# Date 2008-01-16 Time 03:14:41 PST -0800 (1200482081.65 s)
#phil __OFF__

Command line arguments: "../1158.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26658
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1158

-------------------------------------------------------------------------------
  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: (71.655, 47.1647, 85.5261, 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: (71.655, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1679 1.98118
Completeness in resolution range: 0.944913
Completeness with d_max=infinity: 0.942096

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1679
                             d_min =   1.9812

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: (71.655, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1679 1.98118
Completeness in resolution range: 0.944913
Completeness with d_max=infinity: 0.942096

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1683 -  4.2402 [2176/2205]  1961   215   9.9%
  bin  2:  4.2402 -  3.3778 [2090/2106]  1880   210  10.0%
  bin  3:  3.3778 -  2.9544 [2053/2072]  1844   209  10.2%
  bin  4:  2.9544 -  2.6859 [2048/2078]  1853   195   9.5%
  bin  5:  2.6859 -  2.4943 [2048/2067]  1840   208  10.2%
  bin  6:  2.4943 -  2.3478 [2017/2053]  1810   207  10.3%
  bin  7:  2.3478 -  2.2306 [2007/2040]  1807   200  10.0%
  bin  8:  2.2306 -  2.1338 [2010/2044]  1809   201  10.0%
  bin  9:  2.1338 -  2.0518 [2000/2028]  1799   201  10.1%
  bin 10:  2.0518 -  1.9812 [1140/2038]  1027   113   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1158/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:
        1.73 -     2.36: 12
        2.36 -     3.00: 1891
        3.00 -     3.63: 4551
        3.63 -     4.27: 9099
        4.27 -     4.90: 12586
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.729 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.008 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.171 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.180 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28134 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_1158/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1158/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 71.655 47.16465 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4527   r_free= 0.4461   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.253225                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.7297 0.99   1411  159 0.3766 0.3637       6.556      6.5097|
|  2:  4.7297 -  3.7731 0.99   1362  143 0.3553 0.3716      6.7115      6.7249|
|  3:  3.7731 -  3.3018 0.99   1329  154 0.4042 0.3676      6.6041       6.619|
|  4:  3.3018 -  3.0025 0.99   1333  150 0.4301 0.4290      6.4775      6.4275|
|  5:  3.0025 -  2.7887 0.99   1319  146 0.4747 0.5047       6.335      6.3743|
|  6:  2.7887 -  2.6252 0.99   1304  146 0.4828 0.4922      6.2574      6.2449|
|  7:  2.6252 -  2.4943 0.99   1320  139 0.5056 0.4773      6.2437       6.171|
|  8:  2.4943 -  2.3861 0.98   1282  150 0.5035 0.4732      6.1506      6.1755|
|  9:  2.3861 -  2.2946 0.98   1307  148 0.4955 0.4997      6.1089      6.0879|
| 10:  2.2946 -  2.2157 0.98   1291  137 0.4973 0.5199      6.0737       6.106|
| 11:  2.2157 -  2.1466 1.00   1273  141 0.4958 0.4767      6.0311      5.9934|
| 12:  2.1466 -  2.0854 0.97   1283  143 0.5176 0.5375      5.9534      6.0057|
| 13:  2.0854 -  2.0306 0.97   1269  141 0.5212 0.4843      5.8763      5.8109|
| 14:  2.0306 -  1.9812 0.42    547   62 0.5271 0.4588      5.8519      5.7887|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.7297  1411   159  0.73  31.65   0.80     0.76      61536.24|
|  2:  4.7297 -  3.7731  1362   143  0.75  31.18   0.90     0.80      85157.80|
|  3:  3.7731 -  3.3018  1329   154  0.65  39.55   0.85     0.75      93050.11|
|  4:  3.3018 -  3.0025  1333   150  0.57  46.46   0.82     0.66      87989.05|
|  5:  3.0025 -  2.7887  1319   146  0.47  54.56   0.74     0.56      75649.59|
|  6:  2.7887 -  2.6252  1304   146  0.45  56.17   0.76     0.53      66190.01|
|  7:  2.6252 -  2.4943  1320   139  0.46  55.11   0.74     0.51      56036.23|
|  8:  2.4943 -  2.3861  1282   150  0.45  55.85   0.72     0.53      51195.94|
|  9:  2.3861 -  2.2946  1307   148  0.45  56.33   0.74     0.51      45903.25|
| 10:  2.2946 -  2.2157  1291   137  0.42  58.06   0.75     0.49      45191.74|
| 11:  2.2157 -  2.1466  1273   141  0.38  61.31   0.78     0.45      43135.68|
| 12:  2.1466 -  2.0854  1283   143  0.34  64.54   0.74     0.42      42216.76|
| 13:  2.0854 -  2.0306  1269   141  0.34  64.48   0.72     0.42      35693.43|
| 14:  2.0306 -  1.9812   547    62  0.43  57.79   0.72     0.47      26307.52|
|alpha:            min =        0.42 max =            0.80 mean =         0.57|
|beta:             min =    26307.52 max =        93050.11 mean =     59929.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.85|
|phase err.(test): min =        0.00 max =           89.93 mean =        51.79|
|-----------------------------------------------------------------------------|

============================== 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 = 11.367665             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.101   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.884753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.623   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1503 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2611 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3891 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5029 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6529 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7677 |
|-----------------------------------------------------------------------------|
|-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 |       54.034 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.670 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    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 = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4597   r_free= 0.4535   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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.255648                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4449   r_free= 0.4359   ksol= 0.30   Bsol= 20.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.30,7.84,7.56,0.00,0.00,0.00); trace/3= 8.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.249434                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.916891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.172   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.848297              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.078   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4449      final r-factor (work) = 0.3465          |
| start r-factor (free) = 0.4359      final r-factor (free) = 0.3791          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.0504 = 9.92 * 0.50 * 6.2552 + 1.00 * 54.0344                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5108 = 9.92 * 0.50 * 6.1261 + 1.00 * 0.1347                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3465      final r-factor (work) = 0.2955          |
| start r-factor (free) = 0.3791      final r-factor (free) = 0.3451          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2112 = 0.85 * 1.00 * 6.1261 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1068 = 0.85 * 1.00 * 6.0027 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.09   10.92    None  None   None       |
|    all(noH): 2823   0      0.00    62.09   10.92    None  None   None       |
|    Sol.    : 438    0      0.00    55.37   26.51    None  None   None       |
|    Mac.    : 2385   0      0.00    62.09   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 -   6.209: 1238   |   5:    31.045 -  37.254:   88        |
|      1:     6.209 -  12.418:  730   |   6:    37.254 -  43.463:   66        |
|      2:    12.418 -  18.627:  353   |   7:    43.463 -  49.673:   37        |
|      3:    18.627 -  24.836:  160   |   8:    49.673 -  55.882:   16        |
