# Date 2008-01-16 Time 03:37:30 PST -0800 (1200483450.20 s)
#phil __OFF__

Command line arguments: "../1308.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29380
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1308

-------------------------------------------------------------------------------
  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: (72.0062, 47.6339, 88.5498, 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: 3.23, per 1000 atoms: 1.14


================================== 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: (72.0062, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 2.03226
Completeness in resolution range: 0.969993
Completeness with d_max=infinity: 0.966976

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3688
                             d_min =   2.0323

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: (72.0062, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 2.03226
Completeness in resolution range: 0.969993
Completeness with d_max=infinity: 0.966976

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3693 -  4.3484 [2118/2142]  1905   213  10.1%
  bin  2:  4.3484 -  3.4645 [2035/2055]  1832   203  10.0%
  bin  3:  3.4645 -  3.0303 [2014/2033]  1814   200   9.9%
  bin  4:  3.0303 -  2.7550 [1997/2027]  1798   199  10.0%
  bin  5:  2.7550 -  2.5585 [1987/2006]  1787   200  10.1%
  bin  6:  2.5585 -  2.4083 [1958/1983]  1759   199  10.2%
  bin  7:  2.4083 -  2.2881 [1955/1983]  1762   193   9.9%
  bin  8:  2.2881 -  2.1888 [1964/2000]  1769   195   9.9%
  bin  9:  2.1888 -  2.1047 [1943/1985]  1750   193   9.9%
  bin 10:  2.1047 -  2.0323 [1618/1981]  1454   164  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1308/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:
        1.58 -     2.25: 3
        2.25 -     2.91: 1392
        2.91 -     3.57: 4339
        3.57 -     4.24: 8918
        4.24 -     4.90: 12823
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.585 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.268 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.268 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27470 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_1308/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1308/model_refine_001.geo

