# Date 2008-01-16 Time 02:10:42 PST -0800 (1200478242.12 s)
#phil __OFF__

Command line arguments: "../731.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 = 14855
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 731

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.7567, 86.39, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.95354
Completeness in resolution range: 0.938395
Completeness with d_max=infinity: 0.935706

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0485
                             d_min =   1.9535

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0485 1.95354
Completeness in resolution range: 0.938395
Completeness with d_max=infinity: 0.935706

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0489 -  4.1815 [2197/2224]  1976   221  10.1%
  bin  2:  4.1815 -  3.3308 [2111/2131]  1900   211  10.0%
  bin  3:  3.3308 -  2.9133 [2075/2094]  1870   205   9.9%
  bin  4:  2.9133 -  2.6485 [2058/2088]  1849   209  10.2%
  bin  5:  2.6485 -  2.4595 [2046/2065]  1849   197   9.6%
  bin  6:  2.4595 -  2.3151 [2044/2069]  1830   214  10.5%
  bin  7:  2.3151 -  2.1995 [2025/2053]  1819   206  10.2%
  bin  8:  2.1995 -  2.1040 [2009/2045]  1812   197   9.8%
  bin  9:  2.1040 -  2.0232 [2024/2066]  1828   196   9.7%
  bin 10:  2.0232 -  1.9535 [1000/2040]   897   103  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_731/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:
        1.68 -     2.32: 28
        2.32 -     2.97: 1797
        2.97 -     3.61: 4611
        3.61 -     4.26: 9278
        4.26 -     4.90: 12859
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.692 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.757 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28568 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_731/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_731/model_refine_001.geo

CPU time processing inputs: 10.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.75675 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4883   r_free= 0.4847   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.295618                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.6645 0.99   1421  158 0.4274 0.4216      6.6369      6.6859|
|  2:  4.6645 -  3.7208 0.99   1373  155 0.4190 0.3703      6.8377      6.7648|
|  3:  3.7208 -  3.2559 0.99   1343  142 0.4442 0.4333      6.6914      6.6727|
|  4:  3.2559 -  2.9607 0.99   1332  155 0.4814 0.4712      6.5469      6.5171|
|  5:  2.9607 -  2.7498 0.99   1336  149 0.5187 0.5309      6.3781      6.3898|
|  6:  2.7498 -  2.5886 0.99   1330  147 0.5179 0.5333      6.2831      6.2241|
|  7:  2.5886 -  2.4595 0.99   1309  137 0.5177 0.5162      6.2477      6.1763|
|  8:  2.4595 -  2.3529 0.98   1300  152 0.5297 0.5018      6.1724      6.1903|
|  9:  2.3529 -  2.2626 0.98   1305  147 0.5290 0.5475      6.1264      6.1845|
| 10:  2.2626 -  2.1848 1.00   1302  147 0.5266 0.5177      6.0986      6.0653|
| 11:  2.1848 -  2.1166 0.98   1312  138 0.4967 0.4989      6.0333      6.0333|
| 12:  2.1166 -  2.0563 0.98   1289  143 0.5208 0.5704      5.9437      5.9978|
| 13:  2.0563 -  2.0023 0.98   1268  142 0.5502 0.5426      5.8851      5.8125|
| 14:  2.0023 -  1.9535 0.31    410   47 0.5531 0.4773      5.8797      5.8314|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.6645  1421   158  0.61  41.52   0.78     0.68      99478.37|
|  2:  4.6645 -  3.7208  1373   155  0.68  36.98   0.85     0.76     119495.18|
|  3:  3.7208 -  3.2559  1343   142  0.58  45.81   0.85     0.72     121709.91|
|  4:  3.2559 -  2.9607  1332   155  0.48  53.18   0.79     0.59     107569.15|
|  5:  2.9607 -  2.7498  1336   149  0.36  62.58   0.73     0.46      91000.48|
|  6:  2.7498 -  2.5886  1330   147  0.34  64.63   0.71     0.40      78686.42|
|  7:  2.5886 -  2.4595  1309   137  0.30  67.49   0.76     0.36      71204.39|
|  8:  2.4595 -  2.3529  1300   152  0.29  68.18   0.72     0.35      63824.01|
|  9:  2.3529 -  2.2626  1305   147  0.30  67.61   0.73     0.36      57540.28|
| 10:  2.2626 -  2.1848  1302   147  0.32  65.94   0.75     0.39      50543.99|
| 11:  2.1848 -  2.1166  1312   138  0.31  66.87   0.80     0.38      49586.71|
| 12:  2.1166 -  2.0563  1289   143  0.27  69.81   0.76     0.36      45917.38|
| 13:  2.0563 -  2.0023  1268   142  0.26  70.80   0.71     0.35      40049.19|
| 14:  2.0023 -  1.9535   410    47  0.36  63.17   0.73     0.41      28906.57|
|alpha:            min =        0.35 max =            0.76 mean =         0.48|
|beta:             min =    28906.57 max =       121709.91 mean =     76140.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.91|
|phase err.(test): min =        0.00 max =           89.97 mean =        60.14|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.553711             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.349   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.516059              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.429   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       36 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      712 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1523 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2667 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3955 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5152 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6592 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7787 |
|-----------------------------------------------------------------------------|
|-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 |       53.343 |
| 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 |       2.326 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    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 = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4925   r_free= 0.4855   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.297103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4790   r_free= 0.4725   ksol= 0.39   Bsol= 20.00   scale= 0.970   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.44,9.68,6.93,0.00,0.00,0.00); trace/3= 7.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289810                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.459842             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.348   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.557959              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.160   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4790      final r-factor (work) = 0.4104          |
| start r-factor (free) = 0.4725      final r-factor (free) = 0.4393          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 105.1122 = 16.46 * 0.50 * 6.2903 + 1.00 * 53.3433                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4257 = 16.46 * 0.50 * 6.2309 + 1.00 * 0.1456                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4104      final r-factor (work) = 0.3724          |
| start r-factor (free) = 0.4393      final r-factor (free) = 0.4361          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7219 = 1.56 * 1.00 * 6.2309 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6441 = 1.56 * 1.00 * 6.1783 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.94   13.72    None  None   None       |
|    all(noH): 2823   0      0.00    72.94   13.72    None  None   None       |
|    Sol.    : 438    0      0.00    65.09   21.71    None  None   None       |
|    Mac.    : 2385   0      0.00    72.94   12.25    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 -   7.294:  921   |   5:    36.470 -  43.764:   68        |
|      1:     7.294 -  14.588:  824   |   6:    43.764 -  51.059:   34        |
|      2:    14.588 -  21.882:  528   |   7:    51.059 -  58.353:   11        |
|      3:    21.882 -  29.176:  282   |   8:    58.353 -  65.647:    8        |
|      4:    29.176 -  36.470:  146   |   9:    65.647 -  72.941:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3724 r_free = 0.4361             target_work(ml) = 6.172         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3722 r_free = 0.4362             target_work(ml) = 6.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3722   r_free= 0.4362   ksol= 0.39   Bsol= 20.00   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.44,9.68,6.93,0.00,0.00,0.00); trace/3= 7.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.171371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3709   r_free= 0.4327   ksol= 0.37   Bsol= 45.62   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,5.85,4.15,0.00,0.00,0.00); trace/3= 4.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.172329                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.295146              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.357  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.890939              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.767  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3709      final r-factor (work) = 0.3315          |
