# Date 2008-01-16 Time 00:45:25 PST -0800 (1200473125.28 s)
#phil __OFF__

Command line arguments: "../132.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10522
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 132

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 45.9914, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.41, per 1000 atoms: 1.21


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95099
Completeness in resolution range: 0.977544
Completeness with d_max=infinity: 0.974432

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6737
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95099
Completeness in resolution range: 0.977544
Completeness with d_max=infinity: 0.974432

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6741 -  4.1741 [2101/2125]  1892   209   9.9%
  bin  2:  4.1741 -  3.3258 [2030/2049]  1826   204  10.0%
  bin  3:  3.3258 -  2.9091 [1992/2011]  1790   202  10.1%
  bin  4:  2.9091 -  2.6448 [1971/2001]  1777   194   9.8%
  bin  5:  2.6448 -  2.4562 [1962/1981]  1765   197  10.0%
  bin  6:  2.4562 -  2.3119 [1953/1978]  1757   196  10.0%
  bin  7:  2.3119 -  2.1966 [1968/1996]  1771   197  10.0%
  bin  8:  2.1966 -  2.1012 [1928/1964]  1737   191   9.9%
  bin  9:  2.1012 -  2.0206 [1915/1957]  1725   190   9.9%
  bin 10:  2.0206 -  1.9510 [1769/1977]  1590   179  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_132/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: 0.13 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:
        0.74 -     1.57: 6
        1.57 -     2.40: 80
        2.40 -     3.24: 3495
        3.24 -     4.07: 9757
        4.07 -     4.90: 16017
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.741 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.209 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.222 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.227 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.404 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29350 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_132/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_132/model_refine_001.geo

CPU time processing inputs: 9.33


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 45.9914 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5246   r_free= 0.5252   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.312127                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6552 0.99   1372  153 0.4434 0.4550      6.6656      6.7139|
|  2:  4.6552 -  3.7147 0.99   1314  145 0.4839 0.4663      6.8872       6.886|
|  3:  3.7147 -  3.2510 0.99   1287  144 0.5088 0.4965      6.7651      6.8209|
|  4:  3.2510 -  2.9564 0.99   1278  143 0.5143 0.4785      6.5927      6.5343|
|  5:  2.9564 -  2.7460 0.99   1274  141 0.5526 0.5369      6.4151      6.3978|
|  6:  2.7460 -  2.5850 0.99   1274  139 0.5550 0.5960      6.3202       6.286|
|  7:  2.5850 -  2.4562 0.99   1251  141 0.5420 0.4997      6.2641      6.1923|
|  8:  2.4562 -  2.3497 0.98   1265  139 0.5631 0.5780      6.2134      6.2252|
|  9:  2.3497 -  2.2596 0.98   1258  139 0.5507 0.6071      6.1327      6.1661|
| 10:  2.2596 -  2.1819 0.99   1232  137 0.5717 0.5236      6.1411      6.1385|
| 11:  2.1819 -  2.1138 0.98   1252  143 0.5425 0.5939      6.0589      6.1071|
| 12:  2.1138 -  2.0536 0.97   1237  133 0.5413 0.5553      6.0032      6.0348|
| 13:  2.0536 -  1.9997 1.00   1239  143 0.5540 0.5067      5.9039      5.8901|
| 14:  1.9997 -  1.9510 0.85   1097  119 0.5471 0.5299       5.859      5.7554|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6552  1372   153  0.56  45.89   0.78     0.62     113963.91|
|  2:  4.6552 -  3.7147  1314   145  0.57  46.09   0.83     0.66     163279.17|
|  3:  3.7147 -  3.2510  1287   144  0.46  55.21   0.83     0.60     167129.45|
|  4:  3.2510 -  2.9564  1278   143  0.38  61.17   0.79     0.50     136676.20|
|  5:  2.9564 -  2.7460  1274   141  0.29  67.84   0.72     0.37     102053.83|
|  6:  2.7460 -  2.5850  1274   139  0.25  71.42   0.71     0.29      85987.24|
|  7:  2.5850 -  2.4562  1251   141  0.16  77.97   0.73     0.19      79108.80|
|  8:  2.4562 -  2.3497  1265   139  0.15  79.14   0.73     0.18      73350.35|
|  9:  2.3497 -  2.2596  1258   139  0.14  79.22   0.72     0.18      66400.90|
| 10:  2.2596 -  2.1819  1232   137  0.16  77.73   0.74     0.20      59624.37|
| 11:  2.1819 -  2.1138  1252   143  0.14  79.60   0.78     0.18      56245.63|
| 12:  2.1138 -  2.0536  1237   133  0.16  77.83   0.77     0.21      51246.27|
| 13:  2.0536 -  1.9997  1239   143  0.20  75.44   0.75     0.26      42524.29|
| 14:  1.9997 -  1.9510  1097   119  0.27  70.18   0.74     0.31      31926.35|
|alpha:            min =        0.18 max =            0.66 mean =         0.34|
|beta:             min =    31926.35 max =       167129.45 mean =     89081.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.28|
|phase err.(work): min =        0.00 max =           90.00 mean =        68.61|
|phase err.(test): min =        0.00 max =           89.95 mean =        69.07|
|-----------------------------------------------------------------------------|

