# Date 2008-01-16 Time 00:27:21 PST -0800 (1200472041.94 s)
#phil __OFF__

Command line arguments: "../12.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29212
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 12

-------------------------------------------------------------------------------
  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: (68.4938, 45.9914, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


================================== 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: (68.4938, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6393 1.95052
Completeness in resolution range: 0.976813
Completeness with d_max=infinity: 0.973705

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6393
                             d_min =   1.9505

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: (68.4938, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6393 1.95052
Completeness in resolution range: 0.976813
Completeness with d_max=infinity: 0.973705

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6397 -  4.1729 [2105/2130]  1894   211  10.0%
  bin  2:  4.1729 -  3.3249 [2028/2046]  1826   202  10.0%
  bin  3:  3.3249 -  2.9083 [1995/2014]  1796   199  10.0%
  bin  4:  2.9083 -  2.6441 [1973/2003]  1775   198  10.0%
  bin  5:  2.6441 -  2.4556 [1979/1998]  1783   196   9.9%
  bin  6:  2.4556 -  2.3114 [1945/1970]  1746   199  10.2%
  bin  7:  2.3114 -  2.1960 [1945/1973]  1753   192   9.9%
  bin  8:  2.1960 -  2.1007 [1954/1990]  1759   195  10.0%
  bin  9:  2.1007 -  2.0201 [1909/1951]  1716   193  10.1%
  bin 10:  2.0201 -  1.9505 [1756/1979]  1582   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_12/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: 0.13 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:
        0.69 -     1.53: 5
        1.53 -     2.38: 83
        2.38 -     3.22: 3358
        3.22 -     4.06: 9786
        4.06 -     4.90: 16157
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.692 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  0.858 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.296 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.384 3.040 -x+1/2,-y+1,z+1/2
  " OE1 GLN A  55 " - " CB  ASN A 285 "  1.518 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 29384 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_12/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_12/model_refine_001.geo

