# Date 2008-01-16 Time 02:58:10 PST -0800 (1200481090.23 s)
#phil __OFF__

Command line arguments: "../1054.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 = 22339
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1054

-------------------------------------------------------------------------------
  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: (71.3037, 47.3993, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 2.02196
Completeness in resolution range: 0.974529
Completeness with d_max=infinity: 0.971484

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2391
                             d_min =   2.0220

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: (71.3037, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 2.02196
Completeness in resolution range: 0.974529
Completeness with d_max=infinity: 0.971484

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2395 -  4.3261 [2112/2136]  1899   213  10.1%
  bin  2:  4.3261 -  3.4468 [2030/2050]  1828   202  10.0%
  bin  3:  3.4468 -  3.0149 [2001/2020]  1803   198   9.9%
  bin  4:  3.0149 -  2.7410 [1980/2010]  1779   201  10.2%
  bin  5:  2.7410 -  2.5455 [1976/1995]  1778   198  10.0%
  bin  6:  2.5455 -  2.3961 [1964/1989]  1766   198  10.1%
  bin  7:  2.3961 -  2.2765 [1939/1967]  1749   190   9.8%
  bin  8:  2.2765 -  2.1777 [1951/1987]  1755   196  10.0%
  bin  9:  2.1777 -  2.0941 [1937/1979]  1743   194  10.0%
  bin 10:  2.0941 -  2.0220 [1699/1968]  1530   169   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1054/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: 11
        2.42 -     3.04: 2149
        3.04 -     3.66: 4566
        3.66 -     4.28: 8812
        4.28 -     4.90: 12148
  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 207 " - " O   HOH Z 341 "  1.824 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.116 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.181 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.181 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27681 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_1054/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1054/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 71.30375 47.3993 88.1178 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: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4828   r_free= 0.4737   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.281777                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8249 0.99   1375  152 0.3941 0.3661      6.5947      6.4991|
|  2:  4.8249 -  3.8500 0.99   1316  148 0.4000 0.4339      6.7927      6.9107|
|  3:  3.8500 -  3.3693 0.99   1294  144 0.4439 0.4210      6.6926      6.6695|
|  4:  3.3693 -  3.0640 0.99   1285  142 0.4755 0.4074       6.548      6.4289|
|  5:  3.0640 -  2.8459 0.99   1270  141 0.5015 0.4830      6.3793       6.419|
|  6:  2.8459 -  2.6791 0.99   1285  141 0.5162 0.5593      6.2968      6.2011|
|  7:  2.6791 -  2.5455 0.99   1262  144 0.5222 0.4900      6.2492      6.2015|
|  8:  2.5455 -  2.4352 0.98   1260  136 0.5235 0.4604      6.1903      6.1737|
|  9:  2.4352 -  2.3418 0.98   1260  141 0.5178 0.6008      6.1251      6.1669|
| 10:  2.3418 -  2.2612 1.00   1253  141 0.5388 0.5082      6.1277      6.1285|
| 11:  2.2612 -  2.1907 0.97   1257  137 0.5170 0.5283      6.0341      6.0981|
| 12:  2.1907 -  2.1283 0.98   1246  139 0.5300 0.5101      6.0001      6.0208|
| 13:  2.1283 -  2.0724 0.99   1250  139 0.5295 0.4874      5.9003      5.8545|
| 14:  2.0724 -  2.0220 0.81   1017  114 0.5432 0.5291      5.8555      5.7782|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2395 -  4.8249  1375   152  0.71  33.08   0.79     0.74      66285.22|
|  2:  4.8249 -  3.8500  1316   148  0.71  33.93   0.87     0.76     101198.41|
|  3:  3.8500 -  3.3693  1294   144  0.62  42.16   0.81     0.71     107589.98|
|  4:  3.3693 -  3.0640  1285   142  0.53  49.70   0.78     0.60      96361.10|
|  5:  3.0640 -  2.8459  1270   141  0.45  56.09   0.73     0.51      78642.23|
|  6:  2.8459 -  2.6791  1285   141  0.40  59.57   0.71     0.45      71327.95|
|  7:  2.6791 -  2.5455  1262   144  0.37  61.95   0.71     0.42      65341.18|
|  8:  2.5455 -  2.4352  1260   136  0.35  63.87   0.73     0.40      60328.28|
|  9:  2.4352 -  2.3418  1260   141  0.33  65.22   0.70     0.38      56903.67|
| 10:  2.3418 -  2.2612  1253   141  0.33  65.68   0.72     0.37      51886.29|
| 11:  2.2612 -  2.1907  1257   137  0.32  65.82   0.74     0.38      47847.17|
| 12:  2.1907 -  2.1283  1246   139  0.34  64.40   0.72     0.41      42756.06|
| 13:  2.1283 -  2.0724  1250   139  0.32  65.97   0.71     0.38      37064.03|
| 14:  2.0724 -  2.0220  1017   114  0.30  67.65   0.69     0.32      31121.44|
|alpha:            min =        0.32 max =            0.76 mean =         0.49|
|beta:             min =    31121.44 max =       107589.98 mean =     66107.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           90.00 mean =        56.37|
|phase err.(test): min =        0.00 max =           89.89 mean =        56.40|
|-----------------------------------------------------------------------------|

============================== 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 = 14.706483             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.026   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.409609              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.569   (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:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      669 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1471 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2564 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3815 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4975 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6428 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7590 |
|-----------------------------------------------------------------------------|
|-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 |       54.667 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.643 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    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 = 12.423)------------------------------------------|
|    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: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4873   r_free= 0.4767   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.283250                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4750   r_free= 0.4638   ksol= 0.29   Bsol= 20.00   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.05,7.60,10.33,0.00,0.00,0.00); trace/3= 8.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.276259                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.054748             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.897   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.219903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.807   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4750      final r-factor (work) = 0.3856          |
| start r-factor (free) = 0.4638      final r-factor (free) = 0.4130          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.6733 = 13.05 * 0.50 * 6.2822 + 1.00 * 54.6669                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.5009 = 13.05 * 0.50 * 6.1811 + 1.00 * 0.1543                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3856      final r-factor (work) = 0.3422          |
| start r-factor (free) = 0.4130      final r-factor (free) = 0.3940          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5548 = 1.22 * 1.00 * 6.1811 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4526 = 1.22 * 1.00 * 6.0943 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.15  13.01    None  None   None       |
|    all(noH): 2823   0      0.00    108.15  13.01    None  None   None       |
|    Sol.    : 438    0      0.00    108.15  27.93    None  None   None       |
|    Mac.    : 2385   0      0.00    73.76   10.28    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 -  10.815: 1569   |   5:    54.074 -  64.889:   25        |
|      1:    10.815 -  21.630:  734   |   6:    64.889 -  75.704:   11        |
|      2:    21.630 -  32.445:  278   |   7:    75.704 -  86.519:    5        |
|      3:    32.445 -  43.259:  131   |   8:    86.519 -  97.334:    0        |
