# Date 2008-01-16 Time 01:58:26 PST -0800 (1200477506.42 s)
#phil __OFF__

Command line arguments: "../643.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7246
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 643

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 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: 3.30, 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: (70.25, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.98222
Completeness in resolution range: 0.969512
Completeness with d_max=infinity: 0.966499

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   1.9822

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.98222
Completeness in resolution range: 0.969512
Completeness with d_max=infinity: 0.966499

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2414 [2118/2142]  1905   213  10.1%
  bin  2:  4.2414 -  3.3792 [2038/2058]  1835   203  10.0%
  bin  3:  3.3792 -  2.9557 [2012/2031]  1812   200   9.9%
  bin  4:  2.9557 -  2.6872 [2002/2032]  1802   200  10.0%
  bin  5:  2.6872 -  2.4955 [1985/2004]  1785   200  10.1%
  bin  6:  2.4955 -  2.3490 [1957/1982]  1759   198  10.1%
  bin  7:  2.3490 -  2.2317 [1959/1987]  1765   194   9.9%
  bin  8:  2.2317 -  2.1349 [1963/1999]  1769   194   9.9%
  bin  9:  2.1349 -  2.0529 [1944/1986]  1749   195  10.0%
  bin 10:  2.0529 -  1.9822 [1611/1984]  1449   162  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_643/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2211
        3.04 -     3.66: 4706
        3.66 -     4.28: 9097
        4.28 -     4.90: 12387
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.253 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.318 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28411 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_643/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_643/model_refine_001.geo

CPU time processing inputs: 9.36


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 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: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4298   r_free= 0.4163   ksol= 0.00   Bsol= 0.00   scale= 0.827    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.222621                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7305 0.99   1381  153 0.3644 0.3527      6.5213       6.483|
|  2:  4.7305 -  3.7745 0.99   1324  149 0.3230 0.3157      6.6402      6.6044|
|  3:  3.7745 -  3.3032 0.99   1298  142 0.3606 0.3365      6.5413      6.5529|
|  4:  3.3032 -  3.0038 0.99   1289  145 0.4055 0.3664      6.4522      6.3606|
|  5:  3.0038 -  2.7900 0.99   1280  143 0.4526 0.4473      6.3085      6.3495|
|  6:  2.7900 -  2.6264 0.99   1298  140 0.4511 0.5185      6.2374      6.1858|
|  7:  2.6264 -  2.4955 0.99   1269  144 0.4769 0.4441      6.2012      6.1889|
|  8:  2.4955 -  2.3873 0.98   1258  138 0.4858 0.4495      6.1543      6.1457|
|  9:  2.3873 -  2.2958 0.98   1263  143 0.4611 0.4785      6.0714      6.0721|
| 10:  2.2958 -  2.2168 1.00   1263  142 0.4960 0.4704      6.1082      6.0662|
| 11:  2.2168 -  2.1477 0.97   1264  136 0.4998 0.4212      6.0298      5.9734|
| 12:  2.1477 -  2.0865 0.98   1238  140 0.4868 0.4735      5.9667      5.9571|
| 13:  2.0865 -  2.0317 0.99   1287  141 0.4959 0.5053      5.8774       5.853|
| 14:  2.0317 -  1.9822 0.73    918  103 0.5130 0.5160      5.8407      5.7767|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7305  1381   153  0.73  31.41   0.81     0.77      60320.75|
|  2:  4.7305 -  3.7745  1324   149  0.79  27.65   0.91     0.84      71163.01|
|  3:  3.7745 -  3.3032  1298   142  0.72  33.57   0.89     0.82      73206.39|
|  4:  3.3032 -  3.0038  1289   145  0.66  38.78   0.84     0.73      66781.64|
|  5:  3.0038 -  2.7900  1280   143  0.56  47.54   0.78     0.63      60775.96|
|  6:  2.7900 -  2.6264  1298   140  0.52  50.19   0.76     0.58      56849.02|
|  7:  2.6264 -  2.4955  1269   144  0.49  53.17   0.76     0.55      54101.04|
|  8:  2.4955 -  2.3873  1258   138  0.49  53.32   0.76     0.56      49304.33|
|  9:  2.3873 -  2.2958  1263   143  0.52  50.47   0.75     0.58      41850.60|
| 10:  2.2958 -  2.2168  1263   142  0.52  50.27   0.79     0.60      36055.61|
| 11:  2.2168 -  2.1477  1264   136  0.51  51.10   0.77     0.60      34226.93|
| 12:  2.1477 -  2.0865  1238   140  0.46  55.30   0.80     0.55      34864.23|
| 13:  2.0865 -  2.0317  1287   141  0.41  58.96   0.76     0.49      32433.23|
| 14:  2.0317 -  1.9822   918   103  0.42  58.58   0.73     0.44      26299.92|
|alpha:            min =        0.44 max =            0.84 mean =         0.63|
|beta:             min =    26299.92 max =        73206.39 mean =     50572.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           90.00 mean =        46.74|
|phase err.(test): min =        0.00 max =           89.95 mean =        46.96|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.335594              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.840   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.668333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.715   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1503 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2660 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3942 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5088 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6601 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7730 |
|-----------------------------------------------------------------------------|
|-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 |       53.595 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.729 |              |
|-----------------------------------------------------------------------------|

