# Date 2008-01-16 Time 01:56:43 PST -0800 (1200477403.31 s)
#phil __OFF__

Command line arguments: "../621.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22527
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 621

-------------------------------------------------------------------------------
  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: (70.25, 45.9914, 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: 3.36, per 1000 atoms: 1.19


================================== 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: (70.25, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.96293
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948758

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   1.9629

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: (70.25, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.96293
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948758

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2009 [2165/2190]  1946   219  10.1%
  bin  2:  4.2009 -  3.3466 [2074/2094]  1870   204   9.8%
  bin  3:  3.3466 -  2.9271 [2057/2076]  1849   208  10.1%
  bin  4:  2.9271 -  2.6611 [2029/2059]  1827   202  10.0%
  bin  5:  2.6611 -  2.4713 [2011/2030]  1814   197   9.8%
  bin  6:  2.4713 -  2.3261 [2017/2042]  1812   205  10.2%
  bin  7:  2.3261 -  2.2100 [1994/2022]  1793   201  10.1%
  bin  8:  2.2100 -  2.1141 [1990/2026]  1792   198   9.9%
  bin  9:  2.1141 -  2.0329 [1988/2030]  1791   197   9.9%
  bin 10:  2.0329 -  1.9629 [1264/2016]  1136   128  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_621/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:
        1.81 -     2.42: 35
        2.42 -     3.04: 2232
        3.04 -     3.66: 4746
        3.66 -     4.28: 9144
        4.28 -     4.90: 12405
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.842 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.982 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28557 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_621/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_621/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 = 70.25 45.9914 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: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4712   r_free= 0.4641   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.277520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.6858 0.99   1404  156 0.4030 0.3923      6.5945      6.6354|
|  2:  4.6858 -  3.7382 0.99   1348  151 0.3897 0.3551        6.79      6.7011|
|  3:  3.7382 -  3.2713 0.99   1328  143 0.4151 0.3756      6.6551      6.6457|
|  4:  3.2713 -  2.9748 0.99   1325  153 0.4625 0.4440      6.5298      6.4805|
|  5:  2.9748 -  2.7630 0.99   1309  146 0.4999 0.4996      6.3582      6.3863|
|  6:  2.7630 -  2.6009 0.99   1305  142 0.5018 0.5445       6.278      6.2116|
|  7:  2.6009 -  2.4713 0.99   1287  139 0.5052 0.4785      6.2464      6.1998|
|  8:  2.4713 -  2.3641 0.98   1289  146 0.5238 0.4891      6.1776      6.1847|
|  9:  2.3641 -  2.2735 0.98   1269  146 0.5088 0.5346      6.1089      6.1551|
| 10:  2.2735 -  2.1952 1.00   1303  142 0.5186 0.5191      6.1075       6.075|
| 11:  2.1952 -  2.1268 0.98   1281  139 0.5013 0.4856      6.0274      6.0478|
| 12:  2.1268 -  2.0662 0.98   1262  147 0.5122 0.5658      5.9698      6.0235|
| 13:  2.0662 -  2.0119 0.99   1289  135 0.5226 0.5152      5.8701      5.8029|
| 14:  2.0119 -  1.9629 0.48    631   74 0.5606 0.5176      5.8979      5.8098|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.6858  1404   156  0.67  37.18   0.79     0.72      81616.08|
|  2:  4.6858 -  3.7382  1348   151  0.72  33.10   0.87     0.80      98767.02|
|  3:  3.7382 -  3.2713  1328   143  0.63  40.93   0.87     0.76     102939.58|
|  4:  3.2713 -  2.9748  1325   153  0.54  48.60   0.80     0.64      93531.13|
|  5:  2.9748 -  2.7630  1309   146  0.42  58.10   0.75     0.52      81919.46|
|  6:  2.7630 -  2.6009  1305   142  0.39  60.57   0.72     0.45      72322.94|
|  7:  2.6009 -  2.4713  1287   139  0.35  63.39   0.76     0.41      67573.74|
|  8:  2.4713 -  2.3641  1289   146  0.33  65.08   0.73     0.40      61143.47|
|  9:  2.3641 -  2.2735  1269   146  0.36  62.95   0.74     0.42      53983.17|
| 10:  2.2735 -  2.1952  1303   142  0.37  61.94   0.76     0.45      46999.13|
| 11:  2.1952 -  2.1268  1281   139  0.36  62.84   0.78     0.44      45965.38|
| 12:  2.1268 -  2.0662  1262   147  0.30  67.39   0.79     0.39      44601.68|
| 13:  2.0662 -  2.0119  1289   135  0.27  70.18   0.72     0.35      39745.64|
| 14:  2.0119 -  1.9629   631    74  0.32  66.25   0.72     0.36      31102.42|
|alpha:            min =        0.35 max =            0.80 mean =         0.52|
|beta:             min =    31102.42 max =       102939.58 mean =     67585.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.97 mean =        56.41|
|phase err.(test): min =        0.00 max =           89.99 mean =        56.59|
|-----------------------------------------------------------------------------|

============================== 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 = 14.703756             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.928   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.292152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.187   (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:        2 |
| 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:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      699 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1529 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2680 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3962 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5113 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6609 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7784 |
|-----------------------------------------------------------------------------|
|-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 |       53.357 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.043 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    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 = 11.653)------------------------------------------|
|    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: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4777   r_free= 0.4679   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.279992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4625   r_free= 0.4502   ksol= 0.36   Bsol= 2.65   scale= 1.005    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,10.60,7.87,0.00,0.00,0.00); trace/3= 8.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.270651                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.063517             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.212   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.168981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.215   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4625      final r-factor (work) = 0.3823          |
| start r-factor (free) = 0.4502      final r-factor (free) = 0.4054          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.2078 = 12.06 * 0.50 * 6.2753 + 1.00 * 53.3567                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4604 = 12.06 * 0.50 * 6.1879 + 1.00 * 0.1363                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3823      final r-factor (work) = 0.3354          |
| start r-factor (free) = 0.4054      final r-factor (free) = 0.3911          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2480 = 1.17 * 1.00 * 6.1879 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1536 = 1.17 * 1.00 * 6.1057 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.09   13.24    None  None   None       |
|    all(noH): 2823   0      0.00    78.09   13.24    None  None   None       |
|    Sol.    : 438    0      0.00    78.09   24.55    None  None   None       |
|    Mac.    : 2385   0      0.00    72.40   11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.809: 1143   |   5:    39.043 -  46.851:   63        |
|      1:     7.809 -  15.617:  770   |   6:    46.851 -  54.660:   29        |
|      2:    15.617 -  23.426:  430   |   7:    54.660 -  62.468:   16        |
|      3:    23.426 -  31.234:  244   |   8:    62.468 -  70.277:    0        |
