# Date 2008-01-16 Time 02:22:11 PST -0800 (1200478931.11 s)
#phil __OFF__

Command line arguments: "../805.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 = 23821
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 805

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 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: (70.6012, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.9713
Completeness in resolution range: 0.945461
Completeness with d_max=infinity: 0.942595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9858
                             d_min =   1.9713

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.9713
Completeness in resolution range: 0.945461
Completeness with d_max=infinity: 0.942595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9863 -  4.2184 [2180/2209]  1962   218  10.0%
  bin  2:  4.2184 -  3.3607 [2076/2099]  1870   206   9.9%
  bin  3:  3.3607 -  2.9395 [2064/2086]  1855   209  10.1%
  bin  4:  2.9395 -  2.6724 [2051/2070]  1853   198   9.7%
  bin  5:  2.6724 -  2.4818 [2043/2072]  1831   212  10.4%
  bin  6:  2.4818 -  2.3361 [2014/2055]  1816   198   9.8%
  bin  7:  2.3361 -  2.2195 [1997/2033]  1797   200  10.0%
  bin  8:  2.2195 -  2.1231 [2001/2039]  1801   200  10.0%
  bin  9:  2.1231 -  2.0416 [2000/2032]  1796   204  10.2%
  bin 10:  2.0416 -  1.9713 [1163/2024]  1049   114   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_805/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:
        1.81 -     2.42: 24
        2.42 -     3.04: 2187
        3.04 -     3.66: 4691
        3.66 -     4.28: 9007
        4.28 -     4.90: 12406
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.882 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.967 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  2.056 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.065 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28310 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_805/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_805/model_refine_001.geo

CPU time processing inputs: 7.83


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4536   r_free= 0.4487   ksol= 0.00   Bsol= 0.00   scale= 0.811    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.253152                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7052 0.99   1411  155 0.3742 0.3588      6.5487      6.5225|
|  2:  4.7052 -  3.7540 0.99   1361  150 0.3589 0.3800      6.7129      6.7248|
|  3:  3.7540 -  3.2851 0.99   1332  155 0.4036 0.3786      6.6072      6.6168|
|  4:  3.2851 -  2.9874 0.99   1330  146 0.4293 0.4250      6.4726       6.439|
|  5:  2.9874 -  2.7747 0.99   1309  145 0.4737 0.5008      6.3423      6.3701|
|  6:  2.7747 -  2.6120 0.98   1306  145 0.4763 0.5059      6.2433      6.1805|
|  7:  2.6120 -  2.4818 0.99   1322  147 0.4894 0.3993      6.2417      6.1278|
|  8:  2.4818 -  2.3742 0.99   1292  144 0.5017 0.5103      6.1472       6.182|
|  9:  2.3742 -  2.2831 0.98   1299  143 0.5177 0.5148       6.124      6.0999|
| 10:  2.2831 -  2.2046 0.98   1275  140 0.5050 0.5270      6.0898      6.1208|
| 11:  2.2046 -  2.1359 0.98   1285  144 0.5027 0.4604      6.0212      6.0225|
| 12:  2.1359 -  2.0750 0.99   1276  139 0.5224 0.5720      5.9643      6.0148|
| 13:  2.0750 -  2.0205 0.97   1296  145 0.5286 0.4877      5.8718      5.8269|
| 14:  2.0205 -  1.9713 0.42    536   61 0.5356 0.5567      5.8409      5.7568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7052  1411   155  0.73  31.82   0.81     0.75      61385.04|
|  2:  4.7052 -  3.7540  1361   150  0.74  31.31   0.90     0.80      85135.34|
|  3:  3.7540 -  3.2851  1332   155  0.65  39.33   0.85     0.76      92653.42|
|  4:  3.2851 -  2.9874  1330   146  0.58  45.77   0.82     0.66      84247.16|
|  5:  2.9874 -  2.7747  1309   145  0.48  53.40   0.76     0.57      73529.50|
|  6:  2.7747 -  2.6120  1306   145  0.48  53.92   0.76     0.55      61479.42|
|  7:  2.6120 -  2.4818  1322   147  0.50  52.05   0.75     0.55      52982.72|
|  8:  2.4818 -  2.3742  1292   144  0.48  53.51   0.73     0.55      47966.11|
|  9:  2.3742 -  2.2831  1299   143  0.44  56.82   0.74     0.51      46421.22|
| 10:  2.2831 -  2.2046  1275   140  0.40  59.79   0.77     0.48      46584.19|
| 11:  2.2046 -  2.1359  1285   144  0.35  63.45   0.77     0.43      44992.02|
| 12:  2.1359 -  2.0750  1276   139  0.31  66.88   0.75     0.39      44085.71|
| 13:  2.0750 -  2.0205  1296   145  0.29  68.33   0.73     0.37      37891.35|
| 14:  2.0205 -  1.9713   536    61  0.34  64.52   0.73     0.39      29719.66|
|alpha:            min =        0.37 max =            0.80 mean =         0.56|
|beta:             min =    29719.66 max =        92653.42 mean =     59291.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.13|
|phase err.(test): min =        0.00 max =           89.98 mean =        52.22|
|-----------------------------------------------------------------------------|

============================== 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 = 10.393530             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.562   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.872525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.776   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1517 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2622 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3917 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5074 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6544 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7772 |
|-----------------------------------------------------------------------------|
|-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 |       53.718 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.776 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    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 = 11.922)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4605   r_free= 0.4549   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.256270                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4451   r_free= 0.4369   ksol= 0.34   Bsol= 16.36   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.12,9.43,8.51,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.251590                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.283147              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.928   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.816090              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.500   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4451      final r-factor (work) = 0.3494          |
| start r-factor (free) = 0.4369      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.7592 = 9.28 * 0.50 * 6.2568 + 1.00 * 53.7179                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.5678 = 9.28 * 0.50 * 6.1259 + 1.00 * 0.1338                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3494      final r-factor (work) = 0.2981          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.3445          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0137 = 0.82 * 1.00 * 6.1259 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9102 = 0.82 * 1.00 * 6.0007 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.69   11.56    None  None   None       |
|    all(noH): 2823   0      0.00    72.69   11.56    None  None   None       |
|    Sol.    : 438    0      0.00    71.12   27.42    None  None   None       |
|    Mac.    : 2385   0      0.00    72.69   8.64     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 -   7.269: 1364   |   5:    36.344 -  43.613:   77        |
|      1:     7.269 -  14.538:  711   |   6:    43.613 -  50.882:   41        |
|      2:    14.538 -  21.806:  314   |   7:    50.882 -  58.150:   21        |
|      3:    21.806 -  29.075:  161   |   8:    58.150 -  65.419:    9        |
