# Date 2008-01-16 Time 03:28:23 PST -0800 (1200482903.32 s)
#phil __OFF__

Command line arguments: "../1256.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12402
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1256

-------------------------------------------------------------------------------
  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, 46.6953, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


================================== 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, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97112
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937093

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9711

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, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97112
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937093

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2192 [2178/2207]  1965   213   9.8%
  bin  2:  4.2192 -  3.3608 [2107/2123]  1893   214  10.2%
  bin  3:  3.3608 -  2.9395 [2069/2088]  1859   210  10.1%
  bin  4:  2.9395 -  2.6723 [2064/2094]  1865   199   9.6%
  bin  5:  2.6723 -  2.4817 [2038/2057]  1834   204  10.0%
  bin  6:  2.4817 -  2.3359 [2049/2074]  1835   214  10.4%
  bin  7:  2.3359 -  2.2193 [2020/2054]  1817   203  10.0%
  bin  8:  2.2193 -  2.1229 [2010/2040]  1814   196   9.8%
  bin  9:  2.1229 -  2.0414 [1996/2051]  1805   191   9.6%
  bin 10:  2.0414 -  1.9711 [1058/2054]   943   115  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1256/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: 0.12 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:
        1.69 -     2.33: 18
        2.33 -     2.97: 1775
        2.97 -     3.62: 4572
        3.62 -     4.26: 9196
        4.26 -     4.90: 12749
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.690 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.916 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.975 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.048 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28305 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_1256/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1256/model_refine_001.geo