|      4:    31.234 -  39.043:  126   |   9:    70.277 -  78.085:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3354 r_free = 0.3911             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3351 r_free = 0.3907             target_work(ml) = 6.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3351   r_free= 0.3907   ksol= 0.36   Bsol= 2.65   scale= 1.112    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.04,10.60,7.87,0.00,0.00,0.00); trace/3= 8.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.087325                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3313   r_free= 0.3845   ksol= 0.35   Bsol= 35.21   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,6.12,4.69,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.086174                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.798966              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.091  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.594608              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.718  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3313      final r-factor (work) = 0.2676          |
| start r-factor (free) = 0.3845      final r-factor (free) = 0.3274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8790 = 6.80 * 0.50 * 6.1017 + 1.00 * 0.1363                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4434 = 6.80 * 0.50 * 5.9895 + 1.00 * 0.0821                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2676      final r-factor (work) = 0.2472          |
| start r-factor (free) = 0.3274      final r-factor (free) = 0.3140          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5779 = 0.59 * 1.00 * 5.9895 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5009 = 0.59 * 1.00 * 5.8659 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.33   13.27    None  None   None       |
|    all(noH): 2823   0      0.00    84.33   13.27    None  None   None       |
|    Sol.    : 438    0      0.00    84.33   29.87    None  None   None       |
|    Mac.    : 2385   0      0.00    71.63   10.22    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 -   8.433: 1279   |   5:    42.164 -  50.597:   45        |
|      1:     8.433 -  16.866:  771   |   6:    50.597 -  59.030:   30        |
|      2:    16.866 -  25.298:  334   |   7:    59.030 -  67.462:    6        |
|      3:    25.298 -  33.731:  224   |   8:    67.462 -  75.895:    1        |
|      4:    33.731 -  42.164:  132   |   9:    75.895 -  84.328:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2472 r_free = 0.3140             target_work(ml) = 5.845         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2469 r_free = 0.3140             target_work(ml) = 5.845         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2469   r_free= 0.3140   ksol= 0.35   Bsol= 35.21   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,6.12,4.69,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.844738                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2453   r_free= 0.3117   ksol= 0.34   Bsol= 45.64   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.30,3.42,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.842991                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.820383              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.209  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.870309              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.695  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2453      final r-factor (work) = 0.1767          |
| start r-factor (free) = 0.3117      final r-factor (free) = 0.2319          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0890 = 6.82 * 0.50 * 5.8668 + 1.00 * 0.0820                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5571 = 6.82 * 0.50 * 5.7086 + 1.00 * 0.0897                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1767      final r-factor (work) = 0.1513          |
| start r-factor (free) = 0.2319      final r-factor (free) = 0.2083          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6899 = 1.87 * 1.00 * 5.7086 + 1.00 * 0.0131                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2436 = 1.87 * 1.00 * 5.4694 + 1.00 * 0.0141                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.82   13.66    None  None   None       |
|    all(noH): 2823   0      0.00    88.82   13.66    None  None   None       |
|    Sol.    : 438    0      0.00    88.82   37.51    None  None   None       |
|    Mac.    : 2385   0      0.00    85.16   9.29     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 -   8.882: 1550   |   5:    44.411 -  53.293:   98        |
|      1:     8.882 -  17.764:  633   |   6:    53.293 -  62.175:   61        |
|      2:    17.764 -  26.647:  193   |   7:    62.175 -  71.057:   20        |
|      3:    26.647 -  35.529:  129   |   8:    71.057 -  79.940:    2        |
|      4:    35.529 -  44.411:  135   |   9:    79.940 -  88.822:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1513 r_free = 0.2083             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1512 r_free = 0.2079             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.2079   ksol= 0.34   Bsol= 45.64   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.30,3.42,0.00,0.00,0.00); trace/3= 3.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.410082                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1508   r_free= 0.2072   ksol= 0.33   Bsol= 45.64   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,2.00,3.01,0.00,0.00,0.00); trace/3= 2.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.406074                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.973175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.895   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.292286              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.159  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1508      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.2072      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9604 = 3.97 * 0.50 * 5.4720 + 1.00 * 0.0897                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6819 = 3.97 * 0.50 * 5.3425 + 1.00 * 0.0685                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.6030 = 3.29 * 1.00 * 5.3425 + 1.00 * 0.0139                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.3103 = 3.29 * 1.00 * 5.2531 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.91   13.64    None  None   None       |
|    all(noH): 2823   0      0.00    96.91   13.64    None  None   None       |
|    Sol.    : 438    0      0.00    91.67   39.22    None  None   None       |
|    Mac.    : 2385   0      0.00    96.91   8.94     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 -   9.691: 1722   |   5:    48.455 -  58.145:   89        |
|      1:     9.691 -  19.382:  552   |   6:    58.145 -  67.836:   57        |
|      2:    19.382 -  29.073:  155   |   7:    67.836 -  77.527:   23        |
|      3:    29.073 -  38.764:  118   |   8:    77.527 -  87.218:    6        |
|      4:    38.764 -  48.455:   99   |   9:    87.218 -  96.909:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1750             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1210 r_free = 0.1749             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1749   ksol= 0.33   Bsol= 45.64   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,2.00,3.01,0.00,0.00,0.00); trace/3= 2.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1744   ksol= 0.32   Bsol= 45.64   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,1.84,3.17,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228600                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.743667              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.891  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.733612              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.931   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1744      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6485 = 1.74 * 0.50 * 5.2533 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6065 = 1.74 * 0.50 * 5.2233 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8467 = 0.73 * 1.00 * 5.2233 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8454 = 0.73 * 1.00 * 5.2073 + 1.00 * 0.0253                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.38  13.25    None  None   None       |
|    all(noH): 2823   0      0.00    102.38  13.25    None  None   None       |
|    Sol.    : 438    0      1.36    92.14   38.08    None  None   None       |
