# Date 2008-01-16 Time 01:10:49 PST -0800 (1200474649.23 s)
#phil __OFF__

Command line arguments: "../324.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23122
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 324

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.3993, 86.39, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8383 1.97069
Completeness in resolution range: 0.949908
Completeness with d_max=infinity: 0.946969

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8383
                             d_min =   1.9707

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8383 1.97069
Completeness in resolution range: 0.949908
Completeness with d_max=infinity: 0.946969

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8387 -  4.2163 [2178/2206]  1957   221  10.1%
  bin  2:  4.2163 -  3.3594 [2064/2087]  1860   204   9.9%
  bin  3:  3.3594 -  2.9385 [2061/2083]  1855   206  10.0%
  bin  4:  2.9385 -  2.6715 [2034/2053]  1832   202   9.9%
  bin  5:  2.6715 -  2.4810 [2023/2052]  1812   211  10.4%
  bin  6:  2.4810 -  2.3353 [2006/2048]  1812   194   9.7%
  bin  7:  2.3353 -  2.2187 [2002/2038]  1805   197   9.8%
  bin  8:  2.2187 -  2.1224 [1998/2035]  1796   202  10.1%
  bin  9:  2.1224 -  2.0409 [1985/2017]  1788   197   9.9%
  bin 10:  2.0409 -  1.9707 [1238/2003]  1113   125  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_324/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:
        1.63 -     2.29: 15
        2.29 -     2.94: 1617
        2.94 -     3.59: 4505
        3.59 -     4.25: 9214
        4.25 -     4.90: 13022
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.635 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.713 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.844 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.991 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28368 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_324/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_324/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.3993 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4527   r_free= 0.4379   ksol= 0.00   Bsol= 0.00   scale= 0.814    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.250679                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8387 -  4.7024 0.99   1403  157 0.3668 0.3585      6.5308      6.5575|
|  2:  4.7024 -  3.7523 0.99   1363  151 0.3521 0.3650      6.6913       6.727|
|  3:  3.7523 -  3.2838 0.99   1328  149 0.4040 0.3767      6.6019      6.6128|
|  4:  3.2838 -  2.9863 0.99   1312  137 0.4337 0.3942      6.4717      6.3879|
|  5:  2.9863 -  2.7737 0.99   1308  149 0.4793 0.4636      6.3407      6.3681|
|  6:  2.7737 -  2.6111 0.98   1304  149 0.4782 0.5190      6.2538      6.1872|
|  7:  2.6111 -  2.4810 0.99   1298  152 0.4834 0.4618      6.2197      6.1572|
|  8:  2.4810 -  2.3734 0.99   1307  131 0.5024 0.4527      6.1664      6.1368|
|  9:  2.3734 -  2.2824 0.98   1295  148 0.5051 0.5360      6.0921      6.1448|
| 10:  2.2824 -  2.2039 0.98   1273  142 0.5144 0.4553      6.1157      6.0587|
| 11:  2.2039 -  2.1352 0.98   1285  147 0.5129 0.4809      6.0213      6.0223|
| 12:  2.1352 -  2.0743 0.99   1289  137 0.5197 0.5230      5.9654      5.9894|
| 13:  2.0743 -  2.0199 0.97   1268  137 0.5197 0.5173      5.8851      5.8268|
| 14:  2.0199 -  1.9707 0.47    597   73 0.5270 0.4601      5.8854      5.7329|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8387 -  4.7024  1403   157  0.70  33.97   0.81     0.71      67549.67|
|  2:  4.7024 -  3.7523  1363   151  0.74  31.67   0.91     0.79      87084.63|
|  3:  3.7523 -  3.2838  1328   149  0.67  37.86   0.86     0.77      88086.75|
|  4:  3.2838 -  2.9863  1312   137  0.62  42.34   0.82     0.69      73909.91|
|  5:  2.9863 -  2.7737  1308   149  0.52  50.77   0.75     0.59      66469.17|
|  6:  2.7737 -  2.6111  1304   149  0.48  53.51   0.74     0.54      60653.15|
|  7:  2.6111 -  2.4810  1298   152  0.45  55.72   0.77     0.51      57389.07|
|  8:  2.4810 -  2.3734  1307   131  0.46  54.99   0.75     0.53      49771.83|
|  9:  2.3734 -  2.2824  1295   148  0.46  55.53   0.74     0.54      45710.26|
| 10:  2.2824 -  2.2039  1273   142  0.47  54.28   0.75     0.55      40906.13|
| 11:  2.2039 -  2.1352  1285   147  0.44  57.06   0.75     0.53      40279.05|
| 12:  2.1352 -  2.0743  1289   137  0.40  59.76   0.78     0.51      38686.09|
| 13:  2.0743 -  2.0199  1268   137  0.39  60.55   0.74     0.48      33374.92|
| 14:  2.0199 -  1.9707   597    73  0.45  56.15   0.74     0.48      23686.42|
|alpha:            min =        0.48 max =            0.79 mean =         0.59|
|beta:             min =    23686.42 max =        88086.75 mean =     56854.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.96 mean =        49.84|
|phase err.(test): min =        0.00 max =           89.75 mean =        49.92|
|-----------------------------------------------------------------------------|

