# Date 2008-01-16 Time 03:17:48 PST -0800 (1200482268.35 s)
#phil __OFF__

Command line arguments: "../1178.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16377
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1178

-------------------------------------------------------------------------------
  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: (71.655, 47.6339, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96146
Completeness in resolution range: 0.917518
Completeness with d_max=infinity: 0.914818

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9615

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: (71.655, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96146
Completeness in resolution range: 0.917518
Completeness with d_max=infinity: 0.914818

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1985 [2245/2274]  2022   223   9.9%
  bin  2:  4.1985 -  3.3443 [2146/2169]  1931   215  10.0%
  bin  3:  3.3443 -  2.9251 [2118/2143]  1902   216  10.2%
  bin  4:  2.9251 -  2.6592 [2104/2120]  1898   206   9.8%
  bin  5:  2.6592 -  2.4695 [2084/2128]  1880   204   9.8%
  bin  6:  2.4695 -  2.3244 [2081/2109]  1869   212  10.2%
  bin  7:  2.3244 -  2.2084 [2072/2108]  1861   211  10.2%
  bin  8:  2.2084 -  2.1125 [2050/2092]  1848   202   9.9%
  bin  9:  2.1125 -  2.0314 [2034/2107]  1830   204  10.0%
  bin 10:  2.0314 -  1.9615 [ 655/2100]   589    66  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1178/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 23
        2.30 -     2.95: 1649
        2.95 -     3.60: 4501
        3.60 -     4.25: 9155
        4.25 -     4.90: 12857
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.650 3.040 -x+1/2,-y+1,z+1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.697 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.750 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.763 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.789 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28180 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_1178/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1178/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 71.655 47.63395 84.6622 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: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4974   r_free= 0.4925   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.298576                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6835 0.99   1456  165 0.4093 0.3977      6.6286      6.6019|
|  2:  4.6835 -  3.7359 0.99   1395  151 0.4193 0.4465      6.8312      6.9005|
|  3:  3.7359 -  3.2691 0.99   1372  152 0.4690 0.4101      6.6891      6.6614|
|  4:  3.2691 -  2.9727 0.99   1364  149 0.4926 0.4855      6.5259      6.5224|
|  5:  2.9727 -  2.7610 0.98   1353  151 0.5259 0.5510      6.3763       6.375|
|  6:  2.7610 -  2.5991 0.99   1353  156 0.5271 0.5225      6.2884      6.2196|
|  7:  2.5991 -  2.4695 0.98   1340  140 0.5335 0.4500      6.2498      6.1934|
|  8:  2.4695 -  2.3624 0.99   1332  154 0.5414 0.5579      6.1596      6.1973|
|  9:  2.3624 -  2.2718 0.99   1343  152 0.5516 0.5507       6.153      6.1148|
| 10:  2.2718 -  2.1936 0.98   1322  149 0.5184 0.5379      6.0705      6.1379|
| 11:  2.1936 -  2.1252 0.97   1330  134 0.5353 0.5452      6.0418      5.9869|
| 12:  2.1252 -  2.0646 0.99   1320  159 0.5534 0.5512      5.9348      5.9661|
| 13:  2.0646 -  2.0104 0.79   1067  122 0.5508 0.5452      5.8744      5.8412|
| 14:  2.0104 -  1.9615 0.20    283   25 0.5758 0.5185      5.8078        5.82|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6835  1456   165  0.69  35.57   0.79     0.72      76030.01|
|  2:  4.6835 -  3.7359  1395   151  0.67  37.92   0.87     0.73     117855.14|
|  3:  3.7359 -  3.2691  1372   152  0.53  49.32   0.80     0.65     131750.12|
|  4:  3.2691 -  2.9727  1364   149  0.41  59.15   0.78     0.52     121660.77|
|  5:  2.9727 -  2.7610  1353   151  0.32  65.84   0.71     0.41      97704.07|
|  6:  2.7610 -  2.5991  1353   156  0.33  65.24   0.72     0.40      79329.15|
|  7:  2.5991 -  2.4695  1340   140  0.34  64.18   0.72     0.39      65218.04|
|  8:  2.4695 -  2.3624  1332   154  0.32  66.02   0.70     0.39      61455.18|
|  9:  2.3624 -  2.2718  1343   152  0.25  71.30   0.72     0.30      59530.64|
| 10:  2.2718 -  2.1936  1322   149  0.21  74.63   0.73     0.25      58846.63|
| 11:  2.1936 -  2.1252  1330   134  0.16  78.05   0.76     0.20      54370.33|
| 12:  2.1252 -  2.0646  1320   159  0.14  79.74   0.72     0.19      50454.84|
| 13:  2.0646 -  2.0104  1067   122  0.14  79.49   0.70     0.19      43405.92|
| 14:  2.0104 -  1.9615   283    25  0.15  78.87   0.67     0.19      35803.56|
|alpha:            min =        0.19 max =            0.73 mean =         0.41|
|beta:             min =    35803.56 max =       131750.12 mean =     78485.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.99 mean =        63.24|
|phase err.(test): min =        0.00 max =           89.98 mean =        63.31|
|-----------------------------------------------------------------------------|

============================== 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 = 19.829132             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.307   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.895566              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.938   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      698 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1494 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2629 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3901 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5023 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6524 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7759 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.876 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       2.014 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    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 = 12.058)------------------------------------------|
|    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: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5010   r_free= 0.4970   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.299305                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4898   r_free= 0.4803   ksol= 0.30   Bsol= 20.00   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.87,9.09,7.53,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.298017                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.477101             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.454759              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.132   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4898      final r-factor (work) = 0.4282          |
| start r-factor (free) = 0.4803      final r-factor (free) = 0.4551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 102.5888 = 15.48 * 0.50 * 6.2948 + 1.00 * 53.8759                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.3622 = 15.48 * 0.50 * 6.2289 + 1.00 * 0.1593                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4282      final r-factor (work) = 0.3922          |
| start r-factor (free) = 0.4551      final r-factor (free) = 0.4437          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0760 = 1.45 * 1.00 * 6.2289 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0126 = 1.45 * 1.00 * 6.1815 + 1.00 * 0.0200                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.86  15.07    None  None   None       |
|    all(noH): 2823   0      0.00    119.86  15.07    None  None   None       |
|    Sol.    : 438    0      0.00    119.86  27.30    None  None   None       |
|    Mac.    : 2385   0      0.00    98.45   12.83    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 -  11.986: 1409   |   5:    59.929 -  71.915:   24        |
|      1:    11.986 -  23.972:  904   |   6:    71.915 -  83.900:    9        |
|      2:    23.972 -  35.957:  305   |   7:    83.900 -  95.886:    4        |
|      3:    35.957 -  47.943:  108   |   8:    95.886 - 107.872:    3        |