|    Mac.    : 2385   0      0.00    102.38  8.69     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.238: 1817   |   5:    51.190 -  61.428:   63        |
|      1:    10.238 -  20.476:  499   |   6:    61.428 -  71.666:   37        |
|      2:    20.476 -  30.714:  154   |   7:    71.666 -  81.904:   16        |
|      3:    30.714 -  40.952:  124   |   8:    81.904 -  92.142:    8        |
|      4:    40.952 -  51.190:  104   |   9:    92.142 - 102.380:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1672             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1671             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1671   ksol= 0.32   Bsol= 45.64   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,1.84,3.17,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198156                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.6858 0.99   1404  156 0.0986 0.1260      5.3772      5.5528|
|  2:  4.6858 -  3.7382 0.99   1348  151 0.0878 0.1214      5.4658      5.6774|
|  3:  3.7382 -  3.2713 0.99   1328  143 0.1109 0.1518       5.524      5.8715|
|  4:  3.2713 -  2.9748 0.99   1325  153 0.1307 0.1842      5.5127      5.6688|
|  5:  2.9748 -  2.7630 0.99   1309  146 0.1382 0.1850      5.3677      5.6156|
|  6:  2.7630 -  2.6009 0.99   1305  142 0.1259 0.2022      5.2382      5.5435|
|  7:  2.6009 -  2.4713 0.99   1287  139 0.1336 0.1666      5.2146      5.3518|
|  8:  2.4713 -  2.3641 0.98   1289  146 0.1272 0.1745      5.1373      5.3769|
|  9:  2.3641 -  2.2735 0.98   1269  146 0.1275 0.1859      5.1074      5.3533|
| 10:  2.2735 -  2.1952 1.00   1303  142 0.1201 0.1920      5.0249      5.3119|
| 11:  2.1952 -  2.1268 0.98   1281  139 0.1213 0.1965      5.0181      5.3501|
| 12:  2.1268 -  2.0662 0.98   1262  147 0.1190 0.1853      4.9297      5.2414|
| 13:  2.0662 -  2.0119 0.99   1289  135 0.1208 0.1796      4.8323      5.0732|
| 14:  2.0119 -  1.9629 0.48    631   74 0.1055 0.1494      4.7279      4.8836|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.6858  1404   156  0.94   9.22   0.98     0.95       7156.14|
|  2:  4.6858 -  3.7382  1348   151  0.95   8.24   1.02     1.01       9574.70|
|  3:  3.7382 -  3.2713  1328   143  0.93  12.29   1.04     1.03      11696.89|
|  4:  3.2713 -  2.9748  1325   153  0.91  15.07   1.02     1.00      11701.22|
|  5:  2.9748 -  2.7630  1309   146  0.89  16.68   1.00     0.98       9117.77|
|  6:  2.7630 -  2.6009  1305   142  0.89  17.07   0.98     0.96       7585.47|
|  7:  2.6009 -  2.4713  1287   139  0.90  16.40   1.00     0.96       6792.21|
|  8:  2.4713 -  2.3641  1289   146  0.89  16.81   0.99     0.97       6174.47|
|  9:  2.3641 -  2.2735  1269   146  0.90  16.84   1.00     0.96       5883.49|
| 10:  2.2735 -  2.1952  1303   142  0.89  17.58   1.00     0.96       5207.28|
| 11:  2.1952 -  2.1268  1281   139  0.89  17.80   1.00     0.95       5181.42|
| 12:  2.1268 -  2.0662  1262   147  0.90  16.75   1.01     1.00       4479.35|
| 13:  2.0662 -  2.0119  1289   135  0.89  17.86   1.00     0.98       3735.77|
| 14:  2.0119 -  1.9629   631    74  0.91  15.01   0.99     0.96       2961.61|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2961.61 max =        11701.22 mean =      7132.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.00 mean =        14.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1671   ksol= 0.32   Bsol= 46.73   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,-0.54,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1671   ksol= 0.32   Bsol= 46.73   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,-0.54,0.93,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.198160                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.6858 0.99   1404  156 0.0986 0.1262      5.3778      5.5536|
|  2:  4.6858 -  3.7382 0.99   1348  151 0.0878 0.1213      5.4656      5.6762|
|  3:  3.7382 -  3.2713 0.99   1328  143 0.1108 0.1517      5.5235       5.871|
|  4:  3.2713 -  2.9748 0.99   1325  153 0.1307 0.1843      5.5126      5.6689|
|  5:  2.9748 -  2.7630 0.99   1309  146 0.1382 0.1852      5.3678      5.6158|
|  6:  2.7630 -  2.6009 0.99   1305  142 0.1258 0.2020      5.2381      5.5426|
|  7:  2.6009 -  2.4713 0.99   1287  139 0.1337 0.1667      5.2148      5.3523|
|  8:  2.4713 -  2.3641 0.98   1289  146 0.1273 0.1745      5.1374       5.377|
|  9:  2.3641 -  2.2735 0.98   1269  146 0.1275 0.1855      5.1075      5.3524|
| 10:  2.2735 -  2.1952 1.00   1303  142 0.1200 0.1922      5.0251      5.3135|
| 11:  2.1952 -  2.1268 0.98   1281  139 0.1213 0.1967      5.0186      5.3509|
| 12:  2.1268 -  2.0662 0.98   1262  147 0.1189 0.1853      4.9298      5.2418|
| 13:  2.0662 -  2.0119 0.99   1289  135 0.1209 0.1793       4.832       5.072|
| 14:  2.0119 -  1.9629 0.48    631   74 0.1055 0.1490      4.7267      4.8825|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.6858  1404   156  0.94   9.22   0.98     0.95       7166.65|
|  2:  4.6858 -  3.7382  1348   151  0.95   8.24   1.03     1.01       9574.18|
|  3:  3.7382 -  3.2713  1328   143  0.93  12.29   1.04     1.03      11684.41|
|  4:  3.2713 -  2.9748  1325   153  0.91  15.07   1.02     1.00      11695.73|
|  5:  2.9748 -  2.7630  1309   146  0.89  16.67   1.01     0.98       9110.58|
|  6:  2.7630 -  2.6009  1305   142  0.89  17.06   0.99     0.96       7584.54|
|  7:  2.6009 -  2.4713  1287   139  0.90  16.40   1.00     0.97       6793.36|
|  8:  2.4713 -  2.3641  1289   146  0.89  16.82   1.00     0.98       6174.90|
|  9:  2.3641 -  2.2735  1269   146  0.90  16.84   1.00     0.96       5883.16|
| 10:  2.2735 -  2.1952  1303   142  0.89  17.59   1.01     0.96       5212.64|
| 11:  2.1952 -  2.1268  1281   139  0.89  17.83   1.00     0.96       5192.08|
| 12:  2.1268 -  2.0662  1262   147  0.90  16.76   1.02     1.01       4484.82|
| 13:  2.0662 -  2.0119  1289   135  0.89  17.86   1.01     0.99       3732.75|
| 14:  2.0119 -  1.9629   631    74  0.91  14.99   1.00     0.97       2952.42|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2952.42 max =        11695.73 mean =      7132.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.03 mean =        14.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.653)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.41    104.79  15.66    None  None   None       |
|    all(noH): 2823   0      2.41    104.79  15.66    None  None   None       |
|    Sol.    : 438    0      3.77    94.55   40.49    None  None   None       |
|    Mac.    : 2385   0      2.41    104.79  11.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.408 -  12.646: 1817   |   5:    53.597 -  63.835:   63        |
|      1:    12.646 -  22.883:  499   |   6:    63.835 -  74.073:   37        |
|      2:    22.883 -  33.121:  154   |   7:    74.073 -  84.311:   16        |
|      3:    33.121 -  43.359:  124   |   8:    84.311 -  94.549:    8        |
|      4:    43.359 -  53.597:  104   |   9:    94.549 - 104.787:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.281 - 3.827
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 331
   mapped sites are within: 0.706 - 3.827

peak=   10.189 closest distance to " CB  VAL A 230 " =    1.453
peak=    8.518 closest distance to " CG2 VAL A 296 " =    1.308
peak=    8.155 closest distance to " O   HOH Z 130 " =    1.731
peak=    6.482 closest distance to " O   HOH Z  65 " =    1.503
peak=    6.453 closest distance to " CD2 LEU A   5 " =    1.308
peak=    6.163 closest distance to " NE2 GLN A  11 " =    1.180
peak=    5.599 closest distance to " CG  PRO A  54 " =    1.368
peak=    5.440 closest distance to " CG  LEU A   5 " =    1.201
peak=    5.361 closest distance to " O   HOH Z 142 " =    1.986
peak=    5.340 closest distance to " NH2 ARG A  56 " =    2.053
peak=    5.286 closest distance to " O   HOH Z   9 " =    1.711
peak=    5.169 closest distance to " CG  LEU A 228 " =    1.159
peak=    5.167 closest distance to " O   HOH Z   7 " =    1.578
peak=    5.148 closest distance to " CB  PRO A  54 " =    1.084
peak=    5.075 closest distance to " O   HOH Z 425 " =    1.611
peak=    5.052 closest distance to " O   HOH Z 124 " =    1.436
peak=    5.001 closest distance to " O   HOH Z 232 " =    2.227
peak=    4.956 closest distance to " CB  SER A   3 " =    1.420
peak=    4.937 closest distance to " O   HOH Z 427 " =    2.392
peak=    4.847 closest distance to " O   HOH Z 112 " =    1.271
peak=    4.821 closest distance to " O   HOH Z 424 " =    1.211
peak=    4.767 closest distance to " O   HOH Z 380 " =    1.924
