# Date 2008-01-16 Time 01:02:14 PST -0800 (1200474134.65 s)
#phil __OFF__

Command line arguments: "../245.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30346
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 245

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 45.7567, 85.5261, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.95228
Completeness in resolution range: 0.964168
Completeness with d_max=infinity: 0.961187

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7893
                             d_min =   1.9523

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.95228
Completeness in resolution range: 0.964168
Completeness with d_max=infinity: 0.961187

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7897 -  4.1774 [2132/2156]  1918   214  10.0%
  bin  2:  4.1774 -  3.3282 [2038/2058]  1836   202   9.9%
  bin  3:  3.3282 -  2.9111 [2032/2051]  1825   207  10.2%
  bin  4:  2.9111 -  2.6466 [2000/2030]  1803   197   9.8%
  bin  5:  2.6466 -  2.4578 [2010/2029]  1808   202  10.0%
  bin  6:  2.4578 -  2.3135 [1955/1980]  1761   194   9.9%
  bin  7:  2.3135 -  2.1980 [1982/2010]  1781   201  10.1%
  bin  8:  2.1980 -  2.1026 [1977/2013]  1781   196   9.9%
  bin  9:  2.1026 -  2.0219 [1927/1969]  1735   192  10.0%
  bin 10:  2.0219 -  1.9523 [1536/2021]  1382   154  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_245/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: 0.11 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:
        1.36 -     2.07: 24
        2.07 -     2.78: 626
        2.78 -     3.48: 4677
        3.48 -     4.19: 9587
        4.19 -     4.90: 14181
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.359 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.545 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.545 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.573 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.628 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29090 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_245/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_245/model_refine_001.geo

CPU time processing inputs: 8.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 45.75675 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5050   r_free= 0.5056   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.304798                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6593 0.99   1389  153 0.4354 0.4457      6.6509      6.7107|
|  2:  4.6593 -  3.7176 0.99   1330  152 0.4509 0.4201      6.8564      6.8228|
|  3:  3.7176 -  3.2533 0.99   1303  140 0.4822 0.4665      6.7396      6.7801|
|  4:  3.2533 -  2.9585 0.99   1298  149 0.4902 0.4487      6.5733         6.5|
|  5:  2.9585 -  2.7479 0.99   1292  145 0.5319 0.5476      6.3978      6.4243|
|  6:  2.7479 -  2.5868 0.99   1298  139 0.5266 0.5647      6.3066      6.2221|
|  7:  2.5868 -  2.4578 0.99   1280  144 0.5347 0.4917      6.2539       6.226|
|  8:  2.4578 -  2.3513 0.98   1269  141 0.5583 0.5538       6.208      6.1747|
|  9:  2.3513 -  2.2611 0.98   1256  140 0.5174 0.5880      6.1231      6.1932|
| 10:  2.2611 -  2.1833 1.00   1283  143 0.5406 0.5525       6.131      6.1361|
| 11:  2.1833 -  2.1153 0.97   1256  138 0.5299 0.5256      6.0392      6.0801|
| 12:  2.1153 -  2.0550 0.98   1248  138 0.5269 0.5373      5.9934      6.0087|
| 13:  2.0550 -  2.0010 0.99   1291  140 0.5530 0.5520      5.8963       5.851|
| 14:  2.0010 -  1.9523 0.66    837   97 0.5378 0.4982      5.8708      5.7824|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6593  1389   153  0.57  45.48   0.78     0.63     113741.81|
|  2:  4.6593 -  3.7176  1330   152  0.62  42.39   0.85     0.71     144426.88|
|  3:  3.7176 -  3.2533  1303   140  0.51  50.81   0.84     0.66     145196.30|
|  4:  3.2533 -  2.9585  1298   149  0.43  57.46   0.80     0.53     122559.29|
|  5:  2.9585 -  2.7479  1292   145  0.31  66.54   0.73     0.39      97308.13|
|  6:  2.7479 -  2.5868  1298   139  0.26  70.42   0.72     0.30      83931.20|
|  7:  2.5868 -  2.4578  1280   144  0.17  77.17   0.73     0.21      79566.88|
|  8:  2.4578 -  2.3513  1269   141  0.16  78.23   0.73     0.19      72809.68|
|  9:  2.3513 -  2.2611  1256   140  0.16  78.21   0.74     0.19      66739.82|
| 10:  2.2611 -  2.1833  1283   143  0.20  75.29   0.76     0.24      57195.24|
| 11:  2.1833 -  2.1153  1256   138  0.17  77.68   0.77     0.21      55760.73|
| 12:  2.1153 -  2.0550  1248   138  0.17  77.47   0.80     0.22      50300.83|
| 13:  2.0550 -  2.0010  1291   140  0.19  75.86   0.73     0.25      42641.53|
| 14:  2.0010 -  1.9523   837    97  0.34  64.77   0.74     0.38      29878.74|
|alpha:            min =        0.19 max =            0.71 mean =         0.37|
|beta:             min =    29878.74 max =       145196.30 mean =     84930.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.76|
|phase err.(test): min =        0.00 max =           89.97 mean =        66.89|
|-----------------------------------------------------------------------------|

