1317   136  0.85  21.66   1.02     0.98       9677.21|
|  9:  2.3493 -  2.2591  1289   143  0.85  21.49   1.01     0.98       8267.81|
| 10:  2.2591 -  2.1814  1292   148  0.85  21.32   1.00     0.96       8246.07|
| 11:  2.1814 -  2.1134  1283   140  0.84  22.71   1.01     0.95       7339.30|
| 12:  2.1134 -  2.0532  1281   148  0.85  21.72   1.01     0.98       6642.24|
| 13:  2.0532 -  1.9992  1168   130  0.85  21.93   1.00     0.99       5610.26|
| 14:  1.9992 -  1.9506   647    72  0.84  22.23   0.98     0.93       4874.66|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     4874.66 max =        18641.31 mean =     10912.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        19.65|
|phase err.(test): min =        0.00 max =           89.48 mean =        18.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.37  16.80    None  None   None       |
|    all(noH): 2823   0      0.00    110.37  16.80    None  None   None       |
|    Sol.    : 438    0      0.00    110.37  44.58    None  None   None       |
|    Mac.    : 2385   0      0.00    102.23  11.70    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:     0.003 -  11.040: 1543   |   5:    55.186 -  66.222:   87        |
|      1:    11.040 -  22.076:  706   |   6:    66.222 -  77.259:   51        |
|      2:    22.076 -  33.113:  171   |   7:    77.259 -  88.295:   15        |
|      3:    33.113 -  44.149:  112   |   8:    88.295 -  99.331:    8        |
|      4:    44.149 -  55.186:  125   |   9:    99.331 - 110.368:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.441 - 4.458
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 344
   mapped sites are within: 0.758 - 4.458

peak=    8.895 closest distance to " O   HOH Z 138 " =    1.650
peak=    8.827 closest distance to " O   HOH Z 203 " =    1.526
peak=    8.651 closest distance to " CB  VAL A 230 " =    1.359
peak=    7.786 closest distance to " O   HOH Z 403 " =    1.398
peak=    7.591 closest distance to " O   HOH Z 307 " =    1.240
peak=    7.548 closest distance to " O  BHOH Z  74 " =    1.115
peak=    7.341 closest distance to " OD1 ASN A  60 " =    1.043
peak=    6.883 closest distance to " O   HOH Z 159 " =    1.146
peak=    6.843 closest distance to " O   HOH Z 316 " =    1.567
peak=    6.499 closest distance to " O   HOH Z 135 " =    1.356
peak=    6.478 closest distance to " O   HOH Z  37 " =    1.348
peak=    6.438 closest distance to " O   HOH Z  46 " =    1.353
peak=    6.363 closest distance to " O   HOH Z 137 " =    1.354
peak=    6.352 closest distance to " O   HOH Z  45 " =    1.640
peak=    6.214 closest distance to " O   ARG A  56 " =    1.097
peak=    6.159 closest distance to " O   HOH Z  92 " =    1.664
peak=    5.984 closest distance to " O   HOH Z 332 " =    0.993
peak=    5.930 closest distance to " O   HOH Z 117 " =    1.867
peak=    5.916 closest distance to " CD1AILE A 234 " =    1.326
peak=    5.793 closest distance to " CG  GLN A  77 " =    1.222
peak=    5.754 closest distance to " CB  VAL A 296 " =    1.228
peak=    5.664 closest distance to " O   HOH Z 402 " =    1.626
peak=    5.602 closest distance to " CD2 LEU A   5 " =    1.314
peak=    5.551 closest distance to " O   HOH Z 199 " =    1.920
peak=    5.526 closest distance to " O   HOH Z 247 " =    1.859
peak=    5.513 closest distance to " O   HOH Z 342 " =    0.988
peak=    5.364 closest distance to " O   HOH Z 249 " =    1.541
peak=    5.265 closest distance to " O   HOH Z 272 " =    2.022
peak=    5.241 closest distance to " O   HOH Z 422 " =    1.071
peak=    5.225 closest distance to " O   HOH Z 178 " =    1.962
peak=    5.182 closest distance to " O   HOH Z 278 " =    2.351
peak=    5.108 closest distance to " CG  ARG A  66 " =    1.317
peak=    5.097 closest distance to " CG AARG A 275 " =    1.264
peak=    5.084 closest distance to " O   HOH Z 279 " =    1.450
peak=    5.080 closest distance to " O   HOH Z 209 " =    1.399
peak=    5.009 closest distance to " O   SER A  62 " =    0.984
peak=    4.988 closest distance to " O   HOH Z 130 " =    1.246
peak=    4.920 closest distance to " CB  ARG A 275 " =    1.081
peak=    4.890 closest distance to " O   HOH Z 192 " =    1.716
peak=    4.885 closest distance to " O   HOH Z 412 " =    3.508
peak=    4.832 closest distance to " O   HOH Z 116 " =    1.251
peak=    4.826 closest distance to " CA  VAL A  41 " =    0.907
peak=    4.814 closest distance to " OE1 GLU A  44 " =    1.103
peak=    4.807 closest distance to " O   HOH Z  79 " =    1.045
peak=    4.704 closest distance to " CB  GLN A  73 " =    1.089
peak=    4.694 closest distance to " CG  LEU A   5 " =    1.443
peak=    4.685 closest distance to " CA  SER A  62 " =    1.091
peak=    4.652 closest distance to " O   HOH Z 147 " =    1.241
peak=    4.622 closest distance to " O   HOH Z 248 " =    1.383
peak=    4.621 closest distance to " O   HOH Z  49 " =    1.574
peak=    4.596 closest distance to " O   HOH Z 406 " =    1.540
peak=    4.545 closest distance to " O   HOH Z  48 " =    1.628
peak=    4.545 closest distance to " O   HOH Z 146 " =    1.476
peak=    4.529 closest distance to " O   HOH Z 188 " =    1.257
peak=    4.528 closest distance to " O   HOH Z  69 " =    1.322
peak=    4.489 closest distance to " O   HOH Z 124 " =    1.899
peak=    4.481 closest distance to " O   HOH Z 344 " =    1.459
peak=    4.467 closest distance to " O   HOH Z  68 " =    1.922
peak=    4.459 closest distance to " O   HOH Z 126 " =    1.476
peak=    4.449 closest distance to " O   HOH Z 255 " =    1.292
peak=    4.439 closest distance to " O   HOH Z 364 " =    1.633
peak=    4.412 closest distance to " OD2 ASP A 132 " =    2.194
peak=    4.410 closest distance to " O   HOH Z 221 " =    1.355
peak=    4.400 closest distance to " O   HOH Z 389 " =    1.788
peak=    4.367 closest distance to " O   HOH Z 400 " =    0.843
peak=    4.354 closest distance to " O   HOH Z 424 " =    1.090