|      4:    29.075 -  36.344:  119   |   9:    65.419 -  72.688:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2981 r_free = 0.3445             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2976 r_free = 0.3448             target_work(ml) = 5.965         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2976   r_free= 0.3448   ksol= 0.34   Bsol= 16.36   scale= 1.090   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.12,9.43,8.51,0.00,0.00,0.00); trace/3= 8.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.964803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2938   r_free= 0.3389   ksol= 0.33   Bsol= 43.08   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,5.59,5.55,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.964151                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.716539              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.892   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.404162              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.516  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2938      final r-factor (work) = 0.2077          |
| start r-factor (free) = 0.3389      final r-factor (free) = 0.2581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2853 = 3.72 * 0.50 * 6.0010 + 1.00 * 0.1338                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8703 = 3.72 * 0.50 * 5.8142 + 1.00 * 0.0658                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2077      final r-factor (work) = 0.1904          |
| start r-factor (free) = 0.2581      final r-factor (free) = 0.2396          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3632 = 0.40 * 1.00 * 5.8142 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2867 = 0.40 * 1.00 * 5.6317 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.78   11.98    None  None   None       |
|    all(noH): 2823   0      0.00    75.78   11.98    None  None   None       |
|    Sol.    : 438    0      1.78    68.40   32.17    None  None   None       |
|    Mac.    : 2385   0      0.00    75.78   8.27     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 -   7.578: 1454   |   5:    37.891 -  45.469:  105        |
|      1:     7.578 -  15.156:  720   |   6:    45.469 -  53.047:   62        |
|      2:    15.156 -  22.734:  198   |   7:    53.047 -  60.625:   24        |
|      3:    22.734 -  30.313:  126   |   8:    60.625 -  68.203:    7        |
|      4:    30.313 -  37.891:  124   |   9:    68.203 -  75.781:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1904 r_free = 0.2396             target_work(ml) = 5.596         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1902 r_free = 0.2397             target_work(ml) = 5.595         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1902   r_free= 0.2397   ksol= 0.33   Bsol= 43.08   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,5.59,5.55,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.595467                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1888   r_free= 0.2386   ksol= 0.32   Bsol= 43.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,3.60,3.66,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.595503                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.436452              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.906  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.522918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.538  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1888      final r-factor (work) = 0.1361          |
| start r-factor (free) = 0.2386      final r-factor (free) = 0.1794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5791 = 4.44 * 0.50 * 5.6411 + 1.00 * 0.0658                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1964 = 4.44 * 0.50 * 5.4647 + 1.00 * 0.0744                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1361      final r-factor (work) = 0.1256          |
| start r-factor (free) = 0.1794      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8680 = 0.52 * 1.00 * 5.4647 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7625 = 0.52 * 1.00 * 5.2613 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.37   12.34    None  None   None       |
|    all(noH): 2823   0      0.00    82.37   12.34    None  None   None       |
|    Sol.    : 438    0      1.27    69.92   35.01    None  None   None       |
|    Mac.    : 2385   0      0.00    82.37   8.18     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 -   8.237: 1624   |   5:    41.184 -  49.421:  107        |
|      1:     8.237 -  16.474:  612   |   6:    49.421 -  57.658:   67        |
|      2:    16.474 -  24.710:  163   |   7:    57.658 -  65.894:   17        |
|      3:    24.710 -  32.947:  107   |   8:    65.894 -  74.131:    9        |
|      4:    32.947 -  41.184:  115   |   9:    74.131 -  82.368:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1256 r_free = 0.1689             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1254 r_free = 0.1687             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1687   ksol= 0.32   Bsol= 43.08   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,3.60,3.66,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.233556                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1686   ksol= 0.32   Bsol= 43.08   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,2.95,3.12,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.582490              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.593  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.612725              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.842  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1256      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5031 = 3.58 * 0.50 * 5.2638 + 1.00 * 0.0744                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3858 = 3.58 * 0.50 * 5.1967 + 1.00 * 0.0773                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1953 = 0.61 * 1.00 * 5.1967 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1725 = 0.61 * 1.00 * 5.1585 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.27   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    88.27   12.33    None  None   None       |
|    Sol.    : 438    0      1.22    73.83   35.14    None  None   None       |
|    Mac.    : 2385   0      0.00    88.27   8.14     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 -   8.827: 1712   |   5:    44.136 -  52.963:   97        |
|      1:     8.827 -  17.654:  564   |   6:    52.963 -  61.790:   44        |
|      2:    17.654 -  26.482:  156   |   7:    61.790 -  70.617:   19        |
|      3:    26.482 -  35.309:  109   |   8:    70.617 -  79.444:    5        |
|      4:    35.309 -  44.136:  114   |   9:    79.444 -  88.272:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1117 r_free = 0.1590             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1590             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1590   ksol= 0.32   Bsol= 43.08   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,2.95,3.12,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156663                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1590   ksol= 0.32   Bsol= 43.08   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,2.88,3.12,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156607                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.106413              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.122  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.391639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.273  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5100 = 2.11 * 0.50 * 5.1582 + 1.00 * 0.0773                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4983 = 2.11 * 0.50 * 5.1614 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0331 = 0.39 * 1.00 * 5.1614 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0364 = 0.39 * 1.00 * 5.1608 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.70   12.19    None  None   None       |
|    all(noH): 2823   0      0.00    88.70   12.19    None  None   None       |
|    Sol.    : 438    0      1.22    73.34   34.70    None  None   None       |
|    Mac.    : 2385   0      0.00    88.70   8.05     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:     0.000 -   8.870: 1733   |   5:    44.351 -  53.222:   90        |
|      1:     8.870 -  17.741:  552   |   6:    53.222 -  62.092:   44        |
|      2:    17.741 -  26.611:  156   |   7:    62.092 -  70.962:   17        |
|      3:    26.611 -  35.481:  110   |   8:    70.962 -  79.832:    5        |
