# Date 2008-01-16 Time 01:34:42 PST -0800 (1200476082.66 s)
#phil __OFF__

Command line arguments: "../488.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 = 28709
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 488

-------------------------------------------------------------------------------
  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: (69.8988, 45.7567, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (69.8988, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.95292
Completeness in resolution range: 0.951292
Completeness with d_max=infinity: 0.948436

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9529

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: (69.8988, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.95292
Completeness in resolution range: 0.951292
Completeness with d_max=infinity: 0.948436

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.1795 [2165/2190]  1946   219  10.1%
  bin  2:  4.1795 -  3.3295 [2075/2095]  1871   204   9.8%
  bin  3:  3.3295 -  2.9122 [2058/2077]  1850   208  10.1%
  bin  4:  2.9122 -  2.6476 [2029/2059]  1827   202  10.0%
  bin  5:  2.6476 -  2.4587 [2014/2033]  1817   197   9.8%
  bin  6:  2.4587 -  2.3143 [2014/2039]  1809   205  10.2%
  bin  7:  2.3143 -  2.1988 [1995/2023]  1794   201  10.1%
  bin  8:  2.1988 -  2.1033 [1991/2027]  1792   199  10.0%
  bin  9:  2.1033 -  2.0226 [1988/2030]  1791   197   9.9%
  bin 10:  2.0226 -  1.9529 [1260/2019]  1133   127  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_488/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 30
        2.26 -     2.92: 1550
        2.92 -     3.58: 4591
        3.58 -     4.24: 9390
        4.24 -     4.90: 13228
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.602 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.602 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28784 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_488/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_488/model_refine_001.geo

CPU time processing inputs: 9.53


============================ 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 = 69.89875 45.75675 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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4887   r_free= 0.4868   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.295577                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.6619 0.99   1404  156 0.4255 0.4293      6.6344      6.7117|
|  2:  4.6619 -  3.7192 0.99   1348  151 0.4279 0.3851      6.8384      6.7573|
|  3:  3.7192 -  3.2546 0.99   1328  143 0.4507 0.4265      6.7049      6.7187|
|  4:  3.2546 -  2.9596 0.99   1325  153 0.4830 0.4570      6.5549      6.4976|
|  5:  2.9596 -  2.7489 0.99   1311  146 0.5116 0.5250      6.3747      6.4111|
|  6:  2.7489 -  2.5877 0.99   1307  142 0.5188 0.5541      6.2924      6.2172|
|  7:  2.5877 -  2.4587 0.99   1288  139 0.5110 0.4882      6.2549       6.211|
|  8:  2.4587 -  2.3521 0.98   1286  146 0.5365 0.5203      6.1842      6.1879|
|  9:  2.3521 -  2.2619 0.98   1270  147 0.5165 0.5431      6.1182      6.1661|
| 10:  2.2619 -  2.1841 1.00   1305  142 0.5301 0.5541      6.1125      6.0947|
| 11:  2.1841 -  2.1160 0.98   1283  138 0.5050 0.4742      6.0369      6.0605|
| 12:  2.1160 -  2.0556 0.98   1260  147 0.5129 0.5763      5.9684      6.0233|
| 13:  2.0556 -  2.0016 0.99   1289  135 0.5377 0.5078      5.8756      5.8092|
| 14:  2.0016 -  1.9529 0.48    626   74 0.5533 0.5077      5.8978      5.8106|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.6619  1404   156  0.60  42.93   0.78     0.66     104047.40|
|  2:  4.6619 -  3.7192  1348   151  0.66  38.44   0.85     0.75     125270.36|
|  3:  3.7192 -  3.2546  1328   143  0.57  46.34   0.86     0.71     125879.13|
|  4:  3.2546 -  2.9596  1325   153  0.47  54.03   0.80     0.57     109985.82|
|  5:  2.9596 -  2.7489  1311   146  0.35  63.61   0.74     0.44      92115.50|
|  6:  2.7489 -  2.5877  1307   142  0.31  66.59   0.72     0.36      80534.98|
|  7:  2.5877 -  2.4587  1288   139  0.27  69.63   0.76     0.32      74136.06|
|  8:  2.4587 -  2.3521  1286   146  0.26  70.54   0.73     0.31      66431.87|
|  9:  2.3521 -  2.2619  1270   147  0.29  68.48   0.74     0.34      59046.29|
| 10:  2.2619 -  2.1841  1305   142  0.30  67.40   0.76     0.37      51181.06|
| 11:  2.1841 -  2.1160  1283   138  0.28  68.93   0.79     0.35      50506.77|
| 12:  2.1160 -  2.0556  1260   147  0.24  72.41   0.80     0.31      47839.86|
| 13:  2.0556 -  2.0016  1289   135  0.23  73.28   0.72     0.30      41609.67|
| 14:  2.0016 -  1.9529   626    74  0.33  65.15   0.75     0.38      30574.73|
|alpha:            min =        0.30 max =            0.75 mean =         0.45|
|beta:             min =    30574.73 max =       125879.13 mean =     77959.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.98 mean =        61.59|
|phase err.(test): min =        0.00 max =           89.99 mean =        61.70|
|-----------------------------------------------------------------------------|