|      4:    43.259 -  54.074:   69   |   9:    97.334 - 108.148:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3422 r_free = 0.3940             target_work(ml) = 6.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3417 r_free = 0.3943             target_work(ml) = 6.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3417   r_free= 0.3943   ksol= 0.29   Bsol= 20.00   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.05,7.60,10.33,0.00,0.00,0.00); trace/3= 8.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.071369                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3405   r_free= 0.3913   ksol= 0.33   Bsol= 60.29   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.46,5.19,7.28,0.00,0.00,0.00); trace/3= 5.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.072461                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.127358              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.869   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.538097              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.237  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3405      final r-factor (work) = 0.2574          |
| start r-factor (free) = 0.3913      final r-factor (free) = 0.3096          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7635 = 5.13 * 0.50 * 6.0886 + 1.00 * 0.1543                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3577 = 5.13 * 0.50 * 5.9582 + 1.00 * 0.0828                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2574      final r-factor (work) = 0.2358          |
| start r-factor (free) = 0.3096      final r-factor (free) = 0.2868          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2336 = 0.54 * 1.00 * 5.9582 + 1.00 * 0.0275                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1671 = 0.54 * 1.00 * 5.8032 + 1.00 * 0.0444                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.98  12.88    None  None   None       |
|    all(noH): 2823   0      0.00    111.98  12.88    None  None   None       |
|    Sol.    : 438    0      0.00    111.98  33.85    None  None   None       |
|    Mac.    : 2385   0      0.00    71.53   9.03     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.198: 1789   |   5:    55.992 -  67.190:   38        |
|      1:    11.198 -  22.397:  558   |   6:    67.190 -  78.389:    7        |
|      2:    22.397 -  33.595:  204   |   7:    78.389 -  89.587:    3        |
|      3:    33.595 -  44.794:  143   |   8:    89.587 - 100.785:    0        |
|      4:    44.794 -  55.992:   80   |   9:   100.785 - 111.984:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2358 r_free = 0.2868             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2356 r_free = 0.2868             target_work(ml) = 5.774         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2356   r_free= 0.2868   ksol= 0.33   Bsol= 60.29   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.46,5.19,7.28,0.00,0.00,0.00); trace/3= 5.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.774269                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2345   r_free= 0.2861   ksol= 0.33   Bsol= 72.40   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.45,4.99,0.00,0.00,0.00); trace/3= 3.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.776165                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.914060              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.951   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.915769              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.115   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2345      final r-factor (work) = 0.1710          |
| start r-factor (free) = 0.2861      final r-factor (free) = 0.2185          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4451 = 3.91 * 0.50 * 5.8058 + 1.00 * 0.0831                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1354 = 3.91 * 0.50 * 5.6513 + 1.00 * 0.0757                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1544          |
| start r-factor (free) = 0.2185      final r-factor (free) = 0.2072          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8438 = 1.92 * 1.00 * 5.6513 + 1.00 * 0.0173                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4567 = 1.92 * 1.00 * 5.4488 + 1.00 * 0.0180                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.53  13.80    None  None   None       |
|    all(noH): 2823   0      0.00    107.53  13.80    None  None   None       |
|    Sol.    : 438    0      0.00    107.53  40.70    None  None   None       |
|    Mac.    : 2385   0      0.00    82.50   8.86     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.754: 1777   |   5:    53.767 -  64.521:   84        |
|      1:    10.754 -  21.507:  524   |   6:    64.521 -  75.274:   43        |
|      2:    21.507 -  32.260:  153   |   7:    75.274 -  86.028:   13        |
|      3:    32.260 -  43.014:  113   |   8:    86.028 -  96.781:    2        |
|      4:    43.014 -  53.767:  112   |   9:    96.781 - 107.535:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1544 r_free = 0.2072             target_work(ml) = 5.425         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1543 r_free = 0.2074             target_work(ml) = 5.425         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1543   r_free= 0.2074   ksol= 0.33   Bsol= 72.40   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.45,4.99,0.00,0.00,0.00); trace/3= 3.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.424993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1546   r_free= 0.2079   ksol= 0.33   Bsol= 72.40   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.85,4.28,0.00,0.00,0.00); trace/3= 3.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.425667                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.109373              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.050  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.367382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.205  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1546      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.2079      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5499 = 3.11 * 0.50 * 5.4507 + 1.00 * 0.0757                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4171 = 3.11 * 0.50 * 5.3642 + 1.00 * 0.0775                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1848      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9886 = 0.37 * 1.00 * 5.3642 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9575 = 0.37 * 1.00 * 5.2902 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.91  13.16    None  None   None       |
|    all(noH): 2823   0      0.00    103.91  13.16    None  None   None       |
|    Sol.    : 438    0      0.41    103.91  39.11    None  None   None       |
|    Mac.    : 2385   0      0.00    82.72   8.39     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 -  10.391: 1845   |   5:    51.956 -  62.347:   77        |
|      1:    10.391 -  20.782:  484   |   6:    62.347 -  72.738:   46        |
|      2:    20.782 -  31.173:  134   |   7:    72.738 -  83.129:   13        |
|      3:    31.173 -  41.564:  117   |   8:    83.129 -  93.520:    3        |
|      4:    41.564 -  51.956:  102   |   9:    93.520 - 103.911:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1297 r_free = 0.1779             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1296 r_free = 0.1780             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1780   ksol= 0.33   Bsol= 72.40   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.85,4.28,0.00,0.00,0.00); trace/3= 3.20                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.267751                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1297   r_free= 0.1781   ksol= 0.33   Bsol= 72.40   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.73,4.08,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.267650                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.030874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.844  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.694  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1297      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1781      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0931 = 3.03 * 0.50 * 5.2893 + 1.00 * 0.0775                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0271 = 3.03 * 0.50 * 5.2404 + 1.00 * 0.0856                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1229 = 0.21 * 1.00 * 5.2404 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1164 = 0.21 * 1.00 * 5.2183 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.79   12.38    None  None   None       |
|    all(noH): 2823   0      0.00    96.79   12.38    None  None   None       |
|    Sol.    : 438    0      1.40    96.79   35.92    None  None   None       |