CPU time processing inputs: 7.97


============================ 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 46.69535 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4769   r_free= 0.4687   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.277259                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7066 0.99   1416  161 0.3945 0.4092      6.5834      6.5864|
|  2:  4.7066 -  3.7543 0.99   1371  144 0.3958 0.4053      6.7842      6.8203|
|  3:  3.7543 -  3.2852 0.99   1335  150 0.4414 0.4036       6.651      6.6707|
|  4:  3.2852 -  2.9873 0.99   1343  155 0.4545 0.4578      6.5171       6.497|
|  5:  2.9873 -  2.7746 0.99   1323  144 0.4948 0.5219      6.3626      6.3461|
|  6:  2.7746 -  2.6119 0.99   1317  148 0.5068 0.5126      6.2726      6.2675|
|  7:  2.6119 -  2.4817 0.99   1311  138 0.5335 0.4777      6.2625      6.1901|
|  8:  2.4817 -  2.3741 0.98   1297  151 0.5273 0.4874      6.1636      6.1816|
|  9:  2.3741 -  2.2830 0.98   1308  151 0.5180 0.4655      6.1256      6.0527|
| 10:  2.2830 -  2.2044 0.99   1297  141 0.5197 0.5091      6.0829      6.0993|
| 11:  2.2044 -  2.1357 0.99   1307  137 0.5280 0.5239        6.05       6.046|
| 12:  2.1357 -  2.0748 0.97   1272  149 0.5027 0.5693      5.9386      5.9896|
| 13:  2.0748 -  2.0203 0.92   1199  138 0.5478 0.4774      5.8884      5.8176|
| 14:  2.0203 -  1.9711 0.40    534   52 0.5404 0.5485      5.8184      5.8422|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7066  1416   161  0.68  35.75   0.79     0.73      76117.58|
|  2:  4.7066 -  3.7543  1371   144  0.70  35.13   0.88     0.78     106179.10|
|  3:  3.7543 -  3.2852  1335   150  0.59  44.67   0.84     0.72     114603.61|
|  4:  3.2852 -  2.9873  1343   155  0.51  51.31   0.80     0.62     104703.20|
|  5:  2.9873 -  2.7746  1323   144  0.40  59.48   0.73     0.48      86194.04|
|  6:  2.7746 -  2.6119  1317   148  0.38  61.49   0.73     0.46      73854.52|
|  7:  2.6119 -  2.4817  1311   138  0.39  60.82   0.73     0.44      63213.56|
|  8:  2.4817 -  2.3741  1297   151  0.40  59.61   0.71     0.48      55484.44|
|  9:  2.3741 -  2.2830  1308   151  0.41  58.84   0.74     0.48      49142.21|
| 10:  2.2830 -  2.2044  1297   141  0.39  60.53   0.74     0.46      46638.57|
| 11:  2.2044 -  2.1357  1307   137  0.33  65.19   0.76     0.41      46507.15|
| 12:  2.1357 -  2.0748  1272   149  0.27  69.82   0.75     0.33      44840.35|
| 13:  2.0748 -  2.0203  1199   138  0.24  71.89   0.72     0.32      40092.75|
| 14:  2.0203 -  1.9711   534    52  0.28  68.90   0.69     0.33      32653.10|
|alpha:            min =        0.32 max =            0.78 mean =         0.52|
|beta:             min =    32653.10 max =       114603.61 mean =     69268.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.52|
|phase err.(test): min =        0.00 max =           89.93 mean =        56.59|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.407840             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.423   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210671              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.629   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      695 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1508 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2641 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3916 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5078 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6561 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7710 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.747 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.740 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4814   r_free= 0.4765   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.279532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4680   r_free= 0.4580   ksol= 0.33   Bsol= 11.57   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.15,7.44,7.95,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.272949                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.540014             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.962   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.041698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.019   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4680      final r-factor (work) = 0.3872          |
| start r-factor (free) = 0.4580      final r-factor (free) = 0.4138          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.0932 = 12.54 * 0.50 * 6.2753 + 1.00 * 53.7471                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.9250 = 12.54 * 0.50 * 6.1852 + 1.00 * 0.1438                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3872      final r-factor (work) = 0.3405          |
| start r-factor (free) = 0.4138      final r-factor (free) = 0.3873          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4575 = 1.04 * 1.00 * 6.1852 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3670 = 1.04 * 1.00 * 6.0981 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.34   12.68    None  None   None       |
|    all(noH): 2823   0      0.00    78.34   12.68    None  None   None       |
|    Sol.    : 438    0      0.00    66.36   26.59    None  None   None       |
|    Mac.    : 2385   0      0.00    78.34   10.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.834: 1278   |   5:    39.172 -  47.006:   77        |
|      1:     7.834 -  15.669:  702   |   6:    47.006 -  54.840:   32        |
|      2:    15.669 -  23.503:  398   |   7:    54.840 -  62.675:   12        |
|      3:    23.503 -  31.337:  214   |   8:    62.675 -  70.509:    4        |
|      4:    31.337 -  39.172:  103   |   9:    70.509 -  78.343:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3405 r_free = 0.3873             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3399 r_free = 0.3879             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3399   r_free= 0.3879   ksol= 0.33   Bsol= 11.57   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.15,7.44,7.95,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.073575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3369   r_free= 0.3841   ksol= 0.33   Bsol= 34.16   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.30,4.00,5.26,0.00,0.00,0.00); trace/3= 5.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.073507                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.701981              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.260   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.531898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.847  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3369      final r-factor (work) = 0.2387          |
| start r-factor (free) = 0.3841      final r-factor (free) = 0.2958          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6593 = 8.70 * 0.50 * 6.0941 + 1.00 * 0.1438                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9400 = 8.70 * 0.50 * 5.9421 + 1.00 * 0.0859                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2387      final r-factor (work) = 0.2140          |
| start r-factor (free) = 0.2958      final r-factor (free) = 0.2748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1753 = 0.53 * 1.00 * 5.9421 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0656 = 0.53 * 1.00 * 5.7418 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.57   12.79    None  None   None       |
|    all(noH): 2823   0      0.00    78.57   12.79    None  None   None       |
|    Sol.    : 438    0      0.83    70.14   33.09    None  None   None       |
|    Mac.    : 2385   0      0.00    78.57   9.06     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.857: 1381   |   5:    39.283 -  47.139:  100        |
|      1:     7.857 -  15.713:  732   |   6:    47.139 -  54.996:   56        |
|      2:    15.713 -  23.570:  257   |   7:    54.996 -  62.852:   20        |
|      3:    23.570 -  31.426:  138   |   8:    62.852 -  70.709:    8        |
|      4:    31.426 -  39.283:  129   |   9:    70.709 -  78.565:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2140 r_free = 0.2748             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2137 r_free = 0.2748             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2137   r_free= 0.2748   ksol= 0.33   Bsol= 34.16   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.30,4.00,5.26,0.00,0.00,0.00); trace/3= 5.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.703585                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2114   r_free= 0.2706   ksol= 0.34   Bsol= 49.27   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.61,2.27,3.17,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.701020                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.650216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.714  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.753128              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.762  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2114      final r-factor (work) = 0.1654          |
| start r-factor (free) = 0.2706      final r-factor (free) = 0.2152          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7070 = 2.65 * 0.50 * 5.7513 + 1.00 * 0.0859                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4858 = 2.65 * 0.50 * 5.6043 + 1.00 * 0.0595                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1654      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2152      final r-factor (free) = 0.2034          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2323 = 0.75 * 1.00 * 5.6043 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1112 = 0.75 * 1.00 * 5.4414 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.80   13.36    None  None   None       |
|    all(noH): 2823   0      0.00    83.80   13.36    None  None   None       |
|    Sol.    : 438    0      1.80    82.85   37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    83.80   8.96     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.380: 1499   |   5:    41.900 -  50.280:  110        |
|      1:     8.380 -  16.760:  690   |   6:    50.280 -  58.660:   77        |
|      2:    16.760 -  25.140:  188   |   7:    58.660 -  67.040:   31        |
|      3:    25.140 -  33.520:  109   |   8:    67.040 -  75.420:    7        |