peak=    4.743 closest distance to " O   HOH Z 222 " =    1.293
peak=    4.730 closest distance to " CB  VAL A 230 " =    1.141
peak=    4.714 closest distance to " O   HOH Z  78 " =    1.644
peak=    4.701 closest distance to " CD1AILE A 234 " =    1.025
peak=    4.698 closest distance to " O   HOH Z 417 " =    1.492
peak=    4.692 closest distance to " CB  ARG A 275 " =    0.966
peak=    4.667 closest distance to " CG  PRO A 198 " =    1.247
peak=    4.652 closest distance to " O   HOH Z 126 " =    2.014
peak=    4.546 closest distance to " O   HOH Z 423 " =    1.623
peak=    4.531 closest distance to " CB  VAL A 296 " =    1.137
peak=    4.518 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.464 closest distance to " CD2 LEU A 228 " =    1.198
peak=    4.448 closest distance to " O   PRO A 198 " =    1.306
peak=    4.445 closest distance to " O   HOH Z 209 " =    2.360
peak=    4.427 closest distance to " CB  ASN A 148 " =    1.381
peak=    4.416 closest distance to " O   HOH Z   2 " =    1.826
peak=    4.384 closest distance to " CB  GLN A 223 " =    1.500
peak=    4.383 closest distance to " O   HOH Z 369 " =    2.180
peak=    4.366 closest distance to " CB  SER A 216 " =    0.889
peak=    4.365 closest distance to " O   HOH Z 287 " =    1.828
peak=    4.360 closest distance to " CB  SER A  63 " =    1.317
peak=    4.347 closest distance to " O   HOH Z  63 " =    1.556
peak=    4.308 closest distance to " O   HOH Z 316 " =    2.995
peak=    4.242 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.191 closest distance to " O   HOH Z 422 " =    2.552
peak=    4.180 closest distance to " O   HOH Z 392 " =    1.338
peak=    4.174 closest distance to " O   HOH Z  30 " =    1.831
peak=    4.143 closest distance to " CB  GLU A 128 " =    1.072
peak=    4.142 closest distance to " CG  LEU A 167 " =    1.231
peak=    4.110 closest distance to " O   HOH Z 193 " =    1.720
peak=    4.099 closest distance to " O   SER A  87 " =    2.429
peak=    4.087 closest distance to " O   HOH Z 361 " =    1.364
peak=    4.077 closest distance to " O   HOH Z 272 " =    1.821
peak=    4.070 closest distance to " O   HOH Z 419 " =    2.094
peak=    4.064 closest distance to " O   HOH Z 139 " =    1.251
peak=    4.064 closest distance to " O   HOH Z 225 " =    1.539
peak=    4.057 closest distance to " O   HOH Z 298 " =    1.819
peak=    4.039 closest distance to " O   HOH Z 371 " =    2.795
peak=    4.038 closest distance to " O   HOH Z 236 " =    1.580
peak=    4.035 closest distance to " CB  VAL A 202 " =    1.702
peak=    3.999 closest distance to " O   HOH Z  59 " =    1.602
peak=    3.984 closest distance to " O   HOH Z 352 " =    1.710
peak=    3.978 closest distance to " O   HOH Z  68 " =    2.139
peak=    3.973 closest distance to " O   HOH Z 146 " =    1.677
peak=    3.965 closest distance to " O   HOH Z 410 " =    1.461
peak=    3.964 closest distance to " CB  TRP A 266 " =    1.065
peak=    3.939 closest distance to " O   HOH Z   1 " =    1.747
peak=    3.938 closest distance to " CG2 VAL A 257 " =    0.868
peak=    3.935 closest distance to " NH1AARG A 145 " =    1.102
peak=    3.889 closest distance to " O   HOH Z  78 " =    1.898
peak=    3.888 closest distance to " CB  VAL A 265 " =    1.320
peak=    3.881 closest distance to " CA  ASN A 127 " =    1.046
peak=    3.867 closest distance to " O   HOH Z 234 " =    3.566
peak=    3.857 closest distance to " CA  PHE A 283 " =    1.356
peak=    3.850 closest distance to " O   HOH Z 389 " =    1.330
peak=    3.850 closest distance to " O   HOH Z 346 " =    1.651
peak=    3.833 closest distance to " O   HOH Z  97 " =    1.988
peak=    3.832 closest distance to " CA  ASN A 215 " =    1.115
peak=    3.831 closest distance to " O   HOH Z 375 " =    1.025
peak=    3.828 closest distance to " CB  TRP A 179 " =    1.455
peak=    3.824 closest distance to " OG  SER A  62 " =    2.724
peak=    3.824 closest distance to " O   HOH Z 133 " =    1.561
peak=    3.807 closest distance to " CG  GLN A  11 " =    2.152
peak=    3.803 closest distance to " O   HOH Z 214 " =    2.078
peak=    3.802 closest distance to " O   HOH Z  61 " =    1.600
peak=    3.795 closest distance to " O   HOH Z 418 " =    0.956
peak=    3.781 closest distance to " O   HOH Z 368 " =    1.899
peak=    3.776 closest distance to " O   HOH Z 405 " =    1.489
peak=    3.772 closest distance to " OG  SER A  62 " =    3.048
peak=    3.757 closest distance to " CB  ASP A 124 " =    0.855
peak=    3.756 closest distance to " CG  TRP A 179 " =    2.279
peak=    3.735 closest distance to " CA  TYR A  30 " =    0.948
peak=    3.734 closest distance to " O   HOH Z 425 " =    1.967
peak=    3.732 closest distance to " N   GLN A 278 " =    1.172
peak=    3.730 closest distance to " O   HOH Z  59 " =    2.078
peak=    3.728 closest distance to " O   HOH Z 290 " =    0.906
peak=    3.720 closest distance to " NH1 ARG A 138 " =    1.082
peak=    3.716 closest distance to " NH2BARG A 145 " =    2.042
peak=    3.715 closest distance to " O   HOH Z 128 " =    1.951
peak=    3.713 closest distance to " CB BVAL A  41 " =    1.329
peak=    3.700 closest distance to " O   HOH Z  39 " =    1.311
peak=    3.698 closest distance to " CB  ASN A  39 " =    0.934
peak=    3.690 closest distance to " O   HOH Z 263 " =    1.649
peak=    3.688 closest distance to " O   HOH Z 359 " =    1.272
peak=    3.686 closest distance to " O   HOH Z 195 " =    1.430
peak=    3.685 closest distance to " CA  ILE A 234 " =    1.005
peak=    3.685 closest distance to " O   HOH Z 222 " =    2.040
peak=    3.683 closest distance to " O   HOH Z 130 " =    2.348
peak=    3.682 closest distance to " O   HOH Z 366 " =    3.079
peak=    3.677 closest distance to " O   HOH Z 427 " =    1.198
peak=    3.676 closest distance to " O   HOH Z  78 " =    2.478
peak=    3.672 closest distance to " N   PHE A 130 " =    1.266
peak=    3.670 closest distance to " CG  LYS A  76 " =    1.768
peak=    3.657 closest distance to " NZ  LYS A 117 " =    3.086
peak=    3.648 closest distance to " O   HOH Z 158 " =    2.839
peak=    3.647 closest distance to " CB  ASN A 142 " =    0.999
peak=    3.642 closest distance to " CA  ALA A  51 " =    1.080
peak=    3.638 closest distance to " O   HOH Z 368 " =    3.647
peak=    3.635 closest distance to " O   HOH Z 145 " =    1.821
peak=    3.633 closest distance to " ND2 ASN A 187 " =    1.747
peak=    3.633 closest distance to " O   HOH Z 261 " =    2.326
peak=    3.632 closest distance to " O   HOH Z 109 " =    2.333
peak=    3.618 closest distance to " CB  LYS A 117 " =    1.213
peak=    3.605 closest distance to " CE3 TRP A 150 " =    1.030
peak=    3.602 closest distance to " O   HOH Z 362 " =    2.085
peak=    3.599 closest distance to " CB  GLU A 277 " =    3.542
peak=    3.595 closest distance to " CA  ALA A 299 " =    0.965
peak=    3.590 closest distance to " CB  SER A 276 " =    1.176
peak=    3.583 closest distance to " O   HOH Z 193 " =    1.570
peak=    3.570 closest distance to " O   HOH Z 403 " =    1.455
peak=    3.565 closest distance to " O   HOH Z 424 " =    2.319
peak=    3.565 closest distance to " CH2 TRP A 266 " =    1.080
peak=    3.550 closest distance to " O   HOH Z 258 " =    2.200
peak=    3.549 closest distance to " NH2AARG A 190 " =    1.722
peak=    3.548 closest distance to " CD  ARG A 159 " =    0.725
peak=    3.548 closest distance to " O   HOH Z 411 " =    3.616
peak=    3.547 closest distance to " O   HOH Z  55 " =    1.849
peak=    3.544 closest distance to " O   HOH Z 167 " =    1.869
peak=    3.538 closest distance to " CD1 LEU A 281 " =    1.051
peak=    3.538 closest distance to " O   HOH Z 272 " =    2.187
peak=    3.538 closest distance to " O   HOH Z 189 " =    2.640
peak=    3.530 closest distance to " OG BSER A 212 " =    2.858
peak=    3.522 closest distance to " O   HOH Z   9 " =    1.654
peak=    3.522 closest distance to " CB  LEU A 228 " =    1.310
peak=    3.517 closest distance to " CB  THR A 157 " =    1.116
peak=    3.515 closest distance to " CG2 THR A 221 " =    1.259
peak=    3.513 closest distance to " N   ARG A 156 " =    1.285
peak=    3.510 closest distance to " CG BARG A 102 " =    1.938
peak=    3.506 closest distance to " O   HOH Z 193 " =    1.967
peak=    3.506 closest distance to " O   HOH Z  51 " =    1.279
peak=    3.504 closest distance to " O   HOH Z 329 " =    3.827
peak=    3.504 closest distance to " CB  LEU A 143 " =    1.086
peak=    3.502 closest distance to " O  BHOH Z  74 " =    1.362
peak=    3.491 closest distance to " CB  ARG A 190 " =    1.727