CPU time processing inputs: 11.40


============================ 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 = 68.49375 45.9914 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5249   r_free= 0.5242   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.99 A                  |
| x-ray target function (ml) for work reflections: 6.311381                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6397 -  4.6538 0.99   1375  153 0.4430 0.4479       6.662       6.706|
|  2:  4.6538 -  3.7137 0.99   1307  147 0.4778 0.4627      6.8821      6.8857|
|  3:  3.7137 -  3.2501 0.99   1294  142 0.5134 0.4900      6.7647      6.8212|
|  4:  3.2501 -  2.9556 0.99   1284  139 0.5169 0.4672        6.59      6.5246|
|  5:  2.9556 -  2.7453 0.99   1267  144 0.5551 0.5518      6.4175      6.4329|
|  6:  2.7453 -  2.5844 0.99   1276  141 0.5587 0.5737      6.3117      6.2431|
|  7:  2.5844 -  2.4556 0.99   1271  140 0.5459 0.5180      6.2715      6.2002|
|  8:  2.4556 -  2.3491 0.98   1248  140 0.5624 0.5733      6.2078      6.2204|
|  9:  2.3491 -  2.2590 0.98   1251  142 0.5524 0.6030      6.1365      6.1611|
| 10:  2.2590 -  2.1813 0.99   1248  137 0.5597 0.5438       6.135      6.1461|
| 11:  2.1813 -  2.1133 0.98   1251  137 0.5466 0.5937      6.0568       6.083|
| 12:  2.1133 -  2.0531 0.97   1243  141 0.5339 0.5654      5.9992      6.0696|
| 13:  2.0531 -  1.9992 1.00   1249  136 0.5615 0.5328      5.9093      5.8656|
| 14:  1.9992 -  1.9505 0.84   1066  120 0.5455 0.5023      5.8614      5.7707|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6397 -  4.6538  1375   153  0.57  45.08   0.77     0.63     110608.22|
|  2:  4.6538 -  3.7137  1307   147  0.58  45.42   0.84     0.67     159330.14|
|  3:  3.7137 -  3.2501  1294   142  0.46  54.96   0.83     0.61     164134.93|
|  4:  3.2501 -  2.9556  1284   139  0.38  61.00   0.79     0.50     134875.79|
|  5:  2.9556 -  2.7453  1267   144  0.29  68.21   0.72     0.37     102118.05|
|  6:  2.7453 -  2.5844  1276   141  0.24  72.06   0.70     0.28      85927.77|
|  7:  2.5844 -  2.4556  1271   140  0.16  78.23   0.73     0.19      79601.78|
|  8:  2.4556 -  2.3491  1248   140  0.14  79.30   0.73     0.18      72934.40|
|  9:  2.3491 -  2.2590  1251   142  0.14  79.74   0.71     0.17      67425.89|
| 10:  2.2590 -  2.1813  1248   137  0.18  76.95   0.76     0.22      59633.37|
| 11:  2.1813 -  2.1133  1251   137  0.14  79.95   0.77     0.18      56879.03|
| 12:  2.1133 -  2.0531  1243   141  0.15  78.89   0.77     0.19      51249.74|
| 13:  2.0531 -  1.9992  1249   136  0.16  78.18   0.75     0.21      43142.36|
| 14:  1.9992 -  1.9505  1066   120  0.27  69.65   0.74     0.31      31430.91|
|alpha:            min =        0.17 max =            0.67 mean =         0.34|
|beta:             min =    31430.91 max =       164134.93 mean =     88380.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.28|
|phase err.(work): min =        0.00 max =           89.98 mean =        68.82|
|phase err.(test): min =        0.00 max =           89.99 mean =        69.20|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 28.493254             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.741   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.282635              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.228   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.760 -  1.174:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.174 -  1.588:       13 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.588 -  2.002:       64 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.002 -  2.416:      350 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.416 -  2.830:     1107 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.830 -  3.244:     2363 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.244 -  3.658:     3971 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.658 -  4.072:     5494 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.072 -  4.486:     7241 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.486 -  4.900:     8786 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.322 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.082    4.900  0.760 |       4.153 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    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 = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5273   r_free= 0.5258   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.00 A                  |
| x-ray target function (ml) for work reflections: 6.311551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5162   r_free= 0.5128   ksol= 0.40   Bsol= 0.00   scale= 0.959    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.64,7.99,0.00,0.00,0.00); trace/3= 7.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.11 A                  |
| x-ray target function (ml) for work reflections: 6.306027                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.792878             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.446   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.599725              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.761   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5162      final r-factor (work) = 0.4747          |
| start r-factor (free) = 0.5128      final r-factor (free) = 0.4944          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 114.7506 = 19.79 * 0.50 * 6.3082 + 1.00 * 52.3216                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 62.2370 = 19.79 * 0.50 * 6.2731 + 1.00 * 0.1553                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4747      final r-factor (work) = 0.4442          |
| start r-factor (free) = 0.4944      final r-factor (free) = 0.4883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3228 = 2.60 * 1.00 * 6.2731 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.2673 = 2.60 * 1.00 * 6.2486 + 1.00 * 0.0226                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.52   14.47    None  None   None       |
|    all(noH): 2823   0      0.00    68.52   14.47    None  None   None       |
|    Sol.    : 438    0      0.00    57.05   16.47    None  None   None       |
|    Mac.    : 2385   0      0.00    68.52   14.10    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 -   6.852:  680   |   5:    34.262 -  41.114:   84        |
|      1:     6.852 -  13.705:  834   |   6:    41.114 -  47.967:   31        |
|      2:    13.705 -  20.557:  607   |   7:    47.967 -  54.819:   12        |
|      3:    20.557 -  27.410:  381   |   8:    54.819 -  61.672:    5        |
|      4:    27.410 -  34.262:  188   |   9:    61.672 -  68.524:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4442 r_free = 0.4883             target_work(ml) = 6.245         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4437 r_free = 0.4886             target_work(ml) = 6.245         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4437   r_free= 0.4886   ksol= 0.40   Bsol= 0.00   scale= 1.068    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.64,7.99,0.00,0.00,0.00); trace/3= 7.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.244509                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4443   r_free= 0.4860   ksol= 0.38   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.76,6.13,6.47,0.00,0.00,0.00); trace/3= 5.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.246662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.410796             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.135  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.684112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.511  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4443      final r-factor (work) = 0.3987          |
| start r-factor (free) = 0.4860      final r-factor (free) = 0.4550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.0518 = 13.41 * 0.50 * 6.2482 + 1.00 * 0.1553                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.7242 = 13.41 * 0.50 * 6.2082 + 1.00 * 0.0957                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3987      final r-factor (work) = 0.3781          |
| start r-factor (free) = 0.4550      final r-factor (free) = 0.4484          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5416 = 1.68 * 1.00 * 6.2082 + 1.00 * 0.0863                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3930 = 1.68 * 1.00 * 6.1595 + 1.00 * 0.0198                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.09   15.90    None  None   None       |
|    all(noH): 2823   0      0.00    78.09   15.90    None  None   None       |
|    Sol.    : 438    0      0.00    73.20   23.79    None  None   None       |
|    Mac.    : 2385   0      0.00    78.09   14.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.809:  878   |   5:    39.043 -  46.852:   85        |
|      1:     7.809 -  15.617:  748   |   6:    46.852 -  54.660:   36        |
|      2:    15.617 -  23.426:  519   |   7:    54.660 -  62.469:   15        |
|      3:    23.426 -  31.234:  343   |   8:    62.469 -  70.277:   13        |
|      4:    31.234 -  39.043:  182   |   9:    70.277 -  78.086:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3781 r_free = 0.4484             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3781 r_free = 0.4484             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3781   r_free= 0.4484   ksol= 0.38   Bsol= 20.00   scale= 1.087   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.76,6.13,6.47,0.00,0.00,0.00); trace/3= 5.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.147914                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3772   r_free= 0.4476   ksol= 0.36   Bsol= 42.95   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,4.27,4.74,0.00,0.00,0.00); trace/3= 4.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.148117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.891953             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.168  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 7.510086              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.446  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3772      final r-factor (work) = 0.3113          |
| start r-factor (free) = 0.4476      final r-factor (free) = 0.3818          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.7109 = 11.89 * 0.50 * 6.1580 + 1.00 * 0.0957                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.3063 = 11.89 * 0.50 * 6.0867 + 1.00 * 0.1147                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3113      final r-factor (work) = 0.2782          |
| start r-factor (free) = 0.3818      final r-factor (free) = 0.3629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 45.7317 = 7.51 * 1.00 * 6.0867 + 1.00 * 0.0199                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 44.7626 = 7.51 * 1.00 * 5.9560 + 1.00 * 0.0322                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.69  17.98    None  None   None       |
|    all(noH): 2823   0      0.00    123.69  17.98    None  None   None       |
|    Sol.    : 438    0      0.00    105.50  39.22    None  None   None       |
|    Mac.    : 2385   0      0.00    123.69  14.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.369: 1430   |   5:    61.847 -  74.216:   65        |
|      1:    12.369 -  24.739:  695   |   6:    74.216 -  86.586:   35        |
|      2:    24.739 -  37.108:  305   |   7:    86.586 -  98.955:   15        |
|      3:    37.108 -  49.478:  164   |   8:    98.955 - 111.324:    5        |