============================== 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 = 9.064324              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.003   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.755601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.724   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.117 -  1.496:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.496 -  1.874:       14 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.874 -  2.252:      134 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.252 -  2.630:      614 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.630 -  3.009:     1443 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.009 -  3.387:     2533 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.387 -  3.765:     3963 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.765 -  4.143:     5155 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.143 -  4.522:     6652 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.522 -  4.900:     7891 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.621 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.117 |       2.021 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    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 = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4595   r_free= 0.4453   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.253867                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4443   r_free= 0.4319   ksol= 0.35   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.78,9.58,7.97,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.241409                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.867902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.466   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.777034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.789   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4443      final r-factor (work) = 0.3401          |
| start r-factor (free) = 0.4319      final r-factor (free) = 0.3596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.3728 = 8.87 * 0.50 * 6.2590 + 1.00 * 53.6205                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2363 = 8.87 * 0.50 * 6.1134 + 1.00 * 0.1299                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3401      final r-factor (work) = 0.2822          |
| start r-factor (free) = 0.3596      final r-factor (free) = 0.3182          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7646 = 0.78 * 1.00 * 6.1134 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6463 = 0.78 * 1.00 * 5.9623 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.68   11.52    None  None   None       |
|    all(noH): 2823   0      0.00    65.68   11.52    None  None   None       |
|    Sol.    : 438    0      0.00    65.68   27.19    None  None   None       |
|    Mac.    : 2385   0      0.00    60.77   8.64     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 -   6.568: 1222   |   5:    32.842 -  39.410:  112        |
|      1:     6.568 -  13.137:  776   |   6:    39.410 -  45.979:   55        |
|      2:    13.137 -  19.705:  328   |   7:    45.979 -  52.547:   21        |
|      3:    19.705 -  26.274:  166   |   8:    52.547 -  59.115:   21        |
|      4:    26.274 -  32.842:  114   |   9:    59.115 -  65.684:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2822 r_free = 0.3182             target_work(ml) = 5.916         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2817 r_free = 0.3182             target_work(ml) = 5.916         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2817   r_free= 0.3182   ksol= 0.35   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.78,9.58,7.97,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.915550                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2775   r_free= 0.3154   ksol= 0.33   Bsol= 35.92   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.20,5.60,4.92,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.915387                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.659660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.461   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.996  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2775      final r-factor (work) = 0.1810          |
| start r-factor (free) = 0.3154      final r-factor (free) = 0.2208          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0138 = 5.66 * 0.50 * 5.9664 + 1.00 * 0.1299                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2955 = 5.66 * 0.50 * 5.7324 + 1.00 * 0.0738                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1810      final r-factor (work) = 0.1597          |
| start r-factor (free) = 0.2208      final r-factor (free) = 0.2011          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0101 = 0.35 * 1.00 * 5.7324 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9287 = 0.35 * 1.00 * 5.4755 + 1.00 * 0.0240                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.66   11.69    None  None   None       |
|    all(noH): 2823   0      0.00    70.66   11.69    None  None   None       |
|    Sol.    : 438    0      1.40    63.15   32.15    None  None   None       |
|    Mac.    : 2385   0      0.00    70.66   7.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.066: 1455   |   5:    35.330 -  42.396:   99        |
|      1:     7.066 -  14.132:  704   |   6:    42.396 -  49.462:   76        |
|      2:    14.132 -  21.198:  197   |   7:    49.462 -  56.528:   38        |
|      3:    21.198 -  28.264:  120   |   8:    56.528 -  63.594:   21        |
|      4:    28.264 -  35.330:  108   |   9:    63.594 -  70.660:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1597 r_free = 0.2011             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1595 r_free = 0.2009             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1595   r_free= 0.2009   ksol= 0.33   Bsol= 35.92   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.20,5.60,4.92,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.428625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1578   r_free= 0.2000   ksol= 0.32   Bsol= 41.17   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,3.83,4.06,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.425820                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.852505              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.559  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347762              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.784   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1578      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.2000      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6407 = 3.85 * 0.50 * 5.4858 + 1.00 * 0.0737                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3302 = 3.85 * 0.50 * 5.3259 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8669 = 0.35 * 1.00 * 5.3259 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8204 = 0.35 * 1.00 * 5.2016 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.86   11.86    None  None   None       |
|    all(noH): 2823   0      0.00    76.86   11.86    None  None   None       |
|    Sol.    : 438    0      0.72    66.97   34.03    None  None   None       |
|    Mac.    : 2385   0      0.00    76.86   7.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.686: 1607   |   5:    38.428 -  46.114:  102        |
|      1:     7.686 -  15.371:  619   |   6:    46.114 -  53.799:   68        |
|      2:    15.371 -  23.057:  161   |   7:    53.799 -  61.485:   33        |
|      3:    23.057 -  30.743:  109   |   8:    61.485 -  69.171:   15        |
|      4:    30.743 -  38.428:  105   |   9:    69.171 -  76.856:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1598             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1599             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1599   ksol= 0.32   Bsol= 41.17   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,3.83,4.06,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.184496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1599   ksol= 0.33   Bsol= 44.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.28,3.86,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.928398              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.111  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.177766              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.790  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0882 = 1.93 * 0.50 * 5.2032 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0492 = 1.93 * 0.50 * 5.1750 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9401 = 0.18 * 1.00 * 5.1750 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9598 = 0.18 * 1.00 * 5.1701 + 1.00 * 0.0407                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.37   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    76.37   11.65    None  None   None       |
