# Date 2008-01-16 Time 00:39:46 PST -0800 (1200472786.11 s)
#phil __OFF__

Command line arguments: "../114.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32327
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 114

-------------------------------------------------------------------------------
  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, 48.1033, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.95081
Completeness in resolution range: 0.921618
Completeness with d_max=infinity: 0.918895

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0230
                             d_min =   1.9508

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, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.95081
Completeness in resolution range: 0.921618
Completeness with d_max=infinity: 0.918895

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0234 -  4.1756 [2232/2261]  2004   228  10.2%
  bin  2:  4.1756 -  3.3262 [2147/2170]  1936   211   9.8%
  bin  3:  3.3262 -  2.9092 [2113/2138]  1906   207   9.8%
  bin  4:  2.9092 -  2.6448 [2078/2111]  1865   213  10.3%
  bin  5:  2.6448 -  2.4561 [2072/2099]  1864   208  10.0%
  bin  6:  2.4561 -  2.3118 [2084/2112]  1877   207   9.9%
  bin  7:  2.3118 -  2.1964 [2052/2088]  1854   198   9.6%
  bin  8:  2.1964 -  2.1011 [2047/2089]  1840   207  10.1%
  bin  9:  2.1011 -  2.0204 [1985/2110]  1790   195   9.8%
  bin 10:  2.0204 -  1.9508 [ 779/2077]   694    85  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_114/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.82 -     1.64: 9
        1.64 -     2.45: 50
        2.45 -     3.27: 3589
        3.27 -     4.08: 9459
        4.08 -     4.90: 15394
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  0.822 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.153 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.290 3.040 -x+1,y+1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.464 3.270 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.496 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28496 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_114/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_114/model_refine_001.geo