CPU time processing inputs: 8.92


============================ 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 = 72.00625 47.63395 88.54975 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: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5191   r_free= 0.5080   ksol= 0.00   Bsol= 0.00   scale= 0.743    |
|                                                                             |
| 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:   1.03 A                  |
| x-ray target function (ml) for work reflections: 6.309250                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.8499 0.99   1379  152 0.4281 0.4169       6.646      6.5992|
|  2:  4.8499 -  3.8698 0.99   1326  150 0.4662 0.4973      6.8908      6.9766|
|  3:  3.8698 -  3.3866 0.99   1298  142 0.5002 0.4622      6.7525      6.7591|
|  4:  3.3866 -  3.0796 0.99   1285  145 0.5212 0.4402       6.587      6.4911|
|  5:  3.0796 -  2.8604 0.99   1283  142 0.5265 0.5178      6.3997      6.4545|
|  6:  2.8604 -  2.6927 0.99   1292  141 0.5509 0.5666      6.3196      6.2177|
|  7:  2.6927 -  2.5585 0.99   1273  143 0.5603 0.5190      6.2627      6.2451|
|  8:  2.5585 -  2.4476 0.98   1258  138 0.5471 0.4905      6.2048      6.1539|
|  9:  2.4476 -  2.3537 0.98   1264  141 0.5454 0.6281      6.1297      6.1769|
| 10:  2.3537 -  2.2728 1.00   1260  144 0.5652 0.5610      6.1344      6.1745|
| 11:  2.2728 -  2.2019 0.97   1264  136 0.5386 0.5507      6.0519      6.0909|
| 12:  2.2019 -  2.1391 0.98   1236  138 0.5558 0.5365      5.9953      5.9919|
| 13:  2.1391 -  2.0830 0.99   1281  143 0.5434 0.5049      5.9076      5.8701|
| 14:  2.0830 -  2.0323 0.74    931  104 0.5685 0.5239      5.8459      5.7935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.8499  1379   152  0.65  38.31   0.76     0.68      86682.85|
|  2:  4.8499 -  3.8698  1326   150  0.63  41.19   0.83     0.68     136487.78|
|  3:  3.8698 -  3.3866  1298   142  0.51  50.94   0.77     0.61     145391.75|
|  4:  3.3866 -  3.0796  1285   145  0.39  60.34   0.75     0.48     127497.72|
|  5:  3.0796 -  2.8604  1283   142  0.31  66.83   0.69     0.36      97796.79|
|  6:  2.8604 -  2.6927  1292   141  0.26  70.24   0.68     0.30      84444.93|
|  7:  2.6927 -  2.5585  1273   143  0.22  73.40   0.67     0.25      76203.79|
|  8:  2.5585 -  2.4476  1258   138  0.17  77.12   0.70     0.20      71613.82|
|  9:  2.4476 -  2.3537  1264   141  0.13  80.42   0.68     0.15      67214.60|
| 10:  2.3537 -  2.2728  1260   144  0.10  82.28   0.68     0.12      61328.26|
| 11:  2.2728 -  2.2019  1264   136  0.15  78.58   0.72     0.19      56240.61|
| 12:  2.2019 -  2.1391  1236   138  0.17  77.51   0.69     0.20      50272.96|
| 13:  2.1391 -  2.0830  1281   143  0.14  79.62   0.69     0.16      42891.35|
| 14:  2.0830 -  2.0323   931   104  0.15  78.83   0.67     0.16      35261.75|
|alpha:            min =        0.12 max =            0.68 mean =         0.33|
|beta:             min =    35261.75 max =       145391.75 mean =     82698.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.29|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.72|
|phase err.(test): min =        0.00 max =           89.94 mean =        67.61|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 27.069298             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.058   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.052327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.383   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      157 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      670 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1467 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2551 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3801 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4914 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6399 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7495 |
|-----------------------------------------------------------------------------|
|-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 |       55.010 |
| 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 |       1.634 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    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 = 12.637)------------------------------------------|
|    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: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5225   r_free= 0.5140   ksol= 0.00   Bsol= 0.00   scale= 0.718    |
|                                                                             |
| 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:   1.02 A                  |
| x-ray target function (ml) for work reflections: 6.309490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5134   r_free= 0.5028   ksol= 0.26   Bsol= 20.00   scale= 0.917   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,7.40,9.64,0.00,0.00,0.00); trace/3= 8.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.12 A                  |
| x-ray target function (ml) for work reflections: 5.998115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.257113             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.572   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.391859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.783   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5134      final r-factor (work) = 0.4569          |
| start r-factor (free) = 0.5028      final r-factor (free) = 0.4739          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 128.3550 = 23.26 * 0.50 * 6.3074 + 1.00 * 55.0096                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 69.3812 = 23.26 * 0.50 * 5.9519 + 1.00 * 0.1692                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4569      final r-factor (work) = 0.4175          |
| start r-factor (free) = 0.4739      final r-factor (free) = 0.4628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.2506 = 2.39 * 1.00 * 5.9519 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.8966 = 2.39 * 1.00 * 6.2155 + 1.00 * 0.0300                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    140.14  19.16    None  None   None       |
|    all(noH): 2823   0      0.00    140.14  19.16    None  None   None       |
|    Sol.    : 438    0      0.00    140.14  30.53    None  None   None       |
|    Mac.    : 2385   0      0.00    112.54  17.08    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 -  14.014: 1366   |   5:    70.068 -  84.082:   28        |
|      1:    14.014 -  28.027:  797   |   6:    84.082 -  98.096:   15        |
|      2:    28.027 -  42.041:  372   |   7:    98.096 - 112.109:    4        |
|      3:    42.041 -  56.055:  156   |   8:   112.109 - 126.123:    2        |
|      4:    56.055 -  70.068:   81   |   9:   126.123 - 140.137:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4175 r_free = 0.4628             target_work(ml) = 6.204         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4163 r_free = 0.4645             target_work(ml) = 6.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4163   r_free= 0.4645   ksol= 0.26   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.36,7.40,9.64,0.00,0.00,0.00); trace/3= 8.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.204471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4158   r_free= 0.4633   ksol= 0.33   Bsol= 80.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.09,5.28,7.27,0.00,0.00,0.00); trace/3= 5.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.206449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.296606             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.226  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.799111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.401  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4158      final r-factor (work) = 0.3477          |
| start r-factor (free) = 0.4633      final r-factor (free) = 0.4112          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.6820 = 15.30 * 0.50 * 6.2122 + 1.00 * 0.1692                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.1042 = 15.30 * 0.50 * 6.1427 + 1.00 * 0.1233                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3477      final r-factor (work) = 0.3255          |
| start r-factor (free) = 0.4112      final r-factor (free) = 0.3889          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9473 = 0.80 * 1.00 * 6.1427 + 1.00 * 0.0387                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8778 = 0.80 * 1.00 * 6.0559 + 1.00 * 0.0384                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    147.48  16.57    None  None   None       |
|    all(noH): 2823   0      0.00    147.48  16.57    None  None   None       |
|    Sol.    : 438    0      0.00    147.48  34.23    None  None   None       |
|    Mac.    : 2385   0      0.00    106.80  13.33    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 -  14.748: 1659   |   5:    73.738 -  88.486:   17        |
|      1:    14.748 -  29.495:  730   |   6:    88.486 - 103.234:    4        |
|      2:    29.495 -  44.243:  273   |   7:   103.234 - 117.981:    2        |
|      3:    44.243 -  58.991:   90   |   8:   117.981 - 132.729:    0        |
|      4:    58.991 -  73.738:   47   |   9:   132.729 - 147.477:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3255 r_free = 0.3889             target_work(ml) = 6.036         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3254 r_free = 0.3883             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3254   r_free= 0.3883   ksol= 0.33   Bsol= 80.00   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.09,5.28,7.27,0.00,0.00,0.00); trace/3= 5.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.035368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3234   r_free= 0.3856   ksol= 0.33   Bsol= 80.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.04,4.23,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.034218                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.901170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.541   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.841500              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.749   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3234      final r-factor (work) = 0.2510          |
| start r-factor (free) = 0.3856      final r-factor (free) = 0.3158          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.0399 = 7.90 * 0.50 * 6.0539 + 1.00 * 0.1233                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5813 = 7.90 * 0.50 * 5.9445 + 1.00 * 0.0969                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2510      final r-factor (work) = 0.2258          |
| start r-factor (free) = 0.3158      final r-factor (free) = 0.2949          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9691 = 1.84 * 1.00 * 5.9445 + 1.00 * 0.0223                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6894 = 1.84 * 1.00 * 5.7904 + 1.00 * 0.0264                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    151.73  17.30    None  None   None       |
|    all(noH): 2823   0      0.00    151.73  17.30    None  None   None       |
|    Sol.    : 438    0      0.00    151.73  44.60    None  None   None       |
|    Mac.    : 2385   0      0.00    125.43  12.29    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 -  15.173: 1803   |   5:    75.864 -  91.037:   36        |
|      1:    15.173 -  30.346:  534   |   6:    91.037 - 106.210:   15        |
|      2:    30.346 -  45.519:  222   |   7:   106.210 - 121.383:    1        |
|      3:    45.519 -  60.692:  126   |   8:   121.383 - 136.556:    1        |