|-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: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4385   r_free= 0.4217   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.229055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4215   r_free= 0.4031   ksol= 0.37   Bsol= 20.00   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.19,9.41,8.01,0.00,0.00,0.00); trace/3= 8.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.217511                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.761939              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.741   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633755              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.635   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4215      final r-factor (work) = 0.3137          |
| start r-factor (free) = 0.4031      final r-factor (free) = 0.3340          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 74.6751 = 6.76 * 0.50 * 6.2350 + 1.00 * 53.5947                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6140 = 6.76 * 0.50 * 6.0632 + 1.00 * 0.1145                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3137      final r-factor (work) = 0.2478          |
| start r-factor (free) = 0.3340      final r-factor (free) = 0.2849          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8573 = 0.63 * 1.00 * 6.0632 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7367 = 0.63 * 1.00 * 5.8774 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| 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    65.49   10.80    None  None   None       |
|    all(noH): 2823   0      0.00    65.49   10.80    None  None   None       |
|    Sol.    : 438    0      0.00    63.13   27.47    None  None   None       |
|    Mac.    : 2385   0      0.00    65.49   7.74     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 -   6.549: 1321   |   5:    32.746 -  39.295:   97        |
|      1:     6.549 -  13.098:  754   |   6:    39.295 -  45.844:   54        |
|      2:    13.098 -  19.648:  264   |   7:    45.844 -  52.393:   20        |
|      3:    19.648 -  26.197:  176   |   8:    52.393 -  58.942:   10        |
|      4:    26.197 -  32.746:  122   |   9:    58.942 -  65.492:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2478 r_free = 0.2849             target_work(ml) = 5.807         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2472 r_free = 0.2846             target_work(ml) = 5.806         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2472   r_free= 0.2846   ksol= 0.37   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.19,9.41,8.01,0.00,0.00,0.00); trace/3= 8.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.806031                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2414   r_free= 0.2772   ksol= 0.34   Bsol= 36.18   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.74,4.92,4.86,0.00,0.00,0.00); trace/3= 4.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.802369                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.585660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.222   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.676  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2414      final r-factor (work) = 0.1694          |
| start r-factor (free) = 0.2772      final r-factor (free) = 0.2114          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7258 = 2.59 * 0.50 * 5.8876 + 1.00 * 0.1140                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3289 = 2.59 * 0.50 * 5.6244 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1694      final r-factor (work) = 0.1539          |
| start r-factor (free) = 0.2114      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9650 = 0.35 * 1.00 * 5.6244 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8980 = 0.35 * 1.00 * 5.4341 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-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    68.07   11.10    None  None   None       |
|    all(noH): 2823   0      0.00    68.07   11.10    None  None   None       |
|    Sol.    : 438    0      0.00    66.31   31.50    None  None   None       |
|    Mac.    : 2385   0      0.00    68.07   7.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.807: 1504   |   5:    34.036 -  40.843:  131        |
|      1:     6.807 -  13.615:  650   |   6:    40.843 -  47.651:   72        |
|      2:    13.615 -  20.422:  201   |   7:    47.651 -  54.458:   35        |
|      3:    20.422 -  27.229:  103   |   8:    54.458 -  61.265:    9        |
|      4:    27.229 -  34.036:  115   |   9:    61.265 -  68.072:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1539 r_free = 0.1985             target_work(ml) = 5.407         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1538 r_free = 0.1984             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1538   r_free= 0.1984   ksol= 0.34   Bsol= 36.18   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.74,4.92,4.86,0.00,0.00,0.00); trace/3= 4.51                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.406312                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1536   r_free= 0.1973   ksol= 0.32   Bsol= 36.18   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.52,4.50,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.405237                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.776391              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.158  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.429743              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1536      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1973      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8862 = 1.78 * 0.50 * 5.4366 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7787 = 1.78 * 0.50 * 5.3189 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.2531 = 3.43 * 1.00 * 5.3189 + 1.00 * 0.0108                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.9228 = 3.43 * 1.00 * 5.2212 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| 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    83.46   12.01    None  None   None       |
|    all(noH): 2823   0      0.00    83.46   12.01    None  None   None       |
|    Sol.    : 438    0      0.42    81.49   36.14    None  None   None       |
|    Mac.    : 2385   0      0.00    83.46   7.58     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.346: 1719   |   5:    41.728 -  50.074:   98        |
|      1:     8.346 -  16.691:  535   |   6:    50.074 -  58.419:   65        |
|      2:    16.691 -  25.037:  145   |   7:    58.419 -  66.765:   31        |
|      3:    25.037 -  33.382:  109   |   8:    66.765 -  75.110:   17        |
|      4:    33.382 -  41.728:  100   |   9:    75.110 -  83.456:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1220 r_free = 0.1662             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1661             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1661   ksol= 0.32   Bsol= 36.18   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.52,4.50,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206962                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1657   ksol= 0.31   Bsol= 36.18   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.30,4.48,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206540                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.053795              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.813  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.225044              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.074  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4153 = 2.05 * 0.50 * 5.2204 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3755 = 2.05 * 0.50 * 5.1765 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1825 = 0.23 * 1.00 * 5.1765 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1945 = 0.23 * 1.00 * 5.1660 + 1.00 * 0.0319                               |
|-----------------------------------------------------------------------------|
| 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    82.57   11.34    None  None   None       |
|    all(noH): 2823   0      0.00    82.57   11.34    None  None   None       |
|    Sol.    : 438    0      1.30    73.81   33.33    None  None   None       |
|    Mac.    : 2385   0      0.00    82.57   7.30     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 -   8.257: 1781   |   5:    41.285 -  49.542:   78        |
|      1:     8.257 -  16.514:  508   |   6:    49.542 -  57.798:   56        |
|      2:    16.514 -  24.771:  135   |   7:    57.798 -  66.055:   24        |
|      3:    24.771 -  33.028:  128   |   8:    66.055 -  74.312:    9        |
|      4:    33.028 -  41.285:  102   |   9:    74.312 -  82.569:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1575             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1573             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1573   ksol= 0.31   Bsol= 36.18   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,3.30,4.48,0.00,0.00,0.00); trace/3= 3.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153674                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1572   ksol= 0.32   Bsol= 40.36   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,3.17,4.46,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153260                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.370862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.583  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.211145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.992   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6002 = 1.37 * 0.50 * 5.1654 + 1.00 * 0.0597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5831 = 1.37 * 0.50 * 5.1534 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2701 = 1.21 * 1.00 * 5.1534 + 1.00 * 0.0285                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2439 = 1.21 * 1.00 * 5.1437 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    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    87.19   11.60    None  None   None       |
|    all(noH): 2823   0      0.00    87.19   11.60    None  None   None       |
|    Sol.    : 438    0      0.82    76.35   34.64    None  None   None       |
|    Mac.    : 2385   0      0.00    87.19   7.37     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 -   8.719: 1812   |   5:    43.596 -  52.315:   86        |
|      1:     8.719 -  17.438:  469   |   6:    52.315 -  61.034:   48        |
|      2:    17.438 -  26.157:  142   |   7:    61.034 -  69.753:   20        |
|      3:    26.157 -  34.877:  127   |   8:    69.753 -  78.472:   11        |
|      4:    34.877 -  43.596:  106   |   9:    78.472 -  87.191:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1570             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1569             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1569   ksol= 0.32   Bsol= 40.36   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,3.17,4.46,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149390                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7305 0.99   1381  153 0.0997 0.1256      5.3831      5.5118|
|  2:  4.7305 -  3.7745 0.99   1324  149 0.0868 0.1116      5.4366      5.6136|
|  3:  3.7745 -  3.3032 0.99   1298  142 0.1062 0.1456      5.4766      5.8362|
|  4:  3.3032 -  3.0038 0.99   1289  145 0.1218 0.1637      5.4587      5.5978|
|  5:  3.0038 -  2.7900 0.99   1280  143 0.1335 0.1699      5.3402        5.56|
|  6:  2.7900 -  2.6264 0.99   1298  140 0.1190 0.1946      5.2073       5.476|
|  7:  2.6264 -  2.4955 0.99   1269  144 0.1313 0.1555      5.1852      5.3498|
|  8:  2.4955 -  2.3873 0.98   1258  138 0.1185 0.1758      5.0907      5.3696|
|  9:  2.3873 -  2.2958 0.98   1263  143 0.1190 0.1764      5.0556      5.2674|
| 10:  2.2958 -  2.2168 1.00   1263  142 0.1119 0.1698      4.9659      5.2512|
| 11:  2.2168 -  2.1477 0.97   1264  136 0.1134 0.1713      4.9363      5.2376|
| 12:  2.1477 -  2.0865 0.98   1238  140 0.1131 0.1728       4.885      5.2285|
| 13:  2.0865 -  2.0317 0.99   1287  141 0.1150 0.1774      4.8075      5.0768|
| 14:  2.0317 -  1.9822 0.73    918  103 0.1030 0.1686      4.6806      4.9159|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7305  1381   153  0.94   8.80   0.98     0.95       6871.12|
|  2:  4.7305 -  3.7745  1324   149  0.96   7.61   1.02     1.01       8680.03|
|  3:  3.7745 -  3.3032  1298   142  0.94  10.96   1.03     1.02      10084.01|
|  4:  3.3032 -  3.0038  1289   145  0.92  13.52   1.01     0.99      10286.09|
|  5:  3.0038 -  2.7900  1280   143  0.90  15.70   1.00     0.97       8398.75|
|  6:  2.7900 -  2.6264  1298   140  0.90  15.73   0.98     0.96       7076.93|
|  7:  2.6264 -  2.4955  1269   144  0.90  15.88   0.99     0.96       6251.99|
|  8:  2.4955 -  2.3873  1258   138  0.91  15.31   0.99     0.97       5427.76|
|  9:  2.3873 -  2.2958  1263   143  0.91  15.50   1.01     0.97       5242.90|
| 10:  2.2958 -  2.2168  1263   142  0.90  15.37   1.00     0.96       4385.13|
| 11:  2.2168 -  2.1477  1264   136  0.90  16.25   1.00     0.96       4320.81|
| 12:  2.1477 -  2.0865  1238   140  0.91  15.06   1.01     1.01       3926.03|
| 13:  2.0865 -  2.0317  1287   141  0.90  16.16   1.01     0.98       3427.74|
| 14:  2.0317 -  1.9822   918   103  0.92  14.46   0.99     0.95       2665.32|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2665.32 max =        10286.09 mean =      6316.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.96|
|phase err.(test): min =        0.00 max =           87.71 mean =        13.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1569   ksol= 0.32   Bsol= 43.97   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.41,0.89,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149406                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1569   ksol= 0.32   Bsol= 43.97   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.41,0.89,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149406                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7305 0.99   1381  153 0.0997 0.1257      5.3834      5.5122|
|  2:  4.7305 -  3.7745 0.99   1324  149 0.0868 0.1116      5.4367      5.6136|
|  3:  3.7745 -  3.3032 0.99   1298  142 0.1062 0.1456      5.4766      5.8362|
|  4:  3.3032 -  3.0038 0.99   1289  145 0.1218 0.1637      5.4587      5.5979|
|  5:  3.0038 -  2.7900 0.99   1280  143 0.1335 0.1699      5.3401      5.5599|
|  6:  2.7900 -  2.6264 0.99   1298  140 0.1190 0.1946      5.2073      5.4759|
|  7:  2.6264 -  2.4955 0.99   1269  144 0.1313 0.1555      5.1852        5.35|
|  8:  2.4955 -  2.3873 0.98   1258  138 0.1185 0.1757      5.0907      5.3695|
|  9:  2.3873 -  2.2958 0.98   1263  143 0.1190 0.1763      5.0556      5.2673|
| 10:  2.2958 -  2.2168 1.00   1263  142 0.1119 0.1698      4.9659      5.2515|
| 11:  2.2168 -  2.1477 0.97   1264  136 0.1134 0.1713      4.9363      5.2376|
| 12:  2.1477 -  2.0865 0.98   1238  140 0.1131 0.1728       4.885      5.2285|
| 13:  2.0865 -  2.0317 0.99   1287  141 0.1150 0.1774      4.8075      5.0767|
| 14:  2.0317 -  1.9822 0.73    918  103 0.1030 0.1686      4.6804      4.9157|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9944 -  4.7305  1381   153  0.94   8.81   0.98     0.95       6875.87|
|  2:  4.7305 -  3.7745  1324   149  0.96   7.61   1.02     1.01       8683.52|
|  3:  3.7745 -  3.3032  1298   142  0.94  10.96   1.03     1.02      10085.14|
|  4:  3.3032 -  3.0038  1289   145  0.92  13.52   1.01     1.00      10285.67|
|  5:  3.0038 -  2.7900  1280   143  0.90  15.70   1.00     0.97       8396.94|
|  6:  2.7900 -  2.6264  1298   140  0.90  15.73   0.99     0.96       7076.08|
|  7:  2.6264 -  2.4955  1269   144  0.90  15.88   0.99     0.96       6251.60|
|  8:  2.4955 -  2.3873  1258   138  0.91  15.31   1.00     0.97       5427.36|
|  9:  2.3873 -  2.2958  1263   143  0.91  15.50   1.01     0.98       5243.05|
| 10:  2.2958 -  2.2168  1263   142  0.90  15.37   1.01     0.97       4384.98|
| 11:  2.2168 -  2.1477  1264   136  0.90  16.25   1.00     0.96       4321.38|
| 12:  2.1477 -  2.0865  1238   140  0.91  15.06   1.02     1.01       3926.06|
| 13:  2.0865 -  2.0317  1287   141  0.90  16.16   1.01     0.99       3427.28|
| 14:  2.0317 -  1.9822   918   103  0.92  14.45   0.99     0.95       2664.18|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2664.18 max =        10285.67 mean =      6317.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.96|
|phase err.(test): min =        0.00 max =           87.71 mean =        13.52|
|-----------------------------------------------------------------------------|