CPU time processing inputs: 9.34


============================ 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 48.10325 85.95805 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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5195   r_free= 0.5035   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.314182                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.6579 0.99   1452  160 0.4428 0.4397      6.6807      6.7215|
|  2:  4.6579 -  3.7156 0.99   1394  155 0.4596 0.4618      6.8779      6.8701|
|  3:  3.7156 -  3.2513 0.99   1362  151 0.5049 0.4674      6.7304      6.7503|
|  4:  3.2513 -  2.9565 0.98   1356  148 0.5183 0.4696      6.5456      6.5069|
|  5:  2.9565 -  2.7460 0.99   1347  150 0.5597 0.5455      6.3929      6.4111|
|  6:  2.7460 -  2.5849 0.99   1347  154 0.5424 0.5050      6.2902      6.1664|
|  7:  2.5849 -  2.4561 0.98   1317  149 0.5405 0.5314      6.2507      6.2156|
|  8:  2.4561 -  2.3496 0.98   1342  143 0.5464 0.5052      6.1826      6.1916|
|  9:  2.3496 -  2.2594 0.98   1325  144 0.5573 0.5597      6.1207      6.1737|
| 10:  2.2594 -  2.1817 0.99   1337  147 0.5505 0.5775       6.097      6.1119|
| 11:  2.1817 -  2.1137 0.98   1320  148 0.5632 0.5253      6.0302      6.0357|
| 12:  2.1137 -  2.0534 0.97   1300  152 0.5310 0.5400      5.9557      5.9803|
| 13:  2.0534 -  1.9995 0.81   1081  116 0.5558 0.5376      5.8696        5.84|
| 14:  1.9995 -  1.9508 0.26    350   42 0.5861 0.4789      5.9031      5.6988|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0234 -  4.6579  1452   160  0.58  44.13   0.78     0.61     106368.45|
|  2:  4.6579 -  3.7156  1394   155  0.60  43.77   0.84     0.66     145777.91|
|  3:  3.7156 -  3.2513  1362   151  0.49  53.04   0.80     0.62     148261.45|
|  4:  3.2513 -  2.9565  1356   148  0.42  58.33   0.76     0.53     118287.58|
|  5:  2.9565 -  2.7460  1347   150  0.32  66.21   0.70     0.40      95890.34|
|  6:  2.7460 -  2.5849  1347   154  0.27  69.38   0.69     0.32      80757.34|
|  7:  2.5849 -  2.4561  1317   149  0.22  73.57   0.72     0.26      76719.04|
|  8:  2.4561 -  2.3496  1342   143  0.23  73.01   0.70     0.27      66807.46|
|  9:  2.3496 -  2.2594  1325   144  0.24  72.31   0.71     0.30      62782.36|
| 10:  2.2594 -  2.1817  1337   147  0.23  72.87   0.73     0.28      55169.02|
| 11:  2.1817 -  2.1137  1320   148  0.20  75.18   0.74     0.27      54281.98|
| 12:  2.1137 -  2.0534  1300   152  0.18  76.81   0.74     0.24      50905.69|
| 13:  2.0534 -  1.9995  1081   116  0.19  75.96   0.71     0.26      43003.85|
| 14:  1.9995 -  1.9508   350    42  0.25  71.11   0.72     0.28      30238.74|
|alpha:            min =        0.24 max =            0.66 mean =         0.39|
|beta:             min =    30238.74 max =       148261.45 mean =     85109.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.41|
|phase err.(test): min =        0.00 max =           89.98 mean =        65.32|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.243063             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.491   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.057862              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.168   (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 |  0.612 -  1.041:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.041 -  1.470:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.470 -  1.899:       25 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.899 -  2.327:      223 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.327 -  2.756:      927 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.756 -  3.185:     2152 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.185 -  3.614:     3724 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.614 -  4.042:     5434 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.042 -  4.471:     7222 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.471 -  4.900:     8806 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.538 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.612 |       3.420 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    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 = 11.672)------------------------------------------|
|    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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5237   r_free= 0.5079   ksol= 0.00   Bsol= 0.00   scale= 0.737    |
|                                                                             |
| 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:   0.97 A                  |
| x-ray target function (ml) for work reflections: 6.314438                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5133   r_free= 0.4999   ksol= 0.32   Bsol= 3.02   scale= 0.953    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,11.54,6.92,0.00,0.00,0.00); trace/3= 8.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.96 A                  |
| x-ray target function (ml) for work reflections: 6.309586                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.159860             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.902   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.232771              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.206   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5133      final r-factor (work) = 0.4677          |
| start r-factor (free) = 0.4999      final r-factor (free) = 0.4769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 110.8464 = 18.16 * 0.50 * 6.3116 + 1.00 * 53.5379                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.1369 = 18.16 * 0.50 * 6.2769 + 1.00 * 0.1430                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4677      final r-factor (work) = 0.4260          |
| start r-factor (free) = 0.4769      final r-factor (free) = 0.4805          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0297 = 2.23 * 1.00 * 6.2769 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6976 = 2.23 * 1.00 * 6.1238 + 1.00 * 0.0246                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.58  18.79    None  None   None       |
|    all(noH): 2823   0      0.00    104.58  18.79    None  None   None       |
|    Sol.    : 438    0      0.00    104.58  28.09    None  None   None       |
|    Mac.    : 2385   0      0.00    83.06   17.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.458:  994   |   5:    52.289 -  62.747:   65        |
|      1:    10.458 -  20.916:  803   |   6:    62.747 -  73.205:   24        |
|      2:    20.916 -  31.373:  520   |   7:    73.205 -  83.662:   14        |
|      3:    31.373 -  41.831:  272   |   8:    83.662 -  94.120:    5        |
|      4:    41.831 -  52.289:  124   |   9:    94.120 - 104.578:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4260 r_free = 0.4805             target_work(ml) = 6.232         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4253 r_free = 0.4794             target_work(ml) = 6.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4253   r_free= 0.4794   ksol= 0.32   Bsol= 3.02   scale= 1.128    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,11.54,6.92,0.00,0.00,0.00); trace/3= 8.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.231424                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4234   r_free= 0.4731   ksol= 0.28   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,6.16,3.38,0.00,0.00,0.00); trace/3= 4.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.231717                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.615426             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.732445              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.212  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4234      final r-factor (work) = 0.3662          |
| start r-factor (free) = 0.4731      final r-factor (free) = 0.4282          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.9890 = 16.62 * 0.50 * 6.1204 + 1.00 * 0.1424                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4234 = 16.62 * 0.50 * 6.1753 + 1.00 * 0.1212                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3662      final r-factor (work) = 0.3543          |
| start r-factor (free) = 0.4282      final r-factor (free) = 0.4207          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5487 = 0.73 * 1.00 * 6.1753 + 1.00 * 0.0257                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5221 = 0.73 * 1.00 * 6.1244 + 1.00 * 0.0363                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    284.25  18.53    None  None   None       |
|    all(noH): 2823   0      0.00    284.25  18.53    None  None   None       |
|    Sol.    : 438    0      0.00    98.40   29.35    None  None   None       |
|    Mac.    : 2385   0      0.00    284.25  16.54    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 -  28.425: 2250   |   5:   142.126 - 170.551:    0        |
|      1:    28.425 -  56.850:  518   |   6:   170.551 - 198.976:    0        |
|      2:    56.850 -  85.276:   50   |   7:   198.976 - 227.402:    0        |
|      3:    85.276 - 113.701:    4   |   8:   227.402 - 255.827:    0        |
|      4:   113.701 - 142.126:    0   |   9:   255.827 - 284.252:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3543 r_free = 0.4207             target_work(ml) = 6.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3540 r_free = 0.4203             target_work(ml) = 6.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3540   r_free= 0.4203   ksol= 0.28   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,6.16,3.38,0.00,0.00,0.00); trace/3= 4.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.115676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3525   r_free= 0.4185   ksol= 0.31   Bsol= 50.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,3.55,1.74,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.116062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.631805             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.951  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.065237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.556  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3525      final r-factor (work) = 0.2868          |
| start r-factor (free) = 0.4185      final r-factor (free) = 0.3529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.9260 = 14.63 * 0.50 * 6.1243 + 1.00 * 0.1212                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.3601 = 14.63 * 0.50 * 6.0467 + 1.00 * 0.1232                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2868      final r-factor (work) = 0.2560          |
| start r-factor (free) = 0.3529      final r-factor (free) = 0.3280          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4988 = 1.07 * 1.00 * 6.0467 + 1.00 * 0.0576                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3028 = 1.07 * 1.00 * 5.9009 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    184.25  18.10    None  None   None       |
|    all(noH): 2823   0      0.00    184.25  18.10    None  None   None       |
|    Sol.    : 438    0      2.30    107.09  37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    184.25  14.57    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 -  18.425: 1862   |   5:    92.126 - 110.551:    2        |
|      1:    18.425 -  36.850:  628   |   6:   110.551 - 128.976:    0        |
|      2:    36.850 -  55.276:  219   |   7:   128.976 - 147.402:    0        |
|      3:    55.276 -  73.701:   86   |   8:   147.402 - 165.827:    0        |
