# Date 2008-01-16 Time 01:27:01 PST -0800 (1200475621.63 s)
#phil __OFF__

Command line arguments: "../414.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 = 6778
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 414

-------------------------------------------------------------------------------
  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: (69.5475, 46.6953, 87.2539, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (69.5475, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.98067
Completeness in resolution range: 0.963078
Completeness with d_max=infinity: 0.960057

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9236
                             d_min =   1.9807

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: (69.5475, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.98067
Completeness in resolution range: 0.963078
Completeness with d_max=infinity: 0.960057

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9240 -  4.2377 [2145/2169]  1927   218  10.2%
  bin  2:  4.2377 -  3.3764 [2045/2064]  1845   200   9.8%
  bin  3:  3.3764 -  2.9534 [2029/2048]  1825   204  10.1%
  bin  4:  2.9534 -  2.6850 [2002/2032]  1797   205  10.2%
  bin  5:  2.6850 -  2.4935 [2005/2024]  1808   197   9.8%
  bin  6:  2.4935 -  2.3471 [1978/2003]  1780   198  10.0%
  bin  7:  2.3471 -  2.2300 [1978/2006]  1782   196   9.9%
  bin  8:  2.2300 -  2.1332 [1975/2011]  1777   198  10.0%
  bin  9:  2.1332 -  2.0513 [1943/1985]  1748   195  10.0%
  bin 10:  2.0513 -  1.9807 [1489/1998]  1341   148   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_414/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:
        1.75 -     2.38: 18
        2.38 -     3.01: 1974
        3.01 -     3.64: 4614
        3.64 -     4.27: 9152
        4.27 -     4.90: 12634
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.745 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.072 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  2.076 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.107 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28387 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_414/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_414/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 = 69.5475 46.69535 87.2539 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: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4366   r_free= 0.4213   ksol= 0.00   Bsol= 0.00   scale= 0.823    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.230984                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7263 0.99   1394  153 0.3614 0.3386      6.5221      6.4624|
|  2:  4.7263 -  3.7713 0.99   1326  152 0.3256 0.3414      6.6221      6.6921|
|  3:  3.7713 -  3.3005 0.99   1311  145 0.3764 0.3465      6.5576      6.5341|
|  4:  3.3005 -  3.0014 0.99   1300  139 0.4221 0.4078      6.4635      6.4182|
|  5:  3.0014 -  2.7878 0.99   1293  144 0.4510 0.4591      6.3141      6.3311|
|  6:  2.7878 -  2.6243 0.99   1294  149 0.4566 0.5257      6.2372      6.2143|
|  7:  2.6243 -  2.4935 0.99   1284  142 0.4747 0.4671      6.2029      6.1589|
|  8:  2.4935 -  2.3854 0.98   1280  137 0.4846 0.4328       6.155      6.1419|
|  9:  2.3854 -  2.2940 0.98   1261  146 0.4950 0.4665      6.0883      6.1014|
| 10:  2.2940 -  2.2151 0.99   1280  141 0.5104 0.4419       6.128      6.0136|
| 11:  2.2151 -  2.1460 0.98   1260  136 0.5097 0.4499       6.038      6.0082|
| 12:  2.1460 -  2.0848 0.97   1249  141 0.5059 0.4598      5.9671      5.9913|
| 13:  2.0848 -  2.0301 1.00   1265  138 0.4883 0.4566      5.8712      5.8023|
| 14:  2.0301 -  1.9807 0.65    833   96 0.5162 0.4923       5.874      5.7394|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9240 -  4.7263  1394   153  0.73  31.18   0.81     0.76      59592.54|
|  2:  4.7263 -  3.7713  1326   152  0.77  28.93   0.91     0.82      75178.84|
|  3:  3.7713 -  3.3005  1311   145  0.71  34.93   0.88     0.79      79274.29|
|  4:  3.3005 -  3.0014  1300   139  0.63  41.51   0.83     0.70      72871.82|
|  5:  3.0014 -  2.7878  1293   144  0.52  50.05   0.78     0.60      66746.01|
|  6:  2.7878 -  2.6243  1294   149  0.49  53.02   0.75     0.55      61451.81|
|  7:  2.6243 -  2.4935  1284   142  0.46  55.04   0.77     0.53      56929.25|
|  8:  2.4935 -  2.3854  1280   137  0.48  53.78   0.75     0.55      49096.72|
|  9:  2.3854 -  2.2940  1261   146  0.51  51.21   0.75     0.59      42015.08|
| 10:  2.2940 -  2.2151  1280   141  0.53  49.63   0.76     0.61      35886.81|
| 11:  2.2151 -  2.1460  1260   136  0.52  50.91   0.75     0.61      34215.95|
| 12:  2.1460 -  2.0848  1249   141  0.49  53.31   0.79     0.59      33121.49|
| 13:  2.0848 -  2.0301  1265   138  0.46  55.19   0.77     0.55      29771.61|
| 14:  2.0301 -  1.9807   833    96  0.48  53.53   0.74     0.51      23811.93|
|alpha:            min =        0.51 max =            0.82 mean =         0.63|
|beta:             min =    23811.93 max =        79274.29 mean =     52415.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        46.95|
|phase err.(test): min =        0.00 max =           89.92 mean =        47.09|
|-----------------------------------------------------------------------------|

============================== 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 = 7.294579              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.035   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.628229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.592   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      692 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2653 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3920 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5100 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6608 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7719 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.621 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.812 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    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 = 11.807)------------------------------------------|
|    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: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4459   r_free= 0.4276   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.236453                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4284   r_free= 0.4110   ksol= 0.35   Bsol= 20.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.43,8.28,9.57,0.00,0.00,0.00); trace/3= 8.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.223426                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.652638              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.787   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.592377              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.888   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4284      final r-factor (work) = 0.3188          |
| start r-factor (free) = 0.4110      final r-factor (free) = 0.3363          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.3861 = 6.65 * 0.50 * 6.2426 + 1.00 * 53.6213                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3142 = 6.65 * 0.50 * 6.0718 + 1.00 * 0.1175                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3188      final r-factor (work) = 0.2564          |
| start r-factor (free) = 0.3363      final r-factor (free) = 0.2924          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6115 = 0.59 * 1.00 * 6.0718 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4970 = 0.59 * 1.00 * 5.8840 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    52.72   10.58    None  None   None       |
|    all(noH): 2823   0      0.00    52.72   10.58    None  None   None       |
|    Sol.    : 438    0      0.00    52.72   26.67    None  None   None       |
|    Mac.    : 2385   0      0.00    46.35   7.63     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.272: 1094   |   5:    26.361 -  31.634:  117        |
|      1:     5.272 -  10.545:  777   |   6:    31.634 -  36.906:   95        |