|      4:    33.520 -  41.900:  108   |   9:    75.420 -  83.800:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1528 r_free = 0.2034             target_work(ml) = 5.416         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1527 r_free = 0.2033             target_work(ml) = 5.416         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1527   r_free= 0.2033   ksol= 0.34   Bsol= 49.27   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.61,2.27,3.17,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.415519                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1529   r_free= 0.2030   ksol= 0.34   Bsol= 49.27   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,1.88,2.64,0.00,0.00,0.00); trace/3= 2.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.415616                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.052577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.962  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.468801              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.733  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1529      final r-factor (work) = 0.1333          |
| start r-factor (free) = 0.2030      final r-factor (free) = 0.1837          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6465 = 2.05 * 0.50 * 5.4439 + 1.00 * 0.0595                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5580 = 2.05 * 0.50 * 5.3581 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1333      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.1837      final r-factor (free) = 0.1794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5249 = 0.47 * 1.00 * 5.3581 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4987 = 0.47 * 1.00 * 5.2873 + 1.00 * 0.0200                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.14   13.36    None  None   None       |
|    all(noH): 2823   0      0.00    89.14   13.36    None  None   None       |
|    Sol.    : 438    0      2.12    85.36   37.42    None  None   None       |
|    Mac.    : 2385   0      0.00    89.14   8.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.914: 1595   |   5:    44.572 -  53.486:   93        |
|      1:     8.914 -  17.829:  646   |   6:    53.486 -  62.400:   52        |
|      2:    17.829 -  26.743:  171   |   7:    62.400 -  71.315:   28        |
|      3:    26.743 -  35.657:  122   |   8:    71.315 -  80.229:    7        |
|      4:    35.657 -  44.572:  104   |   9:    80.229 -  89.143:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1296 r_free = 0.1794             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1295 r_free = 0.1792             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1295   r_free= 0.1792   ksol= 0.34   Bsol= 49.27   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,1.88,2.64,0.00,0.00,0.00); trace/3= 2.41                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274189                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1295   r_free= 0.1792   ksol= 0.33   Bsol= 50.27   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,1.69,2.45,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273764                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.267864              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.764  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.162170              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.660   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1295      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6978 = 3.27 * 0.50 * 5.2871 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6315 = 3.27 * 0.50 * 5.2357 + 1.00 * 0.0767                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0969 = 1.16 * 1.00 * 5.2357 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0549 = 1.16 * 1.00 * 5.1988 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.23   13.41    None  None   None       |
|    all(noH): 2823   0      0.00    93.23   13.41    None  None   None       |
|    Sol.    : 438    0      2.42    89.74   37.79    None  None   None       |
|    Mac.    : 2385   0      0.00    93.23   8.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.324: 1670   |   5:    46.617 -  55.941:   90        |
|      1:     9.324 -  18.647:  595   |   6:    55.941 -  65.264:   47        |
|      2:    18.647 -  27.970:  166   |   7:    65.264 -  74.588:   20        |
|      3:    27.970 -  37.294:  116   |   8:    74.588 -  83.911:   11        |
|      4:    37.294 -  46.617:  104   |   9:    83.911 -  93.234:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1672             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1670             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1670   ksol= 0.33   Bsol= 50.27   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.35,1.69,2.45,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.193906                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7066 0.99   1416  161 0.0995 0.1402      5.4006      5.6085|
|  2:  4.7066 -  3.7543 0.99   1371  144 0.0874 0.1119       5.458      5.6448|
|  3:  3.7543 -  3.2852 0.99   1335  150 0.1110 0.1678       5.512      5.9075|
|  4:  3.2852 -  2.9873 0.99   1343  155 0.1288 0.1591      5.5131      5.6334|
|  5:  2.9873 -  2.7746 0.99   1323  144 0.1379 0.1872      5.3726      5.6023|
|  6:  2.7746 -  2.6119 0.99   1317  148 0.1271 0.1940      5.2507      5.5103|
|  7:  2.6119 -  2.4817 0.99   1311  138 0.1300 0.1756      5.2118      5.3927|
|  8:  2.4817 -  2.3741 0.98   1297  151 0.1212 0.1834      5.0999      5.4039|
|  9:  2.3741 -  2.2830 0.98   1308  151 0.1242 0.2010      5.0863      5.3839|
| 10:  2.2830 -  2.2044 0.99   1297  141 0.1160 0.1786      4.9934      5.2345|
| 11:  2.2044 -  2.1357 0.99   1307  137 0.1231 0.1930      4.9992      5.3661|
| 12:  2.1357 -  2.0748 0.97   1272  149 0.1141 0.1796      4.9218      5.1656|
| 13:  2.0748 -  2.0203 0.92   1199  138 0.1207 0.1725      4.8371      5.0733|
| 14:  2.0203 -  1.9711 0.40    534   52 0.1016 0.1819       4.648      5.0097|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7066  1416   161  0.94   9.47   0.98     0.96       7919.04|
|  2:  4.7066 -  3.7543  1371   144  0.95   8.46   1.01     1.00       9675.05|
|  3:  3.7543 -  3.2852  1335   150  0.93  12.18   1.03     1.03      11349.84|
|  4:  3.2852 -  2.9873  1343   155  0.91  15.22   1.01     0.98      11935.95|
|  5:  2.9873 -  2.7746  1323   144  0.89  17.02   1.00     0.97       9332.21|
|  6:  2.7746 -  2.6119  1317   148  0.89  17.30   0.99     0.96       7916.60|
|  7:  2.6119 -  2.4817  1311   138  0.90  16.41   0.99     0.97       6904.92|
|  8:  2.4817 -  2.3741  1297   151  0.90  16.60   0.98     0.95       5811.21|
|  9:  2.3741 -  2.2830  1308   151  0.89  17.16   1.01     0.97       5674.28|
| 10:  2.2830 -  2.2044  1297   141  0.90  16.10   1.00     0.97       4814.15|
| 11:  2.2044 -  2.1357  1307   137  0.88  17.92   0.99     0.94       4947.52|
| 12:  2.1357 -  2.0748  1272   149  0.90  16.79   1.01     1.01       4549.37|
| 13:  2.0748 -  2.0203  1199   138  0.89  17.28   1.00     0.99       3759.45|
| 14:  2.0203 -  1.9711   534    52  0.90  15.65   0.99     0.96       2656.25|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2656.25 max =        11935.95 mean =      7196.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.16|
|phase err.(test): min =        0.00 max =           89.58 mean =        14.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1671   ksol= 0.32   Bsol= 52.39   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,-0.45,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194235                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1671   ksol= 0.32   Bsol= 52.39   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.17,-0.45,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194235                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7066 0.99   1416  161 0.0994 0.1359      5.3932      5.6061|
|  2:  4.7066 -  3.7543 0.99   1371  144 0.0881 0.1133      5.4628      5.6603|
|  3:  3.7543 -  3.2852 0.99   1335  150 0.1115 0.1680      5.5185      5.9053|
|  4:  3.2852 -  2.9873 0.99   1343  155 0.1292 0.1594      5.5147       5.635|
|  5:  2.9873 -  2.7746 0.99   1323  144 0.1382 0.1873      5.3717         5.6|
|  6:  2.7746 -  2.6119 0.99   1317  148 0.1272 0.1935      5.2501       5.508|
|  7:  2.6119 -  2.4817 0.99   1311  138 0.1300 0.1758      5.2114       5.393|
|  8:  2.4817 -  2.3741 0.98   1297  151 0.1212 0.1843      5.1007      5.4078|
|  9:  2.3741 -  2.2830 0.98   1308  151 0.1240 0.2008      5.0864      5.3834|
| 10:  2.2830 -  2.2044 0.99   1297  141 0.1158 0.1785      4.9937      5.2337|
| 11:  2.2044 -  2.1357 0.99   1307  137 0.1230 0.1930      4.9987      5.3664|
| 12:  2.1357 -  2.0748 0.97   1272  149 0.1140 0.1796       4.922      5.1658|
| 13:  2.0748 -  2.0203 0.92   1199  138 0.1207 0.1726      4.8372      5.0735|
| 14:  2.0203 -  1.9711 0.40    534   52 0.1017 0.1823      4.6484      5.0105|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7066  1416   161  0.94   9.35   0.97     0.95       7647.31|
|  2:  4.7066 -  3.7543  1371   144  0.95   8.50   1.01     1.00       9723.90|
|  3:  3.7543 -  3.2852  1335   150  0.93  12.30   1.03     1.03      11559.95|
|  4:  3.2852 -  2.9873  1343   155  0.91  15.24   1.01     0.98      11951.70|
|  5:  2.9873 -  2.7746  1323   144  0.89  16.97   0.99     0.97       9289.27|
|  6:  2.7746 -  2.6119  1317   148  0.89  17.28   0.99     0.95       7889.40|
|  7:  2.6119 -  2.4817  1311   138  0.90  16.39   0.99     0.97       6900.16|
|  8:  2.4817 -  2.3741  1297   151  0.90  16.62   0.98     0.94       5831.36|
|  9:  2.3741 -  2.2830  1308   151  0.89  17.18   1.01     0.97       5684.58|
| 10:  2.2830 -  2.2044  1297   141  0.90  16.11   1.00     0.97       4823.40|
| 11:  2.2044 -  2.1357  1307   137  0.88  17.92   0.99     0.94       4945.95|
| 12:  2.1357 -  2.0748  1272   149  0.90  16.80   1.01     1.01       4554.33|
| 13:  2.0748 -  2.0203  1199   138  0.89  17.28   1.00     0.98       3760.55|
| 14:  2.0203 -  1.9711   534    52  0.90  15.66   0.98     0.96       2657.81|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2657.81 max =        11951.70 mean =      7192.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.16|
|phase err.(test): min =        0.00 max =           89.42 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.12    95.35   15.53    None  None   None       |
|    all(noH): 2823   0      2.12    95.35   15.53    None  None   None       |
|    Sol.    : 438    0      4.54    91.85   39.91    None  None   None       |
|    Mac.    : 2385   0      2.12    95.35   11.05    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:     2.117 -  11.440: 1670   |   5:    48.734 -  58.058:   90        |
|      1:    11.440 -  20.764:  595   |   6:    58.058 -  67.381:   47        |
|      2:    20.764 -  30.087:  166   |   7:    67.381 -  76.704:   20        |
|      3:    30.087 -  39.411:  116   |   8:    76.704 -  86.028:   11        |
|      4:    39.411 -  48.734:  104   |   9:    86.028 -  95.351:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.268 - 5.980
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 330
   mapped sites are within: 0.741 - 5.980