============================== 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 = 20.410936             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.285   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.729309              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.625   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      177 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      724 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1536 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2691 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4011 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5162 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6625 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7876 |
|-----------------------------------------------------------------------------|
|-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 |       53.000 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.480 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    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 = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4935   r_free= 0.4873   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.296693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4803   r_free= 0.4750   ksol= 0.38   Bsol= 4.11   scale= 0.978    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.38,9.95,7.27,0.00,0.00,0.00); trace/3= 7.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.289565                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.595197             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.147   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.664109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4803      final r-factor (work) = 0.4163          |
| start r-factor (free) = 0.4750      final r-factor (free) = 0.4473          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 105.2100 = 16.60 * 0.50 * 6.2921 + 1.00 * 53.0003                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.8942 = 16.60 * 0.50 * 6.2369 + 1.00 * 0.1431                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4163      final r-factor (work) = 0.3783          |
| start r-factor (free) = 0.4473      final r-factor (free) = 0.4421          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3933 = 1.66 * 1.00 * 6.2369 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3102 = 1.66 * 1.00 * 6.1836 + 1.00 * 0.0200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.79   14.08    None  None   None       |
|    all(noH): 2823   0      0.00    71.79   14.08    None  None   None       |
|    Sol.    : 438    0      0.00    66.85   21.74    None  None   None       |
|    Mac.    : 2385   0      0.00    71.79   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.179:  865   |   5:    35.897 -  43.077:   83        |
|      1:     7.179 -  14.359:  797   |   6:    43.077 -  50.256:   24        |
|      2:    14.359 -  21.538:  557   |   7:    50.256 -  57.435:   17        |
|      3:    21.538 -  28.718:  294   |   8:    57.435 -  64.615:    3        |
|      4:    28.718 -  35.897:  178   |   9:    64.615 -  71.794:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3783 r_free = 0.4421             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3776 r_free = 0.4424             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3776   r_free= 0.4424   ksol= 0.38   Bsol= 4.11   scale= 1.093    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.38,9.95,7.27,0.00,0.00,0.00); trace/3= 7.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.174520                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3757   r_free= 0.4388   ksol= 0.37   Bsol= 34.32   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,6.02,4.33,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.174788                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.221222              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.767  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.802031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.114  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3757      final r-factor (work) = 0.3347          |
| start r-factor (free) = 0.4388      final r-factor (free) = 0.4098          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6326 = 9.22 * 0.50 * 6.1791 + 1.00 * 0.1431                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3296 = 9.22 * 0.50 * 6.1259 + 1.00 * 0.0855                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3347      final r-factor (work) = 0.3214          |
| start r-factor (free) = 0.4098      final r-factor (free) = 0.3977          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9371 = 0.80 * 1.00 * 6.1259 + 1.00 * 0.0240                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8851 = 0.80 * 1.00 * 6.0752 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.85   13.60    None  None   None       |
|    all(noH): 2823   0      0.00    76.85   13.60    None  None   None       |
|    Sol.    : 438    0      0.00    74.09   24.19    None  None   None       |
|    Mac.    : 2385   0      0.00    76.85   11.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.686: 1027   |   5:    38.427 -  46.113:   55        |
|      1:     7.686 -  15.371:  831   |   6:    46.113 -  53.798:   26        |
|      2:    15.371 -  23.056:  468   |   7:    53.798 -  61.483:    8        |
|      3:    23.056 -  30.742:  274   |   8:    61.483 -  69.169:    3        |
|      4:    30.742 -  38.427:  127   |   9:    69.169 -  76.854:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3214 r_free = 0.3977             target_work(ml) = 6.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3211 r_free = 0.3980             target_work(ml) = 6.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3211   r_free= 0.3980   ksol= 0.37   Bsol= 34.32   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,6.02,4.33,0.00,0.00,0.00); trace/3= 4.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.063835                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3217   r_free= 0.3954   ksol= 0.34   Bsol= 34.32   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,4.31,3.65,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.064467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.421325              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.955  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.007909              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3217      final r-factor (work) = 0.2645          |
| start r-factor (free) = 0.3954      final r-factor (free) = 0.3389          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.6664 = 8.42 * 0.50 * 6.0753 + 1.00 * 0.0855                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.3274 = 8.42 * 0.50 * 5.9891 + 1.00 * 0.1093                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2645      final r-factor (work) = 0.2412          |
| start r-factor (free) = 0.3389      final r-factor (free) = 0.3235          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0489 = 1.01 * 1.00 * 5.9891 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9246 = 1.01 * 1.00 * 5.8626 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.88   14.40    None  None   None       |
|    all(noH): 2823   0      0.00    81.88   14.40    None  None   None       |
|    Sol.    : 438    0      0.00    80.28   33.37    None  None   None       |
|    Mac.    : 2385   0      0.00    81.88   10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.189: 1215   |   5:    40.942 -  49.131:   87        |
|      1:     8.189 -  16.377:  734   |   6:    49.131 -  57.319:   49        |
|      2:    16.377 -  24.565:  368   |   7:    57.319 -  65.508:   23        |
|      3:    24.565 -  32.754:  180   |   8:    65.508 -  73.696:    8        |
|      4:    32.754 -  40.942:  155   |   9:    73.696 -  81.885:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2412 r_free = 0.3235             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2408 r_free = 0.3236             target_work(ml) = 5.838         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2408   r_free= 0.3236   ksol= 0.34   Bsol= 34.32   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,4.31,3.65,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.838326                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2398   r_free= 0.3218   ksol= 0.32   Bsol= 38.52   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.97,2.51,2.91,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.834492                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.712617              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.975   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.256683              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.910  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2398      final r-factor (work) = 0.1926          |
| start r-factor (free) = 0.3218      final r-factor (free) = 0.2569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8512 = 5.71 * 0.50 * 5.8614 + 1.00 * 0.1093                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4880 = 5.71 * 0.50 * 5.7479 + 1.00 * 0.0703                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1926      final r-factor (work) = 0.1774          |
| start r-factor (free) = 0.2569      final r-factor (free) = 0.2319          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4909 = 0.26 * 1.00 * 5.7479 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4514 = 0.26 * 1.00 * 5.5882 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.23   13.59    None  None   None       |