============================== 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 = 36.314592             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.629   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.590984              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.444 -  0.890:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  0.890 -  1.335:        4 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.335 -  1.781:       21 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.781 -  2.226:      167 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.226 -  2.672:      796 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.672 -  3.118:     2058 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.118 -  3.563:     3750 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.563 -  4.009:     5597 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.009 -  4.454:     7580 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.454 -  4.900:     9409 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.304 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.084    4.900  0.444 |       3.732 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    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 = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5274   r_free= 0.5261   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.312246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5170   r_free= 0.5137   ksol= 0.39   Bsol= 0.00   scale= 0.954    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.25,8.41,8.28,0.00,0.00,0.00); trace/3= 7.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.307393                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.126622             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.596913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.563   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5170      final r-factor (work) = 0.4697          |
| start r-factor (free) = 0.5137      final r-factor (free) = 0.4918          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 131.5616 = 25.13 * 0.50 * 6.3087 + 1.00 * 52.3037                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.9622 = 25.13 * 0.50 * 6.2714 + 1.00 * 0.1728                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4697      final r-factor (work) = 0.4340          |
| start r-factor (free) = 0.4918      final r-factor (free) = 0.4885          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3006 = 2.60 * 1.00 * 6.2714 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.2321 = 2.60 * 1.00 * 6.2412 + 1.00 * 0.0242                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.17   16.14    None  None   None       |
|    all(noH): 2823   0      0.00    86.17   16.14    None  None   None       |
|    Sol.    : 438    0      0.00    86.17   20.13    None  None   None       |
|    Mac.    : 2385   0      0.00    74.84   15.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.617:  924   |   5:    43.084 -  51.700:   62        |
|      1:     8.617 -  17.234:  785   |   6:    51.700 -  60.317:   38        |
|      2:    17.234 -  25.850:  562   |   7:    60.317 -  68.934:   12        |
|      3:    25.850 -  34.467:  285   |   8:    68.934 -  77.551:    4        |
|      4:    34.467 -  43.084:  150   |   9:    77.551 -  86.167:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4340 r_free = 0.4885             target_work(ml) = 6.237         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4335 r_free = 0.4883             target_work(ml) = 6.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4335   r_free= 0.4883   ksol= 0.39   Bsol= 0.00   scale= 1.085    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.25,8.41,8.28,0.00,0.00,0.00); trace/3= 7.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.236168                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4335   r_free= 0.4867   ksol= 0.36   Bsol= 20.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,5.67,6.38,0.00,0.00,0.00); trace/3= 5.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.237397                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.544758             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.591  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.262723              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.964  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4335      final r-factor (work) = 0.3907          |
| start r-factor (free) = 0.4867      final r-factor (free) = 0.4555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.4298 = 13.54 * 0.50 * 6.2396 + 1.00 * 0.1728                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.1034 = 13.54 * 0.50 * 6.2030 + 1.00 * 0.0945                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3907      final r-factor (work) = 0.3793          |
| start r-factor (free) = 0.4555      final r-factor (free) = 0.4543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8655 = 1.26 * 1.00 * 6.2030 + 1.00 * 0.0329                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8007 = 1.26 * 1.00 * 6.1648 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.40   16.17    None  None   None       |
|    all(noH): 2823   0      0.00    84.40   16.17    None  None   None       |
|    Sol.    : 438    0      0.00    84.40   22.58    None  None   None       |
|    Mac.    : 2385   0      0.00    81.68   15.00    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:     0.000 -   8.440:  869   |   5:    42.201 -  50.642:   60        |
|      1:     8.440 -  16.881:  858   |   6:    50.642 -  59.082:   27        |
|      2:    16.881 -  25.321:  526   |   7:    59.082 -  67.522:   10        |
|      3:    25.321 -  33.761:  327   |   8:    67.522 -  75.962:    1        |
|      4:    33.761 -  42.201:  138   |   9:    75.962 -  84.403:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3793 r_free = 0.4543             target_work(ml) = 6.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3790 r_free = 0.4544             target_work(ml) = 6.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3790   r_free= 0.4544   ksol= 0.36   Bsol= 20.00   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.02,5.67,6.38,0.00,0.00,0.00); trace/3= 5.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.154874                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3793   r_free= 0.4564   ksol= 0.33   Bsol= 39.50   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.64,3.92,4.56,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.157206                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.279917             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.178833              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.696  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3793      final r-factor (work) = 0.3217          |
| start r-factor (free) = 0.4564      final r-factor (free) = 0.3939          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.8579 = 11.28 * 0.50 * 6.1638 + 1.00 * 0.0941                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.5210 = 11.28 * 0.50 * 6.1028 + 1.00 * 0.1015                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3217      final r-factor (work) = 0.2936          |
| start r-factor (free) = 0.3939      final r-factor (free) = 0.3776          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3131 = 2.18 * 1.00 * 6.1028 + 1.00 * 0.0161                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0935 = 2.18 * 1.00 * 5.9985 + 1.00 * 0.0239                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.91  17.03    None  None   None       |
|    all(noH): 2823   0      0.00    101.91  17.03    None  None   None       |
|    Sol.    : 438    0      0.00    99.92   33.28    None  None   None       |
|    Mac.    : 2385   0      0.00    101.91  14.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.191: 1189   |   5:    50.955 -  61.146:   62        |
|      1:    10.191 -  20.382:  763   |   6:    61.146 -  71.337:   41        |
|      2:    20.382 -  30.573:  407   |   7:    71.337 -  81.527:    9        |
|      3:    30.573 -  40.764:  215   |   8:    81.527 -  91.718:    5        |
|      4:    40.764 -  50.955:  127   |   9:    91.718 - 101.909:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2936 r_free = 0.3776             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2933 r_free = 0.3781             target_work(ml) = 5.976         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2933   r_free= 0.3781   ksol= 0.33   Bsol= 39.50   scale= 1.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.64,3.92,4.56,0.00,0.00,0.00); trace/3= 3.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.975522                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2919   r_free= 0.3766   ksol= 0.34   Bsol= 45.64   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.05,2.90,0.00,0.00,0.00); trace/3= 2.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.971921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.634059              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.856  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308915              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.295  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2919      final r-factor (work) = 0.2392          |
| start r-factor (free) = 0.3766      final r-factor (free) = 0.3148          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9887 = 7.63 * 0.50 * 5.9961 + 1.00 * 0.1015                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6068 = 7.63 * 0.50 * 5.9019 + 1.00 * 0.0792                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2392      final r-factor (work) = 0.2228          |
| start r-factor (free) = 0.3148      final r-factor (free) = 0.2904          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8470 = 0.31 * 1.00 * 5.9019 + 1.00 * 0.0238                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8095 = 0.31 * 1.00 * 5.7863 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.98   15.31    None  None   None       |