|    Sol.    : 438    0      0.86    66.60   33.05    None  None   None       |
|    Mac.    : 2385   0      0.00    76.37   7.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.637: 1636   |   5:    38.186 -  45.823:   94        |
|      1:     7.637 -  15.274:  604   |   6:    45.823 -  53.460:   64        |
|      2:    15.274 -  22.912:  152   |   7:    53.460 -  61.097:   31        |
|      3:    22.912 -  30.549:  115   |   8:    61.097 -  68.735:   12        |
|      4:    30.549 -  38.186:  111   |   9:    68.735 -  76.372:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1564             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1563             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1563   ksol= 0.33   Bsol= 44.50   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.28,3.86,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1563   ksol= 0.33   Bsol= 43.80   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.28,3.86,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164874                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.010459              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.241  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.609385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.309   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8395 = 3.01 * 0.50 * 5.1686 + 1.00 * 0.0595                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8188 = 3.01 * 0.50 * 5.1439 + 1.00 * 0.0761                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2909 = 1.61 * 1.00 * 5.1439 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2622 = 1.61 * 1.00 * 5.1260 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.87   11.87    None  None   None       |
|    all(noH): 2823   0      0.00    81.87   11.87    None  None   None       |
|    Sol.    : 438    0      0.99    73.70   34.43    None  None   None       |
|    Mac.    : 2385   0      0.00    81.87   7.73     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 -   8.187: 1701   |   5:    40.936 -  49.123:   93        |
|      1:     8.187 -  16.374:  550   |   6:    49.123 -  57.311:   63        |
|      2:    16.374 -  24.562:  158   |   7:    57.311 -  65.498:   26        |
|      3:    24.562 -  32.749:  109   |   8:    65.498 -  73.685:    7        |
|      4:    32.749 -  40.936:  110   |   9:    73.685 -  81.872:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1555             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1555             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1555   ksol= 0.33   Bsol= 43.80   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.28,3.86,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132855                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8387 -  4.7024 0.99   1403  157 0.0970 0.1275      5.3653      5.5345|
|  2:  4.7024 -  3.7523 0.99   1363  151 0.0834 0.1102      5.4171      5.6417|
|  3:  3.7523 -  3.2838 0.99   1328  149 0.1038 0.1471      5.4573      5.8172|
|  4:  3.2838 -  2.9863 0.99   1312  137 0.1172 0.1502      5.4225      5.5832|
|  5:  2.9863 -  2.7737 0.99   1308  149 0.1291 0.1630      5.3103      5.4906|
|  6:  2.7737 -  2.6111 0.98   1304  149 0.1217 0.2007      5.1951      5.4989|
|  7:  2.6111 -  2.4810 0.99   1298  152 0.1186 0.1521      5.1443      5.3319|
|  8:  2.4810 -  2.3734 0.99   1307  131 0.1107 0.1713      5.0605      5.3191|
|  9:  2.3734 -  2.2824 0.98   1295  148 0.1167 0.1956      5.0234      5.3538|
| 10:  2.2824 -  2.2039 0.98   1273  142 0.1087 0.1599      4.9622      5.1571|
| 11:  2.2039 -  2.1352 0.98   1285  147 0.1076 0.1738      4.9069      5.2379|
| 12:  2.1352 -  2.0743 0.99   1289  137 0.1061 0.1654      4.8339      5.1367|
| 13:  2.0743 -  2.0199 0.97   1268  137 0.1065 0.1670      4.7644      5.0038|
| 14:  2.0199 -  1.9707 0.47    597   73 0.1065 0.1857      4.7037      4.9718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8387 -  4.7024  1403   157  0.94   8.88   0.98     0.96       6951.13|
|  2:  4.7024 -  3.7523  1363   151  0.95   7.94   1.02     1.00       8864.17|
|  3:  3.7523 -  3.2838  1328   149  0.93  11.18   1.03     1.02      10274.75|
|  4:  3.2838 -  2.9863  1312   137  0.92  13.26   1.01     0.99       9866.67|
|  5:  2.9863 -  2.7737  1308   149  0.90  15.87   1.00     0.97       8193.38|
|  6:  2.7737 -  2.6111  1304   149  0.90  16.16   0.97     0.94       6777.71|
|  7:  2.6111 -  2.4810  1298   152  0.91  15.14   0.98     0.95       6035.92|
|  8:  2.4810 -  2.3734  1307   131  0.91  15.08   0.99     0.97       5446.11|
|  9:  2.3734 -  2.2824  1295   148  0.90  16.29   1.01     0.97       5102.93|
| 10:  2.2824 -  2.2039  1273   142  0.90  16.10   0.99     0.96       4604.25|
| 11:  2.2039 -  2.1352  1285   147  0.90  15.82   1.00     0.96       4263.26|
| 12:  2.1352 -  2.0743  1289   137  0.91  15.08   1.01     0.99       3707.24|
| 13:  2.0743 -  2.0199  1268   137  0.91  15.49   1.00     0.98       3277.57|
| 14:  2.0199 -  1.9707   597    73  0.90  16.09   0.97     0.93       2857.04|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2857.04 max =        10274.75 mean =      6325.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1555   ksol= 0.32   Bsol= 47.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.12,0.81,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132769                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1555   ksol= 0.32   Bsol= 47.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.12,0.81,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132769                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8387 -  4.7024 0.99   1403  157 0.0969 0.1275       5.364      5.5341|
|  2:  4.7024 -  3.7523 0.99   1363  151 0.0835 0.1102      5.4177      5.6426|
|  3:  3.7523 -  3.2838 0.99   1328  149 0.1038 0.1472      5.4578      5.8176|
|  4:  3.2838 -  2.9863 0.99   1312  137 0.1172 0.1500      5.4223      5.5828|
|  5:  2.9863 -  2.7737 0.99   1308  149 0.1291 0.1630      5.3099      5.4902|
|  6:  2.7737 -  2.6111 0.98   1304  149 0.1216 0.2005      5.1947      5.4978|
|  7:  2.6111 -  2.4810 0.99   1298  152 0.1186 0.1522       5.144       5.332|
|  8:  2.4810 -  2.3734 0.99   1307  131 0.1107 0.1712      5.0604       5.319|
|  9:  2.3734 -  2.2824 0.98   1295  148 0.1168 0.1953      5.0235      5.3536|
| 10:  2.2824 -  2.2039 0.98   1273  142 0.1087 0.1599      4.9625      5.1584|
| 11:  2.2039 -  2.1352 0.98   1285  147 0.1075 0.1738       4.907      5.2378|
| 12:  2.1352 -  2.0743 0.99   1289  137 0.1060 0.1656      4.8341      5.1378|
| 13:  2.0743 -  2.0199 0.97   1268  137 0.1065 0.1669      4.7644      5.0027|
| 14:  2.0199 -  1.9707 0.47    597   73 0.1064 0.1856      4.7033      4.9713|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8387 -  4.7024  1403   157  0.94   8.87   0.98     0.96       6922.69|
|  2:  4.7024 -  3.7523  1363   151  0.95   7.93   1.02     1.01       8861.94|
|  3:  3.7523 -  3.2838  1328   149  0.93  11.19   1.03     1.02      10290.78|
|  4:  3.2838 -  2.9863  1312   137  0.92  13.26   1.01     1.00       9864.17|
|  5:  2.9863 -  2.7737  1308   149  0.90  15.86   1.00     0.97       8182.97|
|  6:  2.7737 -  2.6111  1304   149  0.90  16.15   0.98     0.94       6769.85|
|  7:  2.6111 -  2.4810  1298   152  0.91  15.13   0.99     0.95       6031.53|
|  8:  2.4810 -  2.3734  1307   131  0.91  15.08   1.00     0.97       5445.10|
|  9:  2.3734 -  2.2824  1295   148  0.90  16.29   1.01     0.98       5104.60|
| 10:  2.2824 -  2.2039  1273   142  0.90  16.10   1.00     0.97       4607.51|
| 11:  2.2039 -  2.1352  1285   147  0.90  15.83   1.00     0.97       4266.70|
| 12:  2.1352 -  2.0743  1289   137  0.91  15.09   1.01     1.00       3709.94|
| 13:  2.0743 -  2.0199  1268   137  0.91  15.49   1.01     0.99       3276.15|
| 14:  2.0199 -  1.9707   597    73  0.90  16.08   0.98     0.94       2852.07|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2852.07 max =        10290.78 mean =      6322.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.03|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.21    85.08   15.08    None  None   None       |
|    all(noH): 2823   0      3.21    85.08   15.08    None  None   None       |
|    Sol.    : 438    0      4.20    76.91   37.64    None  None   None       |
|    Mac.    : 2385   0      3.21    85.08   10.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.207 -  11.394: 1701   |   5:    44.143 -  52.330:   93        |
|      1:    11.394 -  19.581:  550   |   6:    52.330 -  60.517:   63        |
|      2:    19.581 -  27.768:  158   |   7:    60.517 -  68.704:   26        |
|      3:    27.768 -  35.955:  109   |   8:    68.704 -  76.891:    7        |
|      4:    35.955 -  44.143:  110   |   9:    76.891 -  85.079:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.339 - 4.866
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.718 - 4.866