peak=    4.342 closest distance to " OG ASER A 164 " =    0.826
peak=    4.339 closest distance to " CB  ASN A 187 " =    1.721
peak=    4.302 closest distance to " O   HOH Z 193 " =    1.725
peak=    4.299 closest distance to " NZ  LYS A 117 " =    3.185
peak=    4.291 closest distance to " CB  VAL A 265 " =    1.437
peak=    4.289 closest distance to " ND1 HIS A  81 " =    1.101
peak=    4.268 closest distance to " NZ  LYS A 119 " =    3.089
peak=    4.265 closest distance to " O   HOH Z 232 " =    1.492
peak=    4.252 closest distance to " O   HOH Z 358 " =    1.383
peak=    4.233 closest distance to " O   HOH Z   9 " =    2.446
peak=    4.231 closest distance to " NH2 ARG A  56 " =    1.964
peak=    4.202 closest distance to " O   HOH Z 217 " =    1.967
peak=    4.193 closest distance to " CB  PHE A  59 " =    0.797
peak=    4.192 closest distance to " CE  MET A  93 " =    1.500
peak=    4.189 closest distance to " O   HOH Z 365 " =    1.971
peak=    4.171 closest distance to " NZ  LYS A  76 " =    1.128
peak=    4.152 closest distance to " CD  PRO A  54 " =    0.917
peak=    4.149 closest distance to " CD2 TRP A 179 " =    1.435
peak=    4.146 closest distance to " CB  GLU A 277 " =    0.885
peak=    4.139 closest distance to " CG1 VAL A 296 " =    1.058
peak=    4.127 closest distance to " CB  SER A  62 " =    1.227
peak=    4.104 closest distance to " CG2 THR A 251 " =    1.344
peak=    4.102 closest distance to " O   HOH Z   4 " =    2.117
peak=    4.091 closest distance to " CG  PRO A  54 " =    1.179
peak=    4.082 closest distance to " O   HOH Z 214 " =    1.659
peak=    4.053 closest distance to " O   HOH Z 191 " =    1.444
peak=    4.046 closest distance to " O   HOH Z  78 " =    1.476
peak=    4.042 closest distance to " O   HOH Z 425 " =    1.617
peak=    4.008 closest distance to " O   HOH Z 414 " =    2.613
peak=    3.997 closest distance to " O   HOH Z 237 " =    1.982
peak=    3.996 closest distance to " CD  PRO A 243 " =    1.243
peak=    3.975 closest distance to " O   HOH Z 395 " =    1.352
peak=    3.967 closest distance to " O   HOH Z  60 " =    2.007
peak=    3.960 closest distance to " O   HOH Z 324 " =    1.937
peak=    3.957 closest distance to " CD  ARG A 269 " =    0.995
peak=    3.957 closest distance to " O   HOH Z 361 " =    2.754
peak=    3.956 closest distance to " ND2 ASN A  69 " =    2.581
peak=    3.949 closest distance to " O   HOH Z 406 " =    1.805
peak=    3.948 closest distance to " O   HOH Z 423 " =    1.802
peak=    3.946 closest distance to " O   ASN A 285 " =    0.919
peak=    3.943 closest distance to " ND1 HIS A 115 " =    2.475
peak=    3.937 closest distance to " O   HOH Z 215 " =    1.621
peak=    3.936 closest distance to " O   HOH Z  30 " =    1.451
peak=    3.936 closest distance to " O   HOH Z 238 " =    1.639
peak=    3.923 closest distance to " OG  SER A  95 " =    1.277
peak=    3.921 closest distance to " OE1 GLU A   2 " =    1.473
peak=    3.913 closest distance to " O   HOH Z 126 " =    2.296
peak=    3.904 closest distance to " O   HOH Z  97 " =    1.795
peak=    3.904 closest distance to " O   HOH Z 394 " =    1.879
peak=    3.899 closest distance to " O   HOH Z 156 " =    2.973
peak=    3.885 closest distance to " O   HOH Z 143 " =    1.606
peak=    3.880 closest distance to " CA  VAL A 126 " =    1.243
peak=    3.871 closest distance to " O   HOH Z 245 " =    1.414
peak=    3.867 closest distance to " O   HOH Z 368 " =    1.295
peak=    3.866 closest distance to " CD1 PHE A  61 " =    0.946
peak=    3.858 closest distance to " O   HOH Z 163 " =    1.734
peak=    3.844 closest distance to " CD2 LEU A 228 " =    1.231
peak=    3.844 closest distance to " O   HOH Z 109 " =    1.550
peak=    3.837 closest distance to " CB  ASN A 285 " =    1.010
peak=    3.836 closest distance to " O   HOH Z  47 " =    2.185
peak=    3.836 closest distance to " O   HOH Z 189 " =    2.166
peak=    3.834 closest distance to " O   HOH Z 301 " =    1.548
peak=    3.803 closest distance to " O   HOH Z 291 " =    1.180
peak=    3.792 closest distance to " O   HOH Z 416 " =    1.307
peak=    3.789 closest distance to " O   HOH Z 337 " =    1.766
peak=    3.788 closest distance to " CG1BVAL A 121 " =    1.252
peak=    3.780 closest distance to " O   HOH Z 367 " =    3.141
peak=    3.773 closest distance to " O   HOH Z 208 " =    1.759
peak=    3.771 closest distance to " CG2 VAL A 296 " =    1.045
peak=    3.767 closest distance to " CB  GLN A 194 " =    1.072
peak=    3.757 closest distance to " O   GLN A  55 " =    0.943
peak=    3.755 closest distance to " N   TYR A  15 " =    0.868
peak=    3.745 closest distance to " O   HOH Z 383 " =    2.094
peak=    3.745 closest distance to " CD  GLN A 240 " =    1.273
peak=    3.745 closest distance to " O   HOH Z  40 " =    1.855
peak=    3.742 closest distance to " CE  MET A  40 " =    1.229
peak=    3.741 closest distance to " CG  LYS A 166 " =    1.737
peak=    3.736 closest distance to " O   HOH Z 120 " =    1.380
peak=    3.732 closest distance to " O   HOH Z 110 " =    1.103
peak=    3.706 closest distance to " CB  MET A  47 " =    1.079
peak=    3.700 closest distance to " O   HOH Z 322 " =    1.539
peak=    3.685 closest distance to " CA  CYS A 260 " =    1.060
peak=    3.684 closest distance to " O   HOH Z 276 " =    1.509
peak=    3.676 closest distance to " O   HOH Z 272 " =    2.195
peak=    3.676 closest distance to " O   HOH Z 273 " =    2.743
peak=    3.670 closest distance to " O   HOH Z 132 " =    2.598
peak=    3.666 closest distance to " O   HOH Z 284 " =    1.539
peak=    3.665 closest distance to " O   HOH Z 327 " =    1.649
peak=    3.662 closest distance to " CA  LEU A 282 " =    1.083
peak=    3.659 closest distance to " O   HOH Z 133 " =    1.438
peak=    3.644 closest distance to " O   HOH Z 166 " =    1.866
peak=    3.644 closest distance to " CA  GLY A 196 " =    1.025
peak=    3.637 closest distance to " O   HOH Z 326 " =    1.519