|-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      3.62    90.81   15.22    None  None   None       |
|    all(noH): 2823   0      3.62    90.81   15.22    None  None   None       |
|    Sol.    : 438    0      4.44    79.97   38.26    None  None   None       |
|    Mac.    : 2385   0      3.62    90.81   10.99    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:     3.616 -  12.335: 1812   |   5:    47.212 -  55.931:   86        |
|      1:    12.335 -  21.055:  469   |   6:    55.931 -  64.650:   48        |
|      2:    21.055 -  29.774:  142   |   7:    64.650 -  73.369:   20        |
|      3:    29.774 -  38.493:  127   |   8:    73.369 -  82.089:   11        |
|      4:    38.493 -  47.212:  106   |   9:    82.089 -  90.808:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.328 - 5.632
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 310
   mapped sites are within: 0.706 - 5.632

peak=   11.455 closest distance to " CB  VAL A 230 " =    1.445
peak=    9.417 closest distance to " CG2 VAL A 296 " =    1.349
peak=    6.104 closest distance to " CG  LEU A   5 " =    1.161
peak=    6.084 closest distance to " CD2 LEU A   5 " =    1.186
peak=    5.893 closest distance to " CG  PRO A  54 " =    1.322
peak=    5.785 closest distance to " NE2 GLN A  11 " =    1.168
peak=    5.469 closest distance to " NH2 ARG A  56 " =    2.121
peak=    5.404 closest distance to " CB  GLN A 223 " =    1.425
peak=    5.238 closest distance to " O   HOH Z 144 " =    1.930
peak=    5.169 closest distance to " CG  LEU A 228 " =    1.121
peak=    5.158 closest distance to " CB  PRO A  54 " =    1.017
peak=    4.924 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.843 closest distance to " O   HOH Z 232 " =    2.353
peak=    4.826 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.797 closest distance to " CG  PRO A 198 " =    1.175
peak=    4.793 closest distance to " CB  ARG A 275 " =    0.947
peak=    4.766 closest distance to " O   HOH Z 427 " =    2.816
peak=    4.701 closest distance to " O   HOH Z   9 " =    1.299
peak=    4.657 closest distance to " CB  SER A  63 " =    1.324
peak=    4.612 closest distance to " O   HOH Z 209 " =    2.252
peak=    4.543 closest distance to " CB  ASN A 148 " =    1.369
peak=    4.468 closest distance to " O   HOH Z 298 " =    1.758
peak=    4.463 closest distance to " CB  VAL A 230 " =    1.150
peak=    4.454 closest distance to " CB  SER A   3 " =    1.280
peak=    4.428 closest distance to " O   HOH Z 126 " =    2.043
peak=    4.408 closest distance to " O   HOH Z 425 " =    1.479
peak=    4.402 closest distance to " CG  PRO A 243 " =    1.109
peak=    4.378 closest distance to " CB  TRP A 266 " =    1.053
peak=    4.374 closest distance to " O   HOH Z 316 " =    3.072
peak=    4.355 closest distance to " CD2 LEU A 228 " =    1.150
peak=    4.350 closest distance to " ND2 ASN A 187 " =    1.501
peak=    4.289 closest distance to " O   HOH Z 346 " =    1.585
peak=    4.276 closest distance to " O   HOH Z 287 " =    1.997
peak=    4.275 closest distance to " O   HOH Z 272 " =    1.821
peak=    4.248 closest distance to " CB  VAL A 265 " =    1.288
peak=    4.217 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.177 closest distance to " CB  VAL A 296 " =    1.039
peak=    4.168 closest distance to " O   HOH Z 203 " =    1.762
peak=    4.165 closest distance to " O   PRO A 198 " =    1.579
peak=    4.162 closest distance to " CB  ARG A  79 " =    1.395
peak=    4.148 closest distance to " O   HOH Z  55 " =    2.456
peak=    4.148 closest distance to " CB  SER A 216 " =    0.834
peak=    4.139 closest distance to " O   SER A  87 " =    2.352
peak=    4.134 closest distance to " CB  GLU A 128 " =    1.032
peak=    4.111 closest distance to " CG2 VAL A 257 " =    0.868
peak=    4.108 closest distance to " O   HOH Z  61 " =    1.625
peak=    4.092 closest distance to " O   HOH Z  78 " =    1.655
peak=    4.066 closest distance to " O   HOH Z 234 " =    3.672
peak=    4.060 closest distance to " O   HOH Z 411 " =    3.705
peak=    4.027 closest distance to " CB  GLU A 152 " =    1.240
peak=    4.017 closest distance to " O   HOH Z 193 " =    1.704
peak=    3.997 closest distance to " CG  ARG A  66 " =    2.771
peak=    3.968 closest distance to " CB AVAL A  41 " =    1.253
peak=    3.961 closest distance to " CB  ASN A 142 " =    1.019
peak=    3.960 closest distance to " CG  LEU A 167 " =    1.192
peak=    3.910 closest distance to " CB  ASN A  39 " =    0.954
peak=    3.907 closest distance to " CA  TYR A  30 " =    0.982
peak=    3.898 closest distance to " OG  SER A  97 " =    2.914
peak=    3.898 closest distance to " O   HOH Z  43 " =    1.895
peak=    3.884 closest distance to " O   HOH Z  68 " =    2.183
peak=    3.874 closest distance to " N   PHE A 130 " =    1.247
peak=    3.868 closest distance to " CG1BVAL A  72 " =    1.538
peak=    3.854 closest distance to " O   HOH Z   2 " =    1.515
peak=    3.850 closest distance to " CZ  PHE A 218 " =    1.113
peak=    3.839 closest distance to " O   HOH Z  30 " =    1.512
peak=    3.837 closest distance to " O   HOH Z 368 " =    2.090
peak=    3.828 closest distance to " CB  TRP A 179 " =    1.332
peak=    3.828 closest distance to " O   HOH Z 303 " =    2.120
peak=    3.827 closest distance to " O   HOH Z 313 " =    1.844
peak=    3.822 closest distance to " CB  ASN A 187 " =    1.143
peak=    3.815 closest distance to " CD1AILE A 234 " =    0.950
peak=    3.809 closest distance to " O   HOH Z 158 " =    3.126
peak=    3.806 closest distance to " O   HOH Z  59 " =    1.740
peak=    3.784 closest distance to " O   HOH Z 124 " =    1.328
peak=    3.782 closest distance to " OD1 ASN A  69 " =    2.588
peak=    3.777 closest distance to " CB  VAL A 202 " =    1.649
peak=    3.770 closest distance to " O   HOH Z 261 " =    1.995
peak=    3.765 closest distance to " NZ  LYS A 117 " =    3.017
peak=    3.763 closest distance to " CB  HIS A 108 " =    0.845
peak=    3.748 closest distance to " O   HOH Z 193 " =    1.751
peak=    3.743 closest distance to " CA  THR A 264 " =    0.720
peak=    3.739 closest distance to " O   HOH Z  97 " =    2.083
peak=    3.728 closest distance to " CA  ALA A  51 " =    0.988
peak=    3.727 closest distance to " O   HOH Z 422 " =    2.570
peak=    3.725 closest distance to " CB  LEU A 143 " =    1.166
peak=    3.719 closest distance to " CE  LYS A  76 " =    0.850
peak=    3.714 closest distance to " O   HOH Z 423 " =    2.610
peak=    3.709 closest distance to " O   HOH Z 128 " =    2.107
peak=    3.709 closest distance to " N   ASN A  39 " =    1.198
peak=    3.706 closest distance to " CB  THR A 157 " =    1.127
peak=    3.702 closest distance to " O   HOH Z 389 " =    1.860
peak=    3.696 closest distance to " CA  ASN A 215 " =    1.126