|    all(noH): 2823   0      0.00    98.98   15.31    None  None   None       |
|    Sol.    : 438    0      1.95    97.89   34.84    None  None   None       |
|    Mac.    : 2385   0      0.00    98.98   11.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.898: 1384   |   5:    49.490 -  59.388:   55        |
|      1:     9.898 -  19.796:  721   |   6:    59.388 -  69.287:   26        |
|      2:    19.796 -  29.694:  314   |   7:    69.287 -  79.185:    7        |
|      3:    29.694 -  39.592:  188   |   8:    79.185 -  89.083:    6        |
|      4:    39.592 -  49.490:  118   |   9:    89.083 -  98.981:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2228 r_free = 0.2904             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2224 r_free = 0.2898             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2224   r_free= 0.2898   ksol= 0.34   Bsol= 45.64   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.05,2.90,0.00,0.00,0.00); trace/3= 2.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.741357                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2219   r_free= 0.2884   ksol= 0.33   Bsol= 35.02   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,1.12,2.00,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.738448                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.693540              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.648  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.616   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2219      final r-factor (work) = 0.1841          |
| start r-factor (free) = 0.2884      final r-factor (free) = 0.2394          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8715 = 2.69 * 0.50 * 5.7860 + 1.00 * 0.0792                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6854 = 2.69 * 0.50 * 5.6616 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1841      final r-factor (work) = 0.1682          |
| start r-factor (free) = 0.2394      final r-factor (free) = 0.2230          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9547 = 0.52 * 1.00 * 5.6616 + 1.00 * 0.0324                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8607 = 0.52 * 1.00 * 5.5196 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.96   15.57    None  None   None       |
|    all(noH): 2823   0      0.00    98.96   15.57    None  None   None       |
|    Sol.    : 438    0      2.80    95.89   41.33    None  None   None       |
|    Mac.    : 2385   0      0.00    98.96   10.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.896: 1523   |   5:    49.482 -  59.378:  103        |
|      1:     9.896 -  19.793:  670   |   6:    59.378 -  69.275:   63        |
|      2:    19.793 -  29.689:  187   |   7:    69.275 -  79.171:   12        |
|      3:    29.689 -  39.586:  138   |   8:    79.171 -  89.068:    5        |
|      4:    39.586 -  49.482:  117   |   9:    89.068 -  98.964:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1682 r_free = 0.2230             target_work(ml) = 5.487         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1679 r_free = 0.2226             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1679   r_free= 0.2226   ksol= 0.33   Bsol= 35.02   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.80,1.12,2.00,0.00,0.00,0.00); trace/3= 1.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.485470                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6552 0.99   1372  153 0.1347 0.1663      5.6693      5.7857|
|  2:  4.6552 -  3.7147 0.99   1314  145 0.1251 0.1801      5.7749      6.1212|
|  3:  3.7147 -  3.2510 0.99   1287  144 0.1562 0.1873      5.8439      6.0368|
|  4:  3.2510 -  2.9564 0.99   1278  143 0.1771 0.2325      5.7834      5.9719|
|  5:  2.9564 -  2.7460 0.99   1274  141 0.1978 0.2365       5.659      5.7891|
|  6:  2.7460 -  2.5850 0.99   1274  139 0.1831 0.2353      5.5465      5.6745|
|  7:  2.5850 -  2.4562 0.99   1251  141 0.1864 0.2516      5.4993       5.722|
|  8:  2.4562 -  2.3497 0.98   1265  139 0.1869 0.2466      5.4714      5.6923|
|  9:  2.3497 -  2.2596 0.98   1258  139 0.1831 0.2738      5.4112      5.6514|
| 10:  2.2596 -  2.1819 0.99   1232  137 0.1775 0.2748      5.3561      5.5729|
| 11:  2.1819 -  2.1138 0.98   1252  143 0.1751 0.2359      5.2748        5.54|
| 12:  2.1138 -  2.0536 0.97   1237  133 0.1707 0.2089      5.2184      5.4476|
| 13:  2.0536 -  1.9997 1.00   1239  143 0.1668 0.2475      5.1126      5.3778|
| 14:  1.9997 -  1.9510 0.85   1097  119 0.1745 0.2279      5.0625      5.2414|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6552  1372   153  0.91  13.78   0.99     0.96      13218.82|
|  2:  4.6552 -  3.7147  1314   145  0.92  13.05   1.06     1.04      17690.91|
|  3:  3.7147 -  3.2510  1287   144  0.88  17.73   1.08     1.08      22214.42|
|  4:  3.2510 -  2.9564  1278   143  0.87  19.73   1.05     1.01      19319.00|
|  5:  2.9564 -  2.7460  1274   141  0.84  22.34   1.03     0.98      15244.55|
|  6:  2.7460 -  2.5850  1274   139  0.84  22.33   1.02     0.96      13131.04|
|  7:  2.5850 -  2.4562  1251   141  0.83  23.56   1.04     1.02      12498.52|
|  8:  2.4562 -  2.3497  1265   139  0.83  24.01   1.04     1.00      12109.35|
|  9:  2.3497 -  2.2596  1258   139  0.83  23.58   1.04     1.00      10885.04|
| 10:  2.2596 -  2.1819  1232   137  0.83  23.90   1.05     0.97       9704.32|
| 11:  2.1819 -  2.1138  1252   143  0.83  23.59   1.07     1.01       8350.08|
| 12:  2.1138 -  2.0536  1237   133  0.85  22.29   1.07     1.04       7594.95|
| 13:  2.0536 -  1.9997  1239   143  0.84  22.34   1.07     1.02       6252.04|
| 14:  1.9997 -  1.9510  1097   119  0.85  22.06   1.04     0.98       5141.87|
|alpha:            min =        0.96 max =            1.08 mean =         1.00|
|beta:             min =     5141.87 max =        22214.42 mean =     12515.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.95 mean =        20.93|
|phase err.(test): min =        0.00 max =           89.93 mean =        20.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2223   ksol= 0.31   Bsol= 30.65   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.24,0.65,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.484488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2223   ksol= 0.31   Bsol= 30.65   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.41,-0.24,0.65,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.484488                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6552 0.99   1372  153 0.1338 0.1634      5.6548      5.7659|
|  2:  4.6552 -  3.7147 0.99   1314  145 0.1267 0.1805      5.7758        6.12|
|  3:  3.7147 -  3.2510 0.99   1287  144 0.1565 0.1871      5.8436      6.0304|
|  4:  3.2510 -  2.9564 0.99   1278  143 0.1763 0.2344      5.7823      5.9762|
|  5:  2.9564 -  2.7460 0.99   1274  141 0.1972 0.2372      5.6596      5.7905|
|  6:  2.7460 -  2.5850 0.99   1274  139 0.1827 0.2366      5.5469      5.6772|
|  7:  2.5850 -  2.4562 0.99   1251  141 0.1864 0.2525      5.4996      5.7234|
|  8:  2.4562 -  2.3497 0.98   1265  139 0.1867 0.2467       5.472      5.6955|
|  9:  2.3497 -  2.2596 0.98   1258  139 0.1826 0.2745      5.4106      5.6537|
| 10:  2.2596 -  2.1819 0.99   1232  137 0.1774 0.2740      5.3563      5.5714|
| 11:  2.1819 -  2.1138 0.98   1252  143 0.1751 0.2364       5.275      5.5417|
| 12:  2.1138 -  2.0536 0.97   1237  133 0.1710 0.2086      5.2195      5.4471|
| 13:  2.0536 -  1.9997 1.00   1239  143 0.1670 0.2479      5.1131      5.3785|
| 14:  1.9997 -  1.9510 0.85   1097  119 0.1741 0.2271      5.0617        5.24|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6552  1372   153  0.91  13.31   0.98     0.95      12574.87|
|  2:  4.6552 -  3.7147  1314   145  0.92  12.81   1.05     1.03      17151.29|
|  3:  3.7147 -  3.2510  1287   144  0.88  17.66   1.07     1.06      22065.51|
|  4:  3.2510 -  2.9564  1278   143  0.87  19.68   1.03     1.00      19247.62|
|  5:  2.9564 -  2.7460  1274   141  0.84  22.43   1.01     0.96      15349.03|
|  6:  2.7460 -  2.5850  1274   139  0.84  22.35   1.00     0.93      13177.47|
|  7:  2.5850 -  2.4562  1251   141  0.83  23.61   1.01     0.99      12550.11|
|  8:  2.4562 -  2.3497  1265   139  0.83  24.07   1.01     0.97      12169.69|
|  9:  2.3497 -  2.2596  1258   139  0.83  23.59   1.01     0.97      10908.22|
| 10:  2.2596 -  2.1819  1232   137  0.83  23.93   1.01     0.94       9730.37|
| 11:  2.1819 -  2.1138  1252   143  0.83  23.57   1.04     0.97       8345.08|
| 12:  2.1138 -  2.0536  1237   133  0.85  22.31   1.03     1.01       7612.16|
| 13:  2.0536 -  1.9997  1239   143  0.85  22.34   1.03     0.98       6250.52|
| 14:  1.9997 -  1.9510  1097   119  0.85  22.02   1.00     0.94       5133.01|
|alpha:            min =        0.93 max =            1.06 mean =         0.98|
|beta:             min =     5133.01 max =        22065.51 mean =     12431.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           90.00 mean =        20.88|
|phase err.(test): min =        0.00 max =           89.91 mean =        20.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    99.62   16.22    None  None   None       |
|    all(noH): 2823   0      0.66    99.62   16.22    None  None   None       |
|    Sol.    : 438    0      3.45    96.55   41.99    None  None   None       |
|    Mac.    : 2385   0      0.66    99.62   11.49    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:     0.656 -  10.553: 1523   |   5:    50.138 -  60.035:  103        |
|      1:    10.553 -  20.449:  670   |   6:    60.035 -  69.931:   63        |
|      2:    20.449 -  30.345:  187   |   7:    69.931 -  79.827:   12        |
|      3:    30.345 -  40.242:  138   |   8:    79.827 -  89.724:    5        |
|      4:    40.242 -  50.138:  117   |   9:    89.724 -  99.620:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.240 - 5.533
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 340
   mapped sites are within: 0.701 - 5.533