peak=   10.299 closest distance to " CB  VAL A 230 " =    1.434
peak=    8.993 closest distance to " CG2 VAL A 296 " =    1.288
peak=    7.624 closest distance to " CG  ARG A 138 " =    1.188
peak=    5.982 closest distance to " O   HOH Z 111 " =    2.178
peak=    5.835 closest distance to " O   HOH Z 102 " =    1.062
peak=    5.576 closest distance to " CD1AILE A 234 " =    1.087
peak=    5.572 closest distance to " CG  LEU A   5 " =    1.165
peak=    5.525 closest distance to " CD2 LEU A   5 " =    1.149
peak=    5.317 closest distance to " O   HOH Z 278 " =    0.921
peak=    5.262 closest distance to " NE2 GLN A  11 " =    1.146
peak=    5.221 closest distance to " CB  GLN A 223 " =    1.437
peak=    5.131 closest distance to " O   HOH Z 183 " =    1.479
peak=    5.013 closest distance to " CB  GLN A 183 " =    1.231
peak=    5.013 closest distance to " CG  LEU A 228 " =    1.165
peak=    4.978 closest distance to " O   HOH Z  37 " =    1.287
peak=    4.963 closest distance to " O   HOH Z 112 " =    1.503
peak=    4.927 closest distance to " O   HOH Z 193 " =    1.954
peak=    4.868 closest distance to " O   HOH Z 179 " =    1.025
peak=    4.806 closest distance to " O   HOH Z 186 " =    1.558
peak=    4.775 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.648 closest distance to " CB  SER A  63 " =    1.319
peak=    4.606 closest distance to " CB  VAL A 230 " =    1.226
peak=    4.597 closest distance to " NH1 ARG A  56 " =    1.034
peak=    4.593 closest distance to " O   HOH Z 368 " =    2.054
peak=    4.546 closest distance to " O   HOH Z 298 " =    1.824
peak=    4.487 closest distance to " CB  ASN A 148 " =    1.426
peak=    4.455 closest distance to " O   HOH Z 369 " =    2.003
peak=    4.453 closest distance to " O   HOH Z 427 " =    3.223
peak=    4.450 closest distance to " CB  GLU A 152 " =    1.296
peak=    4.435 closest distance to " O   PRO A 198 " =    1.538
peak=    4.434 closest distance to " O   HOH Z 144 " =    1.507
peak=    4.408 closest distance to " NH2BARG A 102 " =    1.036
peak=    4.406 closest distance to " OD2 ASP A 286 " =    2.917
peak=    4.391 closest distance to " O   HOH Z 303 " =    2.219
peak=    4.381 closest distance to " O   HOH Z  48 " =    1.727
peak=    4.350 closest distance to " O   HOH Z 232 " =    2.281
peak=    4.326 closest distance to " O   HOH Z 247 " =    1.408
peak=    4.315 closest distance to " O   HOH Z  80 " =    1.717
peak=    4.300 closest distance to " O   HOH Z 316 " =    2.993
peak=    4.276 closest distance to " NH1AARG A 145 " =    1.189
peak=    4.240 closest distance to " O   HOH Z   9 " =    2.163
peak=    4.228 closest distance to " CD  ARG A 138 " =    1.108
peak=    4.218 closest distance to " CD2 LEU A 228 " =    1.214
peak=    4.190 closest distance to " CG  PRO A 198 " =    1.233
peak=    4.190 closest distance to " O   HOH Z  78 " =    2.331
peak=    4.174 closest distance to " NH1 ARG A 138 " =    1.061
peak=    4.164 closest distance to " O   HOH Z 272 " =    1.921
peak=    4.151 closest distance to " O   HOH Z 425 " =    1.462
peak=    4.151 closest distance to " CB  SER A   3 " =    1.506
peak=    4.145 closest distance to " O   HOH Z 236 " =    1.962
peak=    4.145 closest distance to " CB  LEU A 228 " =    1.257
peak=    4.101 closest distance to " O   HOH Z 132 " =    2.373
peak=    4.099 closest distance to " CB  TYR A 169 " =    0.942
peak=    4.084 closest distance to " O   HOH Z 410 " =    1.416
peak=    4.081 closest distance to " O   HOH Z 126 " =    1.919
peak=    4.078 closest distance to " O   HOH Z   7 " =    1.198
peak=    4.068 closest distance to " O   HOH Z 371 " =    3.213
peak=    4.067 closest distance to " O   HOH Z 217 " =    3.113
peak=    4.066 closest distance to " OD1 ASN A 217 " =    1.661
peak=    4.046 closest distance to " O   HOH Z 113 " =    2.234
peak=    4.024 closest distance to " O   HOH Z 271 " =    2.173
peak=    4.019 closest distance to " O   HOH Z 108 " =    1.482
peak=    4.014 closest distance to " CG2 THR A 221 " =    1.050
peak=    4.008 closest distance to " CB  GLU A 128 " =    1.107
peak=    4.002 closest distance to " O   HOH Z  44 " =    2.436
peak=    3.998 closest distance to " CG  PRO A 243 " =    1.126
peak=    3.977 closest distance to " O   HOH Z 184 " =    1.489
peak=    3.961 closest distance to " O   HOH Z 117 " =    1.904
peak=    3.955 closest distance to " O   HOH Z 280 " =    3.055
peak=    3.953 closest distance to " CD1 LEU A 300 " =    1.282
peak=    3.935 closest distance to " O   HOH Z 260 " =    1.162
peak=    3.934 closest distance to " O   HOH Z  58 " =    1.742
peak=    3.929 closest distance to " O   HOH Z 411 " =    3.534
peak=    3.920 closest distance to " CB  TRP A 266 " =    1.013
peak=    3.900 closest distance to " O   HOH Z 281 " =    4.353
peak=    3.898 closest distance to " O   HOH Z 437 " =    2.092
peak=    3.892 closest distance to " CD2 LEU A 255 " =    1.640
peak=    3.892 closest distance to " O   HOH Z  88 " =    3.321
peak=    3.838 closest distance to " CB  ASN A 187 " =    1.086
peak=    3.833 closest distance to " CB  VAL A 265 " =    1.206
peak=    3.817 closest distance to " O   HOH Z 263 " =    1.595
peak=    3.812 closest distance to " O   HOH Z 158 " =    2.789
peak=    3.809 closest distance to " O   HOH Z 193 " =    2.167
peak=    3.788 closest distance to " O   HOH Z  92 " =    0.838
peak=    3.775 closest distance to " CB  GLU A 277 " =    3.614
peak=    3.774 closest distance to " CA  ALA A  51 " =    1.079
peak=    3.773 closest distance to " O   ALA A 291 " =    1.704
peak=    3.773 closest distance to " OD1 ASN A  69 " =    2.717
peak=    3.770 closest distance to " CD  ARG A 159 " =    0.855
peak=    3.766 closest distance to " O   HOH Z   9 " =    1.918
peak=    3.765 closest distance to " CB  ASP A 124 " =    0.741
peak=    3.756 closest distance to " O   HOH Z 126 " =    1.540
peak=    3.750 closest distance to " O   HOH Z  78 " =    1.755
peak=    3.749 closest distance to " CG1 ILE A  33 " =    1.268
peak=    3.743 closest distance to " CB  VAL A 202 " =    1.562
peak=    3.743 closest distance to " CG  GLN A  88 " =    1.099
peak=    3.743 closest distance to " CA  ALA A  21 " =    1.205
peak=    3.740 closest distance to " O   SER A  87 " =    2.283
peak=    3.737 closest distance to " CD1 ILE A  33 " =    1.664
peak=    3.714 closest distance to " CA  ASN A 215 " =    1.279
peak=    3.704 closest distance to " CA  LEU A 282 " =    1.102
peak=    3.702 closest distance to " CA  GLY A 267 " =    1.044
peak=    3.699 closest distance to " CB  ASN A 148 " =    1.912
peak=    3.693 closest distance to " O   HOH Z 346 " =    1.538
peak=    3.685 closest distance to " CD ALYS A 290 " =    1.033
peak=    3.681 closest distance to " O   MET A 105 " =    1.828
peak=    3.663 closest distance to " CG  LEU A 167 " =    1.193
peak=    3.660 closest distance to " NE AARG A 275 " =    1.463
peak=    3.658 closest distance to " O   HOH Z  49 " =    2.021
peak=    3.654 closest distance to " O   HOH Z 180 " =    2.092
peak=    3.653 closest distance to " CB  LYS A 117 " =    1.158
peak=    3.649 closest distance to " CB  MET A  40 " =    0.849
peak=    3.639 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.637 closest distance to " O   HOH Z 407 " =    2.033
peak=    3.635 closest distance to " O   HOH Z 295 " =    1.580
peak=    3.635 closest distance to " OE1 GLN A  58 " =    1.299
peak=    3.633 closest distance to " CB  LEU A 237 " =    0.920
peak=    3.626 closest distance to " CD  ARG A  66 " =    2.456
peak=    3.622 closest distance to " O   HOH Z 227 " =    1.863
peak=    3.621 closest distance to " CA  MET A  40 " =    1.113
peak=    3.611 closest distance to " O   HOH Z 126 " =    1.555
peak=    3.611 closest distance to " O   HOH Z 156 " =    2.760
peak=    3.605 closest distance to " O   HOH Z 175 " =    2.252
peak=    3.601 closest distance to " O   HOH Z 108 " =    2.363
peak=    3.600 closest distance to " O   HOH Z  15 " =    1.562
peak=    3.598 closest distance to " O   HOH Z  64 " =    2.324
peak=    3.593 closest distance to " O   ASP A 132 " =    3.732
peak=    3.593 closest distance to " CB  ASP A 140 " =    0.868
peak=    3.591 closest distance to " ND1 HIS A  86 " =    1.764
peak=    3.583 closest distance to " CG  PRO A 280 " =    0.803
peak=    3.583 closest distance to " C   ALA A 299 " =    0.948
peak=    3.580 closest distance to " NE AARG A 102 " =    1.165
peak=    3.578 closest distance to " O   HOH Z 284 " =    1.529
peak=    3.567 closest distance to " CB  MET A  47 " =    1.014
peak=    3.563 closest distance to " CB  TRP A 179 " =    1.470
peak=    3.553 closest distance to " O   HOH Z 134 " =    1.533
peak=    3.551 closest distance to " O   HOH Z 392 " =    2.017
peak=    3.546 closest distance to " O   HOH Z  54 " =    2.402
peak=    3.541 closest distance to " CB  ALA A 291 " =    1.488
peak=    3.537 closest distance to " CB  ARG A  79 " =    1.558
peak=    3.527 closest distance to " O   HOH Z 345 " =    3.440
peak=    3.525 closest distance to " O   HOH Z 222 " =    2.330
peak=    3.522 closest distance to " O   HOH Z 115 " =    2.079
peak=    3.520 closest distance to " O   HOH Z 409 " =    2.879
peak=    3.520 closest distance to " NH2BARG A 145 " =    2.111
peak=    3.516 closest distance to " O   HOH Z   2 " =    1.593
peak=    3.513 closest distance to " CG1BVAL A  72 " =    1.520
peak=    3.511 closest distance to " N   PHE A 130 " =    1.364
peak=    3.508 closest distance to " CA  THR A 221 " =    0.943
peak=    3.508 closest distance to " O   HOH Z 374 " =    2.556
peak=    3.507 closest distance to " CB  SER A 212 " =    1.134
peak=    3.505 closest distance to " CB  GLN A  88 " =    1.253
peak=    3.504 closest distance to " O   HOH Z 133 " =    2.526
peak=    3.502 closest distance to " O   HOH Z 189 " =    2.770
peak=    3.502 closest distance to " CA  TYR A  30 " =    1.022
peak=    3.500 closest distance to " CB  THR A  82 " =    1.274
peak=    3.497 closest distance to " O   HOH Z 133 " =    1.775
peak=    3.497 closest distance to " O   HOH Z  59 " =    2.213
peak=    3.495 closest distance to " CB  ARG A 275 " =    0.856
peak=    3.491 closest distance to " CB  ARG A 139 " =    0.901