peak=    3.692 closest distance to " CA  VAL A  41 " =    0.790
peak=    3.682 closest distance to " O   HOH Z 380 " =    1.637
peak=    3.672 closest distance to " CD1 ILE A  33 " =    1.660
peak=    3.670 closest distance to " O   HOH Z 403 " =    1.653
peak=    3.665 closest distance to " CA  LYS A 290 " =    1.202
peak=    3.663 closest distance to " CB  ARG A 190 " =    1.675
peak=    3.662 closest distance to " O   HOH Z 126 " =    1.612
peak=    3.661 closest distance to " CD BLYS A 290 " =    1.128
peak=    3.656 closest distance to " O   HOH Z   7 " =    1.501
peak=    3.653 closest distance to " O   HOH Z  10 " =    1.714
peak=    3.638 closest distance to " O   HOH Z   9 " =    1.902
peak=    3.636 closest distance to " CB  GLU A 277 " =    3.572
peak=    3.631 closest distance to " OG BSER A 164 " =    2.151
peak=    3.631 closest distance to " O   HOH Z 263 " =    1.566
peak=    3.628 closest distance to " O   HOH Z  88 " =    3.068
peak=    3.626 closest distance to " CB  ARG A  79 " =    0.877
peak=    3.624 closest distance to " O   HOH Z 423 " =    1.505
peak=    3.624 closest distance to " CG  GLN A  88 " =    1.089
peak=    3.622 closest distance to " CG1 VAL A 153 " =    0.930
peak=    3.620 closest distance to " CB  LYS A 117 " =    1.230
peak=    3.618 closest distance to " O   HOH Z 130 " =    2.115
peak=    3.614 closest distance to " O   HOH Z   3 " =    1.949
peak=    3.612 closest distance to " O   HOH Z 280 " =    2.951
peak=    3.612 closest distance to " O   HOH Z 214 " =    2.145
peak=    3.611 closest distance to " CA  ARG A  36 " =    1.061
peak=    3.608 closest distance to " CD2 TRP A 179 " =    1.371
peak=    3.601 closest distance to " O   HOH Z 273 " =    2.796
peak=    3.601 closest distance to " O   HOH Z 435 " =    2.097
peak=    3.599 closest distance to " O   HOH Z 290 " =    1.048
peak=    3.597 closest distance to " CA  PHE A 283 " =    1.199
peak=    3.588 closest distance to " O   HOH Z 419 " =    1.948
peak=    3.585 closest distance to " NH1AARG A 145 " =    1.088
peak=    3.584 closest distance to " CB  ALA A 291 " =    1.462
peak=    3.582 closest distance to " O   HOH Z   1 " =    1.812
peak=    3.582 closest distance to " O   HOH Z  44 " =    1.640
peak=    3.572 closest distance to " CA  ALA A 299 " =    0.990
peak=    3.569 closest distance to " CA  ALA A  21 " =    1.126
peak=    3.562 closest distance to " O   HOH Z 222 " =    2.396
peak=    3.556 closest distance to " CD  LYS A 166 " =    1.367
peak=    3.553 closest distance to " CG BARG A 102 " =    1.838
peak=    3.549 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.545 closest distance to " O   HOH Z 145 " =    1.962
peak=    3.541 closest distance to " O   HOH Z 227 " =    1.701
peak=    3.531 closest distance to " O   HOH Z  97 " =    2.551
peak=    3.530 closest distance to " CG  ARG A 138 " =    1.207
peak=    3.522 closest distance to " O   HOH Z 405 " =    1.157
peak=    3.522 closest distance to " CB  SER A 212 " =    1.229
peak=    3.520 closest distance to " CG1 ILE A  33 " =    1.331
peak=    3.505 closest distance to " CA  ALA A 158 " =    1.247
peak=    3.503 closest distance to " O   HOH Z 344 " =    2.969
peak=    3.501 closest distance to " CB  SER A 273 " =    0.864
peak=    3.498 closest distance to " CB  MET A  40 " =    0.822
peak=    3.497 closest distance to " N   ARG A 156 " =    1.287
peak=    3.494 closest distance to " N   SER A 135 " =    1.324
peak=    3.487 closest distance to " CA  LYS A 117 " =    1.192
peak=    3.484 closest distance to " CB  ASP A 140 " =    0.870
peak=    3.482 closest distance to " CB  ASN A 110 " =    1.127
peak=    3.468 closest distance to " O   GLN A 278 " =    1.402
peak=    3.466 closest distance to " O   HOH Z 371 " =    2.871
peak=    3.453 closest distance to " CB  LEU A 228 " =    1.342
peak=    3.446 closest distance to " CA  SER A  87 " =    1.017
peak=    3.434 closest distance to " O   HOH Z 402 " =    1.355
peak=    3.432 closest distance to " O   HOH Z 353 " =    2.572
peak=    3.425 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.413 closest distance to " O   HOH Z 250 " =    1.339
peak=    3.409 closest distance to " O   HOH Z 172 " =    3.353
peak=    3.406 closest distance to " CE1 TYR A 186 " =    1.323
peak=    3.405 closest distance to " O   HOH Z 193 " =    1.879
peak=    3.404 closest distance to " O   HOH Z  40 " =    2.288
peak=    3.400 closest distance to " CB  THR A  82 " =    1.328
peak=    3.394 closest distance to " CG  MET A 185 " =    1.030
peak=    3.389 closest distance to " CB  THR A  31 " =    1.595
peak=    3.384 closest distance to " O   HOH Z 303 " =    1.761
peak=    3.384 closest distance to " O   HOH Z 305 " =    3.553
peak=    3.383 closest distance to " O   HOH Z 109 " =    2.482
peak=    3.380 closest distance to " O   HOH Z   1 " =    1.722
peak=    3.379 closest distance to " ND1 HIS A  86 " =    1.760
peak=    3.379 closest distance to " O   HOH Z 425 " =    2.038
peak=    3.375 closest distance to " CA  TYR A  30 " =    1.080
peak=    3.374 closest distance to " CA  GLY A 267 " =    0.706
peak=    3.373 closest distance to " O   HOH Z 128 " =    1.941
peak=    3.373 closest distance to " CG2 THR A 221 " =    1.187
peak=    3.372 closest distance to " OD2 ASP A 286 " =    2.731
peak=    3.371 closest distance to " CB  ARG A 139 " =    0.922
peak=    3.368 closest distance to " O   HOH Z 437 " =    1.939
peak=    3.368 closest distance to " NH2BARG A 145 " =    1.998
peak=    3.368 closest distance to " O   HOH Z 227 " =    2.124
peak=    3.361 closest distance to " CG  MET A 185 " =    1.228
peak=    3.358 closest distance to " O   HOH Z 366 " =    2.825
peak=    3.357 closest distance to " CD  ARG A 269 " =    1.035
peak=    3.356 closest distance to " N   GLN A 278 " =    1.190
peak=    3.349 closest distance to " O   HOH Z 261 " =    1.411
peak=    3.348 closest distance to " O   HOH Z 175 " =    2.034
peak=    3.347 closest distance to " O  BHOH Z 338 " =    2.465
peak=    3.345 closest distance to " CD1 LEU A  96 " =    0.769
peak=    3.338 closest distance to " NH2 ARG A 156 " =    1.053
peak=    3.332 closest distance to " O   HOH Z 371 " =    1.651
peak=    3.323 closest distance to " CG1 ILE A 151 " =    1.004
peak=    3.322 closest distance to " CB  SER A  26 " =    1.651
peak=    3.322 closest distance to " O   HOH Z 423 " =    1.633
peak=    3.322 closest distance to " CD1 LEU A 300 " =    1.170
peak=    3.321 closest distance to " CA  ALA A 291 " =    0.875
peak=    3.321 closest distance to " CB  LEU A 255 " =    0.763
peak=    3.319 closest distance to " O   HOH Z 392 " =    3.182
peak=    3.316 closest distance to " OG  SER A  62 " =    2.940
peak=    3.313 closest distance to " CD1 LEU A 228 " =    2.020