|      4:    49.478 -  61.847:  108   |   9:   111.324 - 123.694:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2782 r_free = 0.3629             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2781 r_free = 0.3628             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2781   r_free= 0.3628   ksol= 0.36   Bsol= 42.95   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.22,4.27,4.74,0.00,0.00,0.00); trace/3= 4.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.933849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2766   r_free= 0.3603   ksol= 0.36   Bsol= 42.95   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,2.68,3.30,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.928390                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.909993              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.197   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.309066              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.422  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2766      final r-factor (work) = 0.2367          |
| start r-factor (free) = 0.3603      final r-factor (free) = 0.3136          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7328 = 4.91 * 0.50 * 5.9544 + 1.00 * 0.1147                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4792 = 4.91 * 0.50 * 5.8714 + 1.00 * 0.0650                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2367      final r-factor (work) = 0.2248          |
| start r-factor (free) = 0.3136      final r-factor (free) = 0.2860          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8471 = 0.31 * 1.00 * 5.8714 + 1.00 * 0.0325                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7984 = 0.31 * 1.00 * 5.7859 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.23  14.86    None  None   None       |
|    all(noH): 2823   0      0.00    109.23  14.86    None  None   None       |
|    Sol.    : 438    0      1.21    80.02   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    109.23  10.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.924: 1569   |   5:    54.617 -  65.541:   34        |
|      1:    10.924 -  21.847:  668   |   6:    65.541 -  76.464:   13        |
|      2:    21.847 -  32.770:  266   |   7:    76.464 -  87.388:   11        |
|      3:    32.770 -  43.694:  153   |   8:    87.388 -  98.311:    2        |
|      4:    43.694 -  54.617:  106   |   9:    98.311 - 109.235:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2248 r_free = 0.2860             target_work(ml) = 5.745         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2243 r_free = 0.2855             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2243   r_free= 0.2855   ksol= 0.36   Bsol= 42.95   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,2.68,3.30,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.743183                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2235   r_free= 0.2840   ksol= 0.33   Bsol= 35.91   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,1.35,2.14,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.741860                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.716984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.234  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352762              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.678  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2235      final r-factor (work) = 0.1695          |
| start r-factor (free) = 0.2840      final r-factor (free) = 0.2207          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8189 = 3.72 * 0.50 * 5.7864 + 1.00 * 0.0650                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5303 = 3.72 * 0.50 * 5.6268 + 1.00 * 0.0729                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1695      final r-factor (work) = 0.1541          |
| start r-factor (free) = 0.2207      final r-factor (free) = 0.2057          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9950 = 0.35 * 1.00 * 5.6268 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9297 = 0.35 * 1.00 * 5.4412 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.21  15.02    None  None   None       |
|    all(noH): 2823   0      0.00    104.21  15.02    None  None   None       |
|    Sol.    : 438    0      4.26    81.67   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    104.21  10.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.421: 1646   |   5:    52.105 -  62.526:   93        |
|      1:    10.421 -  20.842:  622   |   6:    62.526 -  72.947:   32        |
|      2:    20.842 -  31.263:  176   |   7:    72.947 -  83.368:   17        |
|      3:    31.263 -  41.684:  122   |   8:    83.368 -  93.789:    0        |
|      4:    41.684 -  52.105:  112   |   9:    93.789 - 104.210:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1541 r_free = 0.2057             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1535 r_free = 0.2047             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1535   r_free= 0.2047   ksol= 0.33   Bsol= 35.91   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,1.35,2.14,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.402447                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6397 -  4.6538 0.99   1375  153 0.1215 0.1624      5.6078      5.7823|
|  2:  4.6538 -  3.7137 0.99   1307  147 0.1115 0.1582      5.6893      5.9839|
|  3:  3.7137 -  3.2501 0.99   1294  142 0.1456 0.1688      5.7798      5.9471|
|  4:  3.2501 -  2.9556 0.99   1284  139 0.1635 0.2373       5.709      6.0006|
|  5:  2.9556 -  2.7453 0.99   1267  144 0.1791 0.2146      5.5864      5.7274|
|  6:  2.7453 -  2.5844 0.99   1276  141 0.1700 0.2151      5.4693       5.583|
|  7:  2.5844 -  2.4556 0.99   1271  140 0.1676 0.2213      5.4017      5.6117|
|  8:  2.4556 -  2.3491 0.98   1248  140 0.1725 0.2275      5.3833      5.6256|
|  9:  2.3491 -  2.2590 0.98   1251  142 0.1652 0.2500      5.3054      5.5666|
| 10:  2.2590 -  2.1813 0.99   1248  137 0.1550 0.2332        5.25      5.4499|
| 11:  2.1813 -  2.1133 0.98   1251  137 0.1585 0.2218      5.1845      5.4742|
| 12:  2.1133 -  2.0531 0.97   1243  141 0.1572 0.1923      5.1479      5.3898|
| 13:  2.0531 -  1.9992 1.00   1249  136 0.1594 0.2198      5.0352      5.2761|
| 14:  1.9992 -  1.9505 0.84   1066  120 0.1632 0.2065      4.9585      5.1637|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6397 -  4.6538  1375   153  0.91  13.40   0.99     0.96      12750.02|
|  2:  4.6538 -  3.7137  1307   147  0.92  11.96   1.06     1.04      15382.27|
|  3:  3.7137 -  3.2501  1294   142  0.89  16.37   1.08     1.07      18913.88|
|  4:  3.2501 -  2.9556  1284   139  0.88  18.31   1.05     1.02      16866.47|
|  5:  2.9556 -  2.7453  1267   144  0.86  20.73   1.03     0.99      13443.22|
|  6:  2.7453 -  2.5844  1276   141  0.86  20.87   1.02     0.96      11178.16|
|  7:  2.5844 -  2.4556  1271   140  0.85  21.13   1.04     1.02      10073.02|
|  8:  2.4556 -  2.3491  1248   140  0.86  21.12   1.04     1.02       9708.08|
|  9:  2.3491 -  2.2590  1251   142  0.86  21.02   1.05     1.02       8567.59|
| 10:  2.2590 -  2.1813  1248   137  0.85  21.88   1.06     1.00       8069.54|
| 11:  2.1813 -  2.1133  1251   137  0.85  21.15   1.08     1.01       6818.65|
| 12:  2.1133 -  2.0531  1243   141  0.86  20.83   1.08     1.07       6582.66|
| 13:  2.0531 -  1.9992  1249   136  0.87  19.93   1.08     1.05       5034.16|
| 14:  1.9992 -  1.9505  1066   120  0.88  18.51   1.05     1.00       3729.01|
|alpha:            min =        0.96 max =            1.07 mean =         1.02|
|beta:             min =     3729.01 max =        18913.88 mean =     10649.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.99 mean =        19.03|
|phase err.(test): min =        0.00 max =           89.16 mean =        18.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1531   r_free= 0.2034   ksol= 0.31   Bsol= 29.52   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.19,0.69,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.400339                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.64 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1531   r_free= 0.2034   ksol= 0.31   Bsol= 29.52   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.19,0.69,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.400339                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6397 -  4.6538 0.99   1375  153 0.1199 0.1560      5.5826      5.7471|
|  2:  4.6538 -  3.7137 0.99   1307  147 0.1122 0.1597      5.6841      5.9879|
|  3:  3.7137 -  3.2501 0.99   1294  142 0.1447 0.1674      5.7779      5.9393|
|  4:  3.2501 -  2.9556 0.99   1284  139 0.1642 0.2387      5.7102      6.0049|
|  5:  2.9556 -  2.7453 0.99   1267  144 0.1785 0.2158      5.5877       5.731|
|  6:  2.7453 -  2.5844 0.99   1276  141 0.1700 0.2145      5.4697      5.5832|
|  7:  2.5844 -  2.4556 0.99   1271  140 0.1671 0.2218      5.4016      5.6132|
|  8:  2.4556 -  2.3491 0.98   1248  140 0.1725 0.2279       5.383      5.6282|
|  9:  2.3491 -  2.2590 0.98   1251  142 0.1650 0.2490      5.3051      5.5646|
| 10:  2.2590 -  2.1813 0.99   1248  137 0.1546 0.2332      5.2495       5.453|
| 11:  2.1813 -  2.1133 0.98   1251  137 0.1586 0.2221      5.1854      5.4764|
| 12:  2.1133 -  2.0531 0.97   1243  141 0.1574 0.1921       5.149      5.3886|
| 13:  2.0531 -  1.9992 1.00   1249  136 0.1594 0.2198      5.0356      5.2754|
| 14:  1.9992 -  1.9505 0.84   1066  120 0.1634 0.2065      4.9599      5.1635|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6397 -  4.6538  1375   153  0.91  12.68   0.98     0.96      11698.46|
|  2:  4.6538 -  3.7137  1307   147  0.93  11.65   1.05     1.03      14818.35|
|  3:  3.7137 -  3.2501  1294   142  0.89  16.30   1.07     1.06      18847.36|
|  4:  3.2501 -  2.9556  1284   139  0.88  18.29   1.03     1.00      16789.73|
|  5:  2.9556 -  2.7453  1267   144  0.86  20.78   1.01     0.97      13537.58|
|  6:  2.7453 -  2.5844  1276   141  0.86  20.89   0.99     0.93      11216.35|
|  7:  2.5844 -  2.4556  1271   140  0.85  21.19   1.01     0.98      10133.99|
|  8:  2.4556 -  2.3491  1248   140  0.85  21.15   1.01     0.98       9703.24|
|  9:  2.3491 -  2.2590  1251   142  0.86  21.04   1.01     0.99       8590.25|
| 10:  2.2590 -  2.1813  1248   137  0.85  21.88   1.01     0.96       8061.81|
| 11:  2.1813 -  2.1133  1251   137  0.85  21.15   1.03     0.97       6832.24|
| 12:  2.1133 -  2.0531  1243   141  0.86  20.82   1.03     1.02       6576.81|
| 13:  2.0531 -  1.9992  1249   136  0.87  19.92   1.03     1.00       5032.53|
| 14:  1.9992 -  1.9505  1066   120  0.88  18.53   1.00     0.95       3738.37|
|alpha:            min =        0.93 max =            1.06 mean =         0.99|
|beta:             min =     3738.37 max =        18847.36 mean =     10530.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.88 mean =        18.95|
|phase err.(test): min =        0.00 max =           88.83 mean =        18.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.090)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    104.89  15.69    None  None   None       |
|    all(noH): 2823   0      0.68    104.89  15.69    None  None   None       |
|    Sol.    : 438    0      4.93    82.35   41.03    None  None   None       |
|    Mac.    : 2385   0      0.68    104.89  11.04    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:     0.676 -  11.097: 1646   |   5:    52.781 -  63.202:   93        |
|      1:    11.097 -  21.518:  622   |   6:    63.202 -  73.623:   32        |
|      2:    21.518 -  31.939:  176   |   7:    73.623 -  84.044:   17        |
|      3:    31.939 -  42.360:  122   |   8:    84.044 -  94.465:    0        |
|      4:    42.360 -  52.781:  112   |   9:    94.465 - 104.886:    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)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.670 - 5.413
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 342
   mapped sites are within: 0.727 - 5.413