peak=   10.716 closest distance to " O   HOH Z  72 " =    1.572
peak=    7.852 closest distance to " CB  VAL A 296 " =    1.473
peak=    7.787 closest distance to " CB  VAL A 230 " =    1.539
peak=    7.567 closest distance to " OD1 ASN A  60 " =    1.413
peak=    7.428 closest distance to " OD1 ASP A  27 " =    1.170
peak=    7.300 closest distance to " O   SER A  62 " =    1.071
peak=    6.971 closest distance to " O   HOH Z 390 " =    1.676
peak=    6.863 closest distance to " O   HOH Z 321 " =    1.127
peak=    6.776 closest distance to " N   PHE A  59 " =    0.955
peak=    6.349 closest distance to " CG2BVAL A 121 " =    1.095
peak=    6.282 closest distance to " O   HOH Z 120 " =    1.370
peak=    6.277 closest distance to " OD2 ASP A  50 " =    1.126
peak=    5.966 closest distance to " O   HOH Z 223 " =    1.477
peak=    5.679 closest distance to " O   HOH Z 381 " =    1.823
peak=    5.631 closest distance to " O   HOH Z 199 " =    1.991
peak=    5.609 closest distance to " O   HOH Z 295 " =    2.465
peak=    5.609 closest distance to " O   HOH Z 205 " =    2.144
peak=    5.590 closest distance to " O   HOH Z 363 " =    1.491
peak=    5.535 closest distance to " O   HOH Z 214 " =    1.925
peak=    5.485 closest distance to " CB  ASN A  60 " =    1.114
peak=    5.467 closest distance to " O   HOH Z 130 " =    1.646
peak=    5.448 closest distance to " N   ASN A  60 " =    1.201
peak=    5.376 closest distance to " O   HOH Z  65 " =    2.048
peak=    5.375 closest distance to " CD  ARG A 138 " =    1.110
peak=    5.327 closest distance to " SG  CYS A 168 " =    1.027
peak=    5.263 closest distance to " O   HOH Z 358 " =    1.676
peak=    5.259 closest distance to " O   HOH Z   9 " =    1.493
peak=    5.247 closest distance to " O   HOH Z  61 " =    1.305
peak=    5.234 closest distance to " O   HOH Z 385 " =    1.523
peak=    5.067 closest distance to " O   HOH Z 410 " =    1.514
peak=    5.033 closest distance to " O   HOH Z 188 " =    1.401
peak=    5.022 closest distance to " OD1 ASN A  45 " =    1.199
peak=    5.021 closest distance to " CG  LEU A   5 " =    1.541
peak=    4.956 closest distance to " O   HOH Z 316 " =    1.167
peak=    4.927 closest distance to " OD1 ASP A 286 " =    1.114
peak=    4.920 closest distance to " O   HOH Z 291 " =    1.645
peak=    4.893 closest distance to " O   HOH Z 192 " =    2.112
peak=    4.884 closest distance to " O   HOH Z 375 " =    1.515
peak=    4.758 closest distance to " O   HOH Z 332 " =    1.288
peak=    4.758 closest distance to " O   HOH Z 167 " =    0.990
peak=    4.743 closest distance to " CA  PHE A  59 " =    1.012
peak=    4.720 closest distance to " O   HOH Z 278 " =    2.447
peak=    4.697 closest distance to " O   HOH Z  53 " =    2.087
peak=    4.677 closest distance to " O   HOH Z 279 " =    1.392
peak=    4.662 closest distance to " NH1 ARG A 159 " =    0.926
peak=    4.650 closest distance to " O   HOH Z 269 " =    2.140
peak=    4.649 closest distance to " O   HOH Z 236 " =    1.701
peak=    4.644 closest distance to " O   HOH Z 126 " =    1.864
peak=    4.571 closest distance to " O   HOH Z 326 " =    1.634
peak=    4.555 closest distance to " CB  ARG A 275 " =    1.310
peak=    4.538 closest distance to " O   HOH Z 426 " =    1.305
peak=    4.529 closest distance to " O   HOH Z 388 " =    1.259
peak=    4.476 closest distance to " O   HOH Z  63 " =    1.778
peak=    4.469 closest distance to " O   HOH Z 139 " =    1.528
peak=    4.459 closest distance to " O   HOH Z 142 " =    2.073
peak=    4.431 closest distance to " CG2 THR A  29 " =    0.944
peak=    4.412 closest distance to " CD  ARG A 138 " =    1.138
peak=    4.398 closest distance to " C   PRO A 198 " =    1.424
peak=    4.381 closest distance to " O   HOH Z 112 " =    1.410
peak=    4.371 closest distance to " N   SER A  63 " =    0.812
peak=    4.369 closest distance to " O   HOH Z 403 " =    2.023
peak=    4.365 closest distance to " O   HOH Z 138 " =    1.047
peak=    4.320 closest distance to " O   HOH Z 428 " =    1.576
peak=    4.299 closest distance to " CD1AILE A 234 " =    0.959
peak=    4.279 closest distance to " O   HOH Z 245 " =    1.291
peak=    4.257 closest distance to " CZ3 TRP A  70 " =    0.903
peak=    4.253 closest distance to " CE  MET A  93 " =    1.365
peak=    4.252 closest distance to " OG ASER A 134 " =    1.326
peak=    4.241 closest distance to " CA  ILE A 234 " =    1.191
peak=    4.207 closest distance to " NH2BARG A 145 " =    1.830
peak=    4.203 closest distance to " O   HOH Z 250 " =    1.212
peak=    4.175 closest distance to " O   HOH Z 316 " =    2.163
peak=    4.167 closest distance to " O   HOH Z 133 " =    2.244
peak=    4.128 closest distance to " NH2 ARG A  56 " =    2.313
peak=    4.081 closest distance to " O   HOH Z 371 " =    1.570
peak=    4.075 closest distance to " NE1 TRP A 266 " =    2.016
peak=    4.072 closest distance to " O   HOH Z  89 " =    1.885
peak=    4.057 closest distance to " CA  PRO A  54 " =    1.025
peak=    4.051 closest distance to " O   ARG A  14 " =    1.005
peak=    4.034 closest distance to " O   HOH Z 116 " =    1.433
peak=    4.025 closest distance to " CG2 THR A 246 " =    1.136
peak=    4.024 closest distance to " CE1 PHE A  61 " =    1.099
peak=    4.012 closest distance to " CZ  PHE A  59 " =    0.925
peak=    4.004 closest distance to " N   LYS A 119 " =    0.914
peak=    4.003 closest distance to " O   HOH Z  97 " =    1.493
peak=    3.999 closest distance to " CE1 PHE A  16 " =    1.107
peak=    3.996 closest distance to " O   HOH Z  58 " =    1.869
peak=    3.985 closest distance to " CB  ASN A 148 " =    2.060
peak=    3.978 closest distance to " O   HOH Z  51 " =    2.302
peak=    3.978 closest distance to " O   HOH Z 347 " =    1.148
peak=    3.954 closest distance to " O   HOH Z 179 " =    1.152
peak=    3.952 closest distance to " O   HOH Z 123 " =    1.444
peak=    3.952 closest distance to " O   HOH Z 429 " =    1.159
peak=    3.949 closest distance to " CA  THR A 264 " =    0.701
peak=    3.931 closest distance to " O   HOH Z 134 " =    1.543
peak=    3.923 closest distance to " CD2 LEU A  25 " =    1.213
peak=    3.921 closest distance to " CB  GLN A  88 " =    1.390
peak=    3.919 closest distance to " O   HOH Z 222 " =    1.286
peak=    3.916 closest distance to " O   HOH Z 415 " =    1.164
peak=    3.914 closest distance to " NE1 TRP A 274 " =    1.157
peak=    3.900 closest distance to " O   HOH Z 427 " =    1.961
peak=    3.896 closest distance to " CE1 PHE A  38 " =    0.777
peak=    3.884 closest distance to " O   ALA A 165 " =    1.060
peak=    3.882 closest distance to " O   HOH Z 270 " =    1.531
peak=    3.849 closest distance to " CD2 HIS A 115 " =    1.007
peak=    3.848 closest distance to " O   HOH Z  54 " =    1.152
peak=    3.847 closest distance to " O   HOH Z 403 " =    1.414
peak=    3.845 closest distance to " O   HOH Z 234 " =    2.240
peak=    3.842 closest distance to " O   HOH Z 344 " =    1.515
peak=    3.835 closest distance to " CB  ALA A   1 " =    1.319
peak=    3.833 closest distance to " O   HOH Z   7 " =    1.778
peak=    3.820 closest distance to " O   HOH Z 384 " =    1.763
peak=    3.820 closest distance to " CE AMET A  47 " =    1.007