|      4:    60.692 -  75.864:   84   |   9:   136.556 - 151.729:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2258 r_free = 0.2949             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2256 r_free = 0.2945             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2256   r_free= 0.2945   ksol= 0.33   Bsol= 80.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.04,4.23,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.763226                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2257   r_free= 0.2945   ksol= 0.34   Bsol= 96.33   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.73,1.98,3.08,0.00,0.00,0.00); trace/3= 2.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.762299                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.071695              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.825   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.039   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2257      final r-factor (work) = 0.1760          |
| start r-factor (free) = 0.2945      final r-factor (free) = 0.2349          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.4699 = 8.07 * 0.50 * 5.7913 + 1.00 * 0.0969                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0036 = 8.07 * 0.50 * 5.6731 + 1.00 * 0.1077                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1760      final r-factor (work) = 0.1634          |
| start r-factor (free) = 0.2349      final r-factor (free) = 0.2223          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3207 = 0.58 * 1.00 * 5.6731 + 1.00 * 0.0242                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2313 = 0.58 * 1.00 * 5.5069 + 1.00 * 0.0313                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    151.01  16.88    None  None   None       |
|    all(noH): 2823   0      0.00    151.01  16.88    None  None   None       |
|    Sol.    : 438    0      1.44    151.01  44.96    None  None   None       |
|    Mac.    : 2385   0      0.00    125.13  11.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  15.101: 1894   |   5:    75.505 -  90.606:   33        |
|      1:    15.101 -  30.202:  464   |   6:    90.606 - 105.707:   18        |
|      2:    30.202 -  45.303:  206   |   7:   105.707 - 120.808:    1        |
|      3:    45.303 -  60.404:  121   |   8:   120.808 - 135.909:    1        |
|      4:    60.404 -  75.505:   84   |   9:   135.909 - 151.010:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1634 r_free = 0.2223             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1631 r_free = 0.2226             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1631   r_free= 0.2226   ksol= 0.34   Bsol= 96.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.73,1.98,3.08,0.00,0.00,0.00); trace/3= 2.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.479054                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1635   r_free= 0.2227   ksol= 0.34   Bsol= 91.49   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.56,2.70,0.00,0.00,0.00); trace/3= 1.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.480454                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.978917              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.840  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.141651              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.181   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1635      final r-factor (work) = 0.1507          |
| start r-factor (free) = 0.2227      final r-factor (free) = 0.2096          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0637 = 3.98 * 0.50 * 5.5070 + 1.00 * 0.1077                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9332 = 3.98 * 0.50 * 5.4514 + 1.00 * 0.0878                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1507      final r-factor (work) = 0.1480          |
| start r-factor (free) = 0.2096      final r-factor (free) = 0.1965          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7981 = 0.14 * 1.00 * 5.4514 + 1.00 * 0.0259                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7766 = 0.14 * 1.00 * 5.4128 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    138.54  14.71    None  None   None       |
|    all(noH): 2823   0      0.00    138.54  14.71    None  None   None       |
|    Sol.    : 438    0      2.75    138.54  38.58    None  None   None       |
|    Mac.    : 2385   0      0.00    113.60  10.33    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 -  13.854: 1957   |   5:    69.270 -  83.124:   22        |
|      1:    13.854 -  27.708:  463   |   6:    83.124 -  96.978:    6        |
|      2:    27.708 -  41.562:  189   |   7:    96.978 - 110.832:    1        |
|      3:    41.562 -  55.416:  125   |   8:   110.832 - 124.686:    1        |
|      4:    55.416 -  69.270:   58   |   9:   124.686 - 138.540:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1480 r_free = 0.1965             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1477 r_free = 0.1962             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1477   r_free= 0.1962   ksol= 0.34   Bsol= 91.49   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.56,2.70,0.00,0.00,0.00); trace/3= 1.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.378914                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.8499 0.99   1379  152 0.1155 0.1508       5.529      5.6866|
|  2:  4.8499 -  3.8698 0.99   1326  150 0.1019 0.1379      5.6132      5.8423|
|  3:  3.8698 -  3.3866 0.99   1298  142 0.1345 0.1730       5.689      5.9767|
|  4:  3.3866 -  3.0796 0.99   1285  145 0.1587 0.1944      5.6865      5.8372|
|  5:  3.0796 -  2.8604 0.99   1283  142 0.1799 0.2326      5.6167      5.8197|
|  6:  2.8604 -  2.6927 0.99   1292  141 0.1726 0.2764      5.5048      5.7574|
|  7:  2.6927 -  2.5585 0.99   1273  143 0.1733 0.1919      5.4366      5.5565|
|  8:  2.5585 -  2.4476 0.98   1258  138 0.1712 0.2113      5.3696      5.5765|
|  9:  2.4476 -  2.3537 0.98   1264  141 0.1614 0.2261       5.286      5.4962|
| 10:  2.3537 -  2.2728 1.00   1260  144 0.1559 0.2045      5.2093      5.4154|
| 11:  2.2728 -  2.2019 0.97   1264  136 0.1549 0.2019      5.1666       5.358|
| 12:  2.2019 -  2.1391 0.98   1236  138 0.1447 0.2218      5.0724      5.4289|
| 13:  2.1391 -  2.0830 0.99   1281  143 0.1557 0.2152      5.0341      5.2425|
| 14:  2.0830 -  2.0323 0.74    931  104 0.1496 0.2158      4.9226      5.1729|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.8499  1379   152  0.92  11.73   0.96     0.93      10314.86|
|  2:  4.8499 -  3.8698  1326   150  0.94  10.57   1.00     0.97      13109.27|
|  3:  3.8698 -  3.3866  1298   142  0.91  14.86   1.01     1.00      16013.05|
|  4:  3.3866 -  3.0796  1285   145  0.88  18.11   1.00     0.97      16451.11|
|  5:  3.0796 -  2.8604  1283   142  0.85  21.65   1.00     0.98      14983.66|
|  6:  2.8604 -  2.6927  1292   141  0.85  21.77   0.97     0.93      12340.45|
|  7:  2.6927 -  2.5585  1273   143  0.85  21.87   1.00     0.96      10980.31|
|  8:  2.5585 -  2.4476  1258   138  0.86  20.78   1.00     0.95       9064.90|
|  9:  2.4476 -  2.3537  1264   141  0.86  20.60   1.01     0.95       8137.19|
| 10:  2.3537 -  2.2728  1260   144  0.87  19.06   1.02     0.96       6317.42|
| 11:  2.2728 -  2.2019  1264   136  0.87  19.84   1.01     0.94       6154.99|
| 12:  2.2019 -  2.1391  1236   138  0.88  18.92   1.02     1.00       5658.74|
| 13:  2.1391 -  2.0830  1281   143  0.86  20.72   1.00     0.98       5258.55|
| 14:  2.0830 -  2.0323   931   104  0.88  18.65   0.97     0.93       3906.74|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     3906.74 max =        16451.11 mean =     10066.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.44|
|phase err.(test): min =        0.00 max =           89.25 mean =        17.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.1954   ksol= 0.33   Bsol= 75.71   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.39,0.95,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.376537                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.1954   ksol= 0.33   Bsol= 75.71   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.39,0.95,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.376537                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.8499 0.99   1379  152 0.1126 0.1445      5.4991      5.6552|
|  2:  4.8499 -  3.8698 0.99   1326  150 0.1018 0.1359      5.6037      5.8308|
|  3:  3.8698 -  3.3866 0.99   1298  142 0.1348 0.1724      5.6881      5.9723|
|  4:  3.3866 -  3.0796 0.99   1285  145 0.1595 0.1950      5.6893      5.8412|
|  5:  3.0796 -  2.8604 0.99   1283  142 0.1805 0.2327      5.6201      5.8221|
|  6:  2.8604 -  2.6927 0.99   1292  141 0.1729 0.2764      5.5067       5.758|
|  7:  2.6927 -  2.5585 0.99   1273  143 0.1735 0.1924      5.4375      5.5572|
|  8:  2.5585 -  2.4476 0.98   1258  138 0.1713 0.2115      5.3701       5.577|
|  9:  2.4476 -  2.3537 0.98   1264  141 0.1616 0.2259      5.2864      5.4955|
| 10:  2.3537 -  2.2728 1.00   1260  144 0.1558 0.2047      5.2094      5.4168|
| 11:  2.2728 -  2.2019 0.97   1264  136 0.1549 0.2019       5.167      5.3589|
| 12:  2.2019 -  2.1391 0.98   1236  138 0.1446 0.2226      5.0726      5.4305|
| 13:  2.1391 -  2.0830 0.99   1281  143 0.1558 0.2150      5.0343      5.2424|
| 14:  2.0830 -  2.0323 0.74    931  104 0.1496 0.2153      4.9221      5.1717|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.8499  1379   152  0.93  11.08   0.95     0.93       9460.22|
|  2:  4.8499 -  3.8698  1326   150  0.94  10.21   0.99     0.97      12527.77|
|  3:  3.8698 -  3.3866  1298   142  0.91  14.78   1.00     0.99      15868.25|
|  4:  3.3866 -  3.0796  1285   145  0.88  18.12   0.99     0.96      16481.70|
|  5:  3.0796 -  2.8604  1283   142  0.85  21.70   0.98     0.96      15061.35|
|  6:  2.8604 -  2.6927  1292   141  0.85  21.80   0.96     0.91      12394.01|
|  7:  2.6927 -  2.5585  1273   143  0.85  21.88   0.98     0.94      10999.13|
|  8:  2.5585 -  2.4476  1258   138  0.86  20.78   0.97     0.93       9071.89|
|  9:  2.4476 -  2.3537  1264   141  0.86  20.59   0.99     0.93       8139.60|
| 10:  2.3537 -  2.2728  1260   144  0.87  19.07   0.99     0.94       6324.44|
| 11:  2.2728 -  2.2019  1264   136  0.87  19.87   0.98     0.92       6170.08|
| 12:  2.2019 -  2.1391  1236   138  0.88  18.93   0.99     0.97       5662.38|
| 13:  2.1391 -  2.0830  1281   143  0.86  20.73   0.97     0.95       5261.27|
| 14:  2.0830 -  2.0323   931   104  0.88  18.64   0.94     0.90       3900.07|
|alpha:            min =        0.90 max =            0.99 mean =         0.94|
|beta:             min =     3900.07 max =        16481.70 mean =      9960.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        18.36|
|phase err.(test): min =        0.00 max =           89.30 mean =        17.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.32    139.86  16.03    None  None   None       |
|    all(noH): 2823   0      1.32    139.86  16.03    None  None   None       |
|    Sol.    : 438    0      4.07    139.86  39.90    None  None   None       |
|    Mac.    : 2385   0      1.32    114.92  11.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.320 -  15.174: 1957   |   5:    70.590 -  84.444:   22        |
|      1:    15.174 -  29.028:  463   |   6:    84.444 -  98.298:    6        |
|      2:    29.028 -  42.882:  189   |   7:    98.298 - 112.152:    1        |
|      3:    42.882 -  56.736:  125   |   8:   112.152 - 126.006:    1        |
|      4:    56.736 -  70.590:   58   |   9:   126.006 - 139.860:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.514 - 5.836
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 348
   mapped sites are within: 0.704 - 5.836