peak=    8.575 closest distance to " CB  VAL A 296 " =    1.429
peak=    8.571 closest distance to " CB  VAL A 230 " =    1.439
peak=    8.241 closest distance to " O   HOH Z 390 " =    1.660
peak=    8.219 closest distance to " O   HOH Z 403 " =    2.472
peak=    8.064 closest distance to " OD1 ASP A  27 " =    1.193
peak=    7.121 closest distance to " CG  ASP A  50 " =    1.315
peak=    6.774 closest distance to " O   HOH Z 381 " =    1.979
peak=    6.627 closest distance to " O   HOH Z 120 " =    1.327
peak=    6.430 closest distance to " OD1 ASN A  60 " =    1.238
peak=    6.269 closest distance to " O   HOH Z  65 " =    1.847
peak=    6.092 closest distance to " O   HOH Z 375 " =    1.865
peak=    6.070 closest distance to " N   PHE A  59 " =    0.863
peak=    5.893 closest distance to " O   HOH Z 321 " =    1.026
peak=    5.813 closest distance to " CD  ARG A 138 " =    1.271
peak=    5.790 closest distance to " O   HOH Z 199 " =    1.809
peak=    5.771 closest distance to " CD2 LEU A   5 " =    1.526
peak=    5.748 closest distance to " O   HOH Z 278 " =    2.033
peak=    5.693 closest distance to " O   HOH Z   9 " =    1.718
peak=    5.640 closest distance to " O   HOH Z 130 " =    1.557
peak=    5.588 closest distance to " O   HOH Z  45 " =    1.348
peak=    5.423 closest distance to " O   HOH Z 385 " =    1.473
peak=    5.378 closest distance to " C   PRO A 198 " =    1.379
peak=    5.317 closest distance to " O   HOH Z 124 " =    1.835
peak=    5.309 closest distance to " O   HOH Z 358 " =    1.741
peak=    5.202 closest distance to " O   SER A  62 " =    0.933
peak=    5.105 closest distance to " CD  ARG A 138 " =    0.946
peak=    5.096 closest distance to " O   HOH Z 193 " =    1.962
peak=    5.047 closest distance to " CD1AILE A 234 " =    0.938
peak=    5.035 closest distance to " O   HOH Z  91 " =    1.110
peak=    5.033 closest distance to " O   HOH Z 410 " =    1.537
peak=    5.000 closest distance to " N   ASN A  60 " =    1.033
peak=    4.968 closest distance to " O   HOH Z 203 " =    2.661
peak=    4.930 closest distance to " O   HOH Z 291 " =    1.665
peak=    4.917 closest distance to " O   HOH Z 349 " =    1.005
peak=    4.909 closest distance to " CG1AVAL A 121 " =    1.015
peak=    4.893 closest distance to " CB  ARG A 275 " =    1.308
peak=    4.884 closest distance to " O   HOH Z 238 " =    1.379
peak=    4.880 closest distance to " CD2 LEU A 228 " =    1.259
peak=    4.869 closest distance to " O   HOH Z 214 " =    1.438
peak=    4.819 closest distance to " O   HOH Z 236 " =    1.850
peak=    4.727 closest distance to " O   HOH Z  28 " =    2.267
peak=    4.678 closest distance to " O   HOH Z 179 " =    1.202
peak=    4.661 closest distance to " O   HOH Z  51 " =    2.296
peak=    4.656 closest distance to " O   HOH Z 363 " =    1.326
peak=    4.638 closest distance to " CB  ASN A  60 " =    1.119
peak=    4.612 closest distance to " O   HOH Z 126 " =    1.891
peak=    4.560 closest distance to " CB  ASN A 148 " =    2.085
peak=    4.538 closest distance to " O   HOH Z 223 " =    1.163
peak=    4.522 closest distance to " O   HOH Z 244 " =    1.402
peak=    4.490 closest distance to " O   HOH Z 279 " =    1.389
peak=    4.486 closest distance to " O   HOH Z 169 " =    1.148
peak=    4.470 closest distance to " O   HOH Z 116 " =    1.334
peak=    4.426 closest distance to " CG2 ILE A 234 " =    1.000
peak=    4.394 closest distance to " OD1 ASP A 286 " =    1.104
peak=    4.364 closest distance to " O   HOH Z  78 " =    1.838
peak=    4.332 closest distance to " NH2BARG A 145 " =    1.676
peak=    4.329 closest distance to " CE AMET A  47 " =    0.973
peak=    4.324 closest distance to " O   HOH Z 388 " =    1.200
peak=    4.321 closest distance to " O   HOH Z 202 " =    1.722
peak=    4.320 closest distance to " CA  ALA A   1 " =    1.349
peak=    4.315 closest distance to " O   HOH Z  63 " =    1.617
peak=    4.314 closest distance to " O   HOH Z 112 " =    1.354
peak=    4.312 closest distance to " O   HOH Z 326 " =    1.140
peak=    4.298 closest distance to " O   HOH Z 222 " =    1.296
peak=    4.293 closest distance to " O   HOH Z 226 " =    1.079
peak=    4.289 closest distance to " OE1 GLN A  55 " =    1.698
peak=    4.265 closest distance to " CE1 PHE A  38 " =    0.843
peak=    4.250 closest distance to " CB  SER A   3 " =    1.155
peak=    4.249 closest distance to " OD1 ASN A  45 " =    1.261
peak=    4.245 closest distance to " O   HOH Z 427 " =    1.297
peak=    4.212 closest distance to " NE1 TRP A 274 " =    1.128
peak=    4.204 closest distance to " O   HOH Z 139 " =    1.321
peak=    4.185 closest distance to " CE  MET A  93 " =    1.288
peak=    4.150 closest distance to " N   ARG A 275 " =    0.815
peak=    4.145 closest distance to " O   HOH Z 414 " =    2.057
peak=    4.139 closest distance to " O   HOH Z 423 " =    2.213
peak=    4.133 closest distance to " O   HOH Z 363 " =    2.789
peak=    4.126 closest distance to " O   HOH Z 384 " =    1.662
peak=    4.094 closest distance to " CG  LEU A   5 " =    1.246
peak=    4.092 closest distance to " O   HOH Z 225 " =    1.523
peak=    4.091 closest distance to " O   HOH Z 209 " =    1.312
peak=    4.086 closest distance to " CG2 THR A  29 " =    0.899
peak=    4.043 closest distance to " O   HOH Z  43 " =    1.316
peak=    4.042 closest distance to " O   HOH Z 428 " =    1.596
peak=    4.038 closest distance to " O   HOH Z 142 " =    1.958
peak=    4.022 closest distance to " O   HOH Z  59 " =    1.650
peak=    4.020 closest distance to " O   HOH Z 143 " =    1.457
peak=    4.019 closest distance to " O   HOH Z 347 " =    1.129
peak=    3.996 closest distance to " O   HOH Z 167 " =    1.022
peak=    3.996 closest distance to " NZ  LYS A 119 " =    2.118
peak=    3.988 closest distance to " O   HOH Z   7 " =    1.927
peak=    3.979 closest distance to " O   HOH Z  97 " =    2.169
peak=    3.976 closest distance to " O   HOH Z 427 " =    1.929
peak=    3.968 closest distance to " O   HOH Z 425 " =    1.953
peak=    3.965 closest distance to " NH1 ARG A 138 " =    0.959
peak=    3.947 closest distance to " O   HOH Z  77 " =    1.225
peak=    3.935 closest distance to " CB  ALA A 114 " =    1.416
peak=    3.929 closest distance to " NE BARG A 145 " =    1.293
peak=    3.929 closest distance to " O   HOH Z 108 " =    1.555
peak=    3.908 closest distance to " O   HOH Z 406 " =    1.635
peak=    3.906 closest distance to " O   HOH Z 130 " =    2.009
peak=    3.906 closest distance to " CD1 LEU A   5 " =    1.633
peak=    3.897 closest distance to " O   HOH Z 411 " =    3.810
peak=    3.892 closest distance to " O   HOH Z  97 " =    1.507
peak=    3.885 closest distance to " N   TYR A  15 " =    1.191
peak=    3.860 closest distance to " O   HOH Z 344 " =    1.540
peak=    3.853 closest distance to " NE BARG A 275 " =    1.386
peak=    3.846 closest distance to " CG2 ILE A  20 " =    1.201
peak=    3.842 closest distance to " O   HOH Z 428 " =    1.389
peak=    3.837 closest distance to " O   VAL A  72 " =    0.980
peak=    3.831 closest distance to " O   HOH Z 357 " =    1.746
peak=    3.798 closest distance to " CD  GLN A  58 " =    5.413
peak=    3.790 closest distance to " O   SER A 271 " =    1.001
peak=    3.785 closest distance to " O   HOH Z 185 " =    1.269