|      4:    73.701 -  92.126:   24   |   9:   165.827 - 184.252:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2560 r_free = 0.3280             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2557 r_free = 0.3280             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2557   r_free= 0.3280   ksol= 0.31   Bsol= 50.00   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,3.55,1.74,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.873264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2549   r_free= 0.3278   ksol= 0.31   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,1.91,0.88,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.872786                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.021984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.444  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.309205              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.079  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2549      final r-factor (work) = 0.2007          |
| start r-factor (free) = 0.3278      final r-factor (free) = 0.2588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7964 = 8.02 * 0.50 * 5.9021 + 1.00 * 0.1232                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3098 = 8.02 * 0.50 * 5.7889 + 1.00 * 0.0906                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2007      final r-factor (work) = 0.1837          |
| start r-factor (free) = 0.2588      final r-factor (free) = 0.2326          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8070 = 0.31 * 1.00 * 5.7889 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7476 = 0.31 * 1.00 * 5.6201 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.39  16.81    None  None   None       |
|    all(noH): 2823   0      0.00    101.39  16.81    None  None   None       |
|    Sol.    : 438    0      4.38    89.61   38.87    None  None   None       |
|    Mac.    : 2385   0      0.00    101.39  12.76    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 -  10.139: 1245   |   5:    50.696 -  60.835:   63        |
|      1:    10.139 -  20.279:  897   |   6:    60.835 -  70.975:   42        |
|      2:    20.279 -  30.418:  256   |   7:    70.975 -  81.114:   14        |
|      3:    30.418 -  40.557:  164   |   8:    81.114 -  91.253:    7        |
|      4:    40.557 -  50.696:  133   |   9:    91.253 - 101.392:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1837 r_free = 0.2326             target_work(ml) = 5.566         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1834 r_free = 0.2323             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1834   r_free= 0.2323   ksol= 0.31   Bsol= 50.00   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,1.91,0.88,0.00,0.00,0.00); trace/3= 0.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.565276                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1830   r_free= 0.2314   ksol= 0.32   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,0.47,-0.08,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.566394                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.215991              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.951  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.121107              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.390  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1830      final r-factor (work) = 0.1510          |
| start r-factor (free) = 0.2314      final r-factor (free) = 0.1968          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1382 = 3.22 * 0.50 * 5.6266 + 1.00 * 0.0906                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8909 = 3.22 * 0.50 * 5.4845 + 1.00 * 0.0718                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1510      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.1968      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6741 = 0.12 * 1.00 * 5.4845 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6592 = 0.12 * 1.00 * 5.3846 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.95    97.20   15.95    None  None   None       |
|    all(noH): 2823   0      1.95    97.20   15.95    None  None   None       |
|    Sol.    : 438    0      5.44    89.24   37.27    None  None   None       |
|    Mac.    : 2385   0      1.95    97.20   12.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.947 -  11.472: 1476   |   5:    49.574 -  59.100:   72        |
|      1:    11.472 -  20.998:  785   |   6:    59.100 -  68.625:   22        |
|      2:    20.998 -  30.523:  183   |   7:    68.625 -  78.151:    8        |
|      3:    30.523 -  40.049:  142   |   8:    78.151 -  87.676:    5        |
|      4:    40.049 -  49.574:  128   |   9:    87.676 -  97.202:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1465 r_free = 0.1896             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1464 r_free = 0.1894             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1894   ksol= 0.32   Bsol= 50.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,0.47,-0.08,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.360746                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.6579 0.99   1452  160 0.1090 0.1494      5.4708       5.669|
|  2:  4.6579 -  3.7156 0.99   1394  155 0.1033 0.1313      5.6026      5.7903|
|  3:  3.7156 -  3.2513 0.99   1362  151 0.1406 0.1883      5.6975      6.0184|
|  4:  3.2513 -  2.9565 0.98   1356  148 0.1656 0.1929      5.6736      5.8067|
|  5:  2.9565 -  2.7460 0.99   1347  150 0.1815 0.2001      5.5683       5.701|
|  6:  2.7460 -  2.5849 0.99   1347  154 0.1676 0.2451      5.4333       5.603|
|  7:  2.5849 -  2.4561 0.98   1317  149 0.1647 0.1920       5.376      5.4982|
|  8:  2.4561 -  2.3496 0.98   1342  143 0.1654 0.2086      5.3117      5.4924|
|  9:  2.3496 -  2.2594 0.98   1325  144 0.1622 0.2299      5.2454      5.5183|
| 10:  2.2594 -  2.1817 0.99   1337  147 0.1549 0.1894      5.2067      5.2905|
| 11:  2.1817 -  2.1137 0.98   1320  148 0.1479 0.2269      5.1134       5.426|
| 12:  2.1137 -  2.0534 0.97   1300  152 0.1494 0.1993       5.046      5.2855|
| 13:  2.0534 -  1.9995 0.81   1081  116 0.1474 0.2118      4.9552      5.1821|
| 14:  1.9995 -  1.9508 0.26    350   42 0.1258 0.1818      4.8505      4.9787|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0234 -  4.6579  1452   160  0.93  10.52   0.97     0.96       8785.42|
|  2:  4.6579 -  3.7156  1394   155  0.94  10.23   1.03     1.02      12509.22|
|  3:  3.7156 -  3.2513  1362   151  0.91  15.16   1.02     1.01      15647.87|
|  4:  3.2513 -  2.9565  1356   148  0.88  18.09   1.02     1.01      15435.00|
|  5:  2.9565 -  2.7460  1347   150  0.86  20.27   1.01     0.97      12631.72|
|  6:  2.7460 -  2.5849  1347   154  0.86  20.75   0.97     0.93      10357.39|
|  7:  2.5849 -  2.4561  1317   149  0.87  19.25   1.00     0.95       8650.86|
|  8:  2.4561 -  2.3496  1342   143  0.87  20.06   1.02     0.99       8214.66|
|  9:  2.3496 -  2.2594  1325   144  0.86  20.21   1.02     0.96       7205.32|
| 10:  2.2594 -  2.1817  1337   147  0.86  20.75   1.02     1.00       7278.21|
| 11:  2.1817 -  2.1137  1320   148  0.87  19.91   1.03     0.98       6075.26|
| 12:  2.1137 -  2.0534  1300   152  0.87  19.46   1.02     1.00       5315.32|
| 13:  2.0534 -  1.9995  1081   116  0.87  19.74   1.03     1.02       4487.08|
| 14:  1.9995 -  1.9508   350    42  0.88  17.70   1.00     0.94       3490.14|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     3490.14 max =        15647.87 mean =      9421.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.92|
|phase err.(test): min =        0.00 max =           89.62 mean =        17.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.1901   ksol= 0.33   Bsol= 49.93   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-0.09,-0.26,-0.00,-0.00,-0.00); trace/3= -0.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.362562                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.1901   ksol= 0.33   Bsol= 49.93   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-0.09,-0.26,-0.00,-0.00,-0.00); trace/3= -0.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.362562                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.6579 0.99   1452  160 0.1104 0.1493      5.4772      5.6745|
|  2:  4.6579 -  3.7156 0.99   1394  155 0.1044 0.1321      5.6127      5.8056|
|  3:  3.7156 -  3.2513 0.99   1362  151 0.1415 0.1893      5.7039      6.0224|
|  4:  3.2513 -  2.9565 0.98   1356  148 0.1663 0.1927      5.6762      5.8059|
|  5:  2.9565 -  2.7460 0.99   1347  150 0.1816 0.2010      5.5701      5.7039|
|  6:  2.7460 -  2.5849 0.99   1347  154 0.1676 0.2453       5.433      5.6053|
|  7:  2.5849 -  2.4561 0.98   1317  149 0.1644 0.1922      5.3755      5.4973|
|  8:  2.4561 -  2.3496 0.98   1342  143 0.1651 0.2096      5.3107      5.4954|
|  9:  2.3496 -  2.2594 0.98   1325  144 0.1622 0.2296      5.2444      5.5147|
| 10:  2.2594 -  2.1817 0.99   1337  147 0.1543 0.1905      5.2063      5.2937|
| 11:  2.1817 -  2.1137 0.98   1320  148 0.1476 0.2266      5.1125      5.4238|
| 12:  2.1137 -  2.0534 0.97   1300  152 0.1495 0.1997      5.0466      5.2871|
| 13:  2.0534 -  1.9995 0.81   1081  116 0.1474 0.2115      4.9548      5.1828|
| 14:  1.9995 -  1.9508 0.26    350   42 0.1258 0.1815      4.8477      4.9772|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0234 -  4.6579  1452   160  0.93  10.56   0.97     0.96       8785.82|
|  2:  4.6579 -  3.7156  1394   155  0.94  10.37   1.02     1.01      12715.47|
|  3:  3.7156 -  3.2513  1362   151  0.90  15.35   1.01     1.00      16009.05|
|  4:  3.2513 -  2.9565  1356   148  0.88  18.13   1.01     1.00      15485.70|
|  5:  2.9565 -  2.7460  1347   150  0.86  20.34   0.99     0.96      12700.62|
|  6:  2.7460 -  2.5849  1347   154  0.86  20.78   0.96     0.92      10406.57|
|  7:  2.5849 -  2.4561  1317   149  0.87  19.26   0.98     0.93       8664.77|
|  8:  2.4561 -  2.3496  1342   143  0.87  20.05   1.00     0.97       8210.84|
|  9:  2.3496 -  2.2594  1325   144  0.86  20.20   1.00     0.94       7209.30|
| 10:  2.2594 -  2.1817  1337   147  0.86  20.74   1.00     0.98       7284.43|
| 11:  2.1817 -  2.1137  1320   148  0.87  19.90   1.00     0.96       6075.44|
| 12:  2.1137 -  2.0534  1300   152  0.87  19.46   1.00     0.97       5320.62|
| 13:  2.0534 -  1.9995  1081   116  0.87  19.71   1.00     0.99       4479.65|
| 14:  1.9995 -  1.9508   350    42  0.88  17.65   0.97     0.92       3467.11|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     3467.11 max =        16009.05 mean =      9479.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.95|
|phase err.(test): min =        0.00 max =           89.90 mean =        17.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.88    97.13   15.88    None  None   None       |
|    all(noH): 2823   0      1.88    97.13   15.88    None  None   None       |
|    Sol.    : 438    0      5.37    89.17   37.20    None  None   None       |
|    Mac.    : 2385   0      1.88    97.13   11.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.877 -  11.402: 1476   |   5:    49.504 -  59.030:   72        |
|      1:    11.402 -  20.928:  785   |   6:    59.030 -  68.555:   22        |
|      2:    20.928 -  30.453:  183   |   7:    68.555 -  78.081:    8        |
|      3:    30.453 -  39.979:  142   |   8:    78.081 -  87.606:    5        |
|      4:    39.979 -  49.504:  128   |   9:    87.606 -  97.132:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.586 - 5.097
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 323
   mapped sites are within: 0.721 - 5.097

