# Date 2008-01-16 Time 05:41:52 PST -0800 (1200490912.39 s)
#phil __OFF__

Command line arguments: "../842.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12103
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 842

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 86.822, 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: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01049
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   2.0105

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01049
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.3010 [2122/2150]  1911   211   9.9%
  bin  2:  4.3010 -  3.4271 [2038/2057]  1832   206  10.1%
  bin  3:  3.4271 -  2.9978 [2024/2044]  1822   202  10.0%
  bin  4:  2.9978 -  2.7254 [1987/2012]  1792   195   9.8%
  bin  5:  2.7254 -  2.5311 [1987/2006]  1787   200  10.1%
  bin  6:  2.5311 -  2.3824 [1966/2011]  1771   195   9.9%
  bin  7:  2.3824 -  2.2635 [1962/1996]  1765   197  10.0%
  bin  8:  2.2635 -  2.1653 [1959/1994]  1758   201  10.3%
  bin  9:  2.1653 -  2.0822 [1945/1975]  1754   191   9.8%
  bin 10:  2.0822 -  2.0105 [1599/2004]  1438   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_842/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:
        1.72 -     2.35: 7
        2.35 -     2.99: 1824
        2.99 -     3.63: 4524
        3.63 -     4.26: 8958
        4.26 -     4.90: 12524
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.718 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.794 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 206 " - " O   HOH Z 342 "  1.840 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.983 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27832 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 =====================


==================== 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/noshake/run_842/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_842/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 86.82195 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4166   r_free= 0.3983   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.236638                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7967 0.99   1380  154 0.3461 0.3663       6.508      6.5044|
|  2:  4.7967 -  3.8278 0.99   1329  146 0.3650 0.3748      6.7907        6.78|
|  3:  3.8278 -  3.3500 0.99   1304  147 0.3924 0.3418      6.6435      6.5519|
|  4:  3.3500 -  3.0465 0.99   1293  138 0.4060 0.3734      6.4867      6.3773|
|  5:  3.0465 -  2.8297 0.99   1282  146 0.4382 0.3927      6.3502       6.321|
|  6:  2.8297 -  2.6638 0.98   1281  142 0.4421 0.4182      6.2425      6.1314|
|  7:  2.6638 -  2.5311 0.99   1275  141 0.4457 0.3735      6.2083      6.0605|
|  8:  2.5311 -  2.4214 0.98   1266  142 0.4444 0.4224      6.1323      6.1371|
|  9:  2.4214 -  2.3285 0.98   1276  146 0.4496 0.4598      6.0737      6.1223|
| 10:  2.3285 -  2.2484 0.97   1232  132 0.4540 0.4198      6.0801      5.9674|
| 11:  2.2484 -  2.1783 0.99   1275  144 0.4500 0.3975      6.0115       5.987|
| 12:  2.1783 -  2.1162 0.98   1271  133 0.4616 0.4724      5.9462      6.0057|
| 13:  2.1162 -  2.0607 0.97   1226  139 0.4513 0.4313      5.8491      5.8529|
| 14:  2.0607 -  2.0105 0.73    940  109 0.4305 0.4820      5.7923      5.7282|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7967  1380   154  0.71  33.71   0.83     0.74      69443.15|
|  2:  4.7967 -  3.8278  1329   146  0.75  30.58   0.91     0.83      83327.73|
|  3:  3.8278 -  3.3500  1304   147  0.69  36.12   0.91     0.84      84154.33|
|  4:  3.3500 -  3.0465  1293   138  0.65  40.01   0.91     0.80      70625.74|
|  5:  3.0465 -  2.8297  1282   146  0.59  44.63   0.90     0.76      56644.79|
|  6:  2.8297 -  2.6638  1281   142  0.59  45.04   0.90     0.74      45341.35|
|  7:  2.6638 -  2.5311  1275   141  0.57  46.10   0.94     0.74      41976.14|
|  8:  2.5311 -  2.4214  1266   142  0.56  47.12   0.94     0.73      39942.68|
|  9:  2.4214 -  2.3285  1276   146  0.54  48.69   0.93     0.74      38066.36|
| 10:  2.3285 -  2.2484  1232   132  0.56  47.26   0.95     0.76      34548.44|
| 11:  2.2484 -  2.1783  1275   144  0.55  48.24   0.95     0.76      32931.15|
| 12:  2.1783 -  2.1162  1271   133  0.51  51.86   0.97     0.72      32951.44|
| 13:  2.1162 -  2.0607  1226   139  0.46  55.11   0.94     0.65      30407.82|
| 14:  2.0607 -  2.0105   940   109  0.45  56.39   0.97     0.58      24777.95|
|alpha:            min =        0.58 max =            0.84 mean =         0.75|
|beta:             min =    24777.95 max =        84154.33 mean =     49801.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.68|
|phase err.(test): min =        0.00 max =           89.95 mean =        44.86|
|-----------------------------------------------------------------------------|