peak=    3.780 closest distance to " OG ASER A 134 " =    1.391
peak=    3.772 closest distance to " CD2 PHE A  59 " =    1.101
peak=    3.767 closest distance to " CA  TYR A  30 " =    1.028
peak=    3.766 closest distance to " O   HOH Z  47 " =    1.695
peak=    3.765 closest distance to " CG  LYS A 166 " =    1.536
peak=    3.752 closest distance to " O   ARG A  14 " =    0.998
peak=    3.747 closest distance to " O   HOH Z 249 " =    1.392
peak=    3.746 closest distance to " O   HOH Z  65 " =    1.562
peak=    3.742 closest distance to " O   HOH Z 130 " =    1.968
peak=    3.736 closest distance to " CB  SER A 273 " =    0.838
peak=    3.733 closest distance to " O   HOH Z 284 " =    1.663
peak=    3.730 closest distance to " O   HOH Z  28 " =    2.071
peak=    3.728 closest distance to " O   HOH Z 134 " =    1.610
peak=    3.721 closest distance to " NE2 GLN A  11 " =    1.011
peak=    3.709 closest distance to " O   HOH Z  30 " =    1.779
peak=    3.702 closest distance to " NH2AARG A 145 " =    2.007
peak=    3.700 closest distance to " O   HOH Z 316 " =    1.147
peak=    3.698 closest distance to " O   HOH Z 346 " =    1.076
peak=    3.697 closest distance to " NH2BARG A 190 " =    1.434
peak=    3.696 closest distance to " CB  VAL A 230 " =    1.200
peak=    3.694 closest distance to " O   HOH Z 371 " =    1.907
peak=    3.691 closest distance to " O   ASP A 286 " =    0.825
peak=    3.687 closest distance to " O   HOH Z 245 " =    1.244
peak=    3.683 closest distance to " CB  ARG A 102 " =    0.812
peak=    3.682 closest distance to " CG  LYS A 119 " =    1.106
peak=    3.679 closest distance to " CB  PRO A 198 " =    1.117
peak=    3.678 closest distance to " C   ALA A   1 " =    1.478
peak=    3.676 closest distance to " CB  ASN A 142 " =    1.230
peak=    3.676 closest distance to " N   GLU A   2 " =    1.451
peak=    3.670 closest distance to " O   HOH Z 194 " =    1.570
peak=    3.669 closest distance to " O   HOH Z 263 " =    1.866
peak=    3.665 closest distance to " CA  PRO A 163 " =    0.882
peak=    3.661 closest distance to " O   HOH Z 176 " =    1.807
peak=    3.659 closest distance to " CB  PRO A  54 " =    1.088
peak=    3.648 closest distance to " CA  PHE A  59 " =    0.875
peak=    3.648 closest distance to " CA  ALA A  21 " =    1.234
peak=    3.645 closest distance to " CA  THR A 264 " =    0.788
peak=    3.642 closest distance to " O   HOH Z  72 " =    0.940
peak=    3.637 closest distance to " CG2 THR A 246 " =    1.040
peak=    3.635 closest distance to " O   HOH Z 132 " =    1.301
peak=    3.635 closest distance to " CZ  PHE A  59 " =    0.866
peak=    3.631 closest distance to " O   HOH Z 415 " =    1.217
peak=    3.630 closest distance to " CB  GLU A   2 " =    1.007
peak=    3.626 closest distance to " O   HOH Z 316 " =    2.301
peak=    3.621 closest distance to " O   HOH Z 422 " =    2.444
peak=    3.617 closest distance to " OG1 THR A 246 " =    1.237
peak=    3.616 closest distance to " O   HOH Z  66 " =    1.349
peak=    3.615 closest distance to " N   ALA A   1 " =    3.317
peak=    3.608 closest distance to " O   HOH Z  46 " =    1.287
peak=    3.607 closest distance to " O   HOH Z 234 " =    1.865
peak=    3.605 closest distance to " O   HOH Z 426 " =    1.143
peak=    3.604 closest distance to " CG  PRO A 213 " =    1.246
peak=    3.597 closest distance to " CG1 ILE A 120 " =    1.167
peak=    3.593 closest distance to " O   HOH Z 123 " =    1.371
peak=    3.592 closest distance to " CD1 TYR A  15 " =    1.039
peak=    3.589 closest distance to " CA  ASN A 284 " =    1.292
peak=    3.588 closest distance to " O   HOH Z 311 " =    1.473
peak=    3.587 closest distance to " O   HOH Z 156 " =    2.620
peak=    3.587 closest distance to " O   HOH Z 416 " =    1.457
peak=    3.585 closest distance to " CA  PHE A 130 " =    1.089
peak=    3.585 closest distance to " O   HOH Z 417 " =    1.156
peak=    3.583 closest distance to " O   HOH Z 331 " =    1.398
peak=    3.573 closest distance to " NH2 ARG A 156 " =    1.024
peak=    3.572 closest distance to " O   HOH Z 260 " =    1.716
peak=    3.572 closest distance to " O   HOH Z 344 " =    2.750
peak=    3.570 closest distance to " CB  SER A 216 " =    0.884
peak=    3.568 closest distance to " O   HOH Z 272 " =    1.775
peak=    3.565 closest distance to " O   HOH Z 153 " =    1.968
peak=    3.562 closest distance to " ND1 HIS A  81 " =    1.175
peak=    3.556 closest distance to " CG  GLN A  88 " =    1.101
peak=    3.555 closest distance to " O   HOH Z 419 " =    1.967
peak=    3.554 closest distance to " O   HOH Z  92 " =    1.618
peak=    3.553 closest distance to " CE2 PHE A  16 " =    0.974
peak=    3.550 closest distance to " NH2 ARG A  56 " =    2.177
peak=    3.545 closest distance to " O   SER A 164 " =    1.230
peak=    3.544 closest distance to " O   HOH Z  39 " =    1.315
peak=    3.543 closest distance to " O   HOH Z 145 " =    2.396
peak=    3.537 closest distance to " CB  LYS A  76 " =    0.978
peak=    3.535 closest distance to " O   HOH Z 114 " =    2.071
peak=    3.531 closest distance to " O   HOH Z 425 " =    1.369
peak=    3.527 closest distance to " CA  ALA A 184 " =    1.874
peak=    3.524 closest distance to " CB  GLN A 223 " =    1.686
peak=    3.518 closest distance to " O   HOH Z 128 " =    1.829
peak=    3.518 closest distance to " O   HOH Z 222 " =    2.139
peak=    3.516 closest distance to " CB  ASN A 187 " =    1.083
peak=    3.508 closest distance to " CG1BVAL A 121 " =    2.139
peak=    3.507 closest distance to " O   HOH Z 418 " =    1.242
peak=    3.506 closest distance to " CA  ILE A 234 " =    1.142
peak=    3.504 closest distance to " O   HOH Z 119 " =    1.463
peak=    3.500 closest distance to " O   HOH Z  78 " =    2.102
peak=    3.499 closest distance to " CB  VAL A 202 " =    1.606
peak=    3.490 closest distance to " O   HOH Z 233 " =    1.443
peak=    3.486 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.484 closest distance to " O   HOH Z 225 " =    1.598
peak=    3.472 closest distance to " O   HOH Z 225 " =    2.265
peak=    3.468 closest distance to " O   HOH Z 259 " =    1.898
peak=    3.464 closest distance to " N   GLU A 277 " =    1.138
peak=    3.458 closest distance to " CB  ARG A 156 " =    1.067
peak=    3.455 closest distance to " O   HOH Z  58 " =    1.914
peak=    3.450 closest distance to " O   PHE A  59 " =    0.894
peak=    3.445 closest distance to " CE1 PHE A  61 " =    1.133
peak=    3.443 closest distance to " CB  TRP A  85 " =    1.498
peak=    3.443 closest distance to " N   GLY A 302 " =    0.991
peak=    3.439 closest distance to " O   HOH Z 261 " =    1.419
peak=    3.437 closest distance to " N   LYS A 119 " =    0.830
peak=    3.430 closest distance to " N   SER A  63 " =    0.794
peak=    3.430 closest distance to " O   ALA A 165 " =    1.111
peak=    3.425 closest distance to " O   HOH Z 100 " =    1.405
peak=    3.422 closest distance to " OE1 GLN A  55 " =    1.398
peak=    3.420 closest distance to " O   HOH Z 108 " =    1.560
peak=    3.417 closest distance to " CA  GLY A 287 " =    1.266
peak=    3.416 closest distance to " O   HOH Z  50 " =    1.994
peak=    3.416 closest distance to " CE1 TYR A 247 " =    1.386