============================== 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 = 28.388473             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.606   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.357650              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.875   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.968 -  1.361:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.361 -  1.754:       16 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.754 -  2.147:       87 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.147 -  2.540:      514 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.540 -  2.934:     1304 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.934 -  3.327:     2499 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.327 -  3.720:     4037 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.720 -  4.113:     5355 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.113 -  4.507:     6970 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.507 -  4.900:     8339 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.623 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.968 |       3.004 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    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 = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5080   r_free= 0.5077   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.305094                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4961   r_free= 0.4955   ksol= 0.39   Bsol= 2.80   scale= 0.969    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.58,9.35,7.43,0.00,0.00,0.00); trace/3= 7.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.299008                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.353343             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.387412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4961      final r-factor (work) = 0.4416          |
| start r-factor (free) = 0.4955      final r-factor (free) = 0.4719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 119.9071 = 21.35 * 0.50 * 6.3020 + 1.00 * 52.6231                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.9838 = 21.35 * 0.50 * 6.2592 + 1.00 * 0.1568                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4416      final r-factor (work) = 0.4039          |
| start r-factor (free) = 0.4719      final r-factor (free) = 0.4653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.9576 = 2.39 * 1.00 * 6.2592 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.8654 = 2.39 * 1.00 * 6.2162 + 1.00 * 0.0248                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.61   15.42    None  None   None       |
|    all(noH): 2823   0      0.00    79.61   15.42    None  None   None       |
|    Sol.    : 438    0      0.00    78.66   21.85    None  None   None       |
|    Mac.    : 2385   0      0.00    79.61   14.24    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.962:  915   |   5:    39.807 -  47.769:   89        |
|      1:     7.962 -  15.923:  774   |   6:    47.769 -  55.730:   38        |
|      2:    15.923 -  23.884:  516   |   7:    55.730 -  63.692:   16        |
|      3:    23.884 -  31.846:  321   |   8:    63.692 -  71.653:    5        |
|      4:    31.846 -  39.807:  146   |   9:    71.653 -  79.615:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4039 r_free = 0.4653             target_work(ml) = 6.208         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4030 r_free = 0.4651             target_work(ml) = 6.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4030   r_free= 0.4651   ksol= 0.39   Bsol= 2.80   scale= 1.093    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.58,9.35,7.43,0.00,0.00,0.00); trace/3= 7.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.207629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4022   r_free= 0.4606   ksol= 0.36   Bsol= 20.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.09,6.13,5.00,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.207388                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.872961             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.500  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.079151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.245  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4022      final r-factor (work) = 0.3618          |
| start r-factor (free) = 0.4606      final r-factor (free) = 0.4344          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.9314 = 10.87 * 0.50 * 6.2126 + 1.00 * 0.1568                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.6213 = 10.87 * 0.50 * 6.1683 + 1.00 * 0.0876                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3618      final r-factor (work) = 0.3504          |
| start r-factor (free) = 0.4344      final r-factor (free) = 0.4232          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6904 = 1.08 * 1.00 * 6.1683 + 1.00 * 0.0339                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6268 = 1.08 * 1.00 * 6.1257 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.92   15.06    None  None   None       |
|    all(noH): 2823   0      0.00    88.92   15.06    None  None   None       |
|    Sol.    : 438    0      0.00    80.83   23.82    None  None   None       |
|    Mac.    : 2385   0      0.00    88.92   13.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.892: 1014   |   5:    44.459 -  53.351:   30        |
|      1:     8.892 -  17.784:  858   |   6:    53.351 -  62.243:   19        |
|      2:    17.784 -  26.675:  546   |   7:    62.243 -  71.135:    4        |
|      3:    26.675 -  35.567:  231   |   8:    71.135 -  80.026:    3        |
|      4:    35.567 -  44.459:  116   |   9:    80.026 -  88.918:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3504 r_free = 0.4232             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3502 r_free = 0.4232             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3502   r_free= 0.4232   ksol= 0.36   Bsol= 20.00   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.09,6.13,5.00,0.00,0.00,0.00); trace/3= 5.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.115116                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3508   r_free= 0.4235   ksol= 0.36   Bsol= 44.68   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,4.56,3.92,0.00,0.00,0.00); trace/3= 3.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.117028                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.706604              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.456  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.024577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.049  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3508      final r-factor (work) = 0.3081          |
| start r-factor (free) = 0.4235      final r-factor (free) = 0.3837          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6257 = 6.71 * 0.50 * 6.1248 + 1.00 * 0.0876                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4439 = 6.71 * 0.50 * 6.0728 + 1.00 * 0.0798                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2876          |
| start r-factor (free) = 0.3837      final r-factor (free) = 0.3745          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3110 = 2.02 * 1.00 * 6.0728 + 1.00 * 0.0161                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1740 = 2.02 * 1.00 * 6.0013 + 1.00 * 0.0239                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.67  16.63    None  None   None       |
|    all(noH): 2823   0      0.00    110.67  16.63    None  None   None       |
|    Sol.    : 438    0      0.00    99.68   31.37    None  None   None       |
|    Mac.    : 2385   0      0.00    110.67  13.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.067: 1276   |   5:    55.333 -  66.400:   43        |
|      1:    11.067 -  22.133:  761   |   6:    66.400 -  77.467:   19        |
|      2:    22.133 -  33.200:  404   |   7:    77.467 -  88.533:    7        |
|      3:    33.200 -  44.267:  213   |   8:    88.533 -  99.600:    1        |
|      4:    44.267 -  55.333:   97   |   9:    99.600 - 110.667:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2876 r_free = 0.3745             target_work(ml) = 5.989         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2875 r_free = 0.3747             target_work(ml) = 5.989         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2875   r_free= 0.3747   ksol= 0.36   Bsol= 44.68   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,4.56,3.92,0.00,0.00,0.00); trace/3= 3.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.989065                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2875   r_free= 0.3738   ksol= 0.36   Bsol= 51.86   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.87,3.07,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.987982                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.243933             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.505  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.369249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.946  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2875      final r-factor (work) = 0.2382          |
| start r-factor (free) = 0.3738      final r-factor (free) = 0.3157          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.8066 = 12.24 * 0.50 * 5.9992 + 1.00 * 0.0798                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3114 = 12.24 * 0.50 * 5.9155 + 1.00 * 0.0967                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2382      final r-factor (work) = 0.2174          |
| start r-factor (free) = 0.3157      final r-factor (free) = 0.2823          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2080 = 0.37 * 1.00 * 5.9155 + 1.00 * 0.0237                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1455 = 0.37 * 1.00 * 5.7839 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.94   14.21    None  None   None       |