| start r-factor (free) = 0.4327      final r-factor (free) = 0.4065          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7552 = 8.30 * 0.50 * 6.1746 + 1.00 * 0.1456                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.4833 = 8.30 * 0.50 * 6.1237 + 1.00 * 0.0846                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3315      final r-factor (work) = 0.3180          |
| start r-factor (free) = 0.4065      final r-factor (free) = 0.3964          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4766 = 0.89 * 1.00 * 6.1237 + 1.00 * 0.0207                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4343 = 0.89 * 1.00 * 6.0700 + 1.00 * 0.0263                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.88  13.71    None  None   None       |
|    all(noH): 2823   0      0.00    111.88  13.71    None  None   None       |
|    Sol.    : 438    0      0.00    66.70   24.10    None  None   None       |
|    Mac.    : 2385   0      0.00    111.88  11.80    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 -  11.188: 1425   |   5:    55.941 -  67.129:    9        |
|      1:    11.188 -  22.376:  862   |   6:    67.129 -  78.317:    1        |
|      2:    22.376 -  33.565:  366   |   7:    78.317 -  89.505:    0        |
|      3:    33.565 -  44.753:  123   |   8:    89.505 - 100.694:    0        |
|      4:    44.753 -  55.941:   36   |   9:   100.694 - 111.882:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3180 r_free = 0.3964             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3178 r_free = 0.3962             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3178   r_free= 0.3962   ksol= 0.37   Bsol= 45.62   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,5.85,4.15,0.00,0.00,0.00); trace/3= 4.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.058511                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3185   r_free= 0.3942   ksol= 0.37   Bsol= 66.31   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,4.08,3.64,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.059366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.428095             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.726   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.769314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.872  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3185      final r-factor (work) = 0.2566          |
| start r-factor (free) = 0.3942      final r-factor (free) = 0.3292          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7716 = 11.43 * 0.50 * 6.0705 + 1.00 * 0.0845                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.2633 = 11.43 * 0.50 * 5.9765 + 1.00 * 0.1131                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2566      final r-factor (work) = 0.2344          |
| start r-factor (free) = 0.3292      final r-factor (free) = 0.3127          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6223 = 0.77 * 1.00 * 5.9765 + 1.00 * 0.0245                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5155 = 0.77 * 1.00 * 5.8371 + 1.00 * 0.0249                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.97  14.04    None  None   None       |
|    all(noH): 2823   0      0.00    111.97  14.04    None  None   None       |
|    Sol.    : 438    0      0.00    70.60   30.27    None  None   None       |
|    Mac.    : 2385   0      0.00    111.97  11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.197: 1522   |   5:    55.986 -  67.183:   11        |
|      1:    11.197 -  22.394:  695   |   6:    67.183 -  78.380:    3        |
|      2:    22.394 -  33.592:  376   |   7:    78.380 -  89.577:    0        |
|      3:    33.592 -  44.789:  173   |   8:    89.577 - 100.775:    0        |
|      4:    44.789 -  55.986:   41   |   9:   100.775 - 111.972:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2344 r_free = 0.3127             target_work(ml) = 5.808         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2340 r_free = 0.3126             target_work(ml) = 5.807         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2340   r_free= 0.3126   ksol= 0.37   Bsol= 66.31   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,4.08,3.64,0.00,0.00,0.00); trace/3= 3.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.806624                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2327   r_free= 0.3110   ksol= 0.35   Bsol= 66.31   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,1.87,2.51,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.803242                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.972334              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.420  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.097204              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.322   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2327      final r-factor (work) = 0.1856          |
| start r-factor (free) = 0.3110      final r-factor (free) = 0.2493          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5455 = 5.97 * 0.50 * 5.8377 + 1.00 * 0.1131                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1439 = 5.97 * 0.50 * 5.7177 + 1.00 * 0.0698                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1856      final r-factor (work) = 0.1614          |
| start r-factor (free) = 0.2493      final r-factor (free) = 0.2198          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2882 = 1.10 * 1.00 * 5.7177 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1143 = 1.10 * 1.00 * 5.5351 + 1.00 * 0.0411                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.20   14.84    None  None   None       |
|    all(noH): 2823   0      0.00    88.20   14.84    None  None   None       |
|    Sol.    : 438    0      1.08    87.65   40.96    None  None   None       |
|    Mac.    : 2385   0      0.00    88.20   10.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.820: 1442   |   5:    44.099 -  52.919:   89        |
|      1:     8.820 -  17.640:  703   |   6:    52.919 -  61.739:   83        |
|      2:    17.640 -  26.459:  197   |   7:    61.739 -  70.558:   42        |
|      3:    26.459 -  35.279:  135   |   8:    70.558 -  79.378:   20        |
|      4:    35.279 -  44.099:  105   |   9:    79.378 -  88.198:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1614 r_free = 0.2198             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1612 r_free = 0.2190             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2190   ksol= 0.35   Bsol= 66.31   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,1.87,2.51,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.468117                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2191   ksol= 0.32   Bsol= 53.69   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,1.20,2.56,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.466084                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.975053              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.720  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.630437              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.971   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.2191      final r-factor (free) = 0.1970          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5346 = 1.98 * 0.50 * 5.5340 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4036 = 1.98 * 0.50 * 5.4188 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1417      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1970      final r-factor (free) = 0.1906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4334 = 0.63 * 1.00 * 5.4188 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3924 = 0.63 * 1.00 * 5.3496 + 1.00 * 0.0199                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.48   14.56    None  None   None       |
|    all(noH): 2823   0      0.00    97.48   14.56    None  None   None       |
|    Sol.    : 438    0      1.41    94.31   41.67    None  None   None       |
|    Mac.    : 2385   0      0.00    97.48   9.58     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.748: 1648   |   5:    48.739 -  58.486:   88        |
|      1:     9.748 -  19.496:  592   |   6:    58.486 -  68.234:   51        |
|      2:    19.496 -  29.243:  175   |   7:    68.234 -  77.982:   32        |