peak=    3.414 closest distance to " CG  PRO A 163 " =    3.650
peak=    3.412 closest distance to " O   HOH Z 130 " =    1.749
peak=    3.409 closest distance to " NH1AARG A 145 " =    0.755
peak=    3.408 closest distance to " O   HOH Z 417 " =    3.174
peak=    3.408 closest distance to " O   HOH Z 373 " =    2.156
peak=    3.404 closest distance to " O   HOH Z   3 " =    2.090
peak=    3.403 closest distance to " O   HOH Z  15 " =    1.239
peak=    3.399 closest distance to " O   HOH Z 193 " =    1.757
peak=    3.390 closest distance to " N   PHE A 130 " =    1.419
peak=    3.389 closest distance to " O   GLY A 147 " =    1.136
peak=    3.385 closest distance to " O   HOH Z 423 " =    2.006
peak=    3.384 closest distance to " O   HOH Z 217 " =    1.798
peak=    3.382 closest distance to " CB  SER A  28 " =    0.998
peak=    3.380 closest distance to " CE1 PHE A  16 " =    0.972
peak=    3.379 closest distance to " O   HOH Z 345 " =    1.698
peak=    3.374 closest distance to " O   HOH Z 214 " =    1.804
peak=    3.367 closest distance to " CA  ASN A 127 " =    1.041
peak=    3.365 closest distance to " O   HOH Z 290 " =    1.256
peak=    3.360 closest distance to " O   HOH Z 368 " =    2.164
peak=    3.354 closest distance to " O   HOH Z 188 " =    0.960
peak=    3.354 closest distance to " O   HOH Z 434 " =    1.525
peak=    3.349 closest distance to " CG  GLN A  77 " =    2.086
peak=    3.347 closest distance to " NE2 GLN A 205 " =    1.338
peak=    3.347 closest distance to " O   HOH Z  53 " =    2.159
peak=    3.345 closest distance to " CB  SER A  62 " =    1.283
peak=    3.339 closest distance to " O   HOH Z 293 " =    1.319
peak=    3.339 closest distance to " O   HOH Z 394 " =    1.697
peak=    3.335 closest distance to " CG  PRO A 198 " =    1.555
peak=    3.334 closest distance to " O   HOH Z 191 " =    2.689
peak=    3.333 closest distance to " O   HOH Z 111 " =    2.475
peak=    3.331 closest distance to " O   SER A  87 " =    2.491
peak=    3.330 closest distance to " NZ  LYS A  48 " =    1.940
peak=    3.325 closest distance to " N   PRO A 243 " =    1.187
peak=    3.323 closest distance to " CA  LEU A 282 " =    1.179
peak=    3.322 closest distance to " NH1 ARG A  14 " =    1.046
peak=    3.319 closest distance to " O   HOH Z 162 " =    1.646
peak=    3.311 closest distance to " O   HOH Z 276 " =    1.670
peak=    3.296 closest distance to " O   HOH Z 172 " =    2.248
peak=    3.287 closest distance to " O   HOH Z 366 " =    2.003
peak=    3.285 closest distance to " CB  THR A 279 " =    1.288
peak=    3.277 closest distance to " CB  TRP A 179 " =    1.173
peak=    3.274 closest distance to " O   HOH Z 350 " =    1.415
peak=    3.273 closest distance to " CB  ARG A  66 " =    1.222
peak=    3.272 closest distance to " CB  ASN A 148 " =    1.441
peak=    3.268 closest distance to " O   HOH Z 356 " =    1.328
peak=    3.267 closest distance to " CA  ASN A  45 " =    1.053
peak=    3.265 closest distance to " CB  GLN A 278 " =    0.727
peak=    3.263 closest distance to " CZ3 TRP A  70 " =    1.005
peak=    3.259 closest distance to " O   HOH Z 223 " =    1.901
peak=    3.259 closest distance to " N   ASP A 286 " =    1.120
peak=    3.257 closest distance to " CB  GLU A 277 " =    1.237
peak=    3.255 closest distance to " N   PHE A  16 " =    1.708
peak=    3.254 closest distance to " O   HOH Z 366 " =    2.311
peak=    3.250 closest distance to " OG BSER A 212 " =    1.954
peak=    3.247 closest distance to " CD1 LEU A 281 " =    1.078
peak=    3.242 closest distance to " O   HOH Z 105 " =    1.168
peak=    3.233 closest distance to " O   HOH Z 153 " =    3.025
peak=    3.232 closest distance to " N   ILE A  33 " =    1.037
peak=    3.231 closest distance to " CB  ALA A 233 " =    1.110
peak=    3.230 closest distance to " O   HOH Z 303 " =    2.293
peak=    3.230 closest distance to " CB  TRP A 266 " =    1.066
peak=    3.230 closest distance to " O   HOH Z 305 " =    2.971
peak=    3.223 closest distance to " CG  GLN A 278 " =    3.613
peak=    3.222 closest distance to " NZ BLYS A 290 " =    1.405
peak=    3.217 closest distance to " O   HOH Z  49 " =    1.200
peak=    3.216 closest distance to " SD  MET A  40 " =    1.470
peak=    3.216 closest distance to " O   HOH Z  98 " =    2.437
peak=    3.214 closest distance to " O   HOH Z 137 " =    1.523
peak=    3.213 closest distance to " CE  LYS A  48 " =    1.275
peak=    3.208 closest distance to " O   HOH Z 232 " =    1.323
peak=    3.201 closest distance to " CB  TRP A 123 " =    1.060
peak=    3.200 closest distance to " O   HOH Z 222 " =    2.540
peak=    3.198 closest distance to " CG  LYS A  76 " =    1.498
peak=    3.198 closest distance to " O   HOH Z  96 " =    1.268
peak=    3.186 closest distance to " CB  LEU A 255 " =    1.197
peak=    3.186 closest distance to " O   HOH Z 104 " =    1.392
peak=    3.184 closest distance to " SD BMET A  47 " =    1.466
peak=    3.184 closest distance to " CA  ARG A  66 " =    1.001
peak=    3.183 closest distance to " O   HOH Z 273 " =    1.274
peak=    3.179 closest distance to " O   HOH Z 126 " =    1.372
peak=    3.173 closest distance to " O   HOH Z 264 " =    1.342
peak=    3.173 closest distance to " O   HOH Z 429 " =    1.055
peak=    3.172 closest distance to " CG  ASN A  60 " =    1.493
peak=    3.169 closest distance to " O   HOH Z 250 " =    1.307
peak=    3.168 closest distance to " CB  SER A  95 " =    0.864
peak=    3.168 closest distance to " OG BSER A 216 " =    1.766
peak=    3.167 closest distance to " O   GLY A 203 " =    1.651
peak=    3.166 closest distance to " O   HOH Z 299 " =    2.912
peak=    3.165 closest distance to " O   HOH Z 278 " =    1.324
peak=    3.164 closest distance to " O   HOH Z  22 " =    1.173
peak=    3.156 closest distance to " O   HOH Z 180 " =    1.400
peak=    3.156 closest distance to " O   HOH Z  88 " =    2.711
peak=    3.156 closest distance to " OG  SER A  62 " =    2.889
peak=    3.153 closest distance to " O   HOH Z 364 " =    1.824
peak=    3.151 closest distance to " O   HOH Z 381 " =    1.921
peak=    3.138 closest distance to " O   HOH Z 400 " =    0.813
peak=    3.133 closest distance to " CB  VAL A 265 " =    1.545
peak=    3.133 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.132 closest distance to " CG2 THR A 294 " =    1.326
peak=    3.127 closest distance to " CD2 LEU A 167 " =    1.302
peak=    3.121 closest distance to " CD2 LEU A 255 " =    1.096
peak=    3.120 closest distance to " O   HOH Z 262 " =    1.238
peak=    3.120 closest distance to " CB  SER A  12 " =    1.494
peak=    3.118 closest distance to " CA  ALA A 299 " =    0.954
peak=    3.116 closest distance to " O   HOH Z 279 " =    2.944
peak=    3.116 closest distance to " CG  ASP A 238 " =    0.840
peak=    3.114 closest distance to " O   HOH Z 257 " =    1.306
peak=    3.113 closest distance to " CB  ALA A 137 " =    0.961
peak=    3.113 closest distance to " O   HOH Z 180 " =    3.010
peak=    3.109 closest distance to " O   HOH Z 343 " =    2.244
peak=    3.078 closest distance to " CG2 ILE A  20 " =    1.795
peak=    3.065 closest distance to " CE  MET A  40 " =    0.940
peak=    3.064 closest distance to " NE2 GLN A  58 " =    3.289
peak=    3.057 closest distance to " O   HOH Z 110 " =    1.671