|    all(noH): 2823   0      0.00    81.23   13.59    None  None   None       |
|    Sol.    : 438    0      2.21    76.59   34.96    None  None   None       |
|    Mac.    : 2385   0      0.00    81.23   9.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.123: 1371   |   5:    40.615 -  48.739:  116        |
|      1:     8.123 -  16.246:  742   |   6:    48.739 -  56.862:   51        |
|      2:    16.246 -  24.369:  238   |   7:    56.862 -  64.985:   14        |
|      3:    24.369 -  32.492:  147   |   8:    64.985 -  73.108:    7        |
|      4:    32.492 -  40.615:  133   |   9:    73.108 -  81.231:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1774 r_free = 0.2319             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1770 r_free = 0.2309             target_work(ml) = 5.539         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1770   r_free= 0.2309   ksol= 0.32   Bsol= 38.52   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.97,2.51,2.91,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.538735                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1768   r_free= 0.2306   ksol= 0.32   Bsol= 35.96   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.34,1.38,2.59,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.537573                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.916104              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.588  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.269098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.303   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1768      final r-factor (work) = 0.1500          |
| start r-factor (free) = 0.2306      final r-factor (free) = 0.2000          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4241 = 1.92 * 0.50 * 5.5882 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2910 = 1.92 * 0.50 * 5.4682 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1500      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.2000      final r-factor (free) = 0.1945          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4847 = 0.27 * 1.00 * 5.4682 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4560 = 0.27 * 1.00 * 5.3748 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.72   13.56    None  None   None       |
|    all(noH): 2823   0      0.00    82.72   13.56    None  None   None       |
|    Sol.    : 438    0      2.58    78.85   36.91    None  None   None       |
|    Mac.    : 2385   0      0.00    82.72   9.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.272: 1453   |   5:    41.361 -  49.633:  104        |
|      1:     8.272 -  16.544:  729   |   6:    49.633 -  57.905:   78        |
|      2:    16.544 -  24.817:  187   |   7:    57.905 -  66.178:   23        |
|      3:    24.817 -  33.089:  123   |   8:    66.178 -  74.450:    7        |
|      4:    33.089 -  41.361:  114   |   9:    74.450 -  82.722:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1433 r_free = 0.1945             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1430 r_free = 0.1939             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1430   r_free= 0.1939   ksol= 0.32   Bsol= 35.96   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.34,1.38,2.59,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.356852                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.6619 0.99   1404  156 0.1124 0.1485      5.4959      5.6749|
|  2:  4.6619 -  3.7192 0.99   1348  151 0.1058 0.1447      5.6208      5.8699|
|  3:  3.7192 -  3.2546 0.99   1328  143 0.1366 0.1701      5.6925      5.9712|
|  4:  3.2546 -  2.9596 0.99   1325  153 0.1600 0.2049      5.6821       5.808|
|  5:  2.9596 -  2.7489 0.99   1311  146 0.1708 0.2264       5.558      5.7918|
|  6:  2.7489 -  2.5877 0.99   1307  142 0.1552 0.2347      5.4145       5.631|
|  7:  2.5877 -  2.4587 0.99   1288  139 0.1616 0.1969       5.389       5.522|
|  8:  2.4587 -  2.3521 0.98   1286  146 0.1576 0.2224      5.3187      5.5857|
|  9:  2.3521 -  2.2619 0.98   1270  147 0.1531 0.2164      5.2603      5.4775|
| 10:  2.2619 -  2.1841 1.00   1305  142 0.1470 0.2213      5.1657      5.4338|
| 11:  2.1841 -  2.1160 0.98   1283  138 0.1455 0.2101      5.1484      5.4052|
| 12:  2.1160 -  2.0556 0.98   1260  147 0.1529 0.2172      5.0994      5.3886|
| 13:  2.0556 -  2.0016 0.99   1289  135 0.1500 0.2104      4.9812      5.1932|
| 14:  2.0016 -  1.9529 0.48    626   74 0.1304 0.1710      4.8599      5.0107|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.6619  1404   156  0.93  11.00   0.98     0.96       9292.48|
|  2:  4.6619 -  3.7192  1348   151  0.94  10.46   1.03     1.01      12674.87|
|  3:  3.7192 -  3.2546  1328   143  0.90  15.21   1.05     1.04      16012.75|
|  4:  3.2546 -  2.9596  1325   153  0.88  18.14   1.02     0.99      16071.80|
|  5:  2.9596 -  2.7489  1311   146  0.86  20.07   1.00     0.97      13080.34|
|  6:  2.7489 -  2.5877  1307   142  0.85  21.01   0.99     0.94      10703.48|
|  7:  2.5877 -  2.4587  1288   139  0.86  20.69   1.01     0.96       9948.25|
|  8:  2.4587 -  2.3521  1286   146  0.86  20.82   1.01     0.98       8998.77|
|  9:  2.3521 -  2.2619  1270   147  0.87  19.97   1.01     0.95       7926.90|
| 10:  2.2619 -  2.1841  1305   142  0.86  20.61   1.02     0.97       6768.36|
| 11:  2.1841 -  2.1160  1283   138  0.87  20.07   1.03     0.97       6648.89|
| 12:  2.1160 -  2.0556  1260   147  0.87  20.09   1.03     1.01       6058.66|
| 13:  2.0556 -  2.0016  1289   135  0.86  20.58   1.02     0.98       4774.00|
| 14:  2.0016 -  1.9529   626    74  0.90  16.73   1.01     0.97       3496.34|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     3496.34 max =        16071.80 mean =      9734.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.86 mean =        18.22|
|phase err.(test): min =        0.00 max =           89.92 mean =        17.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1433   r_free= 0.1939   ksol= 0.32   Bsol= 37.55   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.53,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.356140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1433   r_free= 0.1939   ksol= 0.32   Bsol= 37.55   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,-0.53,0.91,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.356140                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.6619 0.99   1404  156 0.1122 0.1458      5.4876      5.6675|
|  2:  4.6619 -  3.7192 0.99   1348  151 0.1066 0.1464      5.6233      5.8837|
|  3:  3.7192 -  3.2546 0.99   1328  143 0.1372 0.1702      5.6967      5.9733|
|  4:  3.2546 -  2.9596 0.99   1325  153 0.1604 0.2056      5.6834      5.8102|
|  5:  2.9596 -  2.7489 0.99   1311  146 0.1715 0.2255      5.5583      5.7889|
|  6:  2.7489 -  2.5877 0.99   1307  142 0.1550 0.2342      5.4133      5.6297|
|  7:  2.5877 -  2.4587 0.99   1288  139 0.1619 0.1965      5.3883      5.5208|
|  8:  2.4587 -  2.3521 0.98   1286  146 0.1575 0.2227       5.317      5.5856|
|  9:  2.3521 -  2.2619 0.98   1270  147 0.1533 0.2149        5.26      5.4737|
| 10:  2.2619 -  2.1841 1.00   1305  142 0.1465 0.2221      5.1645      5.4367|
| 11:  2.1841 -  2.1160 0.98   1283  138 0.1451 0.2101       5.148       5.406|
| 12:  2.1160 -  2.0556 0.98   1260  147 0.1525 0.2176      5.0989       5.389|
| 13:  2.0556 -  2.0016 0.99   1289  135 0.1498 0.2094      4.9797      5.1895|
| 14:  2.0016 -  1.9529 0.48    626   74 0.1300 0.1706      4.8567      5.0078|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.6619  1404   156  0.93  10.81   0.98     0.96       9070.39|
|  2:  4.6619 -  3.7192  1348   151  0.94  10.45   1.03     1.01      12660.37|
|  3:  3.7192 -  3.2546  1328   143  0.90  15.32   1.04     1.03      16208.14|
|  4:  3.2546 -  2.9596  1325   153  0.88  18.21   1.02     0.98      16147.88|
|  5:  2.9596 -  2.7489  1311   146  0.86  20.08   0.99     0.97      13008.70|
|  6:  2.7489 -  2.5877  1307   142  0.86  20.95   0.98     0.93      10660.09|
|  7:  2.5877 -  2.4587  1288   139  0.86  20.64   1.00     0.96       9899.89|
|  8:  2.4587 -  2.3521  1286   146  0.86  20.82   1.00     0.97       8976.44|
|  9:  2.3521 -  2.2619  1270   147  0.87  19.94   1.00     0.94       7911.90|
| 10:  2.2619 -  2.1841  1305   142  0.86  20.59   1.01     0.96       6765.83|
| 11:  2.1841 -  2.1160  1283   138  0.87  20.09   1.02     0.96       6659.96|
| 12:  2.1160 -  2.0556  1260   147  0.87  20.08   1.02     1.00       6061.14|
| 13:  2.0556 -  2.0016  1289   135  0.86  20.54   1.00     0.97       4754.15|
| 14:  2.0016 -  1.9529   626    74  0.90  16.60   1.00     0.96       3459.07|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3459.07 max =        16208.14 mean =      9719.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.21|
|phase err.(test): min =        0.00 max =           89.82 mean =        17.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.463)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    84.31   15.15    None  None   None       |
|    all(noH): 2823   0      1.59    84.31   15.15    None  None   None       |
|    Sol.    : 438    0      4.17    80.44   38.49    None  None   None       |
|    Mac.    : 2385   0      1.59    84.31   10.86    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:     1.588 -   9.860: 1453   |   5:    42.949 -  51.221:  104        |
|      1:     9.860 -  18.132:  729   |   6:    51.221 -  59.493:   78        |
|      2:    18.132 -  26.404:  187   |   7:    59.493 -  67.765:   23        |
|      3:    26.404 -  34.676:  123   |   8:    67.765 -  76.037:    7        |
|      4:    34.676 -  42.949:  114   |   9:    76.037 -  84.310:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.342 - 5.642
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 334
   mapped sites are within: 0.751 - 5.642