peak=   11.077 closest distance to " CB  VAL A 230 " =    1.463
peak=    6.483 closest distance to " CG  LEU A   5 " =    1.148
peak=    6.281 closest distance to " CB  VAL A 296 " =    1.171
peak=    5.737 closest distance to " NH2 ARG A  56 " =    2.279
peak=    5.644 closest distance to " CG  LEU A 228 " =    1.132
peak=    5.164 closest distance to " NE2 GLN A  11 " =    1.090
peak=    5.107 closest distance to " CG  PRO A  54 " =    1.210
peak=    5.053 closest distance to " CB  ARG A 275 " =    0.945
peak=    4.952 closest distance to " CB  GLN A 183 " =    1.303
peak=    4.900 closest distance to " CB  GLN A 223 " =    1.426
peak=    4.879 closest distance to " CB  VAL A 230 " =    1.173
peak=    4.846 closest distance to " O   HOH Z 142 " =    1.691
peak=    4.844 closest distance to " O   HOH Z 209 " =    2.306
peak=    4.841 closest distance to " CB  SER A  63 " =    1.187
peak=    4.802 closest distance to " CD2 LEU A   5 " =    1.121
peak=    4.782 closest distance to " O   HOH Z  85 " =    1.531
peak=    4.728 closest distance to " O   HOH Z 193 " =    1.756
peak=    4.728 closest distance to " CG2 VAL A 296 " =    0.967
peak=    4.631 closest distance to " O   HOH Z 126 " =    1.827
peak=    4.615 closest distance to " C   PRO A 198 " =    1.425
peak=    4.614 closest distance to " O   SER A  87 " =    2.193
peak=    4.600 closest distance to " O   HOH Z 232 " =    2.358
peak=    4.516 closest distance to " CB  ARG A  79 " =    1.441
peak=    4.502 closest distance to " CB  GLU A 152 " =    1.183
peak=    4.447 closest distance to " O   HOH Z 272 " =    1.876
peak=    4.424 closest distance to " O   HOH Z 346 " =    1.565
peak=    4.423 closest distance to " O   HOH Z 403 " =    1.800
peak=    4.400 closest distance to " O   HOH Z 236 " =    1.957
peak=    4.393 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.361 closest distance to " O   HOH Z 298 " =    1.813
peak=    4.315 closest distance to " O   HOH Z 423 " =    1.826
peak=    4.306 closest distance to " CG1 VAL A 296 " =    1.183
peak=    4.290 closest distance to " O   HOH Z 402 " =    1.441
peak=    4.218 closest distance to " O   HOH Z 234 " =    3.563
peak=    4.214 closest distance to " O   HOH Z  63 " =    2.201
peak=    4.200 closest distance to " CB  PRO A  54 " =    0.863
peak=    4.152 closest distance to " O   HOH Z  97 " =    1.903
peak=    4.147 closest distance to " O   HOH Z 368 " =    2.303
peak=    4.143 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.137 closest distance to " O   HOH Z  54 " =    1.650
peak=    4.125 closest distance to " O   HOH Z 158 " =    3.112
peak=    4.123 closest distance to " OD1 ASN A  69 " =    2.559
peak=    4.106 closest distance to " O   HOH Z  61 " =    1.647
peak=    4.104 closest distance to " O   HOH Z 369 " =    2.320
peak=    4.095 closest distance to " CB  GLU A 277 " =    3.554
peak=    4.093 closest distance to " O   HOH Z 124 " =    1.292
peak=    4.090 closest distance to " O   HOH Z 316 " =    2.976
peak=    4.075 closest distance to " O   HOH Z 126 " =    1.877
peak=    4.062 closest distance to " O   HOH Z  59 " =    2.234
peak=    4.062 closest distance to " CD2 TRP A 179 " =    1.383
peak=    4.058 closest distance to " CG  PRO A 213 " =    1.196
peak=    4.026 closest distance to " O   HOH Z 327 " =    1.561
peak=    4.026 closest distance to " O   HOH Z 265 " =    2.271
peak=    4.010 closest distance to " O   HOH Z 130 " =    2.743
peak=    4.007 closest distance to " CG  PRO A 243 " =    1.153
peak=    4.000 closest distance to " O   HOH Z  43 " =    2.120
peak=    3.998 closest distance to " ND2 ASN A 187 " =    1.531
peak=    3.980 closest distance to " CB  SER A   3 " =    1.244
peak=    3.967 closest distance to " O   HOH Z  80 " =    1.769
peak=    3.961 closest distance to " O   HOH Z 427 " =    2.754
peak=    3.950 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.949 closest distance to " O   HOH Z 280 " =    2.973
peak=    3.943 closest distance to " CB  TRP A 179 " =    1.315
peak=    3.939 closest distance to " N   ASN A  39 " =    1.259
peak=    3.922 closest distance to " CG2 ILE A  20 " =    1.391
peak=    3.919 closest distance to " O   HOH Z  97 " =    2.436
peak=    3.915 closest distance to " O   HOH Z 154 " =    1.481
peak=    3.900 closest distance to " O   HOH Z 371 " =    3.294
peak=    3.884 closest distance to " O   HOH Z 303 " =    2.123
peak=    3.884 closest distance to " O   HOH Z 345 " =    3.007
peak=    3.883 closest distance to " O   HOH Z 389 " =    1.922
peak=    3.879 closest distance to " CB  ARG A 190 " =    1.716
peak=    3.878 closest distance to " O   HOH Z 248 " =    1.560
peak=    3.874 closest distance to " CG1BVAL A  72 " =    1.682
peak=    3.870 closest distance to " CB  SER A  26 " =    1.779
peak=    3.870 closest distance to " CZ  PHE A 218 " =    1.133
peak=    3.869 closest distance to " O   HOH Z 411 " =    3.864
peak=    3.865 closest distance to " O   HOH Z 197 " =    2.804
peak=    3.843 closest distance to " O   HOH Z 128 " =    1.957
peak=    3.837 closest distance to " O   HOH Z 203 " =    1.641
peak=    3.832 closest distance to " CD2 LEU A 228 " =    1.224
peak=    3.816 closest distance to " CB  ARG A 139 " =    1.008
peak=    3.810 closest distance to " O   HOH Z  40 " =    1.739
peak=    3.800 closest distance to " O   HOH Z 414 " =    1.499
peak=    3.799 closest distance to " O   HOH Z 422 " =    2.582
peak=    3.787 closest distance to " O   HOH Z 189 " =    2.636
peak=    3.778 closest distance to " O   HOH Z 147 " =    1.750
peak=    3.772 closest distance to " CD  LYS A 166 " =    1.340
peak=    3.765 closest distance to " CA  ALA A  51 " =    0.980
peak=    3.751 closest distance to " CB  ASP A 140 " =    1.068
peak=    3.747 closest distance to " O   HOH Z  15 " =    2.071
peak=    3.739 closest distance to " O   HOH Z 193 " =    2.078
peak=    3.737 closest distance to " CG1 ILE A  33 " =    1.224
peak=    3.729 closest distance to " CB  TRP A 266 " =    1.025
peak=    3.727 closest distance to " O   HOH Z 214 " =    2.435
peak=    3.715 closest distance to " O   HOH Z 102 " =    1.272
peak=    3.714 closest distance to " CA  ALA A  21 " =    1.151
peak=    3.709 closest distance to " NZ  LYS A 117 " =    3.035
peak=    3.709 closest distance to " O   TRP A 274 " =    1.869
peak=    3.709 closest distance to " O   HOH Z 245 " =    1.407
peak=    3.707 closest distance to " OG BSER A 164 " =    2.179
peak=    3.701 closest distance to " O   HOH Z 227 " =    1.629
peak=    3.696 closest distance to " OE1 GLU A   2 " =    2.123
peak=    3.690 closest distance to " O   HOH Z 425 " =    2.086
peak=    3.683 closest distance to " O   HOH Z 417 " =    3.188
peak=    3.677 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.666 closest distance to " CG  PRO A 198 " =    1.173
peak=    3.658 closest distance to " O   HOH Z 365 " =    2.854
peak=    3.655 closest distance to " OD2 ASP A 298 " =    3.900
peak=    3.647 closest distance to " O   HOH Z  78 " =    1.612
peak=    3.643 closest distance to " CG  GLN A  58 " =    2.782
peak=    3.638 closest distance to " O   HOH Z 344 " =    2.966
peak=    3.637 closest distance to " CA  LYS A 117 " =    1.304
peak=    3.631 closest distance to " O   HOH Z 250 " =    1.481
peak=    3.623 closest distance to " CB  VAL A 202 " =    1.468
peak=    3.620 closest distance to " CB  THR A  52 " =    0.902
peak=    3.617 closest distance to " O   HOH Z 416 " =    2.743
peak=    3.615 closest distance to " CB  GLU A 128 " =    1.163
peak=    3.615 closest distance to " CG1 ILE A  49 " =    1.449
peak=    3.615 closest distance to " CB  THR A  31 " =    1.528
peak=    3.614 closest distance to " O   HOH Z 421 " =    1.674
peak=    3.609 closest distance to " O   ASP A 124 " =    1.214
peak=    3.607 closest distance to " O   HOH Z 261 " =    1.856
peak=    3.604 closest distance to " CB  VAL A 265 " =    1.281
peak=    3.599 closest distance to " CA  ARG A  36 " =    0.978
peak=    3.599 closest distance to " O   HOH Z 426 " =    1.473
peak=    3.598 closest distance to " O   ALA A 165 " =    1.446
peak=    3.594 closest distance to " O   HOH Z 128 " =    2.255
peak=    3.590 closest distance to " O   HOH Z 273 " =    2.849
peak=    3.589 closest distance to " O   HOH Z  35 " =    2.313
peak=    3.584 closest distance to " O   HOH Z 250 " =    1.348
peak=    3.579 closest distance to " O   HOH Z 383 " =    1.893
peak=    3.563 closest distance to " O   HOH Z 299 " =    4.219
peak=    3.562 closest distance to " O   HOH Z 130 " =    2.313
peak=    3.552 closest distance to " CG  GLN A  77 " =    2.314
peak=    3.548 closest distance to " CB  ALA A 295 " =    1.211
peak=    3.548 closest distance to " CA  ASN A 215 " =    1.135
peak=    3.547 closest distance to " NH2 ARG A 156 " =    1.073
peak=    3.543 closest distance to " NE2 GLN A  77 " =    3.214
peak=    3.534 closest distance to " CD  ARG A 159 " =    0.726
peak=    3.533 closest distance to " CA  VAL A  41 " =    0.817
peak=    3.530 closest distance to " O   HOH Z 359 " =    1.431
peak=    3.529 closest distance to " CB  ALA A 248 " =    1.374
peak=    3.520 closest distance to " C   ILE A 106 " =    1.888
peak=    3.517 closest distance to " O   HOH Z 214 " =    2.414
peak=    3.505 closest distance to " O   HOH Z 357 " =    1.906
peak=    3.497 closest distance to " OD1 ASP A 286 " =    1.754
peak=    3.486 closest distance to " CG2 ILE A 120 " =    1.141
peak=    3.484 closest distance to " CG2 THR A 221 " =    1.264