peak=    3.488 closest distance to " CA  ILE A 234 " =    0.986
peak=    3.488 closest distance to " O   HOH Z 116 " =    1.724
peak=    3.482 closest distance to " O   HOH Z  68 " =    1.470
peak=    3.481 closest distance to " O   HOH Z 334 " =    1.629
peak=    3.479 closest distance to " CB  TRP A 150 " =    1.385
peak=    3.478 closest distance to " CD1 LEU A 101 " =    1.160
peak=    3.471 closest distance to " O   HOH Z 124 " =    1.177
peak=    3.469 closest distance to " O   HOH Z  66 " =    2.067
peak=    3.465 closest distance to " O   HOH Z  20 " =    2.154
peak=    3.465 closest distance to " CA  ALA A 158 " =    1.172
peak=    3.465 closest distance to " OD1 ASP A 231 " =    1.881
peak=    3.463 closest distance to " O   HOH Z 171 " =    3.916
peak=    3.463 closest distance to " O   HOH Z 313 " =    1.827
peak=    3.462 closest distance to " CG BARG A 275 " =    1.563
peak=    3.453 closest distance to " NH2 ARG A 219 " =    1.829
peak=    3.451 closest distance to " CB  LEU A 143 " =    1.152
peak=    3.449 closest distance to " CA  ALA A 160 " =    0.878
peak=    3.447 closest distance to " CA  LEU A 101 " =    1.534
peak=    3.444 closest distance to " CB  SER A 216 " =    0.940
peak=    3.433 closest distance to " CA  ALA A 154 " =    1.082
peak=    3.430 closest distance to " O   HOH Z 403 " =    1.688
peak=    3.430 closest distance to " O   HOH Z 302 " =    1.838
peak=    3.428 closest distance to " ND2 ASN A 187 " =    1.575
peak=    3.417 closest distance to " O   HOH Z 244 " =    1.584
peak=    3.416 closest distance to " CA  VAL A 126 " =    1.369
peak=    3.411 closest distance to " O   HOH Z 202 " =    1.201
peak=    3.407 closest distance to " O   HOH Z 332 " =    1.621
peak=    3.404 closest distance to " O   HOH Z  61 " =    1.560
peak=    3.403 closest distance to " N   ARG A 156 " =    1.423
peak=    3.401 closest distance to " O   HOH Z 175 " =    3.569
peak=    3.400 closest distance to " CA  TYR A 186 " =    1.522
peak=    3.395 closest distance to " N   TYR A  15 " =    0.925
peak=    3.392 closest distance to " O   HOH Z 426 " =    1.388
peak=    3.390 closest distance to " O   HOH Z 189 " =    3.540
peak=    3.386 closest distance to " CA  ASN A  74 " =    1.256
peak=    3.383 closest distance to " O   HOH Z  53 " =    2.630
peak=    3.378 closest distance to " CB  LEU A 255 " =    0.867
peak=    3.372 closest distance to " CG  MET A 188 " =    1.459
peak=    3.371 closest distance to " O   HOH Z 255 " =    1.657
peak=    3.370 closest distance to " O   HOH Z 227 " =    2.037
peak=    3.369 closest distance to " O   HOH Z 423 " =    2.709
peak=    3.367 closest distance to " O   HOH Z 344 " =    2.935
peak=    3.360 closest distance to " CG2 VAL A 257 " =    0.890
peak=    3.359 closest distance to " CA  LYS A 117 " =    1.251
peak=    3.356 closest distance to " NE2 GLN A  58 " =    5.580
peak=    3.356 closest distance to " O   HOH Z 128 " =    1.612
peak=    3.348 closest distance to " OG1 THR A 246 " =    3.331
peak=    3.348 closest distance to " O   HOH Z 276 " =    1.268
peak=    3.346 closest distance to " CB  THR A 157 " =    1.057
peak=    3.345 closest distance to " CB  ALA A 161 " =    0.967
peak=    3.343 closest distance to " CG1BVAL A 121 " =    1.010
peak=    3.341 closest distance to " O   HOH Z 298 " =    2.570
peak=    3.341 closest distance to " O   HOH Z   3 " =    1.700
peak=    3.340 closest distance to " CD  LYS A 119 " =    1.536
peak=    3.337 closest distance to " O   HOH Z 128 " =    1.943
peak=    3.334 closest distance to " CB  ASN A 142 " =    0.963
peak=    3.330 closest distance to " CB  TYR A  30 " =    1.437
peak=    3.326 closest distance to " O   HOH Z 145 " =    3.405
peak=    3.323 closest distance to " O   HOH Z  68 " =    2.145
peak=    3.321 closest distance to " O   HOH Z  57 " =    1.238
peak=    3.321 closest distance to " CG1 VAL A 153 " =    0.930
peak=    3.321 closest distance to " O   HOH Z  38 " =    1.840
peak=    3.318 closest distance to " O   HOH Z 290 " =    1.166
peak=    3.311 closest distance to " O   HOH Z 281 " =    1.734
peak=    3.308 closest distance to " O   HOH Z 422 " =    2.729
peak=    3.304 closest distance to " CD  ARG A  14 " =    1.201
peak=    3.295 closest distance to " CD  LYS A 166 " =    1.326
peak=    3.290 closest distance to " O   HOH Z 261 " =    1.747
peak=    3.286 closest distance to " CA  VAL A  41 " =    0.990
peak=    3.285 closest distance to " O   HOH Z 329 " =    3.873
peak=    3.285 closest distance to " CA  ARG A 102 " =    1.193
peak=    3.284 closest distance to " CZ  PHE A 192 " =    1.025
peak=    3.283 closest distance to " OG BSER A 134 " =    3.041
peak=    3.282 closest distance to " O   HOH Z  21 " =    1.679
peak=    3.277 closest distance to " CA  ASN A 127 " =    1.030
peak=    3.272 closest distance to " O   HOH Z 415 " =    5.980
peak=    3.272 closest distance to " CB  ALA A   9 " =    1.618
peak=    3.271 closest distance to " CB  GLU A 236 " =    1.248
peak=    3.267 closest distance to " O   HOH Z 153 " =    1.810
peak=    3.265 closest distance to " O   HOH Z 273 " =    2.675
peak=    3.262 closest distance to " O   GLY A  57 " =    2.539
peak=    3.262 closest distance to " CA  LYS A  48 " =    1.434
peak=    3.261 closest distance to " CB  ALA A 104 " =    0.871
peak=    3.260 closest distance to " CE3 TRP A 274 " =    1.110
peak=    3.255 closest distance to " CB  ALA A 248 " =    1.342
peak=    3.254 closest distance to " O   HOH Z 281 " =    2.217
peak=    3.254 closest distance to " CD1 TRP A 266 " =    1.128
peak=    3.254 closest distance to " O   HOH Z 148 " =    2.147
peak=    3.253 closest distance to " CZ  PHE A 218 " =    1.050
peak=    3.252 closest distance to " CD  ARG A 269 " =    0.872
peak=    3.244 closest distance to " O   HOH Z 151 " =    1.637
peak=    3.242 closest distance to " NH1 ARG A  14 " =    0.994
peak=    3.237 closest distance to " O   HOH Z 197 " =    2.981
peak=    3.233 closest distance to " O   HOH Z 181 " =    2.148
peak=    3.231 closest distance to " CB BVAL A  41 " =    1.341
peak=    3.227 closest distance to " O   ALA A 165 " =    1.370
peak=    3.221 closest distance to " O   GLN A 278 " =    1.212
peak=    3.221 closest distance to " OG  SER A  62 " =    2.969
peak=    3.220 closest distance to " O   HOH Z 236 " =    1.601
peak=    3.217 closest distance to " CG1 ILE A  49 " =    1.538
peak=    3.216 closest distance to " O   HOH Z 173 " =    2.058
peak=    3.205 closest distance to " O   HOH Z  43 " =    2.086
peak=    3.202 closest distance to " O   HOH Z 182 " =    1.329
peak=    3.201 closest distance to " ND1 HIS A  81 " =    1.627
peak=    3.200 closest distance to " O   HOH Z  30 " =    1.327
peak=    3.200 closest distance to " CE1 TYR A 186 " =    1.270
peak=    3.199 closest distance to " OG BSER A 164 " =    2.260
peak=    3.198 closest distance to " O   THR A  31 " =    1.449
peak=    3.195 closest distance to " O   HOH Z 303 " =    1.806
peak=    3.195 closest distance to " CA  ALA A 295 " =    1.096
peak=    3.192 closest distance to " CA  GLY A 211 " =    1.265
peak=    3.185 closest distance to " CD  GLN A 240 " =    1.547
peak=    3.183 closest distance to " CB  TYR A 116 " =    0.977
peak=    3.179 closest distance to " CD2 HIS A  81 " =    1.028
peak=    3.176 closest distance to " O   HOH Z 344 " =    1.212
peak=    3.172 closest distance to " CB  THR A 235 " =    0.973
peak=    3.171 closest distance to " O   HOH Z 130 " =    3.896
peak=    3.169 closest distance to " CA  ASP A 140 " =    1.235
peak=    3.168 closest distance to " O   HOH Z 174 " =    1.119
peak=    3.168 closest distance to " NH2BARG A 190 " =    1.579
peak=    3.168 closest distance to " O   HOH Z   1 " =    1.789
peak=    3.163 closest distance to " CA  ILE A  33 " =    1.741
peak=    3.163 closest distance to " O   HOH Z 288 " =    1.951
peak=    3.159 closest distance to " CB  ILE A 120 " =    1.415
peak=    3.159 closest distance to " O   HOH Z 327 " =    2.354
peak=    3.155 closest distance to " O   HOH Z 286 " =    2.356
peak=    3.154 closest distance to " O   ALA A 158 " =    1.403
peak=    3.153 closest distance to " CB  ALA A  34 " =    0.979
peak=    3.152 closest distance to " O   HOH Z 209 " =    2.627
peak=    3.151 closest distance to " CE  LYS A  48 " =    1.056
peak=    3.149 closest distance to " CA  SER A  87 " =    0.932
peak=    3.148 closest distance to " CG2 VAL A 174 " =    1.317
peak=    3.148 closest distance to " O   HOH Z   4 " =    1.593
peak=    3.144 closest distance to " CG  LEU A  25 " =    1.868
peak=    3.143 closest distance to " CB  VAL A 296 " =    1.010
peak=    3.126 closest distance to " OD1 ASN A  45 " =    1.490
peak=    3.126 closest distance to " N   SER A 134 " =    1.364
peak=    3.125 closest distance to " OG  SER A  22 " =    2.953
peak=    3.124 closest distance to " CG  LYS A  76 " =    1.824
peak=    3.121 closest distance to " CA  ALA A 291 " =    1.018
peak=    3.118 closest distance to " O   HOH Z 380 " =    1.758
peak=    3.117 closest distance to " NH2AARG A 190 " =    1.080
peak=    3.115 closest distance to " OH  TYR A 214 " =    1.267
peak=    3.114 closest distance to " CG2 ILE A 234 " =    0.914
peak=    3.112 closest distance to " O   HOH Z 359 " =    2.064
peak=    3.112 closest distance to " OE2 GLU A  53 " =    2.186
peak=    3.111 closest distance to " O   HOH Z 296 " =    1.642
peak=    3.107 closest distance to " CA  THR A 264 " =    0.766
peak=    3.102 closest distance to " O   HOH Z  93 " =    2.993
peak=    3.094 closest distance to " O   TRP A 274 " =    1.798
peak=    3.091 closest distance to " CB  ASN A  39 " =    0.862
peak=    3.086 closest distance to " CA  TRP A 274 " =    0.951
peak=    3.085 closest distance to " O   HOH Z 172 " =    3.745
peak=    3.082 closest distance to " CB  ALA A 100 " =    1.380
peak=    3.080 closest distance to " O   HOH Z 403 " =    1.359
peak=    3.064 closest distance to " O   HOH Z 203 " =    1.810
peak=    3.057 closest distance to " CZ3 TRP A  92 " =    1.189
peak=    3.055 closest distance to " O   HOH Z 148 " =    3.765
peak=    3.047 closest distance to " O   HOH Z 383 " =    2.306