|      4:    47.943 -  59.929:   56   |   9:   107.872 - 119.858:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3922 r_free = 0.4437             target_work(ml) = 6.170         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3919 r_free = 0.4444             target_work(ml) = 6.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3919   r_free= 0.4444   ksol= 0.30   Bsol= 20.00   scale= 1.087   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.87,9.09,7.53,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.169836                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3913   r_free= 0.4406   ksol= 0.32   Bsol= 38.56   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.94,6.23,5.48,0.00,0.00,0.00); trace/3= 5.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.170667                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.900757             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.131  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.735106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.278  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3913      final r-factor (work) = 0.2984          |
| start r-factor (free) = 0.4406      final r-factor (free) = 0.3713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.4611 = 17.90 * 0.50 * 6.1787 + 1.00 * 0.1593                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.5533 = 17.90 * 0.50 * 6.0812 + 1.00 * 0.1246                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2984      final r-factor (work) = 0.2726          |
| start r-factor (free) = 0.3713      final r-factor (free) = 0.3448          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4901 = 0.74 * 1.00 * 6.0812 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3820 = 0.74 * 1.00 * 5.9405 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.65  14.90    None  None   None       |
|    all(noH): 2823   0      0.00    116.65  14.90    None  None   None       |
|    Sol.    : 438    0      0.00    116.65  32.89    None  None   None       |
|    Mac.    : 2385   0      0.00    93.76   11.60    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 -  11.665: 1504   |   5:    58.323 -  69.987:   19        |
|      1:    11.665 -  23.329:  766   |   6:    69.987 -  81.652:   10        |
|      2:    23.329 -  34.994:  319   |   7:    81.652 -  93.317:    3        |
|      3:    34.994 -  46.658:  135   |   8:    93.317 - 104.981:    2        |
|      4:    46.658 -  58.323:   64   |   9:   104.981 - 116.646:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2726 r_free = 0.3448             target_work(ml) = 5.904         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2725 r_free = 0.3443             target_work(ml) = 5.903         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2725   r_free= 0.3443   ksol= 0.32   Bsol= 38.56   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.94,6.23,5.48,0.00,0.00,0.00); trace/3= 5.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.902594                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2678   r_free= 0.3379   ksol= 0.32   Bsol= 47.76   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.89,2.43,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.900919                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.009099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.255  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.596054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.830  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2678      final r-factor (work) = 0.2025          |
| start r-factor (free) = 0.3379      final r-factor (free) = 0.2581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9865 = 6.01 * 0.50 * 5.9450 + 1.00 * 0.1246                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5189 = 6.01 * 0.50 * 5.8055 + 1.00 * 0.0760                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2025      final r-factor (work) = 0.1804          |
| start r-factor (free) = 0.2581      final r-factor (free) = 0.2349          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4764 = 0.60 * 1.00 * 5.8055 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3509 = 0.60 * 1.00 * 5.6006 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.08  15.37    None  None   None       |
|    all(noH): 2823   0      0.00    101.08  15.37    None  None   None       |
|    Sol.    : 438    0      1.76    101.08  40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    86.37   10.82    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:     0.000 -  10.108: 1479   |   5:    50.541 -  60.649:   86        |
|      1:    10.108 -  20.216:  721   |   6:    60.649 -  70.757:   45        |
|      2:    20.216 -  30.324:  220   |   7:    70.757 -  80.865:   12        |
|      3:    30.324 -  40.433:  130   |   8:    80.865 -  90.973:    7        |
|      4:    40.433 -  50.541:  120   |   9:    90.973 - 101.081:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1804 r_free = 0.2349             target_work(ml) = 5.554         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1801 r_free = 0.2346             target_work(ml) = 5.553         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1801   r_free= 0.2346   ksol= 0.32   Bsol= 47.76   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.89,2.43,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.553423                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1794   r_free= 0.2343   ksol= 0.31   Bsol= 47.76   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,1.59,1.16,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.553931                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.910099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.086  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.230980              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.128  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1794      final r-factor (work) = 0.1486          |
| start r-factor (free) = 0.2343      final r-factor (free) = 0.1985          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2350 = 2.91 * 0.50 * 5.6073 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0384 = 2.91 * 0.50 * 5.4788 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1486      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.1985      final r-factor (free) = 0.1916          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2782 = 0.23 * 1.00 * 5.4788 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2513 = 0.23 * 1.00 * 5.3743 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    90.07   14.90    None  None   None       |
|    all(noH): 2823   0      0.39    90.07   14.90    None  None   None       |
|    Sol.    : 438    0      2.83    90.07   39.07    None  None   None       |
|    Mac.    : 2385   0      0.39    86.97   10.46    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:     0.389 -   9.357: 1405   |   5:    45.230 -  54.199:   88        |
|      1:     9.357 -  18.325:  802   |   6:    54.199 -  63.167:   66        |
|      2:    18.325 -  27.294:  201   |   7:    63.167 -  72.135:   19        |
|      3:    27.294 -  36.262:  105   |   8:    72.135 -  81.104:   11        |
|      4:    36.262 -  45.230:  119   |   9:    81.104 -  90.072:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1426 r_free = 0.1916             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1916             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1916   ksol= 0.31   Bsol= 47.76   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.08,1.59,1.16,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.356964                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1427   r_free= 0.1921   ksol= 0.32   Bsol= 52.14   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,0.85,0.73,0.00,0.00,0.00); trace/3= 0.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.359552                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.082047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.301  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.687  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1427      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1921      final r-factor (free) = 0.1731          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3528 = 3.08 * 0.50 * 5.3772 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2593 = 3.08 * 0.50 * 5.3114 + 1.00 * 0.0742                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1268      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1731      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3796 = 0.45 * 1.00 * 5.3114 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3514 = 0.45 * 1.00 * 5.2460 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.64   14.90    None  None   None       |
|    all(noH): 2823   0      0.00    91.64   14.90    None  None   None       |
|    Sol.    : 438    0      2.62    88.35   39.62    None  None   None       |
|    Mac.    : 2385   0      0.00    91.64   10.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.164: 1409   |   5:    45.820 -  54.985:   91        |