|      2:    10.545 -  15.817:  360   |   7:    36.906 -  42.178:   64        |
|      3:    15.817 -  21.089:  168   |   8:    42.178 -  47.451:   27        |
|      4:    21.089 -  26.361:  116   |   9:    47.451 -  52.723:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2564 r_free = 0.2924             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2560 r_free = 0.2927             target_work(ml) = 5.825         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2560   r_free= 0.2927   ksol= 0.35   Bsol= 20.00   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.43,8.28,9.57,0.00,0.00,0.00); trace/3= 8.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.825013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2508   r_free= 0.2874   ksol= 0.31   Bsol= 20.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.88,4.16,5.98,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.824740                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.517504              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.114   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.337270              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.561  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2508      final r-factor (work) = 0.1647          |
| start r-factor (free) = 0.2874      final r-factor (free) = 0.2030          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4929 = 3.52 * 0.50 * 5.8995 + 1.00 * 0.1172                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9779 = 3.52 * 0.50 * 5.6370 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2030      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9127 = 0.34 * 1.00 * 5.6370 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8300 = 0.34 * 1.00 * 5.3952 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    56.43   10.98    None  None   None       |
|    all(noH): 2823   0      0.00    56.43   10.98    None  None   None       |
|    Sol.    : 438    0      0.63    56.43   30.81    None  None   None       |
|    Mac.    : 2385   0      0.00    54.13   7.34     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 -   5.643: 1274   |   5:    28.216 -  33.859:  106        |
|      1:     5.643 -  11.287:  724   |   6:    33.859 -  39.503:  108        |
|      2:    11.287 -  16.930:  266   |   7:    39.503 -  45.146:   83        |
|      3:    16.930 -  22.573:  127   |   8:    45.146 -  50.789:   40        |
|      4:    22.573 -  28.216:   86   |   9:    50.789 -  56.432:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1487 r_free = 0.1910             target_work(ml) = 5.364         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1486 r_free = 0.1911             target_work(ml) = 5.364         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1486   r_free= 0.1911   ksol= 0.31   Bsol= 20.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.88,4.16,5.98,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.363603                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1476   r_free= 0.1908   ksol= 0.33   Bsol= 41.63   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,3.32,4.86,0.00,0.00,0.00); trace/3= 3.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.362012                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.871443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.384  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.609628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.961  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1476      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8187 = 2.87 * 0.50 * 5.4015 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6404 = 2.87 * 0.50 * 5.2763 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7795 = 2.61 * 1.00 * 5.2763 + 1.00 * 0.0103                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.5362 = 2.61 * 1.00 * 5.1817 + 1.00 * 0.0138                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.48   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    72.48   11.72    None  None   None       |
|    Sol.    : 438    0      0.38    68.14   34.99    None  None   None       |
|    Mac.    : 2385   0      0.00    72.48   7.45     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 -   7.248: 1590   |   5:    36.242 -  43.490:   96        |
|      1:     7.248 -  14.497:  587   |   6:    43.490 -  50.739:   78        |
|      2:    14.497 -  21.745:  187   |   7:    50.739 -  57.987:   61        |
|      3:    21.745 -  28.994:  100   |   8:    57.987 -  65.236:   22        |
|      4:    28.994 -  36.242:   91   |   9:    65.236 -  72.484:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1617             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1617             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1617   ksol= 0.33   Bsol= 41.63   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,3.32,4.86,0.00,0.00,0.00); trace/3= 3.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.174646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1617   ksol= 0.33   Bsol= 41.63   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,3.32,4.86,0.00,0.00,0.00); trace/3= 3.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.174380                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.968378              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.651  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.204253              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.593  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1642 = 1.97 * 0.50 * 5.1810 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1413 = 1.97 * 0.50 * 5.1654 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3997 = 2.20 * 1.00 * 5.1654 + 1.00 * 0.0138                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4056 = 2.20 * 1.00 * 5.1515 + 1.00 * 0.0503                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.02   11.73    None  None   None       |
|    all(noH): 2823   0      0.00    83.02   11.73    None  None   None       |
|    Sol.    : 438    0      0.45    75.74   35.02    None  None   None       |
|    Mac.    : 2385   0      0.00    83.02   7.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.302: 1754   |   5:    41.508 -  49.809:   92        |
|      1:     8.302 -  16.603:  503   |   6:    49.809 -  58.111:   59        |
|      2:    16.603 -  24.905:  153   |   7:    58.111 -  66.412:   30        |
|      3:    24.905 -  33.206:  112   |   8:    66.412 -  74.714:   17        |
|      4:    33.206 -  41.508:  100   |   9:    74.714 -  83.015:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1583             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1583             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1583   ksol= 0.33   Bsol= 41.63   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,3.32,4.86,0.00,0.00,0.00); trace/3= 3.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152402                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1583   ksol= 0.33   Bsol= 41.63   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,3.35,4.89,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.152420                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.633961              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.927  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.589908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.940   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8421 = 2.63 * 0.50 * 5.1516 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8353 = 2.63 * 0.50 * 5.1398 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1930 = 1.59 * 1.00 * 5.1398 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2178 = 1.59 * 1.00 * 5.1390 + 1.00 * 0.0473                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.51   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    83.51   11.65    None  None   None       |
|    Sol.    : 438    0      0.36    75.94   34.90    None  None   None       |