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.375 - 5.527
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.729 - 5.527

peak=   -5.091 closest distance to " CG2 VAL A 230 " =    0.929
peak=   -4.612 closest distance to " O   HOH Z 377 " =    1.531
peak=   -4.451 closest distance to " O   HOH Z 102 " =    1.262
peak=   -4.415 closest distance to " O   HOH Z 231 " =    1.443
peak=   -4.307 closest distance to " CD  ARG A 138 " =    1.167
peak=   -4.194 closest distance to " CD  ARG A  14 " =    3.337
peak=   -4.188 closest distance to " CA  ASP A  27 " =    2.459
peak=   -4.162 closest distance to " OE1 GLN A  88 " =    1.006
peak=   -4.120 closest distance to " O   HOH Z 198 " =    2.512
peak=   -4.106 closest distance to " CD  ARG A 156 " =    1.970
peak=   -4.073 closest distance to " O   ILE A 109 " =    2.648
peak=   -4.016 closest distance to " CG1 VAL A 250 " =    2.618
peak=   -3.977 closest distance to " O   HOH Z  43 " =    1.569
peak=   -3.969 closest distance to " CG  ARG A 138 " =    0.912
peak=   -3.931 closest distance to " C   ASN A 285 " =    2.557
peak=   -3.906 closest distance to " O   HOH Z 266 " =    4.601
peak=   -3.904 closest distance to " O   PRO A 163 " =    1.911
peak=   -3.888 closest distance to " O   HOH Z 290 " =    1.198
peak=   -3.860 closest distance to " N   ALA A  43 " =    2.457
peak=   -3.851 closest distance to " O   HOH Z 274 " =    2.815
peak=   -3.851 closest distance to " OG  SER A  87 " =    1.311
peak=   -3.849 closest distance to " O   HOH Z 350 " =    1.614
peak=   -3.828 closest distance to " CG  GLN A  88 " =    0.827
peak=   -3.822 closest distance to " CD1 LEU A 228 " =    2.404
peak=   -3.810 closest distance to " OG ASER A 134 " =    1.219
peak=   -3.794 closest distance to " CG  GLN A 223 " =    2.242
peak=   -3.784 closest distance to " O   HOH Z 166 " =    1.404
peak=   -3.783 closest distance to " OG BSER A 134 " =    1.285
peak=   -3.753 closest distance to " O   HOH Z  71 " =    1.114
peak=   -3.748 closest distance to " O   HOH Z  13 " =    1.428
peak=   -3.744 closest distance to " O   HOH Z 275 " =    1.626
peak=   -3.731 closest distance to " CG  PRO A 163 " =    2.430
peak=   -3.731 closest distance to " O   HOH Z 388 " =    1.978
peak=   -3.729 closest distance to " C   ALA A 158 " =    1.228
peak=   -3.716 closest distance to " CG1 VAL A 296 " =    1.511
peak=   -3.716 closest distance to " CB  TRP A  85 " =    2.437
peak=   -3.708 closest distance to " N   THR A 157 " =    1.493
peak=   -3.706 closest distance to " O   HOH Z  98 " =    1.591
peak=   -3.700 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.694 closest distance to " CD1 PHE A  59 " =    1.722
peak=   -3.693 closest distance to " CD  LYS A 289 " =    2.554
peak=   -3.689 closest distance to " O   SER A 271 " =    2.349
peak=   -3.662 closest distance to " O   GLY A  80 " =    2.508
peak=   -3.661 closest distance to " OG  SER A  26 " =    1.197
peak=   -3.656 closest distance to " O   SER A 135 " =    1.416
peak=   -3.633 closest distance to " CG2 VAL A 296 " =    1.506
peak=   -3.632 closest distance to " O   PRO A 198 " =    1.352
peak=   -3.619 closest distance to " O   HOH Z 231 " =    0.993
peak=   -3.612 closest distance to " OH  TYR A 214 " =    1.151
peak=   -3.584 closest distance to " OG1 THR A 178 " =    1.260
peak=   -3.576 closest distance to " CB  ALA A  43 " =    2.460
peak=   -3.571 closest distance to " CZ3 TRP A 179 " =    1.185
peak=   -3.566 closest distance to " CG  ASP A 231 " =    0.853
peak=   -3.556 closest distance to " CD1 LEU A 101 " =    2.624
peak=   -3.546 closest distance to " CB  PRO A 163 " =    2.501
peak=   -3.545 closest distance to " NH2AARG A 275 " =    5.527
peak=   -3.544 closest distance to " NH2 ARG A  66 " =    2.142
peak=   -3.541 closest distance to " O   HOH Z 166 " =    1.883
peak=   -3.540 closest distance to " N   ALA A   9 " =    1.516
peak=   -3.540 closest distance to " CB  PRO A 243 " =    2.599
peak=   -3.523 closest distance to " O   HOH Z 389 " =    1.825
peak=   -3.516 closest distance to " O   HOH Z 407 " =    3.343
peak=   -3.512 closest distance to " CD  GLN A  88 " =    2.321
peak=   -3.510 closest distance to " CD2 LEU A 237 " =    2.822
peak=   -3.509 closest distance to " C   ASN A 187 " =    1.673
peak=   -3.497 closest distance to " CA  GLY A 241 " =    2.308
peak=   -3.482 closest distance to " O   GLY A 211 " =    1.477
peak=   -3.480 closest distance to " O   HOH Z 353 " =    2.260
peak=   -3.479 closest distance to " O   HOH Z  65 " =    1.175
peak=   -3.471 closest distance to " O   HOH Z 179 " =    0.827
peak=   -3.471 closest distance to " NH1 ARG A  56 " =    2.382
peak=   -3.463 closest distance to " CG  MET A 105 " =    1.006
peak=   -3.460 closest distance to " C   LEU A 222 " =    0.729
peak=   -3.451 closest distance to " N   ALA A 226 " =    2.058
peak=   -3.442 closest distance to " C   LEU A 143 " =    1.364
peak=   -3.441 closest distance to " CG  ASN A  45 " =    1.745
peak=   -3.440 closest distance to " CG2BVAL A  41 " =    2.740
peak=   -3.432 closest distance to " CD  ARG A 139 " =    1.715
peak=   -3.425 closest distance to " SD BMET A  47 " =    0.897
peak=   -3.421 closest distance to " O   HOH Z  98 " =    2.020
peak=   -3.420 closest distance to " CB  ASN A  39 " =    2.082
peak=   -3.418 closest distance to " C   GLN A 240 " =    2.382
peak=   -3.412 closest distance to " CD2 LEU A 167 " =    1.818
peak=   -3.411 closest distance to " O   PRO A 198 " =    1.376
peak=   -3.408 closest distance to " CB  TYR A 172 " =    2.364
peak=   -3.405 closest distance to " CE1 TYR A 169 " =    2.522
peak=   -3.405 closest distance to " CB  TYR A  15 " =    2.216
peak=   -3.401 closest distance to " O   TYR A  30 " =    2.848
peak=   -3.399 closest distance to " O   HOH Z 436 " =    1.447
peak=   -3.396 closest distance to " O   HOH Z  52 " =    1.713
peak=   -3.395 closest distance to " O   HOH Z 128 " =    3.988
peak=   -3.390 closest distance to " O   HOH Z 426 " =    1.758
peak=   -3.389 closest distance to " O   HOH Z  38 " =    1.676
peak=   -3.387 closest distance to " O   HOH Z 394 " =    1.525
peak=   -3.386 closest distance to " OG1 THR A   4 " =    1.898
peak=   -3.381 closest distance to " O   VAL A 197 " =    1.560
peak=   -3.381 closest distance to " CE2 TYR A  30 " =    2.913
peak=   -3.379 closest distance to " CD  ARG A 195 " =    5.121
peak=   -3.375 closest distance to " CG2 VAL A 296 " =    0.961
peak=   -3.367 closest distance to " O   HOH Z 243 " =    1.616
peak=   -3.365 closest distance to " O   HOH Z 219 " =    1.110
peak=   -3.349 closest distance to " CG  GLU A 152 " =    2.013
peak=   -3.343 closest distance to " ND2 ASN A  45 " =    1.057