peak=    3.484 closest distance to " O   HOH Z 261 " =    2.289
peak=    3.478 closest distance to " O   HOH Z 134 " =    1.331
peak=    3.476 closest distance to " OD2 ASP A 286 " =    2.753
peak=    3.473 closest distance to " O   HOH Z 112 " =    1.685
peak=    3.467 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.452 closest distance to " CG  MET A 185 " =    1.103
peak=    3.448 closest distance to " NH2 ARG A  79 " =    1.326
peak=    3.438 closest distance to " CD1 LEU A 228 " =    1.865
peak=    3.438 closest distance to " N   SER A 135 " =    1.383
peak=    3.436 closest distance to " O   HOH Z  44 " =    1.917
peak=    3.434 closest distance to " CA  ARG A 195 " =    1.293
peak=    3.433 closest distance to " N   ASP A 162 " =    1.250
peak=    3.426 closest distance to " CZ3 TRP A  85 " =    0.957
peak=    3.420 closest distance to " O   HOH Z 380 " =    1.922
peak=    3.415 closest distance to " O   HOH Z 109 " =    2.365
peak=    3.408 closest distance to " CA  ALA A 291 " =    0.887
peak=    3.400 closest distance to " O   HOH Z  48 " =    1.588
peak=    3.397 closest distance to " CB  TRP A 150 " =    1.476
peak=    3.397 closest distance to " O   HOH Z  68 " =    2.226
peak=    3.391 closest distance to " O   HOH Z 437 " =    1.848
peak=    3.390 closest distance to " NH2BARG A 145 " =    2.069
peak=    3.382 closest distance to " O   HOH Z  88 " =    2.547
peak=    3.381 closest distance to " CD  ARG A 269 " =    0.974
peak=    3.378 closest distance to " CB  ASN A 142 " =    1.169
peak=    3.376 closest distance to " CB  ASN A 110 " =    1.133
peak=    3.374 closest distance to " O   HOH Z 188 " =    2.213
peak=    3.372 closest distance to " CB  GLU A  46 " =    1.055
peak=    3.362 closest distance to " O   HOH Z 313 " =    1.788
peak=    3.361 closest distance to " CA  ASP A 140 " =    1.159
peak=    3.361 closest distance to " CB BVAL A  41 " =    1.112
peak=    3.360 closest distance to " O   HOH Z 322 " =    2.120
peak=    3.357 closest distance to " OG  SER A  62 " =    2.811
peak=    3.354 closest distance to " O   HOH Z 367 " =    3.337
peak=    3.353 closest distance to " O   HOH Z 263 " =    1.682
peak=    3.353 closest distance to " O   HOH Z 435 " =    1.943
peak=    3.353 closest distance to " O   HOH Z  48 " =    1.630
peak=    3.349 closest distance to " O   HOH Z 261 " =    1.905
peak=    3.346 closest distance to " O   HOH Z 108 " =    2.471
peak=    3.345 closest distance to " NH2AARG A 275 " =    3.558
peak=    3.343 closest distance to " O   HOH Z 251 " =    1.664
peak=    3.340 closest distance to " O   HOH Z 187 " =    2.289
peak=    3.340 closest distance to " O   HOH Z 419 " =    1.682
peak=    3.340 closest distance to " O   ASN A  74 " =    1.782
peak=    3.337 closest distance to " CD1 ILE A 106 " =    1.095
peak=    3.337 closest distance to " OH  TYR A 116 " =    1.111
peak=    3.335 closest distance to " O   HOH Z 374 " =    2.562
peak=    3.334 closest distance to " O   HOH Z 180 " =    2.213
peak=    3.322 closest distance to " CB  LYS A 290 " =    1.069
peak=    3.320 closest distance to " OE1 GLN A  11 " =    1.750
peak=    3.316 closest distance to " CE  LYS A  76 " =    0.887
peak=    3.315 closest distance to " ND2 ASN A 110 " =    1.562
peak=    3.308 closest distance to " O   HOH Z 420 " =    2.194
peak=    3.305 closest distance to " CG  ARG A  66 " =    0.944
peak=    3.303 closest distance to " N   PHE A 130 " =    1.330
peak=    3.303 closest distance to " O   HOH Z 171 " =    1.926
peak=    3.297 closest distance to " CA  ALA A 158 " =    1.398
peak=    3.294 closest distance to " CA  TYR A 116 " =    1.449
peak=    3.293 closest distance to " CG  LEU A 167 " =    1.200
peak=    3.288 closest distance to " CB  GLN A 205 " =    1.172
peak=    3.286 closest distance to " OE2 GLU A  53 " =    2.008
peak=    3.283 closest distance to " O   HOH Z 325 " =    2.064
peak=    3.278 closest distance to " CD BLYS A 290 " =    1.086
peak=    3.278 closest distance to " O   HOH Z 438 " =    2.583
peak=    3.273 closest distance to " O   HOH Z 423 " =    3.275
peak=    3.271 closest distance to " CB  ALA A   1 " =    1.182
peak=    3.269 closest distance to " O   HOH Z 166 " =    3.755
peak=    3.269 closest distance to " CG BARG A 102 " =    1.796
peak=    3.265 closest distance to " O   HOH Z 185 " =    1.717
peak=    3.264 closest distance to " O   HOH Z  88 " =    3.062
peak=    3.263 closest distance to " OG1 THR A 294 " =    2.327
peak=    3.263 closest distance to " CA  ASP A 162 " =    1.113
peak=    3.261 closest distance to " CB  ALA A 100 " =    1.098
peak=    3.261 closest distance to " O   HOH Z  47 " =    1.720
peak=    3.258 closest distance to " CA  ASP A 191 " =    1.153
peak=    3.258 closest distance to " O   HOH Z 411 " =    1.782
peak=    3.258 closest distance to " O   HOH Z 126 " =    1.520
peak=    3.256 closest distance to " CA  ALA A  84 " =    1.348
peak=    3.255 closest distance to " CA  ASN A 176 " =    1.139
peak=    3.254 closest distance to " OG  SER A  22 " =    2.681
peak=    3.249 closest distance to " NH1AARG A 145 " =    1.185
peak=    3.247 closest distance to " CB  HIS A 108 " =    0.819
peak=    3.245 closest distance to " O   HOH Z 345 " =    1.543
peak=    3.239 closest distance to " CD  LYS A 119 " =    1.886
peak=    3.231 closest distance to " CZ  PHE A  38 " =    1.234
peak=    3.229 closest distance to " O   HOH Z 291 " =    1.514
peak=    3.229 closest distance to " O   HOH Z 189 " =    2.607
peak=    3.220 closest distance to " CA  SER A  32 " =    1.647
peak=    3.219 closest distance to " CG2 ILE A 234 " =    2.131
peak=    3.217 closest distance to " O   HOH Z 257 " =    2.301
peak=    3.215 closest distance to " CG BARG A 275 " =    1.317
peak=    3.214 closest distance to " O   HOH Z 298 " =    4.770
peak=    3.209 closest distance to " O   HOH Z 329 " =    4.036
peak=    3.208 closest distance to " CG2AVAL A 121 " =    2.167
peak=    3.200 closest distance to " CB  ALA A 291 " =    1.330
peak=    3.194 closest distance to " O   HOH Z 162 " =    1.987
peak=    3.192 closest distance to " CD2 TYR A  30 " =    0.909
peak=    3.192 closest distance to " O   HOH Z 162 " =    1.571
peak=    3.191 closest distance to " O   HOH Z 292 " =    1.590
peak=    3.187 closest distance to " O   HOH Z 305 " =    3.464
peak=    3.180 closest distance to " CB  PRO A  90 " =    1.194
peak=    3.173 closest distance to " CB  THR A 157 " =    1.105
peak=    3.170 closest distance to " O   HOH Z 234 " =    1.871
peak=    3.167 closest distance to " CD2 TYR A 186 " =    1.015
peak=    3.167 closest distance to " CG AARG A 275 " =    1.192
peak=    3.161 closest distance to " CD  ARG A  79 " =    1.838
peak=    3.161 closest distance to " CB  LYS A 290 " =    1.272
peak=    3.153 closest distance to " CD2 HIS A  81 " =    0.990
peak=    3.150 closest distance to " O   HOH Z 116 " =    1.753
peak=    3.150 closest distance to " O   HOH Z 279 " =    2.141
peak=    3.148 closest distance to " CD1 LEU A 300 " =    1.254
peak=    3.147 closest distance to " CZ2 TRP A 179 " =    1.731
peak=    3.141 closest distance to " CB  SER A 141 " =    1.096
peak=    3.138 closest distance to " O   HOH Z  14 " =    2.079
peak=    3.133 closest distance to " CA  VAL A 126 " =    1.031
peak=    3.132 closest distance to " O   HOH Z 403 " =    1.430
peak=    3.131 closest distance to " O   HOH Z  49 " =    2.450
peak=    3.130 closest distance to " C   ALA A 299 " =    0.904
peak=    3.130 closest distance to " O   HOH Z 260 " =    1.551
peak=    3.127 closest distance to " CB  MET A  47 " =    1.221
peak=    3.124 closest distance to " N   VAL A 126 " =    1.390
peak=    3.124 closest distance to " O   ALA A   1 " =    1.751
peak=    3.121 closest distance to " OG  SER A 245 " =    1.501
peak=    3.121 closest distance to " O   HOH Z  46 " =    1.408
peak=    3.118 closest distance to " O   HOH Z 406 " =    1.515
peak=    3.116 closest distance to " O   HOH Z 438 " =    1.956
peak=    3.116 closest distance to " CG  MET A 185 " =    0.977
peak=    3.115 closest distance to " CB  THR A 279 " =    1.650
peak=    3.108 closest distance to " O   HOH Z  83 " =    1.570
peak=    3.096 closest distance to " O   HOH Z  61 " =    1.498
peak=    3.096 closest distance to " OD1 ASP A 231 " =    1.913
peak=    3.096 closest distance to " O   HOH Z 368 " =    3.636
peak=    3.090 closest distance to " CA  GLY A 267 " =    0.793
peak=    3.083 closest distance to " NE AARG A 190 " =    2.180
peak=    3.078 closest distance to " CB  ASN A 215 " =    1.124
peak=    3.072 closest distance to " O   HOH Z 281 " =    4.866
peak=    3.071 closest distance to " O   HOH Z  71 " =    2.225
peak=    3.068 closest distance to " NE2 HIS A 207 " =    1.379
peak=    3.059 closest distance to " O   HOH Z 238 " =    2.441
peak=    3.057 closest distance to " O   HOH Z 163 " =    1.794
peak=    3.056 closest distance to " O   HOH Z 302 " =    1.873
peak=    3.055 closest distance to " NZ  LYS A 166 " =    3.043
peak=    3.049 closest distance to " O   HOH Z 175 " =    2.177
peak=    3.045 closest distance to " CB  ILE A 120 " =    1.422
peak=    3.042 closest distance to " CB  ARG A 190 " =    1.090
peak=    3.034 closest distance to " CB  LEU A 255 " =    0.718
peak=    3.026 closest distance to " CA  MET A 105 " =    1.039
peak=    3.025 closest distance to " O   HOH Z 132 " =    2.855
peak=    3.019 closest distance to " O   GLU A   2 " =    1.581