peak=    8.208 closest distance to " CB  VAL A 230 " =    1.447
peak=    6.950 closest distance to " O   HOH Z 135 " =    1.516
peak=    6.576 closest distance to " O   ASN A 285 " =    1.012
peak=    6.367 closest distance to " CG1 ILE A 234 " =    1.440
peak=    6.105 closest distance to " O   HOH Z  46 " =    1.722
peak=    5.974 closest distance to " O   HOH Z 415 " =    1.523
peak=    5.393 closest distance to " O   GLN A  11 " =    1.004
peak=    5.373 closest distance to " O   HOH Z  57 " =    0.992
peak=    5.348 closest distance to " O   HOH Z 126 " =    1.702
peak=    5.245 closest distance to " CG  LEU A   5 " =    1.439
peak=    5.210 closest distance to " NZ  LYS A  76 " =    1.029
peak=    5.200 closest distance to " O   HOH Z 249 " =    1.504
peak=    5.095 closest distance to " O   HOH Z 159 " =    1.148
peak=    5.084 closest distance to " O   HOH Z 210 " =    1.534
peak=    5.037 closest distance to " O   HOH Z 403 " =    1.951
peak=    5.026 closest distance to " CB  ARG A 275 " =    0.986
peak=    5.009 closest distance to " O   HOH Z 404 " =    1.509
peak=    4.976 closest distance to " O   HOH Z  54 " =    1.471
peak=    4.935 closest distance to " O   HOH Z 426 " =    1.223
peak=    4.923 closest distance to " NH2 ARG A 156 " =    1.244
peak=    4.874 closest distance to " O   HOH Z 130 " =    1.335
peak=    4.835 closest distance to " O   HOH Z 128 " =    1.925
peak=    4.820 closest distance to " O   HOH Z 389 " =    1.953
peak=    4.813 closest distance to " O   HOH Z 146 " =    1.814
peak=    4.790 closest distance to " CG  GLN A  77 " =    0.977
peak=    4.778 closest distance to " O   HOH Z  92 " =    1.606
peak=    4.776 closest distance to " O   HOH Z 144 " =    1.745
peak=    4.718 closest distance to " CB  ASN A 285 " =    1.084
peak=    4.713 closest distance to " O   HOH Z 255 " =    1.280
peak=    4.698 closest distance to " CG1 VAL A 296 " =    1.164
peak=    4.674 closest distance to " OD1 ASN A 301 " =    1.029
peak=    4.670 closest distance to " CG AARG A 275 " =    1.224
peak=    4.670 closest distance to " O   HOH Z 433 " =    1.817
peak=    4.663 closest distance to " O   HOH Z 395 " =    1.620
peak=    4.648 closest distance to " CD2 TRP A 179 " =    1.310
peak=    4.635 closest distance to " O   HOH Z 178 " =    0.979
peak=    4.629 closest distance to " CD  ARG A  36 " =    1.433
peak=    4.617 closest distance to " O   HOH Z 193 " =    1.643
peak=    4.613 closest distance to " CB  GLN A  73 " =    1.157
peak=    4.580 closest distance to " CG2 VAL A 296 " =    1.170
peak=    4.564 closest distance to " CB  VAL A 230 " =    1.229
peak=    4.554 closest distance to " O   HOH Z 124 " =    1.734
peak=    4.546 closest distance to " CB  VAL A 296 " =    1.311
peak=    4.490 closest distance to " O   HOH Z 272 " =    1.395
peak=    4.483 closest distance to " CB  SER A 141 " =    0.930
peak=    4.470 closest distance to " OE1 GLN A  11 " =    1.966
peak=    4.448 closest distance to " O   HOH Z  80 " =    2.399
peak=    4.436 closest distance to " CG  ARG A  66 " =    1.110
peak=    4.424 closest distance to " O   HOH Z 248 " =    1.739
peak=    4.410 closest distance to " O   HOH Z 146 " =    1.888
peak=    4.400 closest distance to " NH1 ARG A  36 " =    1.176
peak=    4.399 closest distance to " NH2 ARG A  36 " =    1.255
peak=    4.379 closest distance to " N   ASP A 286 " =    0.951
peak=    4.359 closest distance to " O   HOH Z 422 " =    1.107
peak=    4.354 closest distance to " O   HOH Z  78 " =    1.516
peak=    4.345 closest distance to " O   HOH Z  48 " =    1.708
peak=    4.341 closest distance to " O   HOH Z 247 " =    1.501
peak=    4.317 closest distance to " O   HOH Z 154 " =    1.884
peak=    4.308 closest distance to " O   HOH Z 411 " =    3.454
peak=    4.283 closest distance to " O   HOH Z 236 " =    1.734
peak=    4.279 closest distance to " O   HOH Z  44 " =    1.565
peak=    4.273 closest distance to " CB  SER A  63 " =    1.171
peak=    4.241 closest distance to " OE1 GLU A   2 " =    1.714
peak=    4.200 closest distance to " O   HOH Z 342 " =    0.952
peak=    4.197 closest distance to " O   LEU A  25 " =    1.137
peak=    4.188 closest distance to " O   HOH Z 425 " =    1.763
peak=    4.187 closest distance to " NH1AARG A 275 " =    1.190
peak=    4.168 closest distance to " CE  LYS A 119 " =    1.257
peak=    4.140 closest distance to " CD  ARG A  36 " =    1.412
peak=    4.136 closest distance to " O   HOH Z 435 " =    2.003
peak=    4.128 closest distance to " CZ3 TRP A 266 " =    0.996
peak=    4.101 closest distance to " O   HOH Z 424 " =    1.302
peak=    4.091 closest distance to " CG  PRO A 243 " =    1.382
peak=    4.090 closest distance to " O   HOH Z  49 " =    1.582
peak=    4.087 closest distance to " CG  ARG A  36 " =    1.232
peak=    4.084 closest distance to " OG  SER A  62 " =    2.779
peak=    4.071 closest distance to " OD1 ASN A  60 " =    1.030
peak=    4.057 closest distance to " CD2 LEU A 228 " =    1.204
peak=    4.048 closest distance to " O   HOH Z  40 " =    1.929
peak=    4.018 closest distance to " CA  ILE A 120 " =    1.224
peak=    4.006 closest distance to " O   HOH Z 414 " =    2.776
peak=    4.002 closest distance to " O   HOH Z 357 " =    1.811
peak=    3.989 closest distance to " CB  GLU A 175 " =    1.092
peak=    3.973 closest distance to " O   HOH Z 113 " =    2.442
peak=    3.951 closest distance to " CA  VAL A  41 " =    0.950
peak=    3.947 closest distance to " O   HOH Z 156 " =    3.089
peak=    3.937 closest distance to " CD  LYS A 166 " =    1.630
peak=    3.927 closest distance to " O   HOH Z 394 " =    1.837
peak=    3.924 closest distance to " O   PRO A 198 " =    1.500
peak=    3.923 closest distance to " O   HOH Z 417 " =    1.556
peak=    3.897 closest distance to " O   HOH Z 158 " =    1.519
peak=    3.894 closest distance to " CG2 THR A 220 " =    0.816
peak=    3.881 closest distance to " CA  TRP A  85 " =    1.235
peak=    3.880 closest distance to " CA  ALA A 100 " =    1.299
peak=    3.879 closest distance to " O   HOH Z 369 " =    1.419
peak=    3.858 closest distance to " CB  GLN A  88 " =    1.324
peak=    3.857 closest distance to " O   HOH Z 142 " =    1.642
peak=    3.844 closest distance to " CB  ASN A 187 " =    1.119
peak=    3.842 closest distance to " O   VAL A  72 " =    1.106
peak=    3.826 closest distance to " N   THR A  42 " =    1.506
peak=    3.825 closest distance to " O   HOH Z  92 " =    1.472
peak=    3.824 closest distance to " O   HOH Z 134 " =    2.279
peak=    3.819 closest distance to " CG2 VAL A 197 " =    1.222
peak=    3.807 closest distance to " CD  PRO A  54 " =    0.886
peak=    3.806 closest distance to " CD2 LEU A   5 " =    1.296
peak=    3.799 closest distance to " O   HOH Z 132 " =    2.204
peak=    3.799 closest distance to " O   HOH Z 261 " =    2.448
peak=    3.794 closest distance to " O   VAL A  72 " =    1.217
peak=    3.791 closest distance to " O   HOH Z 278 " =    1.347
peak=    3.789 closest distance to " CG  MET A 185 " =    1.181
peak=    3.785 closest distance to " O   HOH Z 327 " =    1.664
peak=    3.780 closest distance to " CB  GLU A   2 " =    1.159
peak=    3.775 closest distance to " O   HOH Z 214 " =    1.435
peak=    3.767 closest distance to " CB  ALA A 226 " =    1.103
peak=    3.763 closest distance to " O   HOH Z 405 " =    1.491
peak=    3.758 closest distance to " O   ALA A 165 " =    1.338
peak=    3.750 closest distance to " O   HOH Z 315 " =    1.737
peak=    3.749 closest distance to " O   HOH Z 234 " =    3.385
peak=    3.746 closest distance to " CB  GLN A  58 " =    1.192
peak=    3.744 closest distance to " CG1 ILE A  33 " =    1.310
peak=    3.743 closest distance to " CB  GLN A 223 " =    1.433
peak=    3.738 closest distance to " N   TYR A  15 " =    0.741
peak=    3.737 closest distance to " O   HOH Z 267 " =    1.279
peak=    3.726 closest distance to " O   HOH Z 423 " =    1.939
peak=    3.725 closest distance to " O   HOH Z 279 " =    1.261
peak=    3.718 closest distance to " CG  PRO A 198 " =    1.284
peak=    3.715 closest distance to " O   HOH Z 361 " =    2.407
peak=    3.708 closest distance to " ND1 HIS A  81 " =    1.187
peak=    3.697 closest distance to " O   HOH Z 303 " =    2.301
peak=    3.688 closest distance to " O   HOH Z 238 " =    1.938
peak=    3.670 closest distance to " ND2 ASN A  45 " =    1.373
peak=    3.666 closest distance to " CB  GLU A 277 " =    0.882
peak=    3.662 closest distance to " CG2 THR A 251 " =    1.472
peak=    3.657 closest distance to " CB  ASP A 191 " =    1.065
peak=    3.655 closest distance to " O   HOH Z 130 " =    2.390
peak=    3.654 closest distance to " O   HOH Z 418 " =    1.535
peak=    3.654 closest distance to " NE BARG A 190 " =    1.288
peak=    3.631 closest distance to " O   HOH Z 257 " =    2.281
peak=    3.627 closest distance to " CB  THR A 235 " =    1.243
peak=    3.622 closest distance to " O   HOH Z  97 " =    1.349
peak=    3.618 closest distance to " O   HOH Z  63 " =    2.040
peak=    3.616 closest distance to " O   HOH Z 366 " =    2.290
peak=    3.612 closest distance to " CB  SER A  26 " =    1.637
peak=    3.604 closest distance to " O   HOH Z 381 " =    1.508
peak=    3.585 closest distance to " O   HOH Z  44 " =    2.242
peak=    3.582 closest distance to " O   HOH Z  39 " =    2.000
peak=    3.580 closest distance to " CA  SER A  12 " =    1.319
peak=    3.580 closest distance to " O   HOH Z 368 " =    2.953
peak=    3.574 closest distance to " CD  GLN A  73 " =    1.303
peak=    3.570 closest distance to " O   HOH Z  57 " =    2.447
peak=    3.567 closest distance to " O   HOH Z 403 " =    1.469
peak=    3.565 closest distance to " CD  ARG A  24 " =    1.375
peak=    3.564 closest distance to " CB  THR A  31 " =    1.481
peak=    3.542 closest distance to " CA  ALA A 248 " =    1.216
peak=    3.528 closest distance to " O   HOH Z 418 " =    2.933
peak=    3.517 closest distance to " OG  SER A  97 " =    2.895
peak=    3.507 closest distance to " O   HOH Z 137 " =    0.945
peak=    3.502 closest distance to " NE2 GLN A  11 " =    0.972
peak=    3.501 closest distance to " O   HOH Z 143 " =    1.645
peak=    3.500 closest distance to " CA  ARG A  66 " =    0.882