|    Mac.    : 2385   0      0.00    83.51   7.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.351: 1768   |   5:    41.757 -  50.109:   89        |
|      1:     8.351 -  16.703:  492   |   6:    50.109 -  58.460:   59        |
|      2:    16.703 -  25.054:  152   |   7:    58.460 -  66.811:   28        |
|      3:    25.054 -  33.406:  115   |   8:    66.811 -  75.163:   17        |
|      4:    33.406 -  41.757:   99   |   9:    75.163 -  83.514:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1574             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1575             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1575   ksol= 0.33   Bsol= 41.63   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.90,3.35,4.89,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7263 0.99   1394  153 0.0968 0.1258      5.3714      5.5136|
|  2:  4.7263 -  3.7713 0.99   1326  152 0.0821 0.1076      5.4115      5.6075|
|  3:  3.7713 -  3.3005 0.99   1311  145 0.1013 0.1502      5.4479      5.8509|
|  4:  3.3005 -  3.0014 0.99   1300  139 0.1162 0.1616      5.4321      5.5943|
|  5:  3.0014 -  2.7878 0.99   1293  144 0.1274 0.1693      5.3146      5.5519|
|  6:  2.7878 -  2.6243 0.99   1294  149 0.1191 0.1996      5.2035      5.5208|
|  7:  2.6243 -  2.4935 0.99   1284  142 0.1235 0.1587      5.1658        5.33|
|  8:  2.4935 -  2.3854 0.98   1280  137 0.1151 0.1678      5.0777       5.337|
|  9:  2.3854 -  2.2940 0.98   1261  146 0.1167 0.1923      5.0412      5.3473|
| 10:  2.2940 -  2.2151 0.99   1280  141 0.1093 0.1586      4.9539      5.1665|
| 11:  2.2151 -  2.1460 0.98   1260  136 0.1116 0.1791      4.9469      5.2741|
| 12:  2.1460 -  2.0848 0.97   1249  141 0.1124 0.1689      4.8874      5.2332|
| 13:  2.0848 -  2.0301 1.00   1265  138 0.1101 0.1658      4.7916      5.0211|
| 14:  2.0301 -  1.9807 0.65    833   96 0.1003 0.1814      4.6656      4.9502|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9240 -  4.7263  1394   153  0.94   9.27   0.98     0.95       7219.62|
|  2:  4.7263 -  3.7713  1326   152  0.96   7.71   1.02     1.01       8854.21|
|  3:  3.7713 -  3.3005  1311   145  0.94  10.96   1.03     1.02      10053.07|
|  4:  3.3005 -  3.0014  1300   139  0.92  13.30   1.01     1.00      10229.40|
|  5:  3.0014 -  2.7878  1293   144  0.90  15.79   1.00     0.97       8350.83|
|  6:  2.7878 -  2.6243  1294   149  0.90  16.24   0.98     0.96       7196.75|
|  7:  2.6243 -  2.4935  1284   142  0.90  15.66   0.98     0.94       6219.15|
|  8:  2.4935 -  2.3854  1280   137  0.91  15.14   0.99     0.97       5426.84|
|  9:  2.3854 -  2.2940  1261   146  0.91  15.41   1.01     0.98       5211.85|
| 10:  2.2940 -  2.2151  1280   141  0.90  16.23   1.00     0.96       4467.76|
| 11:  2.2151 -  2.1460  1260   136  0.90  16.52   1.00     0.97       4621.70|
| 12:  2.1460 -  2.0848  1249   141  0.91  15.84   1.01     1.00       4081.22|
| 13:  2.0848 -  2.0301  1265   138  0.90  16.00   1.00     0.97       3411.08|
| 14:  2.0301 -  1.9807   833    96  0.92  14.41   0.98     0.95       2583.35|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2583.35 max =        10229.40 mean =      6409.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.11|
|phase err.(test): min =        0.00 max =           89.98 mean =        13.65|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1575   ksol= 0.32   Bsol= 47.10   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,-0.37,1.17,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1575   ksol= 0.32   Bsol= 47.10   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,-0.37,1.17,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138022                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7263 0.99   1394  153 0.0966 0.1261      5.3699      5.5124|
|  2:  4.7263 -  3.7713 0.99   1326  152 0.0824 0.1079       5.413      5.6102|
|  3:  3.7713 -  3.3005 0.99   1311  145 0.1014 0.1503       5.449      5.8511|
|  4:  3.3005 -  3.0014 0.99   1300  139 0.1161 0.1616      5.4316      5.5934|
|  5:  3.0014 -  2.7878 0.99   1293  144 0.1272 0.1690      5.3135      5.5509|
|  6:  2.7878 -  2.6243 0.99   1294  149 0.1190 0.1993      5.2026      5.5196|
|  7:  2.6243 -  2.4935 0.99   1284  142 0.1235 0.1587       5.165      5.3293|
|  8:  2.4935 -  2.3854 0.98   1280  137 0.1150 0.1678      5.0773      5.3369|
|  9:  2.3854 -  2.2940 0.98   1261  146 0.1167 0.1924      5.0411      5.3475|
| 10:  2.2940 -  2.2151 0.99   1280  141 0.1093 0.1585      4.9539      5.1663|
| 11:  2.2151 -  2.1460 0.98   1260  136 0.1116 0.1790      4.9467      5.2736|
| 12:  2.1460 -  2.0848 0.97   1249  141 0.1124 0.1689      4.8872      5.2332|
| 13:  2.0848 -  2.0301 1.00   1265  138 0.1101 0.1658      4.7914      5.0209|
| 14:  2.0301 -  1.9807 0.65    833   96 0.1003 0.1813      4.6652      4.9493|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9240 -  4.7263  1394   153  0.94   9.26   0.98     0.95       7198.04|
|  2:  4.7263 -  3.7713  1326   152  0.95   7.72   1.02     1.01       8868.77|
|  3:  3.7713 -  3.3005  1311   145  0.94  10.98   1.03     1.02      10079.50|
|  4:  3.3005 -  3.0014  1300   139  0.92  13.29   1.02     1.00      10218.33|
|  5:  3.0014 -  2.7878  1293   144  0.90  15.78   1.01     0.98       8335.30|
|  6:  2.7878 -  2.6243  1294   149  0.90  16.23   0.99     0.96       7182.88|
|  7:  2.6243 -  2.4935  1284   142  0.90  15.64   0.99     0.95       6208.08|
|  8:  2.4935 -  2.3854  1280   137  0.91  15.13   1.00     0.98       5422.38|
|  9:  2.3854 -  2.2940  1261   146  0.91  15.41   1.01     0.98       5210.24|
| 10:  2.2940 -  2.2151  1280   141  0.90  16.23   1.00     0.96       4467.03|
| 11:  2.2151 -  2.1460  1260   136  0.90  16.52   1.01     0.97       4619.44|
| 12:  2.1460 -  2.0848  1249   141  0.91  15.83   1.02     1.01       4079.43|
| 13:  2.0848 -  2.0301  1265   138  0.90  16.00   1.00     0.98       3408.49|
| 14:  2.0301 -  1.9807   833    96  0.92  14.40   0.99     0.95       2579.77|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2579.77 max =        10218.33 mean =      6406.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.11|
|phase err.(test): min =        0.00 max =           90.00 mean =        13.64|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.81    87.32   15.45    None  None   None       |
|    all(noH): 2823   0      3.81    87.32   15.45    None  None   None       |
|    Sol.    : 438    0      4.17    79.75   38.71    None  None   None       |
|    Mac.    : 2385   0      3.81    87.32   11.18    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:     3.806 -  12.158: 1768   |   5:    45.564 -  53.915:   89        |
|      1:    12.158 -  20.509:  492   |   6:    53.915 -  62.266:   59        |
|      2:    20.509 -  28.861:  152   |   7:    62.266 -  70.618:   28        |
|      3:    28.861 -  37.212:  115   |   8:    70.618 -  78.969:   17        |
|      4:    37.212 -  45.564:   99   |   9:    78.969 -  87.321:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.246 - 4.087
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 295
   mapped sites are within: 0.711 - 4.087

peak=   11.488 closest distance to " CB  VAL A 230 " =    1.462
peak=    8.832 closest distance to " CG2 VAL A 296 " =    1.283
peak=    6.542 closest distance to " CG  LEU A   5 " =    1.170
peak=    5.968 closest distance to " NE2 GLN A  11 " =    1.204
peak=    5.802 closest distance to " CG  PRO A  54 " =    1.294
peak=    5.739 closest distance to " CG  LEU A 228 " =    1.165
peak=    5.710 closest distance to " O   HOH Z 142 " =    1.866
peak=    5.607 closest distance to " NH2 ARG A  56 " =    2.140
peak=    5.193 closest distance to " CB  GLN A 183 " =    1.271
peak=    5.102 closest distance to " CD2 LEU A   5 " =    1.120
peak=    4.952 closest distance to " CB  ARG A 275 " =    0.965
peak=    4.908 closest distance to " CB  GLN A 223 " =    1.490
peak=    4.709 closest distance to " CB  PRO A  54 " =    0.945
peak=    4.614 closest distance to " ND2 ASN A 187 " =    1.549
peak=    4.523 closest distance to " O   HOH Z 232 " =    2.385