peak=    8.075 closest distance to " O   HOH Z 103 " =    1.032
peak=    7.945 closest distance to " CG2 VAL A 230 " =    1.451
peak=    6.370 closest distance to " CD1AILE A 234 " =    1.451
peak=    6.191 closest distance to " O   HOH Z  70 " =    1.274
peak=    6.123 closest distance to " CG2 VAL A 296 " =    1.259
peak=    5.880 closest distance to " NH1BARG A 275 " =    1.373
peak=    5.726 closest distance to " O   HOH Z  41 " =    1.128
peak=    5.517 closest distance to " O   HOH Z 117 " =    1.490
peak=    5.496 closest distance to " O   HOH Z 102 " =    1.573
peak=    5.265 closest distance to " CG  ARG A 138 " =    1.334
peak=    5.081 closest distance to " O   HOH Z 120 " =    1.231
peak=    5.078 closest distance to " NH1 ARG A  56 " =    1.201
peak=    5.046 closest distance to " O   HOH Z 425 " =    1.964
peak=    4.993 closest distance to " O   HOH Z 411 " =    3.673
peak=    4.916 closest distance to " O   HOH Z 210 " =    1.451
peak=    4.912 closest distance to " CA  VAL A 230 " =    1.132
peak=    4.894 closest distance to " NH1 ARG A 138 " =    1.036
peak=    4.868 closest distance to " CB  SER A  63 " =    1.324
peak=    4.789 closest distance to " O   PRO A 198 " =    1.539
peak=    4.737 closest distance to " CD  ARG A 138 " =    1.137
peak=    4.711 closest distance to " O   HOH Z 250 " =    1.563
peak=    4.670 closest distance to " CG  PRO A 280 " =    1.035
peak=    4.625 closest distance to " NH1AARG A 145 " =    1.305
peak=    4.605 closest distance to " CG  LEU A   5 " =    1.409
peak=    4.592 closest distance to " CB  ASP A 124 " =    0.821
peak=    4.591 closest distance to " CG  PRO A 243 " =    1.181
peak=    4.556 closest distance to " CG  PRO A  54 " =    1.514
peak=    4.524 closest distance to " OD1 ASP A 107 " =    1.043
peak=    4.520 closest distance to " O   HOH Z 182 " =    1.432
peak=    4.481 closest distance to " NH2AARG A 145 " =    0.956
peak=    4.478 closest distance to " CG AARG A 275 " =    1.378
peak=    4.345 closest distance to " O   HOH Z  49 " =    1.833
peak=    4.337 closest distance to " O   HOH Z 261 " =    1.801
peak=    4.334 closest distance to " CZ  PHE A 218 " =    1.230
peak=    4.303 closest distance to " O   HOH Z 130 " =    1.090
peak=    4.294 closest distance to " O   HOH Z  56 " =    1.819
peak=    4.276 closest distance to " CD2 LEU A 228 " =    1.494
peak=    4.272 closest distance to " CB  GLN A 223 " =    1.523
peak=    4.237 closest distance to " O   HOH Z   4 " =    1.922
peak=    4.138 closest distance to " OG  SER A  97 " =    1.213
peak=    4.133 closest distance to " CG  GLN A  55 " =    0.765
peak=    4.106 closest distance to " O   HOH Z  67 " =    1.266
peak=    4.096 closest distance to " CB  ALA A 248 " =    1.165
peak=    4.081 closest distance to " N   SER A 164 " =    0.967
peak=    4.045 closest distance to " O   HOH Z  54 " =    1.567
peak=    4.038 closest distance to " O   HOH Z 213 " =    1.784
peak=    4.017 closest distance to " CG1 VAL A 153 " =    1.141
peak=    4.016 closest distance to " CG  LEU A 228 " =    1.372
peak=    3.991 closest distance to " CD  GLN A  88 " =    1.070
peak=    3.975 closest distance to " CD2 LEU A   5 " =    1.163
peak=    3.970 closest distance to " CD1 LEU A   5 " =    1.391
peak=    3.966 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.964 closest distance to " OD1 ASN A  60 " =    1.143
peak=    3.960 closest distance to " O   HOH Z  76 " =    1.465
peak=    3.944 closest distance to " CB  VAL A 202 " =    1.430
peak=    3.928 closest distance to " CB  ASN A 148 " =    1.498
peak=    3.897 closest distance to " NH2 ARG A  56 " =    1.274
peak=    3.887 closest distance to " O   HOH Z 290 " =    1.943
peak=    3.887 closest distance to " O   HOH Z 298 " =    2.172
peak=    3.886 closest distance to " O   HOH Z  68 " =    2.115
peak=    3.883 closest distance to " O   HOH Z 369 " =    1.819
peak=    3.881 closest distance to " CA  ALA A  51 " =    0.855
peak=    3.875 closest distance to " O   HOH Z 406 " =    1.627
peak=    3.869 closest distance to " O   HOH Z 131 " =    1.442
peak=    3.860 closest distance to " O   HOH Z 126 " =    1.756
peak=    3.856 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.852 closest distance to " CB  TRP A 150 " =    1.365
peak=    3.849 closest distance to " O   HOH Z 272 " =    1.336
peak=    3.848 closest distance to " CZ3 TRP A 274 " =    4.916
peak=    3.840 closest distance to " CA  PRO A  54 " =    1.025
peak=    3.825 closest distance to " CD  LYS A 166 " =    1.517
peak=    3.818 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.816 closest distance to " CB  GLN A 183 " =    1.230
peak=    3.809 closest distance to " O   HOH Z 183 " =    1.990
peak=    3.805 closest distance to " O   ASN A 209 " =    1.463
peak=    3.779 closest distance to " CB  ARG A 190 " =    1.835
peak=    3.779 closest distance to " CG2AVAL A 121 " =    1.971
peak=    3.776 closest distance to " CB  SER A 141 " =    1.069
peak=    3.761 closest distance to " O   HOH Z 177 " =    1.292
peak=    3.758 closest distance to " CB  MET A  40 " =    0.864
peak=    3.754 closest distance to " N   SER A 271 " =    1.095
peak=    3.736 closest distance to " ND2 ASN A 249 " =    2.036
peak=    3.735 closest distance to " CD  PRO A  54 " =    0.940
peak=    3.734 closest distance to " O   TYR A 116 " =    1.253
peak=    3.726 closest distance to " CG2 VAL A 197 " =    1.116
peak=    3.725 closest distance to " C   PRO A  54 " =    0.911
peak=    3.725 closest distance to " CG2 THR A 221 " =    1.179
peak=    3.724 closest distance to " CE3 TRP A  85 " =    1.024
peak=    3.722 closest distance to " CB  ALA A  10 " =    1.330
peak=    3.714 closest distance to " O   HOH Z  91 " =    2.384
peak=    3.713 closest distance to " CB  LEU A 255 " =    1.907
peak=    3.711 closest distance to " CB  GLU A 128 " =    1.165
peak=    3.704 closest distance to " CB  GLN A  89 " =    1.092
peak=    3.703 closest distance to " O   HOH Z 144 " =    1.876
peak=    3.696 closest distance to " CD2 TRP A 179 " =    1.314
peak=    3.690 closest distance to " O   HOH Z 111 " =    1.732
peak=    3.689 closest distance to " CG2 ILE A 120 " =    1.029
peak=    3.685 closest distance to " CB  TYR A  30 " =    1.032
peak=    3.685 closest distance to " O   HOH Z 184 " =    1.957
peak=    3.678 closest distance to " O   HOH Z 324 " =    1.308
peak=    3.674 closest distance to " CA  ASN A 284 " =    0.884
peak=    3.672 closest distance to " O   HOH Z 265 " =    2.024
peak=    3.670 closest distance to " CD1 LEU A 300 " =    1.067
peak=    3.667 closest distance to " O   HOH Z 247 " =    1.693
peak=    3.663 closest distance to " O   HOH Z  27 " =    1.197
peak=    3.659 closest distance to " CA  ASP A 124 " =    0.887
peak=    3.655 closest distance to " O   HOH Z 232 " =    1.921
peak=    3.653 closest distance to " CD ALYS A 290 " =    1.143
peak=    3.649 closest distance to " O   HOH Z 146 " =    1.721
peak=    3.647 closest distance to " O   HOH Z 345 " =    3.703
peak=    3.640 closest distance to " O   HOH Z 303 " =    2.302
peak=    3.639 closest distance to " O   HOH Z 377 " =    1.761
peak=    3.638 closest distance to " O   ALA A 165 " =    1.357
peak=    3.638 closest distance to " CA  ARG A  36 " =    0.982
peak=    3.636 closest distance to " O   HOH Z 234 " =    4.028
peak=    3.617 closest distance to " O   HOH Z 281 " =    4.633
peak=    3.616 closest distance to " CB  ASN A  39 " =    0.704
peak=    3.611 closest distance to " O   HOH Z  38 " =    2.474
peak=    3.608 closest distance to " CA  GLU A 152 " =    1.018
peak=    3.608 closest distance to " O   HOH Z 107 " =    1.277
peak=    3.594 closest distance to " O   HOH Z 250 " =    1.220
peak=    3.585 closest distance to " O   HOH Z 404 " =    1.721
peak=    3.584 closest distance to " NH1 ARG A 269 " =    0.820
peak=    3.582 closest distance to " OE1 GLN A  55 " =    1.504
peak=    3.579 closest distance to " CG2BVAL A  41 " =    1.205
peak=    3.574 closest distance to " CA  GLY A 241 " =    0.738
peak=    3.572 closest distance to " CA  TYR A 116 " =    1.393
peak=    3.568 closest distance to " CB  ALA A 114 " =    0.730
peak=    3.562 closest distance to " CB  ASN A 142 " =    0.812
peak=    3.559 closest distance to " NE2 HIS A 207 " =    1.078
peak=    3.558 closest distance to " CG  GLN A  77 " =    0.829
peak=    3.555 closest distance to " CZ3 TRP A 266 " =    1.114
peak=    3.553 closest distance to " O   HOH Z 287 " =    1.928
peak=    3.543 closest distance to " ND2 ASN A  69 " =    1.241
peak=    3.543 closest distance to " CA  ALA A 295 " =    1.145
peak=    3.542 closest distance to " O   HOH Z 303 " =    1.379
peak=    3.536 closest distance to " O   HOH Z 433 " =    1.907
peak=    3.536 closest distance to " CB  ASN A 187 " =    1.171
peak=    3.527 closest distance to " O   HOH Z 402 " =    1.556
peak=    3.526 closest distance to " O   HOH Z 112 " =    1.405
peak=    3.525 closest distance to " O   HOH Z 427 " =    3.270
peak=    3.523 closest distance to " CB  ALA A 100 " =    1.634
peak=    3.522 closest distance to " O   PHE A 192 " =    1.562
peak=    3.512 closest distance to " O   HOH Z  67 " =    1.646
peak=    3.511 closest distance to " O   HOH Z  32 " =    1.080
peak=    3.507 closest distance to " O   THR A 182 " =    1.409
peak=    3.506 closest distance to " CA  CYS A 260 " =    0.989
peak=    3.504 closest distance to " O   HOH Z 199 " =    1.615
peak=    3.496 closest distance to " O   HOH Z 145 " =    1.806
peak=    3.493 closest distance to " O   HOH Z  69 " =    1.223
peak=    3.489 closest distance to " O   HOH Z 215 " =    1.487
peak=    3.487 closest distance to " O   HOH Z  80 " =    2.648
peak=    3.486 closest distance to " O   HOH Z 171 " =    4.128
peak=    3.486 closest distance to " O   HOH Z 154 " =    1.761
peak=    3.484 closest distance to " O   HOH Z 207 " =    1.615
peak=    3.483 closest distance to " CB  ASN A 215 " =    1.404
peak=    3.483 closest distance to " CB  GLU A 152 " =    1.217
peak=    3.482 closest distance to " O   HOH Z 148 " =    2.017
peak=    3.480 closest distance to " O   GLU A   2 " =    1.775
peak=    3.474 closest distance to " O   HOH Z 359 " =    1.808
peak=    3.470 closest distance to " CG  PRO A 198 " =    1.339
peak=    3.470 closest distance to " O   HOH Z 327 " =    2.203
peak=    3.468 closest distance to " O   HOH Z 298 " =    2.238
peak=    3.466 closest distance to " CB  TRP A 179 " =    1.300
peak=    3.465 closest distance to " CG2 ILE A 234 " =    1.028
peak=    3.462 closest distance to " CB  GLN A  55 " =    0.937
peak=    3.462 closest distance to " CA  SER A  87 " =    0.796
peak=    3.459 closest distance to " NZ  LYS A  76 " =    1.107