|    all(noH): 2823   0      0.00    99.94   14.21    None  None   None       |
|    Sol.    : 438    0      1.37    82.41   33.37    None  None   None       |
|    Mac.    : 2385   0      0.00    99.94   10.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.994: 1463   |   5:    49.969 -  59.963:   40        |
|      1:     9.994 -  19.988:  753   |   6:    59.963 -  69.957:   15        |
|      2:    19.988 -  29.982:  262   |   7:    69.957 -  79.951:    9        |
|      3:    29.982 -  39.975:  170   |   8:    79.951 -  89.944:    2        |
|      4:    39.975 -  49.969:  108   |   9:    89.944 -  99.938:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2174 r_free = 0.2823             target_work(ml) = 5.732         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2167 r_free = 0.2819             target_work(ml) = 5.730         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2167   r_free= 0.2819   ksol= 0.36   Bsol= 51.86   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.87,3.07,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.730473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2165   r_free= 0.2793   ksol= 0.34   Bsol= 46.16   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,1.66,2.41,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.726682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.162349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.161  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.327178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.849  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2165      final r-factor (work) = 0.1751          |
| start r-factor (free) = 0.2793      final r-factor (free) = 0.2312          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2418 = 3.16 * 0.50 * 5.7838 + 1.00 * 0.0967                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9743 = 3.16 * 0.50 * 5.6374 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1751      final r-factor (work) = 0.1616          |
| start r-factor (free) = 0.2312      final r-factor (free) = 0.2187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8543 = 0.33 * 1.00 * 5.6374 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8060 = 0.33 * 1.00 * 5.4888 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.27   14.25    None  None   None       |
|    all(noH): 2823   0      0.00    98.27   14.25    None  None   None       |
|    Sol.    : 438    0      3.40    77.46   37.76    None  None   None       |
|    Mac.    : 2385   0      0.00    98.27   9.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.827: 1594   |   5:    49.135 -  58.962:   91        |
|      1:     9.827 -  19.654:  651   |   6:    58.962 -  68.789:   28        |
|      2:    19.654 -  29.481:  191   |   7:    68.789 -  78.616:   12        |
|      3:    29.481 -  39.308:  133   |   8:    78.616 -  88.443:    3        |
|      4:    39.308 -  49.135:  119   |   9:    88.443 -  98.270:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1616 r_free = 0.2187             target_work(ml) = 5.463         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1613 r_free = 0.2177             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1613   r_free= 0.2177   ksol= 0.34   Bsol= 46.16   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,1.66,2.41,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.460844                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6593 0.99   1389  153 0.1260 0.1589      5.5871      5.7411|
|  2:  4.6593 -  3.7176 0.99   1330  152 0.1226 0.1694      5.7613      6.0776|
|  3:  3.7176 -  3.2533 0.99   1303  140 0.1516 0.1941      5.8179      6.0937|
|  4:  3.2533 -  2.9585 0.99   1298  149 0.1734 0.2329      5.7792      5.9191|
|  5:  2.9585 -  2.7479 0.99   1292  145 0.1883 0.2440      5.6444      5.8593|
|  6:  2.7479 -  2.5868 0.99   1298  139 0.1730 0.2514      5.5102      5.6726|
|  7:  2.5868 -  2.4578 0.99   1280  144 0.1850 0.2191      5.4771      5.6293|
|  8:  2.4578 -  2.3513 0.98   1269  141 0.1757 0.2525      5.4203       5.694|
|  9:  2.3513 -  2.2611 0.98   1256  140 0.1764 0.2487      5.3605      5.5626|
| 10:  2.2611 -  2.1833 1.00   1283  143 0.1652 0.2478       5.297      5.5171|
| 11:  2.1833 -  2.1153 0.97   1256  138 0.1671 0.2492       5.276      5.5692|
| 12:  2.1153 -  2.0550 0.98   1248  138 0.1699 0.2441      5.2187      5.5368|
| 13:  2.0550 -  2.0010 0.99   1291  140 0.1761 0.2388      5.1054      5.2992|
| 14:  2.0010 -  1.9523 0.66    837   97 0.1606 0.1979      4.9897      5.1458|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6593  1389   153  0.92  12.13   0.99     0.97      10861.32|
|  2:  4.6593 -  3.7176  1330   152  0.92  12.31   1.05     1.03      16299.42|
|  3:  3.7176 -  3.2533  1303   140  0.88  18.10   1.06     1.05      22092.73|
|  4:  3.2533 -  2.9585  1298   149  0.86  20.36   1.04     0.98      19874.61|
|  5:  2.9585 -  2.7479  1292   145  0.83  23.13   1.02     0.96      16128.33|
|  6:  2.7479 -  2.5868  1298   139  0.84  22.34   1.01     0.95      12838.57|
|  7:  2.5868 -  2.4578  1280   144  0.83  23.43   1.03     1.00      12091.30|
|  8:  2.4578 -  2.3513  1269   141  0.84  23.00   1.03     1.00      10992.97|
|  9:  2.3513 -  2.2611  1256   140  0.85  22.26   1.03     0.96       9649.04|
| 10:  2.2611 -  2.1833  1283   143  0.83  23.25   1.03     0.97       8921.46|
| 11:  2.1833 -  2.1153  1256   138  0.83  23.75   1.06     0.99       8759.59|
| 12:  2.1153 -  2.0550  1248   138  0.83  23.68   1.06     1.02       8183.87|
| 13:  2.0550 -  2.0010  1291   140  0.84  22.84   1.05     1.01       5917.39|
| 14:  2.0010 -  1.9523   837    97  0.88  18.52   1.04     0.98       4019.97|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     4019.97 max =        22092.73 mean =     12141.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.99 mean =        20.62|
|phase err.(test): min =        0.00 max =           89.64 mean =        19.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2177   ksol= 0.32   Bsol= 35.21   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.37,0.84,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459034                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2177   ksol= 0.32   Bsol= 35.21   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.37,0.84,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459034                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.6593 0.99   1389  153 0.1235 0.1527      5.5607      5.7158|
|  2:  4.6593 -  3.7176 0.99   1330  152 0.1223 0.1676      5.7551      6.0642|
|  3:  3.7176 -  3.2533 0.99   1303  140 0.1512 0.1939      5.8137      6.0949|
|  4:  3.2533 -  2.9585 0.99   1298  149 0.1733 0.2344      5.7796      5.9204|
|  5:  2.9585 -  2.7479 0.99   1292  145 0.1885 0.2444       5.646       5.864|
|  6:  2.7479 -  2.5868 0.99   1298  139 0.1730 0.2531      5.5117      5.6784|
|  7:  2.5868 -  2.4578 0.99   1280  144 0.1848 0.2195      5.4786      5.6296|
|  8:  2.4578 -  2.3513 0.98   1269  141 0.1755 0.2543      5.4224      5.6995|
|  9:  2.3513 -  2.2611 0.98   1256  140 0.1762 0.2494      5.3624      5.5627|
| 10:  2.2611 -  2.1833 1.00   1283  143 0.1653 0.2489      5.2989      5.5206|
| 11:  2.1833 -  2.1153 0.97   1256  138 0.1673 0.2502      5.2777      5.5703|
| 12:  2.1153 -  2.0550 0.98   1248  138 0.1701 0.2450      5.2188      5.5385|
| 13:  2.0550 -  2.0010 0.99   1291  140 0.1767 0.2383      5.1069      5.2967|
| 14:  2.0010 -  1.9523 0.66    837   97 0.1607 0.1980        4.99      5.1454|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.6593  1389   153  0.92  11.84   0.98     0.96      10330.48|
|  2:  4.6593 -  3.7176  1330   152  0.92  12.07   1.04     1.02      15772.98|
|  3:  3.7176 -  3.2533  1303   140  0.88  17.94   1.05     1.04      21778.17|
|  4:  3.2533 -  2.9585  1298   149  0.86  20.40   1.02     0.97      19872.92|
|  5:  2.9585 -  2.7479  1292   145  0.83  23.25   1.00     0.95      16288.54|
|  6:  2.7479 -  2.5868  1298   139  0.84  22.47   0.99     0.93      12971.83|
|  7:  2.5868 -  2.4578  1280   144  0.83  23.53   1.01     0.98      12209.32|
|  8:  2.4578 -  2.3513  1269   141  0.83  23.13   1.00     0.98      11101.60|
|  9:  2.3513 -  2.2611  1256   140  0.85  22.35   1.00     0.93       9729.82|
| 10:  2.2611 -  2.1833  1283   143  0.83  23.33   1.00     0.94       8970.48|
| 11:  2.1833 -  2.1153  1256   138  0.83  23.82   1.03     0.96       8816.33|
| 12:  2.1153 -  2.0550  1248   138  0.83  23.67   1.03     0.99       8180.35|
| 13:  2.0550 -  2.0010  1291   140  0.84  22.86   1.02     0.98       5933.56|
| 14:  2.0010 -  1.9523   837    97  0.88  18.55   1.00     0.95       4029.49|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     4029.49 max =        21778.17 mean =     12089.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.86 mean =        20.62|
|phase err.(test): min =        0.00 max =           89.62 mean =        19.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.289)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    99.49   15.47    None  None   None       |
|    all(noH): 2823   0      1.22    99.49   15.47    None  None   None       |
|    Sol.    : 438    0      4.63    78.69   38.99    None  None   None       |
|    Mac.    : 2385   0      1.22    99.49   11.15    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:     1.223 -  11.050: 1594   |   5:    50.358 -  60.185:   91        |
|      1:    11.050 -  20.877:  651   |   6:    60.185 -  70.012:   28        |
|      2:    20.877 -  30.704:  191   |   7:    70.012 -  79.839:   12        |
|      3:    30.704 -  40.531:  133   |   8:    79.839 -  89.666:    3        |
|      4:    40.531 -  50.358:  119   |   9:    89.666 -  99.493:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 363         
Filter by distance & map next to the model:
   mapped sites are within: 0.443 - 5.420
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 358 from: 363
   mapped sites are within: 0.711 - 5.420