peak=    3.500 closest distance to " CB  ASP A 286 " =    1.158
peak=    3.495 closest distance to " O   HOH Z 116 " =    2.586
peak=    3.495 closest distance to " O   HOH Z 169 " =    2.746
peak=    3.494 closest distance to " O   HOH Z 423 " =    1.996
peak=    3.483 closest distance to " O   HOH Z 203 " =    1.503
peak=    3.477 closest distance to " CB  VAL A 265 " =    1.308
peak=    3.474 closest distance to " O   HOH Z  68 " =    2.091
peak=    3.473 closest distance to " O   HOH Z 296 " =    1.796
peak=    3.471 closest distance to " CB  PRO A 198 " =    1.177
peak=    3.471 closest distance to " O   HOH Z  69 " =    2.282
peak=    3.468 closest distance to " O   HOH Z  85 " =    1.920
peak=    3.462 closest distance to " O   HOH Z 111 " =    1.722
peak=    3.459 closest distance to " CZ  PHE A 218 " =    1.284
peak=    3.458 closest distance to " O   HOH Z 263 " =    1.543
peak=    3.452 closest distance to " CB  SER A  62 " =    1.085
peak=    3.451 closest distance to " O   HOH Z 408 " =    2.419
peak=    3.448 closest distance to " O   HOH Z 128 " =    1.693
peak=    3.447 closest distance to " N   ASP A 162 " =    2.102
peak=    3.443 closest distance to " O   HOH Z 183 " =    1.869
peak=    3.432 closest distance to " O   HOH Z 340 " =    1.636
peak=    3.431 closest distance to " O   HOH Z 366 " =    1.955
peak=    3.429 closest distance to " CB  PRO A 243 " =    1.199
peak=    3.428 closest distance to " O   HOH Z  95 " =    1.835
peak=    3.427 closest distance to " CA  TYR A  30 " =    0.931
peak=    3.424 closest distance to " CB  SER A  97 " =    0.965
peak=    3.424 closest distance to " CB  ARG A  79 " =    1.391
peak=    3.419 closest distance to " O   HOH Z 139 " =    4.163
peak=    3.415 closest distance to " CG2 THR A 294 " =    1.397
peak=    3.414 closest distance to " CB  GLU A 152 " =    1.230
peak=    3.407 closest distance to " O   HOH Z 365 " =    1.630
peak=    3.404 closest distance to " CB  TRP A 179 " =    1.099
peak=    3.402 closest distance to " O   HOH Z   4 " =    1.803
peak=    3.394 closest distance to " O   HOH Z 358 " =    2.403
peak=    3.391 closest distance to " N   LEU A  25 " =    0.982
peak=    3.388 closest distance to " O   HOH Z  88 " =    3.519
peak=    3.385 closest distance to " O   HOH Z 281 " =    4.048
peak=    3.385 closest distance to " O   HOH Z 132 " =    2.856
peak=    3.382 closest distance to " O   HOH Z 287 " =    1.970
peak=    3.379 closest distance to " O   HOH Z 110 " =    1.170
peak=    3.377 closest distance to " CB  SER A  62 " =    3.814
peak=    3.377 closest distance to " CD  ARG A 159 " =    0.856
peak=    3.375 closest distance to " N   PHE A 130 " =    1.327
peak=    3.371 closest distance to " O   HOH Z 272 " =    2.029
peak=    3.364 closest distance to " O   HOH Z 298 " =    5.097
peak=    3.356 closest distance to " NZ  LYS A 117 " =    2.968
peak=    3.356 closest distance to " CB  GLN A 194 " =    1.086
peak=    3.352 closest distance to " O   HOH Z 129 " =    3.200
peak=    3.347 closest distance to " CB  MET A  40 " =    0.738
peak=    3.343 closest distance to " O   PHE A  61 " =    1.297
peak=    3.343 closest distance to " O   HOH Z 382 " =    1.220
peak=    3.341 closest distance to " CE1 HIS A 108 " =    1.232
peak=    3.340 closest distance to " CB  GLN A 183 " =    1.197
peak=    3.332 closest distance to " O   HOH Z 367 " =    1.367
peak=    3.324 closest distance to " CA  ARG A 195 " =    1.126
peak=    3.319 closest distance to " O   HOH Z  52 " =    1.692
peak=    3.312 closest distance to " O   HOH Z  47 " =    1.863
peak=    3.309 closest distance to " O   HOH Z 126 " =    2.460
peak=    3.307 closest distance to " CA  GLN A  11 " =    1.291
peak=    3.304 closest distance to " O   HOH Z 287 " =    2.049
peak=    3.301 closest distance to " CG  PRO A  90 " =    1.242
peak=    3.296 closest distance to " CD2 TYR A  68 " =    0.929
peak=    3.295 closest distance to " OG BSER A 210 " =    1.314
peak=    3.295 closest distance to " O   HOH Z  32 " =    1.774
peak=    3.294 closest distance to " O   HOH Z 415 " =    1.370
peak=    3.291 closest distance to " O  BHOH Z 338 " =    2.405
peak=    3.286 closest distance to " O   ASN A 301 " =    2.549
peak=    3.283 closest distance to " CB  GLN A 278 " =    0.820
peak=    3.279 closest distance to " N   SER A 164 " =    0.996
peak=    3.277 closest distance to " O   HOH Z 340 " =    2.164
peak=    3.274 closest distance to " CD BLYS A 290 " =    1.057
peak=    3.273 closest distance to " O   HOH Z 289 " =    1.628
peak=    3.272 closest distance to " O   HOH Z 265 " =    1.602
peak=    3.271 closest distance to " O   HOH Z 350 " =    1.733
peak=    3.269 closest distance to " N   LYS A 166 " =    0.938
peak=    3.266 closest distance to " CB  GLU A 128 " =    1.253
peak=    3.266 closest distance to " O   HOH Z 399 " =    1.183
peak=    3.266 closest distance to " O   HOH Z 353 " =    1.481
peak=    3.266 closest distance to " OG1 THR A 221 " =    1.126
peak=    3.262 closest distance to " O   SER A  87 " =    2.408
peak=    3.262 closest distance to " O   HOH Z 151 " =    1.804
peak=    3.260 closest distance to " N   ASN A  39 " =    1.210
peak=    3.260 closest distance to " NH1 ARG A  66 " =    3.526
peak=    3.256 closest distance to " CB  ARG A 269 " =    1.713
peak=    3.251 closest distance to " O   HOH Z 277 " =    2.722
peak=    3.248 closest distance to " CG2 ILE A 234 " =    1.056
peak=    3.247 closest distance to " O   HOH Z 154 " =    2.231
peak=    3.247 closest distance to " O   LYS A 289 " =    1.045
peak=    3.245 closest distance to " O   HOH Z  61 " =    1.593
peak=    3.242 closest distance to " O   HOH Z 245 " =    1.398
peak=    3.241 closest distance to " CB  ASN A 148 " =    1.115
peak=    3.238 closest distance to " O   HOH Z 194 " =    1.942
peak=    3.238 closest distance to " O   HOH Z 136 " =    1.340
peak=    3.238 closest distance to " O   HOH Z 383 " =    1.938
peak=    3.231 closest distance to " O   HOH Z  42 " =    2.278
peak=    3.230 closest distance to " CD BLYS A 290 " =    0.909
peak=    3.226 closest distance to " NH1 ARG A  14 " =    1.131
peak=    3.217 closest distance to " OH  TYR A 116 " =    1.154
peak=    3.216 closest distance to " CG2 THR A 221 " =    1.154
peak=    3.214 closest distance to " O   HOH Z 428 " =    3.867
peak=    3.214 closest distance to " O   GLY A  91 " =    1.283
peak=    3.211 closest distance to " O   HOH Z 158 " =    3.202
peak=    3.207 closest distance to " NH1AARG A 275 " =    2.547
peak=    3.204 closest distance to " CD2 LEU A  25 " =    1.171
peak=    3.202 closest distance to " O   HOH Z 196 " =    1.158
peak=    3.202 closest distance to " O   HOH Z 339 " =    1.627
peak=    3.199 closest distance to " NZ  LYS A 193 " =    1.231
peak=    3.195 closest distance to " CG1BVAL A  72 " =    2.426
peak=    3.194 closest distance to " CG1BVAL A 121 " =    1.685
peak=    3.191 closest distance to " CD  ARG A 195 " =    1.230
peak=    3.189 closest distance to " CE3 TRP A 150 " =    1.079
peak=    3.186 closest distance to " O   HOH Z 301 " =    1.843
peak=    3.184 closest distance to " CB  PRO A 213 " =    1.133
peak=    3.183 closest distance to " O   HOH Z  78 " =    1.187
peak=    3.182 closest distance to " CB  ALA A 114 " =    1.363
peak=    3.181 closest distance to " CA  LEU A 282 " =    0.968
peak=    3.180 closest distance to " O   HOH Z 237 " =    2.095
peak=    3.176 closest distance to " CD1 TRP A 274 " =    1.285
peak=    3.175 closest distance to " CZ2 TRP A 274 " =    1.061
peak=    3.175 closest distance to " CB  ALA A 100 " =    1.111
peak=    3.174 closest distance to " O   HOH Z 406 " =    1.650
peak=    3.172 closest distance to " CA  GLN A  58 " =    1.207
peak=    3.171 closest distance to " CA  GLU A 152 " =    0.992
peak=    3.171 closest distance to " O   HOH Z  15 " =    2.114
peak=    3.167 closest distance to " CA  ARG A  36 " =    1.067
peak=    3.156 closest distance to " O   SER A 273 " =    1.810
peak=    3.155 closest distance to " ND1 HIS A  81 " =    1.503
peak=    3.152 closest distance to " CA  GLY A 196 " =    0.743
peak=    3.151 closest distance to " O   HOH Z  40 " =    1.925
peak=    3.145 closest distance to " O   HOH Z 435 " =    3.180
peak=    3.140 closest distance to " O   HOH Z 383 " =    2.135
peak=    3.140 closest distance to " O   HOH Z 412 " =    3.648
peak=    3.139 closest distance to " CG2AVAL A  72 " =    2.110
peak=    3.138 closest distance to " O   HOH Z 230 " =    1.337
peak=    3.136 closest distance to " CB  VAL A 202 " =    1.439
peak=    3.134 closest distance to " CG2 THR A  29 " =    1.124
peak=    3.133 closest distance to " O   HOH Z 337 " =    1.686
peak=    3.133 closest distance to " N   SER A 271 " =    1.099
peak=    3.120 closest distance to " O   HOH Z   9 " =    2.513
peak=    3.118 closest distance to " CE BMET A  47 " =    1.085
peak=    3.117 closest distance to " O   HOH Z 123 " =    2.064
peak=    3.116 closest distance to " O   THR A 264 " =    1.512
peak=    3.110 closest distance to " CB  PRO A 163 " =    4.010
peak=    3.106 closest distance to " O   HOH Z 234 " =    3.761
peak=    3.094 closest distance to " CA  PHE A  59 " =    1.023
peak=    3.091 closest distance to " CA  THR A 294 " =    2.218
peak=    3.091 closest distance to " CZ2 TRP A 150 " =    1.007
peak=    3.088 closest distance to " O   HOH Z 200 " =    3.265
peak=    3.078 closest distance to " N   ALA A  84 " =    0.909
peak=    3.077 closest distance to " O   HOH Z  41 " =    1.820
peak=    3.072 closest distance to " CG  LEU A 228 " =    1.456
peak=    3.068 closest distance to " O   HOH Z 173 " =    2.287
peak=    3.058 closest distance to " O   HOH Z 406 " =    1.298
peak=    3.054 closest distance to " CA  GLN A 223 " =    0.721
peak=    3.049 closest distance to " O   HOH Z 359 " =    1.856
peak=    3.047 closest distance to " O   HOH Z  48 " =    2.828
peak=    3.044 closest distance to " O   ASP A 124 " =    1.621
peak=    3.041 closest distance to " CB  LEU A  25 " =    0.882
peak=    3.028 closest distance to " NE1 TRP A  92 " =    1.111
peak=    3.024 closest distance to " CA  ARG A 195 " =    1.457
peak=    3.015 closest distance to " N   GLY A  75 " =    1.172