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.563 - 4.759
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 204
   mapped sites are within: 0.706 - 4.759

peak=   -5.354 closest distance to " CD  ARG A 138 " =    1.019
peak=   -4.682 closest distance to " O   SER A  62 " =    1.039
peak=   -4.344 closest distance to " N   ASN A  60 " =    0.803
peak=   -4.337 closest distance to " O   PRO A 198 " =    0.964
peak=   -4.314 closest distance to " N   PHE A  59 " =    1.082
peak=   -4.254 closest distance to " N   GLN A  58 " =    0.903
peak=   -4.251 closest distance to " O   SER A 271 " =    1.243
peak=   -4.248 closest distance to " OD2 ASP A  50 " =    1.025
peak=   -4.146 closest distance to " OG ASER A 134 " =    0.974
peak=   -4.140 closest distance to " O   HOH Z 385 " =    0.833
peak=   -4.140 closest distance to " CA  VAL A  67 " =    2.798
peak=   -4.072 closest distance to " O   SER A  22 " =    2.231
peak=   -4.056 closest distance to " O   HOH Z 244 " =    1.132
peak=   -4.054 closest distance to " O   HOH Z  24 " =    1.194
peak=   -4.024 closest distance to " O   HOH Z  88 " =    2.065
peak=   -3.993 closest distance to " CG2 VAL A 230 " =    0.842
peak=   -3.933 closest distance to " OG1 THR A 178 " =    1.004
peak=   -3.919 closest distance to " O   HOH Z 210 " =    1.616
peak=   -3.904 closest distance to " CZ  PHE A  16 " =    0.881
peak=   -3.895 closest distance to " O   VAL A 125 " =    1.985
peak=   -3.874 closest distance to " CG  PHE A 283 " =    2.479
peak=   -3.871 closest distance to " O   SER A 135 " =    1.556
peak=   -3.865 closest distance to " ND2 ASN A 209 " =    1.554
peak=   -3.853 closest distance to " O   LYS A 119 " =    0.860
peak=   -3.850 closest distance to " N   ALA A  64 " =    1.154
peak=   -3.848 closest distance to " CD  ARG A 219 " =    2.517
peak=   -3.845 closest distance to " N   ASP A 286 " =    2.036
peak=   -3.834 closest distance to " N   ARG A 275 " =    0.823
peak=   -3.831 closest distance to " SG  CYS A 168 " =    1.004
peak=   -3.808 closest distance to " O   HOH Z  72 " =    0.964
peak=   -3.800 closest distance to " O   HOH Z  69 " =    1.500
peak=   -3.799 closest distance to " O   HOH Z 347 " =    0.727
peak=   -3.789 closest distance to " N   VAL A 125 " =    1.297
peak=   -3.788 closest distance to " O   HOH Z 169 " =    0.881
peak=   -3.781 closest distance to " O   ILE A  49 " =    1.673
peak=   -3.773 closest distance to " CE  LYS A 166 " =    1.018
peak=   -3.760 closest distance to " O   SER A  22 " =    1.216
peak=   -3.754 closest distance to " CG  PRO A 243 " =    1.307
peak=   -3.735 closest distance to " O   HOH Z 235 " =    1.041
peak=   -3.709 closest distance to " CA  SER A 245 " =    2.281
peak=   -3.698 closest distance to " OD1 ASN A 284 " =    1.285
peak=   -3.691 closest distance to " O   HOH Z 290 " =    0.887
peak=   -3.685 closest distance to " O   TRP A  92 " =    1.476
peak=   -3.646 closest distance to " OD1 ASP A  50 " =    1.320
peak=   -3.643 closest distance to " CG  GLN A  88 " =    0.977
peak=   -3.639 closest distance to " O   HOH Z 256 " =    1.117
peak=   -3.628 closest distance to " CD1 TRP A 179 " =    0.978
peak=   -3.619 closest distance to " O   HOH Z 331 " =    1.409
peak=   -3.617 closest distance to " OG  SER A  97 " =    2.242
peak=   -3.614 closest distance to " O   ALA A 248 " =    1.446
peak=   -3.613 closest distance to " O   HOH Z 430 " =    1.739
peak=   -3.594 closest distance to " O   HOH Z 125 " =    3.241
peak=   -3.593 closest distance to " O   HOH Z  80 " =    1.375
peak=   -3.592 closest distance to " SG BCYS A 201 " =    1.041
peak=   -3.569 closest distance to " O   HOH Z 100 " =    1.016
peak=   -3.552 closest distance to " O   HOH Z 186 " =    1.220
peak=   -3.547 closest distance to " CB  PHE A  59 " =    1.389
peak=   -3.547 closest distance to " CG  LEU A  83 " =    2.187
peak=   -3.546 closest distance to " O   HOH Z  52 " =    1.446
peak=   -3.542 closest distance to " O   HOH Z 126 " =    1.873
peak=   -3.539 closest distance to " CD  ARG A  14 " =    2.863
peak=   -3.536 closest distance to " CG  ASN A  60 " =    1.188
peak=   -3.534 closest distance to " O   ALA A  51 " =    1.188
peak=   -3.528 closest distance to " CD  GLU A 152 " =    2.488
peak=   -3.516 closest distance to " O   ALA A 161 " =    1.764
peak=   -3.514 closest distance to " O   HOH Z 164 " =    4.759
peak=   -3.512 closest distance to " O   HOH Z  53 " =    1.231
peak=   -3.501 closest distance to " O   HOH Z 266 " =    4.450
peak=   -3.498 closest distance to " CB  CYS A 201 " =    1.813
peak=   -3.495 closest distance to " CE2 TYR A  30 " =    2.984
peak=   -3.486 closest distance to " SG  CYS A 168 " =    0.925
peak=   -3.481 closest distance to " O   HOH Z  52 " =    0.884
peak=   -3.480 closest distance to " CA  GLY A 133 " =    1.986
peak=   -3.465 closest distance to " CG2BVAL A 121 " =    0.729
peak=   -3.464 closest distance to " O   HOH Z 179 " =    1.277
peak=   -3.463 closest distance to " O   HOH Z  54 " =    0.792
peak=   -3.461 closest distance to " N   THR A 235 " =    1.071
peak=   -3.454 closest distance to " NH2 ARG A  79 " =    1.890
peak=   -3.450 closest distance to " OD2 ASP A 171 " =    1.430
peak=   -3.446 closest distance to " O   HOH Z 367 " =    4.483
peak=   -3.445 closest distance to " O   ASP A 191 " =    1.858
peak=   -3.438 closest distance to " O   GLU A 152 " =    1.738
peak=   -3.429 closest distance to " CD  PRO A 198 " =    1.224
peak=   -3.420 closest distance to " O   HOH Z  77 " =    1.988
peak=   -3.413 closest distance to " CG1 VAL A 112 " =    2.757
peak=   -3.407 closest distance to " O   SER A 245 " =    1.577
peak=   -3.407 closest distance to " CD1 PHE A  59 " =    1.031
peak=   -3.402 closest distance to " O   HOH Z  65 " =    0.706
peak=   -3.397 closest distance to " ND2 ASN A 127 " =    1.281
peak=   -3.393 closest distance to " CB  ALA A 244 " =    2.145
peak=   -3.379 closest distance to " O   LYS A 117 " =    1.439
peak=   -3.367 closest distance to " O   LYS A 289 " =    2.066
peak=   -3.362 closest distance to " N   GLN A  55 " =    1.120
peak=   -3.362 closest distance to " O   HOH Z 165 " =    2.297
peak=   -3.361 closest distance to " O   HOH Z 130 " =    1.720
peak=   -3.357 closest distance to " O   ILE A 106 " =    1.921
peak=   -3.352 closest distance to " CD2 PHE A  61 " =    1.040
peak=   -3.351 closest distance to " C   ASP A 124 " =    1.958
peak=   -3.351 closest distance to " O   HOH Z 234 " =    1.428
peak=   -3.349 closest distance to " O   HOH Z 279 " =    1.048
peak=   -3.340 closest distance to " O   HOH Z  55 " =    1.296
peak=   -3.339 closest distance to " O   HOH Z  39 " =    1.195
peak=   -3.337 closest distance to " O   HOH Z  86 " =    1.057
peak=   -3.321 closest distance to " OH  TYR A 169 " =    0.758
peak=   -3.319 closest distance to " CD2 LEU A   5 " =    1.001
peak=   -3.317 closest distance to " NE2 GLN A 194 " =    0.954
peak=   -3.309 closest distance to " CG  PRO A 198 " =    1.559
peak=   -3.309 closest distance to " CB  THR A  42 " =    1.425
peak=   -3.309 closest distance to " CD1 TYR A 247 " =    2.544
peak=   -3.305 closest distance to " O   HOH Z 316 " =    1.007
peak=   -3.301 closest distance to " O   HOH Z 287 " =    1.301
peak=   -3.301 closest distance to " CB  ALA A 233 " =    2.324
peak=   -3.301 closest distance to " N   SER A 276 " =    0.923
peak=   -3.295 closest distance to " O   HOH Z 391 " =    2.049
peak=   -3.291 closest distance to " N   ASN A 127 " =    1.198
peak=   -3.291 closest distance to " C   ASN A 176 " =    1.056
peak=   -3.288 closest distance to " O   HOH Z 429 " =    0.821
peak=   -3.287 closest distance to " O   HOH Z 383 " =    0.778
peak=   -3.286 closest distance to " O   HOH Z 195 " =    1.564
peak=   -3.284 closest distance to " OG BSER A  99 " =    1.256
peak=   -3.283 closest distance to " OD1 ASN A 249 " =    1.672
peak=   -3.282 closest distance to " O   HOH Z 298 " =    0.994
peak=   -3.280 closest distance to " O   HOH Z  63 " =    1.123
peak=   -3.274 closest distance to " CG  LEU A   5 " =    0.836
peak=   -3.268 closest distance to " CA  SER A 210 " =    1.148
peak=   -3.268 closest distance to " CG  ARG A 139 " =    1.068
peak=   -3.262 closest distance to " NE2 GLN A  58 " =    3.312
peak=   -3.259 closest distance to " CG  ASP A 286 " =    1.331
peak=   -3.257 closest distance to " O   HOH Z 377 " =    0.878
peak=   -3.257 closest distance to " CD1 LEU A  96 " =    2.093
peak=   -3.256 closest distance to " CB  TRP A 274 " =    2.922
peak=   -3.256 closest distance to " CG1BVAL A  72 " =    1.849
peak=   -3.250 closest distance to " OG  SER A   3 " =    1.091
peak=   -3.246 closest distance to " O   HOH Z 298 " =    2.403
peak=   -3.245 closest distance to " O   PHE A 218 " =    1.399
peak=   -3.245 closest distance to " O   HOH Z 390 " =    2.950
peak=   -3.244 closest distance to " ND2 ASN A 173 " =    1.592
peak=   -3.244 closest distance to " O   GLN A  77 " =    1.790
peak=   -3.239 closest distance to " O   HOH Z 275 " =    1.614
peak=   -3.236 closest distance to " O   HOH Z 274 " =    2.524
peak=   -3.236 closest distance to " CD2 PHE A  61 " =    1.011
peak=   -3.235 closest distance to " O   HOH Z 117 " =    0.993
peak=   -3.230 closest distance to " O   HOH Z  75 " =    1.811
peak=   -3.224 closest distance to " CG1 ILE A 106 " =    0.985
peak=   -3.216 closest distance to " O   HOH Z 307 " =    1.968
peak=   -3.212 closest distance to " CB  ALA A   7 " =    1.974
peak=   -3.209 closest distance to " O   SER A   3 " =    1.348
peak=   -3.207 closest distance to " O   HOH Z 431 " =    1.053
peak=   -3.206 closest distance to " O   HOH Z  93 " =    1.174
peak=   -3.201 closest distance to " CA  SER A   3 " =    2.562
peak=   -3.192 closest distance to " O   HOH Z 140 " =    1.191
peak=   -3.191 closest distance to " OG1 THR A  82 " =    1.579
peak=   -3.187 closest distance to " CG  ASN A  45 " =    1.108
peak=   -3.183 closest distance to " O   HOH Z  79 " =    1.051
peak=   -3.182 closest distance to " O   HOH Z 300 " =    1.089
peak=   -3.175 closest distance to " CG1 VAL A 232 " =    2.092
peak=   -3.174 closest distance to " NE2 GLN A  77 " =    1.982
peak=   -3.173 closest distance to " O   ALA A   8 " =    1.855
peak=   -3.172 closest distance to " O   ALA A   1 " =    0.867
peak=   -3.170 closest distance to " O   HOH Z 248 " =    1.109
peak=   -3.170 closest distance to " CD1 PHE A 225 " =    1.614
peak=   -3.170 closest distance to " O   HOH Z 313 " =    1.344
peak=   -3.170 closest distance to " OE1 GLN A 223 " =    2.055
peak=   -3.168 closest distance to " O   HOH Z 355 " =    1.518
peak=   -3.165 closest distance to " C   ALA A 158 " =    1.310
peak=   -3.164 closest distance to " CA  GLN A  58 " =    1.205
peak=   -3.164 closest distance to " O   HOH Z 194 " =    1.778
peak=   -3.159 closest distance to " CG2 ILE A 109 " =    1.950
peak=   -3.158 closest distance to " N   GLN A  11 " =    1.074
peak=   -3.155 closest distance to " CG  GLN A  58 " =    0.985
peak=   -3.153 closest distance to " O   HOH Z 208 " =    0.948
peak=   -3.148 closest distance to " O   HOH Z 349 " =    0.921
peak=   -3.148 closest distance to " CE1 TYR A 247 " =    2.317
peak=   -3.146 closest distance to " ND2 ASN A 285 " =    2.275
peak=   -3.141 closest distance to " SD  MET A 105 " =    1.919
peak=   -3.139 closest distance to " O   HOH Z 121 " =    3.857
peak=   -3.137 closest distance to " CE2 PHE A 208 " =    1.459
peak=   -3.134 closest distance to " O   HOH Z 264 " =    1.406
peak=   -3.133 closest distance to " CD2 LEU A 237 " =    2.701
peak=   -3.132 closest distance to " O   HOH Z 168 " =    0.784
peak=   -3.132 closest distance to " O   HOH Z  95 " =    1.246
peak=   -3.130 closest distance to " N   ASN A 301 " =    1.605
peak=   -3.124 closest distance to " O   GLY A 136 " =    1.635
peak=   -3.120 closest distance to " O   HOH Z  37 " =    1.337
peak=   -3.117 closest distance to " CD2 TRP A 150 " =    0.923
peak=   -3.110 closest distance to " O   MET A 188 " =    1.508
peak=   -3.109 closest distance to " OD2 ASP A 270 " =    0.815
peak=   -3.104 closest distance to " OD2 ASP A 270 " =    1.055
peak=   -3.102 closest distance to " CB  PHE A 208 " =    2.118
peak=   -3.098 closest distance to " O   HOH Z  16 " =    1.289
peak=   -3.093 closest distance to " O   HOH Z  56 " =    1.997
peak=   -3.086 closest distance to " OG  SER A 288 " =    1.159
peak=   -3.081 closest distance to " O   HOH Z  47 " =    2.016
peak=   -3.048 closest distance to " O   ALA A 161 " =    1.235
peak=   -3.040 closest distance to " OG  SER A 245 " =    1.460
peak=   -3.036 closest distance to " C   PRO A 213 " =    1.428