|    Mac.    : 2385   0      0.00    79.43   8.05     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 -   9.679: 1812   |   5:    48.395 -  58.074:   72        |
|      1:     9.679 -  19.358:  510   |   6:    58.074 -  67.753:   39        |
|      2:    19.358 -  29.037:  144   |   7:    67.753 -  77.432:   13        |
|      3:    29.037 -  38.716:  128   |   8:    77.432 -  87.111:    5        |
|      4:    38.716 -  48.395:   97   |   9:    87.111 -  96.790:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1221 r_free = 0.1676             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1220 r_free = 0.1674             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1674   ksol= 0.33   Bsol= 72.40   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.73,4.08,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212810                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8249 0.99   1375  152 0.1042 0.1362      5.4218      5.5446|
|  2:  4.8249 -  3.8500 0.99   1316  148 0.0885 0.1187      5.4764      5.7026|
|  3:  3.8500 -  3.3693 0.99   1294  144 0.1123 0.1509      5.5307      5.8498|
|  4:  3.3693 -  3.0640 0.99   1285  142 0.1292 0.1696      5.4963      5.6603|
|  5:  3.0640 -  2.8459 0.99   1270  141 0.1497 0.1723      5.4311      5.5735|
|  6:  2.8459 -  2.6791 0.99   1285  141 0.1343 0.2273      5.3022      5.6214|
|  7:  2.6791 -  2.5455 0.99   1262  144 0.1445 0.1717      5.2739      5.4072|
|  8:  2.5455 -  2.4352 0.98   1260  136 0.1341 0.1798      5.1759      5.4233|
|  9:  2.4352 -  2.3418 0.98   1260  141 0.1273 0.1936      5.1086      5.3496|
| 10:  2.3418 -  2.2612 1.00   1253  141 0.1275 0.1787      5.0563      5.2711|
| 11:  2.2612 -  2.1907 0.97   1257  137 0.1268 0.1908      5.0188      5.2736|
| 12:  2.1907 -  2.1283 0.98   1246  139 0.1252 0.1842      4.9478       5.286|
| 13:  2.1283 -  2.0724 0.99   1250  139 0.1242 0.1792      4.8561        5.08|
| 14:  2.0724 -  2.0220 0.81   1017  114 0.1167 0.1846      4.7357      5.0039|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2395 -  4.8249  1375   152  0.94   9.54   0.96     0.94       7913.98|
|  2:  4.8249 -  3.8500  1316   148  0.95   8.65   0.99     0.97       9747.68|
|  3:  3.8500 -  3.3693  1294   144  0.93  11.76   1.01     1.01      11328.42|
|  4:  3.3693 -  3.0640  1285   142  0.92  13.93   0.99     0.97      10684.26|
|  5:  3.0640 -  2.8459  1270   141  0.89  16.92   0.99     0.97       9595.29|
|  6:  2.8459 -  2.6791  1285   141  0.89  17.27   0.97     0.94       8270.24|
|  7:  2.6791 -  2.5455  1262   144  0.89  17.51   0.98     0.95       7494.24|
|  8:  2.5455 -  2.4352  1260   136  0.90  16.62   0.98     0.95       6251.64|
|  9:  2.4352 -  2.3418  1260   141  0.90  16.54   0.99     0.95       5712.90|
| 10:  2.3418 -  2.2612  1253   141  0.89  16.72   0.99     0.95       5050.78|
| 11:  2.2612 -  2.1907  1257   137  0.89  17.16   0.98     0.94       4916.41|
| 12:  2.1907 -  2.1283  1246   139  0.90  16.29   0.99     0.98       4376.40|
| 13:  2.1283 -  2.0724  1250   139  0.90  16.72   0.98     0.96       3657.70|
| 14:  2.0724 -  2.0220  1017   114  0.91  15.04   0.96     0.92       2739.98|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2739.98 max =        11328.42 mean =      7076.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.98|
|phase err.(test): min =        0.00 max =           89.85 mean =        14.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1674   ksol= 0.32   Bsol= 66.05   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,-0.37,1.00,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1674   ksol= 0.32   Bsol= 66.05   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.62,-0.37,1.00,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212622                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.8249 0.99   1375  152 0.1036 0.1358      5.4166      5.5408|
|  2:  4.8249 -  3.8500 0.99   1316  148 0.0880 0.1179      5.4714      5.6958|
|  3:  3.8500 -  3.3693 0.99   1294  144 0.1120 0.1508       5.528      5.8487|
|  4:  3.3693 -  3.0640 0.99   1285  142 0.1295 0.1698      5.4981      5.6612|
|  5:  3.0640 -  2.8459 0.99   1270  141 0.1501 0.1728      5.4337      5.5763|
|  6:  2.8459 -  2.6791 0.99   1285  141 0.1345 0.2276      5.3042      5.6229|
|  7:  2.6791 -  2.5455 0.99   1262  144 0.1447 0.1722      5.2757      5.4093|
|  8:  2.5455 -  2.4352 0.98   1260  136 0.1343 0.1798      5.1769       5.424|
|  9:  2.4352 -  2.3418 0.98   1260  141 0.1273 0.1934      5.1092      5.3493|
| 10:  2.3418 -  2.2612 1.00   1253  141 0.1276 0.1789      5.0568      5.2724|
| 11:  2.2612 -  2.1907 0.97   1257  137 0.1269 0.1909      5.0191      5.2736|
| 12:  2.1907 -  2.1283 0.98   1246  139 0.1252 0.1842       4.948       5.286|
| 13:  2.1283 -  2.0724 0.99   1250  139 0.1242 0.1793      4.8563      5.0803|
| 14:  2.0724 -  2.0220 0.81   1017  114 0.1168 0.1846      4.7357      5.0036|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2395 -  4.8249  1375   152  0.94   9.48   0.96     0.94       7836.12|
|  2:  4.8249 -  3.8500  1316   148  0.95   8.58   0.99     0.97       9655.76|
|  3:  3.8500 -  3.3693  1294   144  0.93  11.68   1.01     1.01      11253.55|
|  4:  3.3693 -  3.0640  1285   142  0.92  13.95   0.99     0.97      10704.75|
|  5:  3.0640 -  2.8459  1270   141  0.89  16.96   0.99     0.97       9641.63|
|  6:  2.8459 -  2.6791  1285   141  0.89  17.31   0.97     0.94       8309.44|
|  7:  2.6791 -  2.5455  1262   144  0.89  17.54   0.98     0.95       7524.06|
|  8:  2.5455 -  2.4352  1260   136  0.90  16.64   0.98     0.95       6264.00|
|  9:  2.4352 -  2.3418  1260   141  0.90  16.56   0.99     0.95       5722.49|
| 10:  2.3418 -  2.2612  1253   141  0.89  16.72   0.99     0.95       5054.42|
| 11:  2.2612 -  2.1907  1257   137  0.89  17.16   0.98     0.94       4920.39|
| 12:  2.1907 -  2.1283  1246   139  0.90  16.30   0.99     0.98       4379.32|
| 13:  2.1283 -  2.0724  1250   139  0.90  16.73   0.98     0.96       3658.53|
| 14:  2.0724 -  2.0220  1017   114  0.91  15.03   0.96     0.92       2738.00|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2738.00 max =        11253.55 mean =      7070.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.98|
|phase err.(test): min =        0.00 max =           89.88 mean =        14.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.423)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.08    99.87   15.46    None  None   None       |
|    all(noH): 2823   0      3.08    99.87   15.46    None  None   None       |
|    Sol.    : 438    0      4.48    99.87   39.00    None  None   None       |
|    Mac.    : 2385   0      3.08    82.51   11.13    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:     3.079 -  12.758: 1812   |   5:    51.474 -  61.153:   72        |
|      1:    12.758 -  22.437:  510   |   6:    61.153 -  70.832:   39        |
|      2:    22.437 -  32.116:  144   |   7:    70.832 -  80.511:   13        |
|      3:    32.116 -  41.795:  128   |   8:    80.511 -  90.190:    5        |
|      4:    41.795 -  51.474:   97   |   9:    90.190 -  99.869:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.277 - 5.981
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 333
   mapped sites are within: 0.702 - 5.981

peak=    9.781 closest distance to " CB  VAL A 230 " =    1.481
peak=    5.711 closest distance to " CG  LEU A   5 " =    1.284
peak=    5.549 closest distance to " CB  GLN A 223 " =    1.527
peak=    5.513 closest distance to " O   HOH Z 111 " =    2.208
peak=    5.277 closest distance to " CG  LEU A 228 " =    1.281
peak=    4.936 closest distance to " CG2 VAL A 296 " =    1.032
peak=    4.856 closest distance to " O   HOH Z 232 " =    2.208
peak=    4.839 closest distance to " CZ  PHE A 218 " =    1.134
peak=    4.819 closest distance to " CB  SER A  63 " =    1.258
peak=    4.779 closest distance to " CD1AILE A 234 " =    1.104
peak=    4.768 closest distance to " CB  VAL A 296 " =    1.101
peak=    4.736 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.706 closest distance to " CG  PRO A 280 " =    0.897
peak=    4.645 closest distance to " CA  VAL A 230 " =    1.233
peak=    4.640 closest distance to " CD2 LEU A   5 " =    1.137
peak=    4.634 closest distance to " O   HOH Z 369 " =    2.052
peak=    4.616 closest distance to " O   HOH Z 425 " =    1.571
peak=    4.561 closest distance to " O   HOH Z 265 " =    2.042
peak=    4.410 closest distance to " CB  ASP A 124 " =    0.767
peak=    4.409 closest distance to " CB  ARG A 190 " =    1.640
peak=    4.369 closest distance to " CB  TRP A 266 " =    1.026
peak=    4.361 closest distance to " CG  PRO A 243 " =    1.129
peak=    4.349 closest distance to " O   HOH Z 368 " =    2.388
peak=    4.340 closest distance to " CG  PRO A 198 " =    1.287
peak=    4.339 closest distance to " O   HOH Z 126 " =    1.679