|      4:    24.836 -  31.045:  134   |   9:    55.882 -  62.091:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2955 r_free = 0.3451             target_work(ml) = 5.963         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2948 r_free = 0.3452             target_work(ml) = 5.962         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2948   r_free= 0.3452   ksol= 0.30   Bsol= 20.00   scale= 1.072   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.30,7.84,7.56,0.00,0.00,0.00); trace/3= 8.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.962442                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2921   r_free= 0.3409   ksol= 0.32   Bsol= 48.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.84,4.61,5.09,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.963301                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.450556              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.223   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.504571              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.515  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2921      final r-factor (work) = 0.1914          |
| start r-factor (free) = 0.3409      final r-factor (free) = 0.2479          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4935 = 7.45 * 0.50 * 6.0019 + 1.00 * 0.1347                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7089 = 7.45 * 0.50 * 5.8058 + 1.00 * 0.0806                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1914      final r-factor (work) = 0.1699          |
| start r-factor (free) = 0.2479      final r-factor (free) = 0.2203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9471 = 0.50 * 1.00 * 5.8058 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8377 = 0.50 * 1.00 * 5.5505 + 1.00 * 0.0371                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.35   11.70    None  None   None       |
|    all(noH): 2823   0      0.00    97.35   11.70    None  None   None       |
|    Sol.    : 438    0      0.69    64.91   32.73    None  None   None       |
|    Mac.    : 2385   0      0.00    97.35   7.84     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 -   9.736: 1810   |   5:    48.677 -  58.413:   50        |
|      1:     9.736 -  19.471:  511   |   6:    58.413 -  68.148:   10        |
|      2:    19.471 -  29.206:  150   |   7:    68.148 -  77.884:    0        |
|      3:    29.206 -  38.942:  158   |   8:    77.884 -  87.619:    0        |
|      4:    38.942 -  48.677:  133   |   9:    87.619 -  97.354:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1699 r_free = 0.2203             target_work(ml) = 5.494         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1698 r_free = 0.2201             target_work(ml) = 5.494         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1698   r_free= 0.2201   ksol= 0.32   Bsol= 48.18   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.84,4.61,5.09,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.493678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1680   r_free= 0.2172   ksol= 0.33   Bsol= 48.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,3.18,3.69,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.493516                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.005827              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.868  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.549623              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.786   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1352          |
| start r-factor (free) = 0.2172      final r-factor (free) = 0.1805          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4415 = 3.01 * 0.50 * 5.5629 + 1.00 * 0.0809                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1930 = 3.01 * 0.50 * 5.4061 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1805      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0023 = 0.55 * 1.00 * 5.4061 + 1.00 * 0.0310                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9128 = 0.55 * 1.00 * 5.2767 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.40   12.26    None  None   None       |
|    all(noH): 2823   0      0.00    77.40   12.26    None  None   None       |
|    Sol.    : 438    0      0.65    76.69   35.64    None  None   None       |
|    Mac.    : 2385   0      0.00    77.40   7.97     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.740: 1582   |   5:    38.698 -  46.438:   95        |
|      1:     7.740 -  15.479:  623   |   6:    46.438 -  54.177:   82        |
|      2:    15.479 -  23.219:  179   |   7:    54.177 -  61.917:   43        |
|      3:    23.219 -  30.958:   94   |   8:    61.917 -  69.656:   16        |
|      4:    30.958 -  38.698:  100   |   9:    69.656 -  77.396:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1277 r_free = 0.1748             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1746             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1746   ksol= 0.33   Bsol= 48.18   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,3.18,3.69,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.259700                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1746   ksol= 0.32   Bsol= 48.18   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,2.80,3.37,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.260832                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.427503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.663  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.242518              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.562  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1137 = 3.43 * 0.50 * 5.2783 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0273 = 3.43 * 0.50 * 5.2213 + 1.00 * 0.0793                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2787 = 0.24 * 1.00 * 5.2213 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2678 = 0.24 * 1.00 * 5.1847 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.49   11.92    None  None   None       |
|    all(noH): 2823   0      0.00    78.49   11.92    None  None   None       |
|    Sol.    : 438    0      1.26    77.22   34.16    None  None   None       |
|    Mac.    : 2385   0      0.00    78.49   7.84     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.849: 1634   |   5:    39.247 -  47.096:   89        |
|      1:     7.849 -  15.699:  595   |   6:    47.096 -  54.946:   64        |
|      2:    15.699 -  23.548:  171   |   7:    54.946 -  62.795:   33        |
|      3:    23.548 -  31.398:  110   |   8:    62.795 -  70.645:   10        |
|      4:    31.398 -  39.247:  110   |   9:    70.645 -  78.494:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1623             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1621             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1621   ksol= 0.32   Bsol= 48.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,2.80,3.37,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.178893                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1621   ksol= 0.32   Bsol= 48.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,2.80,3.37,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.178893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.273009              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.205  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.663422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.290  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9719 = 2.27 * 0.50 * 5.1845 + 1.00 * 0.0797                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9528 = 2.27 * 0.50 * 5.1788 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8038 = 2.66 * 1.00 * 5.1788 + 1.00 * 0.0104                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7795 = 2.66 * 1.00 * 5.1685 + 1.00 * 0.0137                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.93   12.26    None  None   None       |
|    all(noH): 2823   0      0.00    87.93   12.26    None  None   None       |
|    Sol.    : 438    0      1.42    84.22   35.74    None  None   None       |
|    Mac.    : 2385   0      0.00    87.93   7.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.793: 1725   |   5:    43.963 -  52.755:   86        |
|      1:     8.793 -  17.585:  541   |   6:    52.755 -  61.548:   55        |
|      2:    17.585 -  26.378:  157   |   7:    61.548 -  70.341:   23        |
|      3:    26.378 -  35.170:  118   |   8:    70.341 -  79.133:    7        |