peak=    7.979 closest distance to " CB  VAL A 230 " =    1.476
peak=    7.814 closest distance to " O   HOH Z 390 " =    1.323
peak=    7.133 closest distance to " O   HOH Z 268 " =    1.300
peak=    7.001 closest distance to " O   HOH Z  15 " =    1.229
peak=    6.528 closest distance to " O   HOH Z 387 " =    1.838
peak=    6.485 closest distance to " O   HOH Z 130 " =    1.870
peak=    6.266 closest distance to " CG  ARG A 138 " =    1.202
peak=    6.228 closest distance to " OD1 ASP A  27 " =    1.061
peak=    6.092 closest distance to " CD2 LEU A   5 " =    1.572
peak=    5.866 closest distance to " NH1 ARG A 138 " =    1.000
peak=    5.811 closest distance to " NH2 ARG A  56 " =    2.100
peak=    5.703 closest distance to " CG1 VAL A 296 " =    1.152
peak=    5.599 closest distance to " O   HOH Z 415 " =    1.408
peak=    5.555 closest distance to " CD1AILE A 234 " =    1.021
peak=    5.504 closest distance to " O   HOH Z  46 " =    1.356
peak=    5.314 closest distance to " O   HOH Z  65 " =    1.881
peak=    5.289 closest distance to " O   HOH Z   7 " =    2.021
peak=    5.235 closest distance to " CD  ARG A 138 " =    0.883
peak=    5.187 closest distance to " O   PRO A 198 " =    1.474
peak=    5.148 closest distance to " O   HOH Z 350 " =    1.349
peak=    5.122 closest distance to " CB  SER A   3 " =    1.434
peak=    5.083 closest distance to " NZ BLYS A 290 " =    1.101
peak=    5.081 closest distance to " CB  ARG A 275 " =    1.207
peak=    5.074 closest distance to " O   HOH Z   9 " =    1.715
peak=    5.053 closest distance to " O   HOH Z  24 " =    2.090
peak=    5.047 closest distance to " O   HOH Z 403 " =    1.705
peak=    5.027 closest distance to " O   HOH Z 124 " =    1.755
peak=    4.984 closest distance to " CB  VAL A 296 " =    1.248
peak=    4.944 closest distance to " O   HOH Z 418 " =    1.557
peak=    4.936 closest distance to " O   HOH Z 358 " =    1.457
peak=    4.926 closest distance to " O   HOH Z 289 " =    1.341
peak=    4.918 closest distance to " O   HOH Z 142 " =    1.980
peak=    4.849 closest distance to " O   HOH Z  27 " =    1.177
peak=    4.842 closest distance to " O   HOH Z 225 " =    1.809
peak=    4.826 closest distance to " O   HOH Z 428 " =    1.755
peak=    4.777 closest distance to " O   HOH Z 222 " =    1.527
peak=    4.770 closest distance to " O   HOH Z 381 " =    1.070
peak=    4.762 closest distance to " O   HOH Z 417 " =    1.777
peak=    4.761 closest distance to " O   HOH Z 422 " =    1.207
peak=    4.752 closest distance to " CB  VAL A 230 " =    1.273
peak=    4.721 closest distance to " O   HOH Z 139 " =    1.837
peak=    4.717 closest distance to " CG  PRO A 280 " =    0.991
peak=    4.712 closest distance to " O   HOH Z 375 " =    1.312
peak=    4.700 closest distance to " NE2 GLN A  11 " =    1.260
peak=    4.699 closest distance to " O   HOH Z 400 " =    0.873
peak=    4.629 closest distance to " O  BHOH Z  74 " =    1.180
peak=    4.552 closest distance to " O   HOH Z 112 " =    1.559
peak=    4.531 closest distance to " O   HOH Z 389 " =    1.704
peak=    4.508 closest distance to " O   HOH Z 423 " =    1.883
peak=    4.505 closest distance to " CB  PRO A  54 " =    1.177
peak=    4.505 closest distance to " N   GLN A 278 " =    0.954
peak=    4.501 closest distance to " CG2 VAL A 296 " =    0.960
peak=    4.478 closest distance to " O   HOH Z  69 " =    2.279
peak=    4.477 closest distance to " O   HOH Z 410 " =    1.521
peak=    4.443 closest distance to " O   HOH Z  28 " =    1.581
peak=    4.420 closest distance to " O   HOH Z 215 " =    1.552
peak=    4.404 closest distance to " O   HOH Z 425 " =    1.689
peak=    4.395 closest distance to " O   HOH Z  63 " =    1.744
peak=    4.393 closest distance to " CB  SER A 216 " =    0.985
peak=    4.388 closest distance to " O   HOH Z 232 " =    2.193
peak=    4.378 closest distance to " O   HOH Z  78 " =    1.939
peak=    4.345 closest distance to " O   HOH Z  59 " =    1.504
peak=    4.342 closest distance to " O   HOH Z 426 " =    1.178
peak=    4.333 closest distance to " O   HOH Z 371 " =    3.035
peak=    4.331 closest distance to " OE1 GLU A   2 " =    1.984
peak=    4.325 closest distance to " O   HOH Z 133 " =    1.396
peak=    4.322 closest distance to " O   HOH Z 263 " =    1.610
peak=    4.309 closest distance to " CG  LEU A   5 " =    1.294
peak=    4.303 closest distance to " O   HOH Z 127 " =    1.136
peak=    4.276 closest distance to " NH2BARG A 145 " =    1.450
peak=    4.266 closest distance to " OG  SER A 276 " =    0.956
peak=    4.248 closest distance to " O   HOH Z  65 " =    1.520
peak=    4.245 closest distance to " O   HOH Z 416 " =    1.408
peak=    4.234 closest distance to " O   VAL A  72 " =    0.969
peak=    4.204 closest distance to " O   HOH Z 428 " =    1.202
peak=    4.169 closest distance to " O   HOH Z 123 " =    1.392
peak=    4.167 closest distance to " O   HOH Z 356 " =    1.935
peak=    4.151 closest distance to " O   HOH Z 132 " =    1.157
peak=    4.142 closest distance to " O   HOH Z 361 " =    1.711
peak=    4.128 closest distance to " CB  GLU A 277 " =    1.024
peak=    4.095 closest distance to " CE  MET A  93 " =    1.456
peak=    4.081 closest distance to " O   HOH Z 236 " =    1.629
peak=    4.076 closest distance to " O   HOH Z 257 " =    2.263
peak=    4.071 closest distance to " O   HOH Z 214 " =    1.262
peak=    4.068 closest distance to " O   ARG A 275 " =    0.958
peak=    4.068 closest distance to " O   HOH Z  54 " =    1.209
peak=    4.066 closest distance to " CB  GLN A 223 " =    1.495
peak=    4.060 closest distance to " CB  ASN A 148 " =    1.421
peak=    4.059 closest distance to " CB  ALA A 114 " =    1.235
peak=    4.044 closest distance to " O   HOH Z 427 " =    1.262
peak=    4.033 closest distance to " O   HOH Z 419 " =    2.202
peak=    4.027 closest distance to " NE1 TRP A 274 " =    1.145
peak=    4.002 closest distance to " O   HOH Z 363 " =    1.233
peak=    3.993 closest distance to " O   HOH Z 193 " =    1.570
peak=    3.990 closest distance to " CA  ILE A 234 " =    1.067
peak=    3.980 closest distance to " CB  GLU A 128 " =    0.884
peak=    3.956 closest distance to " O   HOH Z 293 " =    1.515
peak=    3.948 closest distance to " O   HOH Z 287 " =    1.764
peak=    3.943 closest distance to " N   GLU A   2 " =    1.324
peak=    3.934 closest distance to " CD2 LEU A 297 " =    0.940
peak=    3.929 closest distance to " CD1 LEU A   5 " =    1.406
peak=    3.926 closest distance to " CB  SER A  62 " =    1.211
peak=    3.925 closest distance to " O   HOH Z  47 " =    1.645
peak=    3.925 closest distance to " CA  ASN A 284 " =    0.964
peak=    3.921 closest distance to " O   HOH Z 402 " =    1.612
peak=    3.916 closest distance to " CB  ASP A 124 " =    1.045
peak=    3.916 closest distance to " O   HOH Z 158 " =    2.800
peak=    3.914 closest distance to " O   HOH Z 399 " =    0.908
peak=    3.901 closest distance to " O   HOH Z 359 " =    1.441
peak=    3.899 closest distance to " O   HOH Z   2 " =    1.718
peak=    3.897 closest distance to " O   HOH Z 126 " =    1.836
peak=    3.887 closest distance to " N   ARG A 275 " =    0.863
peak=    3.885 closest distance to " O   HOH Z 130 " =    2.198
peak=    3.884 closest distance to " O   HOH Z 366 " =    2.755
peak=    3.866 closest distance to " O   HOH Z 380 " =    2.349
peak=    3.865 closest distance to " O   HOH Z 369 " =    1.959
peak=    3.865 closest distance to " CG  LEU A 228 " =    1.121
peak=    3.859 closest distance to " N   TYR A  15 " =    0.935
peak=    3.856 closest distance to " CG2 ILE A 234 " =    0.891
peak=    3.855 closest distance to " O   HOH Z 316 " =    3.015
peak=    3.843 closest distance to " O   HOH Z 344 " =    1.259
peak=    3.833 closest distance to " CG1AVAL A 121 " =    0.838
peak=    3.831 closest distance to " O   HOH Z 414 " =    1.708
peak=    3.829 closest distance to " O   HOH Z 427 " =    2.060
peak=    3.827 closest distance to " O   HOH Z 244 " =    1.390
peak=    3.824 closest distance to " OD1 ASN A  45 " =    1.149
peak=    3.818 closest distance to " O   HOH Z 137 " =    1.620
peak=    3.804 closest distance to " NZ  LYS A 117 " =    1.266
peak=    3.799 closest distance to " OD1 ASP A 286 " =    1.126
peak=    3.795 closest distance to " O   HOH Z 371 " =    1.958
peak=    3.782 closest distance to " O   HOH Z 105 " =    1.159
peak=    3.781 closest distance to " O   HOH Z 422 " =    2.388
peak=    3.770 closest distance to " O   HOH Z 272 " =    1.853
peak=    3.746 closest distance to " O   HOH Z 143 " =    1.597
peak=    3.744 closest distance to " NE2 GLN A  58 " =    5.523
peak=    3.743 closest distance to " O   HOH Z  51 " =    1.527
peak=    3.733 closest distance to " CA  LEU A 282 " =    1.076
peak=    3.731 closest distance to " O   ASN A 285 " =    0.939
peak=    3.716 closest distance to " O   HOH Z  77 " =    1.210
peak=    3.703 closest distance to " O   HOH Z 434 " =    1.401
peak=    3.691 closest distance to " O   HOH Z 119 " =    1.498
peak=    3.683 closest distance to " NE2 GLN A  73 " =    1.619
peak=    3.682 closest distance to " O   HOH Z  61 " =    1.500
peak=    3.677 closest distance to " OG  SER A  62 " =    3.106
peak=    3.676 closest distance to " O   HOH Z 172 " =    1.549
peak=    3.676 closest distance to " O   HOH Z 151 " =    1.685
peak=    3.669 closest distance to " CB  TRP A 266 " =    0.886
peak=    3.669 closest distance to " CG  PRO A  54 " =    1.366
peak=    3.665 closest distance to " CG  PRO A 243 " =    1.163
peak=    3.665 closest distance to " O   HOH Z 128 " =    2.105
peak=    3.659 closest distance to " CG  ARG A 156 " =    1.226
peak=    3.656 closest distance to " CB  LYS A 290 " =    0.789
peak=    3.656 closest distance to " NH2 ARG A 269 " =    0.971
peak=    3.655 closest distance to " ND2BASN A 224 " =    0.813
peak=    3.647 closest distance to " O   HOH Z  91 " =    2.540
peak=    3.636 closest distance to " O   HOH Z   1 " =    1.828
peak=    3.624 closest distance to " CB  ASN A 187 " =    0.982
peak=    3.622 closest distance to " CA  ARG A  36 " =    0.981
peak=    3.617 closest distance to " O   HOH Z 405 " =    2.016
peak=    3.612 closest distance to " O   HOH Z 357 " =    1.553
peak=    3.598 closest distance to " NH2 ARG A 138 " =    1.258
peak=    3.590 closest distance to " O   HOH Z 114 " =    2.012
peak=    3.589 closest distance to " NH2AARG A 145 " =    2.213