peak=    8.537 closest distance to " CB  VAL A 296 " =    1.536
peak=    7.707 closest distance to " CG  ASP A  27 " =    1.304
peak=    7.605 closest distance to " O   HOH Z 390 " =    1.412
peak=    6.941 closest distance to " O   HOH Z 381 " =    1.526
peak=    6.917 closest distance to " CB  VAL A 230 " =    1.487
peak=    6.812 closest distance to " O   HOH Z 268 " =    1.476
peak=    6.310 closest distance to " O   HOH Z 402 " =    1.703
peak=    5.898 closest distance to " CD  ARG A 138 " =    1.020
peak=    5.883 closest distance to " O   HOH Z 387 " =    2.016
peak=    5.619 closest distance to " O   HOH Z 375 " =    1.310
peak=    5.613 closest distance to " OD2 ASP A  50 " =    1.135
peak=    5.513 closest distance to " CG  LEU A   5 " =    1.631
peak=    5.395 closest distance to " O   HOH Z 120 " =    1.260
peak=    5.311 closest distance to " O   HOH Z 291 " =    1.198
peak=    5.305 closest distance to " O   HOH Z 130 " =    1.677
peak=    5.295 closest distance to " O   HOH Z   9 " =    1.644
peak=    5.279 closest distance to " CB  ARG A 275 " =    1.357
peak=    5.273 closest distance to " N   ARG A 275 " =    0.857
peak=    5.226 closest distance to " O   HOH Z 223 " =    1.145
peak=    5.224 closest distance to " OD1 ASP A 286 " =    1.105
peak=    5.139 closest distance to " O   HOH Z 350 " =    1.464
peak=    5.123 closest distance to " O   HOH Z 289 " =    1.525
peak=    5.079 closest distance to " O   HOH Z 139 " =    1.905
peak=    5.039 closest distance to " NH1 ARG A 138 " =    0.978
peak=    4.986 closest distance to " NZ BLYS A 290 " =    1.243
peak=    4.942 closest distance to " C   PRO A 198 " =    1.456
peak=    4.929 closest distance to " O   HOH Z 124 " =    1.772
peak=    4.918 closest distance to " O   HOH Z  24 " =    2.016
peak=    4.912 closest distance to " CD1AILE A 234 " =    0.943
peak=    4.871 closest distance to " NH2 ARG A 269 " =    0.939
peak=    4.871 closest distance to " OD1 ASN A  45 " =    1.150
peak=    4.859 closest distance to " NH2 ARG A  56 " =    2.239
peak=    4.844 closest distance to " O   HOH Z  54 " =    1.383
peak=    4.830 closest distance to " NE1 TRP A 266 " =    2.034
peak=    4.808 closest distance to " CD  ARG A 138 " =    1.145
peak=    4.736 closest distance to " O   HOH Z  46 " =    1.504
peak=    4.697 closest distance to " O   HOH Z  28 " =    1.729
peak=    4.665 closest distance to " O   HOH Z  65 " =    2.202
peak=    4.578 closest distance to " O   HOH Z 130 " =    2.205
peak=    4.574 closest distance to " OD2 ASP A 253 " =    1.086
peak=    4.552 closest distance to " O   HOH Z 410 " =    1.558
peak=    4.546 closest distance to " O   VAL A  72 " =    0.956
peak=    4.546 closest distance to " O   HOH Z 363 " =    1.266
peak=    4.526 closest distance to " O   HOH Z 215 " =    1.683
peak=    4.518 closest distance to " O   HOH Z 244 " =    1.379
peak=    4.494 closest distance to " O   HOH Z 428 " =    1.602
peak=    4.480 closest distance to " O   HOH Z 403 " =    1.839
peak=    4.410 closest distance to " O   HOH Z 363 " =    2.545
peak=    4.406 closest distance to " CA  ASN A 284 " =    0.881
peak=    4.402 closest distance to " O   HOH Z   7 " =    1.987
peak=    4.385 closest distance to " O   HOH Z 426 " =    1.318
peak=    4.384 closest distance to " N   GLU A   2 " =    1.456
peak=    4.380 closest distance to " CE  MET A  93 " =    1.457
peak=    4.363 closest distance to " O   HOH Z 388 " =    1.228
peak=    4.360 closest distance to " O   HOH Z 126 " =    1.986
peak=    4.360 closest distance to " O   HOH Z 293 " =    1.487
peak=    4.352 closest distance to " O   HOH Z 236 " =    1.782
peak=    4.338 closest distance to " O   HOH Z  27 " =    1.245
peak=    4.329 closest distance to " O   HOH Z  59 " =    1.371
peak=    4.303 closest distance to " O   HOH Z 358 " =    1.359
peak=    4.294 closest distance to " C   ASN A 285 " =    0.964
peak=    4.291 closest distance to " O   HOH Z 250 " =    2.183
peak=    4.288 closest distance to " O   HOH Z 422 " =    1.308
peak=    4.280 closest distance to " O   HOH Z 416 " =    1.555
peak=    4.277 closest distance to " N   GLY A 302 " =    0.956
peak=    4.273 closest distance to " O   HOH Z 417 " =    1.575
peak=    4.223 closest distance to " O   THR A 251 " =    0.899
peak=    4.223 closest distance to " O   HOH Z 142 " =    2.248
peak=    4.190 closest distance to " CD1 LEU A   5 " =    0.976
peak=    4.185 closest distance to " O   HOH Z 366 " =    2.413
peak=    4.169 closest distance to " N   TYR A  15 " =    1.042
peak=    4.151 closest distance to " CG2 THR A  29 " =    1.094
peak=    4.140 closest distance to " O   HOH Z  69 " =    1.752
peak=    4.138 closest distance to " NH2BARG A 145 " =    1.888
peak=    4.132 closest distance to " CB  SER A 216 " =    1.008
peak=    4.112 closest distance to " O   ARG A 275 " =    0.943
peak=    4.107 closest distance to " NE1 TRP A 274 " =    1.258
peak=    4.082 closest distance to " O   HOH Z 222 " =    1.493
peak=    4.067 closest distance to " O   HOH Z  53 " =    2.266
peak=    4.060 closest distance to " O   HOH Z  63 " =    1.761
peak=    4.059 closest distance to " CB  VAL A 202 " =    1.566
peak=    4.047 closest distance to " CE2 PHE A  16 " =    0.879
peak=    4.041 closest distance to " O   SER A 271 " =    1.130
peak=    4.037 closest distance to " O   HOH Z 262 " =    2.146
peak=    4.004 closest distance to " O   HOH Z 112 " =    1.674
peak=    3.991 closest distance to " NE2 GLN A  11 " =    1.208
peak=    3.987 closest distance to " O   HOH Z 193 " =    1.496
peak=    3.986 closest distance to " CB  TRP A 266 " =    0.985
peak=    3.972 closest distance to " O   HOH Z 425 " =    1.584
peak=    3.969 closest distance to " O   HOH Z 278 " =    1.603
peak=    3.961 closest distance to " O   ASP A 286 " =    2.237
peak=    3.961 closest distance to " O   HOH Z 179 " =    0.924
peak=    3.959 closest distance to " O   HOH Z 421 " =    2.124
peak=    3.954 closest distance to " CG  PRO A 198 " =    1.382
peak=    3.946 closest distance to " O   HOH Z 427 " =    2.027
peak=    3.946 closest distance to " OE1 GLU A   2 " =    1.917
peak=    3.933 closest distance to " CG1BVAL A 121 " =    2.093
peak=    3.924 closest distance to " CG  GLN A  88 " =    1.074
peak=    3.920 closest distance to " CB  SER A   3 " =    1.268
peak=    3.914 closest distance to " CG2 ILE A 234 " =    0.871
peak=    3.913 closest distance to " O   HOH Z 105 " =    1.156
peak=    3.913 closest distance to " O   HOH Z 400 " =    0.987
peak=    3.898 closest distance to " O   HOH Z  15 " =    1.019
peak=    3.885 closest distance to " O   HOH Z 244 " =    2.022
peak=    3.883 closest distance to " CG  PRO A 243 " =    1.216
peak=    3.875 closest distance to " O   HOH Z  64 " =    2.062
peak=    3.874 closest distance to " CZ3 TRP A  70 " =    1.027
peak=    3.870 closest distance to " O   HOH Z  61 " =    1.566
peak=    3.864 closest distance to " CA  ILE A 234 " =    1.294
peak=    3.853 closest distance to " CG2 THR A 279 " =    1.070
peak=    3.805 closest distance to " CB  SER A  62 " =    1.382
peak=    3.798 closest distance to " O   HOH Z 331 " =    1.361
peak=    3.797 closest distance to " CB  LYS A 290 " =    1.088
peak=    3.785 closest distance to " O   HOH Z  77 " =    1.245
peak=    3.774 closest distance to " OG ASER A 134 " =    1.537
peak=    3.772 closest distance to " O   HOH Z 404 " =    1.315
peak=    3.769 closest distance to " O   HOH Z 419 " =    2.224
peak=    3.765 closest distance to " CB  ALA A 114 " =    1.193
peak=    3.764 closest distance to " CD  GLN A  58 " =    5.420