|      4:    35.481 -  44.351:  113   |   9:    79.832 -  88.703:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1583             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1584             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1584   ksol= 0.32   Bsol= 43.08   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,2.88,3.12,0.00,0.00,0.00); trace/3= 2.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159285                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7052 0.99   1411  155 0.0984 0.1241      5.3659      5.4936|
|  2:  4.7052 -  3.7540 0.99   1361  150 0.0858 0.1138      5.4301      5.6639|
|  3:  3.7540 -  3.2851 0.99   1332  155 0.1054 0.1566      5.4733      5.8546|
|  4:  3.2851 -  2.9874 0.99   1330  146 0.1237 0.1517      5.4632      5.6078|
|  5:  2.9874 -  2.7747 0.99   1309  145 0.1320 0.1755      5.3363      5.5131|
|  6:  2.7747 -  2.6120 0.98   1306  145 0.1240 0.1991      5.2297      5.4964|
|  7:  2.6120 -  2.4818 0.99   1322  147 0.1254 0.1672      5.1797      5.4261|
|  8:  2.4818 -  2.3742 0.99   1292  144 0.1178 0.1670      5.0742      5.2765|
|  9:  2.3742 -  2.2831 0.98   1299  143 0.1195 0.1845      5.0454      5.3266|
| 10:  2.2831 -  2.2046 0.98   1275  140 0.1161 0.1775      4.9871      5.2579|
| 11:  2.2046 -  2.1359 0.98   1285  144 0.1157 0.1699      4.9456       5.264|
| 12:  2.1359 -  2.0750 0.99   1276  139 0.1095 0.1628      4.8619      5.0901|
| 13:  2.0750 -  2.0205 0.97   1296  145 0.1186 0.1832      4.8044      5.0928|
| 14:  2.0205 -  1.9713 0.42    536   61 0.1090 0.1752      4.7081      4.8973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7052  1411   155  0.94   8.47   0.98     0.96       6659.07|
|  2:  4.7052 -  3.7540  1361   150  0.95   7.92   1.01     1.00       8741.10|
|  3:  3.7540 -  3.2851  1332   155  0.93  11.52   1.02     1.02      10661.28|
|  4:  3.2851 -  2.9874  1330   146  0.92  14.21   1.00     0.98      10588.31|
|  5:  2.9874 -  2.7747  1309   145  0.89  16.46   0.99     0.96       8549.35|
|  6:  2.7747 -  2.6120  1306   145  0.90  16.57   0.98     0.96       7490.50|
|  7:  2.6120 -  2.4818  1322   147  0.90  15.71   0.99     0.95       6383.47|
|  8:  2.4818 -  2.3742  1292   144  0.91  15.74   0.99     0.96       5546.73|
|  9:  2.3742 -  2.2831  1299   143  0.90  16.05   1.00     0.97       5147.47|
| 10:  2.2831 -  2.2046  1275   140  0.90  16.01   0.99     0.97       4674.21|
| 11:  2.2046 -  2.1359  1285   144  0.90  16.40   1.00     0.96       4389.74|
| 12:  2.1359 -  2.0750  1276   139  0.92  14.85   1.00     0.98       3856.80|
| 13:  2.0750 -  2.0205  1296   145  0.89  16.96   1.00     1.00       3474.01|
| 14:  2.0205 -  1.9713   536    61  0.90  16.10   0.98     0.95       2875.47|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2875.47 max =        10661.28 mean =      6546.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.36|
|phase err.(test): min =        0.00 max =           89.39 mean =        13.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1584   ksol= 0.32   Bsol= 47.61   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,0.09,0.36,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159137                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1584   ksol= 0.32   Bsol= 47.61   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.45,0.09,0.36,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159137                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7052 0.99   1411  155 0.0984 0.1245      5.3653      5.4948|
|  2:  4.7052 -  3.7540 0.99   1361  150 0.0860 0.1141      5.4322      5.6662|
|  3:  3.7540 -  3.2851 0.99   1332  155 0.1055 0.1568      5.4743       5.855|
|  4:  3.2851 -  2.9874 0.99   1330  146 0.1236 0.1517      5.4629      5.6074|
|  5:  2.9874 -  2.7747 0.99   1309  145 0.1319 0.1754      5.3354       5.512|
|  6:  2.7747 -  2.6120 0.98   1306  145 0.1239 0.1989      5.2289      5.4958|
|  7:  2.6120 -  2.4818 0.99   1322  147 0.1254 0.1673      5.1792       5.426|
|  8:  2.4818 -  2.3742 0.99   1292  144 0.1177 0.1668      5.0737      5.2755|
|  9:  2.3742 -  2.2831 0.98   1299  143 0.1195 0.1847      5.0451      5.3268|
| 10:  2.2831 -  2.2046 0.98   1275  140 0.1161 0.1774      4.9868      5.2574|
| 11:  2.2046 -  2.1359 0.98   1285  144 0.1157 0.1698      4.9453      5.2637|
| 12:  2.1359 -  2.0750 0.99   1276  139 0.1094 0.1629      4.8618      5.0903|
| 13:  2.0750 -  2.0205 0.97   1296  145 0.1186 0.1830      4.8042      5.0922|
| 14:  2.0205 -  1.9713 0.42    536   61 0.1090 0.1751      4.7075       4.897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7052  1411   155  0.94   8.50   0.98     0.96       6672.48|
|  2:  4.7052 -  3.7540  1361   150  0.95   7.95   1.01     1.00       8771.20|
|  3:  3.7540 -  3.2851  1332   155  0.93  11.55   1.02     1.02      10694.06|
|  4:  3.2851 -  2.9874  1330   146  0.92  14.20   1.00     0.98      10583.64|
|  5:  2.9874 -  2.7747  1309   145  0.89  16.45   0.99     0.96       8537.24|
|  6:  2.7747 -  2.6120  1306   145  0.90  16.56   0.98     0.96       7478.06|
|  7:  2.6120 -  2.4818  1322   147  0.90  15.71   0.99     0.96       6376.29|
|  8:  2.4818 -  2.3742  1292   144  0.91  15.73   0.99     0.96       5541.62|
|  9:  2.3742 -  2.2831  1299   143  0.90  16.04   1.00     0.97       5144.04|
| 10:  2.2831 -  2.2046  1275   140  0.90  16.00   1.00     0.97       4671.23|
| 11:  2.2046 -  2.1359  1285   144  0.90  16.39   1.00     0.96       4386.33|
| 12:  2.1359 -  2.0750  1276   139  0.92  14.85   1.00     0.98       3855.63|
| 13:  2.0750 -  2.0205  1296   145  0.89  16.95   1.00     1.00       3471.09|
| 14:  2.0205 -  1.9713   536    61  0.90  16.09   0.98     0.95       2871.29|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2871.29 max =        10694.06 mean =      6547.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.36|
|phase err.(test): min =        0.00 max =           89.08 mean =        13.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.82    91.53   15.01    None  None   None       |
|    all(noH): 2823   0      2.82    91.53   15.01    None  None   None       |
|    Sol.    : 438    0      4.05    76.16   37.53    None  None   None       |
|    Mac.    : 2385   0      2.82    91.53   10.88    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:     2.823 -  11.694: 1733   |   5:    47.175 -  56.045:   90        |
|      1:    11.694 -  20.564:  552   |   6:    56.045 -  64.915:   44        |
|      2:    20.564 -  29.434:  156   |   7:    64.915 -  73.785:   17        |
|      3:    29.434 -  38.304:  110   |   8:    73.785 -  82.656:    5        |
|      4:    38.304 -  47.175:  113   |   9:    82.656 -  91.526:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.373 - 5.980
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 328
   mapped sites are within: 0.745 - 5.980

peak=   10.339 closest distance to " CG2 VAL A 230 " =    1.400
peak=    7.421 closest distance to " CG2 VAL A 296 " =    1.105
peak=    6.399 closest distance to " CG  LEU A   5 " =    1.246
peak=    6.306 closest distance to " NH2 ARG A  56 " =    2.245
peak=    5.571 closest distance to " CG  PRO A  54 " =    1.273
peak=    5.391 closest distance to " CB  GLN A 223 " =    1.401
peak=    5.387 closest distance to " CG  LEU A 228 " =    1.213
peak=    5.303 closest distance to " CB  VAL A 296 " =    1.088
peak=    5.162 closest distance to " CB  SER A  63 " =    1.251
peak=    5.083 closest distance to " CB  PRO A  54 " =    0.901
peak=    5.073 closest distance to " CD2 LEU A   5 " =    1.173
peak=    4.911 closest distance to " CG  PRO A 213 " =    1.217
peak=    4.907 closest distance to " CB  VAL A 230 " =    1.234
peak=    4.845 closest distance to " CB  ARG A 275 " =    0.879
peak=    4.666 closest distance to " CB  GLN A 183 " =    1.310
peak=    4.632 closest distance to " O   HOH Z 316 " =    2.885
peak=    4.550 closest distance to " C   PRO A 198 " =    1.493
peak=    4.534 closest distance to " O   HOH Z  48 " =    1.661
peak=    4.529 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.495 closest distance to " CB  GLU A 152 " =    1.141
peak=    4.479 closest distance to " CG  PRO A 243 " =    1.154
peak=    4.443 closest distance to " OD1 ASN A  69 " =    2.594
peak=    4.433 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.426 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.402 closest distance to " O   HOH Z 193 " =    1.838
peak=    4.391 closest distance to " CB  SER A   3 " =    1.314
peak=    4.383 closest distance to " O   HOH Z 126 " =    1.850
peak=    4.375 closest distance to " CG  PRO A 280 " =    0.777
peak=    4.367 closest distance to " O   SER A  87 " =    2.263