peak=    3.581 closest distance to " NE AARG A 275 " =    1.457
peak=    3.579 closest distance to " CG1BVAL A 121 " =    2.251
peak=    3.578 closest distance to " CB  LEU A 300 " =    0.894
peak=    3.575 closest distance to " CA  ASN A 127 " =    1.045
peak=    3.549 closest distance to " O   HOH Z 213 " =    1.736
peak=    3.541 closest distance to " O   HOH Z 178 " =    1.251
peak=    3.526 closest distance to " CA  ALA A 158 " =    1.037
peak=    3.525 closest distance to " CD2 LEU A 228 " =    1.465
peak=    3.525 closest distance to " CB  VAL A 265 " =    1.342
peak=    3.524 closest distance to " CZ3 TRP A 274 " =    1.443
peak=    3.521 closest distance to " O   HOH Z 353 " =    1.985
peak=    3.517 closest distance to " O   HOH Z 240 " =    2.104
peak=    3.517 closest distance to " CG1 ILE A 120 " =    1.482
peak=    3.513 closest distance to " CB  SER A 210 " =    0.979
peak=    3.511 closest distance to " OG BSER A 258 " =    1.058
peak=    3.501 closest distance to " N   CYS A 260 " =    1.111
peak=    3.499 closest distance to " O   HOH Z  58 " =    1.883
peak=    3.498 closest distance to " O   HOH Z 125 " =    1.802
peak=    3.492 closest distance to " O   HOH Z 153 " =    3.567
peak=    3.492 closest distance to " CA  ALA A 295 " =    0.900
peak=    3.490 closest distance to " O   HOH Z   1 " =    1.577
peak=    3.490 closest distance to " O   HOH Z 406 " =    1.728
peak=    3.483 closest distance to " N   GLN A  73 " =    1.099
peak=    3.481 closest distance to " O   HOH Z 233 " =    1.484
peak=    3.478 closest distance to " O   HOH Z   7 " =    3.254
peak=    3.476 closest distance to " O   HOH Z 362 " =    1.881
peak=    3.473 closest distance to " O   GLY A  17 " =    1.264
peak=    3.473 closest distance to " CG  TRP A 179 " =    2.253
peak=    3.473 closest distance to " CG2 THR A 178 " =    1.183
peak=    3.469 closest distance to " CA  ARG A 195 " =    1.301
peak=    3.462 closest distance to " O   HOH Z  22 " =    1.979
peak=    3.461 closest distance to " O   HOH Z 392 " =    1.680
peak=    3.459 closest distance to " O   HOH Z  95 " =    1.603
peak=    3.457 closest distance to " CG2 THR A 221 " =    1.457
peak=    3.454 closest distance to " O   HOH Z  11 " =    1.640
peak=    3.452 closest distance to " N   GLY A 136 " =    1.134
peak=    3.452 closest distance to " O   HOH Z 434 " =    5.642
peak=    3.447 closest distance to " O   HOH Z 342 " =    1.003
peak=    3.442 closest distance to " CG  PRO A 213 " =    1.256
peak=    3.440 closest distance to " OG BSER A 212 " =    2.619
peak=    3.435 closest distance to " OD1 ASP A 238 " =    0.826
peak=    3.435 closest distance to " O   HOH Z 368 " =    1.724
peak=    3.434 closest distance to " N   PHE A 130 " =    1.232
peak=    3.432 closest distance to " O   HOH Z 425 " =    2.001
peak=    3.430 closest distance to " O   HOH Z  32 " =    1.781
peak=    3.430 closest distance to " CG  LEU A 167 " =    1.288
peak=    3.425 closest distance to " OE1 GLN A  73 " =    2.269
peak=    3.424 closest distance to " CB  ALA A 104 " =    0.772
peak=    3.423 closest distance to " CB  GLU A 277 " =    3.744
peak=    3.422 closest distance to " O   HOH Z 176 " =    2.074
peak=    3.418 closest distance to " CB  ASN A 148 " =    1.918
peak=    3.407 closest distance to " CG2 ILE A  49 " =    1.189
peak=    3.403 closest distance to " CG  GLN A 278 " =    3.931
peak=    3.403 closest distance to " N   ARG A 156 " =    1.331
peak=    3.398 closest distance to " O   HOH Z  69 " =    1.137
peak=    3.396 closest distance to " O   HOH Z  39 " =    1.390
peak=    3.392 closest distance to " O   HOH Z 180 " =    2.109
peak=    3.391 closest distance to " CG  GLN A  88 " =    0.964
peak=    3.391 closest distance to " O   HOH Z 360 " =    1.076
peak=    3.389 closest distance to " OG ASER A 134 " =    1.357
peak=    3.388 closest distance to " CB  SER A  63 " =    1.289
peak=    3.387 closest distance to " OD1 ASP A 200 " =    1.532
peak=    3.385 closest distance to " CD1 LEU A   5 " =    0.797
peak=    3.383 closest distance to " CA  ALA A  21 " =    1.042
peak=    3.371 closest distance to " O   HOH Z 214 " =    1.999
peak=    3.371 closest distance to " O   HOH Z 248 " =    2.010
peak=    3.365 closest distance to " O   HOH Z 128 " =    2.017
peak=    3.363 closest distance to " O   HOH Z 245 " =    1.384
peak=    3.353 closest distance to " O   HOH Z 298 " =    1.737
peak=    3.352 closest distance to " C   GLN A  73 " =    1.166
peak=    3.352 closest distance to " CB  GLU A 152 " =    1.256
peak=    3.348 closest distance to " N   VAL A 296 " =    1.694
peak=    3.346 closest distance to " O   HOH Z 264 " =    1.176
peak=    3.346 closest distance to " O   HOH Z  30 " =    1.265
peak=    3.336 closest distance to " CG1 ILE A  33 " =    1.354
peak=    3.335 closest distance to " CB  VAL A 202 " =    1.730
peak=    3.332 closest distance to " CB  GLN A 183 " =    1.024
peak=    3.327 closest distance to " CG  ASN A 301 " =    1.081
peak=    3.326 closest distance to " CD1 ILE A  33 " =    1.728
peak=    3.317 closest distance to " CD2 LEU A 167 " =    1.179
peak=    3.315 closest distance to " O   HOH Z 384 " =    1.617
peak=    3.314 closest distance to " N   SER A 210 " =    0.875
peak=    3.314 closest distance to " O   HOH Z 184 " =    1.492
peak=    3.311 closest distance to " CA  SER A  87 " =    1.003
peak=    3.311 closest distance to " O   HOH Z 147 " =    1.703
peak=    3.309 closest distance to " CG2AVAL A  72 " =    0.869
peak=    3.309 closest distance to " NH1 ARG A  14 " =    0.918
peak=    3.307 closest distance to " O   HOH Z   6 " =    2.082
peak=    3.303 closest distance to " O   HOH Z 226 " =    1.212
peak=    3.302 closest distance to " O   HOH Z  52 " =    1.178
peak=    3.299 closest distance to " CZ3 TRP A  70 " =    0.875
peak=    3.296 closest distance to " CB  ASP A 140 " =    0.890
peak=    3.295 closest distance to " O   HOH Z 197 " =    2.180
peak=    3.292 closest distance to " O   HOH Z 205 " =    1.260
peak=    3.290 closest distance to " CG2 THR A 294 " =    1.117
peak=    3.281 closest distance to " CB  LYS A 290 " =    0.907
peak=    3.277 closest distance to " O   HOH Z  66 " =    1.213
peak=    3.274 closest distance to " O   HOH Z 302 " =    1.604
peak=    3.265 closest distance to " N   GLY A 302 " =    0.960
peak=    3.261 closest distance to " ND2 ASN A 249 " =    0.751
peak=    3.260 closest distance to " CE1 TYR A  15 " =    1.169
peak=    3.258 closest distance to " NZ  LYS A  76 " =    1.381
peak=    3.257 closest distance to " CG  GLN A 205 " =    1.051
peak=    3.257 closest distance to " O   HOH Z   3 " =    1.555
peak=    3.253 closest distance to " CB  TRP A 179 " =    1.427
peak=    3.253 closest distance to " O   HOH Z  28 " =    1.947
peak=    3.246 closest distance to " N   SER A  97 " =    0.879
peak=    3.244 closest distance to " NH1AARG A 145 " =    0.842
peak=    3.243 closest distance to " O   HOH Z 323 " =    1.858
peak=    3.241 closest distance to " OE1 GLN A  77 " =    1.184
peak=    3.240 closest distance to " CE1 TYR A  68 " =    1.285
peak=    3.239 closest distance to " CA  ARG A 159 " =    1.218
peak=    3.231 closest distance to " O   HOH Z  88 " =    3.569
peak=    3.225 closest distance to " CB  PHE A 225 " =    1.400
peak=    3.219 closest distance to " O   HOH Z 389 " =    1.353
peak=    3.217 closest distance to " OG  SER A  22 " =    2.647
peak=    3.217 closest distance to " O   HOH Z 193 " =    1.964
peak=    3.217 closest distance to " CA  GLN A  55 " =    1.063
peak=    3.216 closest distance to " O   HOH Z 368 " =    3.298
peak=    3.216 closest distance to " CA  ALA A 292 " =    0.953
peak=    3.212 closest distance to " CG2 ILE A 120 " =    0.977
peak=    3.211 closest distance to " O   HOH Z 111 " =    1.829
peak=    3.210 closest distance to " O   HOH Z 120 " =    0.894
peak=    3.209 closest distance to " N   THR A 246 " =    1.410
peak=    3.208 closest distance to " CG2 THR A 279 " =    1.009
peak=    3.206 closest distance to " O   HOH Z  61 " =    1.904
peak=    3.202 closest distance to " O   HOH Z 211 " =    1.282
peak=    3.200 closest distance to " ND1 HIS A  81 " =    1.474
peak=    3.188 closest distance to " CG2 THR A 251 " =    1.718
peak=    3.187 closest distance to " O   HOH Z 204 " =    1.170
peak=    3.178 closest distance to " CE3 TRP A 274 " =    2.127
peak=    3.177 closest distance to " O   HOH Z 222 " =    2.022
peak=    3.173 closest distance to " O   HOH Z  59 " =    1.937
peak=    3.163 closest distance to " O   HOH Z 207 " =    2.564
peak=    3.162 closest distance to " O   HOH Z 158 " =    2.524
peak=    3.158 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.158 closest distance to " CG  GLN A  11 " =    2.247
peak=    3.157 closest distance to " O   ALA A  10 " =    1.020
peak=    3.157 closest distance to " CB  ASN A 110 " =    0.951
peak=    3.157 closest distance to " NH2 ARG A  14 " =    1.301
peak=    3.155 closest distance to " CZ AARG A 102 " =    1.898
peak=    3.152 closest distance to " CB  ASP A 132 " =    3.740
peak=    3.151 closest distance to " OG  SER A  26 " =    1.319
peak=    3.148 closest distance to " O   HOH Z 145 " =    2.716
peak=    3.145 closest distance to " CA  ALA A  51 " =    1.099
peak=    3.144 closest distance to " O   HOH Z 313 " =    1.885
peak=    3.142 closest distance to " CA  ALA A 299 " =    1.011
peak=    3.126 closest distance to " O   HOH Z 344 " =    2.750
peak=    3.122 closest distance to " O   GLY A 302 " =    2.277
peak=    3.121 closest distance to " N   GLN A 103 " =    1.355
peak=    3.121 closest distance to " N   ASN A 209 " =    1.359
peak=    3.116 closest distance to " O   HOH Z  54 " =    1.118
peak=    3.114 closest distance to " O   HOH Z 110 " =    1.797
peak=    3.111 closest distance to " NE BARG A 275 " =    1.137
peak=    3.110 closest distance to " O   HOH Z 357 " =    1.649
peak=    3.108 closest distance to " N   ALA A   1 " =    1.430
peak=    3.103 closest distance to " CB  ALA A 291 " =    0.816
peak=    3.091 closest distance to " NH2AARG A 275 " =    3.745
peak=    3.083 closest distance to " CG2 THR A 246 " =    1.256
peak=    3.078 closest distance to " O   HOH Z 220 " =    1.562
peak=    3.078 closest distance to " OD1 ASN A 217 " =    1.587
peak=    3.073 closest distance to " CE  MET A  40 " =    1.099
peak=    3.072 closest distance to " O   HOH Z  75 " =    1.453
peak=    3.066 closest distance to " O   HOH Z  97 " =    1.969