peak=    3.763 closest distance to " O   HOH Z 431 " =    1.187
peak=    3.762 closest distance to " NH2 ARG A  36 " =    1.217
peak=    3.750 closest distance to " O   HOH Z 434 " =    1.644
peak=    3.747 closest distance to " O   HOH Z 428 " =    1.242
peak=    3.747 closest distance to " NE2 GLN A  73 " =    1.983
peak=    3.741 closest distance to " O   HOH Z 359 " =    1.532
peak=    3.741 closest distance to " O   HOH Z  51 " =    2.021
peak=    3.740 closest distance to " O   HOH Z 211 " =    1.548
peak=    3.739 closest distance to " O   HOH Z  92 " =    1.510
peak=    3.710 closest distance to " O   HOH Z 127 " =    1.009
peak=    3.708 closest distance to " CB  ALA A   1 " =    1.271
peak=    3.708 closest distance to " CG2AVAL A  72 " =    0.980
peak=    3.705 closest distance to " CB  PRO A  54 " =    1.218
peak=    3.700 closest distance to " O   HOH Z 422 " =    2.239
peak=    3.692 closest distance to " O   ALA A 242 " =    0.907
peak=    3.688 closest distance to " O   HOH Z 356 " =    1.784
peak=    3.682 closest distance to " CE AMET A  47 " =    1.163
peak=    3.678 closest distance to " O   HOH Z 389 " =    1.399
peak=    3.676 closest distance to " O   HOH Z 411 " =    1.629
peak=    3.674 closest distance to " NH2 ARG A 138 " =    1.315
peak=    3.670 closest distance to " CE AMET A  47 " =    1.301
peak=    3.664 closest distance to " N   GLU A 277 " =    0.711
peak=    3.660 closest distance to " O   HOH Z  47 " =    1.500
peak=    3.658 closest distance to " N   ARG A 156 " =    1.304
peak=    3.655 closest distance to " O   HOH Z 259 " =    2.400
peak=    3.654 closest distance to " CB  ARG A 138 " =    0.758
peak=    3.650 closest distance to " OG  SER A  62 " =    3.077
peak=    3.649 closest distance to " CB  GLN A 223 " =    1.531
peak=    3.647 closest distance to " O   HOH Z 369 " =    1.401
peak=    3.636 closest distance to " O   HOH Z 123 " =    1.747
peak=    3.622 closest distance to " O   HOH Z 342 " =    1.106
peak=    3.616 closest distance to " NE BARG A 275 " =    1.384
peak=    3.615 closest distance to " CZ  ARG A  14 " =    1.096
peak=    3.614 closest distance to " CG2 ILE A  20 " =    1.093
peak=    3.613 closest distance to " CB  ASN A  74 " =    1.125
peak=    3.610 closest distance to " CB  SER A 276 " =    1.471
peak=    3.609 closest distance to " O   HOH Z 423 " =    2.238
peak=    3.608 closest distance to " OD2 ASP A  27 " =    0.799
peak=    3.600 closest distance to " CG  ARG A 156 " =    1.168
peak=    3.584 closest distance to " CA  LEU A 282 " =    1.008
peak=    3.582 closest distance to " CB  GLU A 152 " =    1.084
peak=    3.579 closest distance to " O   HOH Z  91 " =    1.281
peak=    3.577 closest distance to " NZ  LYS A 119 " =    1.693
peak=    3.572 closest distance to " OD1 ASN A  69 " =    0.992
peak=    3.572 closest distance to " C   THR A  18 " =    1.078
peak=    3.569 closest distance to " O   HOH Z 172 " =    1.417
peak=    3.563 closest distance to " CE1 PHE A  38 " =    0.771
peak=    3.562 closest distance to " CB  ALA A  10 " =    0.903
peak=    3.551 closest distance to " O   HOH Z 226 " =    1.252
peak=    3.549 closest distance to " N   ALA A 160 " =    0.865
peak=    3.548 closest distance to " CB  PRO A  90 " =    1.298
peak=    3.543 closest distance to " O   HOH Z  39 " =    1.453
peak=    3.540 closest distance to " CD2 LEU A 297 " =    0.949
peak=    3.537 closest distance to " ND1 HIS A  81 " =    0.959
peak=    3.533 closest distance to " CB  ALA A 137 " =    0.848
peak=    3.532 closest distance to " O   HOH Z 415 " =    1.445
peak=    3.531 closest distance to " CB  TYR A 169 " =    0.719
peak=    3.524 closest distance to " O   THR A  29 " =    0.944
peak=    3.521 closest distance to " CZ  PHE A  16 " =    0.955
peak=    3.521 closest distance to " NZ  LYS A 117 " =    1.147
peak=    3.516 closest distance to " O   HOH Z 108 " =    2.022
peak=    3.514 closest distance to " OD2 ASP A 286 " =    2.074
peak=    3.509 closest distance to " CZ  PHE A  16 " =    1.066
peak=    3.509 closest distance to " O   HOH Z 204 " =    1.487
peak=    3.506 closest distance to " CB  ASN A 148 " =    1.607
peak=    3.501 closest distance to " O   HOH Z 137 " =    1.469
peak=    3.500 closest distance to " CB  TRP A 123 " =    1.093
peak=    3.499 closest distance to " CB  GLU A 277 " =    1.200
peak=    3.495 closest distance to " O   HOH Z 225 " =    1.545
peak=    3.493 closest distance to " O   HOH Z 434 " =    5.066
peak=    3.485 closest distance to " O   HOH Z 263 " =    1.779
peak=    3.483 closest distance to " O   HOH Z 133 " =    1.336
peak=    3.482 closest distance to " O   HOH Z 161 " =    0.897
peak=    3.481 closest distance to " OG BSER A 212 " =    2.672
peak=    3.475 closest distance to " O   HOH Z 402 " =    1.483
peak=    3.473 closest distance to " O   MET A  40 " =    1.704
peak=    3.472 closest distance to " O   HOH Z  81 " =    0.988
peak=    3.469 closest distance to " N   ASN A  60 " =    1.167
peak=    3.464 closest distance to " N   VAL A  72 " =    0.943
peak=    3.463 closest distance to " CD1 LEU A 281 " =    1.133
peak=    3.463 closest distance to " CE3 TRP A 274 " =    2.075
peak=    3.463 closest distance to " CD2 LEU A  25 " =    1.170
peak=    3.461 closest distance to " CB  ASN A 142 " =    1.182
peak=    3.458 closest distance to " CB  VAL A 230 " =    1.142
peak=    3.457 closest distance to " CD1 ILE A  33 " =    1.359
peak=    3.448 closest distance to " O   GLY A 147 " =    1.228
peak=    3.447 closest distance to " N   GLY A 287 " =    1.004
peak=    3.446 closest distance to " O   HOH Z 414 " =    1.985
peak=    3.434 closest distance to " O   HOH Z 145 " =    2.489
peak=    3.432 closest distance to " O   HOH Z 405 " =    1.908
peak=    3.432 closest distance to " O   ALA A 165 " =    1.265
peak=    3.430 closest distance to " O   HOH Z 159 " =    1.041
peak=    3.430 closest distance to " O   HOH Z 132 " =    1.204
peak=    3.428 closest distance to " O   HOH Z 303 " =    2.093
peak=    3.425 closest distance to " O   HOH Z 153 " =    3.415
peak=    3.424 closest distance to " OD1 ASN A 170 " =    1.698
peak=    3.422 closest distance to " CB  ALA A 233 " =    1.081
peak=    3.422 closest distance to " O   HOH Z 424 " =    1.961
peak=    3.414 closest distance to " CG1AVAL A 121 " =    1.027
peak=    3.414 closest distance to " N   SER A  12 " =    1.522
peak=    3.411 closest distance to " O   HOH Z 427 " =    1.113
peak=    3.410 closest distance to " O   HOH Z  88 " =    3.261
peak=    3.410 closest distance to " N   CYS A 260 " =    1.136
peak=    3.409 closest distance to " O   HOH Z 151 " =    1.948
peak=    3.409 closest distance to " OG1 THR A 246 " =    1.311
peak=    3.409 closest distance to " CG2 THR A 294 " =    1.267
peak=    3.406 closest distance to " CE  LYS A  48 " =    1.182
peak=    3.405 closest distance to " CD  ARG A  79 " =    1.247
peak=    3.401 closest distance to " O   SER A  62 " =    0.918
peak=    3.397 closest distance to " O   HOH Z  22 " =    1.797
peak=    3.392 closest distance to " O   HOH Z 143 " =    1.801
peak=    3.391 closest distance to " CG  GLN A 205 " =    1.199
peak=    3.380 closest distance to " CB  GLN A  77 " =    0.805
peak=    3.380 closest distance to " O   HOH Z  21 " =    1.611
peak=    3.377 closest distance to " CB  GLN A 122 " =    0.952
peak=    3.376 closest distance to " CB  PHE A 204 " =    0.780
peak=    3.371 closest distance to " CG2 VAL A 232 " =    1.161
peak=    3.371 closest distance to " O   HOH Z  89 " =    1.501
peak=    3.368 closest distance to " OG ASER A 258 " =    2.911
peak=    3.368 closest distance to " O   HOH Z 374 " =    2.137