peak=    4.356 closest distance to " CB  GLU A 128 " =    1.065
peak=    4.348 closest distance to " O   HOH Z 232 " =    2.267
peak=    4.340 closest distance to " O   HOH Z 298 " =    1.876
peak=    4.295 closest distance to " CB  ASN A 148 " =    1.319
peak=    4.269 closest distance to " CD2 LEU A 228 " =    1.267
peak=    4.265 closest distance to " O   HOH Z 236 " =    1.806
peak=    4.184 closest distance to " O   HOH Z  97 " =    1.971
peak=    4.171 closest distance to " O   HOH Z 403 " =    1.704
peak=    4.171 closest distance to " CB  GLU A 277 " =    3.593
peak=    4.165 closest distance to " CA  ALA A  21 " =    1.228
peak=    4.165 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.149 closest distance to " O   HOH Z 124 " =    1.395
peak=    4.134 closest distance to " O   HOH Z 128 " =    2.111
peak=    4.131 closest distance to " CB  TYR A 169 " =    0.772
peak=    4.128 closest distance to " O   HOH Z 423 " =    1.809
peak=    4.123 closest distance to " O   HOH Z 234 " =    3.679
peak=    4.115 closest distance to " CG1BVAL A  72 " =    1.642
peak=    4.104 closest distance to " O   HOH Z 280 " =    2.973
peak=    4.097 closest distance to " O   HOH Z 369 " =    2.124
peak=    4.079 closest distance to " O   HOH Z 345 " =    3.250
peak=    4.077 closest distance to " O   HOH Z 368 " =    2.247
peak=    4.074 closest distance to " CB  PRO A  54 " =    1.327
peak=    4.067 closest distance to " NH2 ARG A 156 " =    1.187
peak=    4.059 closest distance to " O   HOH Z  80 " =    1.685
peak=    4.045 closest distance to " O   TRP A 274 " =    1.897
peak=    4.044 closest distance to " O   HOH Z 389 " =    1.954
peak=    4.023 closest distance to " OD2 ASP A 286 " =    2.849
peak=    4.004 closest distance to " O   HOH Z 247 " =    1.313
peak=    3.996 closest distance to " CB  TRP A 179 " =    1.310
peak=    3.986 closest distance to " O   HOH Z 411 " =    3.695
peak=    3.978 closest distance to " O   HOH Z 295 " =    1.523
peak=    3.968 closest distance to " O   HOH Z 426 " =    1.492
peak=    3.962 closest distance to " O   HOH Z 344 " =    2.854
peak=    3.945 closest distance to " O   HOH Z 427 " =    2.954
peak=    3.934 closest distance to " O   HOH Z  20 " =    1.711
peak=    3.927 closest distance to " O   HOH Z  63 " =    1.726
peak=    3.897 closest distance to " CB  ARG A  79 " =    1.409
peak=    3.893 closest distance to " O   HOH Z 142 " =    1.574
peak=    3.892 closest distance to " CB  VAL A 265 " =    1.275
peak=    3.887 closest distance to " O   HOH Z  15 " =    2.180
peak=    3.882 closest distance to " CG  ARG A  66 " =    2.765
peak=    3.875 closest distance to " CB  ALA A 248 " =    1.422
peak=    3.872 closest distance to " O   HOH Z  78 " =    1.682
peak=    3.865 closest distance to " ND2 ASN A 187 " =    1.570
peak=    3.862 closest distance to " CG2 THR A 221 " =    1.150
peak=    3.861 closest distance to " O   HOH Z  59 " =    2.328
peak=    3.830 closest distance to " O   HOH Z 134 " =    1.464
peak=    3.829 closest distance to " O   HOH Z 371 " =    3.316
peak=    3.822 closest distance to " O   HOH Z 346 " =    1.510
peak=    3.819 closest distance to " CG1 ILE A  33 " =    1.326
peak=    3.817 closest distance to " O   HOH Z  54 " =    1.622
peak=    3.808 closest distance to " O   HOH Z  97 " =    2.611
peak=    3.806 closest distance to " CA  ALA A  51 " =    1.013
peak=    3.795 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.786 closest distance to " O   HOH Z 126 " =    1.601
peak=    3.785 closest distance to " NZ  LYS A 117 " =    3.250
peak=    3.765 closest distance to " OG BSER A 164 " =    2.222
peak=    3.764 closest distance to " O   MET A 105 " =    1.821
peak=    3.762 closest distance to " CA  ASP A 140 " =    1.202
peak=    3.757 closest distance to " O   HOH Z 102 " =    1.284
peak=    3.754 closest distance to " O   HOH Z  88 " =    3.134
peak=    3.753 closest distance to " O   HOH Z  61 " =    1.618
peak=    3.750 closest distance to " O   HOH Z 158 " =    3.100
peak=    3.746 closest distance to " O   HOH Z  43 " =    2.210
peak=    3.744 closest distance to " CB  ARG A 139 " =    0.905
peak=    3.744 closest distance to " O   HOH Z 203 " =    1.760
peak=    3.741 closest distance to " CD1 LEU A 300 " =    1.151
peak=    3.733 closest distance to " O   HOH Z 214 " =    2.233
peak=    3.729 closest distance to " O   HOH Z 133 " =    1.645
peak=    3.727 closest distance to " O   HOH Z  48 " =    1.703
peak=    3.726 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.721 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.720 closest distance to " CB  ARG A 190 " =    1.697
peak=    3.712 closest distance to " CA  VAL A  41 " =    0.828
peak=    3.710 closest distance to " O   HOH Z  44 " =    2.349
peak=    3.710 closest distance to " O   HOH Z 133 " =    2.331
peak=    3.709 closest distance to " CD  LYS A 166 " =    1.359
peak=    3.697 closest distance to " CA  ASP A 191 " =    0.841
peak=    3.696 closest distance to " O   HOH Z 193 " =    2.116
peak=    3.690 closest distance to " CA  LYS A 117 " =    1.273
peak=    3.681 closest distance to " O   HOH Z 108 " =    2.478
peak=    3.673 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.670 closest distance to " O   HOH Z  68 " =    1.703
peak=    3.656 closest distance to " O   HOH Z 189 " =    2.627
peak=    3.654 closest distance to " O   HOH Z 263 " =    1.648
peak=    3.648 closest distance to " O   HOH Z 303 " =    2.057
peak=    3.645 closest distance to " O   HOH Z 261 " =    2.068
peak=    3.643 closest distance to " O   HOH Z 197 " =    2.703
peak=    3.643 closest distance to " CA  THR A 221 " =    0.881
peak=    3.643 closest distance to " CG1 VAL A 296 " =    1.173
peak=    3.634 closest distance to " O   HOH Z 383 " =    2.010
peak=    3.631 closest distance to " O   HOH Z 273 " =    2.744
peak=    3.630 closest distance to " CG2 ILE A 120 " =    1.223
peak=    3.624 closest distance to " CB  LEU A 143 " =    1.153
peak=    3.610 closest distance to " CB  ASN A 187 " =    1.340
peak=    3.610 closest distance to " O   HOH Z 329 " =    3.809
peak=    3.602 closest distance to " CB  ALA A 291 " =    1.341
peak=    3.602 closest distance to " CB  ASN A  39 " =    0.840
peak=    3.599 closest distance to " O   HOH Z 402 " =    1.482
peak=    3.599 closest distance to " O   HOH Z 245 " =    1.405
peak=    3.597 closest distance to " O   HOH Z 357 " =    1.992
peak=    3.595 closest distance to " CB  TRP A 266 " =    0.958
peak=    3.594 closest distance to " CD BLYS A 290 " =    1.000
peak=    3.594 closest distance to " CB  ALA A   9 " =    1.611
peak=    3.582 closest distance to " OG  SER A  22 " =    2.833
peak=    3.581 closest distance to " N   ASN A  39 " =    1.213
peak=    3.574 closest distance to " O   HOH Z  85 " =    1.352
peak=    3.570 closest distance to " O   HOH Z 112 " =    1.611
peak=    3.560 closest distance to " CG1 VAL A 153 " =    0.943
peak=    3.558 closest distance to " O   HOH Z 130 " =    2.246
peak=    3.553 closest distance to " O   ASP A 124 " =    1.142
peak=    3.535 closest distance to " CD1 LEU A  96 " =    0.745
peak=    3.529 closest distance to " O   HOH Z  54 " =    2.439
peak=    3.526 closest distance to " O   HOH Z 261 " =    1.854
peak=    3.524 closest distance to " O   HOH Z  40 " =    1.605
peak=    3.523 closest distance to " O   HOH Z 128 " =    2.081
peak=    3.521 closest distance to " CA  ASP A 162 " =    1.134
peak=    3.516 closest distance to " CZ  PHE A 218 " =    1.052
peak=    3.515 closest distance to " CA  THR A 264 " =    0.780
peak=    3.512 closest distance to " CB  SER A 216 " =    0.778
peak=    3.506 closest distance to " O   HOH Z 126 " =    1.835
peak=    3.505 closest distance to " O   HOH Z  49 " =    2.555
peak=    3.500 closest distance to " OD2 ASP A 298 " =    4.009
peak=    3.498 closest distance to " O   HOH Z 281 " =    4.422
peak=    3.496 closest distance to " NH1AARG A 145 " =    1.043
peak=    3.491 closest distance to " O   HOH Z 171 " =    2.448
peak=    3.491 closest distance to " CA  ALA A 295 " =    1.064
peak=    3.491 closest distance to " O   HOH Z  21 " =    1.692
peak=    3.486 closest distance to " CG BARG A 102 " =    1.875
peak=    3.481 closest distance to " O   GLN A 278 " =    1.323
peak=    3.479 closest distance to " CB AVAL A  41 " =    1.082
peak=    3.477 closest distance to " CA  ASN A 176 " =    1.060
peak=    3.475 closest distance to " CD2 HIS A  81 " =    1.136