peak=    4.332 closest distance to " O   PRO A 198 " =    1.558
peak=    4.320 closest distance to " NE2 GLN A  11 " =    1.070
peak=    4.318 closest distance to " O   HOH Z 411 " =    3.817
peak=    4.256 closest distance to " CD  LYS A 166 " =    1.340
peak=    4.246 closest distance to " CG  MET A 185 " =    1.361
peak=    4.245 closest distance to " O   HOH Z 236 " =    2.051
peak=    4.206 closest distance to " O   HOH Z 184 " =    1.596
peak=    4.185 closest distance to " O   HOH Z 303 " =    2.205
peak=    4.177 closest distance to " CG1 VAL A 296 " =    1.211
peak=    4.171 closest distance to " CA  ALA A  51 " =    0.972
peak=    4.148 closest distance to " CB  TYR A 169 " =    0.783
peak=    4.143 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.134 closest distance to " O   SER A  87 " =    2.331
peak=    4.090 closest distance to " O   HOH Z 298 " =    1.961
peak=    4.082 closest distance to " CD2 LEU A 228 " =    1.185
peak=    4.077 closest distance to " O   HOH Z 234 " =    3.749
peak=    4.047 closest distance to " O   HOH Z 261 " =    1.793
peak=    4.047 closest distance to " CB  ARG A  79 " =    1.505
peak=    4.044 closest distance to " CB  ASN A 142 " =    1.087
peak=    4.042 closest distance to " O   HOH Z  76 " =    1.398
peak=    4.029 closest distance to " CD  ARG A  66 " =    2.450
peak=    4.025 closest distance to " O   HOH Z 102 " =    1.380
peak=    4.022 closest distance to " CA  ALA A 295 " =    1.079
peak=    4.018 closest distance to " O   HOH Z  49 " =    1.327
peak=    4.002 closest distance to " CB  VAL A 202 " =    1.546
peak=    3.954 closest distance to " ND2 ASN A 187 " =    1.528
peak=    3.940 closest distance to " CB  GLU A 152 " =    1.155
peak=    3.919 closest distance to " CB  GLU A 277 " =    3.760
peak=    3.899 closest distance to " CD2 TRP A 179 " =    1.301
peak=    3.887 closest distance to " CB  GLU A 128 " =    1.029
peak=    3.883 closest distance to " CG2 THR A 221 " =    0.978
peak=    3.867 closest distance to " O   HOH Z 214 " =    1.423
peak=    3.857 closest distance to " O   HOH Z 193 " =    2.178
peak=    3.854 closest distance to " O   HOH Z 188 " =    3.042
peak=    3.847 closest distance to " O   HOH Z 142 " =    1.665
peak=    3.843 closest distance to " O   HOH Z 359 " =    1.722
peak=    3.833 closest distance to " O   HOH Z 423 " =    1.757
peak=    3.832 closest distance to " O   HOH Z 272 " =    2.015
peak=    3.828 closest distance to " O   HOH Z 422 " =    2.634
peak=    3.827 closest distance to " CA  ARG A 195 " =    1.239
peak=    3.827 closest distance to " NH1AARG A 145 " =    1.281
peak=    3.820 closest distance to " O   HOH Z 427 " =    3.131
peak=    3.818 closest distance to " N   ASN A  39 " =    1.250
peak=    3.816 closest distance to " O   HOH Z 247 " =    1.534
peak=    3.815 closest distance to " CG1 VAL A 153 " =    0.989
peak=    3.815 closest distance to " CB  ALA A 248 " =    1.164
peak=    3.813 closest distance to " CZ3 TRP A 266 " =    1.150
peak=    3.807 closest distance to " O   HOH Z 316 " =    3.206
peak=    3.801 closest distance to " O   HOH Z  43 " =    1.987
peak=    3.799 closest distance to " CD1 LEU A  96 " =    0.815
peak=    3.794 closest distance to " CA  GLY A 267 " =    0.738
peak=    3.793 closest distance to " ND2 ASN A 249 " =    1.944
peak=    3.791 closest distance to " O   HOH Z  63 " =    1.887
peak=    3.791 closest distance to " CB  ASN A 187 " =    2.018
peak=    3.788 closest distance to " CB  ASN A  39 " =    0.823
peak=    3.788 closest distance to " O   HOH Z   9 " =    1.377
peak=    3.782 closest distance to " O   HOH Z 403 " =    1.588
peak=    3.778 closest distance to " O   HOH Z   4 " =    1.731
peak=    3.777 closest distance to " CA  TYR A  30 " =    0.938
peak=    3.777 closest distance to " O   ASP A 124 " =    1.167
peak=    3.774 closest distance to " CA  SER A  87 " =    0.909
peak=    3.774 closest distance to " O   HOH Z 346 " =    1.529
peak=    3.772 closest distance to " CG  ARG A 138 " =    1.224
peak=    3.753 closest distance to " CB  ASP A 140 " =    0.829
peak=    3.752 closest distance to " CB  GLU A  46 " =    0.896
peak=    3.742 closest distance to " CB  LEU A  83 " =    0.702
peak=    3.741 closest distance to " O   HOH Z 406 " =    1.530
peak=    3.739 closest distance to " OG BSER A 164 " =    2.199
peak=    3.739 closest distance to " CB  ASN A 148 " =    1.447
peak=    3.733 closest distance to " NH1 ARG A 138 " =    1.164
peak=    3.731 closest distance to " CD ALYS A 290 " =    1.091
peak=    3.717 closest distance to " CD  ARG A 269 " =    0.945
peak=    3.713 closest distance to " CB  LEU A 143 " =    1.288
peak=    3.713 closest distance to " N   PHE A 130 " =    1.295
peak=    3.713 closest distance to " O   HOH Z 213 " =    1.713
peak=    3.712 closest distance to " O   HOH Z 227 " =    1.811
peak=    3.705 closest distance to " CG2 ILE A 234 " =    0.986
peak=    3.696 closest distance to " CG AARG A 275 " =    1.289
peak=    3.692 closest distance to " CA  ILE A 106 " =    0.776
peak=    3.691 closest distance to " CD  ARG A 159 " =    0.740
peak=    3.688 closest distance to " O   HOH Z  78 " =    1.766
peak=    3.677 closest distance to " CD1 LEU A   5 " =    1.362
peak=    3.669 closest distance to " CB  ARG A 275 " =    0.927
peak=    3.666 closest distance to " O   HOH Z 402 " =    1.519
peak=    3.659 closest distance to " O   HOH Z 214 " =    2.088
peak=    3.653 closest distance to " OD1 ASN A  69 " =    2.485
peak=    3.651 closest distance to " CD  ARG A  66 " =    2.353
peak=    3.651 closest distance to " CB  ALA A 291 " =    1.256
peak=    3.649 closest distance to " CA  ALA A  21 " =    1.154
peak=    3.649 closest distance to " CA  ASP A 162 " =    0.892
peak=    3.645 closest distance to " CB  ALA A   9 " =    1.660
peak=    3.639 closest distance to " OG  SER A 245 " =    1.635
peak=    3.634 closest distance to " O   HOH Z 131 " =    2.318
peak=    3.625 closest distance to " CZ3 TRP A  85 " =    1.059
peak=    3.622 closest distance to " CA  TYR A 116 " =    1.459
peak=    3.618 closest distance to " O   HOH Z  88 " =    3.373
peak=    3.611 closest distance to " CB BVAL A  41 " =    1.265
peak=    3.610 closest distance to " CA  LEU A 282 " =    1.098
peak=    3.597 closest distance to " O   HOH Z 393 " =    3.988
peak=    3.595 closest distance to " NH2AARG A 145 " =    1.176
peak=    3.591 closest distance to " CG  PHE A 204 " =    0.936
peak=    3.590 closest distance to " OG  SER A 276 " =    1.472
peak=    3.589 closest distance to " CG  LEU A 167 " =    1.135
peak=    3.581 closest distance to " ND1 HIS A  81 " =    1.739
peak=    3.578 closest distance to " O   HOH Z  80 " =    1.890
peak=    3.576 closest distance to " O   HOH Z 368 " =    3.461
peak=    3.573 closest distance to " O   HOH Z  21 " =    1.758
peak=    3.567 closest distance to " O   HOH Z  48 " =    1.709
peak=    3.562 closest distance to " CD1 LEU A 300 " =    1.158
peak=    3.559 closest distance to " CB  VAL A 265 " =    1.326
peak=    3.558 closest distance to " O   HOH Z 155 " =    3.444
peak=    3.557 closest distance to " O   HOH Z 210 " =    1.219
peak=    3.554 closest distance to " O   HOH Z 128 " =    1.556
peak=    3.554 closest distance to " CG  ARG A 269 " =    1.818
peak=    3.549 closest distance to " O   ASP A 200 " =    1.629
peak=    3.549 closest distance to " O   HOH Z  19 " =    2.224
peak=    3.544 closest distance to " CG  GLU A  37 " =    0.957
peak=    3.543 closest distance to " O   HOH Z 280 " =    2.956
peak=    3.538 closest distance to " O   HOH Z 285 " =    2.358
peak=    3.536 closest distance to " O   HOH Z  61 " =    1.673
peak=    3.534 closest distance to " CE3 TRP A  85 " =    1.055
peak=    3.531 closest distance to " CZ  PHE A 192 " =    1.004
peak=    3.531 closest distance to " CA  ALA A 160 " =    1.059
peak=    3.525 closest distance to " CZ  PHE A  38 " =    1.156
peak=    3.520 closest distance to " O   HOH Z 130 " =    1.123
peak=    3.516 closest distance to " O   HOH Z 158 " =    3.062
peak=    3.508 closest distance to " OD1 ASN A 217 " =    1.574
peak=    3.495 closest distance to " O   HOH Z 163 " =    1.661
peak=    3.495 closest distance to " CA  ARG A  36 " =    1.129
peak=    3.495 closest distance to " CA  THR A 264 " =    0.732
peak=    3.488 closest distance to " CB  ASN A 187 " =    1.031
peak=    3.485 closest distance to " CZ3 TRP A 274 " =    4.676
peak=    3.483 closest distance to " CB  TRP A 150 " =    1.475
peak=    3.480 closest distance to " CB  SER A   3 " =    1.469
peak=    3.477 closest distance to " O   HOH Z 193 " =    1.766
peak=    3.475 closest distance to " O   HOH Z 251 " =    1.568
peak=    3.474 closest distance to " N   CYS A 260 " =    0.723