peak=   -3.337 closest distance to " O   HOH Z 435 " =    2.760
peak=   -3.331 closest distance to " N   GLN A  58 " =    1.623
peak=   -3.321 closest distance to " NH2 ARG A  79 " =    1.850
peak=   -3.319 closest distance to " O   HOH Z 298 " =    1.305
peak=   -3.318 closest distance to " CB  GLN A  55 " =    1.138
peak=   -3.314 closest distance to " CZ BARG A 275 " =    1.845
peak=   -3.314 closest distance to " CD2 LEU A   5 " =    1.209
peak=   -3.313 closest distance to " O   HOH Z  88 " =    1.898
peak=   -3.311 closest distance to " O   HOH Z 184 " =    1.760
peak=   -3.310 closest distance to " O   HOH Z 292 " =    4.609
peak=   -3.307 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.306 closest distance to " O   HOH Z 222 " =    1.356
peak=   -3.305 closest distance to " OD1 ASN A 148 " =    1.562
peak=   -3.305 closest distance to " O   HOH Z 295 " =    1.371
peak=   -3.301 closest distance to " CB  CYS A 254 " =    2.129
peak=   -3.298 closest distance to " O   HOH Z 317 " =    2.309
peak=   -3.297 closest distance to " CD1 ILE A 199 " =    2.537
peak=   -3.296 closest distance to " CB  SER A  63 " =    3.346
peak=   -3.292 closest distance to " O   HOH Z 306 " =    2.894
peak=   -3.289 closest distance to " CE  MET A 105 " =    2.147
peak=   -3.286 closest distance to " CG  TRP A 266 " =    1.678
peak=   -3.284 closest distance to " CE2 PHE A 283 " =    2.429
peak=   -3.281 closest distance to " O   HOH Z 411 " =    3.793
peak=   -3.279 closest distance to " CH2 TRP A 177 " =    2.265
peak=   -3.266 closest distance to " CE1 PHE A 208 " =    2.041
peak=   -3.266 closest distance to " O   HOH Z 221 " =    1.478
peak=   -3.266 closest distance to " O   SER A  12 " =    1.658
peak=   -3.262 closest distance to " CB  PRO A  54 " =    2.356
peak=   -3.261 closest distance to " CG  LYS A 193 " =    2.403
peak=   -3.258 closest distance to " O   HOH Z 109 " =    1.577
peak=   -3.258 closest distance to " CD2 PHE A  61 " =    1.901
peak=   -3.257 closest distance to " N   VAL A 125 " =    0.869
peak=   -3.254 closest distance to " CG  LEU A 228 " =    0.970
peak=   -3.254 closest distance to " O   HOH Z 211 " =    1.563
peak=   -3.253 closest distance to " CG  ASP A  50 " =    2.121
peak=   -3.248 closest distance to " OG1 THR A  82 " =    1.813
peak=   -3.243 closest distance to " CB  ILE A 239 " =    2.022
peak=   -3.243 closest distance to " CE2 PHE A 218 " =    2.548
peak=   -3.241 closest distance to " O   HOH Z 393 " =    3.719
peak=   -3.238 closest distance to " ND2BASN A 224 " =    1.632
peak=   -3.233 closest distance to " O   ASN A 301 " =    1.487
peak=   -3.232 closest distance to " O   HOH Z 205 " =    2.058
peak=   -3.231 closest distance to " CB  PHE A 192 " =    1.723
peak=   -3.229 closest distance to " CE3 TRP A 150 " =    2.055
peak=   -3.228 closest distance to " CG  PHE A 283 " =    2.621
peak=   -3.223 closest distance to " CA  GLY A  35 " =    2.002
peak=   -3.219 closest distance to " ND2 ASN A  60 " =    1.791
peak=   -3.218 closest distance to " CG  ARG A 259 " =    2.602
peak=   -3.216 closest distance to " OD2 ASP A  50 " =    1.678
peak=   -3.216 closest distance to " O   HOH Z 198 " =    1.524
peak=   -3.213 closest distance to " O   HOH Z 283 " =    1.962
peak=   -3.210 closest distance to " CB  ALA A 248 " =    1.926
peak=   -3.210 closest distance to " O   HOH Z 410 " =    1.929
peak=   -3.209 closest distance to " CB  ARG A  79 " =    2.551
peak=   -3.204 closest distance to " O   HOH Z 132 " =    1.398
peak=   -3.203 closest distance to " O   HOH Z 359 " =    3.346
peak=   -3.201 closest distance to " CG  GLU A   2 " =    2.191
peak=   -3.199 closest distance to " O   HOH Z  44 " =    1.943
peak=   -3.198 closest distance to " CD1 LEU A   5 " =    2.554
peak=   -3.198 closest distance to " N   ALA A 248 " =    1.682
peak=   -3.198 closest distance to " ND2 ASN A 173 " =    1.875
peak=   -3.197 closest distance to " CD  PRO A 213 " =    2.164
peak=   -3.195 closest distance to " O   HOH Z 119 " =    2.508
peak=   -3.193 closest distance to " CB  ALA A 291 " =    2.099
peak=   -3.192 closest distance to " CG1 VAL A 112 " =    2.973
peak=   -3.192 closest distance to " CB  ALA A 227 " =    2.404
peak=   -3.191 closest distance to " OG BSER A 134 " =    1.750
peak=   -3.191 closest distance to " O   HOH Z 426 " =    2.288
peak=   -3.181 closest distance to " O   HOH Z  63 " =    1.269
peak=   -3.181 closest distance to " CG  GLN A 278 " =    2.372
peak=   -3.166 closest distance to " O   THR A  18 " =    1.592
peak=   -3.165 closest distance to " O   GLN A 194 " =    1.342
peak=   -3.163 closest distance to " O   HOH Z 103 " =    1.808
peak=   -3.163 closest distance to " CG2 THR A 178 " =    2.197
peak=   -3.160 closest distance to " OG  SER A 245 " =    1.168
peak=   -3.155 closest distance to " O   HOH Z 184 " =    1.424
peak=   -3.155 closest distance to " CG2 VAL A 112 " =    2.512
peak=   -3.150 closest distance to " NH1AARG A 275 " =    1.892
peak=   -3.150 closest distance to " O   HOH Z 389 " =    4.379
peak=   -3.150 closest distance to " O   HOH Z 396 " =    1.690
peak=   -3.148 closest distance to " OD1 ASN A 249 " =    1.327
peak=   -3.147 closest distance to " O   HOH Z 345 " =    1.998
peak=   -3.137 closest distance to " O   HOH Z 339 " =    1.927
peak=   -3.135 closest distance to " CZ  TYR A 172 " =    1.646
peak=   -3.134 closest distance to " N   GLY A  23 " =    2.224
peak=   -3.132 closest distance to " SG BCYS A 201 " =    2.219
peak=   -3.131 closest distance to " O   HOH Z 210 " =    1.106
peak=   -3.131 closest distance to " CD2 LEU A 300 " =    2.883
peak=   -3.131 closest distance to " CA  SER A  62 " =    2.558
peak=   -3.127 closest distance to " O   MET A  40 " =    2.810
peak=   -3.118 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.116 closest distance to " NZ  LYS A 119 " =    3.321
peak=   -3.113 closest distance to " O   HOH Z 186 " =    1.402
peak=   -3.109 closest distance to " O   HOH Z 313 " =    1.706
peak=   -3.094 closest distance to " O   GLY A 203 " =    2.778
peak=   -3.079 closest distance to " O   HOH Z 234 " =    4.324
peak=   -3.069 closest distance to " O   HOH Z 177 " =    1.478
peak=   -3.068 closest distance to " O   SER A  22 " =    2.304
peak=   -3.066 closest distance to " OE1 GLN A 278 " =    1.201
peak=   -3.055 closest distance to " O   HOH Z  60 " =    2.060
peak=   -3.041 closest distance to " O   HOH Z 350 " =    2.587
peak=   -3.029 closest distance to " N   ALA A 248 " =    2.447
peak=   -3.016 closest distance to " CG2 VAL A 296 " =    1.911
peak=   -3.003 closest distance to " N   MET A 105 " =    2.567
peak=   -2.997 closest distance to " O   HOH Z 102 " =    1.487