|      4:    35.170 -  43.963:  105   |   9:    79.133 -  87.926:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1628             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1627             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1627   ksol= 0.32   Bsol= 48.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,2.80,3.37,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174632                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.7297 0.99   1411  159 0.0985 0.1341      5.3848      5.5542|
|  2:  4.7297 -  3.7731 0.99   1362  143 0.0865 0.1085      5.4406      5.6189|
|  3:  3.7731 -  3.3018 0.99   1329  154 0.1064 0.1619      5.4794      5.8923|
|  4:  3.3018 -  3.0025 0.99   1333  150 0.1229 0.1566      5.4763      5.6091|
|  5:  3.0025 -  2.7887 0.99   1319  146 0.1354 0.1824      5.3539      5.5619|
|  6:  2.7887 -  2.6252 0.99   1304  146 0.1259 0.1913      5.2478      5.5158|
|  7:  2.6252 -  2.4943 0.99   1320  139 0.1292 0.1687       5.205      5.3839|
|  8:  2.4943 -  2.3861 0.98   1282  150 0.1184 0.1789      5.0876      5.3886|
|  9:  2.3861 -  2.2946 0.98   1307  148 0.1207 0.1951      5.0673      5.3646|
| 10:  2.2946 -  2.2157 0.98   1291  137 0.1134 0.1696      4.9776      5.2339|
| 11:  2.2157 -  2.1466 1.00   1273  141 0.1174 0.1827      4.9795      5.3137|
| 12:  2.1466 -  2.0854 0.97   1283  143 0.1103 0.1764      4.8965      5.1354|
| 13:  2.0854 -  2.0306 0.97   1269  141 0.1229 0.1801      4.8312      5.0755|
| 14:  2.0306 -  1.9812 0.42    547   62 0.0957 0.1844      4.6431      4.9864|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.7297  1411   159  0.94   8.78   0.97     0.95       7179.39|
|  2:  4.7297 -  3.7731  1362   143  0.95   8.03   1.01     0.99       9053.76|
|  3:  3.7731 -  3.3018  1329   154  0.93  11.66   1.02     1.02      10652.41|
|  4:  3.3018 -  3.0025  1333   150  0.92  14.26   1.00     0.97      10898.71|
|  5:  3.0025 -  2.7887  1319   146  0.89  16.91   0.99     0.96       9035.78|
|  6:  2.7887 -  2.6252  1304   146  0.89  16.89   0.98     0.96       7809.19|
|  7:  2.6252 -  2.4943  1320   139  0.90  16.11   0.99     0.96       6820.51|
|  8:  2.4943 -  2.3861  1282   150  0.90  16.22   0.98     0.94       5645.02|
|  9:  2.3861 -  2.2946  1307   148  0.90  16.54   1.00     0.96       5525.60|
| 10:  2.2946 -  2.2157  1291   137  0.90  16.09   0.99     0.95       4611.67|
| 11:  2.2157 -  2.1466  1273   141  0.89  17.19   0.99     0.95       4800.20|
| 12:  2.1466 -  2.0854  1283   143  0.91  15.76   0.99     0.98       4276.20|
| 13:  2.0854 -  2.0306  1269   141  0.89  17.53   0.99     0.98       3683.57|
| 14:  2.0306 -  1.9812   547    62  0.91  15.42   0.97     0.94       2625.15|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2625.15 max =        10898.71 mean =      6827.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.71|
|phase err.(test): min =        0.00 max =           88.59 mean =        14.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1627   ksol= 0.32   Bsol= 53.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.23,0.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1627   ksol= 0.32   Bsol= 53.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.23,0.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174525                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.7297 0.99   1411  159 0.0984 0.1345      5.3845      5.5563|
|  2:  4.7297 -  3.7731 0.99   1362  143 0.0867 0.1088      5.4429      5.6213|
|  3:  3.7731 -  3.3018 0.99   1329  154 0.1065 0.1620      5.4801      5.8922|
|  4:  3.3018 -  3.0025 0.99   1333  150 0.1228 0.1565      5.4758      5.6086|
|  5:  3.0025 -  2.7887 0.99   1319  146 0.1353 0.1824       5.353      5.5613|
|  6:  2.7887 -  2.6252 0.99   1304  146 0.1257 0.1910      5.2468      5.5146|
|  7:  2.6252 -  2.4943 0.99   1320  139 0.1291 0.1686      5.2043       5.383|
|  8:  2.4943 -  2.3861 0.98   1282  150 0.1183 0.1789       5.087      5.3881|
|  9:  2.3861 -  2.2946 0.98   1307  148 0.1206 0.1953      5.0671      5.3647|
| 10:  2.2946 -  2.2157 0.98   1291  137 0.1133 0.1694      4.9774      5.2333|
| 11:  2.2157 -  2.1466 1.00   1273  141 0.1173 0.1828      4.9794      5.3141|
| 12:  2.1466 -  2.0854 0.97   1283  143 0.1103 0.1763      4.8967      5.1352|
| 13:  2.0854 -  2.0306 0.97   1269  141 0.1229 0.1801      4.8311      5.0755|
| 14:  2.0306 -  1.9812 0.42    547   62 0.0957 0.1845      4.6433      4.9866|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.7297  1411   159  0.94   8.80   0.97     0.95       7208.11|
|  2:  4.7297 -  3.7731  1362   143  0.95   8.07   1.01     0.99       9091.82|
|  3:  3.7731 -  3.3018  1329   154  0.93  11.68   1.02     1.02      10676.57|
|  4:  3.3018 -  3.0025  1333   150  0.92  14.26   1.00     0.98      10892.03|
|  5:  3.0025 -  2.7887  1319   146  0.89  16.90   0.99     0.97       9021.32|
|  6:  2.7887 -  2.6252  1304   146  0.89  16.87   0.98     0.96       7792.18|
|  7:  2.6252 -  2.4943  1320   139  0.90  16.10   0.99     0.96       6808.23|
|  8:  2.4943 -  2.3861  1282   150  0.90  16.20   0.98     0.95       5638.46|
|  9:  2.3861 -  2.2946  1307   148  0.90  16.54   1.00     0.97       5521.41|
| 10:  2.2946 -  2.2157  1291   137  0.90  16.09   0.99     0.95       4610.26|
| 11:  2.2157 -  2.1466  1273   141  0.89  17.19   0.99     0.95       4798.03|
| 12:  2.1466 -  2.0854  1283   143  0.91  15.77   1.00     0.98       4277.83|
| 13:  2.0854 -  2.0306  1269   141  0.89  17.53   1.00     0.98       3682.98|
| 14:  2.0306 -  1.9812   547    62  0.91  15.43   0.98     0.94       2625.53|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2625.53 max =        10892.03 mean =      6829.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.57 mean =        14.72|
|phase err.(test): min =        0.00 max =           88.60 mean =        14.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.11    91.03   15.36    None  None   None       |
|    all(noH): 2823   0      3.11    91.03   15.36    None  None   None       |
|    Sol.    : 438    0      4.53    87.32   38.85    None  None   None       |
|    Mac.    : 2385   0      3.11    91.03   11.05    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:     3.106 -  11.899: 1725   |   5:    47.069 -  55.861:   86        |
|      1:    11.899 -  20.691:  541   |   6:    55.861 -  64.654:   55        |
|      2:    20.691 -  29.484:  157   |   7:    64.654 -  73.446:   23        |
|      3:    29.484 -  38.276:  118   |   8:    73.446 -  82.239:    7        |
|      4:    38.276 -  47.069:  105   |   9:    82.239 -  91.031:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.386 - 5.954
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 332
   mapped sites are within: 0.710 - 5.954

peak=   10.276 closest distance to " CG2 VAL A 230 " =    1.343
peak=    6.486 closest distance to " CG2 VAL A 296 " =    1.073
peak=    6.233 closest distance to " CG  LEU A   5 " =    1.160
peak=    5.774 closest distance to " O   HOH Z 111 " =    2.159
peak=    5.663 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.605 closest distance to " CG  LEU A 228 " =    1.176
peak=    5.405 closest distance to " CG  PRO A  54 " =    1.264
peak=    5.174 closest distance to " CB  SER A  63 " =    1.354
peak=    5.155 closest distance to " CB  VAL A 230 " =    1.220
peak=    5.122 closest distance to " CB  PRO A  54 " =    0.919
peak=    4.997 closest distance to " CD2 LEU A   5 " =    1.119
peak=    4.917 closest distance to " CB  VAL A 296 " =    1.087
peak=    4.880 closest distance to " CG  PRO A 213 " =    1.230
peak=    4.815 closest distance to " O   HOH Z 232 " =    2.303
peak=    4.706 closest distance to " CB  GLN A 183 " =    1.305
peak=    4.549 closest distance to " CG  PRO A 198 " =    1.274
peak=    4.536 closest distance to " CB  GLU A 128 " =    1.115
peak=    4.527 closest distance to " CG  PRO A 243 " =    1.146
peak=    4.513 closest distance to " O   HOH Z 126 " =    1.895
peak=    4.423 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.410 closest distance to " NE2 GLN A  11 " =    1.088
peak=    4.401 closest distance to " O   HOH Z 112 " =    1.623
peak=    4.382 closest distance to " OD1 ASN A  69 " =    2.654
peak=    4.364 closest distance to " C   PRO A 198 " =    1.551
peak=    4.362 closest distance to " O   HOH Z 427 " =    3.063
peak=    4.342 closest distance to " O   HOH Z 369 " =    2.134
peak=    4.334 closest distance to " O   HOH Z 247 " =    1.360
peak=    4.301 closest distance to " CB  SER A   3 " =    1.365