peak=    4.510 closest distance to " O   HOH Z 427 " =    3.017
peak=    4.474 closest distance to " O   HOH Z   9 " =    1.204
peak=    4.468 closest distance to " CB  ARG A  79 " =    1.464
peak=    4.464 closest distance to " OG  SER A  97 " =    2.938
peak=    4.448 closest distance to " O   HOH Z 346 " =    1.580
peak=    4.415 closest distance to " CG  PRO A 213 " =    1.177
peak=    4.411 closest distance to " O   SER A  87 " =    2.254
peak=    4.385 closest distance to " O   HOH Z 265 " =    2.248
peak=    4.376 closest distance to " C   PRO A 198 " =    1.454
peak=    4.367 closest distance to " O   HOH Z 369 " =    2.211
peak=    4.353 closest distance to " O   HOH Z 209 " =    2.285
peak=    4.293 closest distance to " CB  VAL A 296 " =    1.012
peak=    4.287 closest distance to " O   HOH Z 193 " =    1.663
peak=    4.265 closest distance to " O   HOH Z  61 " =    1.663
peak=    4.233 closest distance to " O   HOH Z 272 " =    1.792
peak=    4.231 closest distance to " O   HOH Z 126 " =    1.914
peak=    4.230 closest distance to " CB  VAL A 230 " =    1.136
peak=    4.229 closest distance to " CB  VAL A 265 " =    1.315
peak=    4.221 closest distance to " CB  TRP A 266 " =    1.048
peak=    4.207 closest distance to " CB  SER A  63 " =    1.243
peak=    4.194 closest distance to " O   HOH Z 158 " =    3.192
peak=    4.181 closest distance to " CZ  PHE A 218 " =    1.152
peak=    4.149 closest distance to " CB  ASN A 148 " =    1.374
peak=    4.147 closest distance to " O   HOH Z 303 " =    2.153
peak=    4.139 closest distance to " O   HOH Z  43 " =    1.991
peak=    4.136 closest distance to " O   HOH Z 402 " =    1.364
peak=    4.088 closest distance to " O   HOH Z  78 " =    1.642
peak=    4.079 closest distance to " O   HOH Z 313 " =    1.855
peak=    4.071 closest distance to " CB  ALA A   9 " =    1.611
peak=    4.068 closest distance to " CB  ARG A 190 " =    1.631
peak=    4.060 closest distance to " O   HOH Z 236 " =    2.158
peak=    4.055 closest distance to " OG ASER A 258 " =    3.051
peak=    4.048 closest distance to " CG  PRO A 198 " =    1.187
peak=    4.035 closest distance to " O   HOH Z 411 " =    3.879
peak=    4.031 closest distance to " CB  GLU A 152 " =    1.222
peak=    3.994 closest distance to " O   HOH Z 423 " =    1.849
peak=    3.969 closest distance to " CG  PRO A 243 " =    1.083
peak=    3.956 closest distance to " CB  VAL A 202 " =    1.636
peak=    3.952 closest distance to " O   HOH Z 298 " =    1.759
peak=    3.949 closest distance to " O   HOH Z 234 " =    3.611
peak=    3.933 closest distance to " O   HOH Z 371 " =    2.891
peak=    3.929 closest distance to " CA  TYR A  30 " =    0.987
peak=    3.927 closest distance to " CB  GLU A 277 " =    3.599
peak=    3.922 closest distance to " CG  MET A 185 " =    1.230
peak=    3.897 closest distance to " CD2 TRP A 179 " =    1.371
peak=    3.880 closest distance to " CB AVAL A  41 " =    1.321
peak=    3.872 closest distance to " O   HOH Z 126 " =    1.894
peak=    3.871 closest distance to " O   HOH Z   9 " =    1.972
peak=    3.861 closest distance to " CB  SER A  26 " =    1.728
peak=    3.849 closest distance to " CB  ASN A  39 " =    0.930
peak=    3.843 closest distance to " O   HOH Z 368 " =    2.141
peak=    3.842 closest distance to " CG  ARG A  66 " =    2.732
peak=    3.822 closest distance to " O   HOH Z 214 " =    2.216
peak=    3.819 closest distance to " CB  ASN A 110 " =    1.081
peak=    3.816 closest distance to " O   HOH Z  59 " =    1.811
peak=    3.815 closest distance to " O   HOH Z 261 " =    1.802
peak=    3.808 closest distance to " CG  LEU A 167 " =    1.238
peak=    3.800 closest distance to " O   HOH Z 425 " =    1.366
peak=    3.799 closest distance to " CA  PHE A 283 " =    1.262
peak=    3.794 closest distance to " O   HOH Z 126 " =    1.617
peak=    3.792 closest distance to " CB  ARG A  79 " =    0.905
peak=    3.792 closest distance to " CB  ASN A 142 " =    1.102
peak=    3.782 closest distance to " OG BSER A 164 " =    2.131
peak=    3.774 closest distance to " CG1BVAL A  72 " =    1.569
peak=    3.766 closest distance to " CB  ASP A 140 " =    1.041
peak=    3.764 closest distance to " OD1 ASN A  69 " =    2.599
peak=    3.760 closest distance to " O   HOH Z 353 " =    2.539
peak=    3.760 closest distance to " O   HOH Z 126 " =    1.524
peak=    3.750 closest distance to " O   HOH Z 251 " =    1.494
peak=    3.736 closest distance to " N   ASN A  39 " =    1.185
peak=    3.730 closest distance to " O   HOH Z 248 " =    1.346
peak=    3.704 closest distance to " O   HOH Z 299 " =    4.087
peak=    3.703 closest distance to " O   HOH Z  10 " =    1.797
peak=    3.700 closest distance to " O   HOH Z  85 " =    1.300
peak=    3.700 closest distance to " NZ  LYS A 117 " =    3.109
peak=    3.700 closest distance to " O   HOH Z 203 " =    1.573
peak=    3.698 closest distance to " O   HOH Z 403 " =    1.610
peak=    3.692 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.690 closest distance to " O   HOH Z 425 " =    2.123
peak=    3.664 closest distance to " CA  ASN A 215 " =    1.067
peak=    3.662 closest distance to " CB  GLU A 128 " =    1.007
peak=    3.653 closest distance to " O  BHOH Z 338 " =    2.350
peak=    3.650 closest distance to " O   HOH Z 258 " =    2.269
peak=    3.647 closest distance to " O   HOH Z 337 " =    3.452
peak=    3.646 closest distance to " O   HOH Z  92 " =    2.409
peak=    3.639 closest distance to " O   HOH Z 180 " =    2.121
peak=    3.637 closest distance to " CB  THR A  31 " =    1.580
peak=    3.634 closest distance to " CB  ALA A 248 " =    1.400
peak=    3.626 closest distance to " CD2 LEU A 228 " =    1.192
peak=    3.620 closest distance to " O   HOH Z 250 " =    1.332
peak=    3.618 closest distance to " O   HOH Z  44 " =    1.688
peak=    3.616 closest distance to " O   HOH Z 422 " =    2.601
peak=    3.604 closest distance to " CB  TRP A 179 " =    1.383
peak=    3.604 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.603 closest distance to " O   HOH Z 128 " =    2.131
peak=    3.602 closest distance to " CG1 ILE A  49 " =    1.453
peak=    3.600 closest distance to " O   HOH Z  80 " =    1.603
peak=    3.583 closest distance to " CD  LYS A 166 " =    1.320
peak=    3.582 closest distance to " N   PHE A 130 " =    1.267
peak=    3.580 closest distance to " O   HOH Z  97 " =    1.988
peak=    3.580 closest distance to " O   HOH Z 261 " =    1.823
peak=    3.580 closest distance to " CD  ARG A 269 " =    1.040
peak=    3.578 closest distance to " O   HOH Z 280 " =    3.001
peak=    3.573 closest distance to " O   HOH Z 193 " =    1.902
peak=    3.570 closest distance to " O   HOH Z 290 " =    0.998
peak=    3.563 closest distance to " CD1 ILE A  33 " =    1.699
peak=    3.558 closest distance to " CG2 VAL A 257 " =    0.808
peak=    3.557 closest distance to " CB  GLN A  88 " =    1.188
peak=    3.544 closest distance to " CB  ASN A 187 " =    1.184
peak=    3.539 closest distance to " O   HOH Z 392 " =    2.991
peak=    3.537 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.530 closest distance to " O   HOH Z  68 " =    2.177
peak=    3.529 closest distance to " CG2 ILE A 120 " =    1.220
peak=    3.528 closest distance to " CG2 ILE A  20 " =    1.471
peak=    3.516 closest distance to " CA  ALA A 233 " =    1.193
peak=    3.512 closest distance to " CA  ARG A  36 " =    1.039
peak=    3.507 closest distance to " O   HOH Z  40 " =    1.405
peak=    3.501 closest distance to " NZ  LYS A  48 " =    1.237
peak=    3.498 closest distance to " O   HOH Z  97 " =    2.448
peak=    3.496 closest distance to " O   HOH Z 128 " =    2.114
peak=    3.489 closest distance to " CB  SER A   3 " =    1.241
peak=    3.488 closest distance to " O   HOH Z 329 " =    4.051
peak=    3.487 closest distance to " CB  THR A 157 " =    1.164
peak=    3.475 closest distance to " CE1 TYR A 186 " =    1.294
peak=    3.474 closest distance to " ND2 ASN A 249 " =    0.877
peak=    3.471 closest distance to " CA  ALA A  51 " =    0.947
peak=    3.465 closest distance to " CB  ARG A 139 " =    0.903