|      3:    29.243 -  38.991:  116   |   8:    77.982 -  87.730:   11        |
|      4:    38.991 -  48.739:  102   |   9:    87.730 -  97.477:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1906             target_work(ml) = 5.332         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1367 r_free = 0.1903             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1903   ksol= 0.32   Bsol= 53.69   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,1.20,2.56,0.00,0.00,0.00); trace/3= 1.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.6645 0.99   1421  158 0.1063 0.1416      5.4523      5.6428|
|  2:  4.6645 -  3.7208 0.99   1373  155 0.0982 0.1286      5.5711        5.81|
|  3:  3.7208 -  3.2559 0.99   1343  142 0.1287 0.1781      5.6439      5.9551|
|  4:  3.2559 -  2.9607 0.99   1332  155 0.1557 0.2027      5.6552      5.8099|
|  5:  2.9607 -  2.7498 0.99   1336  149 0.1634 0.2234      5.5233      5.7658|
|  6:  2.7498 -  2.5886 0.99   1330  147 0.1470 0.2262      5.3802       5.614|
|  7:  2.5886 -  2.4595 0.99   1309  137 0.1521 0.1983      5.3387      5.4828|
|  8:  2.4595 -  2.3529 0.98   1300  152 0.1511 0.2186      5.2856      5.5698|
|  9:  2.3529 -  2.2626 0.98   1305  147 0.1516 0.2267      5.2439      5.5049|
| 10:  2.2626 -  2.1848 1.00   1302  147 0.1427 0.1991      5.1518      5.3677|
| 11:  2.1848 -  2.1166 0.98   1312  138 0.1381 0.2202      5.1249      5.4644|
| 12:  2.1166 -  2.0563 0.98   1289  143 0.1469 0.2119      5.0794      5.3296|
| 13:  2.0563 -  2.0023 0.98   1268  142 0.1437 0.2016      4.9523       5.148|
| 14:  2.0023 -  1.9535 0.31    410   47 0.1248 0.1699      4.8044      4.9906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.6645  1421   158  0.93  10.58   0.97     0.95       8771.80|
|  2:  4.6645 -  3.7208  1373   155  0.94   9.74   1.03     1.01      11825.31|
|  3:  3.7208 -  3.2559  1343   142  0.91  14.58   1.05     1.04      14933.26|
|  4:  3.2559 -  2.9607  1332   155  0.88  18.15   1.02     1.00      15925.26|
|  5:  2.9607 -  2.7498  1336   149  0.86  20.14   1.01     0.98      12730.63|
|  6:  2.7498 -  2.5886  1330   147  0.86  20.55   0.99     0.94      10400.54|
|  7:  2.5886 -  2.4595  1309   137  0.87  19.78   1.00     0.97       9307.41|
|  8:  2.4595 -  2.3529  1300   152  0.86  20.78   1.00     0.95       8568.68|
|  9:  2.3529 -  2.2626  1305   147  0.86  20.45   1.00     0.95       7868.99|
| 10:  2.2626 -  2.1848  1302   147  0.86  20.61   1.01     0.96       6848.51|
| 11:  2.1848 -  2.1166  1312   138  0.87  19.85   1.01     0.95       6495.67|
| 12:  2.1166 -  2.0563  1289   143  0.86  20.91   1.02     1.00       6158.26|
| 13:  2.0563 -  2.0023  1268   142  0.87  20.17   1.00     0.96       4598.08|
| 14:  2.0023 -  1.9535   410    47  0.90  16.44   1.00     0.97       3210.20|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     3210.20 max =        15925.26 mean =      9468.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.05|
|phase err.(test): min =        0.00 max =           89.59 mean =        17.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1903   ksol= 0.32   Bsol= 47.90   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.67,0.92,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1903   ksol= 0.32   Bsol= 47.90   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.67,0.92,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330264                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0489 -  4.6645 0.99   1421  158 0.1062 0.1417      5.4521      5.6416|
|  2:  4.6645 -  3.7208 0.99   1373  155 0.0977 0.1277      5.5677      5.8031|
|  3:  3.7208 -  3.2559 0.99   1343  142 0.1283 0.1773      5.6408      5.9501|
|  4:  3.2559 -  2.9607 0.99   1332  155 0.1557 0.2036      5.6549      5.8116|
|  5:  2.9607 -  2.7498 0.99   1336  149 0.1634 0.2235      5.5236      5.7665|
|  6:  2.7498 -  2.5886 0.99   1330  147 0.1471 0.2261      5.3808      5.6138|
|  7:  2.5886 -  2.4595 0.99   1309  137 0.1522 0.1987      5.3399      5.4845|
|  8:  2.4595 -  2.3529 0.98   1300  152 0.1512 0.2192      5.2867      5.5719|
|  9:  2.3529 -  2.2626 0.98   1305  147 0.1515 0.2263      5.2448      5.5039|
| 10:  2.2626 -  2.1848 1.00   1302  147 0.1426 0.1998      5.1527      5.3706|
| 11:  2.1848 -  2.1166 0.98   1312  138 0.1380 0.2206      5.1255      5.4663|
| 12:  2.1166 -  2.0563 0.98   1289  143 0.1470 0.2116      5.0799      5.3306|
| 13:  2.0563 -  2.0023 0.98   1268  142 0.1437 0.2011      4.9519      5.1454|
| 14:  2.0023 -  1.9535 0.31    410   47 0.1249 0.1692       4.803       4.989|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0489 -  4.6645  1421   158  0.93  10.58   0.97     0.95       8774.73|
|  2:  4.6645 -  3.7208  1373   155  0.94   9.69   1.03     1.01      11748.79|
|  3:  3.7208 -  3.2559  1343   142  0.91  14.50   1.05     1.04      14800.51|
|  4:  3.2559 -  2.9607  1332   155  0.88  18.13   1.02     1.00      15881.01|
|  5:  2.9607 -  2.7498  1336   149  0.86  20.13   1.01     0.97      12730.27|
|  6:  2.7498 -  2.5886  1330   147  0.86  20.57   0.99     0.94      10424.77|
|  7:  2.5886 -  2.4595  1309   137  0.87  19.80   1.00     0.97       9332.80|
|  8:  2.4595 -  2.3529  1300   152  0.86  20.83   0.99     0.95       8596.62|
|  9:  2.3529 -  2.2626  1305   147  0.86  20.49   1.00     0.95       7893.31|
| 10:  2.2626 -  2.1848  1302   147  0.86  20.65   1.01     0.96       6873.34|
| 11:  2.1848 -  2.1166  1312   138  0.87  19.90   1.01     0.95       6522.77|
| 12:  2.1166 -  2.0563  1289   143  0.86  20.94   1.02     1.00       6170.63|
| 13:  2.0563 -  2.0023  1268   142  0.87  20.16   1.00     0.96       4595.07|
| 14:  2.0023 -  1.9535   410    47  0.90  16.39   1.00     0.97       3195.78|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     3195.78 max =        15881.01 mean =      9460.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        18.05|
|phase err.(test): min =        0.00 max =           89.54 mean =        17.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.636)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    99.21   16.29    None  None   None       |
|    all(noH): 2823   0      1.73    99.21   16.29    None  None   None       |
|    Sol.    : 438    0      3.15    96.04   43.41    None  None   None       |
|    Mac.    : 2385   0      1.73    99.21   11.31    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:     1.733 -  11.481: 1648   |   5:    50.471 -  60.219:   88        |
|      1:    11.481 -  21.228:  592   |   6:    60.219 -  69.967:   51        |
|      2:    21.228 -  30.976:  175   |   7:    69.967 -  79.715:   32        |
|      3:    30.976 -  40.724:  116   |   8:    79.715 -  89.462:   11        |
|      4:    40.724 -  50.471:  102   |   9:    89.462 -  99.210:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.670 - 5.935
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 345
   mapped sites are within: 0.700 - 5.935

peak=    9.335 closest distance to " CB  VAL A 296 " =    1.474
peak=    8.036 closest distance to " CG2 VAL A 230 " =    1.479
peak=    7.355 closest distance to " O   HOH Z 130 " =    2.364
peak=    7.304 closest distance to " O   HOH Z 268 " =    1.245
peak=    6.734 closest distance to " CG  ARG A 138 " =    1.247
peak=    6.604 closest distance to " CD2 LEU A   5 " =    1.559
peak=    6.277 closest distance to " O   HOH Z 387 " =    1.535
peak=    6.267 closest distance to " O   HOH Z 390 " =    1.121
peak=    6.240 closest distance to " O   HOH Z 415 " =    1.514
peak=    5.806 closest distance to " CD1AILE A 234 " =    1.112
peak=    5.783 closest distance to " O   HOH Z  65 " =    1.787
peak=    5.700 closest distance to " O   PRO A 198 " =    1.364
peak=    5.589 closest distance to " O   HOH Z 424 " =    1.731
peak=    5.574 closest distance to " NH1 ARG A 138 " =    0.994
peak=    5.509 closest distance to " O   HOH Z 350 " =    1.467
peak=    5.415 closest distance to " O   HOH Z 375 " =    1.347
peak=    5.403 closest distance to " O   HOH Z  46 " =    1.271
peak=    5.273 closest distance to " O   HOH Z 111 " =    2.028
peak=    5.178 closest distance to " O   HOH Z   9 " =    1.923
peak=    5.176 closest distance to " O   HOH Z 403 " =    1.536
peak=    5.168 closest distance to " O   HOH Z 222 " =    1.533
peak=    5.143 closest distance to " CB  SER A 216 " =    1.071
peak=    5.133 closest distance to " O   HOH Z   7 " =    2.159
peak=    5.027 closest distance to " NE2 GLN A  11 " =    1.238
peak=    5.023 closest distance to " O   HOH Z  63 " =    1.863
peak=    4.971 closest distance to " CB  PRO A  54 " =    1.148
peak=    4.965 closest distance to " O   HOH Z 105 " =    1.261
peak=    4.861 closest distance to " O   HOH Z 209 " =    2.415
peak=    4.838 closest distance to " O   HOH Z 417 " =    1.789