============================== 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 = 5.775770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.887   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.321715              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.971   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.718 -  2.036:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.036 -  2.355:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.355 -  2.673:       71 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.673 -  2.991:     1753 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.991 -  3.309:     1878 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.309 -  3.627:     2646 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.627 -  3.945:     4630 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.945 -  4.264:     4328 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.264 -  4.582:     5691 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.582 -  4.900:     6833 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.718 |       0.197 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4166   r_free= 0.3983   ksol= 0.00   Bsol= 0.00   scale= 0.903    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.236638                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4033   r_free= 0.3837   ksol= 0.30   Bsol= 41.11   scale= 0.932   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,5.95,-1.43,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.222202                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.348653              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.498   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.885   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4033      final r-factor (work) = 0.3410          |
| start r-factor (free) = 0.3837      final r-factor (free) = 0.3636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8035 = 5.35 * 0.50 * 6.2212 + 1.00 * 0.1659                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4213 = 5.35 * 0.50 * 6.1037 + 1.00 * 0.0980                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3410      final r-factor (work) = 0.3156          |
| start r-factor (free) = 0.3636      final r-factor (free) = 0.3728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2020 = 0.69 * 1.00 * 6.1037 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1678 = 0.69 * 1.00 * 6.0425 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.48   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    84.48   17.52    None  None   None       |
|    Sol.    : 438    0      2.23    84.48   34.71    None  None   None       |
|    Mac.    : 2385   0      0.00    74.12   14.37    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 -   8.448:  777   |   5:    42.239 -  50.687:  103        |
|      1:     8.448 -  16.896:  917   |   6:    50.687 -  59.135:   56        |
|      2:    16.896 -  25.344:  525   |   7:    59.135 -  67.583:   33        |
|      3:    25.344 -  33.791:  269   |   8:    67.583 -  76.031:    8        |
|      4:    33.791 -  42.239:  133   |   9:    76.031 -  84.479:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3156 r_free = 0.3728             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3153 r_free = 0.3724             target_work(ml) = 6.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3153   r_free= 0.3724   ksol= 0.30   Bsol= 41.11   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.42,5.95,-1.43,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.044926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3143   r_free= 0.3708   ksol= 0.29   Bsol= 54.18   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,3.52,-0.36,0.00,-0.00,-0.00); trace/3= 0.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.046637                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.832016              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.868   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.792740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.552  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3143      final r-factor (work) = 0.2496          |
| start r-factor (free) = 0.3708      final r-factor (free) = 0.2972          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7701 = 7.83 * 0.50 * 6.0450 + 1.00 * 0.0980                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3755 = 7.83 * 0.50 * 5.9403 + 1.00 * 0.1133                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2496      final r-factor (work) = 0.2283          |
| start r-factor (free) = 0.2972      final r-factor (free) = 0.2866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7231 = 0.79 * 1.00 * 5.9403 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6081 = 0.79 * 1.00 * 5.7859 + 1.00 * 0.0214                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.66   17.88    None  None   None       |
|    all(noH): 2823   0      0.00    96.66   17.88    None  None   None       |
|    Sol.    : 438    0      0.46    90.58   39.87    None  None   None       |
|    Mac.    : 2385   0      0.00    96.66   13.85    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 -   9.666: 1076   |   5:    48.328 -  57.994:   90        |
|      1:     9.666 -  19.331:  880   |   6:    57.994 -  67.659:   53        |
|      2:    19.331 -  28.997:  356   |   7:    67.659 -  77.325:   29        |
|      3:    28.997 -  38.662:  204   |   8:    77.325 -  86.990:   17        |