peak=    3.460 closest distance to " O   HOH Z 109 " =    2.538
peak=    3.455 closest distance to " N   ASP A 162 " =    1.241
peak=    3.455 closest distance to " CA  ARG A 195 " =    1.167
peak=    3.452 closest distance to " NE2 GLN A  77 " =    3.185
peak=    3.449 closest distance to " O   HOH Z 366 " =    2.926
peak=    3.447 closest distance to " O   HOH Z 273 " =    2.773
peak=    3.441 closest distance to " O   HOH Z   1 " =    1.806
peak=    3.439 closest distance to " O   HOH Z 437 " =    1.662
peak=    3.438 closest distance to " O   HOH Z 145 " =    3.804
peak=    3.433 closest distance to " O   HOH Z  21 " =    1.767
peak=    3.433 closest distance to " CB  ASP A 124 " =    0.744
peak=    3.432 closest distance to " O   ASP A 124 " =    0.952
peak=    3.427 closest distance to " O   HOH Z 285 " =    2.644
peak=    3.424 closest distance to " O   HOH Z 145 " =    2.166
peak=    3.423 closest distance to " CB  GLU A  46 " =    1.016
peak=    3.423 closest distance to " CA  ASP A 162 " =    1.041
peak=    3.421 closest distance to " OE1 GLU A   2 " =    1.891
peak=    3.405 closest distance to " CB  LYS A 117 " =    1.192
peak=    3.405 closest distance to " O   HOH Z 227 " =    2.153
peak=    3.405 closest distance to " O   HOH Z 245 " =    1.345
peak=    3.401 closest distance to " O   HOH Z 389 " =    1.733
peak=    3.397 closest distance to " CD2 LEU A 297 " =    0.980
peak=    3.396 closest distance to " O   HOH Z 128 " =    2.076
peak=    3.394 closest distance to " O   HOH Z   3 " =    1.896
peak=    3.385 closest distance to " O   HOH Z 172 " =    3.522
peak=    3.384 closest distance to " O   HOH Z 419 " =    1.950
peak=    3.382 closest distance to " O   HOH Z 368 " =    3.583
peak=    3.372 closest distance to " CA  ALA A 158 " =    1.312
peak=    3.371 closest distance to " CB  ASN A 215 " =    1.156
peak=    3.367 closest distance to " CG  GLN A  88 " =    1.042
peak=    3.363 closest distance to " O   HOH Z 233 " =    1.898
peak=    3.361 closest distance to " CB  SER A 273 " =    0.849
peak=    3.360 closest distance to " CD1 LEU A 261 " =    1.215
peak=    3.355 closest distance to " O   HOH Z 327 " =    1.438
peak=    3.353 closest distance to " O   HOH Z 417 " =    3.321
peak=    3.348 closest distance to " O   HOH Z 325 " =    2.214
peak=    3.347 closest distance to " O   HOH Z 133 " =    2.496
peak=    3.345 closest distance to " CG1 VAL A 153 " =    0.951
peak=    3.342 closest distance to " CB  GLN A  89 " =    1.336
peak=    3.342 closest distance to " O   ALA A   1 " =    1.706
peak=    3.342 closest distance to " CB  ALA A 291 " =    1.349
peak=    3.341 closest distance to " O   HOH Z 148 " =    3.435
peak=    3.335 closest distance to " CB  SER A 212 " =    1.213
peak=    3.334 closest distance to " CB  LYS A 290 " =    0.972
peak=    3.331 closest distance to " NH2BARG A 145 " =    2.068
peak=    3.331 closest distance to " CG2AVAL A 121 " =    2.439
peak=    3.328 closest distance to " C   PHE A  59 " =    0.938
peak=    3.326 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.325 closest distance to " CH2 TRP A 266 " =    1.089
peak=    3.323 closest distance to " O   LYS A 290 " =    2.415
peak=    3.321 closest distance to " CD BLYS A 290 " =    1.137
peak=    3.321 closest distance to " CA  ASN A 127 " =    1.031
peak=    3.320 closest distance to " O   HOH Z  30 " =    1.413
peak=    3.320 closest distance to " O   HOH Z 130 " =    2.099
peak=    3.317 closest distance to " O   HOH Z  88 " =    2.743
peak=    3.315 closest distance to " CA  GLY A 267 " =    0.834
peak=    3.314 closest distance to " CB  THR A  52 " =    0.897
peak=    3.314 closest distance to " CG AARG A 275 " =    1.161
peak=    3.312 closest distance to " O   HOH Z 380 " =    1.836
peak=    3.311 closest distance to " O   HOH Z 282 " =    1.959
peak=    3.309 closest distance to " CD1 LEU A  96 " =    0.725
peak=    3.304 closest distance to " O   HOH Z 359 " =    1.330
peak=    3.304 closest distance to " CB  VAL A 268 " =    0.845
peak=    3.294 closest distance to " CA  ALA A  21 " =    1.102
peak=    3.294 closest distance to " CB  PRO A  90 " =    1.164
peak=    3.292 closest distance to " CA  SER A 146 " =    1.760
peak=    3.289 closest distance to " O   HOH Z 407 " =    2.425
peak=    3.287 closest distance to " O   HOH Z 403 " =    1.447
peak=    3.276 closest distance to " CA  THR A 264 " =    0.796
peak=    3.276 closest distance to " CA  LYS A 290 " =    1.203
peak=    3.275 closest distance to " CD  ARG A 195 " =    3.485
peak=    3.270 closest distance to " CB  HIS A 108 " =    0.836
peak=    3.268 closest distance to " CB  ILE A  20 " =    1.515
peak=    3.268 closest distance to " CD1 ILE A 106 " =    0.987
peak=    3.264 closest distance to " O   HOH Z 336 " =    1.722
peak=    3.264 closest distance to " CG  LYS A  76 " =    1.673
peak=    3.263 closest distance to " NH1AARG A 145 " =    1.132
peak=    3.262 closest distance to " O   HOH Z 303 " =    2.904
peak=    3.259 closest distance to " O   HOH Z 305 " =    3.569
peak=    3.256 closest distance to " CD1 ILE A 263 " =    1.305
peak=    3.252 closest distance to " CB  TRP A 150 " =    1.381
peak=    3.249 closest distance to " CB  PHE A 204 " =    0.972
peak=    3.248 closest distance to " O   HOH Z 357 " =    1.940
peak=    3.247 closest distance to " C   ILE A 106 " =    1.900
peak=    3.244 closest distance to " CG  LYS A 119 " =    1.081
peak=    3.244 closest distance to " N   SER A 135 " =    1.299
peak=    3.242 closest distance to " O   HOH Z 302 " =    1.952
peak=    3.240 closest distance to " CG2 VAL A 197 " =    1.067
peak=    3.237 closest distance to " O   HOH Z  61 " =    1.522
peak=    3.236 closest distance to " O   HOH Z 421 " =    1.923
peak=    3.236 closest distance to " CD1 LEU A 228 " =    1.973
peak=    3.235 closest distance to " O   HOH Z  80 " =    2.298
peak=    3.234 closest distance to " OE2 GLU A  53 " =    1.988
peak=    3.230 closest distance to " CB  LEU A  83 " =    0.720
peak=    3.227 closest distance to " CB  SER A 216 " =    0.791
peak=    3.225 closest distance to " CG2 THR A 221 " =    1.219
peak=    3.216 closest distance to " CB  GLN A 278 " =    0.949
peak=    3.214 closest distance to " O   ASN A  74 " =    1.505
peak=    3.213 closest distance to " CA  SER A  87 " =    1.010
peak=    3.212 closest distance to " CA  TYR A 116 " =    1.336
peak=    3.211 closest distance to " O   GLN A 278 " =    1.298
peak=    3.211 closest distance to " O   HOH Z 426 " =    1.560
peak=    3.210 closest distance to " O   HOH Z 291 " =    1.489
peak=    3.208 closest distance to " CG  MET A 185 " =    1.043
peak=    3.207 closest distance to " O   HOH Z   1 " =    1.654
peak=    3.205 closest distance to " O   HOH Z 345 " =    3.208
peak=    3.204 closest distance to " CG  GLN A  77 " =    2.367
peak=    3.202 closest distance to " CG1 ILE A  33 " =    1.242
peak=    3.193 closest distance to " O   HOH Z  88 " =    3.627
peak=    3.190 closest distance to " O   HOH Z 344 " =    2.905
peak=    3.190 closest distance to " CA  MET A 105 " =    0.990
peak=    3.182 closest distance to " CG2 THR A 294 " =    1.581
peak=    3.181 closest distance to " CB  GLN A 205 " =    1.155
peak=    3.181 closest distance to " CD  LYS A 119 " =    1.526
peak=    3.178 closest distance to " CA  ALA A 248 " =    1.274
peak=    3.172 closest distance to " CB  ALA A 114 " =    1.525
peak=    3.171 closest distance to " O   HOH Z 406 " =    1.549
peak=    3.169 closest distance to " CG BARG A 102 " =    1.813
peak=    3.169 closest distance to " CG  LYS A  76 " =    0.998
peak=    3.161 closest distance to " O   HOH Z 409 " =    3.235
peak=    3.159 closest distance to " O   HOH Z 361 " =    3.533
peak=    3.157 closest distance to " CA  TYR A  30 " =    1.055
peak=    3.153 closest distance to " O   HOH Z 279 " =    2.177
peak=    3.149 closest distance to " CB  LEU A 255 " =    0.711
peak=    3.146 closest distance to " O   HOH Z 188 " =    2.387
peak=    3.146 closest distance to " CA  ASP A 191 " =    1.132
peak=    3.140 closest distance to " CA  ARG A 102 " =    1.102
peak=    3.139 closest distance to " OG  SER A  62 " =    2.846