peak=    4.294 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.244 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.239 closest distance to " O   HOH Z 368 " =    2.224
peak=    4.221 closest distance to " CB  ARG A 275 " =    0.860
peak=    4.209 closest distance to " O   HOH Z 316 " =    3.005
peak=    4.195 closest distance to " O   HOH Z  78 " =    1.970
peak=    4.185 closest distance to " O   HOH Z 403 " =    1.752
peak=    4.184 closest distance to " O   HOH Z 298 " =    1.753
peak=    4.181 closest distance to " O   HOH Z 303 " =    2.068
peak=    4.127 closest distance to " O   HOH Z  54 " =    2.400
peak=    4.112 closest distance to " O   HOH Z 272 " =    1.791
peak=    4.106 closest distance to " CB  TYR A 169 " =    0.733
peak=    4.081 closest distance to " CB  TRP A 266 " =    0.981
peak=    4.077 closest distance to " CD2 LEU A 228 " =    1.162
peak=    4.055 closest distance to " O   HOH Z 236 " =    1.950
peak=    4.054 closest distance to " OD2 ASP A 286 " =    2.894
peak=    4.049 closest distance to " O   HOH Z 263 " =    1.664
peak=    4.049 closest distance to " CB  ASP A 124 " =    0.720
peak=    4.025 closest distance to " CA  ALA A  51 " =    1.071
peak=    4.014 closest distance to " O   HOH Z  88 " =    3.309
peak=    4.005 closest distance to " O   HOH Z 423 " =    1.698
peak=    3.998 closest distance to " CA  THR A 221 " =    0.894
peak=    3.990 closest distance to " CD  ARG A 159 " =    0.829
peak=    3.984 closest distance to " CZ  PHE A 192 " =    0.957
peak=    3.976 closest distance to " CD1 LEU A 300 " =    1.161
peak=    3.965 closest distance to " CD BLYS A 290 " =    1.024
peak=    3.962 closest distance to " O   HOH Z 280 " =    2.883
peak=    3.947 closest distance to " O   HOH Z 411 " =    3.613
peak=    3.943 closest distance to " CG1 ILE A  33 " =    1.296
peak=    3.942 closest distance to " CB  GLU A 277 " =    3.682
peak=    3.930 closest distance to " CG2 THR A 221 " =    1.127
peak=    3.923 closest distance to " O   HOH Z 203 " =    1.803
peak=    3.920 closest distance to " O   HOH Z  80 " =    1.832
peak=    3.903 closest distance to " O   SER A  87 " =    2.314
peak=    3.894 closest distance to " ND2 ASN A 249 " =    1.852
peak=    3.892 closest distance to " CB  VAL A 265 " =    1.244
peak=    3.889 closest distance to " CB  SER A 216 " =    0.858
peak=    3.889 closest distance to " CB  LEU A 228 " =    1.266
peak=    3.875 closest distance to " CG1BVAL A  72 " =    1.621
peak=    3.856 closest distance to " CB  SER A 212 " =    1.175
peak=    3.853 closest distance to " CB  VAL A 202 " =    1.578
peak=    3.845 closest distance to " NH1AARG A 145 " =    1.135
peak=    3.843 closest distance to " O   HOH Z  44 " =    2.138
peak=    3.843 closest distance to " O   HOH Z 193 " =    1.794
peak=    3.841 closest distance to " O   HOH Z  20 " =    1.999
peak=    3.839 closest distance to " O   HOH Z 295 " =    1.504
peak=    3.838 closest distance to " CZ  PHE A 218 " =    1.016
peak=    3.823 closest distance to " O   HOH Z 135 " =    1.874
peak=    3.812 closest distance to " O   HOH Z 234 " =    3.739
peak=    3.809 closest distance to " O   HOH Z  78 " =    1.490
peak=    3.808 closest distance to " CG  GLN A  88 " =    1.034
peak=    3.807 closest distance to " CG  MET A 185 " =    1.212
peak=    3.806 closest distance to " CA  MET A  40 " =    1.125
peak=    3.802 closest distance to " O   HOH Z 184 " =    1.491
peak=    3.800 closest distance to " CB  ASP A 140 " =    0.941
peak=    3.796 closest distance to " CB  ARG A  79 " =    1.456
peak=    3.794 closest distance to " CD  ARG A  66 " =    2.537
peak=    3.789 closest distance to " O   HOH Z 425 " =    1.339
peak=    3.789 closest distance to " NH2 ARG A 156 " =    1.162
peak=    3.787 closest distance to " CA  LYS A 117 " =    1.250
peak=    3.780 closest distance to " CB  TRP A 179 " =    1.434
peak=    3.760 closest distance to " O   MET A 105 " =    1.823
peak=    3.757 closest distance to " CA  THR A 264 " =    0.737
peak=    3.755 closest distance to " O   HOH Z 193 " =    2.111
peak=    3.754 closest distance to " CG  ARG A 138 " =    1.146
peak=    3.747 closest distance to " O   TRP A 274 " =    1.840
peak=    3.739 closest distance to " NH1 ARG A  56 " =    1.041
peak=    3.737 closest distance to " O   HOH Z  61 " =    1.631
peak=    3.735 closest distance to " OG BSER A 164 " =    2.162
peak=    3.734 closest distance to " O   HOH Z  15 " =    2.073
peak=    3.733 closest distance to " O   HOH Z 158 " =    2.975
peak=    3.732 closest distance to " O   HOH Z 346 " =    1.651
peak=    3.731 closest distance to " CB  ARG A 190 " =    1.686
peak=    3.724 closest distance to " CB  ALA A   9 " =    1.573
peak=    3.721 closest distance to " ND2 ASN A 187 " =    1.473
peak=    3.719 closest distance to " CA  ASN A 215 " =    1.264
peak=    3.718 closest distance to " O   HOH Z 437 " =    1.951
peak=    3.716 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.715 closest distance to " O   HOH Z 371 " =    3.375
peak=    3.702 closest distance to " O   HOH Z  97 " =    2.026
peak=    3.700 closest distance to " CA  ALA A  21 " =    1.206
peak=    3.698 closest distance to " O   HOH Z  63 " =    1.874
peak=    3.680 closest distance to " O   HOH Z 245 " =    1.352
peak=    3.669 closest distance to " O   HOH Z 128 " =    2.218
peak=    3.669 closest distance to " NZ  LYS A 117 " =    3.287
peak=    3.666 closest distance to " O   HOH Z 145 " =    1.896
peak=    3.658 closest distance to " O   HOH Z 132 " =    2.650
peak=    3.656 closest distance to " O   HOH Z 345 " =    3.504
peak=    3.652 closest distance to " ND1 HIS A  81 " =    1.667
peak=    3.648 closest distance to " CG2 THR A 220 " =    1.017
peak=    3.642 closest distance to " CB  LEU A 143 " =    1.150
peak=    3.639 closest distance to " O   HOH Z 126 " =    1.521
peak=    3.632 closest distance to " O   ALA A 158 " =    1.401
peak=    3.625 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.624 closest distance to " O   HOH Z  68 " =    1.592
peak=    3.616 closest distance to " O   HOH Z 134 " =    1.419
peak=    3.609 closest distance to " O   HOH Z 189 " =    2.768
peak=    3.608 closest distance to " CE1 TYR A 186 " =    1.402
peak=    3.607 closest distance to " CG1 VAL A 296 " =    1.255
peak=    3.601 closest distance to " O   HOH Z 193 " =    1.675
peak=    3.600 closest distance to " O   HOH Z 144 " =    1.542
peak=    3.595 closest distance to " O   HOH Z  43 " =    1.892
peak=    3.595 closest distance to " O   HOH Z 261 " =    2.062
peak=    3.584 closest distance to " CA  ALA A 295 " =    1.092
peak=    3.584 closest distance to " O   HOH Z 271 " =    2.659
peak=    3.570 closest distance to " CB AVAL A  41 " =    1.191
peak=    3.558 closest distance to " CB  ALA A 291 " =    1.388
peak=    3.551 closest distance to " CE  LYS A  76 " =    0.830
peak=    3.543 closest distance to " CB  ASN A 187 " =    1.106
peak=    3.541 closest distance to " CD2 LEU A 255 " =    1.472
peak=    3.540 closest distance to " CB  THR A  82 " =    1.344
peak=    3.534 closest distance to " O   HOH Z 102 " =    1.310
peak=    3.533 closest distance to " O   HOH Z 180 " =    2.119
peak=    3.530 closest distance to " O   HOH Z 171 " =    3.837
peak=    3.529 closest distance to " C   SER A  32 " =    1.087
peak=    3.521 closest distance to " O   HOH Z 133 " =    2.439
peak=    3.514 closest distance to " CG1 ILE A 151 " =    1.036
peak=    3.513 closest distance to " CB  TRP A 150 " =    1.375
peak=    3.511 closest distance to " CB  ALA A 137 " =    1.086
peak=    3.509 closest distance to " O   HOH Z 126 " =    1.852
peak=    3.499 closest distance to " O   HOH Z 197 " =    2.796
peak=    3.497 closest distance to " CA  GLY A 267 " =    0.806
peak=    3.495 closest distance to " O   HOH Z 426 " =    1.548
peak=    3.495 closest distance to " CD1 LEU A   5 " =    1.324
peak=    3.493 closest distance to " O   HOH Z  21 " =    1.661
peak=    3.492 closest distance to " CD  LYS A 166 " =    1.295
peak=    3.488 closest distance to " O   HOH Z 383 " =    2.233
peak=    3.485 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.483 closest distance to " CB  ARG A 139 " =    0.882
peak=    3.481 closest distance to " NZ  LYS A 166 " =    3.192
peak=    3.480 closest distance to " O   HOH Z 214 " =    2.099
peak=    3.480 closest distance to " CA  ARG A 195 " =    1.258
peak=    3.478 closest distance to " O   HOH Z 344 " =    2.980
peak=    3.476 closest distance to " O   HOH Z 183 " =    1.424
peak=    3.476 closest distance to " O   HOH Z 355 " =    1.824