|      4:    38.662 -  48.328:  111   |   9:    86.990 -  96.656:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2283 r_free = 0.2866             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2281 r_free = 0.2865             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2281   r_free= 0.2865   ksol= 0.29   Bsol= 54.18   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,3.52,-0.36,0.00,-0.00,-0.00); trace/3= 0.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.774508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2274   r_free= 0.2844   ksol= 0.32   Bsol= 70.25   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,1.76,0.15,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.773037                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.051335              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.885   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.377045              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.392   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2274      final r-factor (work) = 0.1687          |
| start r-factor (free) = 0.2844      final r-factor (free) = 0.2171          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.4057 = 8.05 * 0.50 * 5.7860 + 1.00 * 0.1133                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8522 = 8.05 * 0.50 * 5.6539 + 1.00 * 0.0915                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1687      final r-factor (work) = 0.1555          |
| start r-factor (free) = 0.2171      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1479 = 0.38 * 1.00 * 5.6539 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1362 = 0.38 * 1.00 * 5.4561 + 1.00 * 1.0790                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.63   17.47    None  None   None       |
|    all(noH): 2823   0      0.00    96.63   17.47    None  None   None       |
|    Sol.    : 438    0      3.56    90.57   40.37    None  None   None       |
|    Mac.    : 2385   0      0.00    96.63   13.26    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 -   9.663: 1146   |   5:    48.317 -  57.980:   93        |
|      1:     9.663 -  19.327:  889   |   6:    57.980 -  67.643:   51        |
|      2:    19.327 -  28.990:  301   |   7:    67.643 -  77.307:   29        |
|      3:    28.990 -  38.653:  182   |   8:    77.307 -  86.970:   18        |
|      4:    38.653 -  48.317:  108   |   9:    86.970 -  96.633:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1555 r_free = 0.2026             target_work(ml) = 5.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1552 r_free = 0.2023             target_work(ml) = 5.422         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2023   ksol= 0.32   Bsol= 70.25   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,1.76,0.15,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.422093                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1553   r_free= 0.2018   ksol= 0.33   Bsol= 69.36   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,0.57,0.11,0.00,0.00,0.00); trace/3= -0.15                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.422099                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.426057              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.426  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.282291              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.165   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1553      final r-factor (work) = 0.1428          |
| start r-factor (free) = 0.2018      final r-factor (free) = 0.1909          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7116 = 2.43 * 0.50 * 5.4570 + 1.00 * 0.0921                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5982 = 2.43 * 0.50 * 5.3879 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1428      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.1909      final r-factor (free) = 0.1832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3153 = 2.28 * 1.00 * 5.3879 + 1.00 * 0.0185                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1583 = 2.28 * 1.00 * 5.3210 + 1.00 * 0.0141                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.46  17.21    None  None   None       |
|    all(noH): 2823   0      0.00    113.46  17.21    None  None   None       |
|    Sol.    : 438    0      0.00    105.89  43.66    None  None   None       |
|    Mac.    : 2385   0      0.00    113.46  12.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.346: 1480   |   5:    56.730 -  68.076:   81        |
|      1:    11.346 -  22.692:  793   |   6:    68.076 -  79.422:   52        |
|      2:    22.692 -  34.038:  165   |   7:    79.422 -  90.768:   17        |
|      3:    34.038 -  45.384:  128   |   8:    90.768 - 102.113:    8        |
|      4:    45.384 -  56.730:   97   |   9:   102.113 - 113.459:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1321 r_free = 0.1832             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1320 r_free = 0.1832             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1832   ksol= 0.33   Bsol= 69.36   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.14,0.57,0.11,0.00,0.00,0.00); trace/3= -0.15                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.294480                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1832   ksol= 0.33   Bsol= 74.92   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.17,0.12,0.16,0.00,0.00,0.00); trace/3= -0.30                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.293987                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.782764              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.998  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.173132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1320      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1832      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4657 = 2.78 * 0.50 * 5.3207 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3899 = 2.78 * 0.50 * 5.2616 + 1.00 * 0.0691                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1724      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9249 = 0.17 * 1.00 * 5.2616 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9160 = 0.17 * 1.00 * 5.2351 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    104.09  16.09    None  None   None       |