peak=    3.629 closest distance to " CA  SER A  12 " =    1.118
peak=    3.629 closest distance to " O   HOH Z 343 " =    2.305
peak=    3.626 closest distance to " O   HOH Z 194 " =    1.886
peak=    3.620 closest distance to " O   HOH Z 136 " =    1.398
peak=    3.616 closest distance to " O   HOH Z  62 " =    1.598
peak=    3.614 closest distance to " CG2 VAL A 197 " =    1.320
peak=    3.610 closest distance to " O   HOH Z  32 " =    1.827
peak=    3.605 closest distance to " O   HOH Z 406 " =    1.433
peak=    3.605 closest distance to " OG BSER A 210 " =    1.141
peak=    3.595 closest distance to " O   HOH Z 151 " =    1.860
peak=    3.594 closest distance to " CB ASER A 164 " =    0.867
peak=    3.593 closest distance to " CB  TRP A 179 " =    0.987
peak=    3.583 closest distance to " CB  PRO A  54 " =    0.762
peak=    3.583 closest distance to " O   HOH Z  92 " =    1.278
peak=    3.577 closest distance to " O   HOH Z 363 " =    1.073
peak=    3.568 closest distance to " O   HOH Z  63 " =    1.915
peak=    3.560 closest distance to " O   HOH Z 423 " =    2.577
peak=    3.553 closest distance to " CB  ARG A 102 " =    0.907
peak=    3.551 closest distance to " OE1 GLN A  11 " =    1.976
peak=    3.548 closest distance to " CA  ARG A  66 " =    1.161
peak=    3.537 closest distance to " O   ARG A 102 " =    2.250
peak=    3.533 closest distance to " CB  SER A 141 " =    0.915
peak=    3.527 closest distance to " O   PRO A 198 " =    1.625
peak=    3.524 closest distance to " CB  ASP A 253 " =    1.152
peak=    3.521 closest distance to " O   HOH Z 271 " =    2.305
peak=    3.520 closest distance to " O   HOH Z 346 " =    1.463
peak=    3.517 closest distance to " O   HOH Z 418 " =    1.264
peak=    3.512 closest distance to " O   HOH Z 371 " =    1.597
peak=    3.511 closest distance to " CA  PRO A 213 " =    0.922
peak=    3.502 closest distance to " O   HOH Z 313 " =    1.560
peak=    3.501 closest distance to " O   HOH Z 128 " =    1.942
peak=    3.493 closest distance to " CB  GLN A 223 " =    1.515
peak=    3.492 closest distance to " O   HOH Z 294 " =    1.686
peak=    3.490 closest distance to " O   ASP A 132 " =    3.789
peak=    3.486 closest distance to " CB  ALA A 100 " =    1.189
peak=    3.486 closest distance to " O   HOH Z 154 " =    1.775
peak=    3.485 closest distance to " O   HOH Z  38 " =    2.385
peak=    3.474 closest distance to " O   HOH Z  80 " =    2.657
peak=    3.473 closest distance to " CA  ILE A 120 " =    1.324
peak=    3.471 closest distance to " O   HOH Z 405 " =    1.963
peak=    3.460 closest distance to " O   HOH Z 369 " =    1.868
peak=    3.456 closest distance to " O   HOH Z 111 " =    1.881
peak=    3.455 closest distance to " O   HOH Z 138 " =    1.250
peak=    3.454 closest distance to " O   HOH Z 150 " =    1.528
peak=    3.450 closest distance to " O   HOH Z 433 " =    1.699
peak=    3.449 closest distance to " O   HOH Z 340 " =    1.787
peak=    3.449 closest distance to " O   HOH Z  91 " =    2.247
peak=    3.449 closest distance to " CE1 PHE A 208 " =    0.975
peak=    3.449 closest distance to " O   HOH Z 210 " =    1.214
peak=    3.442 closest distance to " CG2 THR A 294 " =    1.425
peak=    3.439 closest distance to " O   HOH Z  43 " =    1.932
peak=    3.437 closest distance to " NE2 GLN A  89 " =    0.859
peak=    3.435 closest distance to " O   HOH Z  78 " =    1.314
peak=    3.425 closest distance to " N   PHE A  59 " =    1.303
peak=    3.423 closest distance to " O   HOH Z 263 " =    1.486
peak=    3.420 closest distance to " O   GLY A  23 " =    0.920
peak=    3.418 closest distance to " O   HOH Z 170 " =    1.993
peak=    3.407 closest distance to " O   LEU A 255 " =    3.274
peak=    3.407 closest distance to " CA  THR A 221 " =    1.041
peak=    3.401 closest distance to " CB  ALA A  34 " =    1.025
peak=    3.400 closest distance to " C   GLY A 147 " =    1.048
peak=    3.397 closest distance to " CD BLYS A 290 " =    0.992
peak=    3.395 closest distance to " NH2 ARG A 156 " =    0.961
peak=    3.391 closest distance to " O   HOH Z  95 " =    1.928
peak=    3.387 closest distance to " CB  SER A  32 " =    1.562
peak=    3.386 closest distance to " CA  ALA A 295 " =    0.824
peak=    3.386 closest distance to " CB  ARG A  79 " =    0.889
peak=    3.379 closest distance to " CG2 THR A  18 " =    1.056
peak=    3.377 closest distance to " O   HOH Z 128 " =    2.455
peak=    3.376 closest distance to " N   ALA A 256 " =    1.000
peak=    3.376 closest distance to " O   LYS A 289 " =    1.206
peak=    3.372 closest distance to " O   HOH Z 236 " =    2.443
peak=    3.366 closest distance to " CB  GLN A  58 " =    1.088
peak=    3.362 closest distance to " ND2 ASN A 284 " =    1.172
peak=    3.360 closest distance to " O   HOH Z  77 " =    1.578
peak=    3.348 closest distance to " CB  PRO A 198 " =    1.066
peak=    3.347 closest distance to " NH2BARG A 145 " =    1.868
peak=    3.347 closest distance to " OG ASER A 134 " =    1.788
peak=    3.346 closest distance to " O   HOH Z 436 " =    1.410
peak=    3.344 closest distance to " CG1 VAL A  67 " =    1.061
peak=    3.342 closest distance to " CB  ASP A 132 " =    3.798
peak=    3.342 closest distance to " CA  TYR A  30 " =    1.046
peak=    3.340 closest distance to " CB  ALA A 244 " =    1.035
peak=    3.332 closest distance to " O   HOH Z 219 " =    4.458
peak=    3.331 closest distance to " O   PHE A  59 " =    0.800
peak=    3.330 closest distance to " O   HOH Z 174 " =    1.906
peak=    3.330 closest distance to " O   HOH Z 266 " =    1.758
peak=    3.323 closest distance to " CG  PRO A 280 " =    1.064
peak=    3.319 closest distance to " CB  SER A  99 " =    1.180
peak=    3.319 closest distance to " O   HOH Z 266 " =    2.066
peak=    3.316 closest distance to " NE BARG A 190 " =    1.116
peak=    3.314 closest distance to " CA  ALA A   9 " =    1.146