peak=    3.457 closest distance to " N   CYS A 260 " =    0.816
peak=    3.450 closest distance to " CA  ALA A  21 " =    1.332
peak=    3.450 closest distance to " CG1 ILE A 120 " =    1.110
peak=    3.446 closest distance to " CB  THR A  31 " =    1.404
peak=    3.445 closest distance to " O   HOH Z 124 " =    2.477
peak=    3.442 closest distance to " O   HOH Z 273 " =    1.411
peak=    3.441 closest distance to " CE  LYS A  76 " =    1.016
peak=    3.440 closest distance to " CG1 VAL A 296 " =    1.206
peak=    3.439 closest distance to " O   HOH Z   5 " =    1.824
peak=    3.438 closest distance to " N   PHE A 130 " =    1.198
peak=    3.433 closest distance to " O   HOH Z  59 " =    2.228
peak=    3.432 closest distance to " CB  ALA A 291 " =    1.016
peak=    3.426 closest distance to " O   GLY A 211 " =    1.019
peak=    3.424 closest distance to " O   HOH Z  21 " =    1.705
peak=    3.423 closest distance to " CB  ALA A 161 " =    0.886
peak=    3.423 closest distance to " O   ASP A 124 " =    1.013
peak=    3.419 closest distance to " O   HOH Z 172 " =    5.836
peak=    3.412 closest distance to " CB  VAL A 257 " =    1.005
peak=    3.410 closest distance to " CH2 TRP A  70 " =    0.996
peak=    3.409 closest distance to " O   HOH Z 356 " =    1.826
peak=    3.406 closest distance to " O   HOH Z  96 " =    2.070
peak=    3.401 closest distance to " O   HOH Z  57 " =    1.932
peak=    3.398 closest distance to " CA  MET A 105 " =    0.917
peak=    3.398 closest distance to " O   HOH Z 261 " =    1.961
peak=    3.397 closest distance to " CG  ASP A 231 " =    1.169
peak=    3.396 closest distance to " O   HOH Z 258 " =    2.198
peak=    3.380 closest distance to " CA  ALA A 154 " =    1.038
peak=    3.375 closest distance to " OD1 ASN A 301 " =    1.138
peak=    3.372 closest distance to " N   ASN A  39 " =    1.174
peak=    3.371 closest distance to " CG  GLU A  37 " =    1.041
peak=    3.369 closest distance to " CA  VAL A 153 " =    0.742
peak=    3.365 closest distance to " CB  ALA A 137 " =    0.960
peak=    3.365 closest distance to " O   HOH Z 214 " =    2.024
peak=    3.363 closest distance to " CB  SER A 216 " =    0.910
peak=    3.362 closest distance to " CB  ALA A 104 " =    0.857
peak=    3.357 closest distance to " CA  ASP A 191 " =    0.986
peak=    3.357 closest distance to " CA  LEU A 282 " =    0.813
peak=    3.356 closest distance to " CA  THR A 294 " =    1.605
peak=    3.356 closest distance to " CB  GLU A  46 " =    0.891
peak=    3.355 closest distance to " O   HOH Z 393 " =    3.900
peak=    3.353 closest distance to " O   HOH Z 238 " =    0.754
peak=    3.347 closest distance to " O   HOH Z   9 " =    1.356
peak=    3.347 closest distance to " CB  GLN A  88 " =    1.279
peak=    3.344 closest distance to " CG2 THR A  82 " =    0.826
peak=    3.341 closest distance to " CG1 ILE A 151 " =    1.764
peak=    3.335 closest distance to " CD  ARG A  56 " =    0.933
peak=    3.329 closest distance to " CD2 LEU A 237 " =    0.865
peak=    3.324 closest distance to " O   HOH Z 128 " =    1.521
peak=    3.324 closest distance to " N   VAL A 126 " =    1.662
peak=    3.321 closest distance to " CG  LYS A  76 " =    1.186
peak=    3.315 closest distance to " O   THR A 220 " =    1.330
peak=    3.315 closest distance to " CD1 ILE A 239 " =    1.243
peak=    3.312 closest distance to " CB  VAL A 265 " =    1.361
peak=    3.310 closest distance to " O   HOH Z 343 " =    2.569
peak=    3.310 closest distance to " CA  GLY A 147 " =    0.849
peak=    3.309 closest distance to " O   HOH Z 188 " =    3.382
peak=    3.308 closest distance to " NH1BARG A 102 " =    1.128
peak=    3.307 closest distance to " CA  ARG A 102 " =    1.175
peak=    3.306 closest distance to " O   HOH Z 390 " =    1.126
peak=    3.306 closest distance to " CB  TRP A  92 " =    0.819
peak=    3.305 closest distance to " O   GLY A  91 " =    1.183
peak=    3.305 closest distance to " O   GLY A  98 " =    1.518
peak=    3.303 closest distance to " CB  GLU A 277 " =    3.861
peak=    3.302 closest distance to " CG1 ILE A  49 " =    1.797
peak=    3.302 closest distance to " O   HOH Z   4 " =    1.908
peak=    3.301 closest distance to " CB  PRO A 243 " =    1.306
peak=    3.301 closest distance to " O   ASN A 284 " =    1.778
peak=    3.300 closest distance to " OD1 ASN A 217 " =    1.514
peak=    3.298 closest distance to " O   HOH Z 325 " =    2.243
peak=    3.297 closest distance to " CB  ALA A 248 " =    1.291
peak=    3.296 closest distance to " CA  ALA A 184 " =    1.075
peak=    3.296 closest distance to " CB  ARG A 275 " =    1.063
peak=    3.294 closest distance to " O   HOH Z 258 " =    1.932
peak=    3.294 closest distance to " O   HOH Z  54 " =    1.077
peak=    3.290 closest distance to " O   ASP A 200 " =    1.749
peak=    3.287 closest distance to " CG2 VAL A 296 " =    1.691
peak=    3.287 closest distance to " O   HOH Z 407 " =    2.447
peak=    3.287 closest distance to " NE2 GLN A  11 " =    1.068
peak=    3.285 closest distance to " CG  MET A 188 " =    0.855
peak=    3.282 closest distance to " CB  PHE A  61 " =    0.727
peak=    3.281 closest distance to " CG  PRO A 213 " =    1.341
peak=    3.280 closest distance to " O   HOH Z 155 " =    3.259
peak=    3.278 closest distance to " O   HOH Z  47 " =    1.625
peak=    3.277 closest distance to " O   HOH Z 417 " =    3.083
peak=    3.272 closest distance to " O   THR A 251 " =    1.233
peak=    3.272 closest distance to " O   HOH Z 186 " =    1.946
peak=    3.266 closest distance to " CB  ALA A 242 " =    0.771
peak=    3.265 closest distance to " OG  SER A 245 " =    1.726
peak=    3.261 closest distance to " C   GLN A  58 " =    1.205
peak=    3.261 closest distance to " O   GLN A 103 " =    1.464
peak=    3.260 closest distance to " O   HOH Z 193 " =    1.886
peak=    3.257 closest distance to " O   HOH Z 128 " =    2.483
peak=    3.256 closest distance to " O   HOH Z  88 " =    3.516
peak=    3.254 closest distance to " CA  ARG A 139 " =    1.352
peak=    3.254 closest distance to " CB  ALA A  43 " =    1.164
peak=    3.247 closest distance to " N   LEU A  25 " =    1.404
peak=    3.243 closest distance to " O   HOH Z   1 " =    2.234
peak=    3.235 closest distance to " O   HOH Z 116 " =    1.931
peak=    3.234 closest distance to " O   THR A  52 " =    1.729
peak=    3.229 closest distance to " O   HOH Z 368 " =    2.178
peak=    3.226 closest distance to " O   HOH Z 313 " =    1.740
peak=    3.226 closest distance to " ND1 HIS A  81 " =    1.788
peak=    3.225 closest distance to " ND2 ASN A 187 " =    1.654
peak=    3.224 closest distance to " CB  ILE A 199 " =    0.805
peak=    3.224 closest distance to " O   HOH Z 133 " =    1.566
peak=    3.223 closest distance to " O   MET A 105 " =    1.564
peak=    3.222 closest distance to " CB  PHE A 283 " =    0.880
peak=    3.219 closest distance to " CB  GLU A  37 " =    0.996
peak=    3.219 closest distance to " O   HOH Z 201 " =    2.718
peak=    3.218 closest distance to " CB  GLN A 103 " =    0.959
peak=    3.218 closest distance to " CE1 TYR A  30 " =    1.020
peak=    3.214 closest distance to " CD1 LEU A 261 " =    1.204
peak=    3.212 closest distance to " CB  THR A  52 " =    1.073
peak=    3.211 closest distance to " O   HOH Z  37 " =    1.060
peak=    3.209 closest distance to " CG1 VAL A 174 " =    1.059
peak=    3.209 closest distance to " CB  MET A  47 " =    1.082
peak=    3.208 closest distance to " NH2 ARG A 138 " =    1.073
peak=    3.202 closest distance to " O   HOH Z 346 " =    1.612
peak=    3.202 closest distance to " CZ  PHE A 192 " =    1.138
peak=    3.202 closest distance to " CZ  PHE A  38 " =    1.186
peak=    3.199 closest distance to " CG  GLN A 278 " =    0.919
peak=    3.199 closest distance to " CD1 ILE A 199 " =    0.878
peak=    3.198 closest distance to " CG  PRO A  90 " =    1.366
peak=    3.190 closest distance to " O   HOH Z 437 " =    1.757
peak=    3.187 closest distance to " O   HOH Z 121 " =    4.250
peak=    3.186 closest distance to " O   HOH Z 403 " =    1.905
peak=    3.185 closest distance to " CA  ALA A 233 " =    1.701
peak=    3.183 closest distance to " CA  ALA A   9 " =    0.887
peak=    3.178 closest distance to " CB  PRO A  54 " =    1.145
peak=    3.172 closest distance to " O   HOH Z 152 " =    2.186
peak=    3.170 closest distance to " CB  ARG A 259 " =    1.821
peak=    3.161 closest distance to " O   ALA A  84 " =    1.144
peak=    3.161 closest distance to " O   HOH Z 197 " =    1.995
peak=    3.156 closest distance to " CD1 ILE A  33 " =    1.666
peak=    3.153 closest distance to " OE1 GLU A   2 " =    1.399
peak=    3.152 closest distance to " CD2 LEU A 297 " =    0.716
peak=    3.151 closest distance to " O   HOH Z  85 " =    2.113
peak=    3.149 closest distance to " NE AARG A 275 " =    1.834
peak=    3.143 closest distance to " CA  GLY A  35 " =    0.778
peak=    3.141 closest distance to " CG2 ILE A 106 " =    0.752
peak=    3.136 closest distance to " CB  ALA A   9 " =    1.896
peak=    3.133 closest distance to " OG  SER A   3 " =    1.967
peak=    3.131 closest distance to " CE1 PHE A 155 " =    0.961
peak=    3.117 closest distance to " CB  ILE A 120 " =    1.295
peak=    3.116 closest distance to " CB  MET A 105 " =    1.229
peak=    3.110 closest distance to " CA  ALA A 160 " =    1.007
peak=    3.109 closest distance to " O   HOH Z 425 " =    2.628
peak=    3.106 closest distance to " OE1 GLU A  46 " =    1.319
peak=    3.103 closest distance to " CB  ARG A  79 " =    1.638
peak=    3.100 closest distance to " O   HOH Z 188 " =    2.118
peak=    3.100 closest distance to " CB  ARG A 156 " =    1.161
peak=    3.100 closest distance to " O   ILE A  49 " =    1.112
peak=    3.098 closest distance to " O   HOH Z 379 " =    1.577
peak=    3.096 closest distance to " O   HOH Z 301 " =    1.720
peak=    3.093 closest distance to " CG2 VAL A 268 " =    1.102
peak=    3.092 closest distance to " CA  ALA A 100 " =    1.035
peak=    3.092 closest distance to " O   HOH Z 128 " =    2.096
peak=    3.081 closest distance to " O   HOH Z 146 " =    1.661
peak=    3.078 closest distance to " O   HOH Z 134 " =    2.683
peak=    3.077 closest distance to " CD1 LEU A  96 " =    0.731
peak=    3.074 closest distance to " O   HOH Z 409 " =    2.219
peak=    3.073 closest distance to " CD  ARG A  66 " =    2.248
peak=    3.073 closest distance to " CA  GLY A   6 " =    0.760
peak=    3.060 closest distance to " O   HOH Z 194 " =    2.262
peak=    3.047 closest distance to " NE  ARG A  24 " =    1.229
peak=    3.038 closest distance to " O   THR A 182 " =    1.498
peak=    3.017 closest distance to " CG2 ILE A 120 " =    1.400
peak=    3.017 closest distance to " O   HOH Z 389 " =    1.926