================= 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    :  0.5249 0.5242   6.311381e+00   6.307057e+00
   1_bss:  0.5162 0.5128   6.306027e+00   6.298236e+00
   1_xyz:  0.4747 0.4944   6.269620e+00   6.282629e+00
   1_adp:  0.4442 0.4883   6.245185e+00   6.279091e+00
   1_occ:  0.4437 0.4886   6.244509e+00   6.279344e+00
   2_bss:  0.4443 0.4860   6.246662e+00   6.278819e+00
   2_xyz:  0.3987 0.4550   6.172389e+00   6.244878e+00
   2_adp:  0.3781 0.4484   6.148116e+00   6.235125e+00
   2_occ:  0.3781 0.4484   6.147914e+00   6.235167e+00
   3_bss:  0.3772 0.4476   6.148117e+00   6.235009e+00
   3_xyz:  0.3113 0.3818   6.003282e+00   6.133905e+00
   3_adp:  0.2782 0.3629   5.934045e+00   6.103890e+00
   3_occ:  0.2781 0.3628   5.933849e+00   6.103659e+00
   4_bss:  0.2766 0.3603   5.928390e+00   6.098177e+00
   4_xyz:  0.2367 0.3136   5.798685e+00   5.993360e+00
   4_adp:  0.2248 0.2860   5.744741e+00   5.913797e+00
   4_occ:  0.2243 0.2855   5.743183e+00   5.911267e+00
   5_bss:  0.2235 0.2840   5.741860e+00   5.909803e+00
   5_xyz:  0.1695 0.2207   5.488809e+00   5.686391e+00
   5_adp:  0.1541 0.2057   5.406063e+00   5.626098e+00
   5_occ:  0.1535 0.2047   5.402447e+00   5.621373e+00
   5_bss:  0.1531 0.2034   5.400339e+00   5.619321e+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:  0.403   0.000   6.713   8.639   7.994   0.000   0.000   0.000
   1_xyz:  0.403   0.000   6.713   8.639   7.994   0.000   0.000   0.000
   1_adp:  0.403   0.000   6.713   8.639   7.994   0.000   0.000   0.000
   1_occ:  0.403   0.000   6.713   8.639   7.994   0.000   0.000   0.000
   2_bss:  0.376  20.000   4.758   6.128   6.472   0.000   0.000   0.000
   2_xyz:  0.376  20.000   4.758   6.128   6.472   0.000   0.000   0.000
   2_adp:  0.376  20.000   4.758   6.128   6.472   0.000   0.000   0.000
   2_occ:  0.376  20.000   4.758   6.128   6.472   0.000   0.000   0.000
   3_bss:  0.358  42.947   3.220   4.272   4.742   0.000   0.000   0.000
   3_xyz:  0.358  42.947   3.220   4.272   4.742   0.000   0.000   0.000
   3_adp:  0.358  42.947   3.220   4.272   4.742   0.000   0.000   0.000
   3_occ:  0.358  42.947   3.220   4.272   4.742   0.000   0.000   0.000
   4_bss:  0.358  42.947   2.094   2.675   3.299   0.000   0.000   0.000
   4_xyz:  0.358  42.947   2.094   2.675   3.299   0.000   0.000   0.000
   4_adp:  0.358  42.947   2.094   2.675   3.299   0.000   0.000   0.000
   4_occ:  0.358  42.947   2.094   2.675   3.299   0.000   0.000   0.000
   5_bss:  0.331  35.910   0.882   1.345   2.136   0.000   0.000   0.000
   5_xyz:  0.331  35.910   0.882   1.345   2.136   0.000   0.000   0.000
   5_adp:  0.331  35.910   0.882   1.345   2.136   0.000   0.000   0.000
   5_occ:  0.331  35.910   0.882   1.345   2.136   0.000   0.000   0.000
   5_bss:  0.314  29.518  -0.497  -0.195   0.692  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  68.860 0.2786  0.3399    88372.255
   1_bss:  68.123 0.2872  0.4305    85192.584
   1_xyz:  66.858 0.3022  0.4442    79564.794
   1_adp:  65.715 0.3171  0.4978    78252.911
   1_occ:  65.835 0.3155  0.4938    78328.612
   2_bss:  65.805 0.3157  0.4689    78027.702
   2_xyz:  55.824 0.4453  0.6708    63831.542
   2_adp:  52.273 0.4914  0.7631    60642.824
   2_occ:  52.259 0.4915  0.7628    60642.504
   3_bss:  52.144 0.4929  0.7213    60531.816
   3_xyz:  41.070 0.6297  0.9137    40380.542
   3_adp:  38.240 0.6638  0.9396    36226.501
   3_occ:  38.262 0.6635  0.9394    36214.285
   4_bss:  37.974 0.6665  0.8949    35416.958
   4_xyz:  32.125 0.7338  0.9676    25867.175
   4_adp:  28.229 0.7781  1.0040    21303.949
   4_occ:  28.140 0.7792  1.0054    21187.797
   5_bss:  28.092 0.7795  0.9592    21062.981
   5_xyz:  20.870 0.8539  1.0111    12240.873
   5_adp:  19.059 0.8716  1.0154    10762.399
   5_occ:  18.937 0.8728  1.0161    10648.090
   5_bss:  18.865 0.8733  0.9866    10529.431
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.082   5.2322e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.082   5.2322e+01
   1_xyz:   1.706  0.013  0.107 18.479  0.007  4.102   1.5533e-01
   1_adp:   1.706  0.013  0.107 18.479  0.007  4.102   1.5533e-01
   1_occ:   1.706  0.013  0.107 18.479  0.007  4.102   1.5533e-01
   2_bss:   1.706  0.013  0.107 18.479  0.007  4.102   1.5533e-01
   2_xyz:   1.190  0.008  0.076 16.795  0.005  4.099   9.5722e-02
   2_adp:   1.190  0.008  0.076 16.795  0.005  4.099   9.5722e-02
   2_occ:   1.190  0.008  0.076 16.795  0.005  4.099   9.5722e-02
   3_bss:   1.190  0.008  0.076 16.795  0.005  4.099   9.5722e-02
   3_xyz:   1.373  0.010  0.091 16.762  0.006  4.097   1.1475e-01
   3_adp:   1.373  0.010  0.091 16.762  0.006  4.097   1.1475e-01
   3_occ:   1.373  0.010  0.091 16.762  0.006  4.097   1.1475e-01
   4_bss:   1.373  0.010  0.091 16.762  0.006  4.097   1.1475e-01
   4_xyz:   0.990  0.007  0.068 15.468  0.004  4.108   6.4960e-02
   4_adp:   0.990  0.007  0.068 15.468  0.004  4.108   6.4960e-02
   4_occ:   0.990  0.007  0.068 15.468  0.004  4.108   6.4960e-02
   5_bss:   0.990  0.007  0.068 15.468  0.004  4.108   6.4960e-02
   5_xyz:   1.080  0.007  0.069 15.578  0.004  4.104   7.2885e-02
   5_adp:   1.080  0.007  0.069 15.578  0.004  4.104   7.2885e-02
   5_occ:   1.080  0.007  0.069 15.578  0.004  4.104   7.2885e-02
   5_bss:   1.080  0.007  0.069 15.578  0.004  4.104   7.2885e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.760   6.7647e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.760   6.7647e+00
   1_xyz:  14.225  0.168  0.450 88.507  0.048  2.010   9.4459e-02
   1_adp:  14.225  0.168  0.450 88.507  0.048  2.010   9.4459e-02
   1_occ:  14.225  0.168  0.450 88.507  0.048  2.010   9.4459e-02
   2_bss:  14.225  0.168  0.450 88.507  0.048  2.010   9.4459e-02
   2_xyz:   6.885  0.081  0.262 81.621  0.043  2.009   5.8568e-02
   2_adp:   6.885  0.081  0.262 81.621  0.043  2.009   5.8568e-02
   2_occ:   6.885  0.081  0.262 81.621  0.043  2.009   5.8568e-02
   3_bss:   6.885  0.081  0.262 81.621  0.043  2.009   5.8568e-02
   3_xyz:   8.474  0.086  0.301 78.188  0.058  2.066   1.6316e-01
   3_adp:   8.474  0.086  0.301 78.188  0.058  2.066   1.6316e-01
   3_occ:   8.474  0.086  0.301 78.188  0.058  2.066   1.6316e-01
   4_bss:   8.474  0.086  0.301 78.188  0.058  2.066   1.6316e-01
   4_xyz:   7.329  0.050  0.262 78.562  0.024  2.273   5.9192e-02
   4_adp:   7.329  0.050  0.262 78.562  0.024  2.273   5.9192e-02
   4_occ:   7.329  0.050  0.262 78.562  0.024  2.273   5.9192e-02
   5_bss:   7.329  0.050  0.262 78.562  0.024  2.273   5.9192e-02
   5_xyz:   7.746  0.048  0.236 85.605  0.025  2.294   1.3033e-01
   5_adp:   7.746  0.048  0.236 85.605  0.025  2.294   1.3033e-01
   5_occ:   7.746  0.048  0.236 85.605  0.025  2.294   1.3033e-01
   5_bss:   7.746  0.048  0.236 85.605  0.025  2.294   1.3033e-01
------------------------------------------------------------------------
           |-----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:  68.52   0.00  14.47  68.52   0.00  14.10  57.05   0.00  16.47
   1_occ:  68.52   0.00  14.47  68.52   0.00  14.10  57.05   0.00  16.47
   2_bss:  68.52   0.00  14.47  68.52   0.00  14.10  57.05   0.00  16.47
   2_xyz:  68.52   0.00  14.47  68.52   0.00  14.10  57.05   0.00  16.47
   2_adp:  78.09   0.00  15.90  78.09   0.00  14.45  73.20   0.00  23.79
   2_occ:  78.09   0.00  15.90  78.09   0.00  14.45  73.20   0.00  23.79
   3_bss:  78.09   0.00  15.90  78.09   0.00  14.45  73.20   0.00  23.79
   3_xyz:  78.09   0.00  15.90  78.09   0.00  14.45  73.20   0.00  23.79
   3_adp: 123.69   0.00  17.98 123.69   0.00  14.08 105.50   0.00  39.22
   3_occ: 123.69   0.00  17.98 123.69   0.00  14.08 105.50   0.00  39.22
   4_bss: 123.69   0.00  17.98 123.69   0.00  14.08 105.50   0.00  39.22
   4_xyz: 123.69   0.00  17.98 123.69   0.00  14.08 105.50   0.00  39.22
   4_adp: 109.23   0.00  14.86 109.23   0.00  10.99  80.02   1.21  35.92
   4_occ: 109.23   0.00  14.86 109.23   0.00  10.99  80.02   1.21  35.92
   5_bss: 109.23   0.00  14.86 109.23   0.00  10.99  80.02   1.21  35.92
   5_xyz: 109.23   0.00  14.86 109.23   0.00  10.99  80.02   1.21  35.92
   5_adp: 104.21   0.00  15.02 104.21   0.00  10.37  81.67   4.26  40.35
   5_occ: 104.21   0.00  15.02 104.21   0.00  10.37  81.67   4.26  40.35
   5_bss: 104.89   0.68  15.69 104.89   0.68  11.04  82.35   4.93  41.03
------------------------------------------------------------------------
 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:    1.243    0.024    0.411
   1_adp:    1.243    0.024    0.411
   1_occ:    1.243    0.024    0.411
   2_bss:    1.243    0.024    0.411
   2_xyz:    1.735    0.007    0.567
   2_adp:    1.735    0.007    0.567
   2_occ:    1.735    0.007    0.567
   3_bss:    1.735    0.007    0.567
   3_xyz:    1.846    0.059    0.747
   3_adp:    1.846    0.059    0.747
   3_occ:    1.846    0.059    0.747
   4_bss:    1.846    0.059    0.747
   4_xyz:    1.773    0.026    0.825
   4_adp:    1.773    0.026    0.825
   4_occ:    1.773    0.026    0.825
   5_bss:    1.773    0.026    0.825
   5_xyz:    1.941    0.023    0.934
   5_adp:    1.941    0.023    0.934
   5_occ:    1.941    0.023    0.934
   5_bss:    1.941    0.023    0.934
------------------------------------------------------------------------

CPU time actual refinement: 346.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_12/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_12/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_12/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_12/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_12/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.43 
  Macro-tasks:
    bulk solvent and scale       = 46.24  
    individual site refinement   = 143.31 
    weights calculation          = 32.16  
    collect and process          = 6.25   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 228.10 
  Micro-tasks:
    mask                            = 2.93   
    f_calc                          = 106.98 
    alpha_beta                      = 8.21   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 116.65 
    fmodel                         = 7.88   
    r_factors                      = 0.25   
    phase_errors                   = 9.43   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 253.73 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.932 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    636 calls, 106.57 s
gradients_fft:          581 calls, 103.98 s

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

# Date 2008-01-16 Time 00:33:26 PST -0800 (1200472406.43 s)
Start R-work = 0.5249, R-free = 0.5242 (no bulk solvent and anisotropic scale)
Final R-work = 0.1689, R-free = 0.2176 (no bulk solvent and anisotropic scale)

Start R-work = 0.5162, R-free = 0.5128
Final R-work = 0.1531, R-free = 0.2034