peak=    3.808 closest distance to " O   HOH Z 423 " =    2.244
peak=    3.805 closest distance to " CD1 LEU A   5 " =    1.672
peak=    3.802 closest distance to " OG1 THR A  42 " =    0.875
peak=    3.801 closest distance to " CB  ASN A 187 " =    1.086
peak=    3.798 closest distance to " CG2 ILE A 234 " =    1.099
peak=    3.793 closest distance to " O   HOH Z 360 " =    1.260
peak=    3.788 closest distance to " O   HOH Z 425 " =    1.749
peak=    3.777 closest distance to " O   HOH Z 225 " =    2.007
peak=    3.776 closest distance to " O   HOH Z 427 " =    1.275
peak=    3.774 closest distance to " O   HOH Z 117 " =    1.284
peak=    3.761 closest distance to " O   HOH Z 366 " =    2.151
peak=    3.761 closest distance to " O   HOH Z 428 " =    1.322
peak=    3.753 closest distance to " O   HOH Z 411 " =    3.601
peak=    3.748 closest distance to " N   GLN A  58 " =    0.764
peak=    3.745 closest distance to " O   HOH Z 331 " =    1.617
peak=    3.742 closest distance to " CG  GLN A 205 " =    1.192
peak=    3.731 closest distance to " CG  PRO A 198 " =    1.579
peak=    3.726 closest distance to " OD1 ASP A 238 " =    0.924
peak=    3.718 closest distance to " NH2 ARG A  36 " =    1.163
peak=    3.715 closest distance to " O   HOH Z  59 " =    1.829
peak=    3.714 closest distance to " O   HOH Z  24 " =    1.584
peak=    3.714 closest distance to " O   HOH Z 345 " =    1.660
peak=    3.686 closest distance to " O   HOH Z  39 " =    1.346
peak=    3.686 closest distance to " O   HOH Z 229 " =    1.020
peak=    3.684 closest distance to " CB  ARG A 275 " =    1.082
peak=    3.682 closest distance to " NH1 ARG A  14 " =    1.101
peak=    3.681 closest distance to " CG  LYS A  76 " =    1.495
peak=    3.666 closest distance to " CE2 PHE A  16 " =    0.902
peak=    3.666 closest distance to " O   ASP A 286 " =    0.890
peak=    3.664 closest distance to " O   HOH Z 111 " =    1.711
peak=    3.662 closest distance to " C   VAL A  72 " =    1.023
peak=    3.654 closest distance to " O   HOH Z 153 " =    1.897
peak=    3.654 closest distance to " O   HOH Z 287 " =    1.661
peak=    3.653 closest distance to " OE1 GLN A  58 " =    5.146
peak=    3.650 closest distance to " CD2 LEU A 228 " =    1.298
peak=    3.646 closest distance to " CB  SER A   3 " =    1.237
peak=    3.643 closest distance to " CG2 THR A  52 " =    1.277
peak=    3.638 closest distance to " O   HOH Z 262 " =    1.300
peak=    3.636 closest distance to " O   HOH Z 247 " =    1.333
peak=    3.635 closest distance to " CE1 TYR A 247 " =    1.469
peak=    3.634 closest distance to " O   HOH Z 176 " =    2.053
peak=    3.632 closest distance to " O   HOH Z 302 " =    1.579
peak=    3.626 closest distance to " O   ASN A  60 " =    1.145
peak=    3.623 closest distance to " N   GLU A   2 " =    1.721
peak=    3.621 closest distance to " O   HOH Z  28 " =    2.393
peak=    3.619 closest distance to " CG  GLN A  77 " =    2.065
peak=    3.617 closest distance to " O   HOH Z 124 " =    1.676
peak=    3.613 closest distance to " O   HOH Z 226 " =    1.148
peak=    3.611 closest distance to " CG  LEU A   5 " =    1.147
peak=    3.611 closest distance to " O   HOH Z 126 " =    2.298
peak=    3.611 closest distance to " O   HOH Z  91 " =    1.171
peak=    3.611 closest distance to " O   HOH Z 130 " =    2.056
peak=    3.608 closest distance to " OE2 GLU A 236 " =    1.682
peak=    3.602 closest distance to " CB  ARG A  66 " =    1.131
peak=    3.583 closest distance to " ND1 HIS A  81 " =    1.014
peak=    3.583 closest distance to " CA  ILE A  20 " =    0.915
peak=    3.582 closest distance to " NH1 ARG A 138 " =    0.931
peak=    3.576 closest distance to " O   HOH Z 430 " =    1.776
peak=    3.574 closest distance to " O   HOH Z 134 " =    1.874
peak=    3.570 closest distance to " O   HOH Z 422 " =    2.680
peak=    3.566 closest distance to " CB  ARG A  24 " =    1.647
peak=    3.560 closest distance to " CZ  ARG A 269 " =    1.119
peak=    3.559 closest distance to " CG1BVAL A 121 " =    2.203
peak=    3.556 closest distance to " CG2 ILE A  20 " =    1.239
peak=    3.554 closest distance to " CB  SER A 273 " =    0.907
peak=    3.552 closest distance to " O   HOH Z 334 " =    1.834
peak=    3.544 closest distance to " O   HOH Z 389 " =    1.411
peak=    3.544 closest distance to " O   HOH Z 133 " =    1.345
peak=    3.543 closest distance to " NZ  LYS A 117 " =    1.529
peak=    3.537 closest distance to " OG  SER A  22 " =    1.189
peak=    3.524 closest distance to " CD2 PHE A  61 " =    1.127
peak=    3.522 closest distance to " C   ALA A   1 " =    1.360
peak=    3.521 closest distance to " O   SER A 164 " =    1.486
peak=    3.519 closest distance to " NE2 GLN A  73 " =    1.900
peak=    3.513 closest distance to " NH1AARG A 145 " =    0.801
peak=    3.510 closest distance to " O   HOH Z  32 " =    1.697
peak=    3.510 closest distance to " CB  ASN A 209 " =    1.074
peak=    3.509 closest distance to " CA  TYR A  30 " =    1.039
peak=    3.506 closest distance to " CZ  PHE A  16 " =    1.042
peak=    3.505 closest distance to " O   HOH Z 104 " =    1.429
peak=    3.505 closest distance to " O   ALA A 129 " =    1.014
peak=    3.504 closest distance to " O   HOH Z 363 " =    2.448
peak=    3.498 closest distance to " O   HOH Z 119 " =    1.341
peak=    3.497 closest distance to " O   HOH Z 185 " =    1.343
peak=    3.488 closest distance to " CG  GLN A  11 " =    1.991
peak=    3.484 closest distance to " CB  TRP A 123 " =    1.103
peak=    3.472 closest distance to " CB  MET A  47 " =    1.614
peak=    3.466 closest distance to " O   PHE A  59 " =    0.886
peak=    3.463 closest distance to " O   ASP A 124 " =    1.104
peak=    3.463 closest distance to " O   HOH Z 220 " =    1.454
peak=    3.463 closest distance to " CG BARG A 145 " =    0.917
peak=    3.462 closest distance to " O   HOH Z 249 " =    1.498
peak=    3.462 closest distance to " CA  PRO A 163 " =    1.042
peak=    3.457 closest distance to " CG1 ILE A  49 " =    0.989
peak=    3.447 closest distance to " O   HOH Z 273 " =    1.491
peak=    3.447 closest distance to " CG  GLN A  88 " =    1.039
peak=    3.446 closest distance to " N   ILE A  33 " =    1.420
peak=    3.446 closest distance to " ND2 ASN A  60 " =    2.347
peak=    3.444 closest distance to " CG1 VAL A 265 " =    1.000
peak=    3.442 closest distance to " O   HOH Z 368 " =    1.713
peak=    3.440 closest distance to " O   HOH Z  35 " =    2.252
peak=    3.439 closest distance to " C   ALA A  10 " =    1.222
peak=    3.437 closest distance to " CD1 TYR A  15 " =    1.168
peak=    3.431 closest distance to " C   GLY A 111 " =    1.493
peak=    3.430 closest distance to " OD2 ASP A 238 " =    0.895
peak=    3.428 closest distance to " O   HOH Z 303 " =    2.261
peak=    3.426 closest distance to " OG  SER A  22 " =    2.596
peak=    3.420 closest distance to " O   HOH Z 232 " =    1.390
peak=    3.419 closest distance to " O   HOH Z 311 " =    1.622
peak=    3.419 closest distance to " CA  ALA A 295 " =    1.105
peak=    3.416 closest distance to " O   HOH Z 222 " =    1.974
peak=    3.410 closest distance to " O   HOH Z  27 " =    1.010