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.779 - 5.626

peak=   -5.073 closest distance to " CG2 VAL A 230 " =    0.779
peak=   -4.800 closest distance to " SG  CYS A 254 " =    3.298
peak=   -4.543 closest distance to " CD  ARG A 156 " =    2.014
peak=   -4.526 closest distance to " CD  GLN A  58 " =    1.183
peak=   -4.467 closest distance to " O   HOH Z 266 " =    4.955
peak=   -4.249 closest distance to " CG  GLN A 223 " =    2.187
peak=   -4.232 closest distance to " O   PRO A 163 " =    2.171
peak=   -4.201 closest distance to " C   HIS A 108 " =    1.231
peak=   -4.178 closest distance to " OXT GLY A 302 " =    2.767
peak=   -4.142 closest distance to " OG BSER A 134 " =    1.348
peak=   -4.113 closest distance to " O   HOH Z 231 " =    2.256
peak=   -4.110 closest distance to " CD1 LEU A 101 " =    2.395
peak=   -4.107 closest distance to " CD2 PHE A 192 " =    2.039
peak=   -4.065 closest distance to " CG2BVAL A  41 " =    2.618
peak=   -4.063 closest distance to " O   HOH Z 166 " =    1.750
peak=   -4.016 closest distance to " O   HOH Z 196 " =    2.092
peak=   -4.003 closest distance to " CB  ALA A 291 " =    2.308
peak=   -3.996 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.993 closest distance to " CB  ALA A 248 " =    2.309
peak=   -3.975 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.931 closest distance to " O   HOH Z  13 " =    1.687
peak=   -3.914 closest distance to " O   HOH Z 351 " =    1.521
peak=   -3.886 closest distance to " CB  PRO A 243 " =    2.586
peak=   -3.850 closest distance to " OG  SER A  97 " =    2.279
peak=   -3.848 closest distance to " O   HOH Z 114 " =    3.228
peak=   -3.819 closest distance to " ND2 ASN A  45 " =    1.105
peak=   -3.810 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.763 closest distance to " O   VAL A  67 " =    2.816
peak=   -3.761 closest distance to " N   ALA A 248 " =    1.841
peak=   -3.755 closest distance to " CD1 LEU A 255 " =    2.730
peak=   -3.751 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.742 closest distance to " CG2 THR A 178 " =    2.232
peak=   -3.733 closest distance to " CB  PRO A 163 " =    2.486
peak=   -3.715 closest distance to " O   SER A 210 " =    1.944
peak=   -3.713 closest distance to " CB  ALA A 248 " =    2.061
peak=   -3.704 closest distance to " O   PHE A 218 " =    1.653
peak=   -3.702 closest distance to " N   THR A 235 " =    1.362
peak=   -3.693 closest distance to " CB  ALA A 161 " =    2.550
peak=   -3.686 closest distance to " O   HOH Z  11 " =    1.885
peak=   -3.677 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -3.674 closest distance to " O   HOH Z 166 " =    1.629
peak=   -3.664 closest distance to " O   HOH Z 353 " =    2.151
peak=   -3.659 closest distance to " O   HOH Z  37 " =    1.891
peak=   -3.657 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.649 closest distance to " O   HOH Z 426 " =    1.797
peak=   -3.645 closest distance to " C   ILE A 239 " =    2.172
peak=   -3.633 closest distance to " O   HOH Z 290 " =    1.142
peak=   -3.622 closest distance to " CD2 TYR A 293 " =    2.011
peak=   -3.620 closest distance to " CD  ARG A 139 " =    1.667
peak=   -3.615 closest distance to " CG1 VAL A 296 " =    1.146
peak=   -3.606 closest distance to " O   HOH Z 407 " =    2.829
peak=   -3.599 closest distance to " NE2 GLN A  88 " =    1.844
peak=   -3.588 closest distance to " CD1 PHE A  59 " =    2.024
peak=   -3.572 closest distance to " O   HOH Z 394 " =    1.569
peak=   -3.544 closest distance to " CD  LYS A 289 " =    2.455
peak=   -3.543 closest distance to " O   ASN A  45 " =    1.865
peak=   -3.538 closest distance to " N   ALA A 226 " =    1.933
peak=   -3.533 closest distance to " CB  ASP A 132 " =    2.294
peak=   -3.528 closest distance to " O   VAL A  67 " =    1.874
peak=   -3.525 closest distance to " O   HOH Z 131 " =    4.018
peak=   -3.523 closest distance to " CG1 VAL A 250 " =    2.746
peak=   -3.519 closest distance to " O   PRO A 198 " =    1.261
peak=   -3.508 closest distance to " O   HOH Z 193 " =    1.697
peak=   -3.497 closest distance to " O   HOH Z 102 " =    1.683
peak=   -3.491 closest distance to " ND2 ASN A  39 " =    1.127
peak=   -3.488 closest distance to " CG2 VAL A 296 " =    1.414
peak=   -3.479 closest distance to " OG  SER A   3 " =    1.734
peak=   -3.478 closest distance to " O   HOH Z 423 " =    2.085
peak=   -3.473 closest distance to " CG  ASP A 231 " =    0.844
peak=   -3.472 closest distance to " OD2 ASP A 171 " =    2.265
peak=   -3.468 closest distance to " O   HOH Z  19 " =    2.140
peak=   -3.467 closest distance to " O   VAL A 189 " =    2.646
peak=   -3.463 closest distance to " CB  LEU A  83 " =    2.356
peak=   -3.461 closest distance to " C   ALA A 158 " =    1.253
peak=   -3.461 closest distance to " OD2 ASP A 191 " =    1.517
peak=   -3.459 closest distance to " O   VAL A 174 " =    2.130
peak=   -3.456 closest distance to " O   HOH Z 234 " =    3.931
peak=   -3.450 closest distance to " N   SER A 276 " =    1.389
peak=   -3.447 closest distance to " OG ASER A 134 " =    1.217
peak=   -3.447 closest distance to " O   GLY A  75 " =    1.819
peak=   -3.446 closest distance to " NH2 ARG A  66 " =    1.647
peak=   -3.445 closest distance to " O   HOH Z 185 " =    2.500
peak=   -3.444 closest distance to " OD1 ASN A 148 " =    1.508
peak=   -3.441 closest distance to " CG2 ILE A 263 " =    2.242
peak=   -3.441 closest distance to " O   HOH Z 165 " =    1.934
peak=   -3.433 closest distance to " CB  ASN A  39 " =    2.228
peak=   -3.432 closest distance to " NE2 GLN A  88 " =    1.087
peak=   -3.431 closest distance to " NH2AARG A 275 " =    4.978
peak=   -3.428 closest distance to " O   GLY A  80 " =    2.472
peak=   -3.425 closest distance to " CD1 LEU A  25 " =    2.515
peak=   -3.416 closest distance to " O   HOH Z   6 " =    1.753
peak=   -3.413 closest distance to " NE2 GLN A 194 " =    1.813
peak=   -3.402 closest distance to " CE  MET A 105 " =    2.207
peak=   -3.392 closest distance to " N   PHE A  59 " =    2.187
peak=   -3.390 closest distance to " O   ALA A 161 " =    1.771
peak=   -3.381 closest distance to " CD2 LEU A 300 " =    2.821
peak=   -3.377 closest distance to " O   HOH Z 139 " =    3.179
peak=   -3.371 closest distance to " CB  ASP A 231 " =    2.453
peak=   -3.371 closest distance to " O   HOH Z 283 " =    1.982
peak=   -3.369 closest distance to " N   THR A 157 " =    1.504
peak=   -3.367 closest distance to " CE3 TRP A 150 " =    1.981