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.520 - 4.639
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 209
   mapped sites are within: 0.725 - 4.639

peak=   -5.592 closest distance to " CD  ARG A 138 " =    1.070
peak=   -4.945 closest distance to " CG2 VAL A 230 " =    0.765
peak=   -4.751 closest distance to " CD  ARG A  14 " =    2.968
peak=   -4.501 closest distance to " O   PRO A 198 " =    1.030
peak=   -4.280 closest distance to " O   HOH Z 231 " =    0.829
peak=   -4.258 closest distance to " O   HOH Z 385 " =    0.998
peak=   -4.258 closest distance to " O   HOH Z 242 " =    1.616
peak=   -4.244 closest distance to " OG ASER A 134 " =    0.986
peak=   -4.215 closest distance to " OG  SER A  97 " =    2.218
peak=   -4.213 closest distance to " O   HOH Z  52 " =    0.725
peak=   -4.141 closest distance to " OE1 GLU A 277 " =    2.411
peak=   -4.126 closest distance to " O   HOH Z  95 " =    1.067
peak=   -4.082 closest distance to " CA  GLY A  98 " =    1.732
peak=   -4.077 closest distance to " O   GLN A  11 " =    1.505
peak=   -4.062 closest distance to " O   HOH Z 268 " =    0.867
peak=   -4.057 closest distance to " O   HOH Z 359 " =    1.496
peak=   -4.050 closest distance to " O   HOH Z 377 " =    1.178
peak=   -4.050 closest distance to " CD1 TRP A 179 " =    1.014
peak=   -3.991 closest distance to " OG  SER A 276 " =    0.922
peak=   -3.987 closest distance to " CD2 LEU A   5 " =    0.897
peak=   -3.983 closest distance to " O   HOH Z  76 " =    1.168
peak=   -3.974 closest distance to " O   ALA A  51 " =    1.333
peak=   -3.963 closest distance to " O   HOH Z 313 " =    0.865
peak=   -3.910 closest distance to " CG  PRO A 163 " =    2.436
peak=   -3.905 closest distance to " N   ARG A 275 " =    0.778
peak=   -3.896 closest distance to " O   HOH Z  60 " =    1.505
peak=   -3.863 closest distance to " O   HOH Z 347 " =    0.776
peak=   -3.862 closest distance to " O   HOH Z 235 " =    0.972
peak=   -3.831 closest distance to " O   HOH Z 413 " =    4.092
peak=   -3.791 closest distance to " N   VAL A  72 " =    2.050
peak=   -3.787 closest distance to " CG  TRP A 266 " =    1.811
peak=   -3.781 closest distance to " OG  SER A   3 " =    0.941
peak=   -3.755 closest distance to " O   HOH Z  54 " =    0.770
peak=   -3.744 closest distance to " O   HOH Z 300 " =    0.909
peak=   -3.735 closest distance to " O   HOH Z 290 " =    0.906
peak=   -3.729 closest distance to " OG  SER A 206 " =    1.979
peak=   -3.726 closest distance to " C   VAL A  72 " =    0.940
peak=   -3.718 closest distance to " CG  ASN A 284 " =    1.227
peak=   -3.717 closest distance to " O   HOH Z 163 " =    1.521
peak=   -3.703 closest distance to " O   HOH Z 404 " =    1.130
peak=   -3.698 closest distance to " CD2 LEU A 297 " =    1.082
peak=   -3.686 closest distance to " O   HOH Z 415 " =    0.867
peak=   -3.683 closest distance to " O   HOH Z 298 " =    0.734
peak=   -3.683 closest distance to " CB  ALA A 248 " =    2.053
peak=   -3.677 closest distance to " CG  MET A 105 " =    0.882
peak=   -3.664 closest distance to " O   HOH Z  56 " =    2.169
peak=   -3.658 closest distance to " O   TRP A 179 " =    1.699
peak=   -3.658 closest distance to " CZ  PHE A  38 " =    2.712
peak=   -3.640 closest distance to " CA  GLY A 133 " =    2.063
peak=   -3.639 closest distance to " CA  GLY A  35 " =    1.868
peak=   -3.632 closest distance to " O   HOH Z 131 " =    3.772
peak=   -3.616 closest distance to " O   HOH Z  69 " =    1.893
peak=   -3.608 closest distance to " O   TRP A  92 " =    1.430
peak=   -3.605 closest distance to " C   PHE A 155 " =    0.832
peak=   -3.605 closest distance to " O   HOH Z 381 " =    0.893
peak=   -3.584 closest distance to " CD1 TRP A 274 " =    0.951
peak=   -3.583 closest distance to " O   HOH Z  34 " =    2.071
peak=   -3.582 closest distance to " O   HOH Z  24 " =    1.276
peak=   -3.576 closest distance to " O   HOH Z 205 " =    1.402
peak=   -3.571 closest distance to " O   HOH Z 186 " =    1.359
peak=   -3.571 closest distance to " CD  GLN A  77 " =    1.053
peak=   -3.568 closest distance to " O   ASN A 301 " =    1.312
peak=   -3.568 closest distance to " O   SER A 245 " =    1.184
peak=   -3.560 closest distance to " OE2 GLU A 152 " =    1.016
peak=   -3.557 closest distance to " N   THR A 157 " =    1.622
peak=   -3.556 closest distance to " O   HOH Z 244 " =    1.455
peak=   -3.553 closest distance to " CE2 TYR A  30 " =    2.704
peak=   -3.550 closest distance to " O   GLN A  77 " =    1.637
peak=   -3.533 closest distance to " O   HOH Z 414 " =    1.941
peak=   -3.532 closest distance to " OG BSER A 134 " =    1.668
peak=   -3.517 closest distance to " C   HIS A 108 " =    1.178
peak=   -3.514 closest distance to " CG  GLU A 277 " =    1.139
peak=   -3.512 closest distance to " O   HOH Z 389 " =    2.318
peak=   -3.511 closest distance to " O   HOH Z  13 " =    1.651
peak=   -3.511 closest distance to " ND2 ASN A 252 " =    2.080
peak=   -3.510 closest distance to " O   HOH Z 298 " =    2.795
peak=   -3.501 closest distance to " CG1 VAL A 296 " =    0.933
peak=   -3.494 closest distance to " O   HOH Z  39 " =    0.983
peak=   -3.489 closest distance to " O   HOH Z 431 " =    1.094
peak=   -3.478 closest distance to " O   HOH Z 429 " =    1.524
peak=   -3.465 closest distance to " O   ALA A  10 " =    1.660
peak=   -3.450 closest distance to " N   GLN A  58 " =    1.071
peak=   -3.445 closest distance to " NH2 ARG A  79 " =    2.087
peak=   -3.439 closest distance to " O   HOH Z 264 " =    1.399
peak=   -3.432 closest distance to " O   HOH Z  75 " =    1.704
peak=   -3.431 closest distance to " CA  GLY A 203 " =    2.296
peak=   -3.429 closest distance to " CA  ALA A   1 " =    1.131
peak=   -3.420 closest distance to " O   HOH Z  95 " =    2.135
peak=   -3.419 closest distance to " O   HOH Z 102 " =    1.710
peak=   -3.415 closest distance to " O   HOH Z 416 " =    0.897
peak=   -3.407 closest distance to " CG  ASP A 231 " =    0.784
peak=   -3.404 closest distance to " O   HOH Z 429 " =    2.034
peak=   -3.401 closest distance to " CB  TYR A  68 " =    1.327
peak=   -3.390 closest distance to " CA  GLN A  55 " =    1.140
peak=   -3.379 closest distance to " CB  PRO A 243 " =    2.528
peak=   -3.378 closest distance to " O   HOH Z 426 " =    1.647
peak=   -3.370 closest distance to " CG2 VAL A  78 " =    2.772
peak=   -3.366 closest distance to " O   HOH Z  47 " =    1.659
peak=   -3.364 closest distance to " CB  ASP A  27 " =    2.358
peak=   -3.363 closest distance to " O   HOH Z 231 " =    1.709