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 233         
Filter by distance & map next to the model:
   mapped sites are within: 0.341 - 5.583
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 233
   mapped sites are within: 0.706 - 5.583

peak=   -6.000 closest distance to " CG2 VAL A 230 " =    0.757
peak=   -5.392 closest distance to " CZ  ARG A  36 " =    1.033
peak=   -5.218 closest distance to " O   ASN A 285 " =    0.987
peak=   -4.883 closest distance to " O   GLN A  11 " =    0.927
peak=   -4.689 closest distance to " O   HOH Z 422 " =    0.981
peak=   -4.530 closest distance to " O   HOH Z 340 " =    0.715
peak=   -4.504 closest distance to " OD1 ASN A 301 " =    0.833
peak=   -4.441 closest distance to " O   HOH Z   7 " =    0.828
peak=   -4.435 closest distance to " CG  GLN A  58 " =    1.033
peak=   -4.303 closest distance to " CD1 PHE A  59 " =    1.910
peak=   -4.303 closest distance to " CD  ARG A  14 " =    2.830
peak=   -4.241 closest distance to " N   VAL A  72 " =    1.153
peak=   -4.224 closest distance to " CD1 TRP A 179 " =    0.989
peak=   -4.189 closest distance to " CG  ASP A 286 " =    0.940
peak=   -4.123 closest distance to " O   HOH Z  13 " =    1.716
peak=   -4.119 closest distance to " CB  LEU A 167 " =    1.992
peak=   -4.106 closest distance to " O   HOH Z 120 " =    0.976
peak=   -4.100 closest distance to " O   HOH Z 424 " =    0.903
peak=   -4.089 closest distance to " O   HOH Z  52 " =    2.386
peak=   -4.082 closest distance to " O   HOH Z 384 " =    1.736
peak=   -4.044 closest distance to " O   HOH Z 411 " =    5.125
peak=   -4.026 closest distance to " O   HOH Z  67 " =    1.407
peak=   -4.019 closest distance to " CG  GLN A  73 " =    0.795
peak=   -4.003 closest distance to " CD2 LEU A 237 " =    2.311
peak=   -3.988 closest distance to " C   THR A 279 " =    1.122
peak=   -3.981 closest distance to " CD2 TYR A  30 " =    2.679
peak=   -3.967 closest distance to " O   HOH Z 432 " =    0.754
peak=   -3.967 closest distance to " O   HOH Z 164 " =    5.583
peak=   -3.948 closest distance to " O  BHOH Z 338 " =    1.252
peak=   -3.945 closest distance to " O   PRO A 198 " =    1.259
peak=   -3.935 closest distance to " CD  GLN A 223 " =    0.758
peak=   -3.920 closest distance to " CG  PRO A 243 " =    1.871
peak=   -3.883 closest distance to " O   HOH Z 205 " =    0.759
peak=   -3.873 closest distance to " CG  LEU A   5 " =    0.782
peak=   -3.867 closest distance to " O   HOH Z 425 " =    0.991
peak=   -3.838 closest distance to " CG1 VAL A 296 " =    1.008
peak=   -3.836 closest distance to " O   HOH Z 176 " =    1.246
peak=   -3.800 closest distance to " O   HOH Z 221 " =    0.988
peak=   -3.784 closest distance to " CD  ARG A  36 " =    0.958
peak=   -3.777 closest distance to " CG  ASP A 231 " =    0.788
peak=   -3.774 closest distance to " CD1 LEU A  96 " =    2.109
peak=   -3.758 closest distance to " O   HOH Z 151 " =    0.919
peak=   -3.753 closest distance to " O   HOH Z 137 " =    1.556
peak=   -3.749 closest distance to " O   TYR A  15 " =    1.738
peak=   -3.742 closest distance to " O   HOH Z 166 " =    0.991
peak=   -3.738 closest distance to " O   HOH Z 423 " =    2.786
peak=   -3.733 closest distance to " O   HOH Z  56 " =    1.284
peak=   -3.730 closest distance to " OXT GLY A 302 " =    2.790
peak=   -3.705 closest distance to " O   HOH Z 135 " =    1.530
peak=   -3.680 closest distance to " NH2 ARG A  36 " =    0.963
peak=   -3.678 closest distance to " ND1 HIS A  81 " =    0.891
peak=   -3.666 closest distance to " CG2 VAL A 189 " =    2.085
peak=   -3.661 closest distance to " CG2 THR A  18 " =    2.711
peak=   -3.655 closest distance to " CD  ARG A 156 " =    1.921
peak=   -3.653 closest distance to " O   HOH Z 125 " =    1.201
peak=   -3.641 closest distance to " O   HOH Z 234 " =    3.929
peak=   -3.637 closest distance to " O   HOH Z 146 " =    0.820
peak=   -3.636 closest distance to " CG2 VAL A 296 " =    1.073
peak=   -3.611 closest distance to " CB  SER A  26 " =    1.263
peak=   -3.599 closest distance to " C   LYS A  76 " =    1.655
peak=   -3.583 closest distance to " O   HOH Z 407 " =    0.966
peak=   -3.569 closest distance to " O   HOH Z 428 " =    2.459
peak=   -3.558 closest distance to " CG1 VAL A 112 " =    2.491
peak=   -3.557 closest distance to " O   HOH Z  14 " =    0.816
peak=   -3.547 closest distance to " O   HOH Z  60 " =    1.124
peak=   -3.545 closest distance to " O   HOH Z 120 " =    0.729
peak=   -3.543 closest distance to " C   GLN A 144 " =    0.918
peak=   -3.543 closest distance to " CA  SER A 276 " =    1.440
peak=   -3.543 closest distance to " O   HOH Z 417 " =    0.706
peak=   -3.542 closest distance to " CA  SER A 164 " =    1.752
peak=   -3.538 closest distance to " O   HOH Z 198 " =    0.959
peak=   -3.533 closest distance to " O   HOH Z 130 " =    2.246
peak=   -3.533 closest distance to " O   SER A 273 " =    0.999
peak=   -3.528 closest distance to " O   HOH Z  18 " =    0.968
peak=   -3.527 closest distance to " O   HOH Z 166 " =    1.436
peak=   -3.526 closest distance to " CG2 ILE A  49 " =    2.535
peak=   -3.522 closest distance to " N   LYS A 289 " =    1.073
peak=   -3.512 closest distance to " CG2BVAL A  41 " =    2.306
peak=   -3.512 closest distance to " C   SER A 271 " =    1.227
peak=   -3.507 closest distance to " OD1 ASN A 285 " =    0.994
peak=   -3.505 closest distance to " O   ALA A   7 " =    1.672
peak=   -3.503 closest distance to " C   HIS A 108 " =    1.078
peak=   -3.498 closest distance to " CA  ALA A 114 " =    1.008
peak=   -3.497 closest distance to " O   HOH Z  29 " =    1.211
peak=   -3.495 closest distance to " CD  GLN A  77 " =    0.847
peak=   -3.483 closest distance to " O   VAL A 174 " =    2.140
peak=   -3.480 closest distance to " CG  GLN A 223 " =    1.839
peak=   -3.478 closest distance to " O   HOH Z 251 " =    1.069
peak=   -3.470 closest distance to " OG  SER A  32 " =    1.094
peak=   -3.468 closest distance to " CG2 ILE A  20 " =    2.900
peak=   -3.467 closest distance to " O   HOH Z 135 " =    2.401
peak=   -3.467 closest distance to " CA  GLY A 133 " =    2.029
peak=   -3.460 closest distance to " CA  GLY A 241 " =    3.224
peak=   -3.454 closest distance to " O   HOH Z 378 " =    0.711
peak=   -3.453 closest distance to " O   HOH Z 405 " =    0.925
peak=   -3.451 closest distance to " OG  SER A 206 " =    1.295
peak=   -3.448 closest distance to " O   HOH Z 159 " =    1.132
peak=   -3.446 closest distance to " O   HOH Z 119 " =    1.918
peak=   -3.443 closest distance to " N   VAL A 230 " =    1.107
peak=   -3.429 closest distance to " CE3 TRP A  70 " =    1.725
peak=   -3.421 closest distance to " C   ASP A 286 " =    1.092
peak=   -3.419 closest distance to " O   ASN A 285 " =    1.405
peak=   -3.413 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.408 closest distance to " C   TRP A 274 " =    1.035