|      1:     9.164 -  18.328:  813   |   6:    54.985 -  64.149:   60        |
|      2:    18.328 -  27.492:  178   |   7:    64.149 -  73.313:   25        |
|      3:    27.492 -  36.656:  116   |   8:    73.313 -  82.477:    9        |
|      4:    36.656 -  45.820:  114   |   9:    82.477 -  91.641:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1719             target_work(ml) = 5.245         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1239 r_free = 0.1719             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1719   ksol= 0.32   Bsol= 52.14   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.48,0.85,0.73,0.00,0.00,0.00); trace/3= 0.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.244445                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6835 0.99   1456  165 0.0982 0.1237       5.368        5.53|
|  2:  4.6835 -  3.7359 0.99   1395  151 0.0897 0.1136      5.4571      5.6827|
|  3:  3.7359 -  3.2691 0.99   1372  152 0.1163 0.1807      5.5452      5.9594|
|  4:  3.2691 -  2.9727 0.99   1364  149 0.1447 0.1687      5.5634      5.7002|
|  5:  2.9727 -  2.7610 0.98   1353  151 0.1512 0.1906      5.4496       5.622|
|  6:  2.7610 -  2.5991 0.99   1353  156 0.1420 0.2245      5.3431      5.6021|
|  7:  2.5991 -  2.4695 0.98   1340  140 0.1421 0.1811      5.2846      5.4743|
|  8:  2.4695 -  2.3624 0.99   1332  154 0.1332 0.1799      5.1618      5.3495|
|  9:  2.3624 -  2.2718 0.99   1343  152 0.1270 0.2149         5.1      5.3798|
| 10:  2.2718 -  2.1936 0.98   1322  149 0.1256 0.1840      5.0633       5.356|
| 11:  2.1936 -  2.1252 0.97   1330  134 0.1278 0.1944      5.0181      5.3025|
| 12:  2.1252 -  2.0646 0.99   1320  159 0.1278 0.1990      4.9649      5.2035|
| 13:  2.0646 -  2.0104 0.79   1067  122 0.1278 0.1826      4.8511      5.0541|
| 14:  2.0104 -  1.9615 0.20    283   25 0.1112 0.1834      4.6938       5.033|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6835  1456   165  0.94   8.92   0.97     0.96       7015.50|
|  2:  4.6835 -  3.7359  1395   151  0.95   8.25   1.01     0.99       9196.87|
|  3:  3.7359 -  3.2691  1372   152  0.92  12.82   1.03     1.03      12057.16|
|  4:  3.2691 -  2.9727  1364   149  0.89  16.92   1.00     0.97      12929.31|
|  5:  2.9727 -  2.7610  1353   151  0.87  18.90   0.99     0.97      11017.84|
|  6:  2.7610 -  2.5991  1353   156  0.88  18.80   0.98     0.95       9400.06|
|  7:  2.5991 -  2.4695  1340   140  0.88  18.19   0.98     0.96       8051.47|
|  8:  2.4695 -  2.3624  1332   154  0.89  17.83   0.98     0.94       6480.49|
|  9:  2.3624 -  2.2718  1343   152  0.88  18.04   1.00     0.96       5859.62|
| 10:  2.2718 -  2.1936  1322   149  0.89  17.24   0.99     0.96       5536.42|
| 11:  2.1936 -  2.1252  1330   134  0.88  18.34   0.98     0.94       5220.32|
| 12:  2.1252 -  2.0646  1320   159  0.88  18.44   0.99     0.98       4940.48|
| 13:  2.0646 -  2.0104  1067   122  0.88  18.66   0.99     0.97       3892.23|
| 14:  2.0104 -  1.9615   283    25  0.89  17.25   0.98     0.96       2933.50|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2933.50 max =        12929.31 mean =      7822.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.85 mean =        16.16|
|phase err.(test): min =        0.00 max =           89.17 mean =        15.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1719   ksol= 0.32   Bsol= 52.43   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.16,0.11,0.04,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.244423                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1719   ksol= 0.32   Bsol= 52.43   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.16,0.11,0.04,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.244423                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6835 0.99   1456  165 0.0982 0.1236      5.3677      5.5302|
|  2:  4.6835 -  3.7359 0.99   1395  151 0.0897 0.1136      5.4573      5.6831|
|  3:  3.7359 -  3.2691 0.99   1372  152 0.1164 0.1808      5.5454      5.9597|
|  4:  3.2691 -  2.9727 0.99   1364  149 0.1447 0.1687      5.5633      5.6999|
|  5:  2.9727 -  2.7610 0.98   1353  151 0.1511 0.1906      5.4495      5.6218|
|  6:  2.7610 -  2.5991 0.99   1353  156 0.1419 0.2245       5.343      5.6021|
|  7:  2.5991 -  2.4695 0.98   1340  140 0.1422 0.1812      5.2847      5.4746|
|  8:  2.4695 -  2.3624 0.99   1332  154 0.1331 0.1799       5.162      5.3496|
|  9:  2.3624 -  2.2718 0.99   1343  152 0.1270 0.2150         5.1        5.38|
| 10:  2.2718 -  2.1936 0.98   1322  149 0.1256 0.1840      5.0633      5.3559|
| 11:  2.1936 -  2.1252 0.97   1330  134 0.1278 0.1944      5.0179      5.3017|
| 12:  2.1252 -  2.0646 0.99   1320  159 0.1278 0.1990      4.9647      5.2035|
| 13:  2.0646 -  2.0104 0.79   1067  122 0.1279 0.1825      4.8511      5.0537|
| 14:  2.0104 -  1.9615 0.20    283   25 0.1112 0.1833      4.6936      5.0326|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6835  1456   165  0.94   8.92   0.97     0.96       7016.04|
|  2:  4.6835 -  3.7359  1395   151  0.95   8.25   1.01     0.99       9200.65|
|  3:  3.7359 -  3.2691  1372   152  0.92  12.83   1.03     1.03      12066.17|
|  4:  3.2691 -  2.9727  1364   149  0.89  16.92   1.00     0.97      12928.44|
|  5:  2.9727 -  2.7610  1353   151  0.87  18.89   0.99     0.97      11014.53|
|  6:  2.7610 -  2.5991  1353   156  0.88  18.80   0.98     0.96       9398.24|
|  7:  2.5991 -  2.4695  1340   140  0.88  18.19   0.98     0.96       8050.74|
|  8:  2.4695 -  2.3624  1332   154  0.89  17.84   0.98     0.94       6482.90|
|  9:  2.3624 -  2.2718  1343   152  0.88  18.04   1.00     0.96       5860.63|
| 10:  2.2718 -  2.1936  1322   149  0.89  17.24   0.99     0.96       5536.89|
| 11:  2.1936 -  2.1252  1330   134  0.88  18.33   0.98     0.94       5217.71|
| 12:  2.1252 -  2.0646  1320   159  0.88  18.43   1.00     0.98       4937.42|
| 13:  2.0646 -  2.0104  1067   122  0.88  18.65   0.99     0.97       3890.34|
| 14:  2.0104 -  1.9615   283    25  0.89  17.25   0.98     0.96       2931.27|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2931.27 max =        12928.44 mean =      7822.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.84 mean =        16.16|
|phase err.(test): min =        0.00 max =           89.18 mean =        15.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.058)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    92.34   15.60    None  None   None       |
|    all(noH): 2823   0      0.70    92.34   15.60    None  None   None       |
|    Sol.    : 438    0      3.33    89.06   40.32    None  None   None       |
|    Mac.    : 2385   0      0.70    92.34   11.06    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:     0.703 -   9.867: 1409   |   5:    46.523 -  55.687:   91        |
|      1:     9.867 -  19.031:  813   |   6:    55.687 -  64.851:   60        |
|      2:    19.031 -  28.195:  178   |   7:    64.851 -  74.015:   25        |
|      3:    28.195 -  37.359:  116   |   8:    74.015 -  83.179:    9        |
|      4:    37.359 -  46.523:  114   |   9:    83.179 -  92.344:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.690 - 5.782
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 343
   mapped sites are within: 0.703 - 5.782

peak=    9.301 closest distance to " CG2 VAL A 296 " =    1.474
peak=    8.752 closest distance to " CG2 VAL A 230 " =    1.448
peak=    6.633 closest distance to " O   HOH Z  37 " =    1.574
peak=    6.355 closest distance to " CG  ARG A 138 " =    1.116
peak=    6.188 closest distance to " O   HOH Z 277 " =    1.503
peak=    6.113 closest distance to " CG  LEU A   5 " =    1.308
peak=    5.898 closest distance to " O   HOH Z  11 " =    1.421
peak=    5.887 closest distance to " O   HOH Z 111 " =    2.086
peak=    5.553 closest distance to " O   HOH Z 120 " =    1.093
peak=    5.436 closest distance to " CD2 LEU A   5 " =    1.153
peak=    5.189 closest distance to " O   HOH Z 246 " =    1.622
peak=    5.148 closest distance to " O   HOH Z 124 " =    1.500
peak=    5.090 closest distance to " O   HOH Z 279 " =    1.199
peak=    5.004 closest distance to " O   HOH Z 278 " =    1.106
peak=    4.986 closest distance to " CG  PRO A  54 " =    1.237
peak=    4.969 closest distance to " CB  GLN A 223 " =    1.437
peak=    4.942 closest distance to " O   HOH Z  47 " =    1.996
peak=    4.870 closest distance to " CB  VAL A 230 " =    1.329
peak=    4.865 closest distance to " CB  SER A  63 " =    1.312
peak=    4.838 closest distance to " CD1AILE A 234 " =    1.054
peak=    4.823 closest distance to " O   HOH Z 186 " =    1.405
peak=    4.792 closest distance to " O   HOH Z 126 " =    1.847
peak=    4.759 closest distance to " O   HOH Z 411 " =    3.078