peak=    4.834 closest distance to " O   HOH Z 124 " =    1.702
peak=    4.828 closest distance to " O   HOH Z 214 " =    1.355
peak=    4.729 closest distance to " O   HOH Z 400 " =    0.853
peak=    4.694 closest distance to " O   HOH Z 225 " =    1.690
peak=    4.691 closest distance to " O   HOH Z  63 " =    1.989
peak=    4.687 closest distance to " O   HOH Z 142 " =    2.037
peak=    4.678 closest distance to " O   HOH Z  24 " =    2.111
peak=    4.671 closest distance to " O   HOH Z  27 " =    1.177
peak=    4.664 closest distance to " CE  MET A  93 " =    1.442
peak=    4.622 closest distance to " CB  SER A   3 " =    1.478
peak=    4.573 closest distance to " O   HOH Z 358 " =    1.419
peak=    4.570 closest distance to " O   HOH Z 427 " =    2.245
peak=    4.561 closest distance to " O   HOH Z 418 " =    1.223
peak=    4.531 closest distance to " O   HOH Z  59 " =    1.526
peak=    4.483 closest distance to " O   HOH Z 410 " =    1.587
peak=    4.456 closest distance to " O   HOH Z 127 " =    1.143
peak=    4.449 closest distance to " CG  PRO A 198 " =    1.386
peak=    4.443 closest distance to " NZ BLYS A 290 " =    1.058
peak=    4.421 closest distance to " O   HOH Z 361 " =    1.684
peak=    4.417 closest distance to " OE1 GLU A   2 " =    1.807
peak=    4.412 closest distance to " O   HOH Z 239 " =    1.520
peak=    4.397 closest distance to " CB  VAL A 230 " =    1.228
peak=    4.356 closest distance to " CG  LEU A 228 " =    1.178
peak=    4.353 closest distance to " CB  ARG A 275 " =    1.175
peak=    4.351 closest distance to " O   HOH Z 258 " =    2.278
peak=    4.345 closest distance to " CB  ASP A 124 " =    1.011
peak=    4.323 closest distance to " O   HOH Z 139 " =    1.965
peak=    4.291 closest distance to " O   HOH Z 232 " =    2.079
peak=    4.276 closest distance to " O   HOH Z 360 " =    1.143
peak=    4.255 closest distance to " O   HOH Z 293 " =    1.431
peak=    4.246 closest distance to " CG  PRO A  54 " =    1.451
peak=    4.242 closest distance to " O   HOH Z 133 " =    1.723
peak=    4.236 closest distance to " O   HOH Z 233 " =    1.479
peak=    4.235 closest distance to " O   HOH Z 427 " =    1.192
peak=    4.214 closest distance to " O   HOH Z 380 " =    2.113
peak=    4.197 closest distance to " N   GLN A 278 " =    0.911
peak=    4.184 closest distance to " O   HOH Z 112 " =    1.221
peak=    4.171 closest distance to " CD  ARG A 138 " =    0.923
peak=    4.163 closest distance to " O   HOH Z 316 " =    3.095
peak=    4.160 closest distance to " O   HOH Z 419 " =    2.219
peak=    4.126 closest distance to " O   HOH Z 363 " =    1.211
peak=    4.115 closest distance to " O   HOH Z 414 " =    1.792
peak=    4.101 closest distance to " CG  PRO A 213 " =    1.304
peak=    4.092 closest distance to " NH2AARG A 145 " =    2.309
peak=    4.078 closest distance to " O   HOH Z 423 " =    1.837
peak=    4.066 closest distance to " NZ  LYS A 117 " =    1.201
peak=    4.065 closest distance to " OG  SER A 276 " =    0.945
peak=    4.057 closest distance to " O   HOH Z 303 " =    2.186
peak=    4.057 closest distance to " O  BHOH Z  74 " =    1.276
peak=    4.051 closest distance to " O   HOH Z 130 " =    2.281
peak=    4.044 closest distance to " O   HOH Z 392 " =    1.540
peak=    4.039 closest distance to " O   HOH Z 287 " =    1.663
peak=    4.031 closest distance to " CG2 ILE A 234 " =    0.902
peak=    4.025 closest distance to " O   HOH Z 146 " =    1.766
peak=    4.015 closest distance to " O   HOH Z 426 " =    1.134
peak=    4.009 closest distance to " O   HOH Z 389 " =    1.566
peak=    4.008 closest distance to " O   HOH Z 158 " =    2.644
peak=    4.004 closest distance to " CA  ILE A 234 " =    1.074
peak=    3.994 closest distance to " CG  LEU A   5 " =    1.240
peak=    3.985 closest distance to " O   HOH Z  78 " =    1.816
peak=    3.981 closest distance to " O   HOH Z 236 " =    1.982
peak=    3.977 closest distance to " O   HOH Z 371 " =    2.151
peak=    3.975 closest distance to " O   HOH Z 416 " =    1.466
peak=    3.943 closest distance to " CB  GLU A 128 " =    1.063
peak=    3.937 closest distance to " N   TYR A  15 " =    0.974
peak=    3.917 closest distance to " CA  ASN A 127 " =    1.181
peak=    3.909 closest distance to " CB  GLN A 223 " =    1.361
peak=    3.909 closest distance to " O   HOH Z 132 " =    1.125
peak=    3.909 closest distance to " CG  PRO A 280 " =    0.960
peak=    3.908 closest distance to " OD1 ASP A 200 " =    1.498
peak=    3.900 closest distance to " O   HOH Z 123 " =    1.100
peak=    3.891 closest distance to " O   ASN A 285 " =    0.928
peak=    3.887 closest distance to " CD2 LEU A 228 " =    1.350
peak=    3.880 closest distance to " O   HOH Z 369 " =    2.022
peak=    3.873 closest distance to " CB  ASN A 148 " =    1.415
peak=    3.844 closest distance to " CB  LYS A 290 " =    1.012
peak=    3.836 closest distance to " O   HOH Z 371 " =    2.952
peak=    3.803 closest distance to " O   HOH Z   6 " =    2.126
peak=    3.798 closest distance to " OD2 ASP A  50 " =    1.108
peak=    3.775 closest distance to " CA  ALA A 295 " =    0.945
peak=    3.774 closest distance to " O   HOH Z 384 " =    1.725
peak=    3.773 closest distance to " O   HOH Z 215 " =    1.587
peak=    3.771 closest distance to " CG2 THR A 221 " =    1.239
peak=    3.769 closest distance to " NH2 ARG A 269 " =    0.969
peak=    3.758 closest distance to " CB  ALA A 114 " =    1.226
peak=    3.755 closest distance to " O   HOH Z 217 " =    2.847
peak=    3.736 closest distance to " O   HOH Z 374 " =    1.206
peak=    3.731 closest distance to " O   HOH Z   7 " =    3.056
peak=    3.718 closest distance to " O   HOH Z 342 " =    0.960
peak=    3.713 closest distance to " CG  LEU A 167 " =    1.373
peak=    3.704 closest distance to " O   HOH Z 153 " =    3.462
peak=    3.700 closest distance to " O   HOH Z   1 " =    1.862
peak=    3.699 closest distance to " NE AARG A 275 " =    1.496
peak=    3.689 closest distance to " CA  ALA A  51 " =    1.200
peak=    3.688 closest distance to " NE1 TRP A 274 " =    1.085
peak=    3.684 closest distance to " CB  VAL A 202 " =    1.647
peak=    3.671 closest distance to " N   GLY A 136 " =    1.128
peak=    3.669 closest distance to " CG  PRO A 243 " =    1.103
peak=    3.662 closest distance to " CD  GLN A  58 " =    5.625
peak=    3.662 closest distance to " O   HOH Z 368 " =    3.163
peak=    3.656 closest distance to " ND2 ASN A  60 " =    3.108
peak=    3.653 closest distance to " O   HOH Z 193 " =    1.758
peak=    3.651 closest distance to " CB  SER A  63 " =    1.320
peak=    3.633 closest distance to " CG1BVAL A 121 " =    2.285
peak=    3.609 closest distance to " CB  SER A  62 " =    1.145
peak=    3.606 closest distance to " CA  ALA A  21 " =    1.022
peak=    3.603 closest distance to " N   GLN A  73 " =    1.124
peak=    3.601 closest distance to " CE3 TRP A 274 " =    1.387
peak=    3.594 closest distance to " N   VAL A 296 " =    1.749
peak=    3.590 closest distance to " CB  GLU A 277 " =    3.648
peak=    3.585 closest distance to " O   HOH Z 172 " =    1.753
peak=    3.585 closest distance to " O   HOH Z 356 " =    1.940
peak=    3.584 closest distance to " O   HOH Z  39 " =    1.381
peak=    3.577 closest distance to " O   HOH Z  77 " =    1.187
peak=    3.573 closest distance to " CB  TRP A 266 " =    0.993
peak=    3.570 closest distance to " O   HOH Z  30 " =    1.297
peak=    3.565 closest distance to " O   HOH Z 357 " =    1.349
peak=    3.564 closest distance to " N   SER A  97 " =    0.805
peak=    3.563 closest distance to " O   HOH Z 238 " =    1.239
peak=    3.559 closest distance to " CD  GLN A 240 " =    1.800
peak=    3.557 closest distance to " CB  GLN A 183 " =    1.102
peak=    3.557 closest distance to " O   HOH Z  58 " =    1.995
peak=    3.541 closest distance to " CG  GLN A  11 " =    2.244
peak=    3.539 closest distance to " CG2 ILE A 120 " =    0.964
peak=    3.536 closest distance to " O   HOH Z  47 " =    1.768
peak=    3.536 closest distance to " CA  SER A  87 " =    0.934
peak=    3.535 closest distance to " CA  LEU A 222 " =    1.079
peak=    3.530 closest distance to " N   GLU A   2 " =    1.448
peak=    3.529 closest distance to " O   HOH Z 244 " =    1.540
peak=    3.522 closest distance to " CA  ASN A 284 " =    0.975
peak=    3.521 closest distance to " CB  TRP A 179 " =    1.389
peak=    3.520 closest distance to " CA  ARG A 102 " =    1.114
peak=    3.520 closest distance to " O   HOH Z 378 " =    1.091
peak=    3.511 closest distance to " O   HOH Z 145 " =    2.712
peak=    3.502 closest distance to " O   HOH Z  28 " =    1.519
peak=    3.497 closest distance to " CD BLYS A 290 " =    1.062
peak=    3.492 closest distance to " CB  PHE A 225 " =    1.471
peak=    3.490 closest distance to " O   HOH Z  26 " =    1.663