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 234         
Filter by distance & map next to the model:
   mapped sites are within: 0.329 - 5.289
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 234
   mapped sites are within: 0.700 - 5.289

peak=   -5.227 closest distance to " O   HOH Z 166 " =    1.126
peak=   -4.978 closest distance to " CG2 VAL A 230 " =    0.774
peak=   -4.726 closest distance to " CG1 VAL A 250 " =    2.728
peak=   -4.686 closest distance to " O   HOH Z 103 " =    0.923
peak=   -4.611 closest distance to " CD  ARG A 138 " =    1.200
peak=   -4.579 closest distance to " CD  GLN A  55 " =    0.886
peak=   -4.563 closest distance to " O   HOH Z 255 " =    0.882
peak=   -4.539 closest distance to " O   HOH Z   5 " =    1.549
peak=   -4.522 closest distance to " O   HOH Z 216 " =    1.115
peak=   -4.316 closest distance to " O   HOH Z  44 " =    1.956
peak=   -4.306 closest distance to " OE1 GLN A  88 " =    0.993
peak=   -4.276 closest distance to " O   HOH Z 340 " =    1.072
peak=   -4.248 closest distance to " O   HOH Z  67 " =    0.911
peak=   -4.247 closest distance to " OG  SER A  63 " =    0.843
peak=   -4.229 closest distance to " O   HOH Z  82 " =    0.955
peak=   -4.212 closest distance to " O   HOH Z 103 " =    2.705
peak=   -4.201 closest distance to " O   HOH Z 210 " =    0.723
peak=   -4.141 closest distance to " O   PRO A 198 " =    1.391
peak=   -4.097 closest distance to " O   HOH Z 103 " =    1.190
peak=   -4.063 closest distance to " O   HOH Z  92 " =    0.915
peak=   -4.038 closest distance to " CZ  ARG A 259 " =    0.832
peak=   -4.033 closest distance to " O   GLY A 211 " =    1.446
peak=   -4.005 closest distance to " O   HOH Z 155 " =    1.545
peak=   -3.999 closest distance to " CB  ALA A 291 " =    2.489
peak=   -3.994 closest distance to " O   HOH Z 177 " =    1.231
peak=   -3.965 closest distance to " CA  SER A 271 " =    2.294
peak=   -3.963 closest distance to " CE3 TRP A  70 " =    1.834
peak=   -3.960 closest distance to " CD  GLN A  58 " =    0.787
peak=   -3.907 closest distance to " N   ARG A 275 " =    1.448
peak=   -3.891 closest distance to " O   HOH Z  19 " =    1.762
peak=   -3.876 closest distance to " C   ALA A 158 " =    1.426
peak=   -3.848 closest distance to " CG1 VAL A 232 " =    2.232
peak=   -3.843 closest distance to " CD2 TYR A 293 " =    2.010
peak=   -3.833 closest distance to " OG1 THR A  82 " =    1.409
peak=   -3.830 closest distance to " O   HOH Z 198 " =    0.902
peak=   -3.795 closest distance to " CD2 PHE A  61 " =    2.165
peak=   -3.786 closest distance to " C   PRO A  54 " =    1.072
peak=   -3.773 closest distance to " OG BSER A 164 " =    1.192
peak=   -3.767 closest distance to " CA  GLU A 277 " =    1.254
peak=   -3.759 closest distance to " OG  SER A  97 " =    2.154
peak=   -3.751 closest distance to " O   HOH Z 250 " =    0.819
peak=   -3.724 closest distance to " CD  ARG A  14 " =    3.208
peak=   -3.722 closest distance to " CG  ARG A 269 " =    2.427
peak=   -3.699 closest distance to " N   SER A 212 " =    2.042
peak=   -3.696 closest distance to " CG  LEU A   5 " =    0.795
peak=   -3.693 closest distance to " CB  PRO A 243 " =    2.929
peak=   -3.682 closest distance to " O   GLY A 203 " =    2.583
peak=   -3.678 closest distance to " OE1 GLN A 278 " =    0.778
peak=   -3.650 closest distance to " O   HOH Z 109 " =    1.374
peak=   -3.636 closest distance to " O   HOH Z 120 " =    0.990
peak=   -3.635 closest distance to " O   HOH Z 113 " =    2.105
peak=   -3.629 closest distance to " NH2 ARG A 156 " =    0.925
peak=   -3.627 closest distance to " O   HOH Z  42 " =    0.957
peak=   -3.625 closest distance to " CG2 VAL A 230 " =    2.807
peak=   -3.612 closest distance to " O   HOH Z 183 " =    1.493
peak=   -3.610 closest distance to " O   HOH Z  17 " =    1.162
peak=   -3.605 closest distance to " NH1 ARG A  56 " =    1.179
peak=   -3.603 closest distance to " CE1 PHE A  59 " =    2.059
peak=   -3.600 closest distance to " O   HOH Z 379 " =    0.867
peak=   -3.596 closest distance to " O   HOH Z  37 " =    1.181
peak=   -3.594 closest distance to " O   HOH Z  19 " =    2.102
peak=   -3.593 closest distance to " CG  ASN A  45 " =    0.786
peak=   -3.583 closest distance to " CG1 VAL A 112 " =    2.704
peak=   -3.583 closest distance to " O   HOH Z 207 " =    0.973
peak=   -3.574 closest distance to " O   GLN A  73 " =    0.965
peak=   -3.565 closest distance to " CD2 LEU A 167 " =    1.924
peak=   -3.562 closest distance to " CD  GLN A  11 " =    0.792
peak=   -3.561 closest distance to " O   HOH Z 411 " =    5.289
peak=   -3.547 closest distance to " O   HOH Z   5 " =    0.874
peak=   -3.544 closest distance to " O   HOH Z 198 " =    1.774
peak=   -3.539 closest distance to " NE2 GLN A  55 " =    2.396
peak=   -3.533 closest distance to " O   HOH Z 214 " =    0.801
peak=   -3.532 closest distance to " OG1 THR A  82 " =    1.907
peak=   -3.531 closest distance to " O   VAL A  67 " =    2.793
peak=   -3.528 closest distance to " CG  TRP A 266 " =    1.747
peak=   -3.528 closest distance to " O   HOH Z 111 " =    1.703
peak=   -3.528 closest distance to " O   SER A 164 " =    1.784
peak=   -3.515 closest distance to " CZ2 TRP A  92 " =    2.762
peak=   -3.515 closest distance to " N   THR A  18 " =    1.291
peak=   -3.511 closest distance to " CG  ASP A 231 " =    0.734
peak=   -3.507 closest distance to " O   HOH Z  93 " =    2.315
peak=   -3.500 closest distance to " O   HOH Z 394 " =    1.612
peak=   -3.496 closest distance to " O   HOH Z 102 " =    1.408
peak=   -3.493 closest distance to " OE1 GLN A  88 " =    0.893
peak=   -3.480 closest distance to " CA  GLY A 241 " =    3.193
peak=   -3.475 closest distance to " OE1 GLN A 278 " =    0.987
peak=   -3.473 closest distance to " O   HOH Z 114 " =    1.445
peak=   -3.467 closest distance to " O   HOH Z 100 " =    1.354
peak=   -3.458 closest distance to " CH2 TRP A 150 " =    1.156
peak=   -3.448 closest distance to " NH2 ARG A  79 " =    1.768
peak=   -3.448 closest distance to " O   HOH Z 341 " =    0.830
peak=   -3.447 closest distance to " CG2 VAL A 189 " =    2.215
peak=   -3.446 closest distance to " O   HOH Z 377 " =    0.791
peak=   -3.446 closest distance to " CG  LEU A 281 " =    1.829
peak=   -3.443 closest distance to " CG1 VAL A 296 " =    1.316
peak=   -3.443 closest distance to " CA  ASP A 298 " =    1.171
peak=   -3.430 closest distance to " N   ILE A 120 " =    1.027
peak=   -3.425 closest distance to " O   HOH Z 435 " =    1.694
peak=   -3.425 closest distance to " CA  GLY A  91 " =    2.336
peak=   -3.419 closest distance to " NE2 HIS A  86 " =    0.860
peak=   -3.416 closest distance to " O   HOH Z 351 " =    1.809
peak=   -3.412 closest distance to " O   HOH Z  58 " =    0.719
peak=   -3.410 closest distance to " CG  ARG A 138 " =    0.887
peak=   -3.410 closest distance to " CG  ASP A 298 " =    0.753
peak=   -3.405 closest distance to " O   HOH Z 414 " =    1.036
peak=   -3.403 closest distance to " O   HOH Z 136 " =    1.087