peak=    4.698 closest distance to " O   HOH Z 221 " =    1.442
peak=    4.677 closest distance to " NH1 ARG A 138 " =    1.019
peak=    4.592 closest distance to " O  BHOH Z 338 " =    1.161
peak=    4.548 closest distance to " CG  LEU A 228 " =    1.280
peak=    4.489 closest distance to " O   HOH Z 132 " =    1.139
peak=    4.463 closest distance to " CB  PRO A  54 " =    0.802
peak=    4.438 closest distance to " CG  PRO A 198 " =    1.441
peak=    4.412 closest distance to " CG2 THR A 221 " =    0.993
peak=    4.399 closest distance to " O   HOH Z  61 " =    1.448
peak=    4.392 closest distance to " O   HOH Z  63 " =    1.575
peak=    4.382 closest distance to " O   HOH Z  15 " =    2.044
peak=    4.377 closest distance to " CB  GLU A 152 " =    1.124
peak=    4.353 closest distance to " C   PRO A 198 " =    1.486
peak=    4.350 closest distance to " NH2BARG A 102 " =    0.985
peak=    4.345 closest distance to " O   HOH Z  80 " =    1.950
peak=    4.332 closest distance to " O   HOH Z 394 " =    1.712
peak=    4.326 closest distance to " O   HOH Z 112 " =    1.430
peak=    4.303 closest distance to " CB  TYR A 169 " =    0.898
peak=    4.256 closest distance to " O   HOH Z 163 " =    1.791
peak=    4.256 closest distance to " CD2 LEU A 228 " =    1.173
peak=    4.242 closest distance to " O   HOH Z 433 " =    1.586
peak=    4.234 closest distance to " NH1 ARG A  56 " =    1.085
peak=    4.224 closest distance to " O   HOH Z 403 " =    1.889
peak=    4.224 closest distance to " O   HOH Z 371 " =    3.178
peak=    4.223 closest distance to " CB  GLN A 183 " =    1.247
peak=    4.190 closest distance to " O   HOH Z 272 " =    1.995
peak=    4.188 closest distance to " OE1 GLN A  11 " =    1.881
peak=    4.183 closest distance to " O   HOH Z  68 " =    1.938
peak=    4.182 closest distance to " O   HOH Z  63 " =    1.713
peak=    4.174 closest distance to " O   HOH Z 236 " =    1.792
peak=    4.145 closest distance to " O   HOH Z 389 " =    2.022
peak=    4.140 closest distance to " O   HOH Z 276 " =    1.487
peak=    4.136 closest distance to " O   HOH Z 134 " =    1.754
peak=    4.106 closest distance to " O   HOH Z 182 " =    1.127
peak=    4.104 closest distance to " O   HOH Z  43 " =    1.754
peak=    4.075 closest distance to " CG  PRO A 213 " =    1.301
peak=    4.074 closest distance to " O   HOH Z 108 " =    1.606
peak=    4.067 closest distance to " O   HOH Z 193 " =    1.787
peak=    4.060 closest distance to " O   ASP A 132 " =    3.815
peak=    4.029 closest distance to " O   HOH Z 369 " =    2.177
peak=    4.024 closest distance to " NE2 GLN A  11 " =    1.122
peak=    4.010 closest distance to " O   HOH Z 232 " =    2.202
peak=    4.006 closest distance to " O   HOH Z  30 " =    1.680
peak=    4.003 closest distance to " O   HOH Z  97 " =    1.910
peak=    3.995 closest distance to " O   HOH Z 118 " =    1.744
peak=    3.990 closest distance to " CD1 LEU A 300 " =    1.207
peak=    3.979 closest distance to " O   HOH Z 303 " =    2.238
peak=    3.976 closest distance to " O   HOH Z 386 " =    2.178
peak=    3.973 closest distance to " O   HOH Z 291 " =    1.427
peak=    3.971 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.965 closest distance to " CB  ALA A 100 " =    1.481
peak=    3.964 closest distance to " O   HOH Z  54 " =    1.551
peak=    3.957 closest distance to " CD  ARG A 269 " =    0.900
peak=    3.955 closest distance to " OD2 ASP A 286 " =    2.922
peak=    3.951 closest distance to " O   SER A  87 " =    2.409
peak=    3.948 closest distance to " CG AARG A 275 " =    1.105
peak=    3.948 closest distance to " O   HOH Z 132 " =    2.106
peak=    3.935 closest distance to " O   HOH Z   4 " =    1.756
peak=    3.920 closest distance to " NH2 ARG A 156 " =    1.180
peak=    3.913 closest distance to " CB  ARG A 275 " =    0.909
peak=    3.913 closest distance to " O   HOH Z  40 " =    1.764
peak=    3.911 closest distance to " CB  TRP A 179 " =    1.369
peak=    3.911 closest distance to " CB  LEU A 228 " =    1.324
peak=    3.911 closest distance to " O   HOH Z 128 " =    2.091
peak=    3.910 closest distance to " CA  TYR A  30 " =    0.999
peak=    3.904 closest distance to " O   HOH Z  88 " =    3.006
peak=    3.903 closest distance to " O   HOH Z  78 " =    2.195
peak=    3.900 closest distance to " CA  ALA A  21 " =    1.324
peak=    3.895 closest distance to " O   HOH Z  69 " =    1.241
peak=    3.893 closest distance to " O   HOH Z 280 " =    2.933
peak=    3.890 closest distance to " CB  ASN A 148 " =    1.149
peak=    3.873 closest distance to " CG  PRO A 243 " =    1.188
peak=    3.863 closest distance to " CZ  PHE A 192 " =    1.080
peak=    3.853 closest distance to " CG1 VAL A 153 " =    1.089
peak=    3.851 closest distance to " CB  SER A   3 " =    1.502
peak=    3.849 closest distance to " O   HOH Z 183 " =    1.433
peak=    3.844 closest distance to " O   HOH Z  19 " =    2.478
peak=    3.843 closest distance to " OD1 ASN A  69 " =    2.467
peak=    3.838 closest distance to " CG  ARG A  66 " =    2.787
peak=    3.820 closest distance to " O   HOH Z 184 " =    1.482
peak=    3.812 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.811 closest distance to " O   HOH Z 298 " =    1.804
peak=    3.793 closest distance to " O   HOH Z 192 " =    1.579
peak=    3.789 closest distance to " CE  LYS A 119 " =    1.099
peak=    3.787 closest distance to " CB  TRP A 266 " =    1.018
peak=    3.782 closest distance to " O   HOH Z 210 " =    1.121
peak=    3.774 closest distance to " O   HOH Z 425 " =    1.454
peak=    3.770 closest distance to " C   SER A  32 " =    1.111
peak=    3.769 closest distance to " O   HOH Z 126 " =    2.138
peak=    3.751 closest distance to " CG1 ILE A  33 " =    1.300
peak=    3.740 closest distance to " O   HOH Z  13 " =    1.722
peak=    3.715 closest distance to " CB  VAL A 202 " =    1.552
peak=    3.714 closest distance to " CB  VAL A 265 " =    1.237
peak=    3.709 closest distance to " CB  ASN A 187 " =    1.103
peak=    3.702 closest distance to " CA  ALA A 160 " =    0.909
peak=    3.700 closest distance to " N   ASN A  39 " =    1.309
peak=    3.698 closest distance to " CB  GLU A 277 " =    3.720
peak=    3.693 closest distance to " O   HOH Z 368 " =    2.379
peak=    3.692 closest distance to " O   HOH Z 197 " =    2.099
peak=    3.691 closest distance to " O   HOH Z 271 " =    2.057
peak=    3.688 closest distance to " O   HOH Z 279 " =    2.302
peak=    3.676 closest distance to " O   HOH Z 260 " =    1.269
peak=    3.671 closest distance to " CD  ARG A 159 " =    0.886
peak=    3.663 closest distance to " CA  LYS A 117 " =    1.240
peak=    3.660 closest distance to " O   HOH Z  93 " =    2.749
peak=    3.660 closest distance to " O   HOH Z 427 " =    3.311
peak=    3.656 closest distance to " OE1 GLN A  58 " =    5.782
peak=    3.650 closest distance to " CD BLYS A 290 " =    1.107
peak=    3.645 closest distance to " O   HOH Z 217 " =    1.587
peak=    3.637 closest distance to " CD  ARG A 138 " =    1.324
peak=    3.636 closest distance to " O   HOH Z 225 " =    2.036
peak=    3.635 closest distance to " CB  PRO A 198 " =    1.030
peak=    3.634 closest distance to " N   HIS A 108 " =    1.946
peak=    3.626 closest distance to " CA  ASP A 140 " =    1.342
peak=    3.619 closest distance to " O   HOH Z  48 " =    2.022
peak=    3.615 closest distance to " CB  GLU A 128 " =    1.218
peak=    3.614 closest distance to " O   HOH Z 149 " =    1.500
peak=    3.605 closest distance to " O   HOH Z  92 " =    1.151
peak=    3.602 closest distance to " O   GLY A  91 " =    1.219
peak=    3.600 closest distance to " CG2AVAL A  72 " =    1.807
peak=    3.596 closest distance to " O   ASP A 124 " =    1.091
peak=    3.593 closest distance to " CA  ASP A 191 " =    0.804
peak=    3.591 closest distance to " CB  LEU A 143 " =    1.110
peak=    3.590 closest distance to " CA  GLU A 152 " =    0.885
peak=    3.589 closest distance to " OD1 ASN A 217 " =    1.547
peak=    3.588 closest distance to " O   HOH Z 185 " =    1.755
peak=    3.587 closest distance to " O   HOH Z 423 " =    1.877
peak=    3.584 closest distance to " O   HOH Z  20 " =    2.193
peak=    3.581 closest distance to " O   HOH Z 329 " =    3.658
peak=    3.580 closest distance to " NH1BARG A 145 " =    1.351
peak=    3.576 closest distance to " CD  LYS A 119 " =    1.408
peak=    3.565 closest distance to " O   HOH Z 215 " =    1.531
peak=    3.561 closest distance to " O   HOH Z 104 " =    3.303
peak=    3.560 closest distance to " O   HOH Z 373 " =    1.583
peak=    3.556 closest distance to " O   HOH Z 263 " =    1.476
peak=    3.549 closest distance to " O   HOH Z 196 " =    1.319
peak=    3.548 closest distance to " O   HOH Z  49 " =    2.033