================= 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    :  0.4769 0.4687   6.277259e+00   6.268792e+00
   1_bss:  0.4680 0.4580   6.272949e+00   6.262093e+00
   1_xyz:  0.3872 0.4138   6.157780e+00   6.201723e+00
   1_adp:  0.3405 0.3873   6.074220e+00   6.168469e+00
   1_occ:  0.3399 0.3879   6.073575e+00   6.168510e+00
   2_bss:  0.3369 0.3841   6.073507e+00   6.167662e+00
   2_xyz:  0.2387 0.2958   5.791849e+00   5.963177e+00
   2_adp:  0.2140 0.2748   5.704280e+00   5.892414e+00
   2_occ:  0.2137 0.2748   5.703585e+00   5.892270e+00
   3_bss:  0.2114 0.2706   5.701020e+00   5.888337e+00
   3_xyz:  0.1654 0.2152   5.476490e+00   5.684474e+00
   3_adp:  0.1528 0.2034   5.416016e+00   5.633791e+00
   3_occ:  0.1527 0.2033   5.415519e+00   5.633116e+00
   4_bss:  0.1529 0.2030   5.415616e+00   5.631545e+00
   4_xyz:  0.1333 0.1837   5.298150e+00   5.529774e+00
   4_adp:  0.1296 0.1794   5.274765e+00   5.508616e+00
   4_occ:  0.1295 0.1792   5.274189e+00   5.507899e+00
   5_bss:  0.1295 0.1792   5.273764e+00   5.507903e+00
   5_xyz:  0.1181 0.1691   5.205083e+00   5.456041e+00
   5_adp:  0.1164 0.1672   5.194418e+00   5.449180e+00
   5_occ:  0.1163 0.1670   5.193906e+00   5.448709e+00
   5_bss:  0.1165 0.1671   5.194235e+00   5.449574e+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:  0.330  11.567  10.153   7.435   7.950   0.000   0.000   0.000
   1_xyz:  0.330  11.567  10.153   7.435   7.950   0.000   0.000   0.000
   1_adp:  0.330  11.567  10.153   7.435   7.950   0.000   0.000   0.000
   1_occ:  0.330  11.567  10.153   7.435   7.950   0.000   0.000   0.000
   2_bss:  0.332  34.157   6.301   4.005   5.263   0.000   0.000   0.000
   2_xyz:  0.332  34.157   6.301   4.005   5.263   0.000   0.000   0.000
   2_adp:  0.332  34.157   6.301   4.005   5.263   0.000   0.000   0.000
   2_occ:  0.332  34.157   6.301   4.005   5.263   0.000   0.000   0.000
   3_bss:  0.338  49.266   3.614   2.272   3.174   0.000   0.000   0.000
   3_xyz:  0.338  49.266   3.614   2.272   3.174   0.000   0.000   0.000
   3_adp:  0.338  49.266   3.614   2.272   3.174   0.000   0.000   0.000
   3_occ:  0.338  49.266   3.614   2.272   3.174   0.000   0.000   0.000
   4_bss:  0.338  49.266   2.721   1.883   2.636   0.000   0.000   0.000
   4_xyz:  0.338  49.266   2.721   1.883   2.636   0.000   0.000   0.000
   4_adp:  0.338  49.266   2.721   1.883   2.636   0.000   0.000   0.000
   4_occ:  0.338  49.266   2.721   1.883   2.636   0.000   0.000   0.000
   5_bss:  0.331  50.274   2.349   1.694   2.454   0.000   0.000   0.000
   5_xyz:  0.331  50.274   2.349   1.694   2.454   0.000   0.000   0.000
   5_adp:  0.331  50.274   2.349   1.694   2.454   0.000   0.000   0.000
   5_occ:  0.331  50.274   2.349   1.694   2.454   0.000   0.000   0.000
   5_bss:  0.325  52.391   0.172  -0.454   0.283   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.531 0.4386  0.5154    69267.951
   1_bss:  56.823 0.4328  0.6451    66460.031
   1_xyz:  48.202 0.5413  0.7949    50843.146
   1_adp:  43.697 0.5973  0.9099    44412.177
   1_occ:  43.826 0.5956  0.9062    44556.359
   2_bss:  43.597 0.5983  0.8126    44271.960
   2_xyz:  31.027 0.7453  0.9768    23791.654
   2_adp:  27.869 0.7807  1.0064    20172.094
   2_occ:  27.853 0.7809  1.0066    20144.902
   3_bss:  27.628 0.7831  0.9339    19881.548
   3_xyz:  20.904 0.8526  0.9812    12026.080
   3_adp:  19.479 0.8669  0.9886    10805.176
   3_occ:  19.462 0.8671  0.9886    10786.757
   4_bss:  19.422 0.8674  0.9673    10733.769
   4_xyz:  16.989 0.8897  0.9812     8598.286
   4_adp:  16.400 0.8953  0.9838     8223.184
   4_occ:  16.383 0.8954  0.9838     8211.101
   5_bss:  16.378 0.8954  0.9751     8205.723
   5_xyz:  15.316 0.9043  0.9793     7340.201
   5_adp:  15.111 0.9062  0.9766     7211.001
   5_occ:  15.097 0.9063  0.9766     7196.997
   5_bss:  15.098 0.9064  0.9744     7193.731
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3747e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3747e+01
   1_xyz:   1.702  0.013  0.108 18.371  0.006  4.110   1.4378e-01
   1_adp:   1.702  0.013  0.108 18.371  0.006  4.110   1.4378e-01
   1_occ:   1.702  0.013  0.108 18.371  0.006  4.110   1.4378e-01
   2_bss:   1.702  0.013  0.108 18.371  0.006  4.110   1.4378e-01
   2_xyz:   1.181  0.009  0.083 16.780  0.005  4.112   8.5867e-02
   2_adp:   1.181  0.009  0.083 16.780  0.005  4.112   8.5867e-02
   2_occ:   1.181  0.009  0.083 16.780  0.005  4.112   8.5867e-02
   3_bss:   1.181  0.009  0.083 16.780  0.005  4.112   8.5867e-02
   3_xyz:   0.971  0.006  0.072 15.609  0.004  4.128   5.9482e-02
   3_adp:   0.971  0.006  0.072 15.609  0.004  4.128   5.9482e-02
   3_occ:   0.971  0.006  0.072 15.609  0.004  4.128   5.9482e-02
   4_bss:   0.971  0.006  0.072 15.609  0.004  4.128   5.9482e-02
   4_xyz:   0.967  0.006  0.074 15.489  0.003  4.112   5.8996e-02
   4_adp:   0.967  0.006  0.074 15.489  0.003  4.112   5.8996e-02
   4_occ:   0.967  0.006  0.074 15.489  0.003  4.112   5.8996e-02
   5_bss:   0.967  0.006  0.074 15.489  0.003  4.112   5.8996e-02
   5_xyz:   1.146  0.009  0.086 15.951  0.004  4.116   7.6726e-02
   5_adp:   1.146  0.009  0.086 15.951  0.004  4.116   7.6726e-02
   5_occ:   1.146  0.009  0.086 15.951  0.004  4.116   7.6726e-02
   5_bss:   1.146  0.009  0.086 15.951  0.004  4.116   7.6726e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9684e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9684e+00
   1_xyz:  14.100  0.171  0.472 84.581  0.044  2.186   1.0302e-01
   1_adp:  14.100  0.171  0.472 84.581  0.044  2.186   1.0302e-01
   1_occ:  14.100  0.171  0.472 84.581  0.044  2.186   1.0302e-01
   2_bss:  14.100  0.171  0.472 84.581  0.044  2.186   1.0302e-01
   2_xyz:   8.074  0.070  0.267 82.927  0.049  2.225   5.9481e-02
   2_adp:   8.074  0.070  0.267 82.927  0.049  2.225   5.9481e-02
   2_occ:   8.074  0.070  0.267 82.927  0.049  2.225   5.9481e-02
   3_bss:   8.074  0.070  0.267 82.927  0.049  2.225   5.9481e-02
   3_xyz:   8.689  0.047  0.255 89.208  0.046  2.390   6.1150e-02
   3_adp:   8.689  0.047  0.255 89.208  0.046  2.390   6.1150e-02
   3_occ:   8.689  0.047  0.255 89.208  0.046  2.390   6.1150e-02
   4_bss:   8.689  0.047  0.255 89.208  0.046  2.390   6.1150e-02
   4_xyz:   8.258  0.060  0.321 81.127  0.037  2.354   3.8806e-02
   4_adp:   8.258  0.060  0.321 81.127  0.037  2.354   3.8806e-02
   4_occ:   8.258  0.060  0.321 81.127  0.037  2.354   3.8806e-02
   5_bss:   8.258  0.060  0.321 81.127  0.037  2.354   3.8806e-02
   5_xyz:   9.331  0.071  0.501 84.378  0.030  2.302   5.3628e-02
   5_adp:   9.331  0.071  0.501 84.378  0.030  2.302   5.3628e-02
   5_occ:   9.331  0.071  0.501 84.378  0.030  2.302   5.3628e-02
   5_bss:   9.331  0.071  0.501 84.378  0.030  2.302   5.3628e-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:  78.34   0.00  12.68  78.34   0.00  10.12  66.36   0.00  26.59
   1_occ:  78.34   0.00  12.68  78.34   0.00  10.12  66.36   0.00  26.59
   2_bss:  78.34   0.00  12.68  78.34   0.00  10.12  66.36   0.00  26.59
   2_xyz:  78.34   0.00  12.68  78.34   0.00  10.12  66.36   0.00  26.59
   2_adp:  78.57   0.00  12.79  78.57   0.00   9.06  70.14   0.83  33.09
   2_occ:  78.57   0.00  12.79  78.57   0.00   9.06  70.14   0.83  33.09
   3_bss:  78.57   0.00  12.79  78.57   0.00   9.06  70.14   0.83  33.09
   3_xyz:  78.57   0.00  12.79  78.57   0.00   9.06  70.14   0.83  33.09
   3_adp:  83.80   0.00  13.36  83.80   0.00   8.96  82.85   1.80  37.32
   3_occ:  83.80   0.00  13.36  83.80   0.00   8.96  82.85   1.80  37.32
   4_bss:  83.80   0.00  13.36  83.80   0.00   8.96  82.85   1.80  37.32
   4_xyz:  83.80   0.00  13.36  83.80   0.00   8.96  82.85   1.80  37.32
   4_adp:  89.14   0.00  13.36  89.14   0.00   8.95  85.36   2.12  37.42
   4_occ:  89.14   0.00  13.36  89.14   0.00   8.95  85.36   2.12  37.42
   5_bss:  89.14   0.00  13.36  89.14   0.00   8.95  85.36   2.12  37.42
   5_xyz:  89.14   0.00  13.36  89.14   0.00   8.95  85.36   2.12  37.42
   5_adp:  93.23   0.00  13.41  93.23   0.00   8.94  89.74   2.42  37.79
   5_occ:  93.23   0.00  13.41  93.23   0.00   8.94  89.74   2.42  37.79
   5_bss:  95.35   2.12  15.53  95.35   2.12  11.05  91.85   4.54  39.91
------------------------------------------------------------------------
 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:    1.225    0.025    0.413
   1_adp:    1.225    0.025    0.413
   1_occ:    1.225    0.025    0.413
   2_bss:    1.225    0.025    0.413
   2_xyz:    1.428    0.020    0.596
   2_adp:    1.428    0.020    0.596
   2_occ:    1.428    0.020    0.596
   3_bss:    1.428    0.020    0.596
   3_xyz:    1.562    0.032    0.654
   3_adp:    1.562    0.032    0.654
   3_occ:    1.562    0.032    0.654
   4_bss:    1.562    0.032    0.654
   4_xyz:    1.803    0.036    0.697
   4_adp:    1.803    0.036    0.697
   4_occ:    1.803    0.036    0.697
   5_bss:    1.803    0.036    0.697
   5_xyz:    1.956    0.018    0.719
   5_adp:    1.956    0.018    0.719
   5_occ:    1.956    0.018    0.719
   5_bss:    1.956    0.018    0.719
------------------------------------------------------------------------

CPU time actual refinement: 287.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1256/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_1256/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1256/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1256/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1256/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 287.36 
  Macro-tasks:
    bulk solvent and scale       = 33.49  
    individual site refinement   = 121.56 
    weights calculation          = 26.35  
    collect and process          = 5.26   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 186.74 
  Micro-tasks:
    mask                            = 2.02   
    f_calc                          = 91.25  
    alpha_beta                      = 6.82   
    target                          = 0.92   
    gradients_wrt_atomic_parameters = 100.00 
    fmodel                         = 6.01   
    r_factors                      = 0.17   
    phase_errors                   = 8.65   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 216.06 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.032 micro seconds
Total CPU time: 4.98 minutes
from_scatterers_fft:    648 calls, 91.06 s
gradients_fft:          592 calls, 88.37 s

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

# Date 2008-01-16 Time 03:33:21 PST -0800 (1200483201.57 s)
Start R-work = 0.4769, R-free = 0.4687 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4680, R-free = 0.4580
Final R-work = 0.1165, R-free = 0.1671