|    all(noH): 2823   0      0.85    104.09  16.09    None  None   None       |
|    Sol.    : 438    0      2.47    98.86   39.95    None  None   None       |
|    Mac.    : 2385   0      0.85    104.09  11.71    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:     0.854 -  11.177: 1535   |   5:    52.471 -  62.794:   68        |
|      1:    11.177 -  21.501:  751   |   6:    62.794 -  73.118:   45        |
|      2:    21.501 -  31.824:  172   |   7:    73.118 -  83.441:   13        |
|      3:    31.824 -  42.147:  127   |   8:    83.441 -  93.764:    6        |
|      4:    42.147 -  52.471:  102   |   9:    93.764 - 104.088:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1671             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1672             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1672   ksol= 0.33   Bsol= 74.92   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.17,0.12,0.16,0.00,0.00,0.00); trace/3= -0.30                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218725                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7967 0.99   1380  154 0.1024 0.1313      5.4107      5.5715|
|  2:  4.7967 -  3.8278 0.99   1329  146 0.0881 0.1092      5.4658      5.6574|
|  3:  3.8278 -  3.3500 0.99   1304  147 0.1098 0.1554      5.5172      5.8953|
|  4:  3.3500 -  3.0465 0.99   1293  138 0.1328 0.1728      5.5202       5.666|
|  5:  3.0465 -  2.8297 0.99   1282  146 0.1449 0.1812      5.4185        5.58|
|  6:  2.8297 -  2.6638 0.98   1281  142 0.1432 0.2086      5.3298      5.5456|
|  7:  2.6638 -  2.5311 0.99   1275  141 0.1400 0.1866       5.261      5.4578|
|  8:  2.5311 -  2.4214 0.98   1266  142 0.1335 0.1901      5.1882      5.4428|
|  9:  2.4214 -  2.3285 0.98   1276  146 0.1321 0.1893      5.1168      5.3908|
| 10:  2.3285 -  2.2484 0.97   1232  132 0.1306 0.1832      5.0695      5.2401|
| 11:  2.2484 -  2.1783 0.99   1275  144 0.1275 0.1896      5.0054      5.3262|
| 12:  2.1783 -  2.1162 0.98   1271  133 0.1231 0.1774      4.9401      5.2175|
| 13:  2.1162 -  2.0607 0.97   1226  139 0.1292 0.1737       4.875      5.0646|
| 14:  2.0607 -  2.0105 0.73    940  109 0.1218 0.1911      4.7671      5.0308|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7967  1380   154  0.94   9.52   0.96     0.94       7709.10|
|  2:  4.7967 -  3.8278  1329   146  0.95   8.53   1.00     0.98       9677.77|
|  3:  3.8278 -  3.3500  1304   147  0.93  11.83   1.01     1.01      11309.45|
|  4:  3.3500 -  3.0465  1293   138  0.91  14.78   1.00     0.97      11411.97|
|  5:  3.0465 -  2.8297  1282   146  0.89  17.30   1.00     0.97       9816.67|
|  6:  2.8297 -  2.6638  1281   142  0.89  17.71   0.98     0.95       8525.87|
|  7:  2.6638 -  2.5311  1275   141  0.89  17.20   0.99     0.96       7392.54|
|  8:  2.5311 -  2.4214  1266   142  0.89  17.07   0.99     0.95       6621.87|
|  9:  2.4214 -  2.3285  1276   146  0.89  17.72   0.99     0.94       5858.90|
| 10:  2.3285 -  2.2484  1232   132  0.89  17.12   0.99     0.96       5283.43|
| 11:  2.2484 -  2.1783  1275   144  0.89  17.08   0.99     0.94       4719.60|
| 12:  2.1783 -  2.1162  1271   133  0.90  16.12   0.99     0.98       4305.40|
| 13:  2.1162 -  2.0607  1226   139  0.90  16.87   0.98     0.97       3755.11|
| 14:  2.0607 -  2.0105   940   109  0.89  16.72   0.96     0.92       3042.55|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3042.55 max =        11411.97 mean =      7218.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.30|
|phase err.(test): min =        0.00 max =           89.35 mean =        14.64|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1670   ksol= 0.32   Bsol= 68.82   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-0.12,0.22,-0.00,0.00,0.00); trace/3= -0.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218416                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1670   ksol= 0.32   Bsol= 68.82   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-0.12,0.22,-0.00,0.00,0.00); trace/3= -0.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.218416                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7967 0.99   1380  154 0.1025 0.1293      5.4068      5.5563|
|  2:  4.7967 -  3.8278 0.99   1329  146 0.0887 0.1078      5.4629      5.6481|
|  3:  3.8278 -  3.3500 0.99   1304  147 0.1098 0.1553      5.5156      5.8939|
|  4:  3.3500 -  3.0465 0.99   1293  138 0.1334 0.1734      5.5221       5.667|
|  5:  3.0465 -  2.8297 0.99   1282  146 0.1455 0.1813      5.4207      5.5803|
|  6:  2.8297 -  2.6638 0.98   1281  142 0.1434 0.2080      5.3302      5.5452|