peak=    3.409 closest distance to " CA  ILE A 120 " =    0.891
peak=    3.408 closest distance to " CE2 PHE A  59 " =    0.957
peak=    3.407 closest distance to " NE2 GLN A  11 " =    1.193
peak=    3.407 closest distance to " CA  GLN A  55 " =    1.061
peak=    3.404 closest distance to " NE BARG A 145 " =    1.303
peak=    3.399 closest distance to " N   GLY A 111 " =    1.035
peak=    3.391 closest distance to " O   SER A  26 " =    1.851
peak=    3.389 closest distance to " N   ALA A 160 " =    0.953
peak=    3.382 closest distance to " CB  SER A 216 " =    0.978
peak=    3.378 closest distance to " O   ALA A 242 " =    1.116
peak=    3.376 closest distance to " O   HOH Z 194 " =    1.580
peak=    3.376 closest distance to " O   HOH Z 265 " =    1.364
peak=    3.375 closest distance to " O   HOH Z 176 " =    1.691
peak=    3.373 closest distance to " OG  SER A  62 " =    3.038
peak=    3.371 closest distance to " O   HOH Z 113 " =    1.758
peak=    3.370 closest distance to " O   HOH Z 342 " =    1.043
peak=    3.367 closest distance to " O   HOH Z  47 " =    1.725
peak=    3.365 closest distance to " CE1 TYR A  68 " =    1.030
peak=    3.361 closest distance to " CA  GLY A 287 " =    1.257
peak=    3.357 closest distance to " O   HOH Z  45 " =    1.009
peak=    3.357 closest distance to " O   HOH Z 143 " =    2.390
peak=    3.356 closest distance to " O   HOH Z 369 " =    1.393
peak=    3.356 closest distance to " CG  PRO A  54 " =    1.232
peak=    3.348 closest distance to " O   HOH Z 269 " =    2.107
peak=    3.346 closest distance to " CB  ARG A 102 " =    0.838
peak=    3.344 closest distance to " OD1 ASN A 170 " =    1.589
peak=    3.343 closest distance to " O   ILE A  20 " =    1.432
peak=    3.342 closest distance to " OE1 GLN A  58 " =    1.529
peak=    3.337 closest distance to " CA  ALA A 227 " =    1.066
peak=    3.330 closest distance to " CB  GLU A 152 " =    1.171
peak=    3.330 closest distance to " CB  ARG A 138 " =    0.818
peak=    3.329 closest distance to " O   HOH Z 215 " =    1.598
peak=    3.328 closest distance to " CA  VAL A 126 " =    1.325
peak=    3.328 closest distance to " CB  GLU A   2 " =    0.997
peak=    3.324 closest distance to " CB  LYS A 166 " =    1.010
peak=    3.324 closest distance to " OG1 THR A 246 " =    1.019
peak=    3.322 closest distance to " O   HOH Z 132 " =    1.589
peak=    3.312 closest distance to " CA  LEU A 282 " =    0.947
peak=    3.310 closest distance to " O   HOH Z 186 " =    2.693
peak=    3.310 closest distance to " CD1 ILE A  33 " =    1.419
peak=    3.304 closest distance to " CG  PRO A 163 " =    3.479
peak=    3.299 closest distance to " N   CYS A 260 " =    1.093
peak=    3.294 closest distance to " N   PHE A 130 " =    1.276
peak=    3.291 closest distance to " CD  LYS A 166 " =    1.175
peak=    3.289 closest distance to " NH1AARG A 275 " =    1.376
peak=    3.288 closest distance to " CB  SER A  95 " =    0.791
peak=    3.283 closest distance to " O   HOH Z 197 " =    2.341
peak=    3.281 closest distance to " CZ  PHE A 218 " =    1.482
peak=    3.268 closest distance to " O   HOH Z 148 " =    2.114
peak=    3.267 closest distance to " N   GLY A 302 " =    0.915
peak=    3.265 closest distance to " OG1 THR A 182 " =    1.624
peak=    3.263 closest distance to " C   PHE A 208 " =    1.708
peak=    3.259 closest distance to " CB  SER A  12 " =    1.518
peak=    3.259 closest distance to " CG2AVAL A  41 " =    1.074
peak=    3.258 closest distance to " O   SER A 271 " =    1.184
peak=    3.255 closest distance to " O   HOH Z 425 " =    1.453
peak=    3.238 closest distance to " O   HOH Z 162 " =    1.559
peak=    3.233 closest distance to " O   HOH Z 357 " =    1.698
peak=    3.233 closest distance to " O   HOH Z 406 " =    1.321
peak=    3.229 closest distance to " CE  LYS A  48 " =    1.219
peak=    3.229 closest distance to " O   HOH Z 334 " =    1.724
peak=    3.228 closest distance to " O   ILE A 120 " =    0.881
peak=    3.225 closest distance to " O   HOH Z  65 " =    1.172
peak=    3.223 closest distance to " O   HOH Z 414 " =    1.858
peak=    3.221 closest distance to " CB  PHE A  61 " =    1.390
peak=    3.220 closest distance to " CA  ASN A  45 " =    1.173
peak=    3.209 closest distance to " O   HOH Z   6 " =    1.312
peak=    3.204 closest distance to " O   HOH Z 260 " =    1.691
peak=    3.204 closest distance to " NH2 ARG A 159 " =    0.786
peak=    3.193 closest distance to " CZ  ARG A  14 " =    0.958
peak=    3.190 closest distance to " O   HOH Z  88 " =    2.566
peak=    3.188 closest distance to " O   THR A  42 " =    1.369
peak=    3.177 closest distance to " O   HOH Z 264 " =    1.144
peak=    3.177 closest distance to " O   HOH Z 101 " =    1.369
peak=    3.176 closest distance to " O   HOH Z 108 " =    1.583
peak=    3.176 closest distance to " CB  PHE A 192 " =    1.031
peak=    3.175 closest distance to " O   HOH Z 189 " =    2.196
peak=    3.171 closest distance to " CB  SER A  62 " =    1.270
peak=    3.169 closest distance to " CB  VAL A 202 " =    1.537
peak=    3.162 closest distance to " O  BHOH Z  74 " =    1.127
peak=    3.162 closest distance to " CG  TYR A  68 " =    1.390
peak=    3.160 closest distance to " O   HOH Z 137 " =    1.517
peak=    3.159 closest distance to " NH2AARG A 145 " =    2.068
peak=    3.159 closest distance to " CA  ARG A  36 " =    1.441
peak=    3.158 closest distance to " O   HOH Z  51 " =    2.339
peak=    3.158 closest distance to " NH2AARG A 275 " =    1.890
peak=    3.146 closest distance to " CG1 VAL A 250 " =    1.468
peak=    3.146 closest distance to " NE BARG A 275 " =    1.350
peak=    3.135 closest distance to " CG  LYS A 119 " =    1.086
peak=    3.134 closest distance to " CB  TRP A  85 " =    1.477
peak=    3.132 closest distance to " CA  ALA A 299 " =    0.963
peak=    3.124 closest distance to " SD  MET A  40 " =    1.464
peak=    3.122 closest distance to " O   HOH Z 381 " =    1.834
peak=    3.120 closest distance to " CD  LYS A 166 " =    1.586
peak=    3.119 closest distance to " CA  ALA A  51 " =    0.925
peak=    3.116 closest distance to " O   HOH Z 143 " =    2.602
peak=    3.111 closest distance to " CB  THR A 279 " =    1.428
peak=    3.108 closest distance to " N   TYR A  15 " =    1.256
peak=    3.107 closest distance to " O   HOH Z  66 " =    1.191
peak=    3.106 closest distance to " O   HOH Z 240 " =    2.006
peak=    3.104 closest distance to " O   HOH Z 209 " =    1.220
peak=    3.099 closest distance to " O   HOH Z 222 " =    2.172
peak=    3.092 closest distance to " O   HOH Z  33 " =    2.099
peak=    3.090 closest distance to " N   LEU A 143 " =    1.281
peak=    3.090 closest distance to " O   HOH Z 372 " =    1.395
peak=    3.090 closest distance to " N   ALA A   1 " =    3.027
peak=    3.087 closest distance to " O   HOH Z 199 " =    1.736
peak=    3.080 closest distance to " NE BARG A 275 " =    1.511
peak=    3.077 closest distance to " O   HOH Z 434 " =    5.533
peak=    3.067 closest distance to " O   HOH Z 305 " =    3.185
peak=    3.058 closest distance to " CB  PHE A 130 " =    1.102
peak=    3.052 closest distance to " O   HOH Z  43 " =    1.244
peak=    3.044 closest distance to " CE1 PHE A  16 " =    0.766