peak=    3.543 closest distance to " O   HOH Z 374 " =    3.022
peak=    3.534 closest distance to " O   HOH Z 387 " =    2.562
peak=    3.532 closest distance to " CG1 ILE A  49 " =    1.677
peak=    3.528 closest distance to " CA  ALA A 295 " =    1.106
peak=    3.527 closest distance to " CA  ARG A  36 " =    1.163
peak=    3.522 closest distance to " CD1 TRP A 266 " =    1.140
peak=    3.522 closest distance to " CB  ASP A 124 " =    0.824
peak=    3.521 closest distance to " O   HOH Z  21 " =    1.904
peak=    3.518 closest distance to " CB  LYS A 193 " =    1.167
peak=    3.514 closest distance to " O   HOH Z 437 " =    2.585
peak=    3.506 closest distance to " CB  ALA A  71 " =    1.286
peak=    3.506 closest distance to " O   HOH Z 426 " =    1.399
peak=    3.505 closest distance to " OE1 GLN A  58 " =    1.293
peak=    3.500 closest distance to " CG2 THR A 220 " =    0.932
peak=    3.496 closest distance to " O   HOH Z 346 " =    1.442
peak=    3.494 closest distance to " O   HOH Z 355 " =    1.887
peak=    3.493 closest distance to " CA  ILE A  33 " =    1.577
peak=    3.493 closest distance to " CD1 LEU A   5 " =    1.552
peak=    3.492 closest distance to " N   SER A 164 " =    1.036
peak=    3.484 closest distance to " O   HOH Z 108 " =    2.223
peak=    3.482 closest distance to " O   HOH Z  58 " =    1.643
peak=    3.480 closest distance to " CB  GLU A 236 " =    1.302
peak=    3.477 closest distance to " O   HOH Z 136 " =    1.310
peak=    3.473 closest distance to " NH1 ARG A 269 " =    0.875
peak=    3.472 closest distance to " CB  SER A 141 " =    1.010
peak=    3.471 closest distance to " O   HOH Z 131 " =    2.425
peak=    3.471 closest distance to " O   HOH Z 132 " =    2.615
peak=    3.470 closest distance to " O   HOH Z 261 " =    1.827
peak=    3.469 closest distance to " O   HOH Z 156 " =    2.361
peak=    3.465 closest distance to " CB  ALA A 256 " =    1.185
peak=    3.461 closest distance to " O   HOH Z 102 " =    1.413
peak=    3.461 closest distance to " O   HOH Z 128 " =    2.165
peak=    3.449 closest distance to " CA  THR A 246 " =    1.177
peak=    3.449 closest distance to " O   HOH Z 404 " =    1.521
peak=    3.448 closest distance to " CB  ARG A 139 " =    1.045
peak=    3.448 closest distance to " O   HOH Z 211 " =    2.228
peak=    3.447 closest distance to " O   HOH Z 255 " =    1.746
peak=    3.445 closest distance to " O   HOH Z  89 " =    3.718
peak=    3.444 closest distance to " O   HOH Z 174 " =    2.171
peak=    3.443 closest distance to " O   HOH Z 114 " =    1.560
peak=    3.441 closest distance to " O   HOH Z 422 " =    2.698
peak=    3.439 closest distance to " O   HOH Z 316 " =    2.892
peak=    3.437 closest distance to " CG2 THR A  42 " =    0.893
peak=    3.435 closest distance to " CD2 LEU A 255 " =    1.343
peak=    3.433 closest distance to " CG  GLN A  58 " =    2.498
peak=    3.433 closest distance to " CA  ALA A  51 " =    1.099
peak=    3.428 closest distance to " O   HOH Z 109 " =    2.321
peak=    3.424 closest distance to " O   HOH Z 395 " =    1.357
peak=    3.421 closest distance to " O   HOH Z 327 " =    2.670
peak=    3.421 closest distance to " OG BSER A 164 " =    1.994
peak=    3.420 closest distance to " O   HOH Z 383 " =    2.048
peak=    3.418 closest distance to " O   HOH Z 344 " =    2.916
peak=    3.412 closest distance to " O   HOH Z  54 " =    2.399
peak=    3.411 closest distance to " NH2BARG A 145 " =    2.124
peak=    3.409 closest distance to " O   HOH Z  44 " =    1.780
peak=    3.408 closest distance to " O   HOH Z 214 " =    2.061
peak=    3.403 closest distance to " O   HOH Z 368 " =    2.825
peak=    3.403 closest distance to " O   HOH Z 144 " =    1.494
peak=    3.403 closest distance to " CB  ASP A 140 " =    0.777
peak=    3.402 closest distance to " O   HOH Z 281 " =    3.981
peak=    3.400 closest distance to " O   HOH Z 240 " =    1.888
peak=    3.399 closest distance to " O   HOH Z 410 " =    1.404
peak=    3.398 closest distance to " CD  ARG A  14 " =    1.316
peak=    3.397 closest distance to " CA  GLY A 196 " =    0.915
peak=    3.392 closest distance to " O   HOH Z 374 " =    1.013
peak=    3.381 closest distance to " CA  LEU A 101 " =    1.568
peak=    3.379 closest distance to " CB BVAL A  41 " =    1.225
peak=    3.378 closest distance to " O   HOH Z 406 " =    1.780
peak=    3.376 closest distance to " CA  THR A 221 " =    0.884
peak=    3.370 closest distance to " O   HOH Z  99 " =    2.696
peak=    3.361 closest distance to " O   HOH Z 207 " =    2.613
peak=    3.361 closest distance to " N   LYS A 166 " =    0.899
peak=    3.361 closest distance to " O   HOH Z 203 " =    1.676
peak=    3.356 closest distance to " CA  GLY A  75 " =    1.297
peak=    3.353 closest distance to " O   HOH Z 189 " =    2.711
peak=    3.351 closest distance to " O   HOH Z 365 " =    3.040
peak=    3.347 closest distance to " O   HOH Z 209 " =    2.512
peak=    3.343 closest distance to " O   HOH Z 155 " =    1.554
peak=    3.341 closest distance to " CE1 PHE A 208 " =    1.070
peak=    3.336 closest distance to " CB  ARG A  79 " =    1.439
peak=    3.336 closest distance to " O   HOH Z 434 " =    2.733
peak=    3.332 closest distance to " O   HOH Z 377 " =    1.442
peak=    3.331 closest distance to " O   GLN A 278 " =    1.222
peak=    3.331 closest distance to " CA  LEU A 282 " =    1.031
peak=    3.331 closest distance to " CD  LYS A 166 " =    1.490
peak=    3.323 closest distance to " O   HOH Z 155 " =    2.847
peak=    3.311 closest distance to " CB  ALA A   9 " =    1.555
peak=    3.309 closest distance to " CA  SER A  87 " =    0.909
peak=    3.306 closest distance to " CG2 VAL A 174 " =    1.329
peak=    3.304 closest distance to " O   ALA A 158 " =    1.300
peak=    3.302 closest distance to " OE1 GLU A   2 " =    2.155
peak=    3.302 closest distance to " O   HOH Z 345 " =    3.535
peak=    3.301 closest distance to " CB  GLN A  58 " =    0.792
peak=    3.296 closest distance to " O   HOH Z 374 " =    2.561
peak=    3.294 closest distance to " CA  ALA A 158 " =    1.163
peak=    3.292 closest distance to " CB  ILE A 199 " =    1.094
peak=    3.290 closest distance to " O   HOH Z 243 " =    1.204
peak=    3.288 closest distance to " O   HOH Z 116 " =    1.660
peak=    3.287 closest distance to " O   HOH Z 280 " =    1.660
peak=    3.279 closest distance to " NH1AARG A 145 " =    1.005
peak=    3.277 closest distance to " O   HOH Z 150 " =    3.303
peak=    3.276 closest distance to " O   HOH Z 147 " =    1.732
peak=    3.274 closest distance to " O   HOH Z 128 " =    1.781
peak=    3.269 closest distance to " CE  LYS A 166 " =    1.916
peak=    3.269 closest distance to " CB  SER A 216 " =    0.788
peak=    3.268 closest distance to " CG2 ILE A 106 " =    0.935
peak=    3.261 closest distance to " CA  TYR A 116 " =    1.551
peak=    3.260 closest distance to " CA  GLU A 152 " =    1.519
peak=    3.258 closest distance to " CB  TYR A  30 " =    1.140
peak=    3.256 closest distance to " O   HOH Z 175 " =    3.683
peak=    3.252 closest distance to " CG  GLN A  88 " =    1.058
peak=    3.251 closest distance to " NH1 ARG A  14 " =    1.096
peak=    3.251 closest distance to " O   HOH Z  50 " =    2.116
peak=    3.251 closest distance to " CG1BVAL A 121 " =    1.234
peak=    3.251 closest distance to " O   HOH Z 313 " =    1.849
peak=    3.250 closest distance to " O   HOH Z 423 " =    3.334
peak=    3.244 closest distance to " O   HOH Z 130 " =    1.235
peak=    3.242 closest distance to " O   HOH Z 234 " =    1.818
peak=    3.240 closest distance to " ND1 HIS A  81 " =    1.610
peak=    3.239 closest distance to " N   ALA A 256 " =    0.930
peak=    3.234 closest distance to " CA  MET A  40 " =    1.078
peak=    3.229 closest distance to " CZ3 TRP A  92 " =    1.199
peak=    3.229 closest distance to " OG  SER A  97 " =    3.480
peak=    3.228 closest distance to " O   HOH Z 166 " =    1.463
peak=    3.225 closest distance to " O   HOH Z 420 " =    5.571
peak=    3.223 closest distance to " O   HOH Z 283 " =    1.927
peak=    3.221 closest distance to " O   HOH Z 171 " =    3.836
peak=    3.221 closest distance to " CE1 TYR A 186 " =    1.281
peak=    3.215 closest distance to " CB  GLN A 194 " =    0.837
peak=    3.214 closest distance to " O   HOH Z 368 " =    1.166
peak=    3.205 closest distance to " CG  LYS A 166 " =    1.558
peak=    3.199 closest distance to " OD2 ASP A 286 " =    2.350
peak=    3.197 closest distance to " O   HOH Z  47 " =    1.360
peak=    3.197 closest distance to " O   HOH Z 419 " =    1.709
peak=    3.189 closest distance to " CA  ALA A 291 " =    1.010
peak=    3.185 closest distance to " NH2BARG A 190 " =    1.883
peak=    3.185 closest distance to " CB  GLN A 278 " =    1.213