|  7:  2.6638 -  2.5311 0.99   1275  141 0.1398 0.1872      5.2612      5.4602|
|  8:  2.5311 -  2.4214 0.98   1266  142 0.1335 0.1903      5.1887       5.444|
|  9:  2.4214 -  2.3285 0.98   1276  146 0.1319 0.1888      5.1164      5.3894|
| 10:  2.3285 -  2.2484 0.97   1232  132 0.1305 0.1840      5.0696      5.2423|
| 11:  2.2484 -  2.1783 0.99   1275  144 0.1276 0.1895      5.0056      5.3256|
| 12:  2.1783 -  2.1162 0.98   1271  133 0.1228 0.1781      4.9401      5.2205|
| 13:  2.1162 -  2.0607 0.97   1226  139 0.1292 0.1733      4.8751       5.064|
| 14:  2.0607 -  2.0105 0.73    940  109 0.1218 0.1908      4.7663      5.0291|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7967  1380   154  0.94   9.51   0.96     0.93       7446.67|
|  2:  4.7967 -  3.8278  1329   146  0.95   8.46   1.00     0.98       9474.76|
|  3:  3.8278 -  3.3500  1304   147  0.93  11.75   1.01     1.01      11221.83|
|  4:  3.3500 -  3.0465  1293   138  0.91  14.76   1.00     0.97      11397.86|
|  5:  3.0465 -  2.8297  1282   146  0.89  17.32   0.99     0.97       9823.65|
|  6:  2.8297 -  2.6638  1281   142  0.89  17.72   0.98     0.95       8532.81|
|  7:  2.6638 -  2.5311  1275   141  0.89  17.22   0.98     0.95       7410.16|
|  8:  2.5311 -  2.4214  1266   142  0.89  17.10   0.98     0.94       6640.53|
|  9:  2.4214 -  2.3285  1276   146  0.89  17.72   0.99     0.94       5865.92|
| 10:  2.3285 -  2.2484  1232   132  0.89  17.13   0.99     0.95       5289.51|
| 11:  2.2484 -  2.1783  1275   144  0.89  17.08   0.98     0.94       4727.40|
| 12:  2.1783 -  2.1162  1271   133  0.90  16.15   0.99     0.97       4314.64|
| 13:  2.1162 -  2.0607  1226   139  0.90  16.87   0.97     0.96       3754.00|
| 14:  2.0607 -  2.0105   940   109  0.90  16.70   0.96     0.92       3032.37|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3032.37 max =        11397.86 mean =      7180.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.30|
|phase err.(test): min =        0.00 max =           88.71 mean =        14.62|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.82    104.06  16.06    None  None   None       |
|    all(noH): 2823   0      0.82    104.06  16.06    None  None   None       |
|    Sol.    : 438    0      2.45    98.83   39.92    None  None   None       |
|    Mac.    : 2385   0      0.82    104.06  11.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.825 -  11.148: 1535   |   5:    52.442 -  62.765:   68        |
|      1:    11.148 -  21.472:  751   |   6:    62.765 -  73.089:   45        |
|      2:    21.472 -  31.795:  172   |   7:    73.089 -  83.412:   13        |
|      3:    31.795 -  42.118:  127   |   8:    83.412 -  93.735:    6        |
|      4:    42.118 -  52.442:  102   |   9:    93.735 - 104.059:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.396 - 4.870
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.741 - 4.870

peak=    6.315 closest distance to " O   HOH Z 210 " =    1.399
peak=    5.566 closest distance to " O   HOH Z 111 " =    2.383
peak=    5.371 closest distance to " CB  SER A  63 " =    1.209
peak=    4.884 closest distance to " O   PRO A 198 " =    1.570
peak=    4.802 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.766 closest distance to " O   HOH Z 403 " =    1.810
peak=    4.733 closest distance to " CB  GLN A 223 " =    1.412
peak=    4.729 closest distance to " O   HOH Z 433 " =    1.708
peak=    4.694 closest distance to " O   HOH Z 134 " =    1.842
peak=    4.671 closest distance to " CG  PRO A  54 " =    1.380
peak=    4.545 closest distance to " CG  PRO A  90 " =    1.287
peak=    4.511 closest distance to " O   HOH Z 234 " =    3.842
peak=    4.496 closest distance to " O   HOH Z  49 " =    1.036
peak=    4.484 closest distance to " CG  PRO A 213 " =    1.285
peak=    4.450 closest distance to " CB  ARG A 190 " =    1.805
peak=    4.434 closest distance to " O   HOH Z 209 " =    2.297
peak=    4.416 closest distance to " O   HOH Z 232 " =    2.421
peak=    4.414 closest distance to " O   HOH Z 369 " =    2.061
peak=    4.400 closest distance to " O   HOH Z 176 " =    2.248
peak=    4.393 closest distance to " O   HOH Z  63 " =    1.655
peak=    4.372 closest distance to " CD  LYS A 166 " =    1.441
peak=    4.345 closest distance to " CB  ARG A 275 " =    0.800
peak=    4.292 closest distance to " O   HOH Z 189 " =    2.514
peak=    4.284 closest distance to " O   HOH Z 418 " =    2.064
peak=    4.276 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.273 closest distance to " O   HOH Z 133 " =    2.348
peak=    4.272 closest distance to " CG1 ILE A  33 " =    1.280
peak=    4.236 closest distance to " CA  ALA A  51 " =    0.977
peak=    4.222 closest distance to " O   HOH Z 425 " =    1.550
peak=    4.212 closest distance to " CG  PRO A 198 " =    1.203
peak=    4.207 closest distance to " O   HOH Z  15 " =    2.107
peak=    4.193 closest distance to " O   HOH Z 423 " =    1.857
peak=    4.170 closest distance to " CB  VAL A 202 " =    1.471
peak=    4.130 closest distance to " O   SER A  87 " =    2.296
peak=    4.101 closest distance to " O   HOH Z  44 " =    1.877
peak=    4.100 closest distance to " CB  PRO A  54 " =    0.859
peak=    4.092 closest distance to " O   HOH Z  40 " =    1.897
peak=    4.089 closest distance to " O   HOH Z 128 " =    2.180
peak=    4.088 closest distance to " O   HOH Z  59 " =    2.458