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.468 - 4.799
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 206
   mapped sites are within: 0.707 - 4.799

peak=   -5.112 closest distance to " CD  ARG A 138 " =    0.937
peak=   -5.018 closest distance to " O   SER A  62 " =    0.923
peak=   -4.744 closest distance to " N   PHE A  59 " =    0.918
peak=   -4.468 closest distance to " N   SER A  28 " =    0.917
peak=   -4.453 closest distance to " CB  ASN A  60 " =    1.121
peak=   -4.416 closest distance to " O   ALA A 165 " =    0.919
peak=   -4.356 closest distance to " N   ASN A  60 " =    0.838
peak=   -4.333 closest distance to " OG ASER A 134 " =    0.991
peak=   -4.290 closest distance to " O   GLN A  77 " =    1.371
peak=   -4.273 closest distance to " N   MET A 188 " =    1.842
peak=   -4.263 closest distance to " CD  ARG A  14 " =    3.074
peak=   -4.258 closest distance to " O   SER A  22 " =    1.304
peak=   -4.241 closest distance to " N   GLN A  58 " =    0.934
peak=   -4.231 closest distance to " CA  GLN A  55 " =    1.073
peak=   -4.068 closest distance to " NE1 TRP A  70 " =    1.139
peak=   -4.055 closest distance to " O   SER A 135 " =    1.631
peak=   -4.050 closest distance to " O   HOH Z 401 " =    1.053
peak=   -3.994 closest distance to " CG  ASP A  50 " =    1.032
peak=   -3.918 closest distance to " O   LYS A 119 " =    0.802
peak=   -3.913 closest distance to " CG2 VAL A 230 " =    0.785
peak=   -3.886 closest distance to " CE1 PHE A  16 " =    1.431
peak=   -3.886 closest distance to " CA  GLY A 133 " =    1.816
peak=   -3.885 closest distance to " O   SER A 245 " =    1.491
peak=   -3.862 closest distance to " CA  ASN A  60 " =    1.286
peak=   -3.862 closest distance to " NE2 GLN A 194 " =    1.032
peak=   -3.861 closest distance to " O   VAL A 125 " =    1.744
peak=   -3.852 closest distance to " N   SER A  62 " =    0.972
peak=   -3.845 closest distance to " O   HOH Z 167 " =    0.902
peak=   -3.808 closest distance to " OG1 THR A 178 " =    1.017
peak=   -3.785 closest distance to " NE2 HIS A 115 " =    1.506
peak=   -3.779 closest distance to " CB  ASN A 285 " =    2.076
peak=   -3.779 closest distance to " O   PHE A  61 " =    1.016
peak=   -3.777 closest distance to " CA  TYR A  68 " =    2.729
peak=   -3.759 closest distance to " O   ALA A 100 " =    2.552
peak=   -3.757 closest distance to " CG1BVAL A  72 " =    1.593
peak=   -3.742 closest distance to " O   HOH Z 388 " =    1.929
peak=   -3.734 closest distance to " O   PRO A 198 " =    1.027
peak=   -3.716 closest distance to " O   HOH Z 220 " =    1.621
peak=   -3.707 closest distance to " O   ILE A  49 " =    1.636
peak=   -3.701 closest distance to " CB  PHE A  59 " =    1.038
peak=   -3.680 closest distance to " CE2 PHE A 218 " =    2.379
peak=   -3.668 closest distance to " O   HOH Z 390 " =    2.805
peak=   -3.667 closest distance to " CZ  PHE A  16 " =    0.951
peak=   -3.662 closest distance to " O   HOH Z  24 " =    1.300
peak=   -3.661 closest distance to " O   HOH Z  82 " =    1.327
peak=   -3.659 closest distance to " O   HOH Z  88 " =    2.137
peak=   -3.658 closest distance to " C   SER A  63 " =    0.992
peak=   -3.648 closest distance to " O   HOH Z 298 " =    4.087
peak=   -3.646 closest distance to " O   ALA A  51 " =    1.173
peak=   -3.631 closest distance to " NE2 GLN A  58 " =    3.239
peak=   -3.614 closest distance to " O   ALA A 161 " =    1.702
peak=   -3.613 closest distance to " CD1 TRP A 179 " =    1.148
peak=   -3.609 closest distance to " O   HOH Z 352 " =    1.190
peak=   -3.608 closest distance to " O   HOH Z 101 " =    1.068
peak=   -3.603 closest distance to " O   PRO A 280 " =    1.707
peak=   -3.600 closest distance to " CG  PRO A 243 " =    1.452
peak=   -3.600 closest distance to " N   VAL A 125 " =    1.397
peak=   -3.599 closest distance to " CB  ALA A 244 " =    2.212
peak=   -3.586 closest distance to " CD  ARG A 219 " =    2.537
peak=   -3.584 closest distance to " O   LEU A 101 " =    1.036
peak=   -3.577 closest distance to " N   SER A 164 " =    1.148
peak=   -3.571 closest distance to " O   TRP A  92 " =    1.468
peak=   -3.563 closest distance to " O   HOH Z 267 " =    2.670
peak=   -3.548 closest distance to " OG1 THR A 246 " =    1.240
peak=   -3.546 closest distance to " CA  SER A  63 " =    1.269
peak=   -3.542 closest distance to " O   HOH Z 134 " =    1.608
peak=   -3.533 closest distance to " CE2 TYR A  30 " =    2.944
peak=   -3.532 closest distance to " NH2 ARG A  79 " =    1.664
peak=   -3.521 closest distance to " O   HOH Z  52 " =    1.023
peak=   -3.514 closest distance to " CG1AVAL A 121 " =    0.817
peak=   -3.509 closest distance to " OH  TYR A  68 " =    1.181
peak=   -3.503 closest distance to " CA  ALA A 227 " =    2.421
peak=   -3.495 closest distance to " CG  PRO A 163 " =    2.710
peak=   -3.492 closest distance to " O   HOH Z 385 " =    0.895
peak=   -3.482 closest distance to " C   SER A 288 " =    0.737
peak=   -3.480 closest distance to " NH1 ARG A 159 " =    0.957
peak=   -3.469 closest distance to " O   HOH Z 313 " =    1.439
peak=   -3.467 closest distance to " NE2 GLN A  77 " =    2.052
peak=   -3.464 closest distance to " OG1 THR A 279 " =    1.002
peak=   -3.462 closest distance to " O   HOH Z 268 " =    2.162
peak=   -3.453 closest distance to " O   HOH Z  77 " =    1.855
peak=   -3.451 closest distance to " O   HOH Z 245 " =    1.255
peak=   -3.436 closest distance to " O   HOH Z 220 " =    0.929
peak=   -3.429 closest distance to " O   HOH Z  54 " =    0.792
peak=   -3.421 closest distance to " CG  HIS A 108 " =    1.015
peak=   -3.409 closest distance to " N   THR A 235 " =    1.038
peak=   -3.407 closest distance to " N   HIS A 115 " =    1.787
peak=   -3.405 closest distance to " O   HOH Z 205 " =    1.116
peak=   -3.405 closest distance to " O   HOH Z 266 " =    4.641
peak=   -3.401 closest distance to " CG  PRO A 198 " =    1.580
peak=   -3.400 closest distance to " CG  GLN A  88 " =    0.925
peak=   -3.398 closest distance to " OD2 ASP A 253 " =    0.922
peak=   -3.395 closest distance to " O   HOH Z  93 " =    1.230
peak=   -3.388 closest distance to " CA  GLN A 205 " =    1.091
peak=   -3.385 closest distance to " O   THR A  29 " =    1.064
peak=   -3.384 closest distance to " O   HOH Z 165 " =    2.207
peak=   -3.382 closest distance to " O   HOH Z 373 " =    1.060
peak=   -3.378 closest distance to " O   HOH Z 426 " =    1.915
peak=   -3.373 closest distance to " O   HOH Z 419 " =    0.707
peak=   -3.373 closest distance to " CG BARG A 275 " =    0.722
peak=   -3.368 closest distance to " CD1 TYR A 247 " =    2.442
peak=   -3.367 closest distance to " NE BARG A 145 " =    0.963
peak=   -3.362 closest distance to " CD2 LEU A 237 " =    2.614
peak=   -3.359 closest distance to " CD2 PHE A 208 " =    1.750
peak=   -3.351 closest distance to " O   HOH Z 186 " =    1.243
peak=   -3.351 closest distance to " O   TRP A  70 " =    1.235
peak=   -3.349 closest distance to " O   HOH Z  69 " =    1.260
peak=   -3.342 closest distance to " CD2 PHE A  61 " =    0.778
peak=   -3.341 closest distance to " O   HOH Z 262 " =    1.302
peak=   -3.340 closest distance to " N   VAL A  72 " =    1.767
peak=   -3.334 closest distance to " OG  SER A   3 " =    0.932
peak=   -3.329 closest distance to " O   HOH Z 164 " =    3.638
peak=   -3.326 closest distance to " OD1 ASP A 200 " =    1.134
peak=   -3.323 closest distance to " O   HOH Z 350 " =    0.823
peak=   -3.321 closest distance to " CB  PHE A  59 " =    1.104
peak=   -3.320 closest distance to " CD1 PHE A 192 " =    0.995
peak=   -3.319 closest distance to " O   HOH Z 230 " =    1.460
peak=   -3.318 closest distance to " CB  TYR A  30 " =    1.301
peak=   -3.313 closest distance to " O   LYS A 117 " =    0.958
peak=   -3.307 closest distance to " O   HOH Z 266 " =    4.511
peak=   -3.303 closest distance to " N   GLY A  98 " =    2.204
peak=   -3.296 closest distance to " O   ARG A  56 " =    0.907
peak=   -3.288 closest distance to " O   HOH Z 435 " =    2.096
peak=   -3.284 closest distance to " N   GLN A  55 " =    1.011
peak=   -3.284 closest distance to " O   HOH Z 231 " =    1.694
peak=   -3.283 closest distance to " CZ3 TRP A 274 " =    0.870
peak=   -3.266 closest distance to " O   HOH Z 203 " =    1.346
peak=   -3.262 closest distance to " C   THR A 251 " =    1.626
peak=   -3.261 closest distance to " C   ASN A 142 " =    1.051
peak=   -3.261 closest distance to " O   HOH Z 150 " =    2.901
peak=   -3.258 closest distance to " OG  SER A  22 " =    1.418
peak=   -3.247 closest distance to " CA  GLY A 211 " =    1.181
peak=   -3.245 closest distance to " O   HOH Z 290 " =    0.866
peak=   -3.244 closest distance to " CB  CYS A 201 " =    1.414
peak=   -3.242 closest distance to " O   HOH Z 165 " =    2.173
peak=   -3.239 closest distance to " O   HOH Z 298 " =    2.414
peak=   -3.237 closest distance to " O   ALA A 129 " =    1.050
peak=   -3.236 closest distance to " O   ALA A  10 " =    1.310
peak=   -3.236 closest distance to " O   GLY A 136 " =    1.678
peak=   -3.222 closest distance to " CB  ALA A   1 " =    4.366
peak=   -3.221 closest distance to " ND2 ASN A  69 " =    1.612
peak=   -3.218 closest distance to " CZ3 TRP A 274 " =    1.706
peak=   -3.217 closest distance to " O   HOH Z  55 " =    1.427
peak=   -3.215 closest distance to " O   HOH Z  80 " =    1.530
peak=   -3.213 closest distance to " CD1 TYR A 247 " =    2.222
peak=   -3.211 closest distance to " CB  ARG A 102 " =    1.065
peak=   -3.207 closest distance to " C   ASP A 124 " =    1.923
peak=   -3.205 closest distance to " ND2 ASN A  69 " =    1.853
peak=   -3.204 closest distance to " OD2 ASP A 272 " =    1.312
peak=   -3.204 closest distance to " O   HOH Z 194 " =    1.854
peak=   -3.203 closest distance to " N   MET A  93 " =    0.943
peak=   -3.202 closest distance to " CZ  ARG A  36 " =    1.474
peak=   -3.202 closest distance to " NE  ARG A  79 " =    0.927
peak=   -3.198 closest distance to " ND2 ASN A 284 " =    0.920
peak=   -3.197 closest distance to " CA  ASN A 142 " =    2.083
peak=   -3.195 closest distance to " O   HOH Z 171 " =    1.972
peak=   -3.191 closest distance to " CB  ALA A 233 " =    2.347
peak=   -3.189 closest distance to " C   SER A 276 " =    1.491
peak=   -3.182 closest distance to " CB  SER A 276 " =    1.581
peak=   -3.181 closest distance to " CD  PRO A 198 " =    1.382
peak=   -3.178 closest distance to " SG BCYS A 201 " =    1.019
peak=   -3.175 closest distance to " O   HOH Z 244 " =    1.320
peak=   -3.173 closest distance to " O   HOH Z 431 " =    1.074
peak=   -3.173 closest distance to " CZ2 TRP A  70 " =    2.201
peak=   -3.171 closest distance to " N   LEU A 281 " =    1.961
peak=   -3.171 closest distance to " O   HOH Z 190 " =    1.504
peak=   -3.169 closest distance to " O   HOH Z 426 " =    1.479
peak=   -3.167 closest distance to " NE  ARG A 156 " =    1.344
peak=   -3.164 closest distance to " O   ASP A 107 " =    1.429
peak=   -3.161 closest distance to " CB  VAL A 125 " =    1.162
peak=   -3.161 closest distance to " CB  ALA A  19 " =    2.666
peak=   -3.160 closest distance to " O   HOH Z 316 " =    1.348
peak=   -3.157 closest distance to " CD1 LEU A  96 " =    2.046
peak=   -3.154 closest distance to " O   HOH Z 273 " =    3.239
peak=   -3.151 closest distance to " CA  SER A 164 " =    1.452
peak=   -3.151 closest distance to " CB  ALA A   1 " =    2.972
peak=   -3.142 closest distance to " CB  LEU A 101 " =    1.844
peak=   -3.138 closest distance to " SD  MET A 105 " =    1.754
peak=   -3.137 closest distance to " ND2 ASN A 127 " =    1.188
peak=   -3.135 closest distance to " O   HIS A 115 " =    1.958
peak=   -3.132 closest distance to " C   ASN A 217 " =    1.614
peak=   -3.130 closest distance to " O   HOH Z  72 " =    1.624
peak=   -3.125 closest distance to " O   HOH Z 256 " =    1.117
peak=   -3.124 closest distance to " CG AARG A 145 " =    0.740
peak=   -3.123 closest distance to " O   HOH Z 345 " =    1.938
peak=   -3.123 closest distance to " O   ALA A  43 " =    1.845
peak=   -3.122 closest distance to " CG  ASP A 140 " =    0.897
peak=   -3.111 closest distance to " O   HOH Z 164 " =    4.799
peak=   -3.108 closest distance to " O   HOH Z 163 " =    1.353
peak=   -3.107 closest distance to " ND2 ASN A 209 " =    1.523
peak=   -3.091 closest distance to " O   SER A 276 " =    1.399
peak=   -3.084 closest distance to " N   THR A   4 " =    2.183
peak=   -3.076 closest distance to " N   ALA A 114 " =    2.440
peak=   -3.075 closest distance to " OD1 ASP A 286 " =    1.143
peak=   -3.074 closest distance to " CD2 LEU A 222 " =    2.312
peak=   -3.063 closest distance to " ND1 HIS A 115 " =    1.332
peak=   -3.061 closest distance to " CG  TRP A 266 " =    1.470
peak=   -3.061 closest distance to " O   HOH Z 148 " =    2.874
peak=   -3.054 closest distance to " O   HOH Z 166 " =    1.961
peak=   -3.030 closest distance to " CA  GLN A 205 " =    0.875
peak=   -3.021 closest distance to " O   HOH Z 287 " =    1.576