peak=   -3.363 closest distance to " N   GLN A  58 " =    1.676
peak=   -3.352 closest distance to " C   LEU A 143 " =    0.958
peak=   -3.351 closest distance to " O   HOH Z  15 " =    1.497
peak=   -3.346 closest distance to " O   HOH Z  88 " =    4.286
peak=   -3.345 closest distance to " O   SER A 271 " =    1.947
peak=   -3.343 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.342 closest distance to " O   GLY A 196 " =    1.121
peak=   -3.340 closest distance to " CD2 LEU A 167 " =    1.736
peak=   -3.336 closest distance to " O   ALA A  51 " =    1.242
peak=   -3.335 closest distance to " O   ALA A   1 " =    1.703
peak=   -3.331 closest distance to " CG  GLU A  53 " =    1.595
peak=   -3.328 closest distance to " OXT GLY A 302 " =    3.403
peak=   -3.327 closest distance to " CA  GLY A 203 " =    2.372
peak=   -3.327 closest distance to " O   ARG A  24 " =    1.986
peak=   -3.324 closest distance to " CG1 VAL A 230 " =    1.861
peak=   -3.324 closest distance to " O   HOH Z 389 " =    1.791
peak=   -3.323 closest distance to " O   HOH Z 177 " =    1.667
peak=   -3.322 closest distance to " ND2 ASN A  69 " =    1.788
peak=   -3.318 closest distance to " OD1 ASN A  39 " =    2.143
peak=   -3.318 closest distance to " CZ  PHE A  59 " =    1.570
peak=   -3.311 closest distance to " O   HOH Z 211 " =    1.637
peak=   -3.308 closest distance to " CD  GLN A 223 " =    0.854
peak=   -3.306 closest distance to " CG  ASP A  50 " =    2.262
peak=   -3.305 closest distance to " CE  LYS A 166 " =    3.082
peak=   -3.304 closest distance to " CE1 TYR A 247 " =    2.618
peak=   -3.301 closest distance to " O   HOH Z 136 " =    2.258
peak=   -3.298 closest distance to " O   HOH Z 139 " =    5.140
peak=   -3.291 closest distance to " N   HIS A 115 " =    2.099
peak=   -3.287 closest distance to " O   HOH Z 123 " =    2.337
peak=   -3.286 closest distance to " C   GLN A 205 " =    1.837
peak=   -3.282 closest distance to " O   HOH Z  52 " =    1.618
peak=   -3.280 closest distance to " CG  GLU A 277 " =    1.170
peak=   -3.277 closest distance to " O   ASN A 187 " =    1.520
peak=   -3.274 closest distance to " CA  GLY A  23 " =    1.893
peak=   -3.273 closest distance to " OG BSER A 134 " =    1.698
peak=   -3.272 closest distance to " NE1 TRP A 266 " =    2.462
peak=   -3.271 closest distance to " C   THR A 279 " =    1.165
peak=   -3.271 closest distance to " NH2 ARG A  66 " =    5.016
peak=   -3.271 closest distance to " N   MET A 188 " =    1.900
peak=   -3.264 closest distance to " O   ALA A   8 " =    1.941
peak=   -3.260 closest distance to " NH2 ARG A  79 " =    2.046
peak=   -3.259 closest distance to " O   HOH Z  17 " =    1.345
peak=   -3.258 closest distance to " O   HOH Z 174 " =    4.181
peak=   -3.252 closest distance to " O   HOH Z 191 " =    5.626
peak=   -3.248 closest distance to " O   HOH Z  97 " =    1.211
peak=   -3.246 closest distance to " O   HOH Z 422 " =    1.667
peak=   -3.241 closest distance to " CB  ALA A 291 " =    2.136
peak=   -3.241 closest distance to " CG  GLU A   2 " =    1.854
peak=   -3.240 closest distance to " O   ILE A 234 " =    1.223
peak=   -3.238 closest distance to " O   MET A  40 " =    2.790
peak=   -3.238 closest distance to " O   SER A 273 " =    1.506
peak=   -3.236 closest distance to " C   SER A 206 " =    1.589
peak=   -3.236 closest distance to " CG2 VAL A 189 " =    1.996
peak=   -3.226 closest distance to " CG1 VAL A 112 " =    2.835
peak=   -3.224 closest distance to " O   HOH Z 243 " =    1.888
peak=   -3.222 closest distance to " CA  GLY A 133 " =    1.943
peak=   -3.220 closest distance to " CG  PHE A 283 " =    2.666
peak=   -3.213 closest distance to " CG  ARG A 269 " =    2.192
peak=   -3.213 closest distance to " CZ  PHE A  38 " =    2.048
peak=   -3.212 closest distance to " C   MET A 188 " =    1.475
peak=   -3.208 closest distance to " O   HOH Z 339 " =    1.705
peak=   -3.205 closest distance to " O   LYS A  76 " =    1.657
peak=   -3.204 closest distance to " CE BMET A  47 " =    1.615
peak=   -3.204 closest distance to " O   LEU A 167 " =    1.579
peak=   -3.204 closest distance to " CB  PHE A 208 " =    2.334
peak=   -3.199 closest distance to " NH2 ARG A 159 " =    2.404
peak=   -3.198 closest distance to " OD1 ASN A 301 " =    1.965
peak=   -3.197 closest distance to " O   HOH Z 372 " =    2.303
peak=   -3.191 closest distance to " OG1 THR A  82 " =    1.339
peak=   -3.189 closest distance to " O   TRP A  92 " =    1.916
peak=   -3.181 closest distance to " OG  SER A  26 " =    1.276
peak=   -3.178 closest distance to " CG  GLU A 152 " =    1.366
peak=   -3.176 closest distance to " NE2 GLN A  58 " =    2.493
peak=   -3.172 closest distance to " O   HOH Z 198 " =    2.074
peak=   -3.164 closest distance to " CD1 LEU A 228 " =    2.045
peak=   -3.162 closest distance to " N   THR A  52 " =    1.714
peak=   -3.160 closest distance to " O   ASN A 301 " =    1.456
peak=   -3.152 closest distance to " CG1 VAL A  67 " =    3.193
peak=   -3.145 closest distance to " CD1 TYR A 247 " =    2.407
peak=   -3.141 closest distance to " OG  SER A 206 " =    1.542
peak=   -3.139 closest distance to " O   ALA A  10 " =    1.850
peak=   -3.130 closest distance to " CB  ASP A 132 " =    2.392
peak=   -3.121 closest distance to " O   HOH Z 362 " =    4.365
peak=   -3.121 closest distance to " OG  SER A  62 " =    1.515
peak=   -3.119 closest distance to " O   HOH Z 111 " =    1.729
peak=   -3.118 closest distance to " CG1 VAL A  78 " =    2.762
peak=   -3.117 closest distance to " CB  ALA A  10 " =    2.264
peak=   -3.113 closest distance to " O   LYS A 117 " =    1.642
peak=   -3.097 closest distance to " O   HOH Z  11 " =    2.019
peak=   -3.095 closest distance to " CG2 THR A 221 " =    2.259
peak=   -3.089 closest distance to " O   HOH Z 392 " =    1.871
peak=   -3.080 closest distance to " O   HOH Z 389 " =    4.965
peak=   -3.077 closest distance to " O   HOH Z  71 " =    1.751
peak=   -3.074 closest distance to " O   SER A   3 " =    1.135
peak=   -3.071 closest distance to " OD1 ASP A 200 " =    1.427
peak=   -3.066 closest distance to " O   HOH Z 414 " =    1.936
peak=   -3.064 closest distance to " ND2 ASN A  60 " =    1.442
peak=   -3.062 closest distance to " O   HOH Z  47 " =    1.631
peak=   -3.048 closest distance to " O   HOH Z  90 " =    1.843
peak=   -3.021 closest distance to " O   ASP A 171 " =    1.929
peak=   -3.002 closest distance to " CG2 ILE A  20 " =    2.739