peak=    3.490 closest distance to " CB  ASN A 187 " =    1.069
peak=    3.487 closest distance to " CD  LYS A 166 " =    1.412
peak=    3.487 closest distance to " CD  ARG A 269 " =    1.003
peak=    3.471 closest distance to " O   HOH Z 133 " =    2.488
peak=    3.467 closest distance to " ND2 ASN A 110 " =    1.839
peak=    3.463 closest distance to " CB  ASN A 110 " =    1.052
peak=    3.462 closest distance to " O   HOH Z 414 " =    1.148
peak=    3.462 closest distance to " O   HOH Z 207 " =    2.298
peak=    3.462 closest distance to " OD1 ASN A  69 " =    2.542
peak=    3.456 closest distance to " O   HOH Z 438 " =    2.266
peak=    3.453 closest distance to " CB  SER A  62 " =    1.160
peak=    3.452 closest distance to " O   HOH Z 153 " =    3.668
peak=    3.451 closest distance to " CB  ILE A 234 " =    0.988
peak=    3.451 closest distance to " O   HOH Z  88 " =    3.486
peak=    3.450 closest distance to " O   ASN A 209 " =    1.502
peak=    3.448 closest distance to " O   HOH Z 184 " =    1.317
peak=    3.444 closest distance to " O   HOH Z  50 " =    1.515
peak=    3.444 closest distance to " CG  GLN A  88 " =    1.118
peak=    3.442 closest distance to " O   HOH Z 145 " =    1.894
peak=    3.437 closest distance to " CB  ARG A  79 " =    1.242
peak=    3.432 closest distance to " CG2 ILE A  20 " =    1.727
peak=    3.431 closest distance to " N   SER A 271 " =    0.989
peak=    3.427 closest distance to " CB  MET A  40 " =    0.852
peak=    3.426 closest distance to " CA  ALA A 158 " =    1.146
peak=    3.425 closest distance to " CB  VAL A 250 " =    1.052
peak=    3.424 closest distance to " NZ  LYS A 117 " =    1.181
peak=    3.423 closest distance to " CD  PRO A 243 " =    1.602
peak=    3.419 closest distance to " O   HOH Z 305 " =    3.375
peak=    3.418 closest distance to " OE1 GLN A 240 " =    1.638
peak=    3.417 closest distance to " O   HOH Z 357 " =    2.048
peak=    3.416 closest distance to " CG1 ILE A  33 " =    1.358
peak=    3.412 closest distance to " O   HOH Z 181 " =    2.299
peak=    3.411 closest distance to " CD BLYS A 290 " =    1.088
peak=    3.410 closest distance to " CB  ALA A 291 " =    1.404
peak=    3.407 closest distance to " NE2 GLN A  58 " =    3.773
peak=    3.406 closest distance to " O   HOH Z 334 " =    1.388
peak=    3.403 closest distance to " O   HOH Z 250 " =    1.335
peak=    3.401 closest distance to " O   HOH Z 402 " =    1.398
peak=    3.397 closest distance to " CZ  PHE A 218 " =    1.150
peak=    3.396 closest distance to " N   TYR A  15 " =    0.956
peak=    3.395 closest distance to " O   HOH Z 371 " =    1.845
peak=    3.393 closest distance to " CG  PRO A 243 " =    1.143
peak=    3.389 closest distance to " CB  LEU A 237 " =    0.915
peak=    3.388 closest distance to " NE1 TRP A 274 " =    0.974
peak=    3.385 closest distance to " CA  GLY A 267 " =    1.095
peak=    3.385 closest distance to " CB  LEU A 300 " =    0.872
peak=    3.384 closest distance to " O   HOH Z  44 " =    1.833
peak=    3.383 closest distance to " O   PRO A 198 " =    1.544
peak=    3.382 closest distance to " O   HOH Z 403 " =    1.524
peak=    3.381 closest distance to " CE AMET A  47 " =    1.418
peak=    3.380 closest distance to " CB  GLU A 175 " =    1.044
peak=    3.379 closest distance to " OG BSER A  99 " =    2.125
peak=    3.377 closest distance to " O   HOH Z  10 " =    1.755
peak=    3.377 closest distance to " CD1 ILE A  33 " =    1.799
peak=    3.373 closest distance to " OG BSER A 164 " =    2.138
peak=    3.373 closest distance to " NE AARG A 275 " =    1.327
peak=    3.369 closest distance to " CB  GLN A  88 " =    1.309
peak=    3.365 closest distance to " O   HOH Z 327 " =    1.566
peak=    3.365 closest distance to " O   HOH Z 122 " =    1.980
peak=    3.360 closest distance to " CA  LEU A 282 " =    1.197
peak=    3.359 closest distance to " O   HOH Z 343 " =    3.269
peak=    3.357 closest distance to " CA  THR A 221 " =    0.941
peak=    3.357 closest distance to " CA  ALA A 160 " =    0.940
peak=    3.351 closest distance to " O   HOH Z 145 " =    3.649
peak=    3.349 closest distance to " CB  SER A 212 " =    1.368
peak=    3.348 closest distance to " O   HOH Z  22 " =    2.137
peak=    3.345 closest distance to " O   HOH Z 384 " =    1.279
peak=    3.344 closest distance to " O   HOH Z 128 " =    2.172
peak=    3.340 closest distance to " N   GLU A   2 " =    1.329
peak=    3.336 closest distance to " O   HOH Z  55 " =    1.591
peak=    3.335 closest distance to " CE1 TYR A 186 " =    1.290
peak=    3.332 closest distance to " CA  SER A  87 " =    0.994
peak=    3.332 closest distance to " CG  GLN A  89 " =    1.424
peak=    3.328 closest distance to " OD2 ASP A 286 " =    2.695
peak=    3.314 closest distance to " OE1 GLU A   2 " =    1.973
peak=    3.294 closest distance to " NH1 ARG A  14 " =    0.995
peak=    3.294 closest distance to " CB  ARG A 139 " =    0.956
peak=    3.294 closest distance to " OH  TYR A 116 " =    1.090
peak=    3.292 closest distance to " CB  GLU A 152 " =    1.359
peak=    3.292 closest distance to " O   HOH Z 130 " =    2.469
peak=    3.290 closest distance to " CB  ASN A 215 " =    1.158
peak=    3.288 closest distance to " N   ALA A   1 " =    1.182
peak=    3.285 closest distance to " CA  MET A 105 " =    0.888
peak=    3.285 closest distance to " O   HOH Z 365 " =    1.661
peak=    3.284 closest distance to " O   HOH Z 209 " =    2.439
peak=    3.283 closest distance to " CG  ARG A 138 " =    1.313
peak=    3.276 closest distance to " O   HOH Z 213 " =    2.079
peak=    3.271 closest distance to " CG1 ILE A 151 " =    1.056
peak=    3.271 closest distance to " CE  MET A  93 " =    1.489
peak=    3.271 closest distance to " N   ASN A 127 " =    1.395
peak=    3.269 closest distance to " O   HOH Z  61 " =    1.525
peak=    3.266 closest distance to " OE2 GLU A  53 " =    1.881
peak=    3.264 closest distance to " CB  ALA A 248 " =    1.324
peak=    3.264 closest distance to " N   SER A  97 " =    0.828
peak=    3.263 closest distance to " O   HOH Z 423 " =    1.612
peak=    3.263 closest distance to " O   HOH Z 403 " =    1.277
peak=    3.257 closest distance to " CG2 ILE A  20 " =    1.159
peak=    3.256 closest distance to " O   HOH Z   1 " =    1.675
peak=    3.253 closest distance to " O   HOH Z 175 " =    2.136
peak=    3.243 closest distance to " CB  ALA A 114 " =    1.487
peak=    3.237 closest distance to " O   HOH Z 126 " =    1.482
peak=    3.235 closest distance to " CA  LYS A 117 " =    1.177
peak=    3.234 closest distance to " O   HOH Z 323 " =    1.577
peak=    3.230 closest distance to " ND2 ASN A 249 " =    0.769
peak=    3.227 closest distance to " CA  ALA A 180 " =    1.347
peak=    3.221 closest distance to " O   HOH Z 143 " =    1.429
peak=    3.216 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.215 closest distance to " CG1 ILE A 120 " =    1.343
peak=    3.213 closest distance to " OE2 GLU A   2 " =    1.904
peak=    3.211 closest distance to " CG1 ILE A 263 " =    1.266
peak=    3.210 closest distance to " O   HOH Z 358 " =    1.342
peak=    3.204 closest distance to " CE3 TRP A 274 " =    1.313
peak=    3.203 closest distance to " O   HOH Z 127 " =    1.008
peak=    3.203 closest distance to " CG  GLN A 278 " =    3.682
peak=    3.203 closest distance to " O   HOH Z 110 " =    1.633
peak=    3.200 closest distance to " O   HOH Z 132 " =    2.315
peak=    3.200 closest distance to " O   HOH Z 303 " =    2.804
peak=    3.200 closest distance to " O   HOH Z 125 " =    1.752
peak=    3.199 closest distance to " NE2 GLN A  73 " =    1.525
peak=    3.198 closest distance to " O   HOH Z 392 " =    1.936
peak=    3.198 closest distance to " O   HOH Z 113 " =    2.122
peak=    3.193 closest distance to " O   HOH Z 353 " =    1.808
peak=    3.186 closest distance to " O   TYR A 116 " =    1.307
peak=    3.184 closest distance to " CB  ALA A 114 " =    1.090
peak=    3.182 closest distance to " CA  VAL A  41 " =    0.799
peak=    3.181 closest distance to " O   HOH Z 389 " =    1.560
peak=    3.179 closest distance to " O   HOH Z 118 " =    1.383
peak=    3.178 closest distance to " CB  SER A 210 " =    0.834
peak=    3.177 closest distance to " CA  ILE A 106 " =    0.721
peak=    3.176 closest distance to " CG BARG A 190 " =    1.049
peak=    3.174 closest distance to " CA  LEU A 101 " =    1.561
peak=    3.174 closest distance to " CB  ASP A 140 " =    0.920
peak=    3.173 closest distance to " CA  ALA A 291 " =    0.866
peak=    3.172 closest distance to " CD1 LEU A   5 " =    1.562