peak=    4.080 closest distance to " O   HOH Z  95 " =    1.912
peak=    4.076 closest distance to " O   HOH Z  48 " =    1.929
peak=    4.059 closest distance to " O   HOH Z 412 " =    3.355
peak=    4.053 closest distance to " O   HOH Z  20 " =    1.726
peak=    4.052 closest distance to " O   HOH Z  97 " =    2.065
peak=    4.050 closest distance to " O   HOH Z 154 " =    1.501
peak=    4.040 closest distance to " CB  GLU A 128 " =    1.129
peak=    4.039 closest distance to " NH2 ARG A 156 " =    1.238
peak=    4.036 closest distance to " CB  TRP A 266 " =    0.990
peak=    4.027 closest distance to " CD  ARG A 269 " =    1.053
peak=    4.022 closest distance to " O   HOH Z 265 " =    2.108
peak=    4.020 closest distance to " CB  GLU A 152 " =    1.126
peak=    4.011 closest distance to " O   HOH Z 214 " =    1.416
peak=    3.968 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.959 closest distance to " OE1 GLN A  11 " =    2.098
peak=    3.959 closest distance to " O   HOH Z 406 " =    1.712
peak=    3.955 closest distance to " CG  ARG A  66 " =    2.677
peak=    3.952 closest distance to " O   HOH Z  80 " =    2.108
peak=    3.951 closest distance to " CB  ASN A  39 " =    0.852
peak=    3.917 closest distance to " CB  TRP A 179 " =    1.353
peak=    3.905 closest distance to " CD2 TRP A 179 " =    1.251
peak=    3.895 closest distance to " O   HOH Z 258 " =    2.245
peak=    3.894 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.887 closest distance to " O   ALA A 165 " =    1.320
peak=    3.876 closest distance to " ND2 ASN A 187 " =    1.539
peak=    3.869 closest distance to " CA  ASP A 191 " =    0.900
peak=    3.853 closest distance to " CG AARG A 275 " =    1.086
peak=    3.851 closest distance to " CZ  PHE A 218 " =    1.190
peak=    3.846 closest distance to " CB  ASN A 142 " =    1.142
peak=    3.833 closest distance to " O   HOH Z 357 " =    2.144
peak=    3.831 closest distance to " O   HOH Z 415 " =    1.595
peak=    3.829 closest distance to " CG2BVAL A  41 " =    0.918
peak=    3.812 closest distance to " CB  LEU A 228 " =    1.091
peak=    3.812 closest distance to " CB  ARG A  79 " =    1.269
peak=    3.810 closest distance to " CB  SER A 141 " =    1.049
peak=    3.801 closest distance to " CB  ASN A 285 " =    0.837
peak=    3.799 closest distance to " NE2 GLN A  77 " =    3.332
peak=    3.797 closest distance to " O   HOH Z 284 " =    2.905
peak=    3.792 closest distance to " O   HOH Z 298 " =    1.886
peak=    3.786 closest distance to " CD1 LEU A 300 " =    1.170
peak=    3.784 closest distance to " O   HOH Z 132 " =    2.782
peak=    3.781 closest distance to " O   ASN A  74 " =    1.619
peak=    3.778 closest distance to " O   HOH Z  88 " =    1.612
peak=    3.767 closest distance to " O   HOH Z 362 " =    3.392
peak=    3.766 closest distance to " O   HOH Z  30 " =    1.520
peak=    3.764 closest distance to " CA  ARG A 195 " =    1.088
peak=    3.763 closest distance to " CB  GLU A 277 " =    3.803
peak=    3.749 closest distance to " CB  TYR A 169 " =    0.800
peak=    3.748 closest distance to " CD2 LEU A 297 " =    0.968
peak=    3.744 closest distance to " OG  SER A 276 " =    1.600
peak=    3.735 closest distance to " O   HOH Z 346 " =    1.563
peak=    3.733 closest distance to " O   HOH Z 422 " =    0.916
peak=    3.731 closest distance to " CG2 THR A 220 " =    0.741
peak=    3.729 closest distance to " O   HOH Z 196 " =    1.664
peak=    3.725 closest distance to " CD  PRO A  54 " =    1.013
peak=    3.725 closest distance to " O   THR A 251 " =    1.172
peak=    3.719 closest distance to " CB  GLN A  88 " =    1.116
peak=    3.718 closest distance to " CB  SER A  62 " =    0.839
peak=    3.713 closest distance to " O   HOH Z 246 " =    1.520
peak=    3.712 closest distance to " N   ASN A  39 " =    1.300
peak=    3.704 closest distance to " CG2 VAL A 197 " =    1.156
peak=    3.696 closest distance to " CB  ASP A 124 " =    0.800
peak=    3.695 closest distance to " O   HOH Z 291 " =    1.465
peak=    3.694 closest distance to " CZ3 TRP A  85 " =    1.018
peak=    3.692 closest distance to " O   HOH Z 437 " =    1.824
peak=    3.684 closest distance to " O   HOH Z 345 " =    1.740
peak=    3.683 closest distance to " O   HOH Z 431 " =    1.198
peak=    3.671 closest distance to " O   HOH Z 389 " =    2.019
peak=    3.670 closest distance to " CB  LEU A  83 " =    0.863
peak=    3.650 closest distance to " O   HOH Z 281 " =    4.870
peak=    3.642 closest distance to " OG BSER A 164 " =    2.375
peak=    3.634 closest distance to " O   ASN A 209 " =    1.125
peak=    3.632 closest distance to " O   HOH Z 271 " =    2.634
peak=    3.629 closest distance to " CG  PRO A 243 " =    1.164
peak=    3.615 closest distance to " CA  SER A  87 " =    1.020
peak=    3.610 closest distance to " O   HOH Z 126 " =    1.615
peak=    3.608 closest distance to " O   HOH Z 126 " =    2.006
peak=    3.605 closest distance to " O   HOH Z 203 " =    1.884
peak=    3.605 closest distance to " O  BHOH Z 338 " =    2.166
peak=    3.600 closest distance to " O   HOH Z 415 " =    1.177
peak=    3.596 closest distance to " NE2 GLN A  11 " =    1.153
peak=    3.585 closest distance to " O   HOH Z 147 " =    1.708
peak=    3.581 closest distance to " CG2 THR A 221 " =    0.940
peak=    3.574 closest distance to " O   HOH Z 432 " =    1.910