peak=    3.313 closest distance to " CA  THR A 246 " =    1.177
peak=    3.312 closest distance to " CB  ASN A 187 " =    1.107
peak=    3.306 closest distance to " CA  ARG A 195 " =    1.107
peak=    3.303 closest distance to " O   ALA A  10 " =    1.405
peak=    3.302 closest distance to " CD2 PHE A 218 " =    0.923
peak=    3.300 closest distance to " O   HOH Z 196 " =    1.771
peak=    3.299 closest distance to " O   HOH Z 155 " =    2.337
peak=    3.297 closest distance to " NH1 ARG A  14 " =    0.967
peak=    3.292 closest distance to " O   HOH Z 431 " =    1.639
peak=    3.285 closest distance to " CE  LYS A 119 " =    1.303
peak=    3.285 closest distance to " O   HOH Z 404 " =    1.161
peak=    3.283 closest distance to " O   HOH Z  11 " =    1.208
peak=    3.282 closest distance to " CD1 ILE A 151 " =    1.665
peak=    3.279 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.274 closest distance to " O   HOH Z  44 " =    2.136
peak=    3.274 closest distance to " O   HOH Z 124 " =    2.015
peak=    3.274 closest distance to " O   HOH Z 408 " =    2.062
peak=    3.273 closest distance to " CE1 TYR A 247 " =    1.568
peak=    3.271 closest distance to " O   GLY A 211 " =    1.113
peak=    3.270 closest distance to " O   HOH Z 112 " =    1.769
peak=    3.261 closest distance to " CB  HIS A 108 " =    0.877
peak=    3.260 closest distance to " O   HOH Z 227 " =    1.619
peak=    3.258 closest distance to " NH1AARG A 145 " =    1.016
peak=    3.254 closest distance to " O   HOH Z 192 " =    1.310
peak=    3.253 closest distance to " O   HOH Z 108 " =    1.159
peak=    3.253 closest distance to " O   HOH Z 427 " =    1.017
peak=    3.250 closest distance to " NH2 ARG A  79 " =    1.515
peak=    3.247 closest distance to " O   HOH Z 330 " =    1.426
peak=    3.247 closest distance to " CA  PRO A 163 " =    1.085
peak=    3.230 closest distance to " O   HOH Z 154 " =    1.998
peak=    3.229 closest distance to " O   HOH Z 426 " =    3.264
peak=    3.228 closest distance to " CB  ALA A 226 " =    1.016
peak=    3.226 closest distance to " O   HOH Z 278 " =    1.360
peak=    3.224 closest distance to " O   HOH Z  80 " =    2.118
peak=    3.222 closest distance to " CB  SER A  26 " =    1.612
peak=    3.218 closest distance to " N   TYR A 247 " =    1.594
peak=    3.218 closest distance to " CD  LYS A  76 " =    1.723
peak=    3.215 closest distance to " CG  MET A 185 " =    1.368
peak=    3.213 closest distance to " CB ASER A 164 " =    0.828
peak=    3.211 closest distance to " CB  THR A  52 " =    0.758
peak=    3.206 closest distance to " CA  ILE A 263 " =    1.086
peak=    3.205 closest distance to " O   HOH Z 270 " =    1.823
peak=    3.204 closest distance to " CD1 TRP A 274 " =    1.106
peak=    3.202 closest distance to " O   HOH Z 113 " =    1.923
peak=    3.199 closest distance to " O   HOH Z  94 " =    1.586
peak=    3.198 closest distance to " CE BLYS A 290 " =    1.054
peak=    3.198 closest distance to " CB  TRP A 123 " =    1.071
peak=    3.197 closest distance to " O   HOH Z 374 " =    1.029
peak=    3.196 closest distance to " O   HOH Z 381 " =    1.497
peak=    3.195 closest distance to " CB  VAL A 230 " =    1.150
peak=    3.194 closest distance to " CG2 ILE A 234 " =    1.038
peak=    3.182 closest distance to " N   ASP A 162 " =    1.178
peak=    3.174 closest distance to " CB  SER A  63 " =    1.105
peak=    3.172 closest distance to " O   HOH Z 408 " =    2.039
peak=    3.172 closest distance to " CG2 ILE A 120 " =    1.603
peak=    3.170 closest distance to " CD2 LEU A  25 " =    1.392
peak=    3.168 closest distance to " O   HOH Z  99 " =    2.124
peak=    3.165 closest distance to " O   HOH Z 213 " =    1.665
peak=    3.162 closest distance to " NH2 ARG A  36 " =    1.882
peak=    3.161 closest distance to " CB  LEU A 300 " =    0.982
peak=    3.161 closest distance to " OG BSER A 258 " =    2.669
peak=    3.158 closest distance to " O   HOH Z 259 " =    1.796
peak=    3.157 closest distance to " CB  ALA A 104 " =    0.973
peak=    3.156 closest distance to " CB  PHE A 225 " =    1.350
peak=    3.154 closest distance to " O   HOH Z 123 " =    1.223
peak=    3.152 closest distance to " O   HOH Z 118 " =    1.943
peak=    3.151 closest distance to " O   HOH Z 258 " =    2.946
peak=    3.147 closest distance to " CG2 VAL A 174 " =    1.254
peak=    3.134 closest distance to " CA  LEU A  83 " =    1.334
peak=    3.134 closest distance to " CB BVAL A  41 " =    1.299
peak=    3.132 closest distance to " C   GLY A  23 " =    0.988
peak=    3.127 closest distance to " CG1 ILE A  33 " =    1.495
peak=    3.123 closest distance to " O   HOH Z 405 " =    1.413
peak=    3.122 closest distance to " O   HOH Z 232 " =    1.773
peak=    3.118 closest distance to " CG2 VAL A 126 " =    1.340
peak=    3.112 closest distance to " CA  THR A  18 " =    1.004
peak=    3.110 closest distance to " OG  SER A  26 " =    1.660
peak=    3.109 closest distance to " O   HOH Z 155 " =    1.999
peak=    3.109 closest distance to " OG  SER A  22 " =    2.639
peak=    3.097 closest distance to " O   HOH Z   6 " =    1.589
peak=    3.091 closest distance to " CA  ALA A  21 " =    1.470
peak=    3.090 closest distance to " O   HOH Z 334 " =    1.541
peak=    3.088 closest distance to " OE2 GLU A 277 " =    1.475
peak=    3.084 closest distance to " CB  GLU A   2 " =    1.304
peak=    3.083 closest distance to " O   GLY A  57 " =    0.983
peak=    3.083 closest distance to " O   HOH Z 325 " =    2.310
peak=    3.053 closest distance to " CE  LYS A 117 " =    3.492
peak=    3.053 closest distance to " O   HOH Z 156 " =    1.851
peak=    3.048 closest distance to " OG BSER A 164 " =    2.308
peak=    3.047 closest distance to " CZ  PHE A 218 " =    0.939
peak=    3.034 closest distance to " O   HOH Z 322 " =    2.352

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.697 - 5.690