peak=    3.118 closest distance to " CG  MET A 113 " =    1.074
peak=    3.118 closest distance to " O   HOH Z 222 " =    2.457
peak=    3.110 closest distance to " N   ASN A 127 " =    1.223
peak=    3.104 closest distance to " C   ALA A 299 " =    0.921
peak=    3.100 closest distance to " CB  SER A  62 " =    1.278
peak=    3.094 closest distance to " CD2 TYR A 186 " =    1.055
peak=    3.094 closest distance to " CG1 ILE A 151 " =    1.081
peak=    3.086 closest distance to " CA  LEU A 282 " =    1.155
peak=    3.080 closest distance to " O   HOH Z 412 " =    2.014
peak=    3.077 closest distance to " ND1 HIS A  81 " =    1.734
peak=    3.060 closest distance to " CB  ARG A 138 " =    0.911
peak=    3.057 closest distance to " O   SER A 164 " =    1.324
peak=    3.057 closest distance to " O   HOH Z 116 " =    1.696
peak=    3.053 closest distance to " O   HOH Z 359 " =    3.928
peak=    3.048 closest distance to " O   TRP A 274 " =    1.779
peak=    3.043 closest distance to " CG  LEU A 281 " =    0.996
peak=    3.041 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.006 closest distance to " O   HOH Z 183 " =    1.781

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.758 - 5.518
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.758 - 5.518

peak=   -4.812 closest distance to " OG BSER A 134 " =    1.236
peak=   -4.799 closest distance to " CG2 VAL A 230 " =    0.758
peak=   -4.668 closest distance to " SG  CYS A 254 " =    3.280
peak=   -4.658 closest distance to " O   HOH Z 266 " =    5.256
peak=   -4.477 closest distance to " CD  ARG A 156 " =    2.037
peak=   -4.332 closest distance to " CB  PHE A 192 " =    1.893
peak=   -4.324 closest distance to " CG  GLN A 223 " =    2.128
peak=   -4.278 closest distance to " CG  GLN A  58 " =    1.134
peak=   -4.264 closest distance to " C   HIS A 108 " =    1.217
peak=   -4.206 closest distance to " O   HOH Z 231 " =    2.169
peak=   -4.080 closest distance to " CB  PRO A 243 " =    2.719
peak=   -4.062 closest distance to " O   VAL A  67 " =    2.622
peak=   -4.028 closest distance to " CG1 VAL A  67 " =    2.957
peak=   -4.017 closest distance to " CG2 VAL A 296 " =    1.638
peak=   -3.983 closest distance to " O   HOH Z 114 " =    3.037
peak=   -3.979 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.962 closest distance to " CB  ALA A  43 " =    2.474
peak=   -3.943 closest distance to " O   HOH Z 166 " =    1.940
peak=   -3.917 closest distance to " CE  MET A 105 " =    2.342
peak=   -3.897 closest distance to " O   PRO A 198 " =    1.214
peak=   -3.880 closest distance to " ND2 ASN A 187 " =    1.464
peak=   -3.870 closest distance to " OXT GLY A 302 " =    2.878
peak=   -3.866 closest distance to " CD1 LEU A 255 " =    2.835
peak=   -3.865 closest distance to " O   PRO A 163 " =    2.078
peak=   -3.843 closest distance to " O   HOH Z 394 " =    1.500
peak=   -3.840 closest distance to " O   HOH Z  11 " =    1.901
peak=   -3.825 closest distance to " CE2 TYR A  30 " =    2.710
peak=   -3.815 closest distance to " CE BMET A  47 " =    1.302
peak=   -3.814 closest distance to " CA  ASP A 298 " =    1.117
peak=   -3.814 closest distance to " CG1 VAL A 112 " =    2.875
peak=   -3.806 closest distance to " O   HOH Z 185 " =    2.418
peak=   -3.799 closest distance to " CB  ALA A 248 " =    2.085
peak=   -3.778 closest distance to " C   ILE A 239 " =    2.151
peak=   -3.768 closest distance to " CB  ASP A 171 " =    2.287
peak=   -3.737 closest distance to " ND2 ASN A  45 " =    1.349
peak=   -3.734 closest distance to " O   HOH Z 351 " =    1.490
peak=   -3.701 closest distance to " N   ALA A 248 " =    1.649
peak=   -3.686 closest distance to " O   HOH Z 196 " =    2.221
peak=   -3.684 closest distance to " NE2 GLN A  88 " =    1.889
peak=   -3.671 closest distance to " CB  ALA A 161 " =    2.501
peak=   -3.669 closest distance to " O   PHE A 218 " =    1.525
peak=   -3.664 closest distance to " O   HOH Z  13 " =    1.853
peak=   -3.628 closest distance to " CZ3 TRP A 179 " =    1.229
peak=   -3.613 closest distance to " O   HOH Z  44 " =    2.287
peak=   -3.602 closest distance to " CB  ALA A 291 " =    2.243
peak=   -3.602 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -3.598 closest distance to " O   HOH Z 389 " =    2.047
peak=   -3.587 closest distance to " O   HOH Z 290 " =    1.240
peak=   -3.578 closest distance to " O   SER A 271 " =    2.098
peak=   -3.577 closest distance to " O   HOH Z 102 " =    1.714
peak=   -3.556 closest distance to " CB  ALA A 291 " =    2.281
peak=   -3.556 closest distance to " N   ALA A  43 " =    2.657
peak=   -3.553 closest distance to " O   HOH Z 243 " =    1.906
peak=   -3.546 closest distance to " O   HOH Z 191 " =    5.518
peak=   -3.543 closest distance to " O   HOH Z 198 " =    2.066
peak=   -3.542 closest distance to " O   HOH Z 211 " =    1.497
peak=   -3.522 closest distance to " CA  ASN A 127 " =    1.300
peak=   -3.518 closest distance to " CG  TRP A 266 " =    1.879
peak=   -3.511 closest distance to " ND2 ASN A 249 " =    2.448
peak=   -3.507 closest distance to " CD2 LEU A 237 " =    2.786
peak=   -3.507 closest distance to " O   PRO A 198 " =    1.343
peak=   -3.505 closest distance to " CG2 VAL A 296 " =    0.899
peak=   -3.501 closest distance to " O   ALA A 161 " =    1.755
peak=   -3.499 closest distance to " CD1 PHE A  59 " =    1.943
peak=   -3.494 closest distance to " N   THR A 157 " =    1.460
peak=   -3.472 closest distance to " O   HOH Z 407 " =    2.975
peak=   -3.471 closest distance to " OG  SER A  97 " =    2.276
peak=   -3.469 closest distance to " N   ALA A 226 " =    1.992
peak=   -3.453 closest distance to " OD1 ASN A 148 " =    1.432
peak=   -3.451 closest distance to " CZ  PHE A  59 " =    1.529
peak=   -3.446 closest distance to " O   SER A 210 " =    1.880
peak=   -3.445 closest distance to " O   HOH Z 140 " =    1.621
peak=   -3.445 closest distance to " O   VAL A 189 " =    2.585
peak=   -3.441 closest distance to " CB  PRO A 163 " =    2.454
peak=   -3.429 closest distance to " CG  LEU A 228 " =    1.049
peak=   -3.426 closest distance to " CD  LYS A 289 " =    2.429
peak=   -3.424 closest distance to " O   HOH Z  60 " =    1.989
peak=   -3.424 closest distance to " O   HOH Z 139 " =    3.152
peak=   -3.416 closest distance to " O   HOH Z 103 " =    1.805
peak=   -3.415 closest distance to " NH2AARG A 275 " =    5.092
peak=   -3.410 closest distance to " CA  GLY A 241 " =    3.133
peak=   -3.410 closest distance to " O   SER A  22 " =    2.389
peak=   -3.408 closest distance to " O   ALA A  51 " =    1.290
peak=   -3.395 closest distance to " O   HOH Z 281 " =    2.751
peak=   -3.393 closest distance to " CE2 PHE A 218 " =    2.491
peak=   -3.385 closest distance to " OG  SER A  87 " =    1.421
peak=   -3.381 closest distance to " N   SER A 276 " =    1.294
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.380 closest distance to " O   HOH Z  73 " =    2.319
peak=   -3.379 closest distance to " O   HOH Z 166 " =    1.583
peak=   -3.378 closest distance to " O   HOH Z  38 " =    1.751
peak=   -3.377 closest distance to " OD1 ASN A  39 " =    2.251
peak=   -3.377 closest distance to " CG  ASP A 231 " =    0.815
peak=   -3.370 closest distance to " CB  ASP A 132 " =    2.412
peak=   -3.369 closest distance to " CD2 TYR A 293 " =    2.017
peak=   -3.368 closest distance to " O   HOH Z  90 " =    2.515
peak=   -3.367 closest distance to " CA  GLY A  98 " =    1.882
peak=   -3.366 closest distance to " O   ALA A  10 " =    1.835
peak=   -3.366 closest distance to " CA  GLY A 241 " =    2.312
peak=   -3.358 closest distance to " O   HOH Z 350 " =    1.973
peak=   -3.348 closest distance to " O   HOH Z   9 " =    1.437
peak=   -3.345 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -3.340 closest distance to " CA  GLY A 133 " =    1.909
peak=   -3.340 closest distance to " CG1 VAL A 197 " =    2.275
peak=   -3.338 closest distance to " O   ALA A   8 " =    1.958
peak=   -3.334 closest distance to " OD1 ASN A 187 " =    1.681
peak=   -3.333 closest distance to " C   MET A 188 " =    1.397