peak=    3.473 closest distance to " CB  ALA A 242 " =    0.786
peak=    3.472 closest distance to " O   HOH Z 199 " =    1.687
peak=    3.465 closest distance to " O   HOH Z 313 " =    1.805
peak=    3.464 closest distance to " CB  THR A  31 " =    1.515
peak=    3.464 closest distance to " CB  GLN A  89 " =    1.097
peak=    3.461 closest distance to " CA  MET A 105 " =    0.922
peak=    3.459 closest distance to " O   HOH Z 313 " =    1.666
peak=    3.457 closest distance to " CD  PRO A  54 " =    0.838
peak=    3.455 closest distance to " CD1 ILE A  33 " =    1.823
peak=    3.453 closest distance to " O   HOH Z 248 " =    1.610
peak=    3.447 closest distance to " CE  LYS A  76 " =    0.925
peak=    3.444 closest distance to " O   HOH Z  56 " =    1.690
peak=    3.443 closest distance to " CA  GLY A 211 " =    1.370
peak=    3.441 closest distance to " O   HOH Z  57 " =    1.365
peak=    3.440 closest distance to " O   HOH Z 394 " =    1.673
peak=    3.439 closest distance to " CA  ALA A 291 " =    0.915
peak=    3.435 closest distance to " CG BARG A 275 " =    1.441
peak=    3.432 closest distance to " CA  GLU A 152 " =    0.958
peak=    3.430 closest distance to " O   HOH Z 290 " =    1.248
peak=    3.428 closest distance to " CG1 ILE A  49 " =    1.617
peak=    3.426 closest distance to " CB  ARG A 138 " =    1.038
peak=    3.424 closest distance to " O   HOH Z 383 " =    1.931
peak=    3.416 closest distance to " O   HOH Z 188 " =    1.950
peak=    3.416 closest distance to " CB  SER A 273 " =    0.990
peak=    3.409 closest distance to " O   HOH Z 146 " =    1.538
peak=    3.401 closest distance to " NE2 HIS A 207 " =    1.122
peak=    3.401 closest distance to " CA  VAL A 125 " =    1.222
peak=    3.399 closest distance to " CB  GLN A  88 " =    1.171
peak=    3.398 closest distance to " CB  PRO A  54 " =    0.784
peak=    3.395 closest distance to " CB  SER A  26 " =    1.808
peak=    3.388 closest distance to " O   ASN A 209 " =    1.291
peak=    3.388 closest distance to " O   HOH Z 261 " =    1.830
peak=    3.388 closest distance to " O   HOH Z 273 " =    2.888
peak=    3.388 closest distance to " O   HOH Z 258 " =    2.148
peak=    3.384 closest distance to " O   HOH Z 353 " =    2.542
peak=    3.382 closest distance to " O   ASN A  74 " =    1.556
peak=    3.381 closest distance to " CZ3 TRP A  92 " =    1.423
peak=    3.380 closest distance to " O   HOH Z 183 " =    1.263
peak=    3.378 closest distance to " NH1 ARG A  14 " =    0.981
peak=    3.377 closest distance to " N   SER A 135 " =    1.499
peak=    3.373 closest distance to " O   HOH Z 148 " =    3.245
peak=    3.372 closest distance to " O  BHOH Z 338 " =    2.307
peak=    3.370 closest distance to " O   HOH Z 203 " =    1.776
peak=    3.370 closest distance to " NH2 ARG A 156 " =    1.113
peak=    3.368 closest distance to " CG  MET A 185 " =    1.005
peak=    3.368 closest distance to " O   PHE A 192 " =    1.470
peak=    3.367 closest distance to " CB  PRO A 243 " =    1.216
peak=    3.367 closest distance to " CD  ARG A 219 " =    1.115
peak=    3.360 closest distance to " O   HOH Z 148 " =    2.030
peak=    3.356 closest distance to " CA  ASP A 191 " =    0.949
peak=    3.353 closest distance to " CB  SER A 212 " =    1.315
peak=    3.353 closest distance to " OD2 ASP A 298 " =    3.999
peak=    3.350 closest distance to " O   HOH Z 180 " =    2.030
peak=    3.346 closest distance to " N   ASP A 162 " =    1.262
peak=    3.343 closest distance to " CB  ALA A 104 " =    0.748
peak=    3.341 closest distance to " O   HOH Z 437 " =    1.558
peak=    3.339 closest distance to " O   HOH Z 250 " =    1.339
peak=    3.334 closest distance to " O   HOH Z 109 " =    2.746
peak=    3.330 closest distance to " O   HOH Z 371 " =    2.991
peak=    3.328 closest distance to " CB  ASN A 285 " =    0.940
peak=    3.328 closest distance to " CA  ALA A 154 " =    1.031
peak=    3.318 closest distance to " O   HOH Z 329 " =    3.105
peak=    3.318 closest distance to " CG1 ILE A  33 " =    1.285
peak=    3.315 closest distance to " O   PRO A 213 " =    1.470
peak=    3.315 closest distance to " O   GLN A 278 " =    1.254
peak=    3.313 closest distance to " OG  SER A  22 " =    2.860
peak=    3.310 closest distance to " O   HOH Z 420 " =    5.981
peak=    3.310 closest distance to " CA  VAL A 112 " =    1.072
peak=    3.309 closest distance to " CE3 TRP A 150 " =    1.037
peak=    3.309 closest distance to " O   HOH Z 238 " =    2.135
peak=    3.305 closest distance to " O   HOH Z 299 " =    4.466
peak=    3.303 closest distance to " O   LEU A 228 " =    1.922
peak=    3.303 closest distance to " O   HOH Z 134 " =    2.752
peak=    3.299 closest distance to " OE1 GLN A  55 " =    1.420
peak=    3.298 closest distance to " OG1 THR A 279 " =    1.495
peak=    3.297 closest distance to " CA  ASN A 127 " =    1.117
peak=    3.296 closest distance to " O   ALA A 165 " =    1.420
peak=    3.295 closest distance to " CG1 ILE A 120 " =    1.146
peak=    3.292 closest distance to " CD1 LEU A 101 " =    1.053
peak=    3.292 closest distance to " O   HOH Z 132 " =    2.729
peak=    3.291 closest distance to " O   GLU A   2 " =    1.617
peak=    3.286 closest distance to " CH2 TRP A  70 " =    1.063
peak=    3.285 closest distance to " O   ALA A 158 " =    1.360
peak=    3.276 closest distance to " O   HOH Z  44 " =    1.917
peak=    3.273 closest distance to " CB  ILE A 120 " =    1.326
peak=    3.270 closest distance to " CB  TRP A 179 " =    1.318
peak=    3.270 closest distance to " CA  ALA A 184 " =    0.982
peak=    3.268 closest distance to " O   HOH Z 293 " =    1.820
peak=    3.266 closest distance to " CB  SER A  62 " =    0.899
peak=    3.266 closest distance to " CB  SER A 216 " =    0.869
peak=    3.263 closest distance to " N   VAL A 126 " =    1.603
peak=    3.261 closest distance to " O   HOH Z 117 " =    2.022
peak=    3.260 closest distance to " CG2AVAL A 121 " =    2.173
peak=    3.260 closest distance to " CB  ALA A 100 " =    1.346
peak=    3.260 closest distance to " O   HOH Z 128 " =    2.181
peak=    3.258 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.258 closest distance to " CG1BVAL A  72 " =    1.708
peak=    3.256 closest distance to " O   HOH Z  10 " =    1.795
peak=    3.248 closest distance to " O   HOH Z 298 " =    2.321
peak=    3.248 closest distance to " CA  ASP A 140 " =    1.306
peak=    3.234 closest distance to " CB  THR A  82 " =    1.400
peak=    3.229 closest distance to " CB  SER A 288 " =    1.385
peak=    3.228 closest distance to " CA  ASN A 284 " =    0.922
peak=    3.224 closest distance to " O   HOH Z 141 " =    1.679
peak=    3.223 closest distance to " NZ  LYS A  76 " =    1.474
peak=    3.222 closest distance to " O   HOH Z 391 " =    2.944
peak=    3.220 closest distance to " N   ARG A 190 " =    1.070
peak=    3.216 closest distance to " CB  VAL A 257 " =    0.770
peak=    3.216 closest distance to " O   GLN A  88 " =    1.709
peak=    3.212 closest distance to " O   HOH Z 327 " =    2.241
peak=    3.212 closest distance to " NZ  LYS A  48 " =    1.311
peak=    3.208 closest distance to " CA  ASP A 124 " =    0.817
peak=    3.205 closest distance to " CA  VAL A  41 " =    0.781
peak=    3.205 closest distance to " O   HOH Z  40 " =    1.941
peak=    3.205 closest distance to " O   HOH Z 124 " =    2.059
peak=    3.198 closest distance to " CD  LYS A 119 " =    2.094
peak=    3.197 closest distance to " CA  LYS A 181 " =    1.070
peak=    3.193 closest distance to " O   HOH Z 201 " =    2.852
peak=    3.189 closest distance to " CA  GLN A 223 " =    0.910
peak=    3.187 closest distance to " O   HOH Z  88 " =    3.112
peak=    3.186 closest distance to " CG2 VAL A 197 " =    1.075
peak=    3.185 closest distance to " CB  GLN A 103 " =    0.912
peak=    3.178 closest distance to " O   MET A 105 " =    1.650
peak=    3.177 closest distance to " CB  ASN A 173 " =    0.927
peak=    3.177 closest distance to " O   HOH Z 156 " =    2.935
peak=    3.176 closest distance to " O   THR A 182 " =    1.407
peak=    3.175 closest distance to " CA  ALA A 158 " =    1.190
peak=    3.173 closest distance to " CA  GLN A  88 " =    1.273
peak=    3.173 closest distance to " O   HOH Z 128 " =    2.306
peak=    3.169 closest distance to " CA  ARG A 139 " =    1.198
peak=    3.167 closest distance to " O   HOH Z 130 " =    2.167
peak=    3.164 closest distance to " O   HOH Z 211 " =    1.208
peak=    3.164 closest distance to " CA  GLU A  46 " =    0.741
peak=    3.163 closest distance to " O   ASP A 124 " =    1.797
peak=    3.162 closest distance to " O   TRP A 274 " =    1.846
peak=    3.161 closest distance to " CA  GLY A 241 " =    0.882
peak=    3.159 closest distance to " CA  ALA A 100 " =    1.002
peak=    3.154 closest distance to " CA  GLN A  94 " =    0.794