peak=    3.182 closest distance to " O   HOH Z   1 " =    2.562
peak=    3.180 closest distance to " O   HOH Z  49 " =    0.941
peak=    3.179 closest distance to " CG  MET A 188 " =    1.170
peak=    3.178 closest distance to " CG BARG A 275 " =    1.603
peak=    3.177 closest distance to " CD  ARG A 195 " =    0.923
peak=    3.176 closest distance to " CB  LEU A 237 " =    0.948
peak=    3.176 closest distance to " CA  ASN A 284 " =    1.084
peak=    3.176 closest distance to " O   HOH Z 298 " =    2.345
peak=    3.172 closest distance to " N   TYR A 247 " =    1.227
peak=    3.171 closest distance to " CG AARG A 275 " =    1.199
peak=    3.169 closest distance to " CB  ARG A 259 " =    1.908
peak=    3.168 closest distance to " CB  SER A  28 " =    0.886
peak=    3.165 closest distance to " O   HOH Z 132 " =    2.806
peak=    3.159 closest distance to " O   HOH Z  10 " =    1.872
peak=    3.158 closest distance to " CG  GLN A  77 " =    0.703
peak=    3.154 closest distance to " O   HOH Z 214 " =    2.487
peak=    3.154 closest distance to " CG ALYS A 290 " =    1.043
peak=    3.151 closest distance to " O   HOH Z 344 " =    1.688
peak=    3.146 closest distance to " NE  ARG A 156 " =    1.108
peak=    3.145 closest distance to " CB  TYR A  30 " =    1.469
peak=    3.144 closest distance to " O   HOH Z 173 " =    2.074
peak=    3.141 closest distance to " CD1 LEU A 101 " =    1.232
peak=    3.141 closest distance to " CG2 VAL A 112 " =    1.577
peak=    3.137 closest distance to " O   HOH Z 313 " =    1.718
peak=    3.137 closest distance to " CD  GLU A 236 " =    1.117
peak=    3.133 closest distance to " CD1 LEU A 222 " =    0.878
peak=    3.126 closest distance to " CA  ARG A 195 " =    1.267
peak=    3.125 closest distance to " CA  GLN A 223 " =    0.893
peak=    3.123 closest distance to " CD  ARG A 195 " =    3.572
peak=    3.113 closest distance to " CB  PHE A  61 " =    0.788
peak=    3.104 closest distance to " O   HOH Z 426 " =    2.942
peak=    3.104 closest distance to " O   HOH Z 409 " =    3.229
peak=    3.102 closest distance to " O   HOH Z 148 " =    1.863
peak=    3.099 closest distance to " C   GLY A  80 " =    1.166
peak=    3.095 closest distance to " CA  ALA A 100 " =    1.191
peak=    3.094 closest distance to " CB  ALA A 161 " =    0.984
peak=    3.091 closest distance to " CG2 ILE A 120 " =    1.329
peak=    3.088 closest distance to " CA  VAL A  41 " =    0.861
peak=    3.071 closest distance to " CB  LEU A 261 " =    1.313
peak=    3.069 closest distance to " O   HOH Z 189 " =    1.443
peak=    3.065 closest distance to " CB  PHE A  16 " =    0.991
peak=    3.045 closest distance to " O   HOH Z 244 " =    1.635
peak=    3.028 closest distance to " O   HOH Z 368 " =    3.816
peak=    3.006 closest distance to " CG1 ILE A 151 " =    1.289

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.701 - 5.593
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.701 - 5.593

peak=   -4.873 closest distance to " CG2 VAL A 230 " =    0.921
peak=   -4.575 closest distance to " OG ASER A 134 " =    1.166
peak=   -4.335 closest distance to " O   HOH Z 221 " =    1.067
peak=   -4.320 closest distance to " O   HOH Z 290 " =    1.030
peak=   -4.279 closest distance to " O   HOH Z 184 " =    0.974
peak=   -4.247 closest distance to " O   HOH Z 231 " =    1.534
peak=   -4.206 closest distance to " NH2 ARG A  66 " =    1.454
peak=   -4.170 closest distance to " CG  ASP A 231 " =    0.827
peak=   -4.169 closest distance to " O   HOH Z  17 " =    1.301
peak=   -4.152 closest distance to " CD  ARG A 138 " =    1.530
peak=   -4.147 closest distance to " O   HOH Z  13 " =    1.257
peak=   -4.145 closest distance to " CD1 PHE A  59 " =    1.859
peak=   -4.123 closest distance to " O   HOH Z 151 " =    1.345
peak=   -4.122 closest distance to " O   HOH Z 407 " =    3.470
peak=   -4.115 closest distance to " CD2 LEU A 237 " =    2.642
peak=   -4.110 closest distance to " O   HOH Z  52 " =    2.007
peak=   -4.099 closest distance to " O   HOH Z 166 " =    1.835
peak=   -4.089 closest distance to " OG1 THR A   4 " =    1.916
peak=   -4.050 closest distance to " CG  ARG A 138 " =    1.020
peak=   -4.045 closest distance to " N   ALA A 226 " =    2.070
peak=   -4.044 closest distance to " O   HOH Z 103 " =    2.106
peak=   -3.999 closest distance to " O   HOH Z 266 " =    4.417
peak=   -3.995 closest distance to " O   HOH Z  19 " =    1.926
peak=   -3.988 closest distance to " O   ILE A 109 " =    2.704
peak=   -3.963 closest distance to " C   ASN A 187 " =    1.847
peak=   -3.927 closest distance to " CG2 VAL A 112 " =    2.527
peak=   -3.919 closest distance to " O   HOH Z  15 " =    1.604
peak=   -3.857 closest distance to " OE2 GLU A   2 " =    1.536
peak=   -3.853 closest distance to " O   HOH Z  71 " =    0.857
peak=   -3.841 closest distance to " O   HOH Z 210 " =    0.711
peak=   -3.815 closest distance to " CD  LYS A 289 " =    2.503
peak=   -3.815 closest distance to " O   HOH Z 380 " =    4.597
peak=   -3.794 closest distance to " O   HOH Z 177 " =    1.181
peak=   -3.790 closest distance to " CD  ARG A 156 " =    1.958
peak=   -3.759 closest distance to " CE  MET A  93 " =    1.182
peak=   -3.753 closest distance to " O   HOH Z   5 " =    1.604
peak=   -3.749 closest distance to " N   GLN A  58 " =    1.635
peak=   -3.743 closest distance to " O   HOH Z 243 " =    1.790
peak=   -3.732 closest distance to " CD2 LEU A 143 " =    2.594
peak=   -3.731 closest distance to " CB  GLN A  55 " =    1.425
peak=   -3.724 closest distance to " O   HOH Z  11 " =    1.588
peak=   -3.716 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.714 closest distance to " O   HOH Z 385 " =    3.936
peak=   -3.704 closest distance to " O   HOH Z 241 " =    1.075
peak=   -3.701 closest distance to " CZ  ARG A  66 " =    1.021
peak=   -3.691 closest distance to " CG  MET A 105 " =    0.873
peak=   -3.677 closest distance to " CE2 TYR A  30 " =    2.787
peak=   -3.672 closest distance to " O   HOH Z 189 " =    2.275
peak=   -3.660 closest distance to " O   GLY A 118 " =    2.172
peak=   -3.656 closest distance to " O   HOH Z  94 " =    2.273
peak=   -3.652 closest distance to " O   HOH Z 274 " =    2.622
peak=   -3.644 closest distance to " OG  SER A  26 " =    1.311
peak=   -3.636 closest distance to " CD2 LEU A 167 " =    1.767
peak=   -3.623 closest distance to " O   HOH Z 275 " =    1.464
peak=   -3.617 closest distance to " O   VAL A  67 " =    2.841
peak=   -3.609 closest distance to " O   HOH Z  38 " =    1.134
peak=   -3.605 closest distance to " OD1 ASN A  39 " =    2.344
peak=   -3.604 closest distance to " N   THR A 235 " =    1.269
peak=   -3.595 closest distance to " NE2 GLN A  88 " =    0.924
peak=   -3.568 closest distance to " O   HOH Z  43 " =    1.614
peak=   -3.542 closest distance to " O   HOH Z  60 " =    1.905
peak=   -3.540 closest distance to " CD  GLN A  88 " =    0.793
peak=   -3.538 closest distance to " CB  ASP A 124 " =    2.235
peak=   -3.535 closest distance to " ND2 ASN A  60 " =    1.492
peak=   -3.529 closest distance to " CD2 LEU A 300 " =    2.792
peak=   -3.523 closest distance to " C   GLY A  91 " =    1.537
peak=   -3.517 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.517 closest distance to " OG  SER A  97 " =    2.267
peak=   -3.515 closest distance to " O   GLY A 211 " =    1.589
peak=   -3.512 closest distance to " CG  ARG A 219 " =    2.468
peak=   -3.510 closest distance to " C   ASN A 285 " =    2.571
peak=   -3.509 closest distance to " O   HOH Z 221 " =    1.636
peak=   -3.508 closest distance to " CG  GLU A  53 " =    1.571
peak=   -3.505 closest distance to " O   HOH Z  37 " =    1.553
peak=   -3.498 closest distance to " CG  GLU A 277 " =    1.347
peak=   -3.498 closest distance to " O   HOH Z 156 " =    1.514
peak=   -3.495 closest distance to " O   HOH Z 377 " =    1.027
peak=   -3.494 closest distance to " CD1 TRP A 179 " =    1.104
peak=   -3.492 closest distance to " NH2AARG A 275 " =    5.314
peak=   -3.491 closest distance to " C   LEU A 101 " =    0.940
peak=   -3.489 closest distance to " CH2 TRP A 179 " =    1.063
peak=   -3.480 closest distance to " OG  SER A  87 " =    1.530
peak=   -3.480 closest distance to " O   HOH Z  92 " =    1.169
peak=   -3.466 closest distance to " CA  SER A 164 " =    1.943
peak=   -3.464 closest distance to " OG  SER A  63 " =    1.387
peak=   -3.463 closest distance to " O   HOH Z  55 " =    2.576
peak=   -3.451 closest distance to " CD1 LEU A 101 " =    2.834
peak=   -3.435 closest distance to " CZ  TYR A 172 " =    1.692
peak=   -3.431 closest distance to " CB  ALA A 227 " =    2.428
peak=   -3.426 closest distance to " O   HOH Z 165 " =    2.058