peak=    3.367 closest distance to " N   ILE A  33 " =    1.029
peak=    3.366 closest distance to " O   HOH Z 371 " =    2.443
peak=    3.361 closest distance to " CB  ASP A  27 " =    0.899
peak=    3.349 closest distance to " CD2 LEU A 228 " =    1.305
peak=    3.346 closest distance to " NZ  LYS A 117 " =    3.277
peak=    3.343 closest distance to " CB  THR A  31 " =    1.178
peak=    3.341 closest distance to " CA  ARG A  56 " =    2.045
peak=    3.340 closest distance to " CA  TYR A  30 " =    0.951
peak=    3.337 closest distance to " O   HOH Z 112 " =    2.282
peak=    3.337 closest distance to " O   HOH Z 303 " =    1.518
peak=    3.336 closest distance to " N   TYR A 116 " =    1.370
peak=    3.335 closest distance to " O   HOH Z 225 " =    1.625
peak=    3.333 closest distance to " OG1 THR A 279 " =    0.886
peak=    3.331 closest distance to " OG  SER A  32 " =    1.045
peak=    3.325 closest distance to " CB  SER A 210 " =    0.864
peak=    3.320 closest distance to " CB  ASN A 187 " =    1.038
peak=    3.317 closest distance to " OD1 ASN A  45 " =    3.045
peak=    3.315 closest distance to " O   HOH Z 108 " =    1.453
peak=    3.314 closest distance to " O   HOH Z 431 " =    1.376
peak=    3.313 closest distance to " O   HOH Z 245 " =    1.195
peak=    3.313 closest distance to " C   GLN A  73 " =    1.091
peak=    3.313 closest distance to " CG1 VAL A 265 " =    0.945
peak=    3.309 closest distance to " N   GLN A 278 " =    0.950
peak=    3.309 closest distance to " CA  ALA A  43 " =    0.939
peak=    3.307 closest distance to " O   HOH Z 272 " =    1.866
peak=    3.304 closest distance to " CA  LYS A 290 " =    1.185
peak=    3.298 closest distance to " CD1 TYR A  15 " =    1.174
peak=    3.294 closest distance to " CB  GLN A  73 " =    1.163
peak=    3.294 closest distance to " CA  ALA A 184 " =    1.866
peak=    3.285 closest distance to " OD1 ASP A 272 " =    0.751
peak=    3.281 closest distance to " N   ASN A 127 " =    1.445
peak=    3.279 closest distance to " CZ3 TRP A 123 " =    1.663
peak=    3.278 closest distance to " C   ALA A   1 " =    1.531
peak=    3.275 closest distance to " CG2 THR A 246 " =    0.855
peak=    3.272 closest distance to " N   SER A  97 " =    0.876
peak=    3.272 closest distance to " CB  MET A  47 " =    1.641
peak=    3.269 closest distance to " CA  ASN A 127 " =    1.310
peak=    3.263 closest distance to " CB  ILE A 234 " =    0.965
peak=    3.262 closest distance to " O   HOH Z 222 " =    1.932
peak=    3.262 closest distance to " CG  GLN A  11 " =    2.154
peak=    3.261 closest distance to " CG  LYS A 166 " =    1.556
peak=    3.261 closest distance to " O   HOH Z 205 " =    1.107
peak=    3.257 closest distance to " CB  MET A  47 " =    0.942
peak=    3.256 closest distance to " O   HOH Z 347 " =    1.079
peak=    3.255 closest distance to " CD2 TYR A 169 " =    1.125
peak=    3.252 closest distance to " O   HOH Z 352 " =    1.614
peak=    3.250 closest distance to " CB  ARG A  36 " =    0.965
peak=    3.249 closest distance to " CG  GLN A  77 " =    2.137
peak=    3.247 closest distance to " CB  ALA A 248 " =    1.283
peak=    3.244 closest distance to " ND2BASN A 224 " =    0.858
peak=    3.243 closest distance to " OG BSER A 210 " =    1.559
peak=    3.243 closest distance to " N   GLY A 111 " =    1.464
peak=    3.242 closest distance to " O   HOH Z 271 " =    2.172
peak=    3.241 closest distance to " O   HOH Z 145 " =    2.331
peak=    3.237 closest distance to " CA  GLN A  55 " =    0.822
peak=    3.237 closest distance to " C   SER A 276 " =    1.035
peak=    3.234 closest distance to " O   HOH Z 114 " =    2.811
peak=    3.230 closest distance to " CG2 THR A 251 " =    1.773
peak=    3.225 closest distance to " O   HOH Z  51 " =    1.816
peak=    3.218 closest distance to " O   HOH Z  28 " =    1.725
peak=    3.217 closest distance to " O   HOH Z 119 " =    1.746
peak=    3.213 closest distance to " NH1BARG A 190 " =    1.696
peak=    3.213 closest distance to " CB  LEU A 300 " =    0.949
peak=    3.211 closest distance to " ND2 ASN A 252 " =    1.407
peak=    3.211 closest distance to " O   HOH Z 374 " =    1.278
peak=    3.201 closest distance to " NE AARG A 275 " =    1.552
peak=    3.201 closest distance to " OE1 GLN A  77 " =    1.192
peak=    3.200 closest distance to " O   HOH Z 313 " =    1.656
peak=    3.197 closest distance to " CA  ALA A  51 " =    0.855
peak=    3.196 closest distance to " O   HOH Z 362 " =    1.954
peak=    3.192 closest distance to " O   HOH Z 214 " =    1.125
peak=    3.192 closest distance to " O   HOH Z 104 " =    1.709
peak=    3.189 closest distance to " N   TRP A  85 " =    1.032
peak=    3.180 closest distance to " O   HOH Z 344 " =    1.232
peak=    3.178 closest distance to " O   HOH Z 353 " =    2.022
peak=    3.178 closest distance to " CG2 THR A 220 " =    0.942
peak=    3.178 closest distance to " O   HOH Z 233 " =    1.667
peak=    3.177 closest distance to " CB  PRO A 198 " =    1.054
peak=    3.177 closest distance to " O   SER A 164 " =    1.517
peak=    3.177 closest distance to " O   HOH Z 345 " =    3.786
peak=    3.176 closest distance to " CG  PRO A 213 " =    1.119
peak=    3.174 closest distance to " CB  LEU A  83 " =    0.912
peak=    3.172 closest distance to " O   HOH Z  61 " =    2.016
peak=    3.170 closest distance to " CD1 PHE A 130 " =    0.781
peak=    3.169 closest distance to " O   HOH Z 222 " =    1.624
peak=    3.167 closest distance to " OG1 THR A 246 " =    3.201
peak=    3.165 closest distance to " O   HOH Z 178 " =    1.155
peak=    3.163 closest distance to " O   HOH Z 139 " =    1.909
peak=    3.163 closest distance to " CB  ALA A 104 " =    1.047
peak=    3.163 closest distance to " CB  LYS A  76 " =    0.770
peak=    3.162 closest distance to " O   HOH Z 371 " =    2.312
peak=    3.160 closest distance to " CB  ASP A 124 " =    0.909
peak=    3.160 closest distance to " O   ARG A  79 " =    1.175
peak=    3.160 closest distance to " O   HOH Z 114 " =    2.054
peak=    3.157 closest distance to " NE2 GLN A 205 " =    1.183
peak=    3.156 closest distance to " O   GLY A 302 " =    1.408
peak=    3.153 closest distance to " CB  ALA A 291 " =    1.263
peak=    3.153 closest distance to " CB  ASN A 110 " =    1.021
peak=    3.153 closest distance to " O   HOH Z 406 " =    1.769
peak=    3.150 closest distance to " CE2 TRP A  85 " =    1.206
peak=    3.147 closest distance to " ND2 ASN A 285 " =    0.784
peak=    3.147 closest distance to " O   HOH Z 384 " =    1.710
peak=    3.145 closest distance to " CB  ALA A 180 " =    0.831
peak=    3.132 closest distance to " CA  GLU A 236 " =    1.313
peak=    3.128 closest distance to " CD1 LEU A 237 " =    1.120
peak=    3.125 closest distance to " O   HOH Z 191 " =    4.055
peak=    3.123 closest distance to " O   HOH Z 262 " =    1.264
peak=    3.123 closest distance to " CD2 LEU A 300 " =    0.985
peak=    3.122 closest distance to " O   HOH Z 279 " =    3.089
peak=    3.111 closest distance to " CD  LYS A 166 " =    1.128
peak=    3.109 closest distance to " CA  GLY A  57 " =    1.616
peak=    3.102 closest distance to " NZ  LYS A 181 " =    0.944
peak=    3.096 closest distance to " O   HOH Z 279 " =    1.166
peak=    3.094 closest distance to " O   HOH Z 254 " =    0.971
peak=    3.061 closest distance to " CB  TRP A 179 " =    1.416
peak=    3.054 closest distance to " CB  LYS A 290 " =    0.967
peak=    3.034 closest distance to " O   HOH Z 317 " =    2.586
peak=    3.027 closest distance to " O   HOH Z 284 " =    1.494
peak=    3.006 closest distance to " N   SER A  63 " =    0.849