peak=    3.312 closest distance to " O   HOH Z 409 " =    3.051
peak=    3.310 closest distance to " CB  ALA A   9 " =    1.567
peak=    3.310 closest distance to " OG BSER A 134 " =    3.081
peak=    3.309 closest distance to " CG2 ILE A 120 " =    1.168
peak=    3.305 closest distance to " NE  ARG A  56 " =    3.448
peak=    3.303 closest distance to " CA  ASN A 127 " =    1.028
peak=    3.301 closest distance to " O   HOH Z 126 " =    1.507
peak=    3.298 closest distance to " O   HOH Z 180 " =    2.073
peak=    3.296 closest distance to " O   HOH Z 147 " =    1.688
peak=    3.293 closest distance to " CA  LEU A 282 " =    1.136
peak=    3.292 closest distance to " CG  MET A 113 " =    1.116
peak=    3.288 closest distance to " NH1 ARG A  14 " =    0.937
peak=    3.287 closest distance to " CB  VAL A 268 " =    0.823
peak=    3.285 closest distance to " CB  ASN A 224 " =    0.995
peak=    3.278 closest distance to " CA  SER A 146 " =    1.757
peak=    3.273 closest distance to " O   MET A 105 " =    1.863
peak=    3.273 closest distance to " CB  ASN A 215 " =    1.131
peak=    3.272 closest distance to " CG2 VAL A 197 " =    1.073
peak=    3.272 closest distance to " CD2 LEU A 255 " =    1.613
peak=    3.271 closest distance to " CB  VAL A 250 " =    1.113
peak=    3.271 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.267 closest distance to " NZ  LYS A  48 " =    1.307
peak=    3.266 closest distance to " O   HOH Z  88 " =    2.713
peak=    3.266 closest distance to " ND2 ASN A 249 " =    0.823
peak=    3.265 closest distance to " CE  LYS A  48 " =    1.093
peak=    3.265 closest distance to " CG2 ILE A  20 " =    1.497
peak=    3.264 closest distance to " CG2 THR A 294 " =    1.745
peak=    3.262 closest distance to " O   HOH Z 291 " =    1.482
peak=    3.262 closest distance to " CA  ILE A 234 " =    0.923
peak=    3.259 closest distance to " O   HOH Z 133 " =    1.570
peak=    3.257 closest distance to " O   HOH Z 426 " =    1.835
peak=    3.255 closest distance to " N   SER A 271 " =    0.986
peak=    3.254 closest distance to " CB  TYR A  30 " =    1.608
peak=    3.253 closest distance to " NH1 ARG A 138 " =    1.178
peak=    3.250 closest distance to " O   HOH Z 135 " =    1.959
peak=    3.237 closest distance to " CB  ILE A  20 " =    1.451
peak=    3.234 closest distance to " O   HOH Z 145 " =    3.502
peak=    3.234 closest distance to " O   HOH Z 213 " =    2.193
peak=    3.232 closest distance to " CA  ASP A 162 " =    1.074
peak=    3.232 closest distance to " O   HOH Z 357 " =    1.938
peak=    3.230 closest distance to " CG AARG A 275 " =    1.080
peak=    3.229 closest distance to " CA  ARG A 195 " =    1.206
peak=    3.226 closest distance to " O   HOH Z 132 " =    2.502
peak=    3.225 closest distance to " NZ  LYS A  76 " =    1.555
peak=    3.222 closest distance to " O   HOH Z   2 " =    1.501
peak=    3.219 closest distance to " O   HOH Z 248 " =    1.540
peak=    3.219 closest distance to " O   HOH Z 285 " =    2.757
peak=    3.218 closest distance to " OE2 GLU A   2 " =    1.761
peak=    3.216 closest distance to " OE1 GLU A   2 " =    2.010
peak=    3.213 closest distance to " CA  ARG A 102 " =    1.157
peak=    3.209 closest distance to " O   HOH Z  61 " =    1.528
peak=    3.200 closest distance to " O   HOH Z 336 " =    1.967
peak=    3.198 closest distance to " O   HOH Z 133 " =    2.539
peak=    3.196 closest distance to " O   HOH Z  63 " =    1.311
peak=    3.195 closest distance to " O   HOH Z 238 " =    2.349
peak=    3.190 closest distance to " CG  LYS A 119 " =    1.161
peak=    3.187 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.185 closest distance to " CA  THR A 221 " =    0.927
peak=    3.181 closest distance to " O   PRO A  90 " =    1.512
peak=    3.178 closest distance to " O   HOH Z 359 " =    3.812
peak=    3.175 closest distance to " OG  SER A  62 " =    2.732
peak=    3.174 closest distance to " CZ  PHE A 192 " =    0.938
peak=    3.172 closest distance to " O   HOH Z 153 " =    3.812
peak=    3.170 closest distance to " CA  MET A 105 " =    0.967
peak=    3.170 closest distance to " CD1 ILE A 106 " =    0.955
peak=    3.170 closest distance to " CB  ILE A 120 " =    1.349
peak=    3.170 closest distance to " OE2 GLU A  53 " =    1.947
peak=    3.168 closest distance to " O   HOH Z  21 " =    1.706
peak=    3.167 closest distance to " O   HOH Z 322 " =    1.988
peak=    3.165 closest distance to " CB  ALA A 242 " =    0.864
peak=    3.157 closest distance to " CB  SER A  62 " =    1.247
peak=    3.154 closest distance to " CH2 TRP A 266 " =    1.094
peak=    3.148 closest distance to " CB  LYS A 290 " =    1.156
peak=    3.146 closest distance to " CA  GLN A 194 " =    1.228
peak=    3.145 closest distance to " CG1 ILE A  49 " =    1.445
peak=    3.141 closest distance to " O   HOH Z 329 " =    3.838
peak=    3.137 closest distance to " O   LYS A 290 " =    2.423
peak=    3.135 closest distance to " CD2 LEU A 297 " =    0.892
peak=    3.130 closest distance to " O   HOH Z 345 " =    3.430
peak=    3.129 closest distance to " CG  LEU A 281 " =    1.042
peak=    3.128 closest distance to " O   HOH Z 421 " =    1.959
peak=    3.126 closest distance to " N   ALA A 233 " =    0.761
peak=    3.126 closest distance to " O   PRO A 198 " =    1.231
peak=    3.126 closest distance to " N   VAL A 126 " =    1.256
peak=    3.123 closest distance to " O   HOH Z 325 " =    2.211
peak=    3.112 closest distance to " O   HOH Z  48 " =    1.605
peak=    3.109 closest distance to " OG  SER A 206 " =    1.237
peak=    3.108 closest distance to " CE AMET A  47 " =    1.452
peak=    3.103 closest distance to " N   ALA A 256 " =    1.166
peak=    3.095 closest distance to " CG  GLN A  89 " =    1.445
peak=    3.092 closest distance to " NH1BARG A 145 " =    1.202
peak=    3.090 closest distance to " CG  ARG A 159 " =    0.945
peak=    3.088 closest distance to " O   HOH Z 334 " =    1.523
peak=    3.087 closest distance to " CB  PHE A 204 " =    0.856
peak=    3.080 closest distance to " CD2 TYR A 186 " =    1.039
peak=    3.080 closest distance to " CA  GLY A 136 " =    1.127
peak=    3.075 closest distance to " ND1 HIS A  81 " =    1.661
peak=    3.074 closest distance to " CB  ALA A 137 " =    1.132
peak=    3.063 closest distance to " CB  ALA A 114 " =    1.188
peak=    3.062 closest distance to " CB  TYR A 116 " =    0.832
peak=    3.061 closest distance to " CD1 LEU A 261 " =    1.190
peak=    3.046 closest distance to " O   HOH Z 430 " =    5.632
peak=    3.042 closest distance to " O   HOH Z 156 " =    3.257
peak=    3.026 closest distance to " O   HOH Z 251 " =    1.519
peak=    3.024 closest distance to " CB  ALA A 248 " =    1.522
peak=    2.983 closest distance to " O   HOH Z 438 " =    2.813