peak=    3.171 closest distance to " NZ  LYS A  48 " =    1.235
peak=    3.171 closest distance to " O   HOH Z  93 " =    2.321
peak=    3.167 closest distance to " CB  ALA A 104 " =    0.706
peak=    3.158 closest distance to " CA  ARG A 156 " =    0.987
peak=    3.158 closest distance to " O   HOH Z 385 " =    1.051
peak=    3.154 closest distance to " O   HOH Z 356 " =    1.204
peak=    3.153 closest distance to " O   HOH Z 344 " =    2.899
peak=    3.152 closest distance to " CG AARG A 275 " =    1.197
peak=    3.145 closest distance to " CA  ARG A 102 " =    1.123
peak=    3.137 closest distance to " O   HOH Z 389 " =    2.943
peak=    3.136 closest distance to " CG  GLN A 278 " =    1.224
peak=    3.135 closest distance to " CB  LEU A 255 " =    0.768
peak=    3.125 closest distance to " O   HOH Z 148 " =    2.301
peak=    3.114 closest distance to " NH1BARG A 145 " =    1.310
peak=    3.111 closest distance to " O   HOH Z  59 " =    2.111
peak=    3.109 closest distance to " NH2BARG A 190 " =    1.437
peak=    3.109 closest distance to " O   HOH Z  21 " =    1.633
peak=    3.108 closest distance to " CG2 ILE A 234 " =    0.878
peak=    3.108 closest distance to " O   HOH Z 325 " =    2.070
peak=    3.107 closest distance to " O   HOH Z 383 " =    2.289
peak=    3.103 closest distance to " CD2 PHE A  59 " =    1.237
peak=    3.102 closest distance to " O   HOH Z 129 " =    0.728
peak=    3.097 closest distance to " N   ALA A 233 " =    0.871
peak=    3.097 closest distance to " O   HOH Z 406 " =    1.524
peak=    3.095 closest distance to " CA  LYS A 290 " =    1.336
peak=    3.093 closest distance to " N   SER A 135 " =    1.246
peak=    3.091 closest distance to " NE  ARG A  56 " =    3.494
peak=    3.082 closest distance to " O   HOH Z  40 " =    2.142
peak=    3.078 closest distance to " O   HOH Z 217 " =    1.606
peak=    3.076 closest distance to " O   HOH Z 426 " =    2.073
peak=    3.069 closest distance to " CD  ARG A 195 " =    3.433
peak=    3.061 closest distance to " O   HOH Z 373 " =    1.458
peak=    3.059 closest distance to " O   HOH Z 166 " =    1.525
peak=    3.053 closest distance to " O   HOH Z 368 " =    2.725
peak=    3.047 closest distance to " O   MET A 105 " =    1.710
peak=    3.036 closest distance to " CG2 THR A 246 " =    1.219
peak=    3.032 closest distance to " NZ  LYS A  48 " =    1.875

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.788 - 5.425
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 200
   mapped sites are within: 0.788 - 5.425

peak=   -4.948 closest distance to " CG2 VAL A 230 " =    0.788
peak=   -4.487 closest distance to " OG BSER A 134 " =    1.424
peak=   -4.372 closest distance to " CD  ARG A  14 " =    3.094
peak=   -4.226 closest distance to " CB  PRO A 243 " =    2.591
peak=   -4.130 closest distance to " O   HOH Z 185 " =    2.189
peak=   -4.099 closest distance to " O   SER A 135 " =    1.457
peak=   -4.078 closest distance to " CD  ARG A 156 " =    1.951
peak=   -4.045 closest distance to " CE2 PHE A 218 " =    2.458
peak=   -4.025 closest distance to " CD1 LEU A 255 " =    2.895
peak=   -4.023 closest distance to " CZ2 TRP A 274 " =    0.870
peak=   -4.008 closest distance to " O   PRO A 198 " =    1.142
peak=   -4.007 closest distance to " O   HOH Z 266 " =    4.782
peak=   -3.938 closest distance to " O   HOH Z 131 " =    4.012
peak=   -3.935 closest distance to " N   THR A 157 " =    1.388
peak=   -3.922 closest distance to " CB  ALA A 248 " =    2.028
peak=   -3.913 closest distance to " OG  SER A  87 " =    1.391
peak=   -3.905 closest distance to " O   HOH Z  43 " =    1.789
peak=   -3.893 closest distance to " O   HOH Z 350 " =    1.882
peak=   -3.853 closest distance to " CA  GLY A  98 " =    1.823
peak=   -3.844 closest distance to " ND2 ASN A 187 " =    1.585
peak=   -3.804 closest distance to " CG2 VAL A 296 " =    1.903
peak=   -3.783 closest distance to " O   HOH Z 359 " =    1.678
peak=   -3.778 closest distance to " NH2 ARG A  79 " =    2.029
peak=   -3.760 closest distance to " C   HIS A 108 " =    1.206
peak=   -3.757 closest distance to " O   HOH Z 407 " =    3.133
peak=   -3.754 closest distance to " CA  ASP A  27 " =    2.377
peak=   -3.723 closest distance to " O   SER A  22 " =    2.525
peak=   -3.714 closest distance to " O   HOH Z 231 " =    0.893
peak=   -3.704 closest distance to " CB  TYR A  15 " =    2.104
peak=   -3.703 closest distance to " O   HOH Z 231 " =    1.793
peak=   -3.676 closest distance to " CA  GLY A 133 " =    1.976
peak=   -3.673 closest distance to " O   VAL A  67 " =    2.482
peak=   -3.671 closest distance to " O   PRO A 243 " =    2.391
peak=   -3.660 closest distance to " O   HOH Z 377 " =    1.048
peak=   -3.655 closest distance to " O   VAL A  67 " =    2.955
peak=   -3.648 closest distance to " O   HOH Z  11 " =    1.837
peak=   -3.646 closest distance to " CB  ASP A 132 " =    2.326
peak=   -3.640 closest distance to " O   HOH Z 389 " =    1.371
peak=   -3.639 closest distance to " O   HOH Z 389 " =    2.071
peak=   -3.628 closest distance to " CB  ASN A  39 " =    2.175
peak=   -3.622 closest distance to " CD2 LEU A   5 " =    0.988
peak=   -3.614 closest distance to " CD  LYS A 289 " =    2.383
peak=   -3.600 closest distance to " O   ILE A  49 " =    1.736
peak=   -3.599 closest distance to " O   HOH Z 140 " =    1.299
peak=   -3.595 closest distance to " CB  ALA A  43 " =    2.361
peak=   -3.592 closest distance to " O   HOH Z 290 " =    1.106
peak=   -3.575 closest distance to " CG  GLN A 223 " =    2.322
peak=   -3.569 closest distance to " O   PRO A 163 " =    1.935
peak=   -3.563 closest distance to " O   HOH Z 351 " =    1.524
peak=   -3.559 closest distance to " CD2 TYR A 293 " =    1.808
peak=   -3.554 closest distance to " OG  SER A  63 " =    1.276
peak=   -3.546 closest distance to " O   HOH Z 339 " =    1.827
peak=   -3.545 closest distance to " N   ALA A   1 " =    1.249
peak=   -3.539 closest distance to " N   ALA A  43 " =    2.653
peak=   -3.534 closest distance to " OE1 GLU A 277 " =    2.260
peak=   -3.530 closest distance to " CA  ASN A 127 " =    1.112
peak=   -3.522 closest distance to " OE1 GLN A  88 " =    1.089
peak=   -3.519 closest distance to " CB  GLN A  55 " =    1.243
peak=   -3.514 closest distance to " CE2 TYR A  30 " =    2.598
peak=   -3.510 closest distance to " O   ARG A 145 " =    1.376
peak=   -3.505 closest distance to " O   HOH Z 191 " =    5.425
peak=   -3.497 closest distance to " ND2 ASN A 285 " =    2.019
peak=   -3.483 closest distance to " O   HOH Z 198 " =    2.190
peak=   -3.480 closest distance to " CB  ALA A   7 " =    2.017
peak=   -3.474 closest distance to " O   HOH Z 211 " =    1.321
peak=   -3.454 closest distance to " CA  GLY A 203 " =    2.298
peak=   -3.446 closest distance to " CE2 TYR A 116 " =    3.050
peak=   -3.444 closest distance to " O   HOH Z 427 " =    1.653
peak=   -3.437 closest distance to " CB  TYR A 172 " =    2.451
peak=   -3.432 closest distance to " O   HOH Z 415 " =    1.234
peak=   -3.432 closest distance to " CB  ALA A 161 " =    2.455
peak=   -3.431 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.430 closest distance to " C   MET A 188 " =    1.546
peak=   -3.429 closest distance to " CD  LYS A 166 " =    2.450
peak=   -3.425 closest distance to " CA  GLY A 241 " =    2.200
peak=   -3.422 closest distance to " CG  GLN A  58 " =    1.057
peak=   -3.418 closest distance to " O   GLN A  11 " =    1.527
peak=   -3.414 closest distance to " CD1 PHE A  59 " =    2.004
peak=   -3.411 closest distance to " N   GLN A  58 " =    1.876
peak=   -3.403 closest distance to " O   HOH Z 359 " =    3.444
peak=   -3.403 closest distance to " N   VAL A  72 " =    1.673
peak=   -3.399 closest distance to " OG  SER A  97 " =    2.167
peak=   -3.392 closest distance to " O   HOH Z 385 " =    1.827
peak=   -3.386 closest distance to " C   ALA A 158 " =    1.476
peak=   -3.386 closest distance to " O   HOH Z  60 " =    2.266
peak=   -3.383 closest distance to " CG2 THR A 178 " =    2.176
peak=   -3.382 closest distance to " N   ASP A 171 " =    2.608
peak=   -3.380 closest distance to " N   SER A 276 " =    1.269
peak=   -3.371 closest distance to " O   HOH Z 134 " =    3.730
peak=   -3.367 closest distance to " CZ  PHE A  59 " =    1.459
peak=   -3.364 closest distance to " CD1 LEU A 101 " =    2.276
peak=   -3.364 closest distance to " CG  TRP A 266 " =    1.906
peak=   -3.363 closest distance to " O   ALA A  84 " =    1.709
peak=   -3.360 closest distance to " O   HOH Z 423 " =    2.525
peak=   -3.358 closest distance to " O   HOH Z 114 " =    2.983