peak=    3.475 closest distance to " O   HOH Z 271 " =    2.212
peak=    3.474 closest distance to " CB  ASN A 148 " =    1.911
peak=    3.472 closest distance to " O   HOH Z 420 " =    2.065
peak=    3.470 closest distance to " ND1 HIS A  86 " =    1.684
peak=    3.467 closest distance to " OG  SER A  22 " =    2.927
peak=    3.464 closest distance to " CA  ASP A 140 " =    1.212
peak=    3.457 closest distance to " O   HOH Z  49 " =    2.507
peak=    3.457 closest distance to " O   HOH Z 425 " =    2.065
peak=    3.455 closest distance to " CB  MET A  40 " =    0.819
peak=    3.454 closest distance to " CB  LEU A 255 " =    0.842
peak=    3.454 closest distance to " CB  THR A 157 " =    1.159
peak=    3.448 closest distance to " O   HOH Z 368 " =    3.588
peak=    3.445 closest distance to " CB  ALA A 161 " =    0.947
peak=    3.435 closest distance to " O   GLN A 278 " =    1.343
peak=    3.431 closest distance to " O   HOH Z  58 " =    1.509
peak=    3.427 closest distance to " O   HOH Z 281 " =    4.439
peak=    3.425 closest distance to " CG BARG A 275 " =    1.508
peak=    3.425 closest distance to " CG1 VAL A 153 " =    0.980
peak=    3.424 closest distance to " CD1 LEU A  96 " =    0.740
peak=    3.418 closest distance to " N   ASN A  39 " =    1.252
peak=    3.415 closest distance to " CA  ALA A 299 " =    0.970
peak=    3.414 closest distance to " O   HOH Z 133 " =    1.723
peak=    3.412 closest distance to " O   HOH Z 227 " =    1.666
peak=    3.411 closest distance to " CG2 VAL A 174 " =    1.316
peak=    3.411 closest distance to " CB  MET A  47 " =    1.080
peak=    3.409 closest distance to " CA  SER A  87 " =    0.954
peak=    3.408 closest distance to " O   ASP A 124 " =    1.101
peak=    3.405 closest distance to " CA  ALA A 154 " =    1.143
peak=    3.402 closest distance to " CA  LEU A 282 " =    1.022
peak=    3.401 closest distance to " CG2 VAL A 257 " =    0.870
peak=    3.401 closest distance to " N   ASN A 127 " =    1.230
peak=    3.400 closest distance to " O   HOH Z  68 " =    2.601
peak=    3.398 closest distance to " O   HOH Z  48 " =    1.371
peak=    3.397 closest distance to " N   VAL A 126 " =    1.301
peak=    3.392 closest distance to " O   HOH Z 313 " =    1.813
peak=    3.391 closest distance to " CG1 ILE A  49 " =    1.512
peak=    3.385 closest distance to " O   HOH Z 172 " =    3.748
peak=    3.382 closest distance to " CA  ALA A 158 " =    1.213
peak=    3.382 closest distance to " O   HOH Z 116 " =    1.850
peak=    3.381 closest distance to " O   HOH Z 402 " =    1.465
peak=    3.380 closest distance to " CD1 ILE A 106 " =    0.982
peak=    3.370 closest distance to " CB  ASN A 142 " =    1.039
peak=    3.370 closest distance to " NE2 HIS A 207 " =    1.464
peak=    3.368 closest distance to " O   HOH Z 163 " =    1.499
peak=    3.367 closest distance to " N   SER A 135 " =    1.385
peak=    3.362 closest distance to " ND2 ASN A 110 " =    1.733
peak=    3.359 closest distance to " O   HOH Z  93 " =    2.813
peak=    3.357 closest distance to " O   HOH Z 327 " =    2.300
peak=    3.356 closest distance to " O   HOH Z 128 " =    1.869
peak=    3.355 closest distance to " O   HOH Z 213 " =    1.766
peak=    3.352 closest distance to " CB  GLN A  88 " =    1.291
peak=    3.350 closest distance to " CA  ALA A 291 " =    0.954
peak=    3.346 closest distance to " O   HOH Z 248 " =    1.865
peak=    3.343 closest distance to " O   HOH Z   9 " =    2.115
peak=    3.342 closest distance to " O   HOH Z 286 " =    2.338
peak=    3.336 closest distance to " OD1 ASN A 217 " =    1.676
peak=    3.335 closest distance to " CB  ALA A 248 " =    1.033
peak=    3.330 closest distance to " O   HOH Z 329 " =    3.852
peak=    3.330 closest distance to " NH2 ARG A 219 " =    1.833
peak=    3.329 closest distance to " O   HOH Z  68 " =    2.037
peak=    3.316 closest distance to " O   HOH Z 175 " =    3.541
peak=    3.316 closest distance to " CA  ASP A 191 " =    0.803
peak=    3.308 closest distance to " CA  VAL A  41 " =    0.917
peak=    3.306 closest distance to " O   HOH Z  10 " =    1.841
peak=    3.304 closest distance to " O   HOH Z 109 " =    2.597
peak=    3.303 closest distance to " CA  ARG A  36 " =    1.142
peak=    3.299 closest distance to " O   HOH Z 147 " =    1.709
peak=    3.299 closest distance to " N   TYR A  15 " =    0.877
peak=    3.298 closest distance to " O   HOH Z 410 " =    1.431
peak=    3.296 closest distance to " OE1 GLU A 152 " =    0.871
peak=    3.295 closest distance to " CB  HIS A 108 " =    0.831
peak=    3.294 closest distance to " CB  VAL A 268 " =    0.826
peak=    3.294 closest distance to " CZ  PHE A 192 " =    0.710
peak=    3.285 closest distance to " O   HOH Z 422 " =    2.725
peak=    3.281 closest distance to " CG  LEU A 167 " =    1.161
peak=    3.280 closest distance to " CG  MET A 188 " =    0.942
peak=    3.280 closest distance to " O   HOH Z 298 " =    2.473
peak=    3.279 closest distance to " N   PHE A 130 " =    1.339
peak=    3.271 closest distance to " O   HOH Z  54 " =    1.582
peak=    3.270 closest distance to " CB  LEU A 237 " =    0.745
peak=    3.269 closest distance to " CA  GLY A 211 " =    1.284
peak=    3.267 closest distance to " CB  TYR A  30 " =    1.484
peak=    3.267 closest distance to " CA  GLN A 194 " =    1.189
peak=    3.266 closest distance to " CA  ILE A  33 " =    1.607
peak=    3.265 closest distance to " CG BARG A 102 " =    1.873
peak=    3.265 closest distance to " CB  VAL A 250 " =    1.290
peak=    3.265 closest distance to " C   LYS A 290 " =    1.338
peak=    3.263 closest distance to " OG1 THR A 294 " =    1.720
peak=    3.263 closest distance to " O   HOH Z 407 " =    2.346
peak=    3.262 closest distance to " CD  LYS A 119 " =    1.407
peak=    3.258 closest distance to " CD  ARG A 219 " =    1.038
peak=    3.257 closest distance to " OD1 ASP A 231 " =    1.858
peak=    3.255 closest distance to " OH  TYR A 214 " =    1.247
peak=    3.255 closest distance to " OE1 GLN A  11 " =    1.760
peak=    3.255 closest distance to " CB  SER A  62 " =    1.288
peak=    3.254 closest distance to " CD2 HIS A  81 " =    1.038
peak=    3.252 closest distance to " O   HOH Z 391 " =    3.017
peak=    3.248 closest distance to " O   HOH Z 411 " =    1.873
peak=    3.243 closest distance to " CB  ALA A 248 " =    1.325
peak=    3.239 closest distance to " CE2 TYR A 186 " =    0.901
peak=    3.233 closest distance to " CA  ARG A 102 " =    1.219
peak=    3.231 closest distance to " O   HOH Z 374 " =    2.741
peak=    3.231 closest distance to " O   HOH Z 290 " =    1.067
peak=    3.230 closest distance to " CG  GLN A  58 " =    2.760
peak=    3.230 closest distance to " CB  GLU A  46 " =    1.061
peak=    3.226 closest distance to " CA  ALA A 248 " =    1.237
peak=    3.225 closest distance to " O   ALA A 165 " =    1.438
peak=    3.219 closest distance to " O   HOH Z 166 " =    3.453
peak=    3.217 closest distance to " C   TYR A 214 " =    1.533
peak=    3.216 closest distance to " CB  ASN A 110 " =    1.289
peak=    3.215 closest distance to " CA  ALA A 160 " =    0.857
peak=    3.207 closest distance to " N   SER A 134 " =    1.444
peak=    3.206 closest distance to " CG AARG A 275 " =    1.155
peak=    3.204 closest distance to " CB  GLU A 277 " =    3.864
peak=    3.204 closest distance to " CB  ILE A 120 " =    1.381
peak=    3.202 closest distance to " NE2 GLN A  58 " =    5.862
peak=    3.194 closest distance to " O   HOH Z   4 " =    1.897
peak=    3.188 closest distance to " CA  VAL A 125 " =    1.360
peak=    3.184 closest distance to " O   HOH Z 353 " =    2.821
peak=    3.182 closest distance to " O   HOH Z 118 " =    1.467
peak=    3.181 closest distance to " CG  MET A 185 " =    1.090
peak=    3.181 closest distance to " CG1 VAL A 174 " =    1.195
peak=    3.180 closest distance to " CB  TYR A 116 " =    0.902
peak=    3.180 closest distance to " O   HOH Z  63 " =    0.979
peak=    3.178 closest distance to " OE1 GLU A   2 " =    2.180
peak=    3.175 closest distance to " O   HOH Z 155 " =    3.190
peak=    3.170 closest distance to " O   HOH Z 174 " =    2.622
peak=    3.169 closest distance to " CA  ASN A 176 " =    1.193
peak=    3.165 closest distance to " O   HOH Z 423 " =    2.970
peak=    3.150 closest distance to " O   HOH Z 291 " =    1.607
peak=    3.149 closest distance to " O   HOH Z 227 " =    2.054
peak=    3.144 closest distance to " O   HOH Z 302 " =    1.926
peak=    3.138 closest distance to " O   HOH Z 313 " =    1.723