peak=    3.574 closest distance to " CB  PRO A 198 " =    0.988
peak=    3.567 closest distance to " O   ASP A 124 " =    1.339
peak=    3.567 closest distance to " O   HOH Z 368 " =    2.131
peak=    3.556 closest distance to " O   HOH Z 303 " =    2.342
peak=    3.546 closest distance to " OD1 ASN A  69 " =    2.431
peak=    3.545 closest distance to " CA  ASN A 176 " =    1.281
peak=    3.540 closest distance to " CB  ARG A 190 " =    1.159
peak=    3.538 closest distance to " O   HOH Z   7 " =    0.988
peak=    3.537 closest distance to " CE1 HIS A 108 " =    1.147
peak=    3.532 closest distance to " CB  MET A 105 " =    1.085
peak=    3.520 closest distance to " CB  SER A   3 " =    1.504
peak=    3.518 closest distance to " O   HOH Z 192 " =    1.924
peak=    3.518 closest distance to " O   HOH Z 146 " =    1.547
peak=    3.516 closest distance to " O   HOH Z 374 " =    2.897
peak=    3.502 closest distance to " O   HOH Z  66 " =    2.187
peak=    3.499 closest distance to " O   HOH Z 109 " =    2.162
peak=    3.498 closest distance to " O   HOH Z 234 " =    1.952
peak=    3.496 closest distance to " CB  ASN A 148 " =    1.356
peak=    3.493 closest distance to " O   HOH Z 261 " =    1.994
peak=    3.493 closest distance to " CA  PRO A  54 " =    1.369
peak=    3.488 closest distance to " O   HOH Z  21 " =    1.798
peak=    3.477 closest distance to " O   HOH Z 139 " =    4.861
peak=    3.476 closest distance to " O   ALA A 158 " =    1.207
peak=    3.475 closest distance to " CA  ALA A 295 " =    1.048
peak=    3.466 closest distance to " O   HOH Z 386 " =    2.257
peak=    3.465 closest distance to " O   HOH Z 128 " =    2.102
peak=    3.460 closest distance to " O   HOH Z 421 " =    1.931
peak=    3.459 closest distance to " O   HOH Z 395 " =    1.471
peak=    3.457 closest distance to " O   HOH Z 336 " =    1.662
peak=    3.457 closest distance to " O   HOH Z 163 " =    1.637
peak=    3.456 closest distance to " CA  SER A  12 " =    1.606
peak=    3.456 closest distance to " CZ  PHE A  38 " =    1.281
peak=    3.454 closest distance to " CG1 VAL A 153 " =    1.066
peak=    3.454 closest distance to " CB  ALA A 100 " =    1.456
peak=    3.454 closest distance to " CB  GLU A  46 " =    1.023
peak=    3.452 closest distance to " NZ  LYS A 117 " =    1.714
peak=    3.451 closest distance to " NH2BARG A 145 " =    2.013
peak=    3.450 closest distance to " CA  ALA A 160 " =    1.002
peak=    3.449 closest distance to " O   HOH Z 189 " =    2.982
peak=    3.444 closest distance to " O   HOH Z 174 " =    2.163
peak=    3.437 closest distance to " CG1BVAL A  72 " =    1.813
peak=    3.434 closest distance to " O   HOH Z 327 " =    1.718
peak=    3.433 closest distance to " CA  GLY A 196 " =    0.977
peak=    3.429 closest distance to " O   GLY A  91 " =    1.163
peak=    3.425 closest distance to " O   HOH Z 316 " =    3.216
peak=    3.423 closest distance to " O   HOH Z 200 " =    1.543
peak=    3.419 closest distance to " O   HOH Z  68 " =    2.099
peak=    3.417 closest distance to " CB  ASN A 187 " =    1.152
peak=    3.415 closest distance to " O   HOH Z  47 " =    1.268
peak=    3.413 closest distance to " NZ  LYS A 166 " =    3.154
peak=    3.413 closest distance to " N   CYS A 260 " =    0.828
peak=    3.413 closest distance to " CA  ALA A  21 " =    1.261
peak=    3.412 closest distance to " O   HOH Z 250 " =    1.501
peak=    3.411 closest distance to " CZ3 TRP A 266 " =    1.044
peak=    3.411 closest distance to " CB  PHE A 283 " =    0.780
peak=    3.410 closest distance to " CG2 VAL A  78 " =    1.009
peak=    3.408 closest distance to " N   ILE A  33 " =    0.977
peak=    3.406 closest distance to " O   HOH Z 180 " =    2.282
peak=    3.402 closest distance to " O   HOH Z 294 " =    1.598
peak=    3.401 closest distance to " O   HOH Z 428 " =    1.085
peak=    3.386 closest distance to " CB  ASP A 140 " =    0.787
peak=    3.383 closest distance to " O   HOH Z 380 " =    1.821
peak=    3.383 closest distance to " CA  ASP A 162 " =    1.082
peak=    3.383 closest distance to " O   HOH Z 193 " =    1.737
peak=    3.381 closest distance to " CA  PRO A  90 " =    0.990
peak=    3.379 closest distance to " CE1 TYR A 186 " =    1.245
peak=    3.378 closest distance to " O   HOH Z 214 " =    2.439
peak=    3.374 closest distance to " O   HOH Z 227 " =    1.737
peak=    3.373 closest distance to " O   HOH Z 353 " =    2.769
peak=    3.373 closest distance to " CA  VAL A  41 " =    0.828
peak=    3.371 closest distance to " N   THR A  52 " =    1.096
peak=    3.371 closest distance to " O   HOH Z 173 " =    2.374
peak=    3.354 closest distance to " C   VAL A 265 " =    1.091
peak=    3.354 closest distance to " CG2 VAL A 126 " =    0.845
peak=    3.353 closest distance to " O   HOH Z  90 " =    3.454
peak=    3.352 closest distance to " OG  SER A 245 " =    1.601
peak=    3.350 closest distance to " O   HOH Z 434 " =    2.829
peak=    3.349 closest distance to " NE2 HIS A 115 " =    1.097
peak=    3.347 closest distance to " CA  GLU A 152 " =    0.916
peak=    3.344 closest distance to " CA  GLN A  88 " =    1.279
peak=    3.343 closest distance to " O   HOH Z 199 " =    1.636
peak=    3.337 closest distance to " O   HOH Z  49 " =    1.988
peak=    3.328 closest distance to " O   HOH Z 339 " =    1.330
peak=    3.328 closest distance to " O   HOH Z 245 " =    1.374