peak=    3.467 closest distance to " O   HOH Z 135 " =    1.884
peak=    3.463 closest distance to " O   HOH Z 423 " =    3.187
peak=    3.456 closest distance to " OD1 ASP A 231 " =    1.892
peak=    3.455 closest distance to " O   HOH Z 132 " =    2.785
peak=    3.453 closest distance to " CA  MET A  40 " =    1.093
peak=    3.453 closest distance to " NZ  LYS A  76 " =    1.288
peak=    3.448 closest distance to " NZ  LYS A 166 " =    3.048
peak=    3.447 closest distance to " OE1 GLU A   2 " =    2.101
peak=    3.446 closest distance to " CA  ARG A  36 " =    1.126
peak=    3.444 closest distance to " CG AARG A 275 " =    1.123
peak=    3.443 closest distance to " O   HOH Z 368 " =    3.578
peak=    3.442 closest distance to " ND1 HIS A  81 " =    1.638
peak=    3.435 closest distance to " CB  ALA A 295 " =    1.218
peak=    3.427 closest distance to " CB  LEU A 228 " =    1.348
peak=    3.427 closest distance to " O   HOH Z 227 " =    1.600
peak=    3.426 closest distance to " O   HOH Z 374 " =    2.640
peak=    3.423 closest distance to " O   HOH Z 185 " =    1.755
peak=    3.416 closest distance to " CG1 ILE A  49 " =    1.495
peak=    3.414 closest distance to " CA  GLN A 194 " =    1.209
peak=    3.414 closest distance to " O   HOH Z  68 " =    1.847
peak=    3.410 closest distance to " O   HOH Z 128 " =    1.787
peak=    3.407 closest distance to " N   VAL A 126 " =    1.337
peak=    3.406 closest distance to " NH2BARG A 145 " =    2.212
peak=    3.405 closest distance to " CA  ALA A 158 " =    1.146
peak=    3.404 closest distance to " O   HOH Z 420 " =    2.074
peak=    3.402 closest distance to " O   HOH Z 180 " =    2.132
peak=    3.401 closest distance to " O   ALA A   1 " =    1.502
peak=    3.399 closest distance to " CB  MET A  40 " =    0.862
peak=    3.398 closest distance to " O   HOH Z 313 " =    1.834
peak=    3.398 closest distance to " CG  GLN A  58 " =    2.680
peak=    3.387 closest distance to " O   HOH Z 422 " =    2.692
peak=    3.384 closest distance to " O   HOH Z 227 " =    1.590
peak=    3.383 closest distance to " O   HOH Z 419 " =    1.660
peak=    3.383 closest distance to " O   HOH Z 366 " =    3.053
peak=    3.380 closest distance to " O   ALA A 158 " =    1.329
peak=    3.378 closest distance to " CD2 LEU A 255 " =    1.319
peak=    3.377 closest distance to " N   ARG A 190 " =    1.101
peak=    3.375 closest distance to " C   ALA A 299 " =    0.939
peak=    3.371 closest distance to " OG1 THR A 294 " =    2.310
peak=    3.370 closest distance to " OE1 GLN A  11 " =    1.791
peak=    3.366 closest distance to " CZ  PHE A 192 " =    1.003
peak=    3.363 closest distance to " CG  MET A 185 " =    1.215
peak=    3.357 closest distance to " CG  GLN A  77 " =    2.313
peak=    3.357 closest distance to " CB  PRO A 198 " =    0.987
peak=    3.356 closest distance to " CB  ASP A 140 " =    0.871
peak=    3.353 closest distance to " OD1 ASN A 217 " =    1.677
peak=    3.344 closest distance to " O   HOH Z 367 " =    3.443
peak=    3.341 closest distance to " CA  GLY A 267 " =    0.831
peak=    3.336 closest distance to " CB  SER A 141 " =    1.045
peak=    3.332 closest distance to " CB  ARG A  79 " =    0.877
peak=    3.327 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.320 closest distance to " CB  ASN A 142 " =    1.087
peak=    3.318 closest distance to " C   SER A  32 " =    1.025
peak=    3.315 closest distance to " CG2 ILE A  20 " =    1.483
peak=    3.315 closest distance to " O   HOH Z 411 " =    1.799
peak=    3.308 closest distance to " O   HOH Z 116 " =    1.824
peak=    3.302 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.301 closest distance to " O   ALA A 165 " =    1.354
peak=    3.299 closest distance to " NE2 GLN A  58 " =    5.980
peak=    3.297 closest distance to " CA  LEU A 282 " =    1.086
peak=    3.296 closest distance to " CB  ILE A 120 " =    1.452
peak=    3.295 closest distance to " O   HOH Z 209 " =    2.381
peak=    3.294 closest distance to " O   HOH Z 417 " =    3.058
peak=    3.294 closest distance to " O   GLY A  91 " =    1.203
peak=    3.290 closest distance to " CA  ARG A 195 " =    1.173
peak=    3.290 closest distance to " CB  GLN A  89 " =    1.115
peak=    3.285 closest distance to " CD2 LEU A 297 " =    0.915
peak=    3.284 closest distance to " O   HOH Z 279 " =    2.193
peak=    3.283 closest distance to " O   HOH Z 407 " =    2.737
peak=    3.279 closest distance to " CD2 TRP A 179 " =    1.392
peak=    3.278 closest distance to " CA  SER A  87 " =    0.974
peak=    3.274 closest distance to " CB  TRP A 150 " =    1.493
peak=    3.274 closest distance to " O   HOH Z 435 " =    1.908
peak=    3.270 closest distance to " OD1 ASP A 286 " =    1.720
peak=    3.261 closest distance to " CB  THR A 157 " =    1.058
peak=    3.261 closest distance to " CA  VAL A 126 " =    0.960
peak=    3.258 closest distance to " O   HOH Z 147 " =    1.701
peak=    3.255 closest distance to " O   HOH Z 409 " =    3.287
peak=    3.254 closest distance to " CG2 VAL A 257 " =    0.870
peak=    3.252 closest distance to " O   HOH Z 406 " =    1.570
peak=    3.250 closest distance to " O   HOH Z 425 " =    1.307
peak=    3.247 closest distance to " O   THR A  31 " =    1.482
peak=    3.245 closest distance to " OG  SER A  97 " =    2.577
peak=    3.243 closest distance to " O   ASN A 217 " =    1.277
peak=    3.241 closest distance to " CB  SER A 212 " =    1.195
peak=    3.241 closest distance to " O   HOH Z   4 " =    1.917
peak=    3.240 closest distance to " O   HOH Z 291 " =    1.571
peak=    3.239 closest distance to " O   HOH Z 128 " =    1.893
peak=    3.237 closest distance to " CE1 HIS A 108 " =    1.150
peak=    3.237 closest distance to " CD  ARG A 195 " =    3.463
peak=    3.236 closest distance to " NH1BARG A 190 " =    1.873
peak=    3.236 closest distance to " O   HOH Z 227 " =    2.143
peak=    3.236 closest distance to " CB  THR A  31 " =    1.661
peak=    3.233 closest distance to " OG BSER A 134 " =    2.900
peak=    3.230 closest distance to " CB  SER A  26 " =    1.645
peak=    3.230 closest distance to " CB  LYS A 117 " =    1.150
peak=    3.230 closest distance to " N   SER A 135 " =    1.456
peak=    3.224 closest distance to " CG  LEU A 167 " =    1.110
peak=    3.222 closest distance to " CG2AVAL A 121 " =    2.229
peak=    3.221 closest distance to " O   HOH Z 392 " =    1.564
peak=    3.217 closest distance to " CB  MET A  47 " =    1.115
peak=    3.210 closest distance to " CA  ASN A 215 " =    1.252
peak=    3.209 closest distance to " O   HOH Z 337 " =    3.735
peak=    3.201 closest distance to " O   HOH Z 371 " =    3.480
peak=    3.198 closest distance to " NH1 ARG A  14 " =    1.079
peak=    3.197 closest distance to " CA  ASN A 217 " =    1.360
peak=    3.196 closest distance to " O   SER A  26 " =    1.705
peak=    3.196 closest distance to " CA  ILE A  33 " =    1.498
peak=    3.193 closest distance to " CB  ALA A 248 " =    1.005
peak=    3.192 closest distance to " O   HOH Z 250 " =    1.453
peak=    3.189 closest distance to " CB  ALA A  71 " =    1.282
peak=    3.189 closest distance to " CB  SER A 273 " =    0.806
peak=    3.189 closest distance to " O   HOH Z 163 " =    1.434
peak=    3.188 closest distance to " CA  ALA A 233 " =    1.368
peak=    3.187 closest distance to " O   HOH Z 417 " =    2.227
peak=    3.185 closest distance to " O   HOH Z   9 " =    2.135
peak=    3.185 closest distance to " O   HOH Z  66 " =    1.735
peak=    3.180 closest distance to " CG2 THR A 220 " =    0.853
peak=    3.179 closest distance to " ND1 HIS A  86 " =    1.572
peak=    3.179 closest distance to " CG2 VAL A 197 " =    1.049
peak=    3.177 closest distance to " O   HOH Z 278 " =    1.259
peak=    3.174 closest distance to " O   HOH Z  61 " =    1.640
peak=    3.173 closest distance to " O   HOH Z 271 " =    1.806
peak=    3.173 closest distance to " O   HOH Z 109 " =    2.565
peak=    3.167 closest distance to " CG2 VAL A 202 " =    1.205
peak=    3.167 closest distance to " NH2 ARG A 219 " =    1.772
peak=    3.167 closest distance to " O   HOH Z  63 " =    1.177
peak=    3.162 closest distance to " O   HOH Z 197 " =    1.916
peak=    3.159 closest distance to " CA  ALA A 291 " =    0.930
peak=    3.158 closest distance to " O   HOH Z 404 " =    2.281
peak=    3.147 closest distance to " CB  ALA A 242 " =    0.942
peak=    3.142 closest distance to " O   HOH Z 387 " =    2.997
peak=    3.141 closest distance to " O   HOH Z 345 " =    1.611