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.718 - 5.690

peak=   -5.022 closest distance to " ND1 HIS A  81 " =    0.933
peak=   -4.843 closest distance to " O   HOH Z 159 " =    1.449
peak=   -4.667 closest distance to " O   HOH Z 159 " =    0.863
peak=   -4.536 closest distance to " O   HOH Z 196 " =    1.337
peak=   -4.313 closest distance to " CG2 VAL A 230 " =    0.861
peak=   -4.304 closest distance to " NE1 TRP A 179 " =    1.179
peak=   -4.259 closest distance to " CD1 PHE A  59 " =    1.573
peak=   -4.160 closest distance to " N   GLN A  58 " =    1.023
peak=   -4.138 closest distance to " O   HOH Z  13 " =    1.155
peak=   -4.082 closest distance to " O   HOH Z 221 " =    1.206
peak=   -4.082 closest distance to " O  BHOH Z 338 " =    1.264
peak=   -4.078 closest distance to " O   HOH Z 135 " =    1.205
peak=   -4.077 closest distance to " CA  ASP A  27 " =    2.441
peak=   -4.052 closest distance to " O   HOH Z 130 " =    2.673
peak=   -3.973 closest distance to " O  BHOH Z  74 " =    0.810
peak=   -3.973 closest distance to " O   HOH Z 126 " =    1.852
peak=   -3.955 closest distance to " CA  SER A 164 " =    1.503
peak=   -3.947 closest distance to " O   HOH Z  52 " =    2.428
peak=   -3.925 closest distance to " CE  MET A 105 " =    2.149
peak=   -3.922 closest distance to " O   ARG A  56 " =    0.904
peak=   -3.896 closest distance to " CB  GLN A  58 " =    1.331
peak=   -3.892 closest distance to " N   VAL A  72 " =    1.047
peak=   -3.866 closest distance to " CB  GLN A  73 " =    0.877
peak=   -3.856 closest distance to " O   HOH Z 166 " =    1.861
peak=   -3.854 closest distance to " ND2 ASN A 142 " =    1.825
peak=   -3.853 closest distance to " CG  PRO A 163 " =    1.233
peak=   -3.839 closest distance to " CB  ASP A  50 " =    1.727
peak=   -3.832 closest distance to " CE1 PHE A 225 " =    2.015
peak=   -3.797 closest distance to " SD  MET A  40 " =    1.941
peak=   -3.787 closest distance to " CA  SER A  62 " =    1.187
peak=   -3.780 closest distance to " O   HOH Z 118 " =    5.480
peak=   -3.773 closest distance to " O   HOH Z 423 " =    2.895
peak=   -3.765 closest distance to " O   GLN A  58 " =    0.879
peak=   -3.747 closest distance to " O   LEU A 300 " =    2.432
peak=   -3.736 closest distance to " O   HOH Z 159 " =    1.182
peak=   -3.730 closest distance to " O   HOH Z  69 " =    0.971
peak=   -3.725 closest distance to " O   HOH Z 405 " =    1.418
peak=   -3.722 closest distance to " O   HOH Z 120 " =    1.212
peak=   -3.722 closest distance to " O   GLN A  58 " =    2.245
peak=   -3.716 closest distance to " OG  SER A  26 " =    1.317
peak=   -3.715 closest distance to " O   HOH Z 423 " =    2.909
peak=   -3.714 closest distance to " CD2 LEU A 237 " =    2.620
peak=   -3.710 closest distance to " O   LEU A 143 " =    1.615
peak=   -3.708 closest distance to " CG2 VAL A  78 " =    2.588
peak=   -3.700 closest distance to " O   HOH Z 118 " =    2.811
peak=   -3.697 closest distance to " O   HOH Z 193 " =    1.421
peak=   -3.687 closest distance to " O   HOH Z 362 " =    5.690
peak=   -3.681 closest distance to " O   SER A 273 " =    1.206
peak=   -3.680 closest distance to " O   ALA A 161 " =    1.401
peak=   -3.669 closest distance to " O   HOH Z 248 " =    0.833
peak=   -3.662 closest distance to " CA  ALA A 227 " =    2.391
peak=   -3.634 closest distance to " O   HOH Z 121 " =    3.727
peak=   -3.631 closest distance to " O   HOH Z 210 " =    0.852
peak=   -3.627 closest distance to " NH2 ARG A  66 " =    1.766
peak=   -3.626 closest distance to " O   GLY A 196 " =    2.274
peak=   -3.622 closest distance to " C   HIS A 108 " =    1.213
peak=   -3.616 closest distance to " C   GLY A  91 " =    1.249
peak=   -3.606 closest distance to " O   HOH Z 430 " =    1.438
peak=   -3.602 closest distance to " O   HOH Z 281 " =    3.115
peak=   -3.598 closest distance to " CA  ALA A 114 " =    1.017
peak=   -3.592 closest distance to " CA  GLY A 133 " =    2.028
peak=   -3.591 closest distance to " O   HOH Z 227 " =    0.798
peak=   -3.589 closest distance to " CG2 THR A  18 " =    2.803
peak=   -3.583 closest distance to " CB BSER A 164 " =    0.986
peak=   -3.575 closest distance to " O   ARG A 156 " =    0.739
peak=   -3.572 closest distance to " O   ARG A  66 " =    1.164
peak=   -3.569 closest distance to " O   HOH Z  29 " =    1.413
peak=   -3.566 closest distance to " CG  TYR A 169 " =    2.012
peak=   -3.562 closest distance to " O   HOH Z 340 " =    0.808
peak=   -3.549 closest distance to " O   HOH Z 250 " =    1.516
peak=   -3.547 closest distance to " CG  GLU A   2 " =    1.853
peak=   -3.545 closest distance to " OG1 THR A   4 " =    1.231
peak=   -3.545 closest distance to " CD2 TYR A 293 " =    1.950
peak=   -3.540 closest distance to " O   HOH Z 198 " =    1.456
peak=   -3.539 closest distance to " O   HOH Z 126 " =    2.025
peak=   -3.528 closest distance to " O   HOH Z 146 " =    0.974
peak=   -3.525 closest distance to " O   TYR A  15 " =    1.363
peak=   -3.519 closest distance to " CG BARG A 275 " =    0.903
peak=   -3.517 closest distance to " CZ2 TRP A  92 " =    2.435
peak=   -3.514 closest distance to " OD1 ASN A 110 " =    2.109
peak=   -3.508 closest distance to " O   SER A   3 " =    0.910
peak=   -3.487 closest distance to " CD  ARG A 156 " =    2.122
peak=   -3.475 closest distance to " NE2 GLN A 240 " =    2.151
peak=   -3.463 closest distance to " O   ASN A 187 " =    1.334
peak=   -3.460 closest distance to " O   HOH Z 219 " =    3.334
peak=   -3.459 closest distance to " NE1 TRP A  85 " =    1.212
peak=   -3.452 closest distance to " CG  ASN A  60 " =    0.793
peak=   -3.450 closest distance to " O   SER A  62 " =    0.990
peak=   -3.441 closest distance to " O   HOH Z 235 " =    1.337
peak=   -3.441 closest distance to " O   PRO A 198 " =    1.202
peak=   -3.434 closest distance to " O   HOH Z 426 " =    2.053
peak=   -3.430 closest distance to " O   HOH Z  31 " =    2.238