peak=   -3.333 closest distance to " CG2 ILE A 263 " =    2.238
peak=   -3.331 closest distance to " O   GLY A  80 " =    2.485
peak=   -3.317 closest distance to " CG  PHE A 283 " =    2.633
peak=   -3.317 closest distance to " CE3 TRP A 150 " =    2.181
peak=   -3.312 closest distance to " N   HIS A 115 " =    2.137
peak=   -3.312 closest distance to " O   HOH Z 359 " =    3.132
peak=   -3.308 closest distance to " CG1 VAL A 230 " =    1.891
peak=   -3.302 closest distance to " O   HOH Z 313 " =    1.648
peak=   -3.295 closest distance to " CZ  TYR A 169 " =    1.764
peak=   -3.295 closest distance to " CD  ARG A 139 " =    1.629
peak=   -3.293 closest distance to " CG  LEU A   5 " =    0.932
peak=   -3.292 closest distance to " C   GLY A  17 " =    1.205
peak=   -3.284 closest distance to " O   HOH Z 193 " =    1.549
peak=   -3.282 closest distance to " NH2 ARG A  79 " =    2.022
peak=   -3.280 closest distance to " O   HOH Z  88 " =    4.509
peak=   -3.279 closest distance to " CB  ASN A  39 " =    2.280
peak=   -3.278 closest distance to " N   PHE A  59 " =    2.140
peak=   -3.277 closest distance to " CG2 THR A 178 " =    2.220
peak=   -3.274 closest distance to " O   LEU A 167 " =    1.480
peak=   -3.272 closest distance to " O   MET A  40 " =    2.726
peak=   -3.267 closest distance to " O   HOH Z  43 " =    1.802
peak=   -3.267 closest distance to " O   ALA A 248 " =    1.715
peak=   -3.264 closest distance to " C   LEU A 222 " =    0.861
peak=   -3.261 closest distance to " C   GLN A 205 " =    1.855
peak=   -3.260 closest distance to " C   LEU A 143 " =    1.025
peak=   -3.259 closest distance to " CB  ALA A  10 " =    2.291
peak=   -3.256 closest distance to " CG1 VAL A 125 " =    1.928
peak=   -3.252 closest distance to " CZ2 TRP A 274 " =    0.986
peak=   -3.250 closest distance to " O   HOH Z 295 " =    1.564
peak=   -3.248 closest distance to " CZ2 TRP A  92 " =    2.768
peak=   -3.248 closest distance to " CG2 VAL A 202 " =    2.610
peak=   -3.247 closest distance to " CD  PRO A 213 " =    2.102
peak=   -3.246 closest distance to " N   ALA A 248 " =    2.226
peak=   -3.244 closest distance to " C   ASP A 231 " =    2.428
peak=   -3.243 closest distance to " CD1 LEU A 101 " =    2.265
peak=   -3.239 closest distance to " O   HOH Z 165 " =    1.971
peak=   -3.238 closest distance to " O   TRP A  70 " =    1.428
peak=   -3.236 closest distance to " O   HOH Z 139 " =    5.092
peak=   -3.234 closest distance to " CA  GLY A 203 " =    2.422
peak=   -3.219 closest distance to " CB  TRP A  85 " =    2.625
peak=   -3.210 closest distance to " N   ASP A 171 " =    2.208
peak=   -3.210 closest distance to " OH  TYR A 172 " =    1.775
peak=   -3.209 closest distance to " O   HOH Z 389 " =    1.559
peak=   -3.207 closest distance to " O   SER A 276 " =    1.586
peak=   -3.205 closest distance to " O   HOH Z  47 " =    1.604
peak=   -3.202 closest distance to " O   GLN A 240 " =    2.371
peak=   -3.201 closest distance to " ND2 ASN A  39 " =    1.201
peak=   -3.201 closest distance to " O   ASN A 301 " =    1.594
peak=   -3.199 closest distance to " CB  ALA A  51 " =    1.928
peak=   -3.199 closest distance to " O   ARG A  24 " =    2.049
peak=   -3.191 closest distance to " O   HOH Z 123 " =    2.380
peak=   -3.186 closest distance to " CD2 TYR A 247 " =    2.439
peak=   -3.185 closest distance to " OD2 ASP A 191 " =    1.328
peak=   -3.175 closest distance to " O   HOH Z 131 " =    4.039
peak=   -3.174 closest distance to " OE2 GLU A 152 " =    1.317
peak=   -3.172 closest distance to " O   HOH Z 256 " =    1.335
peak=   -3.166 closest distance to " O   HOH Z  10 " =    1.377
peak=   -3.166 closest distance to " O   ALA A 180 " =    1.366
peak=   -3.166 closest distance to " O   HOH Z 345 " =    1.971
peak=   -3.165 closest distance to " O   HOH Z 371 " =    2.030
peak=   -3.160 closest distance to " N   GLN A  77 " =    1.720
peak=   -3.159 closest distance to " O   HOH Z 210 " =    1.317
peak=   -3.152 closest distance to " O   ALA A   1 " =    1.685
peak=   -3.148 closest distance to " O   GLY A  80 " =    2.511
peak=   -3.144 closest distance to " ND2 ASN A 252 " =    1.890
peak=   -3.139 closest distance to " CD  PRO A 243 " =    2.093
peak=   -3.137 closest distance to " CA  GLY A 133 " =    2.298
peak=   -3.134 closest distance to " CD2 PHE A 225 " =    1.130
peak=   -3.133 closest distance to " OG  SER A 206 " =    1.652
peak=   -3.133 closest distance to " O   ASN A 252 " =    1.337
peak=   -3.130 closest distance to " OG  SER A  62 " =    1.678
peak=   -3.123 closest distance to " O   HOH Z 346 " =    1.742
peak=   -3.123 closest distance to " CE1 HIS A  81 " =    1.458
peak=   -3.122 closest distance to " O   HOH Z 426 " =    1.736
peak=   -3.119 closest distance to " OD1 ASN A 301 " =    2.093
peak=   -3.113 closest distance to " OG  SER A  63 " =    1.209
peak=   -3.110 closest distance to " CG  GLU A   2 " =    2.031
peak=   -3.109 closest distance to " NE2 GLN A 194 " =    1.820
peak=   -3.109 closest distance to " ND2 ASN A  60 " =    1.339
peak=   -3.109 closest distance to " C   ASN A 187 " =    1.825
peak=   -3.105 closest distance to " O   HOH Z 216 " =    1.552
peak=   -3.104 closest distance to " CA  PRO A 243 " =    2.231
peak=   -3.103 closest distance to " O   HOH Z 149 " =    2.346
peak=   -3.099 closest distance to " CG2 THR A  42 " =    1.754
peak=   -3.094 closest distance to " C   GLN A  58 " =    1.989
peak=   -3.092 closest distance to " OG BSER A 134 " =    1.740
peak=   -3.084 closest distance to " O   HOH Z 353 " =    2.074
peak=   -3.073 closest distance to " O   HOH Z  64 " =    2.582
peak=   -3.050 closest distance to " OD2 ASP A  50 " =    2.192
peak=   -3.041 closest distance to " CG1AVAL A  41 " =    2.899

================= 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    :  0.4366 0.4213   6.230984e+00   6.202882e+00
   1_bss:  0.4284 0.4110   6.223426e+00   6.188222e+00
   1_xyz:  0.3188 0.3363   6.013114e+00   6.044558e+00
   1_adp:  0.2564 0.2924   5.826590e+00   5.931910e+00
   1_occ:  0.2560 0.2927   5.825013e+00   5.932945e+00
   2_bss:  0.2508 0.2874   5.824740e+00   5.929006e+00
   2_xyz:  0.1647 0.2030   5.451453e+00   5.622874e+00
   2_adp:  0.1487 0.1910   5.363744e+00   5.554179e+00
   2_occ:  0.1486 0.1911   5.363603e+00   5.554498e+00
   3_bss:  0.1476 0.1908   5.362012e+00   5.552683e+00
   3_xyz:  0.1220 0.1646   5.205198e+00   5.428641e+00
   3_adp:  0.1164 0.1617   5.175023e+00   5.412968e+00
   3_occ:  0.1163 0.1617   5.174646e+00   5.412732e+00
   4_bss:  0.1162 0.1617   5.174380e+00   5.411444e+00
   4_xyz:  0.1134 0.1582   5.155478e+00   5.394540e+00
   4_adp:  0.1124 0.1583   5.152380e+00   5.394479e+00
   4_occ:  0.1124 0.1583   5.152402e+00   5.394630e+00
   5_bss:  0.1124 0.1583   5.152420e+00   5.394644e+00
   5_xyz:  0.1092 0.1575   5.138861e+00   5.393751e+00
   5_adp:  0.1094 0.1574   5.139257e+00   5.393237e+00
   5_occ:  0.1091 0.1575   5.138275e+00   5.392802e+00
   5_bss:  0.1091 0.1575   5.138022e+00   5.392550e+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:  0.353  20.000   7.434   8.280   9.567   0.000   0.000   0.000
   1_xyz:  0.353  20.000   7.434   8.280   9.567   0.000   0.000   0.000
   1_adp:  0.353  20.000   7.434   8.280   9.567   0.000   0.000   0.000
   1_occ:  0.353  20.000   7.434   8.280   9.567   0.000   0.000   0.000
   2_bss:  0.308  20.000   3.883   4.164   5.978   0.000   0.000   0.000
   2_xyz:  0.308  20.000   3.883   4.164   5.978   0.000   0.000   0.000
   2_adp:  0.308  20.000   3.883   4.164   5.978   0.000   0.000   0.000
   2_occ:  0.308  20.000   3.883   4.164   5.978   0.000   0.000   0.000
   3_bss:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   3_xyz:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   3_adp:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   3_occ:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   4_bss:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   4_xyz:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   4_adp:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   4_occ:  0.326  41.634   2.855   3.322   4.865   0.000   0.000   0.000