peak=    3.488 closest distance to " CD1 LEU A   5 " =    1.417
peak=    3.485 closest distance to " O   HOH Z 178 " =    1.211
peak=    3.485 closest distance to " O   HOH Z 359 " =    1.263
peak=    3.485 closest distance to " O   HOH Z 147 " =    1.553
peak=    3.483 closest distance to " CB  TYR A 169 " =    0.700
peak=    3.481 closest distance to " O   HOH Z 263 " =    1.490
peak=    3.478 closest distance to " O   HOH Z  68 " =    2.076
peak=    3.475 closest distance to " NE2 GLN A  73 " =    1.479
peak=    3.463 closest distance to " O   HOH Z 366 " =    2.803
peak=    3.456 closest distance to " CA  ARG A  36 " =    1.065
peak=    3.453 closest distance to " O   HOH Z 176 " =    1.869
peak=    3.449 closest distance to " O   HOH Z  94 " =    2.407
peak=    3.444 closest distance to " O   HOH Z 143 " =    1.538
peak=    3.444 closest distance to " OD2 ASP A 286 " =    2.362
peak=    3.441 closest distance to " CB  ALA A  10 " =    1.003
peak=    3.440 closest distance to " NH1AARG A 145 " =    1.026
peak=    3.438 closest distance to " OD1 ASN A 217 " =    1.658
peak=    3.436 closest distance to " CB  LEU A 300 " =    0.881
peak=    3.433 closest distance to " O   HOH Z 298 " =    1.970
peak=    3.423 closest distance to " C   THR A  18 " =    1.098
peak=    3.423 closest distance to " O   HOH Z 289 " =    1.231
peak=    3.421 closest distance to " O   HOH Z 184 " =    1.652
peak=    3.417 closest distance to " CB  THR A  31 " =    1.728
peak=    3.415 closest distance to " O   HOH Z 431 " =    1.003
peak=    3.409 closest distance to " CD  ARG A 269 " =    0.981
peak=    3.407 closest distance to " CB  SER A 273 " =    0.977
peak=    3.403 closest distance to " CB  LEU A 228 " =    1.385
peak=    3.400 closest distance to " O   HOH Z 227 " =    1.687
peak=    3.400 closest distance to " CA  TRP A  92 " =    1.255
peak=    3.398 closest distance to " O   HOH Z 133 " =    2.568
peak=    3.397 closest distance to " CB  MET A  47 " =    1.045
peak=    3.397 closest distance to " O   HOH Z 245 " =    1.364
peak=    3.396 closest distance to " CA  TYR A  30 " =    0.962
peak=    3.391 closest distance to " O   HOH Z  66 " =    1.166
peak=    3.388 closest distance to " CE3 TRP A  85 " =    0.984
peak=    3.387 closest distance to " N   CYS A 260 " =    1.145
peak=    3.385 closest distance to " O   HOH Z  43 " =    1.397
peak=    3.385 closest distance to " CB  GLU A 277 " =    1.038
peak=    3.384 closest distance to " CG2 THR A 251 " =    1.721
peak=    3.384 closest distance to " O   HOH Z 119 " =    1.441
peak=    3.382 closest distance to " O   HOH Z  44 " =    2.569
peak=    3.379 closest distance to " CB  SER A 210 " =    0.972
peak=    3.377 closest distance to " CG  GLN A 278 " =    4.034
peak=    3.376 closest distance to " O   GLY A 302 " =    2.428
peak=    3.375 closest distance to " CA  ARG A 195 " =    1.303
peak=    3.375 closest distance to " O   HOH Z  91 " =    2.349
peak=    3.374 closest distance to " O   HOH Z  97 " =    1.492
peak=    3.374 closest distance to " CG1 ILE A  33 " =    1.333
peak=    3.373 closest distance to " O   HOH Z 422 " =    2.661
peak=    3.367 closest distance to " O   HOH Z 406 " =    1.784
peak=    3.366 closest distance to " ND2BASN A 224 " =    0.857
peak=    3.363 closest distance to " CA  ALA A 299 " =    0.928
peak=    3.360 closest distance to " O   HOH Z 128 " =    2.015
peak=    3.354 closest distance to " OD1 ASP A 238 " =    0.833
peak=    3.350 closest distance to " O   HOH Z 425 " =    1.952
peak=    3.346 closest distance to " CE  LYS A  48 " =    1.042
peak=    3.343 closest distance to " OE2 GLU A   2 " =    2.042
peak=    3.343 closest distance to " CG  ARG A 159 " =    0.861
peak=    3.343 closest distance to " NH2AARG A 145 " =    1.080
peak=    3.340 closest distance to " O   HOH Z 158 " =    2.638
peak=    3.337 closest distance to " O   HOH Z  88 " =    3.556
peak=    3.332 closest distance to " O   HOH Z 423 " =    1.560
peak=    3.326 closest distance to " CG2 THR A 279 " =    0.972
peak=    3.321 closest distance to " CG1AVAL A 121 " =    0.898
peak=    3.315 closest distance to " CA  LEU A 282 " =    1.069
peak=    3.311 closest distance to " CG2 THR A 178 " =    1.309
peak=    3.310 closest distance to " O   HOH Z 434 " =    1.414
peak=    3.309 closest distance to " O   HOH Z 375 " =    2.137
peak=    3.309 closest distance to " CG1 ILE A 120 " =    1.485
peak=    3.308 closest distance to " CA  ALA A 158 " =    1.145
peak=    3.307 closest distance to " O   HOH Z 148 " =    1.706
peak=    3.303 closest distance to " O   HOH Z 368 " =    1.745
peak=    3.300 closest distance to " CB  ASP A 140 " =    0.953
peak=    3.298 closest distance to " N   ASN A 209 " =    1.466
peak=    3.297 closest distance to " O   HOH Z  50 " =    1.620
peak=    3.291 closest distance to " O   HOH Z 120 " =    0.964
peak=    3.291 closest distance to " CB  LEU A 143 " =    1.017
peak=    3.291 closest distance to " CD2 LEU A 297 " =    0.905
peak=    3.289 closest distance to " O   HOH Z 402 " =    1.443
peak=    3.287 closest distance to " C   ASN A 209 " =    1.813
peak=    3.287 closest distance to " CG  LYS A  76 " =    1.670
peak=    3.286 closest distance to " CE3 TRP A 150 " =    1.126
peak=    3.284 closest distance to " CB  ARG A 138 " =    0.948
peak=    3.281 closest distance to " O   HOH Z 207 " =    2.700
peak=    3.281 closest distance to " O   HOH Z 193 " =    1.439
peak=    3.280 closest distance to " O   HOH Z 353 " =    1.820
peak=    3.279 closest distance to " O   HOH Z 106 " =    2.610
peak=    3.279 closest distance to " CH2 TRP A 150 " =    0.924
peak=    3.278 closest distance to " O   HOH Z 411 " =    3.336
peak=    3.274 closest distance to " N   SER A 210 " =    0.889
peak=    3.272 closest distance to " O   HOH Z  57 " =    1.103
peak=    3.270 closest distance to " O   HOH Z 272 " =    1.849
peak=    3.266 closest distance to " CB  ASN A  39 " =    0.891
peak=    3.263 closest distance to " CE2 PHE A  16 " =    0.840
peak=    3.262 closest distance to " O   HOH Z 405 " =    1.871
peak=    3.260 closest distance to " O   HOH Z 240 " =    2.010
peak=    3.260 closest distance to " OG BSER A 258 " =    0.909
peak=    3.258 closest distance to " O   HOH Z 329 " =    3.960
peak=    3.257 closest distance to " O   HOH Z 353 " =    2.175
peak=    3.256 closest distance to " O   HOH Z  88 " =    2.126
peak=    3.254 closest distance to " O   HOH Z 255 " =    0.924
peak=    3.252 closest distance to " NH1 ARG A  14 " =    1.061
peak=    3.248 closest distance to " CB  VAL A 265 " =    1.373
peak=    3.243 closest distance to " CZ  PHE A 192 " =    0.819
peak=    3.240 closest distance to " CA  GLU A 152 " =    0.950
peak=    3.237 closest distance to " O   HOH Z  54 " =    1.424
peak=    3.233 closest distance to " CB  ASN A 127 " =    0.877
peak=    3.232 closest distance to " CB  SER A 276 " =    1.213
peak=    3.231 closest distance to " CB  ARG A  79 " =    1.174
peak=    3.229 closest distance to " O   HOH Z 151 " =    1.485
peak=    3.229 closest distance to " CB  ALA A 104 " =    0.884
peak=    3.226 closest distance to " CG2 VAL A 202 " =    1.401
peak=    3.223 closest distance to " O   HOH Z 114 " =    1.976
peak=    3.220 closest distance to " O   HOH Z  52 " =    1.054
peak=    3.220 closest distance to " O   HOH Z 158 " =    1.187
peak=    3.219 closest distance to " CA  GLN A  55 " =    1.247
peak=    3.218 closest distance to " CB  ASP A 200 " =    0.966
peak=    3.218 closest distance to " NH1 ARG A  56 " =    1.225
peak=    3.218 closest distance to " O   HOH Z  61 " =    1.789
peak=    3.216 closest distance to " C   VAL A 153 " =    1.137
peak=    3.212 closest distance to " O   HOH Z 282 " =    2.384
peak=    3.211 closest distance to " CB  MET A  40 " =    0.771
peak=    3.208 closest distance to " O   ASN A 301 " =    2.171
peak=    3.203 closest distance to " NZ  LYS A  48 " =    1.917
peak=    3.200 closest distance to " O   HOH Z 110 " =    1.793
peak=    3.198 closest distance to " N   PHE A 130 " =    1.226
peak=    3.196 closest distance to " CA  ALA A 160 " =    1.030
peak=    3.194 closest distance to " CE1 PHE A  38 " =    1.089
peak=    3.192 closest distance to " CG  ARG A 156 " =    1.227
peak=    3.188 closest distance to " NH2BARG A 145 " =    2.043
peak=    3.187 closest distance to " O   HOH Z 417 " =    1.625
peak=    3.184 closest distance to " OG BSER A 212 " =    2.924
peak=    3.184 closest distance to " O   HOH Z 422 " =    0.871
peak=    3.181 closest distance to " CB  ASN A 110 " =    0.945
peak=    3.179 closest distance to " CG2 THR A 220 " =    1.047
peak=    3.175 closest distance to " O   HOH Z 294 " =    1.688
peak=    3.175 closest distance to " O   HOH Z 125 " =    1.770