================= 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    :  0.5246 0.5252   6.312127e+00   6.308192e+00
   1_bss:  0.5170 0.5137   6.307393e+00   6.299295e+00
   1_xyz:  0.4697 0.4918   6.264708e+00   6.281864e+00
   1_adp:  0.4340 0.4885   6.236655e+00   6.279158e+00
   1_occ:  0.4335 0.4883   6.236168e+00   6.279460e+00
   2_bss:  0.4335 0.4867   6.237397e+00   6.278437e+00
   2_xyz:  0.3907 0.4555   6.170720e+00   6.247826e+00
   2_adp:  0.3793 0.4543   6.155002e+00   6.240547e+00
   2_occ:  0.3790 0.4544   6.154874e+00   6.240698e+00
   3_bss:  0.3793 0.4564   6.157206e+00   6.241921e+00
   3_xyz:  0.3217 0.3939   6.034568e+00   6.160605e+00
   3_adp:  0.2936 0.3776   5.975407e+00   6.132542e+00
   3_occ:  0.2933 0.3781   5.975522e+00   6.132810e+00
   4_bss:  0.2919 0.3766   5.971921e+00   6.129252e+00
   4_xyz:  0.2392 0.3148   5.809199e+00   5.998692e+00
   4_adp:  0.2228 0.2904   5.742681e+00   5.922108e+00
   4_occ:  0.2224 0.2898   5.741357e+00   5.920557e+00
   5_bss:  0.2219 0.2884   5.738448e+00   5.916813e+00
   5_xyz:  0.1841 0.2394   5.565122e+00   5.755698e+00
   5_adp:  0.1682 0.2230   5.486826e+00   5.697992e+00
   5_occ:  0.1679 0.2226   5.485470e+00   5.695591e+00
   5_bss:  0.1675 0.2223   5.484488e+00   5.694538e+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:  0.390   0.000   6.251   8.413   8.277   0.000   0.000   0.000
   1_xyz:  0.390   0.000   6.251   8.413   8.277   0.000   0.000   0.000
   1_adp:  0.390   0.000   6.251   8.413   8.277   0.000   0.000   0.000
   1_occ:  0.390   0.000   6.251   8.413   8.277   0.000   0.000   0.000
   2_bss:  0.360  20.000   4.018   5.672   6.380   0.000   0.000   0.000
   2_xyz:  0.360  20.000   4.018   5.672   6.380   0.000   0.000   0.000
   2_adp:  0.360  20.000   4.018   5.672   6.380   0.000   0.000   0.000
   2_occ:  0.360  20.000   4.018   5.672   6.380   0.000   0.000   0.000
   3_bss:  0.331  39.496   2.642   3.923   4.564   0.000   0.000   0.000
   3_xyz:  0.331  39.496   2.642   3.923   4.564   0.000   0.000   0.000
   3_adp:  0.331  39.496   2.642   3.923   4.564   0.000   0.000   0.000
   3_occ:  0.331  39.496   2.642   3.923   4.564   0.000   0.000   0.000
   4_bss:  0.338  45.638   1.609   2.051   2.897   0.000   0.000   0.000
   4_xyz:  0.338  45.638   1.609   2.051   2.897   0.000   0.000   0.000
   4_adp:  0.338  45.638   1.609   2.051   2.897   0.000   0.000   0.000
   4_occ:  0.338  45.638   1.609   2.051   2.897   0.000   0.000   0.000
   5_bss:  0.326  35.021   0.799   1.124   2.003   0.000   0.000   0.000
   5_xyz:  0.326  35.021   0.799   1.124   2.003   0.000   0.000   0.000
   5_adp:  0.326  35.021   0.799   1.124   2.003   0.000   0.000   0.000
   5_occ:  0.326  35.021   0.799   1.124   2.003   0.000   0.000   0.000
   5_bss:  0.313  30.645  -0.412  -0.243   0.654   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  68.659 0.2815  0.3448    89083.502
   1_bss:  68.258 0.2856  0.4296    86271.963
   1_xyz:  64.589 0.3324  0.4898    78287.047
   1_adp:  63.484 0.3468  0.5549    77183.147
   1_occ:  63.662 0.3444  0.5497    77354.366
   2_bss:  63.289 0.3492  0.5223    76857.712
   2_xyz:  55.740 0.4464  0.6723    64512.534
   2_adp:  52.853 0.4841  0.7511    61924.485
   2_occ:  52.852 0.4841  0.7507    61933.801
   3_bss:  52.890 0.4836  0.7095    62357.703
   3_xyz:  43.651 0.5984  0.8757    44686.760
   3_adp:  40.339 0.6388  0.9137    39695.891
   3_occ:  40.375 0.6384  0.9130    39754.455
   4_bss:  40.156 0.6407  0.8657    39139.828
   4_xyz:  32.839 0.7256  0.9566    26571.856
   4_adp:  28.799 0.7719  0.9884    22108.762
   4_occ:  28.732 0.7727  0.9893    22026.596
   5_bss:  28.580 0.7741  0.9578    21644.504
   5_xyz:  22.740 0.8356  1.0014    14426.726
   5_adp:  20.883 0.8544  1.0047    12566.332
   5_occ:  20.845 0.8547  1.0049    12515.872
   5_bss:  20.798 0.8551  0.9802    12432.044
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.084   5.2304e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.084   5.2304e+01
   1_xyz:   1.842  0.015  0.113 18.574  0.007  4.101   1.7282e-01
   1_adp:   1.842  0.015  0.113 18.574  0.007  4.101   1.7282e-01
   1_occ:   1.842  0.015  0.113 18.574  0.007  4.101   1.7282e-01
   2_bss:   1.842  0.015  0.113 18.574  0.007  4.101   1.7282e-01
   2_xyz:   1.186  0.008  0.076 16.908  0.005  4.112   9.4472e-02
   2_adp:   1.186  0.008  0.076 16.908  0.005  4.112   9.4472e-02
   2_occ:   1.186  0.008  0.076 16.908  0.005  4.112   9.4472e-02
   3_bss:   1.186  0.008  0.076 16.908  0.005  4.112   9.4472e-02
   3_xyz:   1.303  0.009  0.088 16.991  0.005  4.098   1.0150e-01
   3_adp:   1.303  0.009  0.088 16.991  0.005  4.098   1.0150e-01
   3_occ:   1.303  0.009  0.088 16.991  0.005  4.098   1.0150e-01
   4_bss:   1.303  0.009  0.088 16.991  0.005  4.098   1.0150e-01
   4_xyz:   1.114  0.008  0.075 16.038  0.004  4.102   7.9168e-02
   4_adp:   1.114  0.008  0.075 16.038  0.004  4.102   7.9168e-02
   4_occ:   1.114  0.008  0.075 16.038  0.004  4.102   7.9168e-02
   5_bss:   1.114  0.008  0.075 16.038  0.004  4.102   7.9168e-02
   5_xyz:   0.927  0.006  0.060 15.545  0.003  4.111   6.0431e-02
   5_adp:   0.927  0.006  0.060 15.545  0.003  4.111   6.0431e-02
   5_occ:   0.927  0.006  0.060 15.545  0.003  4.111   6.0431e-02
   5_bss:   0.927  0.006  0.060 15.545  0.003  4.111   6.0431e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.444   6.7659e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.444   6.7659e+00
   1_xyz:  15.324  0.201  0.492 86.357  0.059  2.010   1.0772e-01
   1_adp:  15.324  0.201  0.492 86.357  0.059  2.010   1.0772e-01
   1_occ:  15.324  0.201  0.492 86.357  0.059  2.010   1.0772e-01
   2_bss:  15.324  0.201  0.492 86.357  0.059  2.010   1.0772e-01
   2_xyz:   7.361  0.093  0.279 77.868  0.044  2.122   5.7338e-02
   2_adp:   7.361  0.093  0.279 77.868  0.044  2.122   5.7338e-02
   2_occ:   7.361  0.093  0.279 77.868  0.044  2.122   5.7338e-02
   3_bss:   7.361  0.093  0.279 77.868  0.044  2.122   5.7338e-02
   3_xyz:   9.170  0.080  0.305 73.947  0.048  2.113   7.8205e-02
   3_adp:   9.170  0.080  0.305 73.947  0.048  2.113   7.8205e-02
   3_occ:   9.170  0.080  0.305 73.947  0.048  2.113   7.8205e-02
   4_bss:   9.170  0.080  0.305 73.947  0.048  2.113   7.8205e-02
   4_xyz:   8.435  0.048  0.353 77.118  0.027  2.036   7.4052e-02
   4_adp:   8.435  0.048  0.353 77.118  0.027  2.036   7.4052e-02
   4_occ:   8.435  0.048  0.353 77.118  0.027  2.036   7.4052e-02
   5_bss:   8.435  0.048  0.353 77.118  0.027  2.036   7.4052e-02
   5_xyz:   7.300  0.039  0.200 89.092  0.025  2.168   1.0417e-01
   5_adp:   7.300  0.039  0.200 89.092  0.025  2.168   1.0417e-01
   5_occ:   7.300  0.039  0.200 89.092  0.025  2.168   1.0417e-01
   5_bss:   7.300  0.039  0.200 89.092  0.025  2.168   1.0417e-01
------------------------------------------------------------------------
           |-----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:  86.17   0.00  16.14  74.84   0.00  15.40  86.17   0.00  20.13
   1_occ:  86.17   0.00  16.14  74.84   0.00  15.40  86.17   0.00  20.13
   2_bss:  86.17   0.00  16.14  74.84   0.00  15.40  86.17   0.00  20.13
   2_xyz:  86.17   0.00  16.14  74.84   0.00  15.40  86.17   0.00  20.13
   2_adp:  84.40   0.00  16.17  81.68   0.00  15.00  84.40   0.00  22.58
   2_occ:  84.40   0.00  16.17  81.68   0.00  15.00  84.40   0.00  22.58
   3_bss:  84.40   0.00  16.17  81.68   0.00  15.00  84.40   0.00  22.58
   3_xyz:  84.40   0.00  16.17  81.68   0.00  15.00  84.40   0.00  22.58
   3_adp: 101.91   0.00  17.03 101.91   0.00  14.04  99.92   0.00  33.28
   3_occ: 101.91   0.00  17.03 101.91   0.00  14.04  99.92   0.00  33.28
   4_bss: 101.91   0.00  17.03 101.91   0.00  14.04  99.92   0.00  33.28
   4_xyz: 101.91   0.00  17.03 101.91   0.00  14.04  99.92   0.00  33.28
   4_adp:  98.98   0.00  15.31  98.98   0.00  11.73  97.89   1.95  34.84
   4_occ:  98.98   0.00  15.31  98.98   0.00  11.73  97.89   1.95  34.84
   5_bss:  98.98   0.00  15.31  98.98   0.00  11.73  97.89   1.95  34.84
   5_xyz:  98.98   0.00  15.31  98.98   0.00  11.73  97.89   1.95  34.84
   5_adp:  98.96   0.00  15.57  98.96   0.00  10.84  95.89   2.80  41.33
   5_occ:  98.96   0.00  15.57  98.96   0.00  10.84  95.89   2.80  41.33
   5_bss:  99.62   0.66  16.22  99.62   0.66  11.49  96.55   3.45  41.99
------------------------------------------------------------------------
 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:    1.300    0.011    0.425
   1_adp:    1.300    0.011    0.425
   1_occ:    1.300    0.011    0.425
   2_bss:    1.300    0.011    0.425
   2_xyz:    1.641    0.038    0.551
   2_adp:    1.641    0.038    0.551
   2_occ:    1.641    0.038    0.551
   3_bss:    1.641    0.038    0.551
   3_xyz:    1.764    0.047    0.722
   3_adp:    1.764    0.047    0.722
   3_occ:    1.764    0.047    0.722
   4_bss:    1.764    0.047    0.722
   4_xyz:    1.782    0.071    0.844
   4_adp:    1.782    0.071    0.844
   4_occ:    1.782    0.071    0.844
   5_bss:    1.782    0.071    0.844
   5_xyz:    1.899    0.042    0.920
   5_adp:    1.899    0.042    0.920
   5_occ:    1.899    0.042    0.920
   5_bss:    1.899    0.042    0.920
------------------------------------------------------------------------

CPU time actual refinement: 369.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_132/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_132/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_132/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_132/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_132/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.85 
  Macro-tasks:
    bulk solvent and scale       = 48.26  
    individual site refinement   = 161.85 
    weights calculation          = 31.74  
    collect and process          = 6.15   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 248.10 
  Micro-tasks:
    mask                            = 2.78   
    f_calc                          = 118.13 
    alpha_beta                      = 8.45   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 124.33 
    fmodel                         = 8.42   
    r_factors                      = 0.25   
    phase_errors                   = 10.00  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 273.78 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.041 micro seconds
Total CPU time: 6.38 minutes
from_scatterers_fft:    677 calls, 117.69 s
gradients_fft:          623 calls, 112.27 s

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

# Date 2008-01-16 Time 00:51:50 PST -0800 (1200473510.19 s)
Start R-work = 0.5246, R-free = 0.5252 (no bulk solvent and anisotropic scale)
Final R-work = 0.1819, R-free = 0.2376 (no bulk solvent and anisotropic scale)

Start R-work = 0.5170, R-free = 0.5137
Final R-work = 0.1675, R-free = 0.2223