peak=   -3.357 closest distance to " OG  SER A   3 " =    1.411
peak=   -3.355 closest distance to " O   HOH Z 364 " =    1.243
peak=   -3.354 closest distance to " CG1 VAL A 197 " =    2.298
peak=   -3.353 closest distance to " OG  SER A 206 " =    1.759
peak=   -3.347 closest distance to " CB  CYS A 201 " =    2.121
peak=   -3.344 closest distance to " CD2 LEU A 237 " =    2.723
peak=   -3.344 closest distance to " CE2 TRP A  70 " =    2.244
peak=   -3.339 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.334 closest distance to " N   ALA A 226 " =    2.126
peak=   -3.331 closest distance to " O   HOH Z  51 " =    0.799
peak=   -3.330 closest distance to " OD2 ASP A 191 " =    1.387
peak=   -3.318 closest distance to " O   GLY A  80 " =    2.452
peak=   -3.313 closest distance to " CB  ALA A 131 " =    1.934
peak=   -3.311 closest distance to " N   PRO A 163 " =    1.585
peak=   -3.304 closest distance to " O   HOH Z 298 " =    1.077
peak=   -3.304 closest distance to " O   HOH Z  39 " =    1.215
peak=   -3.303 closest distance to " CB  VAL A 230 " =    1.009
peak=   -3.302 closest distance to " O   VAL A 197 " =    1.602
peak=   -3.301 closest distance to " CG  ASN A 301 " =    1.993
peak=   -3.299 closest distance to " O   HOH Z 435 " =    2.221
peak=   -3.295 closest distance to " OG  SER A  62 " =    4.390
peak=   -3.293 closest distance to " OE2 GLU A 152 " =    1.093
peak=   -3.275 closest distance to " O   HOH Z 100 " =    1.194
peak=   -3.272 closest distance to " CB  PRO A  90 " =    1.530
peak=   -3.269 closest distance to " O   HOH Z  67 " =    3.144
peak=   -3.268 closest distance to " O   ASN A 301 " =    1.483
peak=   -3.267 closest distance to " CE  LYS A 166 " =    1.126
peak=   -3.264 closest distance to " CG  ARG A 259 " =    2.774
peak=   -3.256 closest distance to " CD2 PHE A  61 " =    2.014
peak=   -3.255 closest distance to " NH2 ARG A 219 " =    1.779
peak=   -3.254 closest distance to " O   HOH Z 166 " =    1.738
peak=   -3.254 closest distance to " CD1 LEU A 101 " =    2.592
peak=   -3.253 closest distance to " C   ARG A 269 " =    1.417
peak=   -3.251 closest distance to " C   GLU A 236 " =    0.888
peak=   -3.249 closest distance to " O   TYR A  30 " =    2.677
peak=   -3.244 closest distance to " CB  PRO A 213 " =    2.164
peak=   -3.244 closest distance to " O   ASP A 191 " =    1.943
peak=   -3.244 closest distance to " ND2 ASN A  69 " =    1.789
peak=   -3.241 closest distance to " CB  ALA A 114 " =    2.309
peak=   -3.237 closest distance to " CG2 VAL A 202 " =    2.659
peak=   -3.236 closest distance to " CB  PHE A 192 " =    1.707
peak=   -3.233 closest distance to " OD1 ASN A 148 " =    1.505
peak=   -3.231 closest distance to " O   HOH Z  90 " =    2.844
peak=   -3.226 closest distance to " O   HOH Z 292 " =    1.609
peak=   -3.225 closest distance to " O   MET A  40 " =    2.767
peak=   -3.211 closest distance to " NH1 ARG A  56 " =    2.372
peak=   -3.210 closest distance to " N   THR A 235 " =    1.189
peak=   -3.209 closest distance to " O   HOH Z  52 " =    1.571
peak=   -3.204 closest distance to " O   HOH Z 353 " =    1.338
peak=   -3.200 closest distance to " O   HOH Z 368 " =    1.311
peak=   -3.199 closest distance to " C   ILE A 239 " =    2.042
peak=   -3.194 closest distance to " O   HOH Z 111 " =    1.068
peak=   -3.193 closest distance to " CZ3 TRP A 179 " =    1.264
peak=   -3.185 closest distance to " C   LEU A 222 " =    0.844
peak=   -3.184 closest distance to " O   HOH Z 368 " =    2.428
peak=   -3.184 closest distance to " C   LEU A 143 " =    1.257
peak=   -3.183 closest distance to " O   HOH Z  65 " =    1.199
peak=   -3.183 closest distance to " O   HOH Z 352 " =    2.150
peak=   -3.180 closest distance to " N   ARG A 138 " =    1.396
peak=   -3.179 closest distance to " CD1 ILE A 239 " =    2.281
peak=   -3.179 closest distance to " O   HOH Z 166 " =    1.656
peak=   -3.179 closest distance to " OG  SER A 245 " =    1.302
peak=   -3.179 closest distance to " CG  PRO A 163 " =    2.542
peak=   -3.178 closest distance to " O   PHE A 218 " =    1.427
peak=   -3.176 closest distance to " O   HOH Z 275 " =    1.593
peak=   -3.175 closest distance to " O   HOH Z 298 " =    2.778
peak=   -3.173 closest distance to " CA  ALA A 227 " =    2.380
peak=   -3.172 closest distance to " N   HIS A 115 " =    2.163
peak=   -3.171 closest distance to " O   HOH Z 134 " =    3.263
peak=   -3.169 closest distance to " CE  LYS A  76 " =    2.813
peak=   -3.165 closest distance to " ND2 ASN A  45 " =    1.140
peak=   -3.165 closest distance to " O   VAL A 189 " =    2.510
peak=   -3.162 closest distance to " C   ASN A 187 " =    1.890
peak=   -3.160 closest distance to " O   HOH Z  60 " =    1.960
peak=   -3.158 closest distance to " O   HOH Z 426 " =    1.665
peak=   -3.156 closest distance to " O   HOH Z 404 " =    1.298
peak=   -3.154 closest distance to " CG  PHE A 283 " =    2.561
peak=   -3.154 closest distance to " C   ASN A 285 " =    2.093
peak=   -3.152 closest distance to " O   HOH Z  93 " =    2.258
peak=   -3.141 closest distance to " ND2 ASN A 209 " =    1.977
peak=   -3.140 closest distance to " O   ALA A 161 " =    1.803
peak=   -3.128 closest distance to " CG2 VAL A 296 " =    1.074
peak=   -3.123 closest distance to " CD1 PHE A  61 " =    2.904
peak=   -3.117 closest distance to " CD2 LEU A 297 " =    1.868
peak=   -3.117 closest distance to " O   HOH Z 216 " =    1.744
peak=   -3.112 closest distance to " O   HOH Z 285 " =    3.045
peak=   -3.108 closest distance to " NH2AARG A 275 " =    5.351
peak=   -3.107 closest distance to " O   HOH Z 193 " =    1.990
peak=   -3.106 closest distance to " O   HOH Z 414 " =    2.139
peak=   -3.091 closest distance to " CZ  TYR A 169 " =    1.681
peak=   -3.090 closest distance to " CB  SER A 210 " =    1.105
peak=   -3.087 closest distance to " O   HOH Z 151 " =    1.625
peak=   -3.087 closest distance to " CE BMET A  47 " =    0.908
peak=   -3.086 closest distance to " CZ3 TRP A 123 " =    1.666
peak=   -3.080 closest distance to " CE  MET A 105 " =    2.425
peak=   -3.077 closest distance to " CE1 PHE A  59 " =    2.053
peak=   -3.072 closest distance to " O   HOH Z 286 " =    1.821
peak=   -3.070 closest distance to " CB  PHE A 130 " =    1.215
peak=   -3.069 closest distance to " O   HOH Z 111 " =    4.366
peak=   -3.065 closest distance to " CG1 VAL A 230 " =    1.821
peak=   -3.063 closest distance to " O   HOH Z 250 " =    1.272
peak=   -3.057 closest distance to " CZ  PHE A 130 " =    0.896
peak=   -3.039 closest distance to " O   HOH Z 421 " =    3.299

================= 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    :  0.4712 0.4641   6.277520e+00   6.262751e+00
   1_bss:  0.4625 0.4502   6.270651e+00   6.251374e+00
   1_xyz:  0.3823 0.4054   6.161957e+00   6.195853e+00
   1_adp:  0.3354 0.3911   6.087883e+00   6.179965e+00
   1_occ:  0.3351 0.3907   6.087325e+00   6.180165e+00
   2_bss:  0.3313 0.3845   6.086174e+00   6.177126e+00
   2_xyz:  0.2676 0.3274   5.900369e+00   6.036658e+00
   2_adp:  0.2472 0.3140   5.844842e+00   6.002348e+00
   2_occ:  0.2469 0.3140   5.844738e+00   6.002646e+00
   3_bss:  0.2453 0.3117   5.842991e+00   5.999376e+00
   3_xyz:  0.1767 0.2319   5.539475e+00   5.745271e+00
   3_adp:  0.1513 0.2083   5.410820e+00   5.647203e+00
   3_occ:  0.1512 0.2079   5.410082e+00   5.646148e+00
   4_bss:  0.1508 0.2072   5.406074e+00   5.641643e+00
   4_xyz:  0.1270 0.1825   5.270264e+00   5.525026e+00
   4_adp:  0.1210 0.1750   5.229826e+00   5.484138e+00
   4_occ:  0.1210 0.1749   5.229575e+00   5.483848e+00
   5_bss:  0.1212 0.1744   5.228600e+00   5.481587e+00
   5_xyz:  0.1189 0.1696   5.209346e+00   5.457859e+00
   5_adp:  0.1181 0.1672   5.199707e+00   5.444955e+00
   5_occ:  0.1178 0.1671   5.198156e+00   5.442957e+00
   5_bss:  0.1178 0.1671   5.198160e+00   5.442905e+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:  0.363   2.653   7.039  10.596   7.868   0.000   0.000   0.000
   1_xyz:  0.363   2.653   7.039  10.596   7.868   0.000   0.000   0.000
   1_adp:  0.363   2.653   7.039  10.596   7.868   0.000   0.000   0.000
   1_occ:  0.363   2.653   7.039  10.596   7.868   0.000   0.000   0.000
   2_bss:  0.353  35.214   3.728   6.122   4.693   0.000   0.000   0.000
   2_xyz:  0.353  35.214   3.728   6.122   4.693   0.000   0.000   0.000
   2_adp:  0.353  35.214   3.728   6.122   4.693   0.000   0.000   0.000
   2_occ:  0.353  35.214   3.728   6.122   4.693   0.000   0.000   0.000
   3_bss:  0.342  45.640   2.344   3.295   3.424   0.000   0.000   0.000