peak=    3.174 closest distance to " O   HOH Z  11 " =    1.057
peak=    3.171 closest distance to " OE1 GLN A 278 " =    1.316
peak=    3.166 closest distance to " O   HOH Z 352 " =    1.476
peak=    3.164 closest distance to " CB  ASN A 142 " =    1.025
peak=    3.164 closest distance to " CA  PHE A 283 " =    1.345
peak=    3.160 closest distance to " O   ALA A 291 " =    1.611
peak=    3.158 closest distance to " O   HOH Z  88 " =    3.857
peak=    3.153 closest distance to " O   HOH Z 214 " =    1.720
peak=    3.153 closest distance to " O   HOH Z 139 " =    5.935
peak=    3.153 closest distance to " O   HOH Z 108 " =    2.132
peak=    3.148 closest distance to " O   ALA A 165 " =    1.279
peak=    3.146 closest distance to " O   HOH Z 196 " =    1.319
peak=    3.145 closest distance to " CG2 VAL A 268 " =    0.845
peak=    3.145 closest distance to " OD1 ASP A 286 " =    1.132
peak=    3.144 closest distance to " O   THR A 251 " =    1.115
peak=    3.141 closest distance to " CD1 LEU A 228 " =    1.675
peak=    3.139 closest distance to " O   HOH Z 279 " =    2.349
peak=    3.136 closest distance to " CD1 ILE A  33 " =    1.714
peak=    3.134 closest distance to " O   VAL A  72 " =    0.879
peak=    3.124 closest distance to " O   HOH Z 389 " =    1.310
peak=    3.115 closest distance to " O   HOH Z 248 " =    2.038
peak=    3.109 closest distance to " O   HOH Z 387 " =    1.959
peak=    3.103 closest distance to " OG BSER A  99 " =    2.182
peak=    3.100 closest distance to " CA  GLY A 267 " =    1.324
peak=    3.098 closest distance to " O   HOH Z  51 " =    1.471
peak=    3.095 closest distance to " O   HOH Z 217 " =    1.679
peak=    3.094 closest distance to " N   LEU A 297 " =    1.062
peak=    3.092 closest distance to " O   HOH Z 287 " =    1.998
peak=    3.083 closest distance to " OG1 THR A 157 " =    1.157
peak=    3.070 closest distance to " O   HOH Z 104 " =    1.403
peak=    3.064 closest distance to " CG2 VAL A 202 " =    1.281
peak=    3.055 closest distance to " O   THR A 220 " =    1.778
peak=    3.053 closest distance to " O   HOH Z  61 " =    1.407
peak=    3.045 closest distance to " O   HOH Z 280 " =    2.705
peak=    3.035 closest distance to " O   HOH Z 323 " =    1.725
peak=    3.013 closest distance to " O   HOH Z 380 " =    1.592

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.682 - 5.922
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.733 - 5.922

peak=   -4.792 closest distance to " CG2 VAL A 230 " =    0.871
peak=   -4.790 closest distance to " CG  MET A 105 " =    0.931
peak=   -4.592 closest distance to " CD  ARG A  14 " =    3.067
peak=   -4.477 closest distance to " CD  ARG A 138 " =    1.197
peak=   -4.406 closest distance to " O   PRO A 198 " =    1.180
peak=   -4.219 closest distance to " OE1 GLU A 277 " =    2.511
peak=   -4.215 closest distance to " N   THR A 157 " =    1.764
peak=   -4.175 closest distance to " CG1 VAL A 296 " =    0.733
peak=   -4.122 closest distance to " OG BSER A 134 " =    1.671
peak=   -4.071 closest distance to " CG BLYS A 290 " =    0.837
peak=   -4.033 closest distance to " OG  SER A  97 " =    2.248
peak=   -3.958 closest distance to " OG ASER A 134 " =    1.079
peak=   -3.941 closest distance to " O   SER A 135 " =    1.515
peak=   -3.919 closest distance to " O   HOH Z 163 " =    1.570
peak=   -3.918 closest distance to " CB  ASP A  27 " =    2.419
peak=   -3.915 closest distance to " O   HOH Z 198 " =    2.273
peak=   -3.878 closest distance to " O   HOH Z  95 " =    1.304
peak=   -3.865 closest distance to " O   HOH Z 415 " =    0.878
peak=   -3.849 closest distance to " NE1 TRP A 179 " =    1.117
peak=   -3.842 closest distance to " CD  LYS A 166 " =    2.619
peak=   -3.840 closest distance to " C   PHE A 155 " =    0.833
peak=   -3.838 closest distance to " O   HOH Z 385 " =    1.078
peak=   -3.826 closest distance to " O   HOH Z 129 " =    4.640
peak=   -3.814 closest distance to " N   LEU A 282 " =    2.287
peak=   -3.812 closest distance to " O   HOH Z 313 " =    1.039
peak=   -3.809 closest distance to " CA  GLY A 133 " =    2.015
peak=   -3.789 closest distance to " O   ALA A  51 " =    1.260
peak=   -3.786 closest distance to " CG  PRO A 163 " =    2.480
peak=   -3.783 closest distance to " CD1 LEU A 222 " =    2.366
peak=   -3.763 closest distance to " O   HOH Z  39 " =    0.993
peak=   -3.743 closest distance to " O   HOH Z 435 " =    2.219
peak=   -3.735 closest distance to " O   HOH Z  76 " =    1.156
peak=   -3.735 closest distance to " O   HOH Z 359 " =    1.536
peak=   -3.730 closest distance to " CD  GLN A  77 " =    1.204
peak=   -3.724 closest distance to " O   HOH Z  52 " =    0.885
peak=   -3.720 closest distance to " OG  SER A  26 " =    0.891
peak=   -3.701 closest distance to " O   HOH Z 286 " =    1.632
peak=   -3.694 closest distance to " O   TRP A 179 " =    1.710
peak=   -3.672 closest distance to " O   HOH Z 268 " =    0.913
peak=   -3.666 closest distance to " O   HOH Z 207 " =    2.111
peak=   -3.659 closest distance to " O   HOH Z 416 " =    0.796
peak=   -3.647 closest distance to " O   HOH Z 231 " =    0.743
peak=   -3.644 closest distance to " O   HOH Z 300 " =    1.011
peak=   -3.624 closest distance to " O   HOH Z 353 " =    1.155
peak=   -3.623 closest distance to " O   ILE A  49 " =    1.627
peak=   -3.592 closest distance to " OG  SER A 206 " =    1.907
peak=   -3.586 closest distance to " O   ILE A 106 " =    2.060
peak=   -3.573 closest distance to " O   THR A 178 " =    0.883
peak=   -3.568 closest distance to " O   HOH Z 431 " =    1.123
peak=   -3.562 closest distance to " CG  TRP A 266 " =    1.877
peak=   -3.560 closest distance to " O   HOH Z 350 " =    2.036
peak=   -3.550 closest distance to " O   HOH Z 235 " =    1.007
peak=   -3.546 closest distance to " O   HOH Z 425 " =    0.747
peak=   -3.545 closest distance to " CG2 ILE A 120 " =    1.298
peak=   -3.543 closest distance to " O   HOH Z 377 " =    1.274
peak=   -3.543 closest distance to " O   HOH Z 298 " =    2.580
peak=   -3.541 closest distance to " CA  GLY A  35 " =    1.907
peak=   -3.537 closest distance to " N   ASP A 270 " =    1.364
peak=   -3.536 closest distance to " O   HOH Z 102 " =    1.731
peak=   -3.533 closest distance to " O   ASN A 301 " =    1.363
peak=   -3.512 closest distance to " O   HOH Z 136 " =    3.064
peak=   -3.508 closest distance to " O   GLN A  11 " =    1.569
peak=   -3.493 closest distance to " O   PHE A 218 " =    1.473
peak=   -3.492 closest distance to " CG  GLU A 277 " =    1.151
peak=   -3.489 closest distance to " NH2AARG A 275 " =    5.428
peak=   -3.480 closest distance to " CA  GLY A  98 " =    1.882
peak=   -3.479 closest distance to " CB  ALA A 114 " =    2.415
peak=   -3.478 closest distance to " O   HOH Z 231 " =    1.862
peak=   -3.476 closest distance to " O   HOH Z 376 " =    2.404
peak=   -3.476 closest distance to " O   GLY A  98 " =    1.988
peak=   -3.465 closest distance to " O   HOH Z  60 " =    1.662
peak=   -3.462 closest distance to " CB  VAL A 230 " =    0.967
peak=   -3.461 closest distance to " CB  PHE A 130 " =    1.141
peak=   -3.457 closest distance to " O   HOH Z  28 " =    1.257
peak=   -3.450 closest distance to " O   ALA A  84 " =    1.746
peak=   -3.449 closest distance to " O   HOH Z 298 " =    0.860
peak=   -3.440 closest distance to " O   HOH Z  77 " =    1.830
peak=   -3.437 closest distance to " O   HOH Z 131 " =    3.662
peak=   -3.429 closest distance to " O   HOH Z 275 " =    1.499
peak=   -3.426 closest distance to " O   SER A   3 " =    2.375
peak=   -3.422 closest distance to " O   HOH Z 352 " =    1.722
peak=   -3.422 closest distance to " O   ALA A 226 " =    1.345
peak=   -3.420 closest distance to " OE1 GLN A  58 " =    2.842
peak=   -3.416 closest distance to " O   HOH Z 140 " =    1.426
peak=   -3.409 closest distance to " O   TRP A  70 " =    1.524
peak=   -3.402 closest distance to " O   HOH Z 412 " =    5.922
peak=   -3.398 closest distance to " O   ASP A 191 " =    1.809
peak=   -3.397 closest distance to " CA  GLY A 203 " =    2.347
peak=   -3.397 closest distance to " O   HOH Z 126 " =    1.681
peak=   -3.395 closest distance to " CB  GLN A  55 " =    1.216
peak=   -3.387 closest distance to " O   VAL A 125 " =    2.200
peak=   -3.383 closest distance to " O   HOH Z 186 " =    1.530
peak=   -3.375 closest distance to " O   ARG A 145 " =    1.585
peak=   -3.371 closest distance to " CA  ASN A 127 " =    1.068
peak=   -3.364 closest distance to " O   SER A 210 " =    1.309
peak=   -3.364 closest distance to " N   ALA A   1 " =    1.185
peak=   -3.362 closest distance to " NE2 GLN A  55 " =    0.858
peak=   -3.359 closest distance to " CG  MET A  40 " =    2.278
peak=   -3.357 closest distance to " O   HOH Z  24 " =    1.242
peak=   -3.353 closest distance to " CB  ALA A 227 " =    2.256