peak=   -3.361 closest distance to " N   HIS A 115 " =    2.151
peak=   -3.355 closest distance to " ND2 ASN A 173 " =    1.581
peak=   -3.354 closest distance to " O   HOH Z 214 " =    1.175
peak=   -3.352 closest distance to " O   ILE A 106 " =    2.131
peak=   -3.350 closest distance to " ND2BASN A 224 " =    1.427
peak=   -3.346 closest distance to " O   ASP A 191 " =    1.887
peak=   -3.334 closest distance to " CG BLYS A 290 " =    0.893
peak=   -3.332 closest distance to " C   TRP A 179 " =    1.037
peak=   -3.331 closest distance to " O   HOH Z 428 " =    1.448
peak=   -3.325 closest distance to " CG1 VAL A 112 " =    2.994
peak=   -3.324 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.322 closest distance to " CA  ASN A 142 " =    1.988
peak=   -3.321 closest distance to " CB  ASN A  45 " =    1.957
peak=   -3.314 closest distance to " O   HOH Z 143 " =    0.926
peak=   -3.310 closest distance to " CG  PRO A 213 " =    2.260
peak=   -3.309 closest distance to " O   HOH Z 189 " =    2.978
peak=   -3.305 closest distance to " CD  GLN A  11 " =    0.892
peak=   -3.299 closest distance to " O   HOH Z 376 " =    2.281
peak=   -3.292 closest distance to " CB  SER A 273 " =    1.776
peak=   -3.292 closest distance to " O   ASP A 286 " =    0.954
peak=   -3.289 closest distance to " CZ2 TRP A 274 " =    0.911
peak=   -3.285 closest distance to " CG2 ILE A  20 " =    2.836
peak=   -3.280 closest distance to " O   HOH Z  60 " =    1.321
peak=   -3.279 closest distance to " O   ILE A  49 " =    1.662
peak=   -3.279 closest distance to " NE1 TRP A 177 " =    1.655
peak=   -3.273 closest distance to " O   HOH Z 140 " =    1.465
peak=   -3.272 closest distance to " O   HOH Z 353 " =    1.334
peak=   -3.270 closest distance to " CG2 ILE A 120 " =    1.338
peak=   -3.269 closest distance to " O   ASP A  27 " =    2.002
peak=   -3.268 closest distance to " NE2 GLN A  55 " =    1.066
peak=   -3.263 closest distance to " NH2 ARG A 159 " =    2.272
peak=   -3.262 closest distance to " O   HOH Z 387 " =    1.148
peak=   -3.261 closest distance to " N   PRO A 163 " =    1.574
peak=   -3.258 closest distance to " CB  ALA A 291 " =    1.778
peak=   -3.256 closest distance to " O   HOH Z 218 " =    3.777
peak=   -3.254 closest distance to " O   HOH Z 421 " =    3.079
peak=   -3.249 closest distance to " CD1 LEU A 297 " =    2.212
peak=   -3.247 closest distance to " O   LEU A 101 " =    1.123
peak=   -3.246 closest distance to " O   HOH Z 136 " =    2.828
peak=   -3.246 closest distance to " O   SER A  22 " =    2.602
peak=   -3.245 closest distance to " CG  ARG A 138 " =    0.954
peak=   -3.244 closest distance to " CG  PRO A 243 " =    1.507
peak=   -3.235 closest distance to " O   GLY A  98 " =    2.054
peak=   -3.232 closest distance to " O   HOH Z 368 " =    1.263
peak=   -3.231 closest distance to " O   GLY A 118 " =    1.048
peak=   -3.225 closest distance to " O   HOH Z 129 " =    4.639
peak=   -3.222 closest distance to " O   ARG A 275 " =    0.784
peak=   -3.219 closest distance to " O   HOH Z 350 " =    2.204
peak=   -3.217 closest distance to " C   ASN A 285 " =    1.936
peak=   -3.214 closest distance to " O   HOH Z  22 " =    2.859
peak=   -3.208 closest distance to " CB  ASN A 301 " =    1.883
peak=   -3.206 closest distance to " O   HOH Z  77 " =    1.742
peak=   -3.205 closest distance to " CA  SER A 276 " =    1.229
peak=   -3.203 closest distance to " CD  GLU A  44 " =    1.141
peak=   -3.197 closest distance to " O   HOH Z  30 " =    0.962
peak=   -3.195 closest distance to " O   HOH Z 165 " =    2.293
peak=   -3.192 closest distance to " O   HOH Z 422 " =    3.428
peak=   -3.182 closest distance to " O   HOH Z 174 " =    2.887
peak=   -3.182 closest distance to " CD  GLN A  58 " =    0.843
peak=   -3.180 closest distance to " C   ILE A 239 " =    1.700
peak=   -3.180 closest distance to " O   HOH Z 157 " =    1.110
peak=   -3.179 closest distance to " O   HOH Z 111 " =    1.071
peak=   -3.179 closest distance to " CB  TYR A  15 " =    2.035
peak=   -3.178 closest distance to " O   HOH Z 374 " =    2.878
peak=   -3.177 closest distance to " CZ3 TRP A  92 " =    0.993
peak=   -3.175 closest distance to " O   HOH Z 207 " =    2.053
peak=   -3.174 closest distance to " N   MET A  40 " =    2.007
peak=   -3.173 closest distance to " O   TYR A  30 " =    1.839
peak=   -3.173 closest distance to " O   HOH Z 275 " =    1.766
peak=   -3.167 closest distance to " O   HOH Z 390 " =    2.478
peak=   -3.165 closest distance to " O   ASP A 200 " =    1.028
peak=   -3.160 closest distance to " N   ALA A   1 " =    1.019
peak=   -3.158 closest distance to " O   HOH Z 373 " =    1.087
peak=   -3.153 closest distance to " CE2 PHE A 218 " =    2.416
peak=   -3.151 closest distance to " O   HOH Z 314 " =    1.048
peak=   -3.146 closest distance to " O   GLY A 136 " =    1.427
peak=   -3.146 closest distance to " CD  GLU A 277 " =    0.800
peak=   -3.145 closest distance to " CE3 TRP A 274 " =    2.437
peak=   -3.145 closest distance to " O   HOH Z  68 " =    1.050
peak=   -3.144 closest distance to " N   VAL A 189 " =    1.661
peak=   -3.143 closest distance to " O   HOH Z 185 " =    2.112
peak=   -3.143 closest distance to " O   THR A 178 " =    0.863
peak=   -3.138 closest distance to " O   HOH Z 364 " =    1.011
peak=   -3.128 closest distance to " CD  LYS A 166 " =    2.605
peak=   -3.122 closest distance to " CG  PHE A 283 " =    2.385
peak=   -3.118 closest distance to " CD2 TYR A 293 " =    1.934
peak=   -3.117 closest distance to " CG  PRO A 213 " =    0.779
peak=   -3.112 closest distance to " O   HOH Z 308 " =    1.570
peak=   -3.108 closest distance to " OE1 GLN A 183 " =    1.624
peak=   -3.108 closest distance to " O   GLN A  73 " =    0.907
peak=   -3.107 closest distance to " O   HOH Z 383 " =    0.734
peak=   -3.104 closest distance to " CG1 ILE A 263 " =    1.936
peak=   -3.095 closest distance to " O   HOH Z 331 " =    1.051
peak=   -3.094 closest distance to " ND2 ASN A  60 " =    1.251
peak=   -3.087 closest distance to " O   HOH Z 208 " =    0.850
peak=   -3.085 closest distance to " CB  PHE A  59 " =    1.881
peak=   -3.085 closest distance to " O   HOH Z 372 " =    1.200
peak=   -3.081 closest distance to " CG2 THR A  31 " =    2.222
peak=   -3.077 closest distance to " OG  SER A  87 " =    1.566
peak=   -3.068 closest distance to " CE2 PHE A  16 " =    2.865
peak=   -3.063 closest distance to " CB  TYR A 172 " =    2.129
peak=   -3.046 closest distance to " CB  PHE A 130 " =    1.214
peak=   -3.028 closest distance to " O   HOH Z  53 " =    1.691