peak=    3.138 closest distance to " CB  PRO A 243 " =    1.175
peak=    3.135 closest distance to " CG  LEU A 281 " =    1.130
peak=    3.130 closest distance to " CB  GLN A 278 " =    0.876
peak=    3.127 closest distance to " CB  LEU A 255 " =    0.805
peak=    3.122 closest distance to " CA  LYS A 290 " =    1.303
peak=    3.116 closest distance to " O   HOH Z  44 " =    1.768
peak=    3.110 closest distance to " OD2 ASP A 200 " =    1.353
peak=    3.110 closest distance to " O   HOH Z  46 " =    1.497
peak=    3.109 closest distance to " CG  GLU A 277 " =    2.252
peak=    3.106 closest distance to " O   HOH Z 282 " =    2.097
peak=    3.104 closest distance to " O   HOH Z 244 " =    1.627
peak=    3.103 closest distance to " CD1 ILE A  33 " =    1.619
peak=    3.095 closest distance to " O   HOH Z 421 " =    1.708
peak=    3.091 closest distance to " O   HOH Z 236 " =    1.675
peak=    3.091 closest distance to " CB  SER A  62 " =    0.766
peak=    3.074 closest distance to " CA  ALA A 160 " =    0.884
peak=    3.074 closest distance to " O   HOH Z 298 " =    4.832
peak=    3.074 closest distance to " O   HOH Z 302 " =    1.867
peak=    3.068 closest distance to " CA  GLY A  80 " =    0.924
peak=    3.067 closest distance to " O   HOH Z 193 " =    1.562
peak=    3.060 closest distance to " OG  SER A  97 " =    3.690
peak=    3.047 closest distance to " CG  GLN A  89 " =    1.536
peak=    3.047 closest distance to " O   HOH Z 353 " =    2.806
peak=    3.047 closest distance to " O   HOH Z 409 " =    3.623
peak=    3.047 closest distance to " O   HOH Z 175 " =    3.475
peak=    3.037 closest distance to " O   HOH Z  98 " =    1.715
peak=    3.034 closest distance to " CB  GLU A 152 " =    1.380
peak=    3.028 closest distance to " O   HOH Z  90 " =    3.281
peak=    3.016 closest distance to " CB  ALA A 100 " =    1.241

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.807 - 5.454
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 200
   mapped sites are within: 0.807 - 5.454

peak=   -5.491 closest distance to " CG2 VAL A 230 " =    0.807
peak=   -4.546 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.427 closest distance to " CG2BVAL A  41 " =    2.623
peak=   -4.326 closest distance to " O   HOH Z 266 " =    4.520
peak=   -4.265 closest distance to " O   HOH Z 290 " =    1.092
peak=   -4.197 closest distance to " CB  ALA A 161 " =    2.553
peak=   -4.084 closest distance to " SG  CYS A 254 " =    3.127
peak=   -4.076 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -4.060 closest distance to " NH2 ARG A  66 " =    1.612
peak=   -4.032 closest distance to " O   HOH Z 196 " =    2.271
peak=   -4.003 closest distance to " CG  ASP A 231 " =    0.834
peak=   -3.995 closest distance to " O   PRO A 163 " =    2.105
peak=   -3.993 closest distance to " O   HOH Z  52 " =    1.664
peak=   -3.990 closest distance to " C   HIS A 108 " =    1.202
peak=   -3.969 closest distance to " O   HOH Z 166 " =    1.765
peak=   -3.960 closest distance to " OXT GLY A 302 " =    2.824
peak=   -3.946 closest distance to " O   HOH Z  13 " =    1.494
peak=   -3.918 closest distance to " O   HOH Z  17 " =    1.386
peak=   -3.878 closest distance to " O   HOH Z 103 " =    1.836
peak=   -3.864 closest distance to " O   HOH Z 351 " =    1.526
peak=   -3.846 closest distance to " CD1 LEU A 101 " =    2.598
peak=   -3.843 closest distance to " CD2 LEU A 237 " =    2.703
peak=   -3.832 closest distance to " CD  LYS A 289 " =    2.527
peak=   -3.812 closest distance to " OG ASER A 134 " =    1.331
peak=   -3.776 closest distance to " O   HOH Z 231 " =    1.957
peak=   -3.756 closest distance to " OG  SER A  97 " =    2.320
peak=   -3.746 closest distance to " NH2AARG A 275 " =    5.146
peak=   -3.735 closest distance to " O   ALA A 256 " =    1.604
peak=   -3.731 closest distance to " CD2 LEU A 300 " =    2.823
peak=   -3.725 closest distance to " OE1 GLN A 223 " =    2.130
peak=   -3.713 closest distance to " CD1 PHE A  59 " =    1.885
peak=   -3.710 closest distance to " O   HOH Z 198 " =    2.541
peak=   -3.705 closest distance to " CG2 THR A   4 " =    1.930
peak=   -3.704 closest distance to " N   ALA A  43 " =    2.497
peak=   -3.703 closest distance to " N   ALA A 226 " =    2.054
peak=   -3.695 closest distance to " N   GLN A  58 " =    1.769
peak=   -3.685 closest distance to " O   HOH Z  43 " =    1.624
peak=   -3.672 closest distance to " O   HOH Z  19 " =    2.155
peak=   -3.671 closest distance to " CD1 LEU A 228 " =    2.340
peak=   -3.665 closest distance to " O   HOH Z 292 " =    4.450
peak=   -3.661 closest distance to " ND2 ASN A  45 " =    0.991
peak=   -3.650 closest distance to " CD1 LEU A 101 " =    2.785
peak=   -3.648 closest distance to " N   THR A 235 " =    1.311
peak=   -3.643 closest distance to " OG  SER A  62 " =    1.565
peak=   -3.641 closest distance to " CZ3 TRP A 179 " =    1.279
peak=   -3.640 closest distance to " OG BSER A 134 " =    1.743
peak=   -3.637 closest distance to " CB  PRO A 243 " =    2.666
peak=   -3.616 closest distance to " C   ALA A 158 " =    1.250
peak=   -3.610 closest distance to " O   HOH Z 151 " =    1.466
peak=   -3.606 closest distance to " O   HOH Z 222 " =    1.386
peak=   -3.604 closest distance to " CG  GLU A  53 " =    1.548
peak=   -3.596 closest distance to " O   HOH Z 407 " =    3.116
peak=   -3.591 closest distance to " O   HOH Z 353 " =    2.220
peak=   -3.574 closest distance to " CE  MET A 105 " =    2.113
peak=   -3.570 closest distance to " O   HOH Z 283 " =    1.860
peak=   -3.568 closest distance to " N   SER A 212 " =    1.925
peak=   -3.564 closest distance to " CG1 VAL A 296 " =    1.255
peak=   -3.559 closest distance to " CB  TYR A  15 " =    2.237
peak=   -3.543 closest distance to " OG BSER A 134 " =    1.217
peak=   -3.539 closest distance to " O   HOH Z 389 " =    1.778
peak=   -3.539 closest distance to " O   HOH Z 377 " =    2.079
peak=   -3.535 closest distance to " CB  PRO A 163 " =    2.666
peak=   -3.522 closest distance to " CA  ASP A 298 " =    1.051
peak=   -3.519 closest distance to " O   VAL A 125 " =    2.245
peak=   -3.512 closest distance to " O   HOH Z 252 " =    4.006
peak=   -3.512 closest distance to " ND2 ASN A 187 " =    1.721
peak=   -3.511 closest distance to " CD  ARG A 139 " =    1.593
peak=   -3.509 closest distance to " NE2 GLN A  88 " =    2.125
peak=   -3.506 closest distance to " CG2 ILE A 263 " =    2.345
peak=   -3.504 closest distance to " O   VAL A  67 " =    2.573
peak=   -3.499 closest distance to " O   HOH Z  71 " =    1.161
peak=   -3.492 closest distance to " O   HOH Z 311 " =    3.645
peak=   -3.492 closest distance to " NH2 ARG A 159 " =    2.284
peak=   -3.491 closest distance to " O   HOH Z 165 " =    1.989
peak=   -3.491 closest distance to " CG  MET A 105 " =    0.893
peak=   -3.491 closest distance to " O   HOH Z 241 " =    1.284
peak=   -3.490 closest distance to " CB  ALA A 248 " =    1.977
peak=   -3.489 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.488 closest distance to " O   HOH Z 426 " =    1.727
peak=   -3.486 closest distance to " C   MET A 188 " =    1.519
peak=   -3.482 closest distance to " CG  GLU A 277 " =    1.071
peak=   -3.473 closest distance to " O   HOH Z 118 " =    3.072
peak=   -3.473 closest distance to " O   GLY A 196 " =    1.091
peak=   -3.465 closest distance to " O   ALA A 161 " =    1.650
peak=   -3.465 closest distance to " O   HOH Z 166 " =    1.610
peak=   -3.463 closest distance to " CD1 LEU A  25 " =    2.471
peak=   -3.461 closest distance to " N   THR A 157 " =    1.560
peak=   -3.460 closest distance to " N   SER A 276 " =    1.327
peak=   -3.456 closest distance to " OG  SER A  26 " =    1.303
peak=   -3.453 closest distance to " O   HOH Z 234 " =    4.211
peak=   -3.452 closest distance to " CG2 VAL A 296 " =    1.488
peak=   -3.452 closest distance to " O   HOH Z  10 " =    1.615
peak=   -3.447 closest distance to " N   ALA A 248 " =    1.647
peak=   -3.442 closest distance to " N   ALA A 248 " =    2.199
peak=   -3.419 closest distance to " CA  GLY A 203 " =    2.206
peak=   -3.416 closest distance to " O   HOH Z 423 " =    2.258
peak=   -3.408 closest distance to " O   PRO A 198 " =    1.212
peak=   -3.405 closest distance to " O   HOH Z 377 " =    1.495
peak=   -3.405 closest distance to " O   HOH Z 185 " =    2.286
peak=   -3.403 closest distance to " CG  PHE A 283 " =    2.734
peak=   -3.402 closest distance to " C   ASN A 187 " =    1.923