peak=   -3.350 closest distance to " O   HOH Z  54 " =    0.856
peak=   -3.350 closest distance to " CE2 TYR A  30 " =    2.572
peak=   -3.349 closest distance to " CD1 TRP A 274 " =    1.013
peak=   -3.337 closest distance to " CD  LYS A 289 " =    2.344
peak=   -3.334 closest distance to " O   HOH Z 389 " =    2.272
peak=   -3.333 closest distance to " O   HOH Z 139 " =    1.996
peak=   -3.333 closest distance to " NE2 GLN A  11 " =    1.352
peak=   -3.327 closest distance to " CA  GLY A  23 " =    2.070
peak=   -3.321 closest distance to " N   GLN A  58 " =    1.105
peak=   -3.314 closest distance to " CB  TYR A  68 " =    1.226
peak=   -3.313 closest distance to " O   ALA A  10 " =    1.761
peak=   -3.312 closest distance to " O   HOH Z 420 " =    3.123
peak=   -3.312 closest distance to " C   ILE A 239 " =    1.919
peak=   -3.308 closest distance to " CG  ARG A 219 " =    2.405
peak=   -3.305 closest distance to " CD2 TYR A 116 " =    2.108
peak=   -3.300 closest distance to " CD  ARG A 139 " =    1.812
peak=   -3.292 closest distance to " CB  ASN A  39 " =    2.258
peak=   -3.289 closest distance to " CD2 TYR A 293 " =    1.892
peak=   -3.286 closest distance to " O   HOH Z 275 " =    1.744
peak=   -3.282 closest distance to " O   HOH Z  88 " =    2.260
peak=   -3.281 closest distance to " N   VAL A 125 " =    1.084
peak=   -3.275 closest distance to " CA  GLY A  57 " =    2.099
peak=   -3.271 closest distance to " CD1 LEU A   5 " =    2.490
peak=   -3.266 closest distance to " CB  PRO A 243 " =    2.566
peak=   -3.264 closest distance to " O   GLY A  80 " =    2.469
peak=   -3.263 closest distance to " CZ2 TRP A 274 " =    0.928
peak=   -3.261 closest distance to " O   HOH Z 111 " =    1.954
peak=   -3.261 closest distance to " O   HOH Z 308 " =    1.490
peak=   -3.260 closest distance to " O   HOH Z 185 " =    2.200
peak=   -3.258 closest distance to " O   ALA A   1 " =    1.295
peak=   -3.257 closest distance to " O   HOH Z 388 " =    2.260
peak=   -3.246 closest distance to " O   HOH Z 125 " =    3.861
peak=   -3.245 closest distance to " NE2 GLN A 223 " =    1.513
peak=   -3.244 closest distance to " CB  ALA A 248 " =    1.990
peak=   -3.237 closest distance to " OG  SER A 276 " =    0.908
peak=   -3.233 closest distance to " OE2 GLU A 152 " =    2.211
peak=   -3.233 closest distance to " N   ALA A  43 " =    2.563
peak=   -3.231 closest distance to " O   ASP A 298 " =    1.901
peak=   -3.226 closest distance to " O   HOH Z 266 " =    4.758
peak=   -3.225 closest distance to " CB  ALA A  43 " =    2.296
peak=   -3.222 closest distance to " OG  SER A  63 " =    1.488
peak=   -3.219 closest distance to " O   HOH Z  68 " =    1.264
peak=   -3.214 closest distance to " OE1 GLN A  58 " =    5.358
peak=   -3.212 closest distance to " CG  PHE A  59 " =    1.830
peak=   -3.212 closest distance to " N   SER A 276 " =    1.096
peak=   -3.211 closest distance to " O   HOH Z 420 " =    4.359
peak=   -3.210 closest distance to " CE3 TRP A 150 " =    2.438
peak=   -3.209 closest distance to " CD2 LEU A   5 " =    0.914
peak=   -3.208 closest distance to " OE2 GLU A 152 " =    0.974
peak=   -3.207 closest distance to " N   PRO A 163 " =    1.417
peak=   -3.207 closest distance to " CA  GLN A 240 " =    1.387
peak=   -3.202 closest distance to " CG2 THR A  31 " =    2.256
peak=   -3.200 closest distance to " CG  GLN A 240 " =    2.348
peak=   -3.199 closest distance to " O   GLY A 211 " =    1.181
peak=   -3.199 closest distance to " O   HOH Z 300 " =    2.335
peak=   -3.193 closest distance to " CG  ASP A 231 " =    0.747
peak=   -3.179 closest distance to " O   HOH Z 371 " =    1.478
peak=   -3.178 closest distance to " O   HOH Z 290 " =    1.160
peak=   -3.177 closest distance to " CD2 LEU A 237 " =    2.564
peak=   -3.176 closest distance to " OG  SER A  32 " =    1.179
peak=   -3.176 closest distance to " O   VAL A 197 " =    1.595
peak=   -3.175 closest distance to " O   GLU A 277 " =    2.236
peak=   -3.175 closest distance to " O   HOH Z  11 " =    1.954
peak=   -3.175 closest distance to " OE1 GLN A 223 " =    2.352
peak=   -3.175 closest distance to " O   HOH Z 111 " =    1.089
peak=   -3.174 closest distance to " O   HOH Z 124 " =    4.297
peak=   -3.172 closest distance to " C   SER A 206 " =    1.508
peak=   -3.171 closest distance to " ND2BASN A 224 " =    1.555
peak=   -3.171 closest distance to " O   HOH Z 143 " =    1.025
peak=   -3.170 closest distance to " OD1 ASN A 249 " =    1.550
peak=   -3.168 closest distance to " OG  SER A  63 " =    1.573
peak=   -3.163 closest distance to " O   HOH Z 165 " =    2.251
peak=   -3.163 closest distance to " O   HOH Z 179 " =    1.575
peak=   -3.162 closest distance to " O   HOH Z 211 " =    1.291
peak=   -3.160 closest distance to " O   HOH Z  30 " =    1.118
peak=   -3.160 closest distance to " N   VAL A  72 " =    1.959
peak=   -3.159 closest distance to " O   HOH Z  54 " =    1.244
peak=   -3.159 closest distance to " O   HOH Z 426 " =    1.537
peak=   -3.157 closest distance to " NH2 ARG A  79 " =    1.993
peak=   -3.147 closest distance to " O   HOH Z  52 " =    1.977
peak=   -3.142 closest distance to " C   VAL A  72 " =    0.905
peak=   -3.138 closest distance to " CB  ALA A 291 " =    2.029
peak=   -3.136 closest distance to " CD1 ILE A 239 " =    2.467
peak=   -3.135 closest distance to " CG  GLN A  88 " =    0.824
peak=   -3.134 closest distance to " O   HOH Z 361 " =    4.048
peak=   -3.131 closest distance to " CB  ASN A 301 " =    1.922
peak=   -3.130 closest distance to " O   HOH Z   1 " =    3.764
peak=   -3.118 closest distance to " O   HOH Z 393 " =    4.507
peak=   -3.115 closest distance to " O   HOH Z 364 " =    1.014
peak=   -3.114 closest distance to " CA  GLY A  23 " =    2.798
peak=   -3.112 closest distance to " CD  ARG A 156 " =    1.794
peak=   -3.108 closest distance to " CB  TYR A 172 " =    2.257
peak=   -3.107 closest distance to " O   HOH Z 368 " =    2.577
peak=   -3.107 closest distance to " CA  HIS A  86 " =    2.143
peak=   -3.104 closest distance to " C   PHE A  59 " =    1.119
peak=   -3.102 closest distance to " O   HOH Z 337 " =    1.540
peak=   -3.101 closest distance to " CZ  TYR A 169 " =    1.858
peak=   -3.100 closest distance to " O   HOH Z  60 " =    1.552
peak=   -3.093 closest distance to " O   HOH Z 429 " =    1.511
peak=   -3.087 closest distance to " CB  TYR A  15 " =    2.129
peak=   -3.086 closest distance to " OD2 ASP A 272 " =    1.379
peak=   -3.077 closest distance to " N   LYS A 166 " =    1.921
peak=   -3.066 closest distance to " CG2 ILE A 151 " =    2.382
peak=   -3.059 closest distance to " OG  SER A 245 " =    1.369
peak=   -3.055 closest distance to " N   THR A 235 " =    1.119
peak=   -3.054 closest distance to " CD2 TYR A 169 " =    2.368
peak=   -3.051 closest distance to " O   HOH Z 414 " =    1.923
peak=   -3.027 closest distance to " O   HOH Z  40 " =    4.147

================= 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    :  0.4883 0.4847   6.295618e+00   6.282368e+00
   1_bss:  0.4790 0.4725   6.289810e+00   6.274372e+00
   1_xyz:  0.4104 0.4393   6.215601e+00   6.247662e+00
   1_adp:  0.3724 0.4361   6.171603e+00   6.243461e+00
   1_occ:  0.3722 0.4362   6.171371e+00   6.243901e+00
   2_bss:  0.3709 0.4327   6.172329e+00   6.242749e+00
   2_xyz:  0.3315 0.4065   6.079962e+00   6.193515e+00
   2_adp:  0.3180 0.3964   6.058819e+00   6.180184e+00
   2_occ:  0.3178 0.3962   6.058511e+00   6.180005e+00
   3_bss:  0.3185 0.3942   6.059366e+00   6.179275e+00
   3_xyz:  0.2566 0.3292   5.876080e+00   6.039913e+00
   3_adp:  0.2344 0.3127   5.807504e+00   5.996321e+00
   3_occ:  0.2340 0.3126   5.806624e+00   5.996241e+00
   4_bss:  0.2327 0.3110   5.803242e+00   5.991954e+00
   4_xyz:  0.1856 0.2493   5.592900e+00   5.804327e+00
   4_adp:  0.1614 0.2198   5.469982e+00   5.696625e+00
   4_occ:  0.1612 0.2190   5.468117e+00   5.694209e+00
   5_bss:  0.1612 0.2191   5.466084e+00   5.692303e+00
   5_xyz:  0.1417 0.1970   5.361709e+00   5.598680e+00
   5_adp:  0.1369 0.1906   5.331567e+00   5.565555e+00
   5_occ:  0.1367 0.1903   5.330411e+00   5.564295e+00
   5_bss:  0.1367 0.1903   5.330264e+00   5.563864e+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:  0.392  20.000   6.443   9.678   6.930   0.000   0.000   0.000
   1_xyz:  0.392  20.000   6.443   9.678   6.930   0.000   0.000   0.000
   1_adp:  0.392  20.000   6.443   9.678   6.930   0.000   0.000   0.000
   1_occ:  0.392  20.000   6.443   9.678   6.930   0.000   0.000   0.000
   2_bss:  0.374  45.625   3.654   5.854   4.148   0.000   0.000   0.000
   2_xyz:  0.374  45.625   3.654   5.854   4.148   0.000   0.000   0.000
   2_adp:  0.374  45.625   3.654   5.854   4.148   0.000   0.000   0.000
   2_occ:  0.374  45.625   3.654   5.854   4.148   0.000   0.000   0.000