peak=    3.151 closest distance to " CB  ALA A  43 " =    0.955
peak=    3.151 closest distance to " O   HOH Z 371 " =    2.366
peak=    3.149 closest distance to " O   HOH Z 350 " =    1.630
peak=    3.148 closest distance to " CG  LYS A  76 " =    0.995
peak=    3.142 closest distance to " NH1 ARG A  56 " =    1.136
peak=    3.141 closest distance to " O   HOH Z 197 " =    1.944
peak=    3.139 closest distance to " N   ALA A 256 " =    1.141
peak=    3.138 closest distance to " O   HOH Z  78 " =    2.263
peak=    3.134 closest distance to " O   HOH Z 156 " =    2.653
peak=    3.133 closest distance to " O   HOH Z 145 " =    1.366
peak=    3.132 closest distance to " N   ARG A 156 " =    1.497
peak=    3.123 closest distance to " O   HOH Z 301 " =    1.762
peak=    3.119 closest distance to " O   HOH Z 162 " =    2.149
peak=    3.118 closest distance to " CB  ALA A   1 " =    4.857
peak=    3.114 closest distance to " CB  PHE A 204 " =    1.007
peak=    3.107 closest distance to " CG2 ILE A  20 " =    1.442
peak=    3.106 closest distance to " OG BSER A 134 " =    2.833
peak=    3.101 closest distance to " O   HOH Z 116 " =    1.840
peak=    3.087 closest distance to " OG1 THR A 294 " =    2.449
peak=    3.084 closest distance to " CG BARG A 102 " =    1.810
peak=    3.082 closest distance to " CD  ARG A 195 " =    1.008
peak=    3.082 closest distance to " CD1 ILE A 199 " =    0.928
peak=    3.076 closest distance to " O   HOH Z 409 " =    2.959
peak=    3.059 closest distance to " CB  LEU A 300 " =    0.895
peak=    3.057 closest distance to " CA  SER A  26 " =    0.963
peak=    3.056 closest distance to " O   HOH Z 344 " =    3.063
peak=    3.053 closest distance to " CG  MET A 113 " =    1.740
peak=    3.050 closest distance to " CB  PRO A  54 " =    1.269

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.626 - 5.409
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 219
   mapped sites are within: 0.705 - 5.409

peak=   -5.904 closest distance to " CG2 VAL A 230 " =    0.734
peak=   -4.943 closest distance to " O   HOH Z 211 " =    0.716
peak=   -4.592 closest distance to " O   HOH Z 210 " =    0.705
peak=   -4.584 closest distance to " CD  GLN A  58 " =    0.890
peak=   -4.401 closest distance to " CB  PRO A 243 " =    2.717
peak=   -4.384 closest distance to " CG1 VAL A 250 " =    2.772
peak=   -4.342 closest distance to " CG1 VAL A 296 " =    1.189
peak=   -4.304 closest distance to " O   HOH Z 166 " =    1.678
peak=   -4.223 closest distance to " CG1 VAL A 112 " =    2.648
peak=   -4.191 closest distance to " CA  ASP A 298 " =    1.085
peak=   -4.145 closest distance to " O   HOH Z 394 " =    1.513
peak=   -4.093 closest distance to " O   HOH Z 216 " =    0.978
peak=   -4.078 closest distance to " CB  ALA A 161 " =    2.690
peak=   -4.023 closest distance to " O   HOH Z 133 " =    1.040
peak=   -4.021 closest distance to " O   HOH Z 196 " =    2.480
peak=   -4.019 closest distance to " CD  ARG A 156 " =    2.140
peak=   -4.014 closest distance to " CE3 TRP A  70 " =    1.829
peak=   -3.987 closest distance to " CG1 VAL A 112 " =    2.658
peak=   -3.964 closest distance to " CD  ARG A  14 " =    3.273
peak=   -3.959 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.926 closest distance to " CD1 PHE A  59 " =    2.098
peak=   -3.921 closest distance to " OE1 GLN A  88 " =    0.840
peak=   -3.912 closest distance to " O   HOH Z 290 " =    1.189
peak=   -3.908 closest distance to " C   ALA A 158 " =    1.363
peak=   -3.906 closest distance to " O   HOH Z  10 " =    1.644
peak=   -3.875 closest distance to " O   HOH Z 351 " =    1.641
peak=   -3.833 closest distance to " O   HOH Z 377 " =    0.993
peak=   -3.795 closest distance to " O   HOH Z 411 " =    5.409
peak=   -3.786 closest distance to " O   PRO A 198 " =    1.315
peak=   -3.759 closest distance to " O   SER A 271 " =    2.196
peak=   -3.752 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.751 closest distance to " OD1 ASN A 148 " =    1.468
peak=   -3.750 closest distance to " CD  GLN A  55 " =    0.915
peak=   -3.744 closest distance to " CG2BVAL A  41 " =    2.722
peak=   -3.738 closest distance to " CZ2 TRP A  92 " =    2.838
peak=   -3.727 closest distance to " O   HOH Z  93 " =    2.240
peak=   -3.701 closest distance to " CD2 TYR A 293 " =    2.037
peak=   -3.691 closest distance to " O   HOH Z  37 " =    2.123
peak=   -3.689 closest distance to " O   GLY A 203 " =    2.424
peak=   -3.689 closest distance to " CG  ARG A 269 " =    2.337
peak=   -3.676 closest distance to " O   HOH Z  52 " =    1.650
peak=   -3.667 closest distance to " O   HOH Z 434 " =    1.775
peak=   -3.667 closest distance to " O   HOH Z  73 " =    2.391
peak=   -3.666 closest distance to " CG  GLN A 223 " =    2.332
peak=   -3.650 closest distance to " CA  GLY A 241 " =    2.373
peak=   -3.636 closest distance to " O   GLY A  80 " =    2.681
peak=   -3.630 closest distance to " O   HOH Z 231 " =    1.171
peak=   -3.629 closest distance to " N   THR A  18 " =    1.352
peak=   -3.628 closest distance to " CZ3 TRP A 179 " =    1.139
peak=   -3.626 closest distance to " O   PRO A 163 " =    2.153
peak=   -3.622 closest distance to " O   HOH Z 359 " =    2.924
peak=   -3.617 closest distance to " O   HOH Z 183 " =    1.122
peak=   -3.613 closest distance to " CA  GLY A 241 " =    3.168
peak=   -3.602 closest distance to " CG  HIS A  86 " =    1.197
peak=   -3.598 closest distance to " CG2 THR A 178 " =    2.406
peak=   -3.589 closest distance to " CD2 PHE A  61 " =    2.596
peak=   -3.587 closest distance to " OD1 ASN A 249 " =    2.493
peak=   -3.582 closest distance to " CD  GLN A 223 " =    1.189
peak=   -3.579 closest distance to " O   HOH Z  44 " =    0.909
peak=   -3.578 closest distance to " CG  GLU A 277 " =    1.346
peak=   -3.577 closest distance to " OG  SER A  97 " =    2.305
peak=   -3.573 closest distance to " N   ALA A  43 " =    2.685
peak=   -3.565 closest distance to " CA  SER A  62 " =    2.745
peak=   -3.553 closest distance to " O   HOH Z 210 " =    0.706
peak=   -3.549 closest distance to " O   HOH Z 251 " =    4.940
peak=   -3.542 closest distance to " NE2 GLN A 194 " =    1.897
peak=   -3.523 closest distance to " C   HIS A 108 " =    1.162
peak=   -3.522 closest distance to " O   HOH Z 407 " =    3.368
peak=   -3.521 closest distance to " C   LEU A 143 " =    1.109
peak=   -3.520 closest distance to " CG  LEU A   5 " =    0.886
peak=   -3.519 closest distance to " O   VAL A  67 " =    2.606
peak=   -3.519 closest distance to " ND2 ASN A  45 " =    2.301
peak=   -3.511 closest distance to " O   HOH Z 185 " =    2.492
peak=   -3.510 closest distance to " N   PHE A  59 " =    1.997
peak=   -3.497 closest distance to " N   THR A  52 " =    1.629
peak=   -3.495 closest distance to " O   HOH Z 231 " =    2.202
peak=   -3.493 closest distance to " O   SER A 276 " =    1.795
peak=   -3.490 closest distance to " O   HOH Z 177 " =    1.807
peak=   -3.490 closest distance to " O   HOH Z 232 " =    1.729
peak=   -3.489 closest distance to " CA  GLY A 133 " =    2.316
peak=   -3.481 closest distance to " OD1 ASP A 171 " =    1.710
peak=   -3.479 closest distance to " N   ALA A 226 " =    2.173
peak=   -3.467 closest distance to " CB  ALA A 129 " =    2.461
peak=   -3.452 closest distance to " CB  ALA A 256 " =    2.793
peak=   -3.448 closest distance to " NE2 GLN A  55 " =    2.443
peak=   -3.439 closest distance to " CD1 LEU A 101 " =    2.710
peak=   -3.435 closest distance to " CB  ALA A 248 " =    2.153
peak=   -3.428 closest distance to " CB  PRO A 163 " =    2.531
peak=   -3.427 closest distance to " O   HOH Z  60 " =    2.142
peak=   -3.424 closest distance to " O   VAL A 189 " =    2.625
peak=   -3.424 closest distance to " O   HOH Z  17 " =    1.396
peak=   -3.418 closest distance to " CG2 VAL A 189 " =    2.024
peak=   -3.416 closest distance to " O   HOH Z  43 " =    1.576
peak=   -3.412 closest distance to " CB  ALA A  10 " =    2.269
peak=   -3.402 closest distance to " O   HOH Z  38 " =    1.519
peak=   -3.397 closest distance to " NH2 ARG A  79 " =    1.681
peak=   -3.397 closest distance to " O   HOH Z 149 " =    2.164
peak=   -3.397 closest distance to " CE3 TRP A 150 " =    2.314
peak=   -3.393 closest distance to " NH2 ARG A 159 " =    2.460
peak=   -3.389 closest distance to " CD1 ILE A  33 " =    2.515
peak=   -3.387 closest distance to " O   HOH Z 234 " =    4.503
peak=   -3.386 closest distance to " NE2 GLN A 103 " =    1.830
peak=   -3.381 closest distance to " NE2 GLN A  88 " =    1.006
peak=   -3.380 closest distance to " CD1 LEU A 228 " =    2.438
peak=   -3.372 closest distance to " CD2 LEU A 167 " =    1.852
peak=   -3.369 closest distance to " CD1 LEU A 101 " =    2.477
peak=   -3.366 closest distance to " C   MET A 188 " =    1.310
peak=   -3.365 closest distance to " CG  MET A 105 " =    0.962