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.460 - 4.879
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 204
   mapped sites are within: 0.714 - 4.879

peak=   -5.892 closest distance to " CD  ARG A 138 " =    1.011
peak=   -4.474 closest distance to " O   HOH Z 313 " =    0.867
peak=   -4.418 closest distance to " N   ARG A 275 " =    0.799
peak=   -4.397 closest distance to " OG  SER A  97 " =    2.224
peak=   -4.344 closest distance to " OG ASER A 134 " =    0.896
peak=   -4.330 closest distance to " O   PRO A 198 " =    1.036
peak=   -4.221 closest distance to " O   SER A 135 " =    1.526
peak=   -4.151 closest distance to " CG  ASN A 284 " =    1.229
peak=   -4.119 closest distance to " CG2 VAL A 230 " =    0.741
peak=   -4.109 closest distance to " O   VAL A  72 " =    0.785
peak=   -4.081 closest distance to " CD2 LEU A 297 " =    1.167
peak=   -4.075 closest distance to " O   HOH Z  69 " =    1.303
peak=   -4.052 closest distance to " CD  ARG A  14 " =    2.963
peak=   -4.046 closest distance to " O   HOH Z 244 " =    1.154
peak=   -4.031 closest distance to " O   HOH Z  52 " =    0.860
peak=   -4.018 closest distance to " CG  ASP A 253 " =    0.952
peak=   -4.004 closest distance to " O   LYS A  76 " =    0.880
peak=   -3.989 closest distance to " CB  TRP A 274 " =    2.691
peak=   -3.963 closest distance to " O   ALA A  10 " =    1.406
peak=   -3.940 closest distance to " CA  GLY A 133 " =    2.144
peak=   -3.926 closest distance to " O   HOH Z  95 " =    0.974
peak=   -3.907 closest distance to " C   SER A 276 " =    1.372
peak=   -3.887 closest distance to " O   HOH Z 385 " =    1.046
peak=   -3.886 closest distance to " OG  SER A   3 " =    0.881
peak=   -3.873 closest distance to " O   ASP A 286 " =    1.076
peak=   -3.869 closest distance to " O   HOH Z 268 " =    0.997
peak=   -3.861 closest distance to " CE2 PHE A 218 " =    2.593
peak=   -3.842 closest distance to " OG BSER A 212 " =    2.292
peak=   -3.815 closest distance to " CG  TRP A 266 " =    1.741
peak=   -3.791 closest distance to " O   SER A  22 " =    1.110
peak=   -3.774 closest distance to " CG  GLN A  73 " =    1.218
peak=   -3.765 closest distance to " O   ILE A  49 " =    1.691
peak=   -3.693 closest distance to " O   HOH Z  24 " =    1.236
peak=   -3.693 closest distance to " O   HOH Z 186 " =    1.252
peak=   -3.693 closest distance to " CD  GLU A  44 " =    1.210
peak=   -3.688 closest distance to " O   HOH Z 264 " =    0.985
peak=   -3.673 closest distance to " O   HOH Z  82 " =    1.421
peak=   -3.651 closest distance to " CA  GLY A  98 " =    1.536
peak=   -3.636 closest distance to " O   HOH Z 359 " =    1.788
peak=   -3.632 closest distance to " O   HOH Z 368 " =    1.180
peak=   -3.626 closest distance to " O   HOH Z  30 " =    0.903
peak=   -3.618 closest distance to " OG  SER A 276 " =    0.916
peak=   -3.611 closest distance to " CD1 TRP A 179 " =    1.152
peak=   -3.592 closest distance to " O   HOH Z 163 " =    1.758
peak=   -3.588 closest distance to " O   SER A 273 " =    0.837
peak=   -3.585 closest distance to " C   SER A 288 " =    0.822
peak=   -3.582 closest distance to " CZ  PHE A  16 " =    1.138
peak=   -3.580 closest distance to " CD  GLN A  77 " =    0.794
peak=   -3.576 closest distance to " CB  PHE A  59 " =    1.691
peak=   -3.574 closest distance to " CG1AVAL A  72 " =    2.027
peak=   -3.570 closest distance to " CB  TYR A  30 " =    1.203
peak=   -3.568 closest distance to " O   ILE A 106 " =    2.221
peak=   -3.566 closest distance to " O   TRP A  92 " =    1.467
peak=   -3.561 closest distance to " ND2 ASN A 173 " =    1.625
peak=   -3.558 closest distance to " CB  ASN A 285 " =    1.988
peak=   -3.556 closest distance to " O   HOH Z 221 " =    0.969
peak=   -3.556 closest distance to " CA  GLY A  35 " =    1.790
peak=   -3.555 closest distance to " O   THR A  82 " =    1.023
peak=   -3.555 closest distance to " O   GLN A  77 " =    1.875
peak=   -3.552 closest distance to " O   HOH Z 290 " =    0.936
peak=   -3.542 closest distance to " CG  HIS A 108 " =    1.098
peak=   -3.538 closest distance to " O   HOH Z 300 " =    0.784
peak=   -3.519 closest distance to " O   HOH Z 217 " =    1.147
peak=   -3.514 closest distance to " O   HOH Z 435 " =    2.555
peak=   -3.506 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.504 closest distance to " CG  ASP A  50 " =    1.028
peak=   -3.501 closest distance to " C   ASN A 301 " =    1.214
peak=   -3.501 closest distance to " O   VAL A 174 " =    2.452
peak=   -3.490 closest distance to " CD1 PHE A  38 " =    0.958
peak=   -3.483 closest distance to " O   HOH Z 140 " =    1.846
peak=   -3.481 closest distance to " N   GLN A  58 " =    1.014
peak=   -3.479 closest distance to " O   HOH Z 298 " =    2.704
peak=   -3.479 closest distance to " O   HOH Z 422 " =    3.188
peak=   -3.474 closest distance to " C   PHE A  59 " =    0.995
peak=   -3.473 closest distance to " O   HOH Z 404 " =    1.038
peak=   -3.463 closest distance to " O   HOH Z  60 " =    1.326
peak=   -3.453 closest distance to " CD1 TRP A 274 " =    0.978
peak=   -3.445 closest distance to " CE1 PHE A  16 " =    1.404
peak=   -3.440 closest distance to " OE1 GLU A 277 " =    2.265
peak=   -3.432 closest distance to " CA  ALA A   1 " =    1.054
peak=   -3.432 closest distance to " OG1 THR A 178 " =    1.057
peak=   -3.431 closest distance to " O   THR A 178 " =    0.854
peak=   -3.430 closest distance to " CG1BVAL A  72 " =    2.177
peak=   -3.429 closest distance to " O   HOH Z  72 " =    0.973
peak=   -3.427 closest distance to " O   GLY A 136 " =    1.444
peak=   -3.427 closest distance to " CZ  ARG A  36 " =    1.369
peak=   -3.422 closest distance to " O   HOH Z  95 " =    1.781
peak=   -3.421 closest distance to " O   HOH Z 220 " =    1.943
peak=   -3.420 closest distance to " O   HOH Z 377 " =    1.110
peak=   -3.414 closest distance to " O   HOH Z  86 " =    0.931
peak=   -3.408 closest distance to " O   SER A 245 " =    1.243
peak=   -3.403 closest distance to " ND2 ASN A 209 " =    1.639
peak=   -3.402 closest distance to " CD2 LEU A   5 " =    0.839
peak=   -3.400 closest distance to " CG  PRO A 243 " =    1.854
peak=   -3.389 closest distance to " N   THR A 279 " =    1.322
peak=   -3.388 closest distance to " NH2 ARG A 138 " =    0.863
peak=   -3.371 closest distance to " O   HOH Z 397 " =    1.685
peak=   -3.370 closest distance to " CG  GLN A  88 " =    1.047
peak=   -3.370 closest distance to " O   HOH Z  88 " =    1.234
peak=   -3.367 closest distance to " CA  GLY A 133 " =    2.036
peak=   -3.367 closest distance to " O   HOH Z  60 " =    1.684
peak=   -3.357 closest distance to " O   HOH Z 354 " =    2.605
peak=   -3.356 closest distance to " O   TRP A 179 " =    1.742
peak=   -3.347 closest distance to " O   HOH Z 165 " =    2.138
peak=   -3.344 closest distance to " O   HOH Z 131 " =    4.042
peak=   -3.340 closest distance to " O   HOH Z  75 " =    1.422
peak=   -3.337 closest distance to " O   HOH Z 335 " =    1.173
peak=   -3.321 closest distance to " N   VAL A 189 " =    1.545
peak=   -3.321 closest distance to " CD1 TYR A 247 " =    2.444
peak=   -3.320 closest distance to " O   GLN A  11 " =    1.627
peak=   -3.320 closest distance to " OD2 ASP A 191 " =    1.269
peak=   -3.317 closest distance to " O   GLY A 287 " =    2.103
peak=   -3.317 closest distance to " OG1 THR A 246 " =    0.845
peak=   -3.317 closest distance to " N   ARG A  66 " =    1.477
peak=   -3.311 closest distance to " C   ASN A 110 " =    1.149
peak=   -3.299 closest distance to " C   GLU A   2 " =    1.975
peak=   -3.298 closest distance to " CB  SER A 245 " =    1.991
peak=   -3.298 closest distance to " CD2 TRP A 150 " =    1.144
peak=   -3.293 closest distance to " O   HOH Z 298 " =    0.891
peak=   -3.293 closest distance to " CG  LEU A 228 " =    0.996
peak=   -3.291 closest distance to " CG BLYS A 290 " =    0.818
peak=   -3.286 closest distance to " CA  ASN A 142 " =    1.895
peak=   -3.284 closest distance to " OE1 GLN A 223 " =    2.194
peak=   -3.283 closest distance to " CE3 TRP A 179 " =    2.421
peak=   -3.282 closest distance to " N   THR A 220 " =    1.513
peak=   -3.281 closest distance to " N   ILE A  33 " =    1.878
peak=   -3.279 closest distance to " OG1 THR A 251 " =    0.770
peak=   -3.277 closest distance to " N   ALA A  64 " =    1.103
peak=   -3.276 closest distance to " O   TRP A 150 " =    1.431
peak=   -3.275 closest distance to " CG  PRO A 163 " =    2.500
peak=   -3.271 closest distance to " CA  GLY A  57 " =    1.903
peak=   -3.270 closest distance to " O   LEU A 101 " =    1.058
peak=   -3.270 closest distance to " O   SER A  22 " =    2.402
peak=   -3.269 closest distance to " O   ALA A  51 " =    1.280
peak=   -3.267 closest distance to " SG  CYS A 168 " =    1.184
peak=   -3.266 closest distance to " O   HOH Z 195 " =    1.730
peak=   -3.266 closest distance to " CG  GLN A  11 " =    2.018
peak=   -3.261 closest distance to " O   HOH Z 286 " =    1.466
peak=   -3.257 closest distance to " O   LEU A 222 " =    1.399
peak=   -3.251 closest distance to " CB  THR A  29 " =    1.825
peak=   -3.249 closest distance to " O   SER A 271 " =    1.527
peak=   -3.249 closest distance to " O   HOH Z 406 " =    0.754
peak=   -3.248 closest distance to " O   ARG A 159 " =    1.585
peak=   -3.244 closest distance to " O   ALA A 165 " =    1.183
peak=   -3.240 closest distance to " OD2 ASP A 272 " =    1.166
peak=   -3.238 closest distance to " O   HOH Z 193 " =    1.664
peak=   -3.235 closest distance to " O   HOH Z 256 " =    0.950
peak=   -3.228 closest distance to " CE2 TRP A 274 " =    1.440
peak=   -3.227 closest distance to " N   THR A 157 " =    1.657
peak=   -3.222 closest distance to " CA  GLY A  17 " =    2.017
peak=   -3.221 closest distance to " O   HOH Z  71 " =    1.168
peak=   -3.218 closest distance to " CA  TYR A  68 " =    1.175
peak=   -3.203 closest distance to " CA  GLY A 203 " =    2.448
peak=   -3.202 closest distance to " CD  LYS A  76 " =    0.733
peak=   -3.202 closest distance to " CG1 ILE A 234 " =    1.074
peak=   -3.200 closest distance to " CD  PRO A 213 " =    2.180
peak=   -3.198 closest distance to " O   HOH Z 343 " =    1.856
peak=   -3.197 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.196 closest distance to " O   HOH Z 336 " =    4.879
peak=   -3.193 closest distance to " N   ILE A 263 " =    0.951
peak=   -3.189 closest distance to " SG BCYS A 201 " =    2.476
peak=   -3.188 closest distance to " C   PRO A  54 " =    1.631
peak=   -3.186 closest distance to " N   SER A  28 " =    0.831
peak=   -3.183 closest distance to " O   SER A  62 " =    1.112
peak=   -3.181 closest distance to " O   HOH Z 431 " =    0.945
peak=   -3.181 closest distance to " N   ALA A 244 " =    1.107
peak=   -3.178 closest distance to " CB  ALA A   1 " =    2.763
peak=   -3.173 closest distance to " C   ASP A 124 " =    2.073
peak=   -3.170 closest distance to " CZ  PHE A  16 " =    0.894
peak=   -3.169 closest distance to " ND2 ASN A 285 " =    2.091
peak=   -3.162 closest distance to " O   SER A  26 " =    1.554
peak=   -3.154 closest distance to " O   HOH Z 257 " =    1.050
peak=   -3.152 closest distance to " O   HOH Z 368 " =    2.845
peak=   -3.149 closest distance to " CA  VAL A  67 " =    2.675
peak=   -3.149 closest distance to " CG  LEU A   5 " =    1.000
peak=   -3.147 closest distance to " O   PRO A  54 " =    1.315
peak=   -3.146 closest distance to " C   TRP A 274 " =    0.821
peak=   -3.141 closest distance to " CA  GLN A  55 " =    1.468
peak=   -3.135 closest distance to " C   GLU A 236 " =    0.780
peak=   -3.129 closest distance to " C   ASN A 285 " =    1.094
peak=   -3.123 closest distance to " N   GLN A  11 " =    0.948
peak=   -3.122 closest distance to " OE1 GLN A 183 " =    1.457
peak=   -3.121 closest distance to " CA  SER A  63 " =    1.281
peak=   -3.116 closest distance to " NE1 TRP A 177 " =    1.626
peak=   -3.112 closest distance to " CZ2 TRP A  70 " =    2.313
peak=   -3.112 closest distance to " O   GLY A 118 " =    1.137
peak=   -3.112 closest distance to " O   HOH Z 276 " =    1.288
peak=   -3.107 closest distance to " OG BSER A 134 " =    2.216
peak=   -3.106 closest distance to " CB  TRP A  85 " =    2.070
peak=   -3.106 closest distance to " OD1 ASN A 127 " =    1.175
peak=   -3.104 closest distance to " CZ BARG A 145 " =    0.950
peak=   -3.102 closest distance to " O   GLN A  88 " =    1.302
peak=   -3.098 closest distance to " OE1 GLU A  44 " =    1.057
peak=   -3.097 closest distance to " CG2 VAL A  78 " =    2.601
peak=   -3.094 closest distance to " O   HOH Z 428 " =    1.725
peak=   -3.038 closest distance to " N   ARG A 275 " =    1.014
peak=   -3.037 closest distance to " O   HOH Z  56 " =    0.714