peak=   -3.426 closest distance to " O   VAL A 174 " =    1.979
peak=   -3.426 closest distance to " O   HOH Z 384 " =    1.048
peak=   -3.426 closest distance to " OG ASER A 134 " =    1.265
peak=   -3.425 closest distance to " OG BSER A  99 " =    1.609
peak=   -3.419 closest distance to " O   HOH Z 422 " =    2.211
peak=   -3.416 closest distance to " O   HOH Z  92 " =    1.423
peak=   -3.405 closest distance to " N   PHE A  59 " =    1.119
peak=   -3.403 closest distance to " NH1 ARG A 195 " =    2.626
peak=   -3.399 closest distance to " O   VAL A 197 " =    1.182
peak=   -3.397 closest distance to " CG2 THR A 279 " =    1.257
peak=   -3.385 closest distance to " O   HOH Z 388 " =    1.755
peak=   -3.378 closest distance to " OXT GLY A 302 " =    3.471
peak=   -3.377 closest distance to " O   HOH Z  79 " =    0.795
peak=   -3.374 closest distance to " CE3 TRP A 150 " =    2.288
peak=   -3.372 closest distance to " O   SER A  99 " =    1.486
peak=   -3.372 closest distance to " CB  GLN A 223 " =    1.678
peak=   -3.370 closest distance to " O   HOH Z 117 " =    1.314
peak=   -3.369 closest distance to " CD  GLN A  88 " =    2.494
peak=   -3.364 closest distance to " O   HOH Z 434 " =    5.435
peak=   -3.364 closest distance to " O   GLN A 144 " =    0.839
peak=   -3.363 closest distance to " O   HOH Z 119 " =    1.941
peak=   -3.344 closest distance to " CB  PRO A 163 " =    3.013
peak=   -3.340 closest distance to " CG1 VAL A 257 " =    2.116
peak=   -3.338 closest distance to " CB  ALA A   7 " =    2.278
peak=   -3.334 closest distance to " O   TRP A  85 " =    2.168
peak=   -3.333 closest distance to " OG  SER A  63 " =    1.069
peak=   -3.330 closest distance to " CG  LEU A 282 " =    2.576
peak=   -3.329 closest distance to " O   HOH Z 166 " =    1.243
peak=   -3.328 closest distance to " OG  SER A 206 " =    1.716
peak=   -3.327 closest distance to " CG  ARG A 219 " =    2.261
peak=   -3.323 closest distance to " O   HOH Z 222 " =    2.922
peak=   -3.317 closest distance to " O   HOH Z 138 " =    1.677
peak=   -3.317 closest distance to " O   HOH Z 283 " =    1.483
peak=   -3.312 closest distance to " O   GLY A  23 " =    0.905
peak=   -3.311 closest distance to " OG BSER A  99 " =    1.171
peak=   -3.308 closest distance to " O   HOH Z  37 " =    1.065
peak=   -3.302 closest distance to " O   HOH Z 282 " =    1.181
peak=   -3.300 closest distance to " O   HOH Z 353 " =    1.064
peak=   -3.299 closest distance to " OD1 ASP A 200 " =    1.164
peak=   -3.294 closest distance to " O   HOH Z 267 " =    0.826
peak=   -3.289 closest distance to " CB  ALA A  51 " =    1.759
peak=   -3.289 closest distance to " O   HOH Z  12 " =    3.192
peak=   -3.287 closest distance to " O   SER A 271 " =    1.485
peak=   -3.280 closest distance to " O   ALA A 161 " =    2.468
peak=   -3.280 closest distance to " N   VAL A 125 " =    1.998
peak=   -3.277 closest distance to " O   LYS A 193 " =    1.550
peak=   -3.272 closest distance to " O   PHE A  59 " =    2.374
peak=   -3.268 closest distance to " CE  MET A  93 " =    1.183
peak=   -3.267 closest distance to " O   ALA A  10 " =    1.122
peak=   -3.266 closest distance to " O   SER A  62 " =    1.454
peak=   -3.261 closest distance to " CB  LEU A 167 " =    1.897
peak=   -3.256 closest distance to " CG  GLU A  46 " =    2.533
peak=   -3.244 closest distance to " O   HOH Z  25 " =    2.345
peak=   -3.237 closest distance to " CD  ARG A  14 " =    2.803
peak=   -3.233 closest distance to " O   HOH Z 400 " =    1.054
peak=   -3.230 closest distance to " O   HOH Z  46 " =    0.967
peak=   -3.226 closest distance to " O   HOH Z 350 " =    1.145
peak=   -3.226 closest distance to " O   HOH Z 424 " =    1.050
peak=   -3.224 closest distance to " O   HOH Z 413 " =    1.211
peak=   -3.223 closest distance to " OG BSER A 134 " =    1.547
peak=   -3.219 closest distance to " O   HOH Z 391 " =    1.418
peak=   -3.218 closest distance to " CB  PRO A 163 " =    2.171
peak=   -3.217 closest distance to " O   HOH Z 368 " =    2.364
peak=   -3.217 closest distance to " O   HOH Z 307 " =    1.169
peak=   -3.212 closest distance to " O   HOH Z  11 " =    1.426
peak=   -3.210 closest distance to " O   HOH Z 265 " =    1.526
peak=   -3.209 closest distance to " O   HOH Z 284 " =    1.139
peak=   -3.207 closest distance to " NE  ARG A  24 " =    1.289
peak=   -3.206 closest distance to " O   HOH Z 274 " =    2.558
peak=   -3.201 closest distance to " O   MET A 113 " =    1.170
peak=   -3.198 closest distance to " O   HOH Z 179 " =    1.904
peak=   -3.197 closest distance to " O   LEU A 282 " =    2.352
peak=   -3.192 closest distance to " C   THR A 279 " =    1.008
peak=   -3.184 closest distance to " O   GLN A  11 " =    1.200
peak=   -3.182 closest distance to " OG1 THR A  82 " =    1.645
peak=   -3.182 closest distance to " O   HOH Z 384 " =    1.702
peak=   -3.181 closest distance to " N   ALA A 226 " =    1.943
peak=   -3.177 closest distance to " CD  PRO A 198 " =    1.603
peak=   -3.173 closest distance to " O   HOH Z 416 " =    0.934
peak=   -3.172 closest distance to " O   HOH Z 145 " =    2.325
peak=   -3.150 closest distance to " CD  GLN A  11 " =    1.017
peak=   -3.147 closest distance to " CG2 VAL A 112 " =    2.540
peak=   -3.145 closest distance to " N   SER A  62 " =    0.718
peak=   -3.141 closest distance to " SD  MET A  40 " =    2.710
peak=   -3.139 closest distance to " O   HOH Z  62 " =    1.201
peak=   -3.135 closest distance to " N   GLY A  17 " =    1.467
peak=   -3.134 closest distance to " NZ  LYS A 166 " =    1.377
peak=   -3.127 closest distance to " O   HOH Z 371 " =    2.221
peak=   -3.122 closest distance to " O   HOH Z 192 " =    1.478
peak=   -3.120 closest distance to " CB  ASP A 200 " =    2.716
peak=   -3.119 closest distance to " O   ILE A 120 " =    0.861
peak=   -3.111 closest distance to " O   HOH Z  91 " =    2.272