peak=   -3.402 closest distance to " O   SER A 141 " =    1.872
peak=   -3.399 closest distance to " O   HOH Z 133 " =    1.070
peak=   -3.397 closest distance to " CB  PHE A 130 " =    1.262
peak=   -3.397 closest distance to " O   HOH Z 120 " =    4.637
peak=   -3.395 closest distance to " CA  VAL A 121 " =    1.502
peak=   -3.392 closest distance to " NH2 ARG A  79 " =    2.279
peak=   -3.387 closest distance to " O   HOH Z 182 " =    2.794
peak=   -3.384 closest distance to " CG  GLN A  58 " =    1.526
peak=   -3.384 closest distance to " O   SER A 276 " =    1.729
peak=   -3.377 closest distance to " CD1 LEU A   5 " =    2.537
peak=   -3.377 closest distance to " O   ASN A  74 " =    1.949
peak=   -3.371 closest distance to " CB  ARG A  36 " =    1.420
peak=   -3.368 closest distance to " N   PHE A  59 " =    1.923
peak=   -3.361 closest distance to " O   HOH Z 211 " =    0.922
peak=   -3.359 closest distance to " O   HOH Z 251 " =    4.862
peak=   -3.358 closest distance to " O   PRO A 163 " =    2.001
peak=   -3.347 closest distance to " O   HOH Z  64 " =    1.405
peak=   -3.335 closest distance to " CG1 VAL A 125 " =    1.828
peak=   -3.335 closest distance to " O   HOH Z 100 " =    0.789
peak=   -3.333 closest distance to " C   SER A 273 " =    1.136
peak=   -3.331 closest distance to " CH2 TRP A 179 " =    1.121
peak=   -3.326 closest distance to " O   HOH Z  60 " =    0.955
peak=   -3.326 closest distance to " CB  ARG A  79 " =    2.480
peak=   -3.325 closest distance to " OE1 GLN A 240 " =    0.791
peak=   -3.324 closest distance to " O   HOH Z  33 " =    0.841
peak=   -3.319 closest distance to " O   HOH Z 118 " =    5.003
peak=   -3.316 closest distance to " O   HOH Z 329 " =    0.919
peak=   -3.307 closest distance to " CB  ILE A 120 " =    0.986
peak=   -3.305 closest distance to " OD1 ASN A  69 " =    0.824
peak=   -3.304 closest distance to " O   HOH Z 115 " =    1.196
peak=   -3.291 closest distance to " CB  PRO A 163 " =    2.574
peak=   -3.286 closest distance to " N   SER A 134 " =    1.196
peak=   -3.277 closest distance to " CA  GLY A  75 " =    2.519
peak=   -3.276 closest distance to " O   HOH Z  70 " =    1.994
peak=   -3.275 closest distance to " CG2 THR A 251 " =    1.809
peak=   -3.272 closest distance to " CG  ARG A 259 " =    2.439
peak=   -3.271 closest distance to " C   LEU A 228 " =    2.192
peak=   -3.269 closest distance to " CG  PRO A 163 " =    2.166
peak=   -3.268 closest distance to " O   HOH Z 140 " =    1.264
peak=   -3.257 closest distance to " ND2 ASN A 249 " =    1.034
peak=   -3.257 closest distance to " CD1 LEU A 101 " =    2.704
peak=   -3.254 closest distance to " O   HOH Z 215 " =    1.026
peak=   -3.252 closest distance to " O   HOH Z 109 " =    0.746
peak=   -3.251 closest distance to " CD2 TRP A 274 " =    0.791
peak=   -3.240 closest distance to " CD1 PHE A  61 " =    1.215
peak=   -3.237 closest distance to " CA  TRP A 274 " =    0.950
peak=   -3.237 closest distance to " O   HOH Z 177 " =    1.406
peak=   -3.234 closest distance to " CA  VAL A 296 " =    0.984
peak=   -3.230 closest distance to " O   HOH Z 317 " =    1.882
peak=   -3.228 closest distance to " O   HOH Z 304 " =    1.409
peak=   -3.227 closest distance to " O   HOH Z 359 " =    3.124
peak=   -3.224 closest distance to " CG  MET A 105 " =    0.986
peak=   -3.223 closest distance to " O   VAL A 189 " =    2.426
peak=   -3.222 closest distance to " CG  ARG A 219 " =    2.411
peak=   -3.221 closest distance to " O   HOH Z   5 " =    1.976
peak=   -3.218 closest distance to " O   HOH Z 175 " =    4.407
peak=   -3.213 closest distance to " O   HOH Z 407 " =    3.619
peak=   -3.209 closest distance to " O   HOH Z 139 " =    4.559
peak=   -3.208 closest distance to " CD2 LEU A 297 " =    2.020
peak=   -3.202 closest distance to " C   MET A 188 " =    1.573
peak=   -3.199 closest distance to " O   HOH Z 118 " =    1.137
peak=   -3.198 closest distance to " CB  SER A 276 " =    1.077
peak=   -3.198 closest distance to " C   LEU A 222 " =    0.849
peak=   -3.197 closest distance to " CG  ARG A 259 " =    1.610
peak=   -3.197 closest distance to " O   HOH Z 149 " =    2.007
peak=   -3.196 closest distance to " CZ  PHE A 283 " =    2.015
peak=   -3.190 closest distance to " CG2 THR A 178 " =    2.421
peak=   -3.189 closest distance to " NH2 ARG A  66 " =    2.119
peak=   -3.186 closest distance to " CG  ARG A 219 " =    2.688
peak=   -3.179 closest distance to " O   HOH Z 154 " =    0.963
peak=   -3.178 closest distance to " CG  LEU A   5 " =    1.115
peak=   -3.178 closest distance to " OD1 ASN A 173 " =    1.253
peak=   -3.169 closest distance to " OE2 GLU A 152 " =    1.871
peak=   -3.165 closest distance to " O   HOH Z 373 " =    0.777
peak=   -3.156 closest distance to " CD2 TRP A 177 " =    1.396
peak=   -3.155 closest distance to " O   HOH Z  83 " =    1.324
peak=   -3.155 closest distance to " O   HOH Z 208 " =    0.803
peak=   -3.152 closest distance to " O   HOH Z 437 " =    1.120
peak=   -3.150 closest distance to " CG1 VAL A  78 " =    2.700
peak=   -3.149 closest distance to " O   HOH Z 396 " =    2.088
peak=   -3.149 closest distance to " NH2AARG A 275 " =    5.160
peak=   -3.149 closest distance to " O   HOH Z 371 " =    1.128
peak=   -3.144 closest distance to " OD1 ASN A 176 " =    1.389
peak=   -3.142 closest distance to " C   LEU A 143 " =    1.324
peak=   -3.141 closest distance to " C   ASP A 270 " =    1.005
peak=   -3.139 closest distance to " O   HOH Z 151 " =    0.834
peak=   -3.139 closest distance to " O   HOH Z 410 " =    1.478
peak=   -3.135 closest distance to " O   HOH Z  81 " =    1.648
peak=   -3.129 closest distance to " CD1 TYR A 247 " =    2.558
peak=   -3.125 closest distance to " CD2 TYR A 169 " =    2.350
peak=   -3.125 closest distance to " O   HOH Z 411 " =    1.513
peak=   -3.120 closest distance to " CG2 VAL A 296 " =    0.703
peak=   -3.119 closest distance to " N   ALA A 184 " =    1.553
peak=   -3.118 closest distance to " O   TYR A  30 " =    2.371
peak=   -3.115 closest distance to " O   HOH Z 171 " =    2.552
peak=   -3.115 closest distance to " O   HOH Z 152 " =    1.503
peak=   -3.113 closest distance to " O   VAL A 121 " =    0.903
peak=   -3.111 closest distance to " O   HOH Z 234 " =    4.925
peak=   -3.108 closest distance to " CD  PRO A 243 " =    1.835
peak=   -3.105 closest distance to " OE1 GLU A  44 " =    0.742
peak=   -3.104 closest distance to " O   HOH Z 329 " =    0.700
peak=   -3.089 closest distance to " CB  ARG A  79 " =    2.504
peak=   -3.083 closest distance to " CB  SER A 146 " =    2.192
peak=   -3.079 closest distance to " O   HOH Z  99 " =    5.236
peak=   -3.073 closest distance to " CA  GLU A   2 " =    2.437
peak=   -3.073 closest distance to " C   VAL A 265 " =    0.939
peak=   -3.055 closest distance to " N   GLY A 241 " =    2.417
peak=   -3.051 closest distance to " CG1BVAL A  72 " =    2.576
peak=   -3.041 closest distance to " O   HOH Z 290 " =    1.479