peak=   -3.364 closest distance to " O   HOH Z 136 " =    2.590
peak=   -3.363 closest distance to " CD  GLN A  88 " =    0.817
peak=   -3.359 closest distance to " O   HOH Z 241 " =    1.147
peak=   -3.358 closest distance to " CE2 TRP A  70 " =    2.279
peak=   -3.355 closest distance to " ND2 ASN A 249 " =    2.489
peak=   -3.352 closest distance to " CG  GLU A  53 " =    1.605
peak=   -3.350 closest distance to " CG2BVAL A  41 " =    1.813
peak=   -3.345 closest distance to " O   HOH Z 438 " =    3.129
peak=   -3.341 closest distance to " CZ  ARG A 259 " =    0.824
peak=   -3.340 closest distance to " CD  PRO A 243 " =    1.937
peak=   -3.335 closest distance to " CG  LYS A 166 " =    2.160
peak=   -3.333 closest distance to " CD1 ILE A 199 " =    2.619
peak=   -3.331 closest distance to " CB  VAL A 230 " =    1.050
peak=   -3.329 closest distance to " O   ASP A  27 " =    2.052
peak=   -3.329 closest distance to " CG2 VAL A 296 " =    1.206
peak=   -3.328 closest distance to " O   HOH Z 371 " =    1.441
peak=   -3.327 closest distance to " CA  GLY A 203 " =    2.477
peak=   -3.327 closest distance to " O   HOH Z  40 " =    2.288
peak=   -3.323 closest distance to " CE  LYS A  76 " =    2.609
peak=   -3.321 closest distance to " O   HOH Z 411 " =    1.737
peak=   -3.317 closest distance to " O   HOH Z  19 " =    2.063
peak=   -3.316 closest distance to " O   HOH Z 285 " =    1.889
peak=   -3.313 closest distance to " O   HOH Z  58 " =    0.760
peak=   -3.308 closest distance to " NH2AARG A 275 " =    5.344
peak=   -3.307 closest distance to " CD1 LEU A   5 " =    2.499
peak=   -3.305 closest distance to " O   HOH Z 145 " =    0.834
peak=   -3.303 closest distance to " O   HOH Z 111 " =    1.765
peak=   -3.300 closest distance to " O   SER A 210 " =    1.913
peak=   -3.293 closest distance to " O   GLN A  94 " =    2.334
peak=   -3.292 closest distance to " CD  GLN A  11 " =    1.110
peak=   -3.289 closest distance to " O   HOH Z 166 " =    1.629
peak=   -3.287 closest distance to " O   HOH Z 134 " =    2.886
peak=   -3.285 closest distance to " O   HOH Z 136 " =    0.807
peak=   -3.285 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.284 closest distance to " O   HOH Z  49 " =    1.087
peak=   -3.282 closest distance to " ND2 ASN A  60 " =    1.340
peak=   -3.278 closest distance to " O   HOH Z 193 " =    1.606
peak=   -3.275 closest distance to " OG ASER A 134 " =    1.532
peak=   -3.269 closest distance to " O   HOH Z 236 " =    1.363
peak=   -3.269 closest distance to " C   LYS A  76 " =    1.651
peak=   -3.263 closest distance to " O   HOH Z 317 " =    2.110
peak=   -3.263 closest distance to " O   GLY A 262 " =    2.524
peak=   -3.258 closest distance to " O   HOH Z 184 " =    1.659
peak=   -3.254 closest distance to " CD  PRO A 213 " =    2.204
peak=   -3.250 closest distance to " N   ALA A 248 " =    2.566
peak=   -3.250 closest distance to " CD  LYS A 289 " =    2.433
peak=   -3.247 closest distance to " O   HOH Z 252 " =    3.688
peak=   -3.246 closest distance to " CB  ALA A  43 " =    2.633
peak=   -3.245 closest distance to " CG  TRP A 266 " =    1.841
peak=   -3.245 closest distance to " O   HOH Z 175 " =    4.095
peak=   -3.244 closest distance to " O   HOH Z 377 " =    1.902
peak=   -3.243 closest distance to " CD2 PHE A 192 " =    2.058
peak=   -3.237 closest distance to " O   ALA A 227 " =    1.537
peak=   -3.233 closest distance to " O   HOH Z 431 " =    2.027
peak=   -3.233 closest distance to " CG1 VAL A  67 " =    2.678
peak=   -3.229 closest distance to " N   SER A 276 " =    1.577
peak=   -3.227 closest distance to " CG1BVAL A  72 " =    2.521
peak=   -3.224 closest distance to " CD2 PHE A 225 " =    1.174
peak=   -3.223 closest distance to " CE BMET A  47 " =    1.722
peak=   -3.216 closest distance to " CB  TRP A  85 " =    2.686
peak=   -3.216 closest distance to " O   GLY A 211 " =    1.496
peak=   -3.215 closest distance to " O   HOH Z 106 " =    1.965
peak=   -3.213 closest distance to " NE2 GLN A 194 " =    2.008
peak=   -3.208 closest distance to " ND2 ASN A  69 " =    1.448
peak=   -3.204 closest distance to " O   HOH Z  11 " =    1.845
peak=   -3.199 closest distance to " O   HOH Z 165 " =    1.905
peak=   -3.193 closest distance to " CG  LEU A   5 " =    1.454
peak=   -3.188 closest distance to " CG1 VAL A 125 " =    1.930
peak=   -3.180 closest distance to " CA  GLY A  98 " =    2.162
peak=   -3.179 closest distance to " O   HOH Z 150 " =    1.870
peak=   -3.179 closest distance to " O   HOH Z 100 " =    0.948
peak=   -3.177 closest distance to " CZ  TYR A 169 " =    1.733
peak=   -3.172 closest distance to " C   ASP A 270 " =    1.268
peak=   -3.167 closest distance to " CG  PRO A 163 " =    2.261
peak=   -3.162 closest distance to " O   HOH Z 198 " =    1.299
peak=   -3.157 closest distance to " OG BSER A 210 " =    1.612
peak=   -3.155 closest distance to " OE2 GLU A 277 " =    2.856
peak=   -3.154 closest distance to " O   HOH Z 409 " =    4.765
peak=   -3.153 closest distance to " O   GLY A  80 " =    2.642
peak=   -3.153 closest distance to " O   HOH Z 426 " =    1.829
peak=   -3.148 closest distance to " O   HOH Z 259 " =    4.122
peak=   -3.146 closest distance to " NH2 ARG A  36 " =    2.404
peak=   -3.140 closest distance to " O   HOH Z 227 " =    1.179
peak=   -3.135 closest distance to " ND2 ASN A  69 " =    1.931
peak=   -3.132 closest distance to " O   TYR A 186 " =    1.893
peak=   -3.130 closest distance to " CH2 TRP A 150 " =    1.140
peak=   -3.128 closest distance to " C   ALA A 165 " =    1.952
peak=   -3.124 closest distance to " CZ  PHE A 192 " =    2.857
peak=   -3.124 closest distance to " CD1 TYR A 247 " =    2.344
peak=   -3.116 closest distance to " O   HOH Z 396 " =    1.928
peak=   -3.115 closest distance to " ND2 ASN A  45 " =    1.190
peak=   -3.115 closest distance to " C   GLN A  58 " =    2.005
peak=   -3.108 closest distance to " O   HOH Z 275 " =    1.626
peak=   -3.107 closest distance to " O   HOH Z 265 " =    1.763
peak=   -3.104 closest distance to " OG BSER A 134 " =    1.990
peak=   -3.096 closest distance to " OH  TYR A 247 " =    1.890
peak=   -3.092 closest distance to " O   HOH Z 298 " =    3.043
peak=   -3.092 closest distance to " O   HOH Z  60 " =    2.363
peak=   -3.091 closest distance to " CA  SER A  62 " =    2.538
peak=   -3.085 closest distance to " O   HOH Z 435 " =    2.668
peak=   -3.078 closest distance to " O   HOH Z   6 " =    1.626
peak=   -3.077 closest distance to " CD  GLN A  73 " =    0.751
peak=   -3.067 closest distance to " CB  ASP A 171 " =    2.365
peak=   -3.062 closest distance to " N   TYR A  68 " =    3.012
peak=   -3.057 closest distance to " CE1 TYR A 247 " =    2.665
peak=   -3.055 closest distance to " CG2BVAL A  41 " =    1.290
peak=   -3.052 closest distance to " OD1 ASN A 173 " =    1.443
peak=   -3.045 closest distance to " O   LYS A 289 " =    2.991
peak=   -3.021 closest distance to " O   HOH Z 110 " =    1.445

================= 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    :  0.4828 0.4737   6.281777e+00   6.265694e+00
   1_bss:  0.4750 0.4638   6.276259e+00   6.257638e+00
   1_xyz:  0.3856 0.4130   6.154118e+00   6.186323e+00
   1_adp:  0.3422 0.3940   6.072353e+00   6.151154e+00
   1_occ:  0.3417 0.3943   6.071369e+00   6.151928e+00
   2_bss:  0.3405 0.3913   6.072461e+00   6.150836e+00
   2_xyz:  0.2574 0.3096   5.842915e+00   5.979782e+00
   2_adp:  0.2358 0.2868   5.774596e+00   5.928110e+00
   2_occ:  0.2356 0.2868   5.774269e+00   5.928082e+00
   3_bss:  0.2345 0.2861   5.776165e+00   5.928883e+00
   3_xyz:  0.1710 0.2185   5.495406e+00   5.690978e+00
   3_adp:  0.1544 0.2072   5.424726e+00   5.643990e+00
   3_occ:  0.1543 0.2074   5.424993e+00   5.644963e+00
   4_bss:  0.1546 0.2079   5.425667e+00   5.643893e+00
   4_xyz:  0.1327 0.1848   5.298381e+00   5.531547e+00
   4_adp:  0.1297 0.1779   5.267907e+00   5.493143e+00
   4_occ:  0.1296 0.1780   5.267751e+00   5.493330e+00
   5_bss:  0.1297 0.1781   5.267650e+00   5.493291e+00
   5_xyz:  0.1216 0.1689   5.215046e+00   5.449309e+00
   5_adp:  0.1221 0.1676   5.213421e+00   5.441556e+00
   5_occ:  0.1220 0.1674   5.212810e+00   5.441006e+00
   5_bss:  0.1220 0.1674   5.212622e+00   5.440763e+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:  0.295  20.000   7.053   7.603  10.333   0.000   0.000   0.000
   1_xyz:  0.295  20.000   7.053   7.603  10.333   0.000   0.000   0.000
   1_adp:  0.295  20.000   7.053   7.603  10.333   0.000   0.000   0.000
   1_occ:  0.295  20.000   7.053   7.603  10.333   0.000   0.000   0.000
   2_bss:  0.330  60.293   4.458   5.188   7.278   0.000   0.000   0.000
   2_xyz:  0.330  60.293   4.458   5.188   7.278   0.000   0.000   0.000
   2_adp:  0.330  60.293   4.458   5.188   7.278   0.000   0.000   0.000