peak=   -3.425 closest distance to " O   HOH Z 265 " =    1.623
peak=   -3.424 closest distance to " CG1 VAL A 112 " =    2.608
peak=   -3.414 closest distance to " CD2 TYR A 293 " =    2.153
peak=   -3.399 closest distance to " CD  ARG A 195 " =    5.011
peak=   -3.398 closest distance to " O   HOH Z 402 " =    1.375
peak=   -3.398 closest distance to " O   HOH Z 179 " =    2.335
peak=   -3.395 closest distance to " O   HOH Z 388 " =    1.813
peak=   -3.392 closest distance to " O   HOH Z 234 " =    4.377
peak=   -3.387 closest distance to " O   HOH Z  97 " =    1.386
peak=   -3.387 closest distance to " O   HOH Z 377 " =    1.975
peak=   -3.386 closest distance to " CG  ASP A  50 " =    2.162
peak=   -3.386 closest distance to " O   HOH Z 108 " =    2.274
peak=   -3.385 closest distance to " O   HOH Z 292 " =    4.408
peak=   -3.380 closest distance to " C   HIS A 108 " =    1.114
peak=   -3.378 closest distance to " CE  MET A 105 " =    2.252
peak=   -3.377 closest distance to " O   LEU A 255 " =    1.690
peak=   -3.377 closest distance to " CG  GLU A 152 " =    2.351
peak=   -3.372 closest distance to " O   HOH Z 396 " =    1.552
peak=   -3.366 closest distance to " CB  CYS A 254 " =    2.313
peak=   -3.360 closest distance to " O   HOH Z 231 " =    1.158
peak=   -3.345 closest distance to " CB  ALA A 248 " =    1.893
peak=   -3.339 closest distance to " OE1 GLN A  88 " =    1.012
peak=   -3.338 closest distance to " O   PRO A 198 " =    1.292
peak=   -3.330 closest distance to " CD  ARG A 139 " =    1.615
peak=   -3.328 closest distance to " O   HOH Z 423 " =    2.258
peak=   -3.319 closest distance to " O   HOH Z 166 " =    1.829
peak=   -3.311 closest distance to " O   MET A  47 " =    2.622
peak=   -3.307 closest distance to " O   ALA A   1 " =    1.866
peak=   -3.303 closest distance to " C   THR A 279 " =    1.167
peak=   -3.298 closest distance to " O   HOH Z  48 " =    1.042
peak=   -3.283 closest distance to " OD2 ASP A  65 " =    1.573
peak=   -3.282 closest distance to " CA  ASN A 127 " =    1.004
peak=   -3.275 closest distance to " O   HOH Z 283 " =    1.916
peak=   -3.274 closest distance to " OD1 ASN A 148 " =    1.586
peak=   -3.273 closest distance to " CZ3 TRP A  92 " =    1.206
peak=   -3.271 closest distance to " CB  SER A  63 " =    3.266
peak=   -3.269 closest distance to " O   HOH Z   6 " =    2.027
peak=   -3.268 closest distance to " CB  ALA A 114 " =    2.249
peak=   -3.266 closest distance to " O   HOH Z 367 " =    1.543
peak=   -3.263 closest distance to " CG  ARG A 269 " =    2.222
peak=   -3.262 closest distance to " ND2BASN A 224 " =    1.828
peak=   -3.254 closest distance to " NH1 ARG A  56 " =    2.413
peak=   -3.254 closest distance to " CG  TRP A 266 " =    1.803
peak=   -3.249 closest distance to " O   HOH Z 262 " =    2.350
peak=   -3.248 closest distance to " O   HOH Z  93 " =    1.640
peak=   -3.243 closest distance to " O   ASP A 191 " =    1.435
peak=   -3.240 closest distance to " O   HOH Z 124 " =    1.481
peak=   -3.240 closest distance to " CD1 LEU A 228 " =    2.532
peak=   -3.237 closest distance to " CD2 LEU A 237 " =    2.761
peak=   -3.236 closest distance to " OD2 ASP A 171 " =    1.856
peak=   -3.231 closest distance to " CG  ARG A  66 " =    2.440
peak=   -3.231 closest distance to " CG1 VAL A 296 " =    1.445
peak=   -3.231 closest distance to " CD  GLN A 223 " =    0.701
peak=   -3.230 closest distance to " O   HOH Z 185 " =    2.111
peak=   -3.228 closest distance to " O   GLY A 196 " =    1.190
peak=   -3.226 closest distance to " CE2 TYR A 293 " =    2.598
peak=   -3.226 closest distance to " CE3 TRP A 150 " =    2.167
peak=   -3.219 closest distance to " O   HOH Z 120 " =    1.244
peak=   -3.209 closest distance to " NE2 GLN A  58 " =    0.878
peak=   -3.205 closest distance to " O   HOH Z  39 " =    1.958
peak=   -3.202 closest distance to " N   THR A 220 " =    2.257
peak=   -3.201 closest distance to " CB  PHE A 208 " =    2.234
peak=   -3.185 closest distance to " CB  ALA A 100 " =    2.064
peak=   -3.184 closest distance to " O   ALA A 100 " =    2.321
peak=   -3.180 closest distance to " C   LEU A 143 " =    1.340
peak=   -3.179 closest distance to " N   SER A 276 " =    1.458
peak=   -3.178 closest distance to " N   ALA A  43 " =    2.480
peak=   -3.172 closest distance to " CD  LYS A 119 " =    1.001
peak=   -3.166 closest distance to " O   ASP A 270 " =    1.757
peak=   -3.159 closest distance to " CA  GLY A 203 " =    2.218
peak=   -3.157 closest distance to " OH  TYR A 169 " =    1.056
peak=   -3.156 closest distance to " CG  PHE A  59 " =    2.626
peak=   -3.155 closest distance to " O   HOH Z 252 " =    1.040
peak=   -3.153 closest distance to " O   HOH Z 402 " =    1.198
peak=   -3.153 closest distance to " OG  SER A  62 " =    4.498
peak=   -3.151 closest distance to " O   HOH Z 303 " =    1.381
peak=   -3.142 closest distance to " NH2 ARG A 159 " =    2.438
peak=   -3.136 closest distance to " CG  ARG A 259 " =    2.777
peak=   -3.134 closest distance to " OD1 ASP A 191 " =    1.690
peak=   -3.134 closest distance to " O   ASN A 301 " =    1.325
peak=   -3.134 closest distance to " CG  GLN A  58 " =    1.177
peak=   -3.129 closest distance to " O   SER A  32 " =    1.339
peak=   -3.123 closest distance to " CB  PRO A 163 " =    2.745
peak=   -3.121 closest distance to " O   ALA A 161 " =    1.546
peak=   -3.118 closest distance to " O   HOH Z  98 " =    1.453
peak=   -3.117 closest distance to " O   VAL A  67 " =    2.481
peak=   -3.116 closest distance to " CA  GLY A 241 " =    3.095
peak=   -3.115 closest distance to " O   ALA A 158 " =    1.126
peak=   -3.114 closest distance to " CD2 LEU A   5 " =    1.048
peak=   -3.114 closest distance to " O   HOH Z 252 " =    4.185
peak=   -3.109 closest distance to " O   HOH Z 399 " =    2.222
peak=   -3.107 closest distance to " ND2 ASN A  45 " =    1.067
peak=   -3.107 closest distance to " O   HOH Z 157 " =    3.705
peak=   -3.098 closest distance to " O   HOH Z 186 " =    0.915
peak=   -3.096 closest distance to " O   HOH Z 171 " =    2.345
peak=   -3.095 closest distance to " O   HOH Z 420 " =    5.593
peak=   -3.088 closest distance to " NH1 ARG A 195 " =    2.357
peak=   -3.085 closest distance to " O   HOH Z 435 " =    2.608
peak=   -3.083 closest distance to " O   HOH Z 351 " =    1.578
peak=   -3.078 closest distance to " CD1 ILE A 263 " =    2.409
peak=   -3.073 closest distance to " O   HOH Z 427 " =    1.473
peak=   -3.073 closest distance to " NE2 HIS A  86 " =    1.024
peak=   -3.072 closest distance to " CA  GLY A 133 " =    1.851
peak=   -3.071 closest distance to " O   HOH Z 246 " =    1.277
peak=   -3.050 closest distance to " CD  ARG A  14 " =    3.150
peak=   -3.035 closest distance to " C   ALA A 158 " =    0.799
peak=   -3.013 closest distance to " O   HOH Z 426 " =    2.280

================= 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    :  0.4974 0.4925   6.298576e+00   6.290431e+00
   1_bss:  0.4898 0.4803   6.298017e+00   6.286030e+00
   1_xyz:  0.4282 0.4551   6.217832e+00   6.254020e+00
   1_adp:  0.3922 0.4437   6.170398e+00   6.241265e+00
   1_occ:  0.3919 0.4444   6.169836e+00   6.241427e+00
   2_bss:  0.3913 0.4406   6.170667e+00   6.239677e+00
   2_xyz:  0.2984 0.3713   5.977833e+00   6.126358e+00
   2_adp:  0.2726 0.3448   5.903525e+00   6.068396e+00
   2_occ:  0.2725 0.3443   5.902594e+00   6.067991e+00
   3_bss:  0.2678 0.3379   5.900919e+00   6.065309e+00
   3_xyz:  0.2025 0.2581   5.651636e+00   5.848023e+00
   3_adp:  0.1804 0.2349   5.554183e+00   5.763273e+00
   3_occ:  0.1801 0.2346   5.553423e+00   5.762749e+00
   4_bss:  0.1794 0.2343   5.553931e+00   5.762501e+00
   4_xyz:  0.1486 0.1985   5.388075e+00   5.608117e+00
   4_adp:  0.1426 0.1916   5.357314e+00   5.575490e+00
   4_occ:  0.1425 0.1916   5.356964e+00   5.575306e+00
   5_bss:  0.1427 0.1921   5.359552e+00   5.577681e+00
   5_xyz:  0.1268 0.1731   5.256017e+00   5.483500e+00
   5_adp:  0.1239 0.1719   5.244764e+00   5.480079e+00
   5_occ:  0.1239 0.1719   5.244445e+00   5.479766e+00
   5_bss:  0.1239 0.1719   5.244423e+00   5.479757e+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:  0.300  20.000   7.869   9.094   7.528   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.869   9.094   7.528   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.869   9.094   7.528   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.869   9.094   7.528   0.000   0.000   0.000
   2_bss:  0.321  38.564   4.936   6.235   5.477   0.000   0.000   0.000
   2_xyz:  0.321  38.564   4.936   6.235   5.477   0.000   0.000   0.000
   2_adp:  0.321  38.564   4.936   6.235   5.477   0.000   0.000   0.000
   2_occ:  0.321  38.564   4.936   6.235   5.477   0.000   0.000   0.000