   5_bss:  0.326  41.634   2.904   3.352   4.885   0.000   0.000   0.000
   5_xyz:  0.326  41.634   2.904   3.352   4.885   0.000   0.000   0.000
   5_adp:  0.326  41.634   2.904   3.352   4.885   0.000   0.000   0.000
   5_occ:  0.326  41.634   2.904   3.352   4.885   0.000   0.000   0.000
   5_bss:  0.322  47.095  -0.801  -0.370   1.170   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.959 0.5601  0.6307    52413.886
   1_bss:  46.765 0.5604  0.8146    49546.526
   1_xyz:  35.579 0.6941  0.9709    30153.919
   1_adp:  29.178 0.7674  1.0506    21875.561
   1_occ:  29.189 0.7672  1.0494    21862.100
   2_bss:  28.929 0.7699  0.9172    21521.954
   2_xyz:  19.411 0.8670  0.9992    10364.776
   2_adp:  17.582 0.8844  1.0095     9044.771
   2_occ:  17.593 0.8843  1.0093     9042.276
   3_bss:  17.503 0.8853  0.9746     9018.822
   3_xyz:  14.891 0.9075  0.9838     6913.086
   3_adp:  14.571 0.9103  0.9809     6668.385
   3_occ:  14.561 0.9104  0.9809     6662.734
   4_bss:  14.560 0.9104  0.9805     6653.535
   4_xyz:  14.117 0.9143  0.9818     6428.837
   4_adp:  14.093 0.9146  0.9778     6431.153
   4_occ:  14.095 0.9146  0.9777     6430.319
   5_bss:  14.096 0.9146  0.9789     6430.956
   5_xyz:  14.084 0.9146  0.9798     6425.847
   5_adp:  14.069 0.9147  0.9764     6415.808
   5_occ:  14.065 0.9147  0.9761     6409.121
   5_bss:  14.061 0.9148  0.9795     6405.565
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3621e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3621e+01
   1_xyz:   1.529  0.011  0.101 17.808  0.006  4.120   1.1750e-01
   1_adp:   1.529  0.011  0.101 17.808  0.006  4.120   1.1750e-01
   1_occ:   1.529  0.011  0.101 17.808  0.006  4.120   1.1750e-01
   2_bss:   1.529  0.011  0.101 17.808  0.006  4.120   1.1750e-01
   2_xyz:   1.011  0.007  0.077 16.036  0.004  4.121   6.3707e-02
   2_adp:   1.011  0.007  0.077 16.036  0.004  4.121   6.3707e-02
   2_occ:   1.011  0.007  0.077 16.036  0.004  4.121   6.3707e-02
   3_bss:   1.011  0.007  0.077 16.036  0.004  4.121   6.3707e-02
   3_xyz:   1.035  0.007  0.082 15.725  0.004  4.128   6.5060e-02
   3_adp:   1.035  0.007  0.082 15.725  0.004  4.128   6.5060e-02
   3_occ:   1.035  0.007  0.082 15.725  0.004  4.128   6.5060e-02
   4_bss:   1.035  0.007  0.082 15.725  0.004  4.128   6.5060e-02
   4_xyz:   0.957  0.006  0.077 15.414  0.003  4.116   5.7517e-02
   4_adp:   0.957  0.006  0.077 15.414  0.003  4.116   5.7517e-02
   4_occ:   0.957  0.006  0.077 15.414  0.003  4.116   5.7517e-02
   5_bss:   0.957  0.006  0.077 15.414  0.003  4.116   5.7517e-02
   5_xyz:   1.049  0.008  0.084 15.505  0.004  4.118   6.6210e-02
   5_adp:   1.049  0.008  0.084 15.505  0.004  4.118   6.6210e-02
   5_occ:   1.049  0.008  0.084 15.505  0.004  4.118   6.6210e-02
   5_bss:   1.049  0.008  0.084 15.505  0.004  4.118   6.6210e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9514e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9514e+00
   1_xyz:  12.702  0.140  0.397 89.614  0.035  2.228   8.6234e-02
   1_adp:  12.702  0.140  0.397 89.614  0.035  2.228   8.6234e-02
   1_occ:  12.702  0.140  0.397 89.614  0.035  2.228   8.6234e-02
   2_bss:  12.702  0.140  0.397 89.614  0.035  2.228   8.6234e-02
   2_xyz:   6.708  0.080  0.357 88.341  0.034  2.293   5.1327e-02
   2_adp:   6.708  0.080  0.357 88.341  0.034  2.293   5.1327e-02
   2_occ:   6.708  0.080  0.357 88.341  0.034  2.293   5.1327e-02
   3_bss:   6.708  0.080  0.357 88.341  0.034  2.293   5.1327e-02
   3_xyz:   6.384  0.047  0.505 82.770  0.035  2.246   4.6114e-02
   3_adp:   6.384  0.047  0.505 82.770  0.035  2.246   4.6114e-02
   3_occ:   6.384  0.047  0.505 82.770  0.035  2.246   4.6114e-02
   4_bss:   6.384  0.047  0.505 82.770  0.035  2.246   4.6114e-02
   4_xyz:   6.255  0.044  0.445 83.893  0.036  2.366   3.9390e-02
   4_adp:   6.255  0.044  0.445 83.893  0.036  2.366   3.9390e-02
   4_occ:   6.255  0.044  0.445 83.893  0.036  2.366   3.9390e-02
   5_bss:   6.255  0.044  0.445 83.893  0.036  2.366   3.9390e-02
   5_xyz:   6.529  0.050  0.513 83.035  0.038  2.292   4.7106e-02
   5_adp:   6.529  0.050  0.513 83.035  0.038  2.292   4.7106e-02
   5_occ:   6.529  0.050  0.513 83.035  0.038  2.292   4.7106e-02
   5_bss:   6.529  0.050  0.513 83.035  0.038  2.292   4.7106e-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:  52.72   0.00  10.58  46.35   0.00   7.63  52.72   0.00  26.67
   1_occ:  52.72   0.00  10.58  46.35   0.00   7.63  52.72   0.00  26.67
   2_bss:  52.72   0.00  10.58  46.35   0.00   7.63  52.72   0.00  26.67
   2_xyz:  52.72   0.00  10.58  46.35   0.00   7.63  52.72   0.00  26.67
   2_adp:  56.43   0.00  10.98  54.13   0.00   7.34  56.43   0.63  30.81
   2_occ:  56.43   0.00  10.98  54.13   0.00   7.34  56.43   0.63  30.81
   3_bss:  56.43   0.00  10.98  54.13   0.00   7.34  56.43   0.63  30.81
   3_xyz:  56.43   0.00  10.98  54.13   0.00   7.34  56.43   0.63  30.81
   3_adp:  72.48   0.00  11.72  72.48   0.00   7.45  68.14   0.38  34.99
   3_occ:  72.48   0.00  11.72  72.48   0.00   7.45  68.14   0.38  34.99
   4_bss:  72.48   0.00  11.72  72.48   0.00   7.45  68.14   0.38  34.99
   4_xyz:  72.48   0.00  11.72  72.48   0.00   7.45  68.14   0.38  34.99
   4_adp:  83.02   0.00  11.73  83.02   0.00   7.45  75.74   0.45  35.02
   4_occ:  83.02   0.00  11.73  83.02   0.00   7.45  75.74   0.45  35.02
   5_bss:  83.02   0.00  11.73  83.02   0.00   7.45  75.74   0.45  35.02
   5_xyz:  83.02   0.00  11.73  83.02   0.00   7.45  75.74   0.45  35.02
   5_adp:  83.51   0.00  11.65  83.51   0.00   7.38  75.94   0.36  34.90
   5_occ:  83.51   0.00  11.65  83.51   0.00   7.38  75.94   0.36  34.90
   5_bss:  87.32   3.81  15.45  87.32   3.81  11.18  79.75   4.17  38.71
------------------------------------------------------------------------
 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:    1.226    0.022    0.401
   1_adp:    1.226    0.022    0.401
   1_occ:    1.226    0.022    0.401
   2_bss:    1.226    0.022    0.401
   2_xyz:    1.489    0.038    0.507
   2_adp:    1.489    0.038    0.507
   2_occ:    1.489    0.038    0.507
   3_bss:    1.489    0.038    0.507
   3_xyz:    1.530    0.027    0.542
   3_adp:    1.530    0.027    0.542
   3_occ:    1.530    0.027    0.542
   4_bss:    1.530    0.027    0.542
   4_xyz:    1.637    0.027    0.554
   4_adp:    1.637    0.027    0.554
   4_occ:    1.637    0.027    0.554
   5_bss:    1.637    0.027    0.554
   5_xyz:    1.680    0.033    0.561
   5_adp:    1.680    0.033    0.561
   5_occ:    1.680    0.033    0.561
   5_bss:    1.680    0.033    0.561
------------------------------------------------------------------------

CPU time actual refinement: 330.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_414/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_414/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_414/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_414/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_414/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.23 
  Macro-tasks:
    bulk solvent and scale       = 46.42  
    individual site refinement   = 125.73 
    weights calculation          = 31.88  
    collect and process          = 6.50   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.64 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 99.47  
    alpha_beta                      = 8.55   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.11 
    fmodel                         = 7.96   
    r_factors                      = 0.24   
    phase_errors                   = 10.94  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 239.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.679 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    663 calls, 99.04 s
gradients_fft:          608 calls, 96.28 s

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

# Date 2008-01-16 Time 01:32:44 PST -0800 (1200475964.01 s)
Start R-work = 0.4366, R-free = 0.4213 (no bulk solvent and anisotropic scale)
Final R-work = 0.1275, R-free = 0.1745 (no bulk solvent and anisotropic scale)

Start R-work = 0.4284, R-free = 0.4110
Final R-work = 0.1091, R-free = 0.1575