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.783 - 5.430
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.783 - 5.430

peak=   -4.827 closest distance to " CG2 VAL A 230 " =    0.783
peak=   -4.390 closest distance to " CD  ARG A 156 " =    2.055
peak=   -4.356 closest distance to " CB  PRO A 243 " =    2.666
peak=   -4.305 closest distance to " O   HOH Z 435 " =    2.853
peak=   -4.291 closest distance to " OG BSER A 134 " =    1.201
peak=   -4.263 closest distance to " SG  CYS A 254 " =    3.316
peak=   -4.175 closest distance to " O   HOH Z 266 " =    5.122
peak=   -4.135 closest distance to " CG  GLN A 223 " =    2.136
peak=   -4.011 closest distance to " CB  PHE A 192 " =    1.901
peak=   -4.007 closest distance to " C   HIS A 108 " =    1.167
peak=   -4.004 closest distance to " O   PRO A 198 " =    1.176
peak=   -3.982 closest distance to " CE2 TYR A  30 " =    2.787
peak=   -3.962 closest distance to " O   HOH Z 351 " =    1.493
peak=   -3.936 closest distance to " O   HOH Z 231 " =    1.991
peak=   -3.930 closest distance to " CB  ALA A 161 " =    2.590
peak=   -3.923 closest distance to " OD1 ASN A 187 " =    1.632
peak=   -3.917 closest distance to " O   HOH Z 290 " =    1.107
peak=   -3.913 closest distance to " CB  ALA A  43 " =    2.503
peak=   -3.885 closest distance to " CG2 VAL A 296 " =    1.811
peak=   -3.861 closest distance to " O   HOH Z 114 " =    2.944
peak=   -3.857 closest distance to " CB  ALA A 248 " =    2.066
peak=   -3.839 closest distance to " N   ALA A  43 " =    2.493
peak=   -3.834 closest distance to " O   HOH Z 185 " =    2.270
peak=   -3.829 closest distance to " CE2 PHE A 218 " =    2.519
peak=   -3.817 closest distance to " CG1 VAL A 112 " =    2.827
peak=   -3.776 closest distance to " CD  GLN A  58 " =    1.111
peak=   -3.727 closest distance to " O   HOH Z 140 " =    1.471
peak=   -3.727 closest distance to " ND2 ASN A  45 " =    1.476
peak=   -3.722 closest distance to " CE  MET A 105 " =    2.330
peak=   -3.716 closest distance to " CB  PRO A 280 " =    2.025
peak=   -3.698 closest distance to " O   VAL A  67 " =    2.584
peak=   -3.689 closest distance to " CA  VAL A  67 " =    2.920
peak=   -3.687 closest distance to " O   HOH Z 166 " =    2.129
peak=   -3.669 closest distance to " O   HOH Z 102 " =    1.635
peak=   -3.664 closest distance to " CD2 LEU A 237 " =    2.849
peak=   -3.661 closest distance to " N   THR A 157 " =    1.404
peak=   -3.660 closest distance to " O   HOH Z  11 " =    1.886
peak=   -3.641 closest distance to " O   HOH Z 350 " =    1.830
peak=   -3.641 closest distance to " O   HOH Z 389 " =    2.007
peak=   -3.640 closest distance to " CA  GLY A 203 " =    2.348
peak=   -3.638 closest distance to " ND2 ASN A 187 " =    1.578
peak=   -3.636 closest distance to " O   HOH Z 394 " =    1.502
peak=   -3.629 closest distance to " CZ  PHE A  59 " =    1.467
peak=   -3.627 closest distance to " C   MET A 188 " =    1.498
peak=   -3.622 closest distance to " CG  PHE A 283 " =    2.705
peak=   -3.614 closest distance to " O   HOH Z  52 " =    1.448
peak=   -3.610 closest distance to " O   SER A  22 " =    2.264
peak=   -3.609 closest distance to " N   ALA A 226 " =    2.088
peak=   -3.599 closest distance to " CZ3 TRP A 179 " =    1.226
peak=   -3.597 closest distance to " O   ARG A 145 " =    1.544
peak=   -3.595 closest distance to " CG2 THR A 178 " =    2.222
peak=   -3.591 closest distance to " CA  ASN A 127 " =    1.218
peak=   -3.590 closest distance to " CB  ALA A 291 " =    2.238
peak=   -3.588 closest distance to " C   LEU A 222 " =    0.808
peak=   -3.575 closest distance to " O   HOH Z 313 " =    1.525
peak=   -3.572 closest distance to " CA  GLY A 241 " =    2.250
peak=   -3.569 closest distance to " OXT GLY A 302 " =    2.945
peak=   -3.567 closest distance to " O   ALA A 161 " =    1.644
peak=   -3.567 closest distance to " O   PRO A 163 " =    1.983
peak=   -3.556 closest distance to " CG  TRP A 266 " =    1.914
peak=   -3.555 closest distance to " O   HOH Z 166 " =    2.097
peak=   -3.552 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.551 closest distance to " N   GLN A  58 " =    1.831
peak=   -3.545 closest distance to " N   ALA A 248 " =    1.576
peak=   -3.539 closest distance to " C   ALA A 158 " =    1.307
peak=   -3.517 closest distance to " O   HOH Z  43 " =    1.834
peak=   -3.507 closest distance to " CB  ALA A 248 " =    2.410
peak=   -3.507 closest distance to " CD1 LEU A 228 " =    2.177
peak=   -3.505 closest distance to " CD  LYS A 289 " =    2.492
peak=   -3.504 closest distance to " NH2 ARG A  79 " =    2.014
peak=   -3.501 closest distance to " O   HOH Z 134 " =    3.002
peak=   -3.498 closest distance to " O   HOH Z  60 " =    2.056
peak=   -3.496 closest distance to " CE3 TRP A 150 " =    2.022
peak=   -3.493 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.492 closest distance to " O   HOH Z 281 " =    2.774
peak=   -3.474 closest distance to " CB  TYR A  15 " =    2.154
peak=   -3.470 closest distance to " CD2 LEU A   5 " =    1.095
peak=   -3.463 closest distance to " O   HOH Z 423 " =    1.209
peak=   -3.460 closest distance to " CD1 LEU A 101 " =    2.363
peak=   -3.441 closest distance to " O   SER A 271 " =    2.190
peak=   -3.438 closest distance to " OD2 ASP A 191 " =    1.347
peak=   -3.435 closest distance to " O   HOH Z 243 " =    1.961
peak=   -3.432 closest distance to " OD2 ASP A 171 " =    2.160
peak=   -3.430 closest distance to " C   GLY A  17 " =    1.230
peak=   -3.428 closest distance to " O   HOH Z 211 " =    1.471
peak=   -3.418 closest distance to " O   HOH Z 359 " =    1.651
peak=   -3.417 closest distance to " O   HOH Z 191 " =    5.430
peak=   -3.416 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -3.413 closest distance to " O   HOH Z 198 " =    2.110
peak=   -3.408 closest distance to " O   HOH Z 359 " =    3.363
peak=   -3.401 closest distance to " CD1 LEU A 101 " =    2.841
peak=   -3.399 closest distance to " O   HOH Z  90 " =    2.698
peak=   -3.389 closest distance to " CB  ALA A 291 " =    2.289
peak=   -3.389 closest distance to " O   HOH Z 388 " =    2.153
peak=   -3.378 closest distance to " O   HOH Z 165 " =    2.066
peak=   -3.378 closest distance to " CZ  TYR A 169 " =    1.594
peak=   -3.376 closest distance to " O   GLY A  80 " =    2.426
peak=   -3.370 closest distance to " O   VAL A 189 " =    2.597
peak=   -3.368 closest distance to " NE2 GLN A  88 " =    1.997
peak=   -3.367 closest distance to " O   HOH Z 262 " =    2.800
peak=   -3.359 closest distance to " CA  GLY A  98 " =    1.921
peak=   -3.357 closest distance to " O   HOH Z  56 " =    2.403