================= 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    :  0.4527 0.4379   6.250679e+00   6.232097e+00
   1_bss:  0.4443 0.4319   6.241409e+00   6.224388e+00
   1_xyz:  0.3401 0.3596   6.062044e+00   6.102546e+00
   1_adp:  0.2822 0.3182   5.916434e+00   6.013439e+00
   1_occ:  0.2817 0.3182   5.915550e+00   6.013598e+00
   2_bss:  0.2775 0.3154   5.915387e+00   6.012431e+00
   2_xyz:  0.1810 0.2208   5.537576e+00   5.714640e+00
   2_adp:  0.1597 0.2011   5.429493e+00   5.619572e+00
   2_occ:  0.1595 0.2009   5.428625e+00   5.619239e+00
   3_bss:  0.1578 0.2000   5.425820e+00   5.614016e+00
   3_xyz:  0.1243 0.1652   5.222492e+00   5.443077e+00
   3_adp:  0.1187 0.1598   5.184839e+00   5.410580e+00
   3_occ:  0.1185 0.1599   5.184496e+00   5.410619e+00
   4_bss:  0.1188 0.1599   5.185292e+00   5.408635e+00
   4_xyz:  0.1152 0.1571   5.166625e+00   5.394890e+00
   4_adp:  0.1160 0.1564   5.167149e+00   5.390379e+00
   4_occ:  0.1156 0.1563   5.164821e+00   5.388724e+00
   5_bss:  0.1156 0.1563   5.164874e+00   5.388763e+00
   5_xyz:  0.1105 0.1541   5.134856e+00   5.373462e+00
   5_adp:  0.1086 0.1555   5.132989e+00   5.382455e+00
   5_occ:  0.1086 0.1555   5.132855e+00   5.382337e+00
   5_bss:  0.1086 0.1555   5.132769e+00   5.382304e+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:  0.352  20.001   7.781   9.580   7.965   0.000   0.000   0.000
   1_xyz:  0.352  20.001   7.781   9.580   7.965   0.000   0.000   0.000
   1_adp:  0.352  20.001   7.781   9.580   7.965   0.000   0.000   0.000
   1_occ:  0.352  20.001   7.781   9.580   7.965   0.000   0.000   0.000
   2_bss:  0.329  35.924   4.196   5.605   4.922   0.000   0.000   0.000
   2_xyz:  0.329  35.924   4.196   5.605   4.922   0.000   0.000   0.000
   2_adp:  0.329  35.924   4.196   5.605   4.922   0.000   0.000   0.000
   2_occ:  0.329  35.924   4.196   5.605   4.922   0.000   0.000   0.000
   3_bss:  0.316  41.171   2.468   3.826   4.061   0.000   0.000   0.000
   3_xyz:  0.316  41.171   2.468   3.826   4.061   0.000   0.000   0.000
   3_adp:  0.316  41.171   2.468   3.826   4.061   0.000   0.000   0.000
   3_occ:  0.316  41.171   2.468   3.826   4.061   0.000   0.000   0.000
   4_bss:  0.327  44.504   2.153   3.278   3.858   0.000   0.000   0.000
   4_xyz:  0.327  44.504   2.153   3.278   3.858   0.000   0.000   0.000
   4_adp:  0.327  44.504   2.153   3.278   3.858   0.000   0.000   0.000
   4_occ:  0.327  44.504   2.153   3.278   3.858   0.000   0.000   0.000
   5_bss:  0.327  43.798   2.153   3.278   3.858   0.000   0.000   0.000
   5_xyz:  0.327  43.798   2.153   3.278   3.858   0.000   0.000   0.000
   5_adp:  0.327  43.798   2.153   3.278   3.858   0.000   0.000   0.000
   5_occ:  0.327  43.798   2.153   3.278   3.858   0.000   0.000   0.000
   5_bss:  0.324  47.005  -0.928   0.116   0.812   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.850 0.5241  0.5948    56849.944
   1_bss:  49.931 0.5213  0.7654    55055.305
   1_xyz:  39.570 0.6468  0.9218    35995.799
   1_adp:  33.182 0.7226  1.0285    27472.902
   1_occ:  33.209 0.7223  1.0271    27480.670
   2_bss:  32.961 0.7250  0.9080    27178.249
   2_xyz:  22.136 0.8398  1.0066    12737.888
   2_adp:  19.525 0.8659  1.0230    10497.491
   2_occ:  19.527 0.8659  1.0228    10488.421
   3_bss:  19.387 0.8671  0.9704    10338.172
   3_xyz:  15.415 0.9029  0.9891     7171.193
   3_adp:  14.678 0.9094  0.9900     6752.964
   3_occ:  14.680 0.9094  0.9898     6748.372
   4_bss:  14.669 0.9095  0.9773     6741.729
   4_xyz:  14.219 0.9135  0.9775     6508.949
   4_adp:  14.096 0.9147  0.9769     6456.033
   4_occ:  14.058 0.9150  0.9768     6439.091
   5_bss:  14.059 0.9150  0.9768     6439.596
   5_xyz:  13.788 0.9169  0.9778     6247.973
   5_adp:  13.982 0.9154  0.9727     6325.185
   5_occ:  13.981 0.9154  0.9727     6324.741
   5_bss:  13.980 0.9154  0.9766     6322.107
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3621e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3621e+01
   1_xyz:   1.623  0.013  0.107 17.851  0.006  4.110   1.2986e-01
   1_adp:   1.623  0.013  0.107 17.851  0.006  4.110   1.2986e-01
   1_occ:   1.623  0.013  0.107 17.851  0.006  4.110   1.2986e-01
   2_bss:   1.623  0.013  0.107 17.851  0.006  4.110   1.2986e-01
   2_xyz:   1.112  0.008  0.078 16.063  0.004  4.124   7.3791e-02
   2_adp:   1.112  0.008  0.078 16.063  0.004  4.124   7.3791e-02
   2_occ:   1.112  0.008  0.078 16.063  0.004  4.124   7.3791e-02
   3_bss:   1.112  0.008  0.078 16.063  0.004  4.124   7.3791e-02
   3_xyz:   1.106  0.008  0.086 15.776  0.004  4.124   7.1223e-02
   3_adp:   1.106  0.008  0.086 15.776  0.004  4.124   7.1223e-02
   3_occ:   1.106  0.008  0.086 15.776  0.004  4.124   7.1223e-02
   4_bss:   1.106  0.008  0.086 15.776  0.004  4.124   7.1223e-02
   4_xyz:   0.986  0.007  0.078 15.438  0.004  4.118   5.9502e-02
   4_adp:   0.986  0.007  0.078 15.438  0.004  4.118   5.9502e-02
   4_occ:   0.986  0.007  0.078 15.438  0.004  4.118   5.9502e-02
   5_bss:   0.986  0.007  0.078 15.438  0.004  4.118   5.9502e-02
   5_xyz:   1.144  0.009  0.092 15.676  0.004  4.121   7.6050e-02
   5_adp:   1.144  0.009  0.092 15.676  0.004  4.121   7.6050e-02
   5_occ:   1.144  0.009  0.092 15.676  0.004  4.121   7.6050e-02
   5_bss:   1.144  0.009  0.092 15.676  0.004  4.121   7.6050e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.117   6.9498e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.117   6.9498e+00
   1_xyz:  14.933  0.156  0.506 85.155  0.038  2.322   9.7071e-02
   1_adp:  14.933  0.156  0.506 85.155  0.038  2.322   9.7071e-02
   1_occ:  14.933  0.156  0.506 85.155  0.038  2.322   9.7071e-02
   2_bss:  14.933  0.156  0.506 85.155  0.038  2.322   9.7071e-02
   2_xyz:   7.463  0.119  0.261 84.077  0.039  2.206   6.5616e-02
   2_adp:   7.463  0.119  0.261 84.077  0.039  2.206   6.5616e-02
   2_occ:   7.463  0.119  0.261 84.077  0.039  2.206   6.5616e-02
   3_bss:   7.463  0.119  0.261 84.077  0.039  2.206   6.5616e-02
   3_xyz:   7.229  0.054  0.519 82.670  0.041  2.254   6.1212e-02
   3_adp:   7.229  0.054  0.519 82.670  0.041  2.254   6.1212e-02
   3_occ:   7.229  0.054  0.519 82.670  0.041  2.254   6.1212e-02
   4_bss:   7.229  0.054  0.519 82.670  0.041  2.254   6.1212e-02
   4_xyz:   6.957  0.045  0.398 82.107  0.038  2.312   3.9644e-02
   4_adp:   6.957  0.045  0.398 82.107  0.038  2.312   3.9644e-02
   4_occ:   6.957  0.045  0.398 82.107  0.038  2.312   3.9644e-02
   5_bss:   6.957  0.045  0.398 82.107  0.038  2.312   3.9644e-02
   5_xyz:   7.893  0.053  0.600 82.618  0.040  2.291   5.6005e-02
   5_adp:   7.893  0.053  0.600 82.618  0.040  2.291   5.6005e-02
   5_occ:   7.893  0.053  0.600 82.618  0.040  2.291   5.6005e-02
   5_bss:   7.893  0.053  0.600 82.618  0.040  2.291   5.6005e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  65.68   0.00  11.52  60.77   0.00   8.64  65.68   0.00  27.19
   1_occ:  65.68   0.00  11.52  60.77   0.00   8.64  65.68   0.00  27.19
   2_bss:  65.68   0.00  11.52  60.77   0.00   8.64  65.68   0.00  27.19
   2_xyz:  65.68   0.00  11.52  60.77   0.00   8.64  65.68   0.00  27.19
   2_adp:  70.66   0.00  11.69  70.66   0.00   7.94  63.15   1.40  32.15
   2_occ:  70.66   0.00  11.69  70.66   0.00   7.94  63.15   1.40  32.15
   3_bss:  70.66   0.00  11.69  70.66   0.00   7.94  63.15   1.40  32.15
   3_xyz:  70.66   0.00  11.69  70.66   0.00   7.94  63.15   1.40  32.15
   3_adp:  76.86   0.00  11.86  76.86   0.00   7.79  66.97   0.72  34.03
   3_occ:  76.86   0.00  11.86  76.86   0.00   7.79  66.97   0.72  34.03
   4_bss:  76.86   0.00  11.86  76.86   0.00   7.79  66.97   0.72  34.03
   4_xyz:  76.86   0.00  11.86  76.86   0.00   7.79  66.97   0.72  34.03
   4_adp:  76.37   0.00  11.65  76.37   0.00   7.72  66.60   0.86  33.05
   4_occ:  76.37   0.00  11.65  76.37   0.00   7.72  66.60   0.86  33.05
   5_bss:  76.37   0.00  11.65  76.37   0.00   7.72  66.60   0.86  33.05
   5_xyz:  76.37   0.00  11.65  76.37   0.00   7.72  66.60   0.86  33.05
   5_adp:  81.87   0.00  11.87  81.87   0.00   7.73  73.70   0.99  34.43
   5_occ:  81.87   0.00  11.87  81.87   0.00   7.73  73.70   0.99  34.43
   5_bss:  85.08   3.21  15.08  85.08   3.21  10.93  76.91   4.20  37.64
------------------------------------------------------------------------
 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:    1.212    0.015    0.411
   1_adp:    1.212    0.015    0.411
   1_occ:    1.212    0.015    0.411
   2_bss:    1.212    0.015    0.411
   2_xyz:    1.604    0.050    0.556
   2_adp:    1.604    0.050    0.556
   2_occ:    1.604    0.050    0.556
   3_bss:    1.604    0.050    0.556
   3_xyz:    1.548    0.058    0.598
   3_adp:    1.548    0.058    0.598
   3_occ:    1.548    0.058    0.598
   4_bss:    1.548    0.058    0.598
   4_xyz:    1.721    0.074    0.613
   4_adp:    1.721    0.074    0.613
   4_occ:    1.721    0.074    0.613
   5_bss:    1.721    0.074    0.613
   5_xyz:    1.721    0.062    0.623
   5_adp:    1.721    0.062    0.623
   5_occ:    1.721    0.062    0.623
   5_bss:    1.721    0.062    0.623
------------------------------------------------------------------------

CPU time actual refinement: 341.18


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_324/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_324/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_324/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_324/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_324/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.02 
  Macro-tasks:
    bulk solvent and scale       = 40.84  
    individual site refinement   = 139.29 
    weights calculation          = 32.57  
    collect and process          = 6.58   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 219.43 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 106.48 
    alpha_beta                      = 8.33   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 117.02 
    fmodel                         = 7.39   
    r_factors                      = 0.15   
    phase_errors                   = 10.94  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 253.56 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.805 micro seconds
Total CPU time: 5.91 minutes
from_scatterers_fft:    659 calls, 106.10 s
gradients_fft:          604 calls, 103.91 s

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

# Date 2008-01-16 Time 01:16:43 PST -0800 (1200475003.77 s)
Start R-work = 0.4527, R-free = 0.4379 (no bulk solvent and anisotropic scale)
Final R-work = 0.1267, R-free = 0.1711 (no bulk solvent and anisotropic scale)

Start R-work = 0.4443, R-free = 0.4319
Final R-work = 0.1086, R-free = 0.1555