peak=    3.137 closest distance to " O   HOH Z 420 " =    5.954
peak=    3.136 closest distance to " O   ASN A 217 " =    1.311
peak=    3.132 closest distance to " O   HOH Z 332 " =    1.579
peak=    3.131 closest distance to " O   HOH Z 345 " =    1.636
peak=    3.129 closest distance to " O   HOH Z 128 " =    2.212
peak=    3.128 closest distance to " O   HOH Z 392 " =    1.415
peak=    3.127 closest distance to " CG  LEU A  25 " =    1.906
peak=    3.124 closest distance to " O   HOH Z 273 " =    2.727
peak=    3.117 closest distance to " O   HOH Z 367 " =    3.458
peak=    3.115 closest distance to " O   THR A 220 " =    1.272
peak=    3.114 closest distance to " O   HOH Z  53 " =    2.555
peak=    3.105 closest distance to " O   HOH Z 417 " =    2.862
peak=    3.104 closest distance to " OG  SER A 206 " =    1.162
peak=    3.102 closest distance to " CB  ASN A 224 " =    1.006
peak=    3.098 closest distance to " CA  GLU A 152 " =    0.819
peak=    3.093 closest distance to " OG1 THR A 246 " =    3.201
peak=    3.093 closest distance to " CA  TRP A 274 " =    0.903
peak=    3.090 closest distance to " NE  ARG A  79 " =    1.238
peak=    3.090 closest distance to " NH2BARG A 145 " =    2.053
peak=    3.086 closest distance to " CB  ALA A 104 " =    0.798
peak=    3.081 closest distance to " CB  PHE A 283 " =    0.894
peak=    3.078 closest distance to " O   HOH Z 357 " =    2.015
peak=    3.067 closest distance to " O   HOH Z 343 " =    3.017
peak=    3.058 closest distance to " CB  ALA A 114 " =    1.125
peak=    3.058 closest distance to " O   HOH Z 301 " =    1.894
peak=    3.049 closest distance to " C   GLY A  80 " =    1.133
peak=    3.045 closest distance to " CG2 VAL A 202 " =    1.154
peak=    3.041 closest distance to " CB  ALA A 100 " =    1.335
peak=    3.026 closest distance to " CB  PRO A 243 " =    1.158
peak=    3.023 closest distance to " O   HOH Z  22 " =    2.546
peak=    3.021 closest distance to " O   HOH Z  48 " =    1.254

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.584
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.779 - 5.584

peak=   -4.988 closest distance to " CG2 VAL A 230 " =    0.944
peak=   -4.453 closest distance to " CD  ARG A 156 " =    1.979
peak=   -4.238 closest distance to " CG  LEU A 101 " =    2.564
peak=   -4.174 closest distance to " OE1 GLN A 223 " =    2.154
peak=   -4.157 closest distance to " O   HOH Z 266 " =    4.770
peak=   -4.143 closest distance to " SG  CYS A 254 " =    3.163
peak=   -4.107 closest distance to " O   ILE A 109 " =    2.660
peak=   -4.059 closest distance to " O   HOH Z  52 " =    1.612
peak=   -4.006 closest distance to " O   HOH Z 231 " =    1.923
peak=   -3.957 closest distance to " CD2 LEU A 300 " =    2.816
peak=   -3.956 closest distance to " CG1 VAL A 296 " =    1.290
peak=   -3.938 closest distance to " O   HOH Z 103 " =    1.808
peak=   -3.908 closest distance to " O   HOH Z  19 " =    2.303
peak=   -3.890 closest distance to " O   SER A 271 " =    2.263
peak=   -3.887 closest distance to " O   HOH Z 290 " =    1.240
peak=   -3.883 closest distance to " O   PRO A 163 " =    2.049
peak=   -3.871 closest distance to " CG1 VAL A 250 " =    2.693
peak=   -3.862 closest distance to " CE2 TYR A  30 " =    2.777
peak=   -3.859 closest distance to " CD  LYS A 289 " =    2.499
peak=   -3.850 closest distance to " OD1 ASN A 148 " =    1.524
peak=   -3.843 closest distance to " NE2 GLN A  88 " =    2.191
peak=   -3.834 closest distance to " O   HOH Z 166 " =    1.910
peak=   -3.794 closest distance to " CG  ARG A 269 " =    2.321
peak=   -3.775 closest distance to " NH2AARG A 275 " =    5.347
peak=   -3.764 closest distance to " O   HOH Z  38 " =    1.443
peak=   -3.756 closest distance to " CB  ALA A  43 " =    2.545
peak=   -3.753 closest distance to " CG  TRP A 266 " =    1.778
peak=   -3.750 closest distance to " OG  SER A  97 " =    2.287
peak=   -3.748 closest distance to " CG2BVAL A  41 " =    2.582
peak=   -3.745 closest distance to " C   ASN A 187 " =    1.792
peak=   -3.744 closest distance to " CB  PRO A 243 " =    2.615
peak=   -3.743 closest distance to " CZ3 TRP A 179 " =    1.175
peak=   -3.742 closest distance to " O   HOH Z 275 " =    1.503
peak=   -3.740 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.722 closest distance to " CD1 LEU A 228 " =    2.378
peak=   -3.701 closest distance to " O   HOH Z 436 " =    1.541
peak=   -3.698 closest distance to " O   HOH Z 389 " =    1.856
peak=   -3.681 closest distance to " O   HOH Z 426 " =    1.643
peak=   -3.678 closest distance to " N   ALA A 226 " =    2.175
peak=   -3.665 closest distance to " O   HOH Z 118 " =    2.926
peak=   -3.664 closest distance to " O   HOH Z 353 " =    2.190
peak=   -3.663 closest distance to " CD1 LEU A   5 " =    2.549
peak=   -3.662 closest distance to " NH2 ARG A  66 " =    1.947
peak=   -3.660 closest distance to " OG ASER A 134 " =    1.195
peak=   -3.659 closest distance to " OG  SER A  87 " =    1.528
peak=   -3.653 closest distance to " O   HOH Z  43 " =    1.642
peak=   -3.640 closest distance to " CA  GLY A 203 " =    2.376
peak=   -3.638 closest distance to " CD  ARG A 139 " =    1.542
peak=   -3.633 closest distance to " OG BSER A 134 " =    1.243
peak=   -3.626 closest distance to " CB  ALA A 291 " =    2.179
peak=   -3.626 closest distance to " O   HOH Z 377 " =    1.875
peak=   -3.622 closest distance to " O   HOH Z  11 " =    1.970
peak=   -3.618 closest distance to " CD2 TYR A 293 " =    2.104
peak=   -3.618 closest distance to " ND2 ASN A  45 " =    0.997
peak=   -3.617 closest distance to " C   ALA A 158 " =    1.253
peak=   -3.614 closest distance to " N   THR A 157 " =    1.586
peak=   -3.604 closest distance to " O   HOH Z 196 " =    2.273
peak=   -3.603 closest distance to " CG  PHE A 283 " =    2.854
peak=   -3.593 closest distance to " O   HOH Z 394 " =    1.594
peak=   -3.593 closest distance to " O   HOH Z  10 " =    1.569
peak=   -3.587 closest distance to " OG  SER A  26 " =    1.400
peak=   -3.586 closest distance to " CA  ASP A 298 " =    1.023
peak=   -3.584 closest distance to " CA  GLY A 241 " =    3.046
peak=   -3.581 closest distance to " CD1 LEU A 101 " =    2.638
peak=   -3.577 closest distance to " O   GLY A 211 " =    1.549
peak=   -3.577 closest distance to " O   HOH Z 184 " =    1.594
peak=   -3.570 closest distance to " OXT GLY A 302 " =    2.956
peak=   -3.561 closest distance to " N   ALA A  43 " =    2.365
peak=   -3.558 closest distance to " O   HOH Z 350 " =    1.689
peak=   -3.557 closest distance to " O   HOH Z  13 " =    1.479
peak=   -3.554 closest distance to " CG2 VAL A 112 " =    2.599
peak=   -3.554 closest distance to " O   HOH Z 283 " =    2.006
peak=   -3.551 closest distance to " CG2 VAL A 296 " =    1.524
peak=   -3.536 closest distance to " O   HOH Z 407 " =    3.239
peak=   -3.535 closest distance to " OE1 GLN A  58 " =    1.116
peak=   -3.533 closest distance to " CG1 VAL A 112 " =    2.615
peak=   -3.502 closest distance to " O   HOH Z 351 " =    1.494
peak=   -3.499 closest distance to " CG1 VAL A 112 " =    2.963
peak=   -3.492 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.489 closest distance to " CD2 LEU A 167 " =    1.751
peak=   -3.484 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.472 closest distance to " O   VAL A 125 " =    2.303
peak=   -3.455 closest distance to " CB  PRO A 163 " =    2.609
peak=   -3.445 closest distance to " O   HOH Z 241 " =    1.239
peak=   -3.443 closest distance to " O   HOH Z 243 " =    1.774
peak=   -3.441 closest distance to " O   LEU A 167 " =    1.478
peak=   -3.437 closest distance to " CG  GLU A  53 " =    1.441
peak=   -3.436 closest distance to " CD1 PHE A  59 " =    1.860
peak=   -3.436 closest distance to " OD1 ASN A 187 " =    1.541
peak=   -3.435 closest distance to " O   HOH Z 311 " =    3.826
peak=   -3.434 closest distance to " OD2 ASP A 171 " =    1.782
peak=   -3.433 closest distance to " O   GLY A 203 " =    2.407
peak=   -3.432 closest distance to " CB  PHE A 192 " =    1.823
peak=   -3.426 closest distance to " CG1 VAL A 197 " =    2.330
peak=   -3.421 closest distance to " O   HOH Z 207 " =    2.178
peak=   -3.413 closest distance to " N   GLN A  58 " =    1.747
peak=   -3.410 closest distance to " C   ASN A 285 " =    2.579
peak=   -3.408 closest distance to " O   VAL A  67 " =    2.547
peak=   -3.403 closest distance to " O   HOH Z 388 " =    2.022
peak=   -3.402 closest distance to " OG BSER A 134 " =    1.749
peak=   -3.402 closest distance to " O   HOH Z 222 " =    1.454