   2_occ:  0.330  60.293   4.458   5.188   7.278   0.000   0.000   0.000
   3_bss:  0.332  72.398   2.889   3.446   4.990   0.000   0.000   0.000
   3_xyz:  0.332  72.398   2.889   3.446   4.990   0.000   0.000   0.000
   3_adp:  0.332  72.398   2.889   3.446   4.990   0.000   0.000   0.000
   3_occ:  0.332  72.398   2.889   3.446   4.990   0.000   0.000   0.000
   4_bss:  0.328  72.398   2.481   2.853   4.276   0.000   0.000   0.000
   4_xyz:  0.328  72.398   2.481   2.853   4.276   0.000   0.000   0.000
   4_adp:  0.328  72.398   2.481   2.853   4.276   0.000   0.000   0.000
   4_occ:  0.328  72.398   2.481   2.853   4.276   0.000   0.000   0.000
   5_bss:  0.330  72.398   2.433   2.733   4.081   0.000   0.000   0.000
   5_xyz:  0.330  72.398   2.433   2.733   4.081   0.000   0.000   0.000
   5_adp:  0.330  72.398   2.433   2.733   4.081   0.000   0.000   0.000
   5_occ:  0.330  72.398   2.433   2.733   4.081   0.000   0.000   0.000
   5_bss:  0.321  66.053  -0.622  -0.375   0.997  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.369 0.4403  0.4927    66108.910
   1_bss:  55.113 0.4560  0.6536    64585.852
   1_xyz:  47.478 0.5505  0.7649    48377.115
   1_adp:  43.548 0.5994  0.8587    42878.311
   1_occ:  43.539 0.5995  0.8582    42921.630
   2_bss:  43.400 0.6012  0.7859    42769.854
   2_xyz:  32.534 0.7289  0.9373    25711.362
   2_adp:  29.478 0.7638  0.9643    22092.355
   2_occ:  29.505 0.7634  0.9633    22092.608
   3_bss:  29.501 0.7636  0.9018    22159.228
   3_xyz:  21.235 0.8495  0.9685    12181.180
   3_adp:  19.704 0.8649  0.9670    10899.777
   3_occ:  19.736 0.8645  0.9666    10909.529
   4_bss:  19.702 0.8648  0.9470    10873.567
   4_xyz:  17.136 0.8882  0.9623     8533.621
   4_adp:  16.140 0.8974  0.9601     7922.462
   4_occ:  16.150 0.8973  0.9599     7920.188
   5_bss:  16.155 0.8972  0.9558     7929.828
   5_xyz:  15.152 0.9059  0.9608     7163.389
   5_adp:  14.928 0.9080  0.9574     7086.523
   5_occ:  14.913 0.9081  0.9575     7076.792
   5_bss:  14.911 0.9081  0.9574     7070.442
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4667e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4667e+01
   1_xyz:   1.777  0.015  0.113 18.267  0.007  4.112   1.5434e-01
   1_adp:   1.777  0.015  0.113 18.267  0.007  4.112   1.5434e-01
   1_occ:   1.777  0.015  0.113 18.267  0.007  4.112   1.5434e-01
   2_bss:   1.777  0.015  0.113 18.267  0.007  4.112   1.5434e-01
   2_xyz:   1.157  0.009  0.075 16.525  0.005  4.132   8.2830e-02
   2_adp:   1.157  0.009  0.075 16.525  0.005  4.132   8.2830e-02
   2_occ:   1.157  0.009  0.075 16.525  0.005  4.132   8.2830e-02
   3_bss:   1.157  0.009  0.075 16.525  0.005  4.132   8.2830e-02
   3_xyz:   1.143  0.009  0.085 16.126  0.004  4.135   7.5713e-02
   3_adp:   1.143  0.009  0.085 16.126  0.004  4.135   7.5713e-02
   3_occ:   1.143  0.009  0.085 16.126  0.004  4.135   7.5713e-02
   4_bss:   1.143  0.009  0.085 16.126  0.004  4.135   7.5713e-02
   4_xyz:   1.134  0.010  0.087 15.982  0.004  4.150   7.7462e-02
   4_adp:   1.134  0.010  0.087 15.982  0.004  4.150   7.7462e-02
   4_occ:   1.134  0.010  0.087 15.982  0.004  4.150   7.7462e-02
   5_bss:   1.134  0.010  0.087 15.982  0.004  4.150   7.7462e-02
   5_xyz:   1.178  0.012  0.092 15.784  0.004  4.117   8.5595e-02
   5_adp:   1.178  0.012  0.092 15.784  0.004  4.117   8.5595e-02
   5_occ:   1.178  0.012  0.092 15.784  0.004  4.117   8.5595e-02
   5_bss:   1.178  0.012  0.092 15.784  0.004  4.117   8.5595e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0883e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0883e+00
   1_xyz:  15.140  0.178  0.479 86.277  0.037  2.303   1.1420e-01
   1_adp:  15.140  0.178  0.479 86.277  0.037  2.303   1.1420e-01
   1_occ:  15.140  0.178  0.479 86.277  0.037  2.303   1.1420e-01
   2_bss:  15.140  0.178  0.479 86.277  0.037  2.303   1.1420e-01
   2_xyz:   7.938  0.085  0.269 87.379  0.040  2.089   1.4260e-01
   2_adp:   7.938  0.085  0.269 87.379  0.040  2.089   1.4260e-01
   2_occ:   7.938  0.085  0.269 87.379  0.040  2.089   1.4260e-01
   3_bss:   7.938  0.085  0.269 87.379  0.040  2.089   1.4260e-01
   3_xyz:   7.568  0.099  0.293 89.451  0.043  2.332   6.1438e-02
   3_adp:   7.568  0.099  0.293 89.451  0.043  2.332   6.1438e-02
   3_occ:   7.568  0.099  0.293 89.451  0.043  2.332   6.1438e-02
   4_bss:   7.568  0.099  0.293 89.451  0.043  2.332   6.1438e-02
   4_xyz:   9.597  0.064  0.407 83.066  0.033  2.293   4.6370e-02
   4_adp:   9.597  0.064  0.407 83.066  0.033  2.293   4.6370e-02
   4_occ:   9.597  0.064  0.407 83.066  0.033  2.293   4.6370e-02
   5_bss:   9.597  0.064  0.407 83.066  0.033  2.293   4.6370e-02
   5_xyz:   8.013  0.049  0.563 82.460  0.035  2.355   5.7050e-02
   5_adp:   8.013  0.049  0.563 82.460  0.035  2.355   5.7050e-02
   5_occ:   8.013  0.049  0.563 82.460  0.035  2.355   5.7050e-02
   5_bss:   8.013  0.049  0.563 82.460  0.035  2.355   5.7050e-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: 108.15   0.00  13.01  73.76   0.00  10.28 108.15   0.00  27.93
   1_occ: 108.15   0.00  13.01  73.76   0.00  10.28 108.15   0.00  27.93
   2_bss: 108.15   0.00  13.01  73.76   0.00  10.28 108.15   0.00  27.93
   2_xyz: 108.15   0.00  13.01  73.76   0.00  10.28 108.15   0.00  27.93
   2_adp: 111.98   0.00  12.88  71.53   0.00   9.03 111.98   0.00  33.85
   2_occ: 111.98   0.00  12.88  71.53   0.00   9.03 111.98   0.00  33.85
   3_bss: 111.98   0.00  12.88  71.53   0.00   9.03 111.98   0.00  33.85
   3_xyz: 111.98   0.00  12.88  71.53   0.00   9.03 111.98   0.00  33.85
   3_adp: 107.53   0.00  13.80  82.50   0.00   8.86 107.53   0.00  40.70
   3_occ: 107.53   0.00  13.80  82.50   0.00   8.86 107.53   0.00  40.70
   4_bss: 107.53   0.00  13.80  82.50   0.00   8.86 107.53   0.00  40.70
   4_xyz: 107.53   0.00  13.80  82.50   0.00   8.86 107.53   0.00  40.70
   4_adp: 103.91   0.00  13.16  82.72   0.00   8.39 103.91   0.41  39.11
   4_occ: 103.91   0.00  13.16  82.72   0.00   8.39 103.91   0.41  39.11
   5_bss: 103.91   0.00  13.16  82.72   0.00   8.39 103.91   0.41  39.11
   5_xyz: 103.91   0.00  13.16  82.72   0.00   8.39 103.91   0.41  39.11
   5_adp:  96.79   0.00  12.38  79.43   0.00   8.05  96.79   1.40  35.92
   5_occ:  96.79   0.00  12.38  79.43   0.00   8.05  96.79   1.40  35.92
   5_bss:  99.87   3.08  15.46  82.51   3.08  11.13  99.87   4.48  39.00
------------------------------------------------------------------------
 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:    1.283    0.013    0.419
   1_adp:    1.283    0.013    0.419
   1_occ:    1.283    0.013    0.419
   2_bss:    1.283    0.013    0.419
   2_xyz:    1.785    0.024    0.571
   2_adp:    1.785    0.024    0.571
   2_occ:    1.785    0.024    0.571
   3_bss:    1.785    0.024    0.571
   3_xyz:    1.657    0.043    0.657
   3_adp:    1.657    0.043    0.657
   3_occ:    1.657    0.043    0.657
   4_bss:    1.657    0.043    0.657
   4_xyz:    1.807    0.035    0.707
   4_adp:    1.807    0.035    0.707
   4_occ:    1.807    0.035    0.707
   5_bss:    1.807    0.035    0.707
   5_xyz:    1.820    0.051    0.722
   5_adp:    1.820    0.051    0.722
   5_occ:    1.820    0.051    0.722
   5_bss:    1.820    0.051    0.722
------------------------------------------------------------------------

CPU time actual refinement: 321.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1054/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_1054/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1054/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1054/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1054/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.28 
  Macro-tasks:
    bulk solvent and scale       = 41.63  
    individual site refinement   = 127.41 
    weights calculation          = 31.84  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 207.53 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 97.14  
    alpha_beta                      = 8.31   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 106.19 
    fmodel                         = 7.33   
    r_factors                      = 0.33   
    phase_errors                   = 10.58  
    foms                           = 0.17   
    TOTAL for micro-tasks          = 233.51 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.596 micro seconds
Total CPU time: 5.58 minutes
from_scatterers_fft:    628 calls, 96.78 s
gradients_fft:          573 calls, 93.72 s

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

# Date 2008-01-16 Time 03:03:44 PST -0800 (1200481424.16 s)
Start R-work = 0.4828, R-free = 0.4737 (no bulk solvent and anisotropic scale)
Final R-work = 0.1383, R-free = 0.1826 (no bulk solvent and anisotropic scale)

Start R-work = 0.4750, R-free = 0.4638
Final R-work = 0.1220, R-free = 0.1674