peak=   -3.399 closest distance to " O   HOH Z 411 " =    1.417
peak=   -3.396 closest distance to " O   GLY A 241 " =    2.214
peak=   -3.395 closest distance to " CB  ALA A 248 " =    2.186
peak=   -3.392 closest distance to " OD1 ASP A 298 " =    2.335
peak=   -3.391 closest distance to " O   ALA A 161 " =    1.399
peak=   -3.383 closest distance to " C   TRP A  70 " =    1.408
peak=   -3.383 closest distance to " CD1 TYR A 169 " =    2.122
peak=   -3.379 closest distance to " CA  ALA A 137 " =    2.550
peak=   -3.374 closest distance to " O   LEU A 300 " =    2.452
peak=   -3.372 closest distance to " C   ALA A 160 " =    1.546
peak=   -3.372 closest distance to " OE2 GLU A   2 " =    1.463
peak=   -3.371 closest distance to " O   HOH Z 368 " =    1.635
peak=   -3.364 closest distance to " O   HOH Z 126 " =    1.983
peak=   -3.363 closest distance to " CD  ARG A 195 " =    4.970
peak=   -3.363 closest distance to " O   HOH Z 353 " =    1.112
peak=   -3.358 closest distance to " CB  ALA A 161 " =    2.377
peak=   -3.357 closest distance to " OG BSER A 212 " =    1.473
peak=   -3.354 closest distance to " O   HOH Z 130 " =    1.114
peak=   -3.343 closest distance to " NE1 TRP A 266 " =    2.096
peak=   -3.342 closest distance to " CG AARG A 102 " =    2.028
peak=   -3.330 closest distance to " O   HOH Z 391 " =    1.062
peak=   -3.329 closest distance to " CA  SER A 210 " =    0.833
peak=   -3.328 closest distance to " OG BSER A  99 " =    1.173
peak=   -3.326 closest distance to " N   ALA A  43 " =    2.825
peak=   -3.325 closest distance to " CE  MET A 105 " =    2.047
peak=   -3.316 closest distance to " N   THR A 235 " =    1.146
peak=   -3.316 closest distance to " O   HOH Z 165 " =    2.163
peak=   -3.314 closest distance to " O   HOH Z 351 " =    1.565
peak=   -3.313 closest distance to " O   HOH Z 109 " =    2.833
peak=   -3.311 closest distance to " OD2 ASP A 298 " =    0.772
peak=   -3.307 closest distance to " CG1AVAL A 121 " =    2.664
peak=   -3.302 closest distance to " C   ASN A 148 " =    1.502
peak=   -3.300 closest distance to " O   HOH Z  37 " =    1.563
peak=   -3.296 closest distance to " NE1 TRP A 177 " =    2.068
peak=   -3.294 closest distance to " CB  ASP A 286 " =    1.076
peak=   -3.292 closest distance to " CG BARG A 275 " =    0.918
peak=   -3.285 closest distance to " O   HOH Z 423 " =    2.624
peak=   -3.281 closest distance to " O   HOH Z 433 " =    0.944
peak=   -3.281 closest distance to " O   HOH Z 362 " =    3.597
peak=   -3.281 closest distance to " O   HOH Z 233 " =    2.412
peak=   -3.277 closest distance to " NH2 ARG A  79 " =    2.069
peak=   -3.271 closest distance to " N   ARG A 275 " =    1.096
peak=   -3.270 closest distance to " CB  HIS A  86 " =    2.339
peak=   -3.264 closest distance to " O   GLU A 236 " =    1.244
peak=   -3.255 closest distance to " C   LEU A   5 " =    1.188
peak=   -3.253 closest distance to " O   ASN A 187 " =    1.559
peak=   -3.248 closest distance to " CE1 TYR A 247 " =    2.432
peak=   -3.240 closest distance to " O   HOH Z 435 " =    1.158
peak=   -3.239 closest distance to " CD2 LEU A 300 " =    2.573
peak=   -3.239 closest distance to " O   HOH Z 196 " =    1.535
peak=   -3.236 closest distance to " O   HOH Z 123 " =    0.833
peak=   -3.236 closest distance to " O   HOH Z 126 " =    1.979
peak=   -3.236 closest distance to " O   SER A  95 " =    1.513
peak=   -3.236 closest distance to " N   ASP A 191 " =    1.595
peak=   -3.235 closest distance to " CD2 LEU A 237 " =    2.670
peak=   -3.229 closest distance to " O   ASP A 171 " =    2.036
peak=   -3.228 closest distance to " O   HOH Z 350 " =    2.369
peak=   -3.228 closest distance to " NH2AARG A 275 " =    0.921
peak=   -3.227 closest distance to " CA  ASP A 298 " =    1.099
peak=   -3.221 closest distance to " O   SER A   3 " =    0.941
peak=   -3.220 closest distance to " OG  SER A 141 " =    1.859
peak=   -3.220 closest distance to " C   GLY A 147 " =    1.581
peak=   -3.213 closest distance to " O   HOH Z 388 " =    1.453
peak=   -3.213 closest distance to " O   HOH Z 249 " =    0.894
peak=   -3.212 closest distance to " O   HOH Z 173 " =    2.757
peak=   -3.211 closest distance to " O   GLY A  23 " =    1.122
peak=   -3.207 closest distance to " CA  VAL A 197 " =    0.968
peak=   -3.206 closest distance to " O   HOH Z 377 " =    0.735
peak=   -3.201 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.200 closest distance to " OG  SER A  62 " =    0.761
peak=   -3.187 closest distance to " O   HOH Z 259 " =    1.093
peak=   -3.184 closest distance to " CG  ARG A 219 " =    2.189
peak=   -3.175 closest distance to " O   HOH Z 193 " =    1.597
peak=   -3.174 closest distance to " CB  PHE A  59 " =    2.379
peak=   -3.174 closest distance to " CZ3 TRP A  92 " =    1.067
peak=   -3.170 closest distance to " O   THR A  31 " =    1.455
peak=   -3.159 closest distance to " O   HOH Z   9 " =    2.663
peak=   -3.159 closest distance to " OG  SER A 245 " =    1.316
peak=   -3.156 closest distance to " CD1 LEU A   5 " =    1.964
peak=   -3.153 closest distance to " O   HOH Z 150 " =    1.334
peak=   -3.150 closest distance to " N   GLY A  75 " =    1.139
peak=   -3.147 closest distance to " C   MET A 188 " =    1.308
peak=   -3.146 closest distance to " N   ASP A 286 " =    1.096
peak=   -3.140 closest distance to " CG1 VAL A 197 " =    2.299
peak=   -3.138 closest distance to " O   ALA A  34 " =    2.521
peak=   -3.138 closest distance to " O   TRP A  92 " =    2.324
peak=   -3.134 closest distance to " CG1 VAL A 296 " =    1.370
peak=   -3.134 closest distance to " O   HOH Z 359 " =    3.163
peak=   -3.130 closest distance to " NZ  LYS A  76 " =    1.775
peak=   -3.130 closest distance to " O   HOH Z  92 " =    1.413
peak=   -3.127 closest distance to " CG  GLU A  53 " =    1.284
peak=   -3.126 closest distance to " OG  SER A  97 " =    2.200
peak=   -3.118 closest distance to " O   HOH Z 124 " =    1.328
peak=   -3.114 closest distance to " SD  MET A 105 " =    2.331
peak=   -3.109 closest distance to " O   HOH Z 164 " =    4.732
peak=   -3.108 closest distance to " CG  GLN A 223 " =    1.096
peak=   -3.104 closest distance to " O   HOH Z 174 " =    1.895
peak=   -3.101 closest distance to " CA  THR A 220 " =    1.371
peak=   -3.093 closest distance to " O   GLN A  94 " =    2.211
peak=   -3.080 closest distance to " O   HOH Z 115 " =    1.232
peak=   -3.077 closest distance to " OXT GLY A 302 " =    3.604
peak=   -3.069 closest distance to " O   HOH Z 261 " =    0.951
peak=   -3.069 closest distance to " O   HOH Z 289 " =    1.733
peak=   -3.050 closest distance to " O   HOH Z 145 " =    2.514
peak=   -3.049 closest distance to " CD  LYS A 289 " =    2.365
peak=   -3.048 closest distance to " OD1 ASN A 301 " =    1.036
peak=   -3.046 closest distance to " O   HOH Z  28 " =    1.968
peak=   -3.039 closest distance to " O   HOH Z 156 " =    2.075