peak=   -3.111 closest distance to " CD  GLN A  58 " =    3.147
peak=   -3.109 closest distance to " O   THR A  31 " =    1.358
peak=   -3.106 closest distance to " CA  GLY A  17 " =    1.566
peak=   -3.103 closest distance to " O   HOH Z  37 " =    1.426
peak=   -3.098 closest distance to " CA  TYR A  68 " =    2.589
peak=   -3.091 closest distance to " O   HOH Z 313 " =    1.352
peak=   -3.091 closest distance to " O   HOH Z 263 " =    0.789
peak=   -3.089 closest distance to " O   HOH Z 405 " =    0.825
peak=   -3.083 closest distance to " NE1 TRP A 266 " =    2.329
peak=   -3.083 closest distance to " C   THR A 264 " =    1.406
peak=   -3.082 closest distance to " OD1 ASP A 270 " =    1.562
peak=   -3.079 closest distance to " CE  LYS A 166 " =    1.243
peak=   -3.075 closest distance to " O   HOH Z 426 " =    1.819
peak=   -3.075 closest distance to " O   HOH Z 407 " =    3.135
peak=   -3.066 closest distance to " O   HOH Z  60 " =    1.690
peak=   -3.043 closest distance to " O   HOH Z 400 " =    1.348
peak=   -3.038 closest distance to " O   HOH Z  60 " =    1.532
peak=   -3.038 closest distance to " O   HOH Z  78 " =    1.124

================= 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    :  0.5282 0.5214   6.316943e+00   6.308544e+00
   1_bss:  0.5220 0.5157   6.315055e+00   6.303631e+00
   1_xyz:  0.4681 0.4910   6.265437e+00   6.287380e+00
   1_adp:  0.4375 0.4922   6.238393e+00   6.284531e+00
   1_occ:  0.4370 0.4909   6.237199e+00   6.283826e+00
   2_bss:  0.4365 0.4830   6.238348e+00   6.282700e+00
   2_xyz:  0.3851 0.4456   6.153486e+00   6.236752e+00
   2_adp:  0.3658 0.4368   6.129273e+00   6.225749e+00
   2_occ:  0.3657 0.4367   6.128778e+00   6.225256e+00
   3_bss:  0.3628 0.4325   6.126511e+00   6.223897e+00
   3_xyz:  0.3011 0.3754   5.988883e+00   6.128725e+00
   3_adp:  0.2669 0.3541   5.920398e+00   6.097480e+00
   3_occ:  0.2667 0.3537   5.919559e+00   6.096984e+00
   4_bss:  0.2666 0.3521   5.915766e+00   6.093204e+00
   4_xyz:  0.2255 0.3005   5.772744e+00   5.978385e+00
   4_adp:  0.2128 0.2720   5.700001e+00   5.885803e+00
   4_occ:  0.2125 0.2717   5.699451e+00   5.885283e+00
   5_bss:  0.2120 0.2710   5.699592e+00   5.884721e+00
   5_xyz:  0.1662 0.2219   5.490769e+00   5.710945e+00
   5_adp:  0.1493 0.2043   5.395041e+00   5.625239e+00
   5_occ:  0.1490 0.2043   5.394550e+00   5.625541e+00
   5_bss:  0.1491 0.2041   5.395630e+00   5.625201e+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:  0.344   0.000   6.735   9.893   7.847   0.000   0.000   0.000
   1_xyz:  0.344   0.000   6.735   9.893   7.847   0.000   0.000   0.000
   1_adp:  0.344   0.000   6.735   9.893   7.847   0.000   0.000   0.000
   1_occ:  0.344   0.000   6.735   9.893   7.847   0.000   0.000   0.000
   2_bss:  0.377  50.000   3.603   6.254   5.213   0.000   0.000   0.000
   2_xyz:  0.377  50.000   3.603   6.254   5.213   0.000   0.000   0.000
   2_adp:  0.377  50.000   3.603   6.254   5.213   0.000   0.000   0.000
   2_occ:  0.377  50.000   3.603   6.254   5.213   0.000   0.000   0.000
   3_bss:  0.335  51.645   1.126   3.424   2.773   0.000   0.000   0.000
   3_xyz:  0.335  51.645   1.126   3.424   2.773   0.000   0.000   0.000
   3_adp:  0.335  51.645   1.126   3.424   2.773   0.000   0.000   0.000
   3_occ:  0.335  51.645   1.126   3.424   2.773   0.000   0.000   0.000
   4_bss:  0.326  51.645   0.619   2.454   1.922   0.000   0.000   0.000
   4_xyz:  0.326  51.645   0.619   2.454   1.922   0.000   0.000   0.000
   4_adp:  0.326  51.645   0.619   2.454   1.922   0.000   0.000   0.000
   4_occ:  0.326  51.645   0.619   2.454   1.922   0.000   0.000   0.000
   5_bss:  0.327  43.926  -0.485   1.470   0.971   0.000   0.000   0.000
   5_xyz:  0.327  43.926  -0.485   1.470   0.971   0.000   0.000   0.000
   5_adp:  0.327  43.926  -0.485   1.470   0.971   0.000   0.000   0.000
   5_occ:  0.327  43.926  -0.485   1.470   0.971   0.000   0.000   0.000
   5_bss:  0.327  43.929  -1.069   0.715   0.287   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  69.002 0.2765  0.3317    89171.323
   1_bss:  69.219 0.2723  0.4089    87704.357
   1_xyz:  67.434 0.2942  0.4290    79963.256
   1_adp:  63.854 0.3419  0.5750    77917.919
   1_occ:  63.894 0.3412  0.5712    77587.980
   2_bss:  63.241 0.3496  0.5362    76521.725
   2_xyz:  54.217 0.4653  0.7207    60119.391
   2_adp:  51.799 0.4962  0.7877    56524.943
   2_occ:  51.738 0.4970  0.7888    56377.388
   3_bss:  51.448 0.5003  0.7266    55610.049
   3_xyz:  41.665 0.6215  0.8907    39905.058
   3_adp:  39.005 0.6533  0.9015    35684.803
   3_occ:  38.946 0.6540  0.9022    35599.120
   4_bss:  38.724 0.6564  0.8796    35054.218
   4_xyz:  32.150 0.7324  0.9569    24974.593
   4_adp:  27.559 0.7844  0.9927    19805.165
   4_occ:  27.544 0.7846  0.9928    19807.406
   5_bss:  27.516 0.7850  0.9568    19783.372
   5_xyz:  22.031 0.8414  0.9963    13117.992
   5_adp:  19.572 0.8659  1.0001    10895.244
   5_occ:  19.572 0.8660  1.0000    10904.364
   5_bss:  19.566 0.8661  0.9755    10910.448
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2935e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2935e+01
   1_xyz:   2.085  0.017  0.123 18.875  0.009  4.103   2.1178e-01
   1_adp:   2.085  0.017  0.123 18.875  0.009  4.103   2.1178e-01
   1_occ:   2.085  0.017  0.123 18.875  0.009  4.103   2.1178e-01
   2_bss:   2.085  0.017  0.123 18.875  0.009  4.103   2.1178e-01
   2_xyz:   1.447  0.010  0.092 18.212  0.005  4.097   1.3465e-01
   2_adp:   1.447  0.010  0.092 18.212  0.005  4.097   1.3465e-01
   2_occ:   1.447  0.010  0.092 18.212  0.005  4.097   1.3465e-01
   3_bss:   1.447  0.010  0.092 18.212  0.005  4.097   1.3465e-01
   3_xyz:   1.368  0.010  0.091 17.438  0.005  4.101   1.1036e-01
   3_adp:   1.368  0.010  0.091 17.438  0.005  4.101   1.1036e-01
   3_occ:   1.368  0.010  0.091 17.438  0.005  4.101   1.1036e-01
   4_bss:   1.368  0.010  0.091 17.438  0.005  4.101   1.1036e-01