================= 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    :  0.5191 0.5080   6.309250e+00   6.300837e+00
   1_bss:  0.5134 0.5028   5.998115e+00   5.988951e+00
   1_xyz:  0.4569 0.4739   6.250059e+00   6.265490e+00
   1_adp:  0.4175 0.4628   6.204164e+00   6.253525e+00
   1_occ:  0.4163 0.4645   6.204471e+00   6.254839e+00
   2_bss:  0.4158 0.4633   6.206449e+00   6.255044e+00
   2_xyz:  0.3477 0.4112   6.080463e+00   6.183080e+00
   2_adp:  0.3255 0.3889   6.035853e+00   6.152211e+00
   2_occ:  0.3254 0.3883   6.035368e+00   6.152219e+00
   3_bss:  0.3234 0.3856   6.034218e+00   6.150190e+00
   3_xyz:  0.2510 0.3158   5.835239e+00   5.997544e+00
   3_adp:  0.2258 0.2949   5.764176e+00   5.954593e+00
   3_occ:  0.2256 0.2945   5.763226e+00   5.953412e+00
   4_bss:  0.2257 0.2945   5.762299e+00   5.952554e+00
   4_xyz:  0.1760 0.2349   5.536404e+00   5.756243e+00
   4_adp:  0.1634 0.2223   5.479293e+00   5.709770e+00
   4_occ:  0.1631 0.2226   5.479054e+00   5.710089e+00
   5_bss:  0.1635 0.2227   5.480454e+00   5.710616e+00
   5_xyz:  0.1507 0.2096   5.416580e+00   5.651777e+00
   5_adp:  0.1480 0.1965   5.379785e+00   5.594311e+00
   5_occ:  0.1477 0.1962   5.378914e+00   5.593887e+00
   5_bss:  0.1474 0.1954   5.376537e+00   5.591019e+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:  0.262  20.000   7.364   7.399   9.641   0.000   0.000   0.000
   1_xyz:  0.262  20.000   7.364   7.399   9.641   0.000   0.000   0.000
   1_adp:  0.262  20.000   7.364   7.399   9.641   0.000   0.000   0.000
   1_occ:  0.262  20.000   7.364   7.399   9.641   0.000   0.000   0.000
   2_bss:  0.328  80.000   5.093   5.280   7.269   0.000   0.000   0.000
   2_xyz:  0.328  80.000   5.093   5.280   7.269   0.000   0.000   0.000
   2_adp:  0.328  80.000   5.093   5.280   7.269   0.000   0.000   0.000
   2_occ:  0.328  80.000   5.093   5.280   7.269   0.000   0.000   0.000
   3_bss:  0.332  80.000   2.632   3.042   4.225   0.000   0.000   0.000
   3_xyz:  0.332  80.000   2.632   3.042   4.225   0.000   0.000   0.000
   3_adp:  0.332  80.000   2.632   3.042   4.225   0.000   0.000   0.000
   3_occ:  0.332  80.000   2.632   3.042   4.225   0.000   0.000   0.000
   4_bss:  0.344  96.326   1.734   1.977   3.081   0.000   0.000   0.000
   4_xyz:  0.344  96.326   1.734   1.977   3.081   0.000   0.000   0.000
   4_adp:  0.344  96.326   1.734   1.977   3.081   0.000   0.000   0.000
   4_occ:  0.344  96.326   1.734   1.977   3.081   0.000   0.000   0.000
   5_bss:  0.341  91.490   1.374   1.558   2.703   0.000   0.000   0.000
   5_xyz:  0.341  91.490   1.374   1.558   2.703   0.000   0.000   0.000
   5_adp:  0.341  91.490   1.374   1.558   2.703   0.000   0.000   0.000
   5_occ:  0.341  91.490   1.374   1.558   2.703   0.000   0.000   0.000
   5_bss:  0.328  75.708  -0.560  -0.388   0.948   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.709 0.2925  0.3315    82700.863
   1_bss:  67.205 0.2984  0.4218    81832.527
   1_xyz:  59.765 0.3944  0.5496    68690.049
   1_adp:  57.177 0.4281  0.6650    64982.828
   1_occ:  57.574 0.4229  0.6550    65619.340
   2_bss:  57.598 0.4227  0.6118    65836.446
   2_xyz:  46.925 0.5577  0.8164    48362.724
   2_adp:  43.267 0.6031  0.8709    42977.061
   2_occ:  43.273 0.6030  0.8699    42913.823
   3_bss:  43.129 0.6046  0.7982    42518.022
   3_xyz:  33.367 0.7194  0.9216    27022.738
   3_adp:  30.750 0.7493  0.9243    23686.504
   3_occ:  30.718 0.7496  0.9240    23604.222
   4_bss:  30.630 0.7504  0.8919    23455.575
   4_xyz:  23.390 0.8271  0.9593    14369.221
   4_adp:  21.678 0.8451  0.9657    12937.369
   4_occ:  21.693 0.8449  0.9653    12940.528
   5_bss:  21.700 0.8449  0.9521    12963.158
   5_xyz:  19.897 0.8630  0.9605    11300.867
   5_adp:  18.364 0.8779  0.9619    10087.641
   5_occ:  18.352 0.8780  0.9618    10066.347
   5_bss:  18.278 0.8785  0.9438     9960.608
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.5010e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.5010e+01
   1_xyz:   1.853  0.015  0.116 18.513  0.008  4.110   1.6925e-01
   1_adp:   1.853  0.015  0.116 18.513  0.008  4.110   1.6925e-01
   1_occ:   1.853  0.015  0.116 18.513  0.008  4.110   1.6925e-01
   2_bss:   1.853  0.015  0.116 18.513  0.008  4.110   1.6925e-01
   2_xyz:   1.458  0.011  0.097 17.253  0.005  4.113   1.2333e-01
   2_adp:   1.458  0.011  0.097 17.253  0.005  4.113   1.2333e-01
   2_occ:   1.458  0.011  0.097 17.253  0.005  4.113   1.2333e-01
   3_bss:   1.458  0.011  0.097 17.253  0.005  4.113   1.2333e-01
   3_xyz:   1.243  0.011  0.085 15.991  0.006  4.112   9.6939e-02
   3_adp:   1.243  0.011  0.085 15.991  0.006  4.112   9.6939e-02
   3_occ:   1.243  0.011  0.085 15.991  0.006  4.112   9.6939e-02
   4_bss:   1.243  0.011  0.085 15.991  0.006  4.112   9.6939e-02
   4_xyz:   1.340  0.013  0.096 16.098  0.005  4.138   1.0766e-01
   4_adp:   1.340  0.013  0.096 16.098  0.005  4.138   1.0766e-01
   4_occ:   1.340  0.013  0.096 16.098  0.005  4.138   1.0766e-01
   5_bss:   1.340  0.013  0.096 16.098  0.005  4.138   1.0766e-01
   5_xyz:   1.226  0.011  0.090 15.671  0.004  4.121   8.7769e-02
   5_adp:   1.226  0.011  0.090 15.671  0.004  4.121   8.7769e-02
   5_occ:   1.226  0.011  0.090 15.671  0.004  4.121   8.7769e-02
   5_bss:   1.226  0.011  0.090 15.671  0.004  4.121   8.7769e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.1328e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.1328e+00
   1_xyz:  15.328  0.182  0.473 86.813  0.052  2.092   1.1828e-01
   1_adp:  15.328  0.182  0.473 86.813  0.052  2.092   1.1828e-01
   1_occ:  15.328  0.182  0.473 86.813  0.052  2.092   1.1828e-01
   2_bss:  15.328  0.182  0.473 86.813  0.052  2.092   1.1828e-01
   2_xyz:  10.091  0.123  0.351 80.622  0.022  1.969   1.0349e-01
   2_adp:  10.091  0.123  0.351 80.622  0.022  1.969   1.0349e-01
   2_occ:  10.091  0.123  0.351 80.622  0.022  1.969   1.0349e-01
   3_bss:  10.091  0.123  0.351 80.622  0.022  1.969   1.0349e-01
   3_xyz:   7.656  0.063  0.284 78.627  0.047  2.251   1.3012e-01
   3_adp:   7.656  0.063  0.284 78.627  0.047  2.251   1.3012e-01
   3_occ:   7.656  0.063  0.284 78.627  0.047  2.251   1.3012e-01
   4_bss:   7.656  0.063  0.284 78.627  0.047  2.251   1.3012e-01
   4_xyz:  10.002  0.076  0.393 86.195  0.033  2.148   1.0076e-01
   4_adp:  10.002  0.076  0.393 86.195  0.033  2.148   1.0076e-01
   4_occ:  10.002  0.076  0.393 86.195  0.033  2.148   1.0076e-01
   5_bss:  10.002  0.076  0.393 86.195  0.033  2.148   1.0076e-01
   5_xyz:   9.081  0.066  0.480 83.288  0.045  2.210   5.1378e-02
   5_adp:   9.081  0.066  0.480 83.288  0.045  2.210   5.1378e-02
   5_occ:   9.081  0.066  0.480 83.288  0.045  2.210   5.1378e-02
   5_bss:   9.081  0.066  0.480 83.288  0.045  2.210   5.1378e-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: 140.14   0.00  19.16 112.54   0.00  17.08 140.14   0.00  30.53
   1_occ: 140.14   0.00  19.16 112.54   0.00  17.08 140.14   0.00  30.53
   2_bss: 140.14   0.00  19.16 112.54   0.00  17.08 140.14   0.00  30.53
   2_xyz: 140.14   0.00  19.16 112.54   0.00  17.08 140.14   0.00  30.53
   2_adp: 147.48   0.00  16.57 106.80   0.00  13.33 147.48   0.00  34.23
   2_occ: 147.48   0.00  16.57 106.80   0.00  13.33 147.48   0.00  34.23
   3_bss: 147.48   0.00  16.57 106.80   0.00  13.33 147.48   0.00  34.23
   3_xyz: 147.48   0.00  16.57 106.80   0.00  13.33 147.48   0.00  34.23
   3_adp: 151.73   0.00  17.30 125.43   0.00  12.29 151.73   0.00  44.60
   3_occ: 151.73   0.00  17.30 125.43   0.00  12.29 151.73   0.00  44.60
   4_bss: 151.73   0.00  17.30 125.43   0.00  12.29 151.73   0.00  44.60
   4_xyz: 151.73   0.00  17.30 125.43   0.00  12.29 151.73   0.00  44.60
   4_adp: 151.01   0.00  16.88 125.13   0.00  11.72 151.01   1.44  44.96
   4_occ: 151.01   0.00  16.88 125.13   0.00  11.72 151.01   1.44  44.96
   5_bss: 151.01   0.00  16.88 125.13   0.00  11.72 151.01   1.44  44.96
   5_xyz: 151.01   0.00  16.88 125.13   0.00  11.72 151.01   1.44  44.96
   5_adp: 138.54   0.00  14.71 113.60   0.00  10.33 138.54   2.75  38.58
   5_occ: 138.54   0.00  14.71 113.60   0.00  10.33 138.54   2.75  38.58
   5_bss: 139.86   1.32  16.03 114.92   1.32  11.65 139.86   4.07  39.90
------------------------------------------------------------------------
 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:    1.256    0.013    0.418
   1_adp:    1.256    0.013    0.418
   1_occ:    1.256    0.013    0.418
   2_bss:    1.256    0.013    0.418
   2_xyz:    2.022    0.038    0.636
   2_adp:    2.022    0.038    0.636
   2_occ:    2.022    0.038    0.636
   3_bss:    2.022    0.038    0.636
   3_xyz:    1.707    0.054    0.754
   3_adp:    1.707    0.054    0.754
   3_occ:    1.707    0.054    0.754
   4_bss:    1.707    0.054    0.754
   4_xyz:    1.911    0.035    0.877
   4_adp:    1.911    0.035    0.877
   4_occ:    1.911    0.035    0.877
   5_bss:    1.911    0.035    0.877
   5_xyz:    1.904    0.092    0.907
   5_adp:    1.904    0.092    0.907
   5_occ:    1.904    0.092    0.907
   5_bss:    1.904    0.092    0.907
------------------------------------------------------------------------

CPU time actual refinement: 357.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1308/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_1308/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1308/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1308/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1308/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.56 
  Macro-tasks:
    bulk solvent and scale       = 60.47  
    individual site refinement   = 145.29 
    weights calculation          = 30.58  
    collect and process          = 6.21   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 242.65 
  Micro-tasks:
    mask                            = 2.81   
    f_calc                          = 105.36 
    alpha_beta                      = 8.15   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 116.66 
    fmodel                         = 10.18  
    r_factors                      = 0.35   
    phase_errors                   = 9.97   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 254.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.924 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    655 calls, 105.07 s
gradients_fft:          601 calls, 103.12 s

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

# Date 2008-01-16 Time 03:43:39 PST -0800 (1200483819.71 s)
Start R-work = 0.5191, R-free = 0.5080 (no bulk solvent and anisotropic scale)
Final R-work = 0.1626, R-free = 0.2104 (no bulk solvent and anisotropic scale)

Start R-work = 0.5134, R-free = 0.5028
Final R-work = 0.1474, R-free = 0.1954