peak=   -3.357 closest distance to " O   HOH Z   9 " =    1.448
peak=   -3.355 closest distance to " CB  ASN A  39 " =    2.235
peak=   -3.346 closest distance to " C   LEU A 143 " =    1.058
peak=   -3.345 closest distance to " CG  GLN A 278 " =    2.165
peak=   -3.344 closest distance to " ND2 ASN A 252 " =    1.867
peak=   -3.342 closest distance to " O   HOH Z 103 " =    1.731
peak=   -3.340 closest distance to " O   ALA A  10 " =    1.783
peak=   -3.336 closest distance to " CD2 TYR A 247 " =    2.474
peak=   -3.332 closest distance to " O   SER A 135 " =    1.444
peak=   -3.329 closest distance to " CZ2 TRP A 274 " =    0.887
peak=   -3.329 closest distance to " O   ALA A  51 " =    1.369
peak=   -3.328 closest distance to " NH2AARG A 275 " =    5.166
peak=   -3.327 closest distance to " O   HOH Z 348 " =    1.841
peak=   -3.324 closest distance to " OG  SER A  87 " =    1.424
peak=   -3.324 closest distance to " N   PHE A  59 " =    2.165
peak=   -3.310 closest distance to " OH  TYR A 214 " =    1.150
peak=   -3.310 closest distance to " CB  ALA A   7 " =    2.199
peak=   -3.309 closest distance to " O   HOH Z 407 " =    3.023
peak=   -3.307 closest distance to " NZ  LYS A 119 " =    3.368
peak=   -3.306 closest distance to " O   HOH Z 423 " =    2.136
peak=   -3.302 closest distance to " CE BMET A  47 " =    1.585
peak=   -3.298 closest distance to " ND2 ASN A 249 " =    2.284
peak=   -3.293 closest distance to " CA  ASP A  27 " =    2.358
peak=   -3.286 closest distance to " O   GLY A 203 " =    2.436
peak=   -3.281 closest distance to " O   HOH Z  51 " =    1.180
peak=   -3.274 closest distance to " OG  SER A  97 " =    2.183
peak=   -3.273 closest distance to " N   ASN A  60 " =    1.370
peak=   -3.269 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.267 closest distance to " CD2 TYR A 293 " =    1.996
peak=   -3.265 closest distance to " O   HOH Z 166 " =    1.511
peak=   -3.263 closest distance to " CG1 VAL A 197 " =    2.294
peak=   -3.261 closest distance to " O   HOH Z 309 " =    2.425
peak=   -3.256 closest distance to " N   THR A  52 " =    1.751
peak=   -3.250 closest distance to " OH  TYR A 169 " =    0.955
peak=   -3.247 closest distance to " CG  MET A 105 " =    0.917
peak=   -3.243 closest distance to " O   HOH Z 256 " =    1.240
peak=   -3.243 closest distance to " O   HOH Z 389 " =    1.421
peak=   -3.242 closest distance to " O   ALA A 180 " =    1.236
peak=   -3.238 closest distance to " O   HOH Z 111 " =    4.380
peak=   -3.238 closest distance to " N   SER A 276 " =    1.294
peak=   -3.237 closest distance to " C   ASP A 231 " =    2.420
peak=   -3.236 closest distance to " O   HOH Z 134 " =    3.699
peak=   -3.232 closest distance to " O   HOH Z  65 " =    1.178
peak=   -3.231 closest distance to " CG2 ILE A 263 " =    2.360
peak=   -3.229 closest distance to " CD  PRO A 213 " =    2.065
peak=   -3.228 closest distance to " O   HOH Z 295 " =    1.598
peak=   -3.228 closest distance to " O   HOH Z 377 " =    1.079
peak=   -3.227 closest distance to " CE1 TYR A 169 " =    2.538
peak=   -3.224 closest distance to " NE2 GLN A 223 " =    1.743
peak=   -3.222 closest distance to " OD1 ASN A 148 " =    1.389
peak=   -3.221 closest distance to " CB  TYR A 172 " =    2.437
peak=   -3.219 closest distance to " OE1 GLN A  88 " =    1.090
peak=   -3.219 closest distance to " O   HOH Z 369 " =    2.292
peak=   -3.218 closest distance to " ND2 ASN A  39 " =    1.459
peak=   -3.217 closest distance to " O   PRO A 198 " =    1.319
peak=   -3.217 closest distance to " C   ASN A 187 " =    1.798
peak=   -3.217 closest distance to " ND2BASN A 224 " =    1.691
peak=   -3.216 closest distance to " NH1 ARG A  36 " =    1.883
peak=   -3.209 closest distance to " O   HOH Z 426 " =    1.679
peak=   -3.207 closest distance to " O   HOH Z  63 " =    1.766
peak=   -3.206 closest distance to " OG ASER A 134 " =    1.131
peak=   -3.202 closest distance to " O   HOH Z  13 " =    1.921
peak=   -3.197 closest distance to " O   HOH Z 275 " =    1.382
peak=   -3.197 closest distance to " CG1 VAL A 296 " =    1.338
peak=   -3.197 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.192 closest distance to " O   HOH Z 139 " =    3.066
peak=   -3.191 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.189 closest distance to " C   LYS A  76 " =    1.582
peak=   -3.184 closest distance to " CD1 ILE A 199 " =    2.504
peak=   -3.177 closest distance to " OE2 GLU A 152 " =    1.199
peak=   -3.176 closest distance to " CD  ARG A 139 " =    1.598
peak=   -3.175 closest distance to " O   MET A  40 " =    2.712
peak=   -3.173 closest distance to " ND2 ASN A  69 " =    1.766
peak=   -3.172 closest distance to " O   HOH Z 123 " =    2.481
peak=   -3.169 closest distance to " CA  GLY A  57 " =    2.081
peak=   -3.169 closest distance to " N   SER A 212 " =    1.950
peak=   -3.168 closest distance to " O   TRP A  70 " =    1.430
peak=   -3.163 closest distance to " CA  GLY A 241 " =    3.075
peak=   -3.159 closest distance to " O   HOH Z 131 " =    4.043
peak=   -3.158 closest distance to " O   HOH Z 111 " =    2.345
peak=   -3.154 closest distance to " O   HOH Z 371 " =    2.290
peak=   -3.150 closest distance to " OG  SER A 206 " =    1.645
peak=   -3.148 closest distance to " O   ARG A  24 " =    2.008
peak=   -3.147 closest distance to " CG  GLU A 277 " =    1.183
peak=   -3.145 closest distance to " O   HOH Z 151 " =    2.014
peak=   -3.145 closest distance to " CD2 LEU A 300 " =    2.566
peak=   -3.141 closest distance to " CA  GLY A 133 " =    1.963
peak=   -3.141 closest distance to " CG2 VAL A 202 " =    2.688
peak=   -3.138 closest distance to " NH2BARG A 275 " =    1.651
peak=   -3.125 closest distance to " O   HOH Z 357 " =    1.923
peak=   -3.122 closest distance to " N   HIS A 115 " =    2.152
peak=   -3.117 closest distance to " O   HOH Z 417 " =    2.676
peak=   -3.116 closest distance to " O   GLN A 240 " =    2.007
peak=   -3.107 closest distance to " CB  ALA A   9 " =    2.555
peak=   -3.105 closest distance to " O   ILE A 106 " =    2.112
peak=   -3.086 closest distance to " CD1 TYR A 247 " =    2.701
peak=   -3.085 closest distance to " ND2 ASN A  60 " =    1.745
peak=   -3.081 closest distance to " O   VAL A 125 " =    2.438
peak=   -3.079 closest distance to " CH2 TRP A 179 " =    1.936
peak=   -3.076 closest distance to " O   HOH Z 231 " =    1.447
peak=   -3.076 closest distance to " N   ALA A 248 " =    2.546
peak=   -3.073 closest distance to " OG  SER A  62 " =    1.657
peak=   -3.072 closest distance to " OXT GLY A 302 " =    3.487
peak=   -3.071 closest distance to " CG  ARG A 269 " =    2.367
peak=   -3.020 closest distance to " CD2 LEU A 300 " =    2.850