   3_bss:  0.368  66.309   2.964   4.076   3.638   0.000   0.000   0.000
   3_xyz:  0.368  66.309   2.964   4.076   3.638   0.000   0.000   0.000
   3_adp:  0.368  66.309   2.964   4.076   3.638   0.000   0.000   0.000
   3_occ:  0.368  66.309   2.964   4.076   3.638   0.000   0.000   0.000
   4_bss:  0.346  66.309   1.437   1.868   2.505   0.000   0.000   0.000
   4_xyz:  0.346  66.309   1.437   1.868   2.505   0.000   0.000   0.000
   4_adp:  0.346  66.309   1.437   1.868   2.505   0.000   0.000   0.000
   4_occ:  0.346  66.309   1.437   1.868   2.505   0.000   0.000   0.000
   5_bss:  0.325  53.688   1.436   1.203   2.565   0.000   0.000   0.000
   5_xyz:  0.325  53.688   1.436   1.203   2.565   0.000   0.000   0.000
   5_adp:  0.325  53.688   1.436   1.203   2.565   0.000   0.000   0.000
   5_occ:  0.325  53.688   1.436   1.203   2.565   0.000   0.000   0.000
   5_bss:  0.317  47.900  -0.255  -0.667   0.921   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.930 0.3951  0.4753    76138.134
   1_bss:  58.904 0.4077  0.6129    73700.478
   1_xyz:  53.815 0.4720  0.6943    63406.419
   1_adp:  53.071 0.4811  0.7562    62341.752
   1_occ:  53.143 0.4803  0.7545    62602.323
   2_bss:  52.840 0.4840  0.6843    62039.335
   2_xyz:  46.948 0.5568  0.7813    49994.711
   2_adp:  44.780 0.5843  0.8204    47433.881
   2_occ:  44.789 0.5841  0.8199    47409.253
   3_bss:  44.554 0.5869  0.7949    46999.363
   3_xyz:  34.988 0.7008  0.9297    30394.998
   3_adp:  32.356 0.7314  0.9607    26788.940
   3_occ:  32.355 0.7313  0.9600    26736.029
   4_bss:  32.149 0.7334  0.9079    26352.325
   4_xyz:  25.027 0.8103  0.9614    16208.407
   4_adp:  21.581 0.8459  0.9718    12639.073
   4_occ:  21.508 0.8465  0.9715    12527.230
   5_bss:  21.460 0.8468  0.9641    12438.362
   5_xyz:  18.903 0.8718  0.9773    10063.320
   5_adp:  18.006 0.8807  0.9740     9511.838
   5_occ:  17.978 0.8809  0.9737     9468.594
   5_bss:  17.983 0.8808  0.9734     9461.181
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3343e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3343e+01
   1_xyz:   1.694  0.013  0.106 18.338  0.007  4.106   1.4561e-01
   1_adp:   1.694  0.013  0.106 18.338  0.007  4.106   1.4561e-01
   1_occ:   1.694  0.013  0.106 18.338  0.007  4.106   1.4561e-01
   2_bss:   1.694  0.013  0.106 18.338  0.007  4.106   1.4561e-01
   2_xyz:   1.150  0.008  0.078 16.200  0.004  4.122   8.4584e-02
   2_adp:   1.150  0.008  0.078 16.200  0.004  4.122   8.4584e-02
   2_occ:   1.150  0.008  0.078 16.200  0.004  4.122   8.4584e-02
   3_bss:   1.150  0.008  0.078 16.200  0.004  4.122   8.4584e-02
   3_xyz:   1.378  0.010  0.096 16.871  0.005  4.103   1.1311e-01
   3_adp:   1.378  0.010  0.096 16.871  0.005  4.103   1.1311e-01
   3_occ:   1.378  0.010  0.096 16.871  0.005  4.103   1.1311e-01
   4_bss:   1.378  0.010  0.096 16.871  0.005  4.103   1.1311e-01
   4_xyz:   1.054  0.007  0.076 15.723  0.004  4.115   6.9838e-02
   4_adp:   1.054  0.007  0.076 15.723  0.004  4.115   6.9838e-02
   4_occ:   1.054  0.007  0.076 15.723  0.004  4.115   6.9838e-02
   5_bss:   1.054  0.007  0.076 15.723  0.004  4.115   6.9838e-02
   5_xyz:   0.892  0.005  0.065 15.200  0.003  4.112   5.2324e-02
   5_adp:   0.892  0.005  0.065 15.200  0.003  4.112   5.2324e-02
   5_occ:   0.892  0.005  0.065 15.200  0.003  4.112   5.2324e-02
   5_bss:   0.892  0.005  0.065 15.200  0.003  4.112   5.2324e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9116e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9116e+00
   1_xyz:  13.026  0.192  0.422 84.893  0.036  2.136   1.0026e-01
   1_adp:  13.026  0.192  0.422 84.893  0.036  2.136   1.0026e-01
   1_occ:  13.026  0.192  0.422 84.893  0.036  2.136   1.0026e-01
   2_bss:  13.026  0.192  0.422 84.893  0.036  2.136   1.0026e-01
   2_xyz:   7.731  0.102  0.292 79.307  0.052  2.017   8.9644e-02
   2_adp:   7.731  0.102  0.292 79.307  0.052  2.017   8.9644e-02
   2_occ:   7.731  0.102  0.292 79.307  0.052  2.017   8.9644e-02
   3_bss:   7.731  0.102  0.292 79.307  0.052  2.017   8.9644e-02
   3_xyz:   7.278  0.056  0.364 85.092  0.033  2.020   7.0513e-02
   3_adp:   7.278  0.056  0.364 85.092  0.033  2.020   7.0513e-02
   3_occ:   7.278  0.056  0.364 85.092  0.033  2.020   7.0513e-02
   4_bss:   7.278  0.056  0.364 85.092  0.033  2.020   7.0513e-02
   4_xyz:   6.362  0.057  0.263 84.235  0.027  2.309   5.5595e-02
   4_adp:   6.362  0.057  0.263 84.235  0.027  2.309   5.5595e-02
   4_occ:   6.362  0.057  0.263 84.235  0.027  2.309   5.5595e-02
   5_bss:   6.362  0.057  0.263 84.235  0.027  2.309   5.5595e-02
   5_xyz:   7.468  0.038  0.196 80.137  0.025  2.366   4.1075e-02
   5_adp:   7.468  0.038  0.196 80.137  0.025  2.366   4.1075e-02
   5_occ:   7.468  0.038  0.196 80.137  0.025  2.366   4.1075e-02
   5_bss:   7.468  0.038  0.196 80.137  0.025  2.366   4.1075e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  72.94   0.00  13.72  72.94   0.00  12.25  65.09   0.00  21.71
   1_occ:  72.94   0.00  13.72  72.94   0.00  12.25  65.09   0.00  21.71
   2_bss:  72.94   0.00  13.72  72.94   0.00  12.25  65.09   0.00  21.71
   2_xyz:  72.94   0.00  13.72  72.94   0.00  12.25  65.09   0.00  21.71
   2_adp: 111.88   0.00  13.71 111.88   0.00  11.80  66.70   0.00  24.10
   2_occ: 111.88   0.00  13.71 111.88   0.00  11.80  66.70   0.00  24.10
   3_bss: 111.88   0.00  13.71 111.88   0.00  11.80  66.70   0.00  24.10
   3_xyz: 111.88   0.00  13.71 111.88   0.00  11.80  66.70   0.00  24.10
   3_adp: 111.97   0.00  14.04 111.97   0.00  11.06  70.60   0.00  30.27
   3_occ: 111.97   0.00  14.04 111.97   0.00  11.06  70.60   0.00  30.27
   4_bss: 111.97   0.00  14.04 111.97   0.00  11.06  70.60   0.00  30.27
   4_xyz: 111.97   0.00  14.04 111.97   0.00  11.06  70.60   0.00  30.27
   4_adp:  88.20   0.00  14.84  88.20   0.00  10.04  87.65   1.08  40.96
   4_occ:  88.20   0.00  14.84  88.20   0.00  10.04  87.65   1.08  40.96
   5_bss:  88.20   0.00  14.84  88.20   0.00  10.04  87.65   1.08  40.96
   5_xyz:  88.20   0.00  14.84  88.20   0.00  10.04  87.65   1.08  40.96
   5_adp:  97.48   0.00  14.56  97.48   0.00   9.58  94.31   1.41  41.67
   5_occ:  97.48   0.00  14.56  97.48   0.00   9.58  94.31   1.41  41.67
   5_bss:  99.21   1.73  16.29  99.21   1.73  11.31  96.04   3.15  43.41
------------------------------------------------------------------------
 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:    1.248    0.016    0.412
   1_adp:    1.248    0.016    0.412
   1_occ:    1.248    0.016    0.412
   2_bss:    1.248    0.016    0.412
   2_xyz:    1.595    0.036    0.546
   2_adp:    1.595    0.036    0.546
   2_occ:    1.595    0.036    0.546
   3_bss:    1.595    0.036    0.546
   3_xyz:    1.703    0.057    0.717
   3_adp:    1.703    0.057    0.717
   3_occ:    1.703    0.057    0.717
   4_bss:    1.703    0.057    0.717
   4_xyz:    2.044    0.052    0.817
   4_adp:    2.044    0.052    0.817
   4_occ:    2.044    0.052    0.817
   5_bss:    2.044    0.052    0.817
   5_xyz:    2.061    0.065    0.844
   5_adp:    2.061    0.065    0.844
   5_occ:    2.061    0.065    0.844
   5_bss:    2.061    0.065    0.844
------------------------------------------------------------------------

CPU time actual refinement: 391.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_731/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_731/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_731/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_731/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_731/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 391.13 
  Macro-tasks:
    bulk solvent and scale       = 41.64  
    individual site refinement   = 178.06 
    weights calculation          = 34.77  
    collect and process          = 6.50   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 261.13 
  Micro-tasks:
    mask                            = 2.59   
    f_calc                          = 127.47 
    alpha_beta                      = 8.48   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 140.66 
    fmodel                         = 7.80   
    r_factors                      = 0.14   
    phase_errors                   = 9.79   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 298.36 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.314 micro seconds
Total CPU time: 6.76 minutes
from_scatterers_fft:    687 calls, 127.11 s
gradients_fft:          633 calls, 125.64 s

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

# Date 2008-01-16 Time 02:17:26 PST -0800 (1200478646.22 s)
Start R-work = 0.4883, R-free = 0.4847 (no bulk solvent and anisotropic scale)
Final R-work = 0.1516, R-free = 0.2037 (no bulk solvent and anisotropic scale)

Start R-work = 0.4790, R-free = 0.4725
Final R-work = 0.1367, R-free = 0.1903