================= 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    :  0.4887 0.4868   6.295577e+00   6.286758e+00
   1_bss:  0.4803 0.4750   6.289565e+00   6.278215e+00
   1_xyz:  0.4163 0.4473   6.220468e+00   6.250447e+00
   1_adp:  0.3783 0.4421   6.175137e+00   6.246439e+00
   1_occ:  0.3776 0.4424   6.174520e+00   6.246819e+00
   2_bss:  0.3757 0.4388   6.174788e+00   6.244943e+00
   2_xyz:  0.3347 0.4098   6.083996e+00   6.199230e+00
   2_adp:  0.3214 0.3977   6.063700e+00   6.182197e+00
   2_occ:  0.3211 0.3980   6.063835e+00   6.182503e+00
   3_bss:  0.3217 0.3954   6.064467e+00   6.181759e+00
   3_xyz:  0.2645 0.3389   5.901335e+00   6.060400e+00
   3_adp:  0.2412 0.3235   5.838713e+00   6.025244e+00
   3_occ:  0.2408 0.3236   5.838326e+00   6.025882e+00
   4_bss:  0.2398 0.3218   5.834492e+00   6.022562e+00
   4_xyz:  0.1926 0.2569   5.622239e+00   5.834975e+00
   4_adp:  0.1774 0.2319   5.541203e+00   5.753272e+00
   4_occ:  0.1770 0.2309   5.538735e+00   5.749878e+00
   5_bss:  0.1768 0.2306   5.537573e+00   5.748042e+00
   5_xyz:  0.1500 0.2000   5.395113e+00   5.613521e+00
   5_adp:  0.1433 0.1945   5.358375e+00   5.581265e+00
   5_occ:  0.1430 0.1939   5.356852e+00   5.578936e+00
   5_bss:  0.1433 0.1939   5.356140e+00   5.578982e+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:  0.378   4.113   6.383   9.954   7.268   0.000   0.000   0.000
   1_xyz:  0.378   4.113   6.383   9.954   7.268   0.000   0.000   0.000
   1_adp:  0.378   4.113   6.383   9.954   7.268   0.000   0.000   0.000
   1_occ:  0.378   4.113   6.383   9.954   7.268   0.000   0.000   0.000
   2_bss:  0.369  34.321   3.375   6.016   4.334   0.000   0.000   0.000
   2_xyz:  0.369  34.321   3.375   6.016   4.334   0.000   0.000   0.000
   2_adp:  0.369  34.321   3.375   6.016   4.334   0.000   0.000   0.000
   2_occ:  0.369  34.321   3.375   6.016   4.334   0.000   0.000   0.000
   3_bss:  0.342  34.321   2.789   4.314   3.652   0.000   0.000   0.000
   3_xyz:  0.342  34.321   2.789   4.314   3.652   0.000   0.000   0.000
   3_adp:  0.342  34.321   2.789   4.314   3.652   0.000   0.000   0.000
   3_occ:  0.342  34.321   2.789   4.314   3.652   0.000   0.000   0.000
   4_bss:  0.317  38.523   1.971   2.509   2.906   0.000   0.000   0.000
   4_xyz:  0.317  38.523   1.971   2.509   2.906   0.000   0.000   0.000
   4_adp:  0.317  38.523   1.971   2.509   2.906   0.000   0.000   0.000
   4_occ:  0.317  38.523   1.971   2.509   2.906   0.000   0.000   0.000
   5_bss:  0.319  35.964   1.337   1.379   2.592   0.000   0.000   0.000
   5_xyz:  0.319  35.964   1.337   1.379   2.592   0.000   0.000   0.000
   5_adp:  0.319  35.964   1.337   1.379   2.592   0.000   0.000   0.000
   5_occ:  0.319  35.964   1.337   1.379   2.592   0.000   0.000   0.000
   5_bss:  0.319  37.551  -0.384  -0.530   0.913   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.603 0.3734  0.4477    77957.751
   1_bss:  60.540 0.3863  0.5781    74937.011
   1_xyz:  54.394 0.4645  0.6846    63956.612
   1_adp:  53.256 0.4789  0.7562    62658.224
   1_occ:  53.282 0.4786  0.7543    62777.567
   2_bss:  52.797 0.4847  0.6869    62051.671
   2_xyz:  46.833 0.5587  0.7891    50570.568
   2_adp:  44.599 0.5869  0.8278    47637.533
   2_occ:  44.663 0.5861  0.8267    47740.550
   3_bss:  44.520 0.5876  0.7999    47333.642
   3_xyz:  35.741 0.6925  0.9235    31706.398
   3_adp:  33.355 0.7204  0.9442    28616.569
   3_occ:  33.390 0.7200  0.9432    28622.185
   4_bss:  33.166 0.7223  0.9083    28181.439
   4_xyz:  25.639 0.8043  0.9751    17126.533
   4_adp:  22.591 0.8364  0.9883    13998.527
   4_occ:  22.490 0.8374  0.9886    13862.755
   5_bss:  22.431 0.8378  0.9635    13758.641
   5_xyz:  19.039 0.8711  0.9816    10402.011
   5_adp:  18.203 0.8792  0.9792     9792.530
   5_occ:  18.151 0.8796  0.9792     9735.005
   5_bss:  18.130 0.8798  0.9724     9719.862
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3000e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3000e+01
   1_xyz:   1.684  0.013  0.105 18.273  0.007  4.105   1.4313e-01
   1_adp:   1.684  0.013  0.105 18.273  0.007  4.105   1.4313e-01
   1_occ:   1.684  0.013  0.105 18.273  0.007  4.105   1.4313e-01
   2_bss:   1.684  0.013  0.105 18.273  0.007  4.105   1.4313e-01
   2_xyz:   1.152  0.008  0.076 16.112  0.005  4.117   8.5472e-02
   2_adp:   1.152  0.008  0.076 16.112  0.005  4.117   8.5472e-02
   2_occ:   1.152  0.008  0.076 16.112  0.005  4.117   8.5472e-02
   3_bss:   1.152  0.008  0.076 16.112  0.005  4.117   8.5472e-02
   3_xyz:   1.311  0.010  0.095 16.637  0.005  4.108   1.0927e-01
   3_adp:   1.311  0.010  0.095 16.637  0.005  4.108   1.0927e-01
   3_occ:   1.311  0.010  0.095 16.637  0.005  4.108   1.0927e-01
   4_bss:   1.311  0.010  0.095 16.637  0.005  4.108   1.0927e-01
   4_xyz:   1.058  0.007  0.077 15.863  0.004  4.106   7.0298e-02
   4_adp:   1.058  0.007  0.077 15.863  0.004  4.106   7.0298e-02
   4_occ:   1.058  0.007  0.077 15.863  0.004  4.106   7.0298e-02
   5_bss:   1.058  0.007  0.077 15.863  0.004  4.106   7.0298e-02
   5_xyz:   0.890  0.005  0.064 15.277  0.003  4.112   5.2221e-02
   5_adp:   0.890  0.005  0.064 15.277  0.003  4.112   5.2221e-02
   5_occ:   0.890  0.005  0.064 15.277  0.003  4.112   5.2221e-02
   5_bss:   0.890  0.005  0.064 15.277  0.003  4.112   5.2221e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8660e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8660e+00
   1_xyz:  13.078  0.191  0.414 84.644  0.043  2.160   9.7212e-02
   1_adp:  13.078  0.191  0.414 84.644  0.043  2.160   9.7212e-02
   1_occ:  13.078  0.191  0.414 84.644  0.043  2.160   9.7212e-02
   2_bss:  13.078  0.191  0.414 84.644  0.043  2.160   9.7212e-02
   2_xyz:   7.013  0.099  0.278 78.697  0.045  1.962   5.3498e-02
   2_adp:   7.013  0.099  0.278 78.697  0.045  1.962   5.3498e-02
   2_occ:   7.013  0.099  0.278 78.697  0.045  1.962   5.3498e-02
   3_bss:   7.013  0.099  0.278 78.697  0.045  1.962   5.3498e-02
   3_xyz:   8.325  0.081  0.328 75.789  0.032  2.084   1.8897e-01
   3_adp:   8.325  0.081  0.328 75.789  0.032  2.084   1.8897e-01
   3_occ:   8.325  0.081  0.328 75.789  0.032  2.084   1.8897e-01
   4_bss:   8.325  0.081  0.328 75.789  0.032  2.084   1.8897e-01
   4_xyz:   8.374  0.074  0.324 77.752  0.033  2.300   5.9048e-02
   4_adp:   8.374  0.074  0.324 77.752  0.033  2.300   5.9048e-02
   4_occ:   8.374  0.074  0.324 77.752  0.033  2.300   5.9048e-02
   5_bss:   8.374  0.074  0.324 77.752  0.033  2.300   5.9048e-02
   5_xyz:   6.486  0.048  0.191 81.778  0.038  2.322   4.0371e-02
   5_adp:   6.486  0.048  0.191 81.778  0.038  2.322   4.0371e-02
   5_occ:   6.486  0.048  0.191 81.778  0.038  2.322   4.0371e-02
   5_bss:   6.486  0.048  0.191 81.778  0.038  2.322   4.0371e-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:  71.79   0.00  14.08  71.79   0.00  12.68  66.85   0.00  21.74
   1_occ:  71.79   0.00  14.08  71.79   0.00  12.68  66.85   0.00  21.74
   2_bss:  71.79   0.00  14.08  71.79   0.00  12.68  66.85   0.00  21.74
   2_xyz:  71.79   0.00  14.08  71.79   0.00  12.68  66.85   0.00  21.74
   2_adp:  76.85   0.00  13.60  76.85   0.00  11.66  74.09   0.00  24.19
   2_occ:  76.85   0.00  13.60  76.85   0.00  11.66  74.09   0.00  24.19
   3_bss:  76.85   0.00  13.60  76.85   0.00  11.66  74.09   0.00  24.19
   3_xyz:  76.85   0.00  13.60  76.85   0.00  11.66  74.09   0.00  24.19
   3_adp:  81.88   0.00  14.40  81.88   0.00  10.92  80.28   0.00  33.37
   3_occ:  81.88   0.00  14.40  81.88   0.00  10.92  80.28   0.00  33.37
   4_bss:  81.88   0.00  14.40  81.88   0.00  10.92  80.28   0.00  33.37
   4_xyz:  81.88   0.00  14.40  81.88   0.00  10.92  80.28   0.00  33.37
   4_adp:  81.23   0.00  13.59  81.23   0.00   9.67  76.59   2.21  34.96
   4_occ:  81.23   0.00  13.59  81.23   0.00   9.67  76.59   2.21  34.96
   5_bss:  81.23   0.00  13.59  81.23   0.00   9.67  76.59   2.21  34.96
   5_xyz:  81.23   0.00  13.59  81.23   0.00   9.67  76.59   2.21  34.96
   5_adp:  82.72   0.00  13.56  82.72   0.00   9.27  78.85   2.58  36.91
   5_occ:  82.72   0.00  13.56  82.72   0.00   9.27  78.85   2.58  36.91
   5_bss:  84.31   1.59  15.15  84.31   1.59  10.86  80.44   4.17  38.49
------------------------------------------------------------------------
 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:    1.257    0.015    0.410
   1_adp:    1.257    0.015    0.410
   1_occ:    1.257    0.015    0.410
   2_bss:    1.257    0.015    0.410
   2_xyz:    1.599    0.034    0.537
   2_adp:    1.599    0.034    0.537
   2_occ:    1.599    0.034    0.537
   3_bss:    1.599    0.034    0.537
   3_xyz:    1.655    0.085    0.696
   3_adp:    1.655    0.085    0.696
   3_occ:    1.655    0.085    0.696
   4_bss:    1.655    0.085    0.696
   4_xyz:    1.860    0.044    0.796
   4_adp:    1.860    0.044    0.796
   4_occ:    1.860    0.044    0.796
   5_bss:    1.860    0.044    0.796
   5_xyz:    1.968    0.060    0.843
   5_adp:    1.968    0.060    0.843
   5_occ:    1.968    0.060    0.843
   5_bss:    1.968    0.060    0.843
------------------------------------------------------------------------

CPU time actual refinement: 346.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_488/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_488/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_488/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_488/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_488/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.26 
  Macro-tasks:
    bulk solvent and scale       = 42.29  
    individual site refinement   = 149.47 
    weights calculation          = 32.18  
    collect and process          = 6.41   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 230.49 
  Micro-tasks:
    mask                            = 3.02   
    f_calc                          = 106.76 
    alpha_beta                      = 8.50   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.93 
    fmodel                         = 7.16   
    r_factors                      = 0.23   
    phase_errors                   = 9.78   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 255.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.808 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    651 calls, 106.42 s
gradients_fft:          596 calls, 105.07 s

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

# Date 2008-01-16 Time 01:40:41 PST -0800 (1200476441.43 s)
Start R-work = 0.4887, R-free = 0.4868 (no bulk solvent and anisotropic scale)
Final R-work = 0.1586, R-free = 0.2078 (no bulk solvent and anisotropic scale)

Start R-work = 0.4803, R-free = 0.4750
Final R-work = 0.1433, R-free = 0.1939