peak=   -3.402 closest distance to " N   SER A 212 " =    1.973
peak=   -3.397 closest distance to " O   HOH Z  92 " =    1.698
peak=   -3.397 closest distance to " O   PRO A 198 " =    1.270
peak=   -3.397 closest distance to " CG  GLU A 277 " =    1.087
peak=   -3.396 closest distance to " O   HOH Z 211 " =    1.570
peak=   -3.394 closest distance to " CB  ALA A 248 " =    2.036
peak=   -3.385 closest distance to " O   HOH Z 231 " =    1.346
peak=   -3.373 closest distance to " CB  TRP A  85 " =    2.464
peak=   -3.370 closest distance to " CG  ASP A  50 " =    2.429
peak=   -3.368 closest distance to " C   ALA A   8 " =    1.553
peak=   -3.364 closest distance to " CG  ARG A  66 " =    2.397
peak=   -3.363 closest distance to " O   HOH Z 234 " =    4.384
peak=   -3.359 closest distance to " O   HOH Z 185 " =    2.388
peak=   -3.357 closest distance to " OG  SER A  62 " =    1.767
peak=   -3.354 closest distance to " CB  VAL A 230 " =    1.078
peak=   -3.354 closest distance to " CE  MET A 105 " =    2.127
peak=   -3.342 closest distance to " O   HOH Z 166 " =    1.564
peak=   -3.341 closest distance to " O   HOH Z 372 " =    2.446
peak=   -3.338 closest distance to " O   HOH Z  60 " =    2.053
peak=   -3.337 closest distance to " CZ  TYR A 169 " =    1.702
peak=   -3.332 closest distance to " O   HOH Z 292 " =    4.576
peak=   -3.330 closest distance to " O   HOH Z 165 " =    2.011
peak=   -3.329 closest distance to " CB  ASN A  39 " =    2.101
peak=   -3.320 closest distance to " OD1 ASP A 191 " =    1.549
peak=   -3.318 closest distance to " CG  GLU A   2 " =    1.792
peak=   -3.314 closest distance to " O   GLY A 196 " =    1.191
peak=   -3.313 closest distance to " ND2 ASN A  60 " =    1.427
peak=   -3.312 closest distance to " CE2 PHE A 218 " =    2.588
peak=   -3.312 closest distance to " CE1 TYR A 169 " =    2.497
peak=   -3.312 closest distance to " O   HOH Z 431 " =    1.661
peak=   -3.311 closest distance to " CA  ASN A 127 " =    1.069
peak=   -3.309 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.290 closest distance to " N   SER A 276 " =    1.346
peak=   -3.288 closest distance to " CE3 TRP A 150 " =    2.142
peak=   -3.280 closest distance to " CZ  PHE A  59 " =    1.617
peak=   -3.278 closest distance to " O   HOH Z 252 " =    3.928
peak=   -3.277 closest distance to " CB  CYS A 254 " =    2.156
peak=   -3.273 closest distance to " CG  ARG A 259 " =    2.546
peak=   -3.272 closest distance to " O   HOH Z 128 " =    2.505
peak=   -3.269 closest distance to " O   VAL A 197 " =    1.387
peak=   -3.269 closest distance to " O   VAL A 189 " =    2.618
peak=   -3.258 closest distance to " CD2 LEU A 237 " =    2.820
peak=   -3.255 closest distance to " CG1 VAL A 296 " =    1.259
peak=   -3.252 closest distance to " CE BMET A  47 " =    1.855
peak=   -3.251 closest distance to " C   SER A 206 " =    1.516
peak=   -3.251 closest distance to " CG  HIS A  86 " =    0.909
peak=   -3.251 closest distance to " CB  ALA A 291 " =    2.330
peak=   -3.243 closest distance to " O   HOH Z 191 " =    5.584
peak=   -3.243 closest distance to " ND2BASN A 224 " =    1.657
peak=   -3.240 closest distance to " CA  GLY A 241 " =    2.247
peak=   -3.230 closest distance to " O   ASN A 301 " =    1.385
peak=   -3.230 closest distance to " C   LEU A 222 " =    0.787
peak=   -3.230 closest distance to " O   LYS A 117 " =    1.709
peak=   -3.229 closest distance to " O   ALA A   7 " =    1.599
peak=   -3.228 closest distance to " OH  TYR A 169 " =    1.043
peak=   -3.227 closest distance to " O   HOH Z 417 " =    2.815
peak=   -3.223 closest distance to " C   LEU A 143 " =    1.201
peak=   -3.223 closest distance to " O   GLY A  80 " =    2.490
peak=   -3.222 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.220 closest distance to " O   HOH Z  98 " =    2.058
peak=   -3.216 closest distance to " C   GLN A  58 " =    2.242
peak=   -3.215 closest distance to " CG  GLN A  88 " =    0.859
peak=   -3.212 closest distance to " O   HOH Z 111 " =    2.367
peak=   -3.212 closest distance to " O   HOH Z 435 " =    2.713
peak=   -3.207 closest distance to " C   MET A 188 " =    1.406
peak=   -3.207 closest distance to " O   MET A  40 " =    2.715
peak=   -3.202 closest distance to " O   HOH Z 292 " =    1.960
peak=   -3.202 closest distance to " CB  ALA A 227 " =    2.374
peak=   -3.198 closest distance to " O   HOH Z 120 " =    4.261
peak=   -3.192 closest distance to " CB  ASP A 132 " =    2.282
peak=   -3.179 closest distance to " CB  TYR A  15 " =    2.271
peak=   -3.179 closest distance to " O   HOH Z 189 " =    1.988
peak=   -3.178 closest distance to " O   HOH Z 177 " =    1.628
peak=   -3.178 closest distance to " O   HOH Z 310 " =    1.880
peak=   -3.178 closest distance to " NH2 ARG A  79 " =    1.979
peak=   -3.177 closest distance to " CG  PRO A 163 " =    2.444
peak=   -3.172 closest distance to " O   HOH Z  55 " =    2.561
peak=   -3.168 closest distance to " NE2 GLN A 103 " =    1.760
peak=   -3.161 closest distance to " O   HOH Z  90 " =    1.492
peak=   -3.159 closest distance to " C   GLN A 240 " =    2.397
peak=   -3.154 closest distance to " NH1 ARG A 195 " =    2.321
peak=   -3.152 closest distance to " CD2 TYR A 247 " =    2.161
peak=   -3.152 closest distance to " O   HOH Z 409 " =    4.665
peak=   -3.147 closest distance to " N   MET A 105 " =    2.862
peak=   -3.146 closest distance to " O   HOH Z 139 " =    2.994
peak=   -3.145 closest distance to " OG  SER A 206 " =    1.802
peak=   -3.143 closest distance to " O   HOH Z  60 " =    1.925
peak=   -3.143 closest distance to " O   ALA A 161 " =    1.611
peak=   -3.137 closest distance to " O   HOH Z 148 " =    1.777
peak=   -3.134 closest distance to " O   HOH Z  71 " =    1.278
peak=   -3.134 closest distance to " OD2 ASP A 171 " =    2.254
peak=   -3.130 closest distance to " CD  GLN A 223 " =    1.479
peak=   -3.129 closest distance to " O   PRO A 198 " =    1.395
peak=   -3.128 closest distance to " O   HOH Z 396 " =    1.771
peak=   -3.124 closest distance to " CG  LYS A 166 " =    2.071
peak=   -3.123 closest distance to " O   HOH Z 266 " =    4.909
peak=   -3.121 closest distance to " O   HOH Z 317 " =    2.273
peak=   -3.112 closest distance to " CD2 PHE A  61 " =    2.404
peak=   -3.097 closest distance to " CA  SER A 135 " =    1.305
peak=   -3.097 closest distance to " O   HOH Z   6 " =    1.830
peak=   -3.087 closest distance to " O   HOH Z 174 " =    2.463
peak=   -3.068 closest distance to " O   HOH Z 108 " =    1.823
peak=   -3.055 closest distance to " N   SER A   3 " =    2.160
peak=   -3.044 closest distance to " CG2 THR A 178 " =    2.233

================= 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    :  0.4527 0.4461   6.253225e+00   6.241106e+00
   1_bss:  0.4449 0.4359   6.249434e+00   6.234928e+00
   1_xyz:  0.3465 0.3791   6.083315e+00   6.145379e+00
   1_adp:  0.2955 0.3451   5.963383e+00   6.080667e+00
   1_occ:  0.2948 0.3452   5.962442e+00   6.081298e+00
   2_bss:  0.2921 0.3409   5.963301e+00   6.078944e+00
   2_xyz:  0.1914 0.2479   5.605961e+00   5.803645e+00
   2_adp:  0.1699 0.2203   5.494101e+00   5.699355e+00
   2_occ:  0.1698 0.2201   5.493678e+00   5.699189e+00
   3_bss:  0.1680 0.2172   5.493516e+00   5.697364e+00
   3_xyz:  0.1352 0.1805   5.301396e+00   5.525903e+00
   3_adp:  0.1277 0.1748   5.260028e+00   5.492770e+00
   3_occ:  0.1276 0.1746   5.259700e+00   5.492552e+00
   4_bss:  0.1278 0.1746   5.260832e+00   5.493222e+00
   4_xyz:  0.1162 0.1643   5.184806e+00   5.431279e+00
   4_adp:  0.1157 0.1623   5.179112e+00   5.421991e+00
   4_occ:  0.1157 0.1621   5.178893e+00   5.421838e+00
   5_bss:  0.1157 0.1621   5.178893e+00   5.421838e+00
   5_xyz:  0.1151 0.1613   5.176150e+00   5.417498e+00
   5_adp:  0.1134 0.1628   5.174770e+00   5.425714e+00
   5_occ:  0.1134 0.1627   5.174632e+00   5.425622e+00
   5_bss:  0.1133 0.1627   5.174525e+00   5.425666e+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:  0.300  20.000   9.296   7.839   7.558   0.000   0.000   0.000
   1_xyz:  0.300  20.000   9.296   7.839   7.558   0.000   0.000   0.000
   1_adp:  0.300  20.000   9.296   7.839   7.558   0.000   0.000   0.000
   1_occ:  0.300  20.000   9.296   7.839   7.558   0.000   0.000   0.000
   2_bss:  0.319  48.181   5.839   4.610   5.090   0.000   0.000   0.000
   2_xyz:  0.319  48.181   5.839   4.610   5.090   0.000   0.000   0.000
   2_adp:  0.319  48.181   5.839   4.610   5.090   0.000   0.000   0.000
   2_occ:  0.319  48.181   5.839   4.610   5.090   0.000   0.000   0.000