================= 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    :  0.5195 0.5035   6.314182e+00   6.305243e+00
   1_bss:  0.5133 0.4999   6.309586e+00   6.304111e+00
   1_xyz:  0.4677 0.4769   6.155452e+00   6.163251e+00
   1_adp:  0.4260 0.4805   6.232257e+00   6.282876e+00
   1_occ:  0.4253 0.4794   6.231424e+00   6.282212e+00
   2_bss:  0.4234 0.4731   6.231717e+00   6.281351e+00
   2_xyz:  0.3662 0.4282   6.133051e+00   6.229544e+00
   2_adp:  0.3543 0.4207   6.116432e+00   6.219818e+00
   2_occ:  0.3540 0.4203   6.115676e+00   6.219622e+00
   3_bss:  0.3525 0.4185   6.116062e+00   6.220182e+00
   3_xyz:  0.2868 0.3529   5.946543e+00   6.097710e+00
   3_adp:  0.2560 0.3280   5.873913e+00   6.049069e+00
   3_occ:  0.2557 0.3280   5.873264e+00   6.048595e+00
   4_bss:  0.2549 0.3278   5.872786e+00   6.046523e+00
   4_xyz:  0.2007 0.2588   5.653501e+00   5.857029e+00
   4_adp:  0.1837 0.2326   5.566152e+00   5.755482e+00
   4_occ:  0.1834 0.2323   5.565276e+00   5.755094e+00
   5_bss:  0.1830 0.2314   5.566394e+00   5.753347e+00
   5_xyz:  0.1510 0.1968   5.395282e+00   5.599429e+00
   5_adp:  0.1465 0.1896   5.361397e+00   5.556163e+00
   5_occ:  0.1464 0.1894   5.360746e+00   5.556106e+00
   5_bss:  0.1465 0.1901   5.362562e+00   5.558490e+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:  0.315   3.019   7.020  11.543   6.922   0.000   0.000   0.000
   1_xyz:  0.315   3.019   7.020  11.543   6.922   0.000   0.000   0.000
   1_adp:  0.315   3.019   7.020  11.543   6.922   0.000   0.000   0.000
   1_occ:  0.315   3.019   7.020  11.543   6.922   0.000   0.000   0.000
   2_bss:  0.284  20.000   3.077   6.164   3.376   0.000   0.000   0.000
   2_xyz:  0.284  20.000   3.077   6.164   3.376   0.000   0.000   0.000
   2_adp:  0.284  20.000   3.077   6.164   3.376   0.000   0.000   0.000
   2_occ:  0.284  20.000   3.077   6.164   3.376   0.000   0.000   0.000
   3_bss:  0.314  50.001   0.811   3.547   1.743   0.000   0.000   0.000
   3_xyz:  0.314  50.001   0.811   3.547   1.743   0.000   0.000   0.000
   3_adp:  0.314  50.001   0.811   3.547   1.743   0.000   0.000   0.000
   3_occ:  0.314  50.001   0.811   3.547   1.743   0.000   0.000   0.000
   4_bss:  0.314  50.001  -0.477   1.910   0.880   0.000   0.000   0.000
   4_xyz:  0.314  50.001  -0.477   1.910   0.880   0.000   0.000   0.000
   4_adp:  0.314  50.001  -0.477   1.910   0.880   0.000   0.000   0.000
   4_occ:  0.314  50.001  -0.477   1.910   0.880   0.000   0.000   0.000
   5_bss:  0.321  50.001  -1.841   0.467  -0.077   0.000  -0.000  -0.000
   5_xyz:  0.321  50.001  -1.841   0.467  -0.077   0.000  -0.000  -0.000
   5_adp:  0.321  50.001  -1.841   0.467  -0.077   0.000  -0.000  -0.000
   5_occ:  0.321  50.001  -1.841   0.467  -0.077   0.000  -0.000  -0.000
   5_bss:  0.327  49.931  -2.252  -0.087  -0.259  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.405 0.3242  0.3902    85097.356
   1_bss:  66.612 0.3071  0.4666    84979.577
   1_xyz:  61.335 0.3750  0.5638    74885.259
   1_adp:  58.978 0.4056  0.7025    72747.394
   1_occ:  58.881 0.4068  0.7031    72529.778
   2_bss:  58.288 0.4145  0.6259    71521.610
   2_xyz:  51.382 0.5012  0.7563    56820.859
   2_adp:  49.655 0.5233  0.8102    54542.680
   2_occ:  49.620 0.5237  0.8095    54431.885
   3_bss:  49.372 0.5268  0.7585    54209.464
   3_xyz:  38.574 0.6583  0.9165    35039.287
   3_adp:  35.586 0.6938  0.9329    30637.425
   3_occ:  35.552 0.6943  0.9332    30596.956
   4_bss:  35.424 0.6957  0.8943    30409.258
   4_xyz:  26.777 0.7917  0.9827    18059.112
   4_adp:  23.229 0.8298  1.0032    14494.363
   4_occ:  23.202 0.8301  1.0040    14489.335
   5_bss:  23.162 0.8305  0.9600    14461.545
   5_xyz:  19.054 0.8704  0.9805    10129.551
   5_adp:  17.881 0.8819  0.9830     9413.710
   5_occ:  17.869 0.8821  0.9833     9419.898
   5_bss:  17.904 0.8818  0.9676     9478.075
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3538e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3538e+01
   1_xyz:   1.636  0.012  0.103 18.676  0.006  4.116   1.4297e-01
   1_adp:   1.636  0.012  0.103 18.676  0.006  4.116   1.4297e-01
   1_occ:   1.636  0.012  0.103 18.676  0.006  4.116   1.4297e-01
   2_bss:   1.636  0.012  0.103 18.676  0.006  4.116   1.4297e-01
   2_xyz:   1.382  0.011  0.089 17.700  0.005  4.102   1.2117e-01
   2_adp:   1.382  0.011  0.089 17.700  0.005  4.102   1.2117e-01
   2_occ:   1.382  0.011  0.089 17.700  0.005  4.102   1.2117e-01
   3_bss:   1.382  0.011  0.089 17.700  0.005  4.102   1.2117e-01
   3_xyz:   1.441  0.012  0.098 17.491  0.006  4.102   1.2318e-01
   3_adp:   1.441  0.012  0.098 17.491  0.006  4.102   1.2318e-01
   3_occ:   1.441  0.012  0.098 17.491  0.006  4.102   1.2318e-01
   4_bss:   1.441  0.012  0.098 17.491  0.006  4.102   1.2318e-01
   4_xyz:   1.222  0.009  0.083 16.382  0.005  4.106   9.0620e-02
   4_adp:   1.222  0.009  0.083 16.382  0.005  4.106   9.0620e-02
   4_occ:   1.222  0.009  0.083 16.382  0.005  4.106   9.0620e-02
   5_bss:   1.222  0.009  0.083 16.382  0.005  4.106   9.0620e-02
   5_xyz:   1.098  0.007  0.080 15.747  0.004  4.117   7.1826e-02
   5_adp:   1.098  0.007  0.080 15.747  0.004  4.117   7.1826e-02
   5_occ:   1.098  0.007  0.080 15.747  0.004  4.117   7.1826e-02
   5_bss:   1.098  0.007  0.080 15.747  0.004  4.117   7.1826e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.612   6.9281e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.612   6.9281e+00
   1_xyz:  13.950  0.151  0.433 86.337  0.043  2.045   9.0602e-02
   1_adp:  13.950  0.151  0.433 86.337  0.043  2.045   9.0602e-02
   1_occ:  13.950  0.151  0.433 86.337  0.043  2.045   9.0602e-02
   2_bss:  13.950  0.151  0.433 86.337  0.043  2.045   9.0602e-02
   2_xyz:   9.143  0.156  0.276 84.500  0.052  1.970   1.0230e-01
   2_adp:   9.143  0.156  0.276 84.500  0.052  1.970   1.0230e-01
   2_occ:   9.143  0.156  0.276 84.500  0.052  1.970   1.0230e-01
   3_bss:   9.143  0.156  0.276 84.500  0.052  1.970   1.0230e-01
   3_xyz:   9.090  0.110  0.411 86.851  0.056  2.094   1.0722e-01
   3_adp:   9.090  0.110  0.411 86.851  0.056  2.094   1.0722e-01
   3_occ:   9.090  0.110  0.411 86.851  0.056  2.094   1.0722e-01
   4_bss:   9.090  0.110  0.411 86.851  0.056  2.094   1.0722e-01
   4_xyz:   6.625  0.088  0.266 82.522  0.032  2.042   8.5169e-02
   4_adp:   6.625  0.088  0.266 82.522  0.032  2.042   8.5169e-02
   4_occ:   6.625  0.088  0.266 82.522  0.032  2.042   8.5169e-02
   5_bss:   6.625  0.088  0.266 82.522  0.032  2.042   8.5169e-02
   5_xyz:   7.357  0.070  0.413 80.841  0.040  2.158   5.2052e-02
   5_adp:   7.357  0.070  0.413 80.841  0.040  2.158   5.2052e-02
   5_occ:   7.357  0.070  0.413 80.841  0.040  2.158   5.2052e-02
   5_bss:   7.357  0.070  0.413 80.841  0.040  2.158   5.2052e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp: 104.58   0.00  18.79  83.06   0.00  17.08 104.58   0.00  28.09
   1_occ: 104.58   0.00  18.79  83.06   0.00  17.08 104.58   0.00  28.09
   2_bss: 104.58   0.00  18.79  83.06   0.00  17.08 104.58   0.00  28.09
   2_xyz: 104.58   0.00  18.79  83.06   0.00  17.08 104.58   0.00  28.09
   2_adp: 284.25   0.00  18.53 284.25   0.00  16.54  98.40   0.00  29.35
   2_occ: 284.25   0.00  18.53 284.25   0.00  16.54  98.40   0.00  29.35
   3_bss: 284.25   0.00  18.53 284.25   0.00  16.54  98.40   0.00  29.35
   3_xyz: 284.25   0.00  18.53 284.25   0.00  16.54  98.40   0.00  29.35
   3_adp: 184.25   0.00  18.10 184.25   0.00  14.57 107.09   2.30  37.32
   3_occ: 184.25   0.00  18.10 184.25   0.00  14.57 107.09   2.30  37.32
   4_bss: 184.25   0.00  18.10 184.25   0.00  14.57 107.09   2.30  37.32
   4_xyz: 184.25   0.00  18.10 184.25   0.00  14.57 107.09   2.30  37.32
   4_adp: 101.39   0.00  16.81 101.39   0.00  12.76  89.61   4.38  38.87
   4_occ: 101.39   0.00  16.81 101.39   0.00  12.76  89.61   4.38  38.87
   5_bss: 101.39   0.00  16.81 101.39   0.00  12.76  89.61   4.38  38.87
   5_xyz: 101.39   0.00  16.81 101.39   0.00  12.76  89.61   4.38  38.87
   5_adp:  97.20   1.95  15.95  97.20   1.95  12.03  89.24   5.44  37.27
   5_occ:  97.20   1.95  15.95  97.20   1.95  12.03  89.24   5.44  37.27
   5_bss:  97.13   1.88  15.88  97.13   1.88  11.96  89.17   5.37  37.20
------------------------------------------------------------------------
 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:    1.139    0.005    0.400
   1_adp:    1.139    0.005    0.400
   1_occ:    1.139    0.005    0.400
   2_bss:    1.139    0.005    0.400
   2_xyz:    1.602    0.019    0.598
   2_adp:    1.602    0.019    0.598
   2_occ:    1.602    0.019    0.598
   3_bss:    1.602    0.019    0.598
   3_xyz:    1.724    0.035    0.774
   3_adp:    1.724    0.035    0.774
   3_occ:    1.724    0.035    0.774
   4_bss:    1.724    0.035    0.774
   4_xyz:    2.004    0.032    0.893
   4_adp:    2.004    0.032    0.893
   4_occ:    2.004    0.032    0.893
   5_bss:    2.004    0.032    0.893
   5_xyz:    2.082    0.049    0.957
   5_adp:    2.082    0.049    0.957
   5_occ:    2.082    0.049    0.957
   5_bss:    2.082    0.049    0.957
------------------------------------------------------------------------

CPU time actual refinement: 369.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_114/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_114/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_114/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_114/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_114/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 369.35 
  Macro-tasks:
    bulk solvent and scale       = 46.21  
    individual site refinement   = 168.16 
    weights calculation          = 32.60  
    collect and process          = 6.38   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 253.49 
  Micro-tasks:
    mask                            = 3.07   
    f_calc                          = 116.16 
    alpha_beta                      = 8.60   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 129.18 
    fmodel                         = 8.04   
    r_factors                      = 0.28   
    phase_errors                   = 9.62   
    foms                           = 0.29   
    TOTAL for micro-tasks          = 276.40 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.009 micro seconds
Total CPU time: 6.39 minutes
from_scatterers_fft:    657 calls, 115.73 s
gradients_fft:          601 calls, 114.48 s

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

# Date 2008-01-16 Time 00:46:09 PST -0800 (1200473169.75 s)
Start R-work = 0.5195, R-free = 0.5035 (no bulk solvent and anisotropic scale)
Final R-work = 0.1664, R-free = 0.2079 (no bulk solvent and anisotropic scale)

Start R-work = 0.5133, R-free = 0.4999
Final R-work = 0.1465, R-free = 0.1901