peak=   -3.398 closest distance to " O   HOH Z 431 " =    1.732
peak=   -3.393 closest distance to " CE3 TRP A 150 " =    2.015
peak=   -3.389 closest distance to " CD2 TYR A 293 " =    2.100
peak=   -3.389 closest distance to " CG  TRP A 266 " =    1.832
peak=   -3.388 closest distance to " O   HOH Z  11 " =    1.867
peak=   -3.384 closest distance to " O   HOH Z 275 " =    1.507
peak=   -3.379 closest distance to " CD2 LEU A 167 " =    1.717
peak=   -3.371 closest distance to " NE2 GLN A 103 " =    1.727
peak=   -3.365 closest distance to " CG  ASP A  50 " =    2.420
peak=   -3.356 closest distance to " OD1 ASN A 148 " =    1.563
peak=   -3.356 closest distance to " O   HOH Z  15 " =    1.573
peak=   -3.355 closest distance to " CD  GLN A  58 " =    1.194
peak=   -3.354 closest distance to " O   HOH Z 262 " =    2.663
peak=   -3.344 closest distance to " O   HOH Z  92 " =    1.674
peak=   -3.343 closest distance to " CG1 VAL A 112 " =    2.806
peak=   -3.339 closest distance to " CG2 VAL A 112 " =    2.607
peak=   -3.326 closest distance to " O   HOH Z 150 " =    1.704
peak=   -3.325 closest distance to " CZ  PHE A  59 " =    1.671
peak=   -3.323 closest distance to " OG  SER A  87 " =    1.431
peak=   -3.317 closest distance to " SG ACYS A 201 " =    2.397
peak=   -3.307 closest distance to " CE2 PHE A 218 " =    2.624
peak=   -3.306 closest distance to " CB  ASN A  39 " =    2.107
peak=   -3.306 closest distance to " CA  GLY A 133 " =    1.973
peak=   -3.305 closest distance to " O   SER A 271 " =    2.007
peak=   -3.304 closest distance to " CG  GLU A   2 " =    1.761
peak=   -3.295 closest distance to " CB  ALA A 291 " =    2.370
peak=   -3.294 closest distance to " NH2 ARG A  79 " =    1.923
peak=   -3.292 closest distance to " CG  LYS A 193 " =    2.289
peak=   -3.292 closest distance to " CD1 ILE A 263 " =    2.410
peak=   -3.282 closest distance to " O   MET A  40 " =    2.696
peak=   -3.275 closest distance to " CG  LEU A 228 " =    0.965
peak=   -3.274 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.269 closest distance to " NZ  LYS A 119 " =    3.555
peak=   -3.266 closest distance to " CE BMET A  47 " =    2.022
peak=   -3.265 closest distance to " C   SER A 206 " =    1.584
peak=   -3.251 closest distance to " CA  ASN A 127 " =    1.037
peak=   -3.247 closest distance to " O   GLY A 203 " =    2.439
peak=   -3.247 closest distance to " O   GLY A 211 " =    1.496
peak=   -3.244 closest distance to " OD2 ASP A 171 " =    2.249
peak=   -3.243 closest distance to " CG2 THR A 178 " =    2.162
peak=   -3.243 closest distance to " C   ASN A 285 " =    2.491
peak=   -3.243 closest distance to " O   HOH Z 191 " =    5.454
peak=   -3.233 closest distance to " CB  ALA A 291 " =    2.209
peak=   -3.230 closest distance to " CB  ALA A  10 " =    2.183
peak=   -3.227 closest distance to " O   HOH Z  63 " =    0.896
peak=   -3.227 closest distance to " CD  GLN A  88 " =    1.053
peak=   -3.227 closest distance to " CZ  TYR A 169 " =    1.747
peak=   -3.226 closest distance to " O   HOH Z 123 " =    2.327
peak=   -3.220 closest distance to " OD2 ASP A 171 " =    1.798
peak=   -3.214 closest distance to " O   HOH Z 193 " =    1.758
peak=   -3.213 closest distance to " N   GLY A  23 " =    2.094
peak=   -3.208 closest distance to " O   SER A  95 " =    1.573
peak=   -3.203 closest distance to " O   HOH Z  38 " =    1.648
peak=   -3.202 closest distance to " O   HOH Z 339 " =    1.879
peak=   -3.201 closest distance to " OD1 ASN A 187 " =    1.691
peak=   -3.200 closest distance to " CG  ARG A 269 " =    2.254
peak=   -3.196 closest distance to " O   HOH Z 211 " =    1.589
peak=   -3.194 closest distance to " CD  ARG A 195 " =    5.075
peak=   -3.194 closest distance to " CG1 VAL A  78 " =    2.465
peak=   -3.191 closest distance to " O   HOH Z 388 " =    2.015
peak=   -3.185 closest distance to " C   LEU A 222 " =    0.853
peak=   -3.184 closest distance to " NE  ARG A 259 " =    1.074
peak=   -3.181 closest distance to " CA  GLY A 133 " =    2.219
peak=   -3.170 closest distance to " O   HOH Z 184 " =    1.567
peak=   -3.167 closest distance to " CG  PRO A 243 " =    1.721
peak=   -3.167 closest distance to " CB  GLN A  11 " =    1.901
peak=   -3.160 closest distance to " OG1 THR A  82 " =    1.416
peak=   -3.159 closest distance to " OD1 ASP A 191 " =    1.592
peak=   -3.151 closest distance to " O   LYS A 117 " =    1.689
peak=   -3.144 closest distance to " O   LEU A 167 " =    1.483
peak=   -3.141 closest distance to " ND2 ASN A  60 " =    1.572
peak=   -3.140 closest distance to " N   PHE A  59 " =    2.255
peak=   -3.139 closest distance to " N   GLN A  77 " =    1.519
peak=   -3.136 closest distance to " CB  PHE A 192 " =    1.907
peak=   -3.135 closest distance to " O   HOH Z 350 " =    1.765
peak=   -3.130 closest distance to " NE1 TRP A 266 " =    2.264
peak=   -3.128 closest distance to " CG  PRO A 163 " =    2.613
peak=   -3.127 closest distance to " O   VAL A 197 " =    1.300
peak=   -3.125 closest distance to " CE  MET A  93 " =    1.193
peak=   -3.125 closest distance to " O   HOH Z 265 " =    2.018
peak=   -3.121 closest distance to " O   HOH Z 414 " =    1.524
peak=   -3.120 closest distance to " O   HOH Z 292 " =    2.915
peak=   -3.119 closest distance to " O   SER A 258 " =    1.890
peak=   -3.118 closest distance to " OXT GLY A 302 " =    3.393
peak=   -3.116 closest distance to " O   HOH Z 422 " =    1.578
peak=   -3.115 closest distance to " O   HOH Z 128 " =    2.471
peak=   -3.111 closest distance to " CB  PHE A 208 " =    2.291
peak=   -3.109 closest distance to " O   HOH Z 414 " =    1.383
peak=   -3.108 closest distance to " O   HOH Z 174 " =    2.222
peak=   -3.108 closest distance to " O   GLY A  80 " =    2.520
peak=   -3.105 closest distance to " C   GLN A 205 " =    2.003
peak=   -3.088 closest distance to " CB  SER A 245 " =    2.321
peak=   -3.086 closest distance to " C   VAL A 265 " =    0.855
peak=   -3.076 closest distance to " O   HOH Z  47 " =    1.537
peak=   -3.075 closest distance to " OD1 ASN A  39 " =    1.255
peak=   -3.053 closest distance to " CG2 VAL A 189 " =    1.977
peak=   -3.051 closest distance to " O   HOH Z 417 " =    2.715
peak=   -2.837 closest distance to " CZ  ARG A  66 " =    1.222

================= 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    :  0.4536 0.4487   6.253152e+00   6.240328e+00
   1_bss:  0.4451 0.4369   6.251590e+00   6.230860e+00
   1_xyz:  0.3494 0.3794   6.085556e+00   6.136571e+00
   1_adp:  0.2981 0.3445   5.965310e+00   6.070012e+00
   1_occ:  0.2976 0.3448   5.964803e+00   6.070250e+00
   2_bss:  0.2938 0.3389   5.964151e+00   6.066585e+00
   2_xyz:  0.2077 0.2581   5.674440e+00   5.845906e+00
   2_adp:  0.1904 0.2396   5.595812e+00   5.777796e+00
   2_occ:  0.1902 0.2397   5.595467e+00   5.777964e+00
   3_bss:  0.1888 0.2386   5.595503e+00   5.776835e+00
   3_xyz:  0.1361 0.1794   5.297736e+00   5.514594e+00
   3_adp:  0.1256 0.1689   5.234356e+00   5.461987e+00
   3_occ:  0.1254 0.1687   5.233556e+00   5.461405e+00
   4_bss:  0.1256 0.1686   5.235643e+00   5.462615e+00
   4_xyz:  0.1137 0.1596   5.166001e+00   5.409843e+00
   4_adp:  0.1117 0.1590   5.156951e+00   5.405717e+00
   4_occ:  0.1117 0.1590   5.156663e+00   5.405575e+00
   5_bss:  0.1117 0.1590   5.156607e+00   5.405589e+00
   5_xyz:  0.1126 0.1587   5.160872e+00   5.404190e+00
   5_adp:  0.1127 0.1583   5.159219e+00   5.401285e+00
   5_occ:  0.1127 0.1584   5.159285e+00   5.401554e+00
   5_bss:  0.1126 0.1584   5.159137e+00   5.401551e+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:  0.339  16.362   7.116   9.428   8.510   0.000   0.000   0.000
   1_xyz:  0.339  16.362   7.116   9.428   8.510   0.000   0.000   0.000
   1_adp:  0.339  16.362   7.116   9.428   8.510   0.000   0.000   0.000
   1_occ:  0.339  16.362   7.116   9.428   8.510   0.000   0.000   0.000
   2_bss:  0.334  43.076   3.787   5.593   5.545   0.000   0.000   0.000
   2_xyz:  0.334  43.076   3.787   5.593   5.545   0.000   0.000   0.000
   2_adp:  0.334  43.076   3.787   5.593   5.545   0.000   0.000   0.000
   2_occ:  0.334  43.076   3.787   5.593   5.545   0.000   0.000   0.000
   3_bss:  0.322  43.077   2.483   3.604   3.656   0.000   0.000   0.000
   3_xyz:  0.322  43.077   2.483   3.604   3.656   0.000   0.000   0.000
   3_adp:  0.322  43.077   2.483   3.604   3.656   0.000   0.000   0.000
   3_occ:  0.322  43.077   2.483   3.604   3.656   0.000   0.000   0.000
   4_bss:  0.323  43.085   2.229   2.952   3.115   0.000   0.000   0.000