================= 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    :  0.4298 0.4163   6.222621e+00   6.196231e+00
   1_bss:  0.4215 0.4031   6.217511e+00   6.181592e+00
   1_xyz:  0.3137 0.3340   6.004573e+00   6.043651e+00
   1_adp:  0.2478 0.2849   5.807379e+00   5.914122e+00
   1_occ:  0.2472 0.2846   5.806031e+00   5.915137e+00
   2_bss:  0.2414 0.2772   5.802369e+00   5.908279e+00
   2_xyz:  0.1694 0.2114   5.485570e+00   5.656866e+00
   2_adp:  0.1539 0.1985   5.406670e+00   5.599038e+00
   2_occ:  0.1538 0.1984   5.406312e+00   5.598776e+00
   3_bss:  0.1536 0.1973   5.405237e+00   5.595596e+00
   3_xyz:  0.1279 0.1702   5.244140e+00   5.460131e+00
   3_adp:  0.1220 0.1662   5.207717e+00   5.433520e+00
   3_occ:  0.1219 0.1661   5.206962e+00   5.432545e+00
   4_bss:  0.1220 0.1657   5.206540e+00   5.431552e+00
   4_xyz:  0.1137 0.1602   5.161617e+00   5.407111e+00
   4_adp:  0.1142 0.1575   5.154372e+00   5.388957e+00
   4_occ:  0.1141 0.1573   5.153674e+00   5.388256e+00
   5_bss:  0.1141 0.1572   5.153260e+00   5.387831e+00
   5_xyz:  0.1141 0.1559   5.150245e+00   5.382173e+00
   5_adp:  0.1128 0.1570   5.150056e+00   5.390634e+00
   5_occ:  0.1127 0.1569   5.149390e+00   5.389815e+00
   5_bss:  0.1127 0.1569   5.149406e+00   5.389831e+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:  0.366  20.001   7.192   9.411   8.005   0.000   0.000   0.000
   1_xyz:  0.366  20.001   7.192   9.411   8.005   0.000   0.000   0.000
   1_adp:  0.366  20.001   7.192   9.411   8.005   0.000   0.000   0.000
   1_occ:  0.366  20.001   7.192   9.411   8.005   0.000   0.000   0.000
   2_bss:  0.342  36.180   3.744   4.915   4.864   0.000   0.000   0.000
   2_xyz:  0.342  36.180   3.744   4.915   4.864   0.000   0.000   0.000
   2_adp:  0.342  36.180   3.744   4.915   4.864   0.000   0.000   0.000
   2_occ:  0.342  36.180   3.744   4.915   4.864   0.000   0.000   0.000
   3_bss:  0.324  36.180   3.167   3.519   4.495   0.000   0.000   0.000
   3_xyz:  0.324  36.180   3.167   3.519   4.495   0.000   0.000   0.000
   3_adp:  0.324  36.180   3.167   3.519   4.495   0.000   0.000   0.000
   3_occ:  0.324  36.180   3.167   3.519   4.495   0.000   0.000   0.000
   4_bss:  0.313  36.180   3.123   3.303   4.477   0.000   0.000   0.000
   4_xyz:  0.313  36.180   3.123   3.303   4.477   0.000   0.000   0.000
   4_adp:  0.313  36.180   3.123   3.303   4.477   0.000   0.000   0.000
   4_occ:  0.313  36.180   3.123   3.303   4.477   0.000   0.000   0.000
   5_bss:  0.321  40.358   3.082   3.167   4.456   0.000   0.000   0.000
   5_xyz:  0.321  40.358   3.082   3.167   4.456   0.000   0.000   0.000
   5_adp:  0.321  40.358   3.082   3.167   4.456   0.000   0.000   0.000
   5_occ:  0.321  40.358   3.082   3.167   4.456   0.000   0.000   0.000
   5_bss:  0.321  43.974  -0.481  -0.413   0.894   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.762 0.5621  0.6301    50572.845
   1_bss:  46.658 0.5609  0.8015    47872.893
   1_xyz:  35.848 0.6909  0.9612    30481.747
   1_adp:  27.977 0.7812  1.0626    20808.934
   1_occ:  28.022 0.7806  1.0605    20779.362
   2_bss:  27.633 0.7845  0.9310    20262.540
   2_xyz:  20.110 0.8607  0.9893    11138.737
   2_adp:  18.531 0.8760  0.9974     9862.108
   2_occ:  18.523 0.8761  0.9973     9844.262
   3_bss:  18.434 0.8768  0.9696     9752.724
   3_xyz:  15.558 0.9019  0.9849     7324.550
   3_adp:  14.933 0.9074  0.9844     6969.904
   3_occ:  14.912 0.9076  0.9845     6956.308
   4_bss:  14.889 0.9078  0.9809     6951.154
   4_xyz:  14.319 0.9126  0.9822     6552.329
   4_adp:  13.889 0.9162  0.9825     6342.311
   4_occ:  13.875 0.9163  0.9825     6329.422
   5_bss:  13.862 0.9164  0.9804     6326.526
   5_xyz:  13.750 0.9173  0.9808     6240.177
   5_adp:  13.932 0.9159  0.9774     6325.665
   5_occ:  13.914 0.9160  0.9774     6317.035
   5_bss:  13.914 0.9160  0.9791     6317.421
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3595e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3595e+01
   1_xyz:   1.495  0.011  0.099 17.842  0.006  4.119   1.1454e-01
   1_adp:   1.495  0.011  0.099 17.842  0.006  4.119   1.1454e-01
   1_occ:   1.495  0.011  0.099 17.842  0.006  4.119   1.1454e-01
   2_bss:   1.495  0.011  0.099 17.842  0.006  4.119   1.1454e-01
   2_xyz:   0.937  0.006  0.071 15.819  0.004  4.118   5.7503e-02
   2_adp:   0.937  0.006  0.071 15.819  0.004  4.118   5.7503e-02
   2_occ:   0.937  0.006  0.071 15.819  0.004  4.118   5.7503e-02
   3_bss:   0.937  0.006  0.071 15.819  0.004  4.118   5.7503e-02
   3_xyz:   0.927  0.005  0.073 15.646  0.003  4.121   5.4480e-02
   3_adp:   0.927  0.005  0.073 15.646  0.003  4.121   5.4480e-02
   3_occ:   0.927  0.005  0.073 15.646  0.003  4.121   5.4480e-02
   4_bss:   0.927  0.005  0.073 15.646  0.003  4.121   5.4480e-02
   4_xyz:   0.977  0.006  0.078 15.804  0.003  4.124   5.9775e-02
   4_adp:   0.977  0.006  0.078 15.804  0.003  4.124   5.9775e-02
   4_occ:   0.977  0.006  0.078 15.804  0.003  4.124   5.9775e-02
   5_bss:   0.977  0.006  0.078 15.804  0.003  4.124   5.9775e-02
   5_xyz:   0.882  0.005  0.071 15.296  0.003  4.114   5.0845e-02
   5_adp:   0.882  0.005  0.071 15.296  0.003  4.114   5.0845e-02
   5_occ:   0.882  0.005  0.071 15.296  0.003  4.114   5.0845e-02
   5_bss:   0.882  0.005  0.071 15.296  0.003  4.114   5.0845e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9487e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9487e+00
   1_xyz:  12.285  0.140  0.420 89.345  0.032  2.271   8.3936e-02
   1_adp:  12.285  0.140  0.420 89.345  0.032  2.271   8.3936e-02
   1_occ:  12.285  0.140  0.420 89.345  0.032  2.271   8.3936e-02
   2_bss:  12.285  0.140  0.420 89.345  0.032  2.271   8.3936e-02
   2_xyz:   5.698  0.055  0.316 82.069  0.042  2.328   3.8020e-02
   2_adp:   5.698  0.055  0.316 82.069  0.042  2.328   3.8020e-02
   2_occ:   5.698  0.055  0.316 82.069  0.042  2.328   3.8020e-02
   3_bss:   5.698  0.055  0.316 82.069  0.042  2.328   3.8020e-02
   3_xyz:   7.009  0.050  0.375 83.339  0.025  2.321   4.4874e-02
   3_adp:   7.009  0.050  0.375 83.339  0.025  2.321   4.4874e-02
   3_occ:   7.009  0.050  0.375 83.339  0.025  2.321   4.4874e-02
   4_bss:   7.009  0.050  0.375 83.339  0.025  2.321   4.4874e-02
   4_xyz:   8.561  0.054  0.456 83.486  0.036  2.328   3.7813e-02
   4_adp:   8.561  0.054  0.456 83.486  0.036  2.328   3.7813e-02
   4_occ:   8.561  0.054  0.456 83.486  0.036  2.328   3.7813e-02
   5_bss:   8.561  0.054  0.456 83.486  0.036  2.328   3.7813e-02
   5_xyz:   6.546  0.040  0.376 83.637  0.033  2.350   2.7857e-02
   5_adp:   6.546  0.040  0.376 83.637  0.033  2.350   2.7857e-02
   5_occ:   6.546  0.040  0.376 83.637  0.033  2.350   2.7857e-02
   5_bss:   6.546  0.040  0.376 83.637  0.033  2.350   2.7857e-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:  65.49   0.00  10.80  65.49   0.00   7.74  63.13   0.00  27.47
   1_occ:  65.49   0.00  10.80  65.49   0.00   7.74  63.13   0.00  27.47
   2_bss:  65.49   0.00  10.80  65.49   0.00   7.74  63.13   0.00  27.47
   2_xyz:  65.49   0.00  10.80  65.49   0.00   7.74  63.13   0.00  27.47
   2_adp:  68.07   0.00  11.10  68.07   0.00   7.36  66.31   0.00  31.50
   2_occ:  68.07   0.00  11.10  68.07   0.00   7.36  66.31   0.00  31.50
   3_bss:  68.07   0.00  11.10  68.07   0.00   7.36  66.31   0.00  31.50
   3_xyz:  68.07   0.00  11.10  68.07   0.00   7.36  66.31   0.00  31.50
   3_adp:  83.46   0.00  12.01  83.46   0.00   7.58  81.49   0.42  36.14
   3_occ:  83.46   0.00  12.01  83.46   0.00   7.58  81.49   0.42  36.14
   4_bss:  83.46   0.00  12.01  83.46   0.00   7.58  81.49   0.42  36.14
   4_xyz:  83.46   0.00  12.01  83.46   0.00   7.58  81.49   0.42  36.14
   4_adp:  82.57   0.00  11.34  82.57   0.00   7.30  73.81   1.30  33.33
   4_occ:  82.57   0.00  11.34  82.57   0.00   7.30  73.81   1.30  33.33
   5_bss:  82.57   0.00  11.34  82.57   0.00   7.30  73.81   1.30  33.33
   5_xyz:  82.57   0.00  11.34  82.57   0.00   7.30  73.81   1.30  33.33
   5_adp:  87.19   0.00  11.60  87.19   0.00   7.37  76.35   0.82  34.64
   5_occ:  87.19   0.00  11.60  87.19   0.00   7.37  76.35   0.82  34.64
   5_bss:  90.81   3.62  15.22  90.81   3.62  10.99  79.97   4.44  38.26
------------------------------------------------------------------------
 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:    1.173    0.017    0.400
   1_adp:    1.173    0.017    0.400
   1_occ:    1.173    0.017    0.400
   2_bss:    1.173    0.017    0.400
   2_xyz:    1.379    0.023    0.495
   2_adp:    1.379    0.023    0.495
   2_occ:    1.379    0.023    0.495
   3_bss:    1.379    0.023    0.495
   3_xyz:    1.451    0.029    0.526
   3_adp:    1.451    0.029    0.526
   3_occ:    1.451    0.029    0.526
   4_bss:    1.451    0.029    0.526
   4_xyz:    1.570    0.035    0.548
   4_adp:    1.570    0.035    0.548
   4_occ:    1.570    0.035    0.548
   5_bss:    1.570    0.035    0.548
   5_xyz:    1.604    0.026    0.552
   5_adp:    1.604    0.026    0.552
   5_occ:    1.604    0.026    0.552
   5_bss:    1.604    0.026    0.552
------------------------------------------------------------------------

CPU time actual refinement: 319.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_643/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_643/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_643/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_643/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_643/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.00 
  Macro-tasks:
    bulk solvent and scale       = 40.10  
    individual site refinement   = 127.31 
    weights calculation          = 32.33  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 206.41 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 96.28  
    alpha_beta                      = 8.11   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 106.53 
    fmodel                         = 7.10   
    r_factors                      = 0.29   
    phase_errors                   = 10.61  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 232.12 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.523 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    640 calls, 95.97 s
gradients_fft:          585 calls, 93.22 s

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

# Date 2008-01-16 Time 02:03:57 PST -0800 (1200477837.84 s)
Start R-work = 0.4298, R-free = 0.4163 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1740 (no bulk solvent and anisotropic scale)

Start R-work = 0.4215, R-free = 0.4031
Final R-work = 0.1127, R-free = 0.1569