================= 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    :  0.5050 0.5056   6.304798e+00   6.298036e+00
   1_bss:  0.4961 0.4955   6.299008e+00   6.289731e+00
   1_xyz:  0.4416 0.4719   6.244940e+00   6.269230e+00
   1_adp:  0.4039 0.4653   6.208412e+00   6.264863e+00
   1_occ:  0.4030 0.4651   6.207629e+00   6.265562e+00
   2_bss:  0.4022 0.4606   6.207388e+00   6.263631e+00
   2_xyz:  0.3618 0.4344   6.130960e+00   6.230296e+00
   2_adp:  0.3504 0.4232   6.115107e+00   6.218504e+00
   2_occ:  0.3502 0.4232   6.115116e+00   6.218610e+00
   3_bss:  0.3508 0.4235   6.117028e+00   6.218777e+00
   3_xyz:  0.3081 0.3837   6.025300e+00   6.156428e+00
   3_adp:  0.2876 0.3745   5.988716e+00   6.141862e+00
   3_occ:  0.2875 0.3747   5.989065e+00   6.142280e+00
   4_bss:  0.2875 0.3738   5.987982e+00   6.141701e+00
   4_xyz:  0.2382 0.3157   5.816973e+00   6.005917e+00
   4_adp:  0.2174 0.2823   5.732128e+00   5.915651e+00
   4_occ:  0.2167 0.2819   5.730473e+00   5.914065e+00
   5_bss:  0.2165 0.2793   5.726682e+00   5.909296e+00
   5_xyz:  0.1751 0.2312   5.529922e+00   5.734472e+00
   5_adp:  0.1616 0.2187   5.463311e+00   5.685148e+00
   5_occ:  0.1613 0.2177   5.460844e+00   5.681556e+00
   5_bss:  0.1611 0.2177   5.459034e+00   5.680168e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.390   2.805   6.582   9.349   7.426   0.000   0.000   0.000
   1_xyz:  0.390   2.805   6.582   9.349   7.426   0.000   0.000   0.000
   1_adp:  0.390   2.805   6.582   9.349   7.426   0.000   0.000   0.000
   1_occ:  0.390   2.805   6.582   9.349   7.426   0.000   0.000   0.000
   2_bss:  0.360  20.001   4.094   6.134   5.003   0.000   0.000   0.000
   2_xyz:  0.360  20.001   4.094   6.134   5.003   0.000   0.000   0.000
   2_adp:  0.360  20.001   4.094   6.134   5.003   0.000   0.000   0.000
   2_occ:  0.360  20.001   4.094   6.134   5.003   0.000   0.000   0.000
   3_bss:  0.362  44.682   2.982   4.561   3.916   0.000   0.000   0.000
   3_xyz:  0.362  44.682   2.982   4.561   3.916   0.000   0.000   0.000
   3_adp:  0.362  44.682   2.982   4.561   3.916   0.000   0.000   0.000
   3_occ:  0.362  44.682   2.982   4.561   3.916   0.000   0.000   0.000
   4_bss:  0.355  51.863   1.935   2.875   3.068   0.000   0.000   0.000
   4_xyz:  0.355  51.863   1.935   2.875   3.068   0.000   0.000   0.000
   4_adp:  0.355  51.863   1.935   2.875   3.068   0.000   0.000   0.000
   4_occ:  0.355  51.863   1.935   2.875   3.068   0.000   0.000   0.000
   5_bss:  0.342  46.162   1.180   1.664   2.410   0.000   0.000   0.000
   5_xyz:  0.342  46.162   1.180   1.664   2.410   0.000   0.000   0.000
   5_adp:  0.342  46.162   1.180   1.664   2.410   0.000   0.000   0.000
   5_occ:  0.342  46.162   1.180   1.664   2.410   0.000   0.000   0.000
   5_bss:  0.319  35.212  -0.471  -0.373   0.844   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.773 0.3059  0.3695    84935.487
   1_bss:  66.181 0.3126  0.4660    82357.727
   1_xyz:  59.434 0.3997  0.5906    71698.766
   1_adp:  58.206 0.4155  0.6586    70516.895
   1_occ:  58.145 0.4164  0.6590    70614.109
   2_bss:  57.705 0.4218  0.6134    69633.339
   2_xyz:  51.236 0.5036  0.7336    58192.613
   2_adp:  49.019 0.5321  0.7890    55175.315
   2_occ:  49.044 0.5317  0.7882    55208.180
   3_bss:  48.974 0.5326  0.7573    55303.166
   3_xyz:  42.775 0.6088  0.8589    43518.721
   3_adp:  41.020 0.6304  0.8827    41086.780
   3_occ:  41.092 0.6295  0.8815    41164.354
   4_bss:  40.941 0.6312  0.8460    40897.371
   4_xyz:  33.097 0.7227  0.9465    26863.414
   4_adp:  28.424 0.7760  0.9787    21462.607
   4_occ:  28.349 0.7768  0.9792    21328.075
   5_bss:  28.137 0.7788  0.9495    20863.833
   5_xyz:  22.066 0.8420  0.9917    13638.099
   5_adp:  20.623 0.8565  0.9906    12278.835
   5_occ:  20.526 0.8574  0.9909    12142.224
   5_bss:  20.529 0.8571  0.9709    12089.988
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2623e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2623e+01
   1_xyz:   1.760  0.014  0.109 18.357  0.007  4.103   1.5681e-01
   1_adp:   1.760  0.014  0.109 18.357  0.007  4.103   1.5681e-01
   1_occ:   1.760  0.014  0.109 18.357  0.007  4.103   1.5681e-01
   2_bss:   1.760  0.014  0.109 18.357  0.007  4.103   1.5681e-01
   2_xyz:   1.174  0.008  0.075 16.199  0.005  4.116   8.7563e-02
   2_adp:   1.174  0.008  0.075 16.199  0.005  4.116   8.7563e-02
   2_occ:   1.174  0.008  0.075 16.199  0.005  4.116   8.7563e-02
   3_bss:   1.174  0.008  0.075 16.199  0.005  4.116   8.7563e-02
   3_xyz:   1.118  0.008  0.077 16.138  0.004  4.105   7.9776e-02
   3_adp:   1.118  0.008  0.077 16.138  0.004  4.105   7.9776e-02
   3_occ:   1.118  0.008  0.077 16.138  0.004  4.105   7.9776e-02
   4_bss:   1.118  0.008  0.077 16.138  0.004  4.105   7.9776e-02
   4_xyz:   1.262  0.010  0.090 16.435  0.005  4.103   9.6674e-02
   4_adp:   1.262  0.010  0.090 16.435  0.005  4.103   9.6674e-02
   4_occ:   1.262  0.010  0.090 16.435  0.005  4.103   9.6674e-02
   5_bss:   1.262  0.010  0.090 16.435  0.005  4.103   9.6674e-02
   5_xyz:   0.976  0.006  0.065 15.826  0.003  4.113   6.0473e-02
   5_adp:   0.976  0.006  0.065 15.826  0.003  4.113   6.0473e-02
   5_occ:   0.976  0.006  0.065 15.826  0.003  4.113   6.0473e-02
   5_bss:   0.976  0.006  0.065 15.826  0.003  4.113   6.0473e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.968   6.8131e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.968   6.8131e+00
   1_xyz:  14.666  0.198  0.456 84.692  0.049  2.007   1.0166e-01
   1_adp:  14.666  0.198  0.456 84.692  0.049  2.007   1.0166e-01
   1_occ:  14.666  0.198  0.456 84.692  0.049  2.007   1.0166e-01
   2_bss:  14.666  0.198  0.456 84.692  0.049  2.007   1.0166e-01
   2_xyz:   6.874  0.093  0.266 73.878  0.048  2.065   5.4701e-02
   2_adp:   6.874  0.093  0.266 73.878  0.048  2.065   5.4701e-02
   2_occ:   6.874  0.093  0.266 73.878  0.048  2.065   5.4701e-02
   3_bss:   6.874  0.093  0.266 73.878  0.048  2.065   5.4701e-02
   3_xyz:   8.622  0.108  0.276 73.967  0.024  2.175   6.7905e-02
   3_adp:   8.622  0.108  0.276 73.967  0.024  2.175   6.7905e-02
   3_occ:   8.622  0.108  0.276 73.967  0.024  2.175   6.7905e-02
   4_bss:   8.622  0.108  0.276 73.967  0.024  2.175   6.7905e-02
   4_xyz:   7.354  0.051  0.351 83.791  0.039  2.089   8.2540e-02
   4_adp:   7.354  0.051  0.351 83.791  0.039  2.089   8.2540e-02
   4_occ:   7.354  0.051  0.351 83.791  0.039  2.089   8.2540e-02
   5_bss:   7.354  0.051  0.351 83.791  0.039  2.089   8.2540e-02
   5_xyz:   7.365  0.056  0.210 78.928  0.024  2.304   4.6253e-02
   5_adp:   7.365  0.056  0.210 78.928  0.024  2.304   4.6253e-02
   5_occ:   7.365  0.056  0.210 78.928  0.024  2.304   4.6253e-02
   5_bss:   7.365  0.056  0.210 78.928  0.024  2.304   4.6253e-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:  79.61   0.00  15.42  79.61   0.00  14.24  78.66   0.00  21.85
   1_occ:  79.61   0.00  15.42  79.61   0.00  14.24  78.66   0.00  21.85
   2_bss:  79.61   0.00  15.42  79.61   0.00  14.24  78.66   0.00  21.85
   2_xyz:  79.61   0.00  15.42  79.61   0.00  14.24  78.66   0.00  21.85
   2_adp:  88.92   0.00  15.06  88.92   0.00  13.45  80.83   0.00  23.82
   2_occ:  88.92   0.00  15.06  88.92   0.00  13.45  80.83   0.00  23.82
   3_bss:  88.92   0.00  15.06  88.92   0.00  13.45  80.83   0.00  23.82
   3_xyz:  88.92   0.00  15.06  88.92   0.00  13.45  80.83   0.00  23.82
   3_adp: 110.67   0.00  16.63 110.67   0.00  13.93  99.68   0.00  31.37
   3_occ: 110.67   0.00  16.63 110.67   0.00  13.93  99.68   0.00  31.37
   4_bss: 110.67   0.00  16.63 110.67   0.00  13.93  99.68   0.00  31.37
   4_xyz: 110.67   0.00  16.63 110.67   0.00  13.93  99.68   0.00  31.37
   4_adp:  99.94   0.00  14.21  99.94   0.00  10.69  82.41   1.37  33.37
   4_occ:  99.94   0.00  14.21  99.94   0.00  10.69  82.41   1.37  33.37
   5_bss:  99.94   0.00  14.21  99.94   0.00  10.69  82.41   1.37  33.37
   5_xyz:  99.94   0.00  14.21  99.94   0.00  10.69  82.41   1.37  33.37
   5_adp:  98.27   0.00  14.25  98.27   0.00   9.93  77.46   3.40  37.76
   5_occ:  98.27   0.00  14.25  98.27   0.00   9.93  77.46   3.40  37.76
   5_bss:  99.49   1.22  15.47  99.49   1.22  11.15  78.69   4.63  38.99
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.279    0.009    0.416
   1_adp:    1.279    0.009    0.416
   1_occ:    1.279    0.009    0.416
   2_bss:    1.279    0.009    0.416
   2_xyz:    1.710    0.024    0.537
   2_adp:    1.710    0.024    0.537
   2_occ:    1.710    0.024    0.537
   3_bss:    1.710    0.024    0.537
   3_xyz:    1.498    0.017    0.629
   3_adp:    1.498    0.017    0.629
   3_occ:    1.498    0.017    0.629
   4_bss:    1.498    0.017    0.629
   4_xyz:    1.761    0.060    0.797
   4_adp:    1.761    0.060    0.797
   4_occ:    1.761    0.060    0.797
   5_bss:    1.761    0.060    0.797
   5_xyz:    1.897    0.035    0.875
   5_adp:    1.897    0.035    0.875
   5_occ:    1.897    0.035    0.875
   5_bss:    1.897    0.035    0.875
------------------------------------------------------------------------

CPU time actual refinement: 284.88


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_245/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_245/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_245/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_245/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_245/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 284.75 
  Macro-tasks:
    bulk solvent and scale       = 38.91  
    individual site refinement   = 124.40 
    weights calculation          = 26.35  
    collect and process          = 5.16   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 194.90 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 86.60  
    alpha_beta                      = 6.95   
    target                          = 0.94   
    gradients_wrt_atomic_parameters = 96.89  
    fmodel                         = 6.44   
    r_factors                      = 0.24   
    phase_errors                   = 7.92   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 208.61 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 3.988 micro seconds
Total CPU time: 4.94 minutes
from_scatterers_fft:    618 calls, 86.34 s
gradients_fft:          563 calls, 85.43 s

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

# Date 2008-01-16 Time 01:07:09 PST -0800 (1200474429.97 s)
Start R-work = 0.5050, R-free = 0.5056 (no bulk solvent and anisotropic scale)
Final R-work = 0.1755, R-free = 0.2310 (no bulk solvent and anisotropic scale)

Start R-work = 0.4961, R-free = 0.4955
Final R-work = 0.1611, R-free = 0.2177