   4_xyz:  0.323  43.085   2.229   2.952   3.115   0.000   0.000   0.000
   4_adp:  0.323  43.085   2.229   2.952   3.115   0.000   0.000   0.000
   4_occ:  0.323  43.085   2.229   2.952   3.115   0.000   0.000   0.000
   5_bss:  0.323  43.085   2.307   2.883   3.116   0.000   0.000   0.000
   5_xyz:  0.323  43.085   2.307   2.883   3.116   0.000   0.000   0.000
   5_adp:  0.323  43.085   2.307   2.883   3.116   0.000   0.000   0.000
   5_occ:  0.323  43.085   2.307   2.883   3.116   0.000   0.000   0.000
   5_bss:  0.321  47.606  -0.448   0.092   0.356   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.140 0.4940  0.5640    59298.451
   1_bss:  52.325 0.4888  0.7074    56875.276
   1_xyz:  42.136 0.6150  0.8784    39845.651
   1_adp:  36.396 0.6846  0.9846    31830.568
   1_occ:  36.428 0.6842  0.9835    31885.088
   2_bss:  36.115 0.6878  0.8780    31475.752
   2_xyz:  26.079 0.7997  0.9882    17452.332
   2_adp:  23.470 0.8277  1.0113    14824.745
   2_occ:  23.486 0.8275  1.0109    14830.421
   3_bss:  23.432 0.8280  0.9504    14803.155
   3_xyz:  16.840 0.8903  0.9893     8178.479
   3_adp:  15.674 0.9008  0.9940     7418.484
   3_occ:  15.656 0.9010  0.9939     7412.182
   4_bss:  15.684 0.9008  0.9763     7461.047
   4_xyz:  14.552 0.9104  0.9786     6672.762
   4_adp:  14.434 0.9116  0.9755     6620.889
   4_occ:  14.429 0.9116  0.9754     6623.819
   5_bss:  14.427 0.9117  0.9757     6624.327
   5_xyz:  14.372 0.9122  0.9750     6581.199
   5_adp:  14.301 0.9127  0.9726     6542.609
   5_occ:  14.304 0.9127  0.9724     6546.997
   5_bss:  14.305 0.9127  0.9743     6548.651
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3718e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3718e+01
   1_xyz:   1.657  0.013  0.107 17.944  0.007  4.112   1.3379e-01
   1_adp:   1.657  0.013  0.107 17.944  0.007  4.112   1.3379e-01
   1_occ:   1.657  0.013  0.107 17.944  0.007  4.112   1.3379e-01
   2_bss:   1.657  0.013  0.107 17.944  0.007  4.112   1.3379e-01
   2_xyz:   1.021  0.007  0.070 15.944  0.005  4.127   6.5823e-02
   2_adp:   1.021  0.007  0.070 15.944  0.005  4.127   6.5823e-02
   2_occ:   1.021  0.007  0.070 15.944  0.005  4.127   6.5823e-02
   3_bss:   1.021  0.007  0.070 15.944  0.005  4.127   6.5823e-02
   3_xyz:   1.121  0.009  0.085 15.555  0.004  4.113   7.4363e-02
   3_adp:   1.121  0.009  0.085 15.555  0.004  4.113   7.4363e-02
   3_occ:   1.121  0.009  0.085 15.555  0.004  4.113   7.4363e-02
   4_bss:   1.121  0.009  0.085 15.555  0.004  4.113   7.4363e-02
   4_xyz:   1.151  0.009  0.092 15.780  0.004  4.117   7.7344e-02
   4_adp:   1.151  0.009  0.092 15.780  0.004  4.117   7.7344e-02
   4_occ:   1.151  0.009  0.092 15.780  0.004  4.117   7.7344e-02
   5_bss:   1.151  0.009  0.092 15.780  0.004  4.117   7.7344e-02
   5_xyz:   1.016  0.007  0.081 15.228  0.004  4.117   6.2266e-02
   5_adp:   1.016  0.007  0.081 15.228  0.004  4.117   6.2266e-02
   5_occ:   1.016  0.007  0.081 15.228  0.004  4.117   6.2266e-02
   5_bss:   1.016  0.007  0.081 15.228  0.004  4.117   6.2266e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9643e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9643e+00
   1_xyz:  14.729  0.158  0.499 87.719  0.053  2.247   9.8837e-02
   1_adp:  14.729  0.158  0.499 87.719  0.053  2.247   9.8837e-02
   1_occ:  14.729  0.158  0.499 87.719  0.053  2.247   9.8837e-02
   2_bss:  14.729  0.158  0.499 87.719  0.053  2.247   9.8837e-02
   2_xyz:   6.492  0.056  0.257 87.122  0.032  2.284   6.5146e-02
   2_adp:   6.492  0.056  0.257 87.122  0.032  2.284   6.5146e-02
   2_occ:   6.492  0.056  0.257 87.122  0.032  2.284   6.5146e-02
   3_bss:   6.492  0.056  0.257 87.122  0.032  2.284   6.5146e-02
   3_xyz:   7.024  0.059  0.553 80.782  0.035  2.293   8.4977e-02
   3_adp:   7.024  0.059  0.553 80.782  0.035  2.293   8.4977e-02
   3_occ:   7.024  0.059  0.553 80.782  0.035  2.293   8.4977e-02
   4_bss:   7.024  0.059  0.553 80.782  0.035  2.293   8.4977e-02
   4_xyz:   7.681  0.053  0.703 82.673  0.034  2.329   6.1025e-02
   4_adp:   7.681  0.053  0.703 82.673  0.034  2.329   6.1025e-02
   4_occ:   7.681  0.053  0.703 82.673  0.034  2.329   6.1025e-02
   5_bss:   7.681  0.053  0.703 82.673  0.034  2.329   6.1025e-02
   5_xyz:   7.056  0.038  0.553 82.066  0.032  2.377   4.9666e-02
   5_adp:   7.056  0.038  0.553 82.066  0.032  2.377   4.9666e-02
   5_occ:   7.056  0.038  0.553 82.066  0.032  2.377   4.9666e-02
   5_bss:   7.056  0.038  0.553 82.066  0.032  2.377   4.9666e-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:  72.69   0.00  11.56  72.69   0.00   8.64  71.12   0.00  27.42
   1_occ:  72.69   0.00  11.56  72.69   0.00   8.64  71.12   0.00  27.42
   2_bss:  72.69   0.00  11.56  72.69   0.00   8.64  71.12   0.00  27.42
   2_xyz:  72.69   0.00  11.56  72.69   0.00   8.64  71.12   0.00  27.42
   2_adp:  75.78   0.00  11.98  75.78   0.00   8.27  68.40   1.78  32.17
   2_occ:  75.78   0.00  11.98  75.78   0.00   8.27  68.40   1.78  32.17
   3_bss:  75.78   0.00  11.98  75.78   0.00   8.27  68.40   1.78  32.17
   3_xyz:  75.78   0.00  11.98  75.78   0.00   8.27  68.40   1.78  32.17
   3_adp:  82.37   0.00  12.34  82.37   0.00   8.18  69.92   1.27  35.01
   3_occ:  82.37   0.00  12.34  82.37   0.00   8.18  69.92   1.27  35.01
   4_bss:  82.37   0.00  12.34  82.37   0.00   8.18  69.92   1.27  35.01
   4_xyz:  82.37   0.00  12.34  82.37   0.00   8.18  69.92   1.27  35.01
   4_adp:  88.27   0.00  12.33  88.27   0.00   8.14  73.83   1.22  35.14
   4_occ:  88.27   0.00  12.33  88.27   0.00   8.14  73.83   1.22  35.14
   5_bss:  88.27   0.00  12.33  88.27   0.00   8.14  73.83   1.22  35.14
   5_xyz:  88.27   0.00  12.33  88.27   0.00   8.14  73.83   1.22  35.14
   5_adp:  88.70   0.00  12.19  88.70   0.00   8.05  73.34   1.22  34.70
   5_occ:  88.70   0.00  12.19  88.70   0.00   8.05  73.34   1.22  34.70
   5_bss:  91.53   2.82  15.01  91.53   2.82  10.88  76.16   4.05  37.53
------------------------------------------------------------------------
 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:    1.204    0.018    0.412
   1_adp:    1.204    0.018    0.412
   1_occ:    1.204    0.018    0.412
   2_bss:    1.204    0.018    0.412
   2_xyz:    1.583    0.021    0.536
   2_adp:    1.583    0.021    0.536
   2_occ:    1.583    0.021    0.536
   3_bss:    1.583    0.021    0.536
   3_xyz:    1.548    0.029    0.614
   3_adp:    1.548    0.029    0.614
   3_occ:    1.548    0.029    0.614
   4_bss:    1.548    0.029    0.614
   4_xyz:    1.560    0.059    0.636
   4_adp:    1.560    0.059    0.636
   4_occ:    1.560    0.059    0.636
   5_bss:    1.560    0.059    0.636
   5_xyz:    1.652    0.057    0.644
   5_adp:    1.652    0.057    0.644
   5_occ:    1.652    0.057    0.644
   5_bss:    1.652    0.057    0.644
------------------------------------------------------------------------

CPU time actual refinement: 273.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_805/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_805/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_805/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_805/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_805/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 273.34 
  Macro-tasks:
    bulk solvent and scale       = 34.87  
    individual site refinement   = 110.43 
    weights calculation          = 26.81  
    collect and process          = 5.55   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 177.76 
  Micro-tasks:
    mask                            = 1.52   
    f_calc                          = 82.68  
    alpha_beta                      = 7.18   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 91.25  
    fmodel                         = 6.20   
    r_factors                      = 0.28   
    phase_errors                   = 8.87   
    foms                           = 0.18   
    TOTAL for micro-tasks          = 199.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.886 micro seconds
Total CPU time: 4.75 minutes
from_scatterers_fft:    629 calls, 82.35 s
gradients_fft:          574 calls, 80.26 s

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

# Date 2008-01-16 Time 02:26:55 PST -0800 (1200479215.09 s)
Start R-work = 0.4536, R-free = 0.4487 (no bulk solvent and anisotropic scale)
Final R-work = 0.1294, R-free = 0.1746 (no bulk solvent and anisotropic scale)

Start R-work = 0.4451, R-free = 0.4369
Final R-work = 0.1126, R-free = 0.1584