   3_xyz:  0.342  45.640   2.344   3.295   3.424   0.000   0.000   0.000
   3_adp:  0.342  45.640   2.344   3.295   3.424   0.000   0.000   0.000
   3_occ:  0.342  45.640   2.344   3.295   3.424   0.000   0.000   0.000
   4_bss:  0.329  45.640   1.816   1.999   3.011   0.000   0.000   0.000
   4_xyz:  0.329  45.640   1.816   1.999   3.011   0.000   0.000   0.000
   4_adp:  0.329  45.640   1.816   1.999   3.011   0.000   0.000   0.000
   4_occ:  0.329  45.640   1.816   1.999   3.011   0.000   0.000   0.000
   5_bss:  0.322  45.640   1.897   1.836   3.169   0.000   0.000   0.000
   5_xyz:  0.322  45.640   1.897   1.836   3.169   0.000   0.000   0.000
   5_adp:  0.322  45.640   1.897   1.836   3.169   0.000   0.000   0.000
   5_occ:  0.322  45.640   1.897   1.836   3.169   0.000   0.000   0.000
   5_bss:  0.320  46.730  -0.386  -0.542   0.928   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.430 0.4396  0.5158    67584.902
   1_bss:  55.837 0.4457  0.6651    64508.924
   1_xyz:  47.970 0.5442  0.7979    50337.850
   1_adp:  44.754 0.5847  0.9035    46566.705
   1_occ:  44.819 0.5839  0.9016    46639.164
   2_bss:  44.175 0.5918  0.8079    45736.568
   2_xyz:  34.626 0.7053  0.9414    29631.956
   2_adp:  32.254 0.7329  0.9737    26723.401
   2_occ:  32.289 0.7325  0.9730    26767.454
   3_bss:  32.005 0.7355  0.9142    26407.200
   3_xyz:  22.927 0.8321  0.9935    13894.748
   3_adp:  20.048 0.8609  0.9995    11106.075
   3_occ:  20.025 0.8611  0.9994    11069.623
   4_bss:  19.907 0.8620  0.9731    10918.274
   4_xyz:  17.160 0.8875  0.9843     8442.468
   4_adp:  16.148 0.8969  0.9797     7808.267
   4_occ:  16.147 0.8968  0.9794     7792.662
   5_bss:  16.104 0.8972  0.9801     7734.044
   5_xyz:  15.510 0.9025  0.9819     7317.379
   5_adp:  15.174 0.9056  0.9775     7164.610
   5_occ:  15.141 0.9058  0.9773     7133.164
   5_bss:  15.143 0.9058  0.9811     7133.110
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3357e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3357e+01
   1_xyz:   1.650  0.013  0.104 18.224  0.006  4.107   1.3634e-01
   1_adp:   1.650  0.013  0.104 18.224  0.006  4.107   1.3634e-01
   1_occ:   1.650  0.013  0.104 18.224  0.006  4.107   1.3634e-01
   2_bss:   1.650  0.013  0.104 18.224  0.006  4.107   1.3634e-01
   2_xyz:   1.139  0.008  0.082 15.999  0.005  4.121   8.2137e-02
   2_adp:   1.139  0.008  0.082 15.999  0.005  4.121   8.2137e-02
   2_occ:   1.139  0.008  0.082 15.999  0.005  4.121   8.2137e-02
   3_bss:   1.139  0.008  0.082 15.999  0.005  4.121   8.2137e-02
   3_xyz:   1.210  0.009  0.088 16.322  0.004  4.120   8.9697e-02
   3_adp:   1.210  0.009  0.088 16.322  0.004  4.120   8.9697e-02
   3_occ:   1.210  0.009  0.088 16.322  0.004  4.120   8.9697e-02
   4_bss:   1.210  0.009  0.088 16.322  0.004  4.120   8.9697e-02
   4_xyz:   1.057  0.007  0.080 16.027  0.004  4.108   6.8519e-02
   4_adp:   1.057  0.007  0.080 16.027  0.004  4.108   6.8519e-02
   4_occ:   1.057  0.007  0.080 16.027  0.004  4.108   6.8519e-02
   5_bss:   1.057  0.007  0.080 16.027  0.004  4.108   6.8519e-02
   5_xyz:   0.898  0.005  0.070 15.401  0.003  4.110   5.2686e-02
   5_adp:   0.898  0.005  0.070 15.401  0.003  4.110   5.2686e-02
   5_occ:   0.898  0.005  0.070 15.401  0.003  4.110   5.2686e-02
   5_bss:   0.898  0.005  0.070 15.401  0.003  4.110   5.2686e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9155e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9155e+00
   1_xyz:  12.938  0.180  0.408 89.201  0.034  2.134   9.6026e-02
   1_adp:  12.938  0.180  0.408 89.201  0.034  2.134   9.6026e-02
   1_occ:  12.938  0.180  0.408 89.201  0.034  2.134   9.6026e-02
   2_bss:  12.938  0.180  0.408 89.201  0.034  2.134   9.6026e-02
   2_xyz:   6.827  0.085  0.302 79.517  0.039  2.163   6.0992e-02
   2_adp:   6.827  0.085  0.302 79.517  0.039  2.163   6.0992e-02
   2_occ:   6.827  0.085  0.302 79.517  0.039  2.163   6.0992e-02
   3_bss:   6.827  0.085  0.302 79.517  0.039  2.163   6.0992e-02
   3_xyz:   7.373  0.063  0.472 80.378  0.034  2.193   1.6889e-01
   3_adp:   7.373  0.063  0.472 80.378  0.034  2.193   1.6889e-01
   3_occ:   7.373  0.063  0.472 80.378  0.034  2.193   1.6889e-01
   4_bss:   7.373  0.063  0.472 80.378  0.034  2.193   1.6889e-01
   4_xyz:   8.367  0.053  0.428 82.562  0.037  2.279   5.2326e-02
   4_adp:   8.367  0.053  0.428 82.562  0.037  2.279   5.2326e-02
   4_occ:   8.367  0.053  0.428 82.562  0.037  2.279   5.2326e-02
   5_bss:   8.367  0.053  0.428 82.562  0.037  2.279   5.2326e-02
   5_xyz:   6.843  0.039  0.356 82.215  0.038  2.342   3.0998e-02
   5_adp:   6.843  0.039  0.356 82.215  0.038  2.342   3.0998e-02
   5_occ:   6.843  0.039  0.356 82.215  0.038  2.342   3.0998e-02
   5_bss:   6.843  0.039  0.356 82.215  0.038  2.342   3.0998e-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:  78.09   0.00  13.24  72.40   0.00  11.16  78.09   0.00  24.55
   1_occ:  78.09   0.00  13.24  72.40   0.00  11.16  78.09   0.00  24.55
   2_bss:  78.09   0.00  13.24  72.40   0.00  11.16  78.09   0.00  24.55
   2_xyz:  78.09   0.00  13.24  72.40   0.00  11.16  78.09   0.00  24.55
   2_adp:  84.33   0.00  13.27  71.63   0.00  10.22  84.33   0.00  29.87
   2_occ:  84.33   0.00  13.27  71.63   0.00  10.22  84.33   0.00  29.87
   3_bss:  84.33   0.00  13.27  71.63   0.00  10.22  84.33   0.00  29.87
   3_xyz:  84.33   0.00  13.27  71.63   0.00  10.22  84.33   0.00  29.87
   3_adp:  88.82   0.00  13.66  85.16   0.00   9.29  88.82   0.00  37.51
   3_occ:  88.82   0.00  13.66  85.16   0.00   9.29  88.82   0.00  37.51
   4_bss:  88.82   0.00  13.66  85.16   0.00   9.29  88.82   0.00  37.51
   4_xyz:  88.82   0.00  13.66  85.16   0.00   9.29  88.82   0.00  37.51
   4_adp:  96.91   0.00  13.64  96.91   0.00   8.94  91.67   0.00  39.22
   4_occ:  96.91   0.00  13.64  96.91   0.00   8.94  91.67   0.00  39.22
   5_bss:  96.91   0.00  13.64  96.91   0.00   8.94  91.67   0.00  39.22
   5_xyz:  96.91   0.00  13.64  96.91   0.00   8.94  91.67   0.00  39.22
   5_adp: 102.38   0.00  13.25 102.38   0.00   8.69  92.14   1.36  38.08
   5_occ: 102.38   0.00  13.25 102.38   0.00   8.69  92.14   1.36  38.08
   5_bss: 104.79   2.41  15.66 104.79   2.41  11.10  94.55   3.77  40.49
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.238    0.022    0.408
   1_adp:    1.238    0.022    0.408
   1_occ:    1.238    0.022    0.408
   2_bss:    1.238    0.022    0.408
   2_xyz:    1.448    0.019    0.564
   2_adp:    1.448    0.019    0.564
   2_occ:    1.448    0.019    0.564
   3_bss:    1.448    0.019    0.564
   3_xyz:    1.717    0.047    0.701
   3_adp:    1.717    0.047    0.701
   3_occ:    1.717    0.047    0.701
   4_bss:    1.717    0.047    0.701
   4_xyz:    1.861    0.030    0.730
   4_adp:    1.861    0.030    0.730
   4_occ:    1.861    0.030    0.730
   5_bss:    1.861    0.030    0.730
   5_xyz:    1.869    0.019    0.740
   5_adp:    1.869    0.019    0.740
   5_occ:    1.869    0.019    0.740
   5_bss:    1.869    0.019    0.740
------------------------------------------------------------------------

CPU time actual refinement: 337.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_621/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_621/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_621/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_621/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_621/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.44 
  Macro-tasks:
    bulk solvent and scale       = 42.80  
    individual site refinement   = 139.94 
    weights calculation          = 33.30  
    collect and process          = 6.83   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 223.02 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 102.93 
    alpha_beta                      = 8.47   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 112.85 
    fmodel                         = 7.44   
    r_factors                      = 0.19   
    phase_errors                   = 10.61  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 246.39 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.757 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    632 calls, 102.57 s
gradients_fft:          576 calls,  99.54 s

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

# Date 2008-01-16 Time 02:02:34 PST -0800 (1200477754.99 s)
Start R-work = 0.4712, R-free = 0.4641 (no bulk solvent and anisotropic scale)
Final R-work = 0.1344, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4625, R-free = 0.4502
Final R-work = 0.1178, R-free = 0.1671