   3_bss:  0.323  47.759   2.413   2.885   2.432   0.000   0.000   0.000
   3_xyz:  0.323  47.759   2.413   2.885   2.432   0.000   0.000   0.000
   3_adp:  0.323  47.759   2.413   2.885   2.432   0.000   0.000   0.000
   3_occ:  0.323  47.759   2.413   2.885   2.432   0.000   0.000   0.000
   4_bss:  0.315  47.759   1.085   1.594   1.158   0.000   0.000   0.000
   4_xyz:  0.315  47.759   1.085   1.594   1.158   0.000   0.000   0.000
   4_adp:  0.315  47.759   1.085   1.594   1.158   0.000   0.000   0.000
   4_occ:  0.315  47.759   1.085   1.594   1.158   0.000   0.000   0.000
   5_bss:  0.323  52.139   0.475   0.855   0.733   0.000   0.000   0.000
   5_xyz:  0.323  52.139   0.475   0.855   0.733   0.000   0.000   0.000
   5_adp:  0.323  52.139   0.475   0.855   0.733   0.000   0.000   0.000
   5_occ:  0.323  52.139   0.475   0.855   0.733   0.000   0.000   0.000
   5_bss:  0.321  52.429  -0.155   0.114   0.042   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.247 0.3507  0.4148    78474.043
   1_bss:  63.552 0.3444  0.5036    75834.262
   1_xyz:  58.366 0.4102  0.5878    64539.055
   1_adp:  56.559 0.4330  0.6719    60954.061
   1_occ:  56.636 0.4320  0.6701    61136.200
   2_bss:  56.289 0.4363  0.6264    60593.828
   2_xyz:  41.398 0.6239  0.9090    39455.587
   2_adp:  36.891 0.6783  0.9849    32756.199
   2_occ:  36.852 0.6787  0.9853    32674.896
   3_bss:  36.588 0.6816  0.8917    32346.569
   3_xyz:  26.280 0.7966  0.9817    17647.851
   3_adp:  23.271 0.8284  0.9946    14455.021
   3_occ:  23.260 0.8285  0.9943    14437.776
   4_bss:  23.237 0.8288  0.9495    14439.309
   4_xyz:  19.088 0.8697  0.9778    10198.396
   4_adp:  18.210 0.8786  0.9823     9610.893
   4_occ:  18.214 0.8785  0.9819     9621.011
   5_bss:  18.253 0.8783  0.9621     9698.450
   5_xyz:  16.210 0.8963  0.9696     7892.313
   5_adp:  16.093 0.8975  0.9665     7825.085
   5_occ:  16.083 0.8976  0.9664     7821.454
   5_bss:  16.082 0.8976  0.9670     7821.701
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3876e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3876e+01
   1_xyz:   1.810  0.014  0.112 18.275  0.007  4.109   1.5928e-01
   1_adp:   1.810  0.014  0.112 18.275  0.007  4.109   1.5928e-01
   1_occ:   1.810  0.014  0.112 18.275  0.007  4.109   1.5928e-01
   2_bss:   1.810  0.014  0.112 18.275  0.007  4.109   1.5928e-01
   2_xyz:   1.452  0.012  0.096 17.068  0.007  4.115   1.2461e-01
   2_adp:   1.452  0.012  0.096 17.068  0.007  4.115   1.2461e-01
   2_occ:   1.452  0.012  0.096 17.068  0.007  4.115   1.2461e-01
   3_bss:   1.452  0.012  0.096 17.068  0.007  4.115   1.2461e-01
   3_xyz:   1.138  0.008  0.080 15.848  0.004  4.112   7.6037e-02
   3_adp:   1.138  0.008  0.080 15.848  0.004  4.112   7.6037e-02
   3_occ:   1.138  0.008  0.080 15.848  0.004  4.112   7.6037e-02
   4_bss:   1.138  0.008  0.080 15.848  0.004  4.112   7.6037e-02
   4_xyz:   1.051  0.007  0.077 15.634  0.004  4.121   6.6381e-02
   4_adp:   1.051  0.007  0.077 15.634  0.004  4.121   6.6381e-02
   4_occ:   1.051  0.007  0.077 15.634  0.004  4.121   6.6381e-02
   5_bss:   1.051  0.007  0.077 15.634  0.004  4.121   6.6381e-02
   5_xyz:   1.128  0.009  0.084 15.696  0.004  4.114   7.4234e-02
   5_adp:   1.128  0.009  0.084 15.696  0.004  4.114   7.4234e-02
   5_occ:   1.128  0.009  0.084 15.696  0.004  4.114   7.4234e-02
   5_bss:   1.128  0.009  0.084 15.696  0.004  4.114   7.4234e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9828e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9828e+00
   1_xyz:  15.998  0.185  0.513 86.235  0.051  2.198   1.0799e-01
   1_adp:  15.998  0.185  0.513 86.235  0.051  2.198   1.0799e-01
   1_occ:  15.998  0.185  0.513 86.235  0.051  2.198   1.0799e-01
   2_bss:  15.998  0.185  0.513 86.235  0.051  2.198   1.0799e-01
   2_xyz:   8.787  0.121  0.321 85.770  0.056  2.155   9.0135e-02
   2_adp:   8.787  0.121  0.321 85.770  0.056  2.155   9.0135e-02
   2_occ:   8.787  0.121  0.321 85.770  0.056  2.155   9.0135e-02
   3_bss:   8.787  0.121  0.321 85.770  0.056  2.155   9.0135e-02
   3_xyz:   7.164  0.052  0.274 79.380  0.048  2.356   6.0352e-02
   3_adp:   7.164  0.052  0.274 79.380  0.048  2.356   6.0352e-02
   3_occ:   7.164  0.052  0.274 79.380  0.048  2.356   6.0352e-02
   4_bss:   7.164  0.052  0.274 79.380  0.048  2.356   6.0352e-02
   4_xyz:   7.591  0.045  0.342 88.979  0.034  2.321   4.3544e-02
   4_adp:   7.591  0.045  0.342 88.979  0.034  2.321   4.3544e-02
   4_occ:   7.591  0.045  0.342 88.979  0.034  2.321   4.3544e-02
   5_bss:   7.591  0.045  0.342 88.979  0.034  2.321   4.3544e-02
   5_xyz:   8.758  0.053  0.442 82.043  0.040  2.361   5.3104e-02
   5_adp:   8.758  0.053  0.442 82.043  0.040  2.361   5.3104e-02
   5_occ:   8.758  0.053  0.442 82.043  0.040  2.361   5.3104e-02
   5_bss:   8.758  0.053  0.442 82.043  0.040  2.361   5.3104e-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: 119.86   0.00  15.07  98.45   0.00  12.83 119.86   0.00  27.30
   1_occ: 119.86   0.00  15.07  98.45   0.00  12.83 119.86   0.00  27.30
   2_bss: 119.86   0.00  15.07  98.45   0.00  12.83 119.86   0.00  27.30
   2_xyz: 119.86   0.00  15.07  98.45   0.00  12.83 119.86   0.00  27.30
   2_adp: 116.65   0.00  14.90  93.76   0.00  11.60 116.65   0.00  32.89
   2_occ: 116.65   0.00  14.90  93.76   0.00  11.60 116.65   0.00  32.89
   3_bss: 116.65   0.00  14.90  93.76   0.00  11.60 116.65   0.00  32.89
   3_xyz: 116.65   0.00  14.90  93.76   0.00  11.60 116.65   0.00  32.89
   3_adp: 101.08   0.00  15.37  86.37   0.00  10.82 101.08   1.76  40.13
   3_occ: 101.08   0.00  15.37  86.37   0.00  10.82 101.08   1.76  40.13
   4_bss: 101.08   0.00  15.37  86.37   0.00  10.82 101.08   1.76  40.13
   4_xyz: 101.08   0.00  15.37  86.37   0.00  10.82 101.08   1.76  40.13
   4_adp:  90.07   0.39  14.90  86.97   0.39  10.46  90.07   2.83  39.07
   4_occ:  90.07   0.39  14.90  86.97   0.39  10.46  90.07   2.83  39.07
   5_bss:  90.07   0.39  14.90  86.97   0.39  10.46  90.07   2.83  39.07
   5_xyz:  90.07   0.39  14.90  86.97   0.39  10.46  90.07   2.83  39.07
   5_adp:  91.64   0.00  14.90  91.64   0.00  10.36  88.35   2.62  39.62
   5_occ:  91.64   0.00  14.90  91.64   0.00  10.36  88.35   2.62  39.62
   5_bss:  92.34   0.70  15.60  92.34   0.70  11.06  89.06   3.33  40.32
------------------------------------------------------------------------
 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:    1.185    0.033    0.418
   1_adp:    1.185    0.033    0.418
   1_occ:    1.185    0.033    0.418
   2_bss:    1.185    0.033    0.418
   2_xyz:    1.737    0.045    0.657
   2_adp:    1.737    0.045    0.657
   2_occ:    1.737    0.045    0.657
   3_bss:    1.737    0.045    0.657
   3_xyz:    1.759    0.031    0.751
   3_adp:    1.759    0.031    0.751
   3_occ:    1.759    0.031    0.751
   4_bss:    1.759    0.031    0.751
   4_xyz:    1.774    0.061    0.813
   4_adp:    1.774    0.061    0.813
   4_occ:    1.774    0.061    0.813
   5_bss:    1.774    0.061    0.813
   5_xyz:    1.794    0.047    0.841
   5_adp:    1.794    0.047    0.841
   5_occ:    1.794    0.047    0.841
   5_bss:    1.794    0.047    0.841
------------------------------------------------------------------------

CPU time actual refinement: 354.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1178/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_1178/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1178/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1178/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1178/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.44 
  Macro-tasks:
    bulk solvent and scale       = 41.56  
    individual site refinement   = 148.79 
    weights calculation          = 31.90  
    collect and process          = 6.19   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 228.58 
  Micro-tasks:
    mask                            = 2.63   
    f_calc                          = 114.56 
    alpha_beta                      = 8.09   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 123.32 
    fmodel                         = 7.13   
    r_factors                      = 0.19   
    phase_errors                   = 9.83   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 267.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.994 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    643 calls, 114.22 s
gradients_fft:          587 calls, 110.29 s

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

# Date 2008-01-16 Time 03:23:55 PST -0800 (1200482635.12 s)
Start R-work = 0.4974, R-free = 0.4925 (no bulk solvent and anisotropic scale)
Final R-work = 0.1401, R-free = 0.1886 (no bulk solvent and anisotropic scale)

Start R-work = 0.4898, R-free = 0.4803
Final R-work = 0.1239, R-free = 0.1719