   3_bss:  0.329  48.181   3.598   3.177   3.694   0.000   0.000   0.000
   3_xyz:  0.329  48.181   3.598   3.177   3.694   0.000   0.000   0.000
   3_adp:  0.329  48.181   3.598   3.177   3.694   0.000   0.000   0.000
   3_occ:  0.329  48.181   3.598   3.177   3.694   0.000   0.000   0.000
   4_bss:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   4_xyz:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   4_adp:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   4_occ:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   5_bss:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   5_xyz:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   5_adp:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   5_occ:  0.323  48.181   2.990   2.804   3.372   0.000   0.000   0.000
   5_bss:  0.319  53.447  -0.103  -0.233   0.336   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.840 0.4982  0.5687    59931.292
   1_bss:  52.378 0.4889  0.7059    57893.576
   1_xyz:  42.922 0.6057  0.8568    41327.744
   1_adp:  37.257 0.6743  0.9546    33115.694
   1_occ:  37.284 0.6739  0.9534    33156.722
   2_bss:  37.133 0.6757  0.8600    33012.827
   2_xyz:  24.614 0.8147  0.9945    15780.918
   2_adp:  21.238 0.8498  1.0217    12516.985
   2_occ:  21.240 0.8497  1.0215    12513.912
   3_bss:  21.161 0.8505  0.9617    12467.353
   3_xyz:  16.877 0.8906  0.9811     8457.446
   3_adp:  16.127 0.8975  0.9830     7929.163
   3_occ:  16.121 0.8975  0.9829     7924.029
   4_bss:  16.129 0.8975  0.9669     7940.319
   4_xyz:  14.834 0.9083  0.9724     6945.568
   4_adp:  14.604 0.9104  0.9728     6833.680
   4_occ:  14.602 0.9104  0.9726     6830.286
   5_bss:  14.602 0.9104  0.9726     6830.286
   5_xyz:  14.457 0.9117  0.9720     6746.757
   5_adp:  14.661 0.9100  0.9670     6829.540
   5_occ:  14.659 0.9100  0.9669     6828.143
   5_bss:  14.661 0.9100  0.9687     6830.475
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4034e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4034e+01
   1_xyz:   1.656  0.013  0.106 17.925  0.007  4.112   1.3474e-01
   1_adp:   1.656  0.013  0.106 17.925  0.007  4.112   1.3474e-01
   1_occ:   1.656  0.013  0.106 17.925  0.007  4.112   1.3474e-01
   2_bss:   1.656  0.013  0.106 17.925  0.007  4.112   1.3474e-01
   2_xyz:   1.152  0.009  0.080 16.315  0.005  4.132   8.0555e-02
   2_adp:   1.152  0.009  0.080 16.315  0.005  4.132   8.0555e-02
   2_occ:   1.152  0.009  0.080 16.315  0.005  4.132   8.0555e-02
   3_bss:   1.152  0.009  0.080 16.315  0.005  4.132   8.0555e-02
   3_xyz:   1.068  0.008  0.081 15.875  0.004  4.130   6.8081e-02
   3_adp:   1.068  0.008  0.081 15.875  0.004  4.130   6.8081e-02
   3_occ:   1.068  0.008  0.081 15.875  0.004  4.130   6.8081e-02
   4_bss:   1.068  0.008  0.081 15.875  0.004  4.130   6.8081e-02
   4_xyz:   1.145  0.010  0.091 15.795  0.004  4.137   7.9300e-02
   4_adp:   1.145  0.010  0.091 15.795  0.004  4.137   7.9300e-02
   4_occ:   1.145  0.010  0.091 15.795  0.004  4.137   7.9300e-02
   5_bss:   1.145  0.010  0.091 15.795  0.004  4.137   7.9300e-02
   5_xyz:   1.048  0.008  0.084 15.476  0.004  4.120   6.7025e-02
   5_adp:   1.048  0.008  0.084 15.476  0.004  4.120   6.7025e-02
   5_occ:   1.048  0.008  0.084 15.476  0.004  4.120   6.7025e-02
   5_bss:   1.048  0.008  0.084 15.476  0.004  4.120   6.7025e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0061e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0061e+00
   1_xyz:  14.719  0.162  0.477 84.964  0.044  2.256   1.0008e-01
   1_adp:  14.719  0.162  0.477 84.964  0.044  2.256   1.0008e-01
   1_occ:  14.719  0.162  0.477 84.964  0.044  2.256   1.0008e-01
   2_bss:  14.719  0.162  0.477 84.964  0.044  2.256   1.0008e-01
   2_xyz:   7.511  0.117  0.241 86.773  0.040  2.288   7.7814e-02
   2_adp:   7.511  0.117  0.241 86.773  0.040  2.288   7.7814e-02
   2_occ:   7.511  0.117  0.241 86.773  0.040  2.288   7.7814e-02
   3_bss:   7.511  0.117  0.241 86.773  0.040  2.288   7.7814e-02
   3_xyz:   8.138  0.054  0.487 82.825  0.042  2.386   4.5376e-02
   3_adp:   8.138  0.054  0.487 82.825  0.042  2.386   4.5376e-02
   3_occ:   8.138  0.054  0.487 82.825  0.042  2.386   4.5376e-02
   4_bss:   8.138  0.054  0.487 82.825  0.042  2.386   4.5376e-02
   4_xyz:   7.673  0.065  0.639 83.130  0.043  2.302   9.1954e-02
   4_adp:   7.673  0.065  0.639 83.130  0.043  2.302   9.1954e-02
   4_occ:   7.673  0.065  0.639 83.130  0.043  2.302   9.1954e-02
   5_bss:   7.673  0.065  0.639 83.130  0.043  2.302   9.1954e-02
   5_xyz:   7.840  0.043  0.553 83.356  0.041  2.358   4.5268e-02
   5_adp:   7.840  0.043  0.553 83.356  0.041  2.358   4.5268e-02
   5_occ:   7.840  0.043  0.553 83.356  0.041  2.358   4.5268e-02
   5_bss:   7.840  0.043  0.553 83.356  0.041  2.358   4.5268e-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:  62.09   0.00  10.92  62.09   0.00   8.05  55.37   0.00  26.51
   1_occ:  62.09   0.00  10.92  62.09   0.00   8.05  55.37   0.00  26.51
   2_bss:  62.09   0.00  10.92  62.09   0.00   8.05  55.37   0.00  26.51
   2_xyz:  62.09   0.00  10.92  62.09   0.00   8.05  55.37   0.00  26.51
   2_adp:  97.35   0.00  11.70  97.35   0.00   7.84  64.91   0.69  32.73
   2_occ:  97.35   0.00  11.70  97.35   0.00   7.84  64.91   0.69  32.73
   3_bss:  97.35   0.00  11.70  97.35   0.00   7.84  64.91   0.69  32.73
   3_xyz:  97.35   0.00  11.70  97.35   0.00   7.84  64.91   0.69  32.73
   3_adp:  77.40   0.00  12.26  77.40   0.00   7.97  76.69   0.65  35.64
   3_occ:  77.40   0.00  12.26  77.40   0.00   7.97  76.69   0.65  35.64
   4_bss:  77.40   0.00  12.26  77.40   0.00   7.97  76.69   0.65  35.64
   4_xyz:  77.40   0.00  12.26  77.40   0.00   7.97  76.69   0.65  35.64
   4_adp:  78.49   0.00  11.92  78.49   0.00   7.84  77.22   1.26  34.16
   4_occ:  78.49   0.00  11.92  78.49   0.00   7.84  77.22   1.26  34.16
   5_bss:  78.49   0.00  11.92  78.49   0.00   7.84  77.22   1.26  34.16
   5_xyz:  78.49   0.00  11.92  78.49   0.00   7.84  77.22   1.26  34.16
   5_adp:  87.93   0.00  12.26  87.93   0.00   7.94  84.22   1.42  35.74
   5_occ:  87.93   0.00  12.26  87.93   0.00   7.94  84.22   1.42  35.74
   5_bss:  91.03   3.11  15.36  91.03   3.11  11.05  87.32   4.53  38.85
------------------------------------------------------------------------
 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:    1.201    0.020    0.412
   1_adp:    1.201    0.020    0.412
   1_occ:    1.201    0.020    0.412
   2_bss:    1.201    0.020    0.412
   2_xyz:    1.414    0.033    0.563
   2_adp:    1.414    0.033    0.563
   2_occ:    1.414    0.033    0.563
   3_bss:    1.414    0.033    0.563
   3_xyz:    1.462    0.031    0.608
   3_adp:    1.462    0.031    0.608
   3_occ:    1.462    0.031    0.608
   4_bss:    1.462    0.031    0.608
   4_xyz:    1.609    0.034    0.635
   4_adp:    1.609    0.034    0.635
   4_occ:    1.609    0.034    0.635
   5_bss:    1.609    0.034    0.635
   5_xyz:    1.693    0.039    0.643
   5_adp:    1.693    0.039    0.643
   5_occ:    1.693    0.039    0.643
   5_bss:    1.693    0.039    0.643
------------------------------------------------------------------------

CPU time actual refinement: 339.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1158/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_1158/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1158/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1158/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1158/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.36 
  Macro-tasks:
    bulk solvent and scale       = 40.01  
    individual site refinement   = 138.08 
    weights calculation          = 33.44  
    collect and process          = 6.59   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.23 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 106.47 
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 116.08 
    fmodel                         = 7.12   
    r_factors                      = 0.39   
    phase_errors                   = 10.74  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 252.33 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.803 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    638 calls, 106.11 s
gradients_fft:          583 calls, 103.00 s

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

# Date 2008-01-16 Time 03:20:34 PST -0800 (1200482434.50 s)
Start R-work = 0.4527, R-free = 0.4461 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.4449, R-free = 0.4359
Final R-work = 0.1133, R-free = 0.1627