   4_xyz:   1.021  0.007  0.067 16.020  0.004  4.115   6.6639e-02
   4_adp:   1.021  0.007  0.067 16.020  0.004  4.115   6.6639e-02
   4_occ:   1.021  0.007  0.067 16.020  0.004  4.115   6.6639e-02
   5_bss:   1.021  0.007  0.067 16.020  0.004  4.115   6.6639e-02
   5_xyz:   1.216  0.009  0.087 15.911  0.005  4.105   8.4050e-02
   5_adp:   1.216  0.009  0.087 15.911  0.005  4.105   8.4050e-02
   5_occ:   1.216  0.009  0.087 15.911  0.005  4.105   8.4050e-02
   5_bss:   1.216  0.009  0.087 15.911  0.005  4.105   8.4050e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.993   6.8479e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.993   6.8479e+00
   1_xyz:  17.605  0.209  0.604 89.007  0.061  1.900   1.2554e-01
   1_adp:  17.605  0.209  0.604 89.007  0.061  1.900   1.2554e-01
   1_occ:  17.605  0.209  0.604 89.007  0.061  1.900   1.2554e-01
   2_bss:  17.605  0.209  0.604 89.007  0.061  1.900   1.2554e-01
   2_xyz:  10.512  0.094  0.367 83.597  0.052  1.860   9.9782e-02
   2_adp:  10.512  0.094  0.367 83.597  0.052  1.860   9.9782e-02
   2_occ:  10.512  0.094  0.367 83.597  0.052  1.860   9.9782e-02
   3_bss:  10.512  0.094  0.367 83.597  0.052  1.860   9.9782e-02
   3_xyz:   9.953  0.053  0.351 77.237  0.028  2.102   9.3382e-02
   3_adp:   9.953  0.053  0.351 77.237  0.028  2.102   9.3382e-02
   3_occ:   9.953  0.053  0.351 77.237  0.028  2.102   9.3382e-02
   4_bss:   9.953  0.053  0.351 77.237  0.028  2.102   9.3382e-02
   4_xyz:   6.678  0.045  0.231 82.702  0.033  2.195   4.7698e-02
   4_adp:   6.678  0.045  0.231 82.702  0.033  2.195   4.7698e-02
   4_occ:   6.678  0.045  0.231 82.702  0.033  2.195   4.7698e-02
   5_bss:   6.678  0.045  0.231 82.702  0.033  2.195   4.7698e-02
   5_xyz:   7.469  0.054  0.523 82.614  0.043  2.180   6.1283e-02
   5_adp:   7.469  0.054  0.523 82.614  0.043  2.180   6.1283e-02
   5_occ:   7.469  0.054  0.523 82.614  0.043  2.180   6.1283e-02
   5_bss:   7.469  0.054  0.523 82.614  0.043  2.180   6.1283e-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:  99.26   0.00  17.24  86.91   0.00  16.21  99.26   0.00  22.88
   1_occ:  99.26   0.00  17.24  86.91   0.00  16.21  99.26   0.00  22.88
   2_bss:  99.26   0.00  17.24  86.91   0.00  16.21  99.26   0.00  22.88
   2_xyz:  99.26   0.00  17.24  86.91   0.00  16.21  99.26   0.00  22.88
   2_adp: 104.81   0.00  17.67 104.81   0.00  15.94 102.89   0.00  27.04
   2_occ: 104.81   0.00  17.67 104.81   0.00  15.94 102.89   0.00  27.04
   3_bss: 104.81   0.00  17.67 104.81   0.00  15.94 102.89   0.00  27.04
   3_xyz: 104.81   0.00  17.67 104.81   0.00  15.94 102.89   0.00  27.04
   3_adp: 114.24   0.00  19.43 106.31   0.00  15.44 114.24   0.00  41.16
   3_occ: 114.24   0.00  19.43 106.31   0.00  15.44 114.24   0.00  41.16
   4_bss: 114.24   0.00  19.43 106.31   0.00  15.44 114.24   0.00  41.16
   4_xyz: 114.24   0.00  19.43 106.31   0.00  15.44 114.24   0.00  41.16
   4_adp: 113.92   0.00  17.45 101.92   0.00  13.06 113.92   2.73  41.35
   4_occ: 113.92   0.00  17.45 101.92   0.00  13.06 113.92   2.73  41.35
   5_bss: 113.92   0.00  17.45 101.92   0.00  13.06 113.92   2.73  41.35
   5_xyz: 113.92   0.00  17.45 101.92   0.00  13.06 113.92   2.73  41.35
   5_adp: 110.37   0.00  16.80 102.22   0.00  11.69 110.37   0.00  44.58
   5_occ: 110.37   0.00  16.80 102.22   0.00  11.69 110.37   0.00  44.58
   5_bss: 110.37   0.00  16.80 102.23   0.00  11.70 110.37   0.00  44.58
------------------------------------------------------------------------
 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:    1.287    0.032    0.443
   1_adp:    1.287    0.032    0.443
   1_occ:    1.287    0.032    0.443
   2_bss:    1.287    0.032    0.443
   2_xyz:    2.044    0.049    0.640
   2_adp:    2.044    0.049    0.640
   2_occ:    2.044    0.049    0.640
   3_bss:    2.044    0.049    0.640
   3_xyz:    1.917    0.059    0.798
   3_adp:    1.917    0.059    0.798
   3_occ:    1.917    0.059    0.798
   4_bss:    1.917    0.059    0.798
   4_xyz:    2.068    0.050    0.889
   4_adp:    2.068    0.050    0.889
   4_occ:    2.068    0.050    0.889
   5_bss:    2.068    0.050    0.889
   5_xyz:    2.132    0.055    0.997
   5_adp:    2.132    0.055    0.997
   5_occ:    2.132    0.055    0.997
   5_bss:    2.132    0.055    0.997
------------------------------------------------------------------------

CPU time actual refinement: 335.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_99/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_99/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_99/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_99/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_99/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.00 
  Macro-tasks:
    bulk solvent and scale       = 39.94  
    individual site refinement   = 144.66 
    weights calculation          = 32.72  
    collect and process          = 6.23   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 223.67 
  Micro-tasks:
    mask                            = 3.08   
    f_calc                          = 105.01 
    alpha_beta                      = 8.28   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.58 
    fmodel                         = 6.67   
    r_factors                      = 0.24   
    phase_errors                   = 9.43   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 248.71 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.798 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    591 calls, 104.71 s
gradients_fft:          535 calls, 102.20 s

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

# Date 2008-01-16 Time 00:45:20 PST -0800 (1200473120.20 s)
Start R-work = 0.5282, R-free = 0.5214 (no bulk solvent and anisotropic scale)
Final R-work = 0.1653, R-free = 0.2195 (no bulk solvent and anisotropic scale)

Start R-work = 0.5220, R-free = 0.5157
Final R-work = 0.1491, R-free = 0.2041