peak=    3.324 closest distance to " CB  MET A  40 " =    0.884
peak=    3.321 closest distance to " O   HOH Z 394 " =    4.064
peak=    3.320 closest distance to " N   GLY A  98 " =    1.146
peak=    3.319 closest distance to " O   HOH Z 118 " =    1.029
peak=    3.319 closest distance to " CA  LYS A 117 " =    1.295
peak=    3.316 closest distance to " CA  GLY A 241 " =    0.786
peak=    3.315 closest distance to " OE1 GLN A  58 " =    3.200
peak=    3.314 closest distance to " O   HOH Z 185 " =    1.764
peak=    3.310 closest distance to " N   SER A 164 " =    0.977
peak=    3.308 closest distance to " NH1AARG A 145 " =    1.128
peak=    3.302 closest distance to " CG2 THR A  29 " =    1.319
peak=    3.300 closest distance to " CG1 ILE A 120 " =    1.146
peak=    3.300 closest distance to " CA  THR A 221 " =    1.650
peak=    3.300 closest distance to " OE1 GLU A   2 " =    1.550
peak=    3.299 closest distance to " CB  ALA A 248 " =    1.241
peak=    3.292 closest distance to " O   HOH Z 418 " =    3.041
peak=    3.290 closest distance to " NE1 TRP A 274 " =    0.784
peak=    3.287 closest distance to " CB  ALA A 291 " =    1.220
peak=    3.287 closest distance to " O   HOH Z 298 " =    4.402
peak=    3.286 closest distance to " CB  ALA A  71 " =    1.274
peak=    3.283 closest distance to " O   HOH Z  22 " =    2.594
peak=    3.283 closest distance to " OH  TYR A 116 " =    1.289
peak=    3.283 closest distance to " O   HOH Z 313 " =    1.814
peak=    3.282 closest distance to " O   HOH Z 371 " =    2.986
peak=    3.279 closest distance to " CB  LEU A   5 " =    1.137
peak=    3.279 closest distance to " O   HOH Z 435 " =    2.888
peak=    3.275 closest distance to " CA  TYR A 116 " =    1.393
peak=    3.275 closest distance to " CA  ASN A 217 " =    1.351
peak=    3.275 closest distance to " CD  ARG A 195 " =    0.989
peak=    3.274 closest distance to " O   HOH Z 162 " =    1.851
peak=    3.273 closest distance to " CA  LEU A  83 " =    1.448
peak=    3.273 closest distance to " CG  MET A 185 " =    1.115
peak=    3.269 closest distance to " NH1 ARG A  14 " =    1.175
peak=    3.266 closest distance to " O   HOH Z 394 " =    1.725
peak=    3.264 closest distance to " CG  GLU A  37 " =    0.985
peak=    3.261 closest distance to " O   HOH Z   6 " =    1.152
peak=    3.259 closest distance to " O   HOH Z 261 " =    2.119
peak=    3.257 closest distance to " O   HOH Z 334 " =    1.512
peak=    3.254 closest distance to " O   HOH Z 255 " =    1.974
peak=    3.252 closest distance to " OH  TYR A  30 " =    1.317
peak=    3.251 closest distance to " O   HOH Z  78 " =    2.276
peak=    3.251 closest distance to " O   HOH Z 146 " =    1.255
peak=    3.243 closest distance to " ND2 ASN A 301 " =    1.124
peak=    3.242 closest distance to " CB  TYR A 116 " =    1.255
peak=    3.240 closest distance to " O   HOH Z 150 " =    1.847
peak=    3.238 closest distance to " CA  ALA A 158 " =    1.191
peak=    3.236 closest distance to " O   TYR A 116 " =    1.412
peak=    3.235 closest distance to " CA  ALA A 100 " =    1.244
peak=    3.233 closest distance to " CB  MET A  47 " =    0.951
peak=    3.231 closest distance to " CA  VAL A 125 " =    1.136
peak=    3.228 closest distance to " OG  SER A  62 " =    2.958
peak=    3.228 closest distance to " O   HOH Z  88 " =    3.446
peak=    3.226 closest distance to " CA  THR A 246 " =    1.051
peak=    3.226 closest distance to " O   HOH Z 377 " =    1.368
peak=    3.225 closest distance to " O   HOH Z 279 " =    2.148
peak=    3.223 closest distance to " OG1 THR A 294 " =    2.438
peak=    3.220 closest distance to " OD1 ASN A 301 " =    1.154
peak=    3.220 closest distance to " CA  LYS A 166 " =    1.483
peak=    3.219 closest distance to " CA  ASP A 124 " =    0.772
peak=    3.217 closest distance to " O   HOH Z 301 " =    1.569
peak=    3.210 closest distance to " O   HOH Z 420 " =    2.081
peak=    3.208 closest distance to " CB  VAL A 265 " =    1.304
peak=    3.206 closest distance to " OD2 ASP A 298 " =    3.827
peak=    3.205 closest distance to " CB  GLN A  89 " =    1.243
peak=    3.199 closest distance to " NZ  LYS A 117 " =    2.986
peak=    3.198 closest distance to " C   ILE A 106 " =    1.881
peak=    3.196 closest distance to " O   HOH Z 248 " =    1.783
peak=    3.194 closest distance to " CA  GLN A 223 " =    0.805
peak=    3.192 closest distance to " O   HOH Z  83 " =    1.718
peak=    3.192 closest distance to " CD1 LEU A  96 " =    0.749
peak=    3.192 closest distance to " O  BHOH Z  74 " =    1.418
peak=    3.190 closest distance to " O   HOH Z 141 " =    1.629
peak=    3.190 closest distance to " CB  PRO A  90 " =    1.193
peak=    3.189 closest distance to " O   HOH Z  54 " =    1.595
peak=    3.187 closest distance to " CG2 ILE A 120 " =    1.061
peak=    3.186 closest distance to " CA  MET A 105 " =    1.061
peak=    3.184 closest distance to " CG2 ILE A  20 " =    1.485
peak=    3.179 closest distance to " O   HOH Z 368 " =    4.529
peak=    3.177 closest distance to " O   HOH Z 128 " =    1.769
peak=    3.174 closest distance to " CB  ARG A 219 " =    1.614
peak=    3.173 closest distance to " O   HOH Z 387 " =    2.660
peak=    3.172 closest distance to " O   HOH Z 402 " =    2.754
peak=    3.171 closest distance to " O   HOH Z 299 " =    2.396
peak=    3.169 closest distance to " O   HOH Z 183 " =    1.572
peak=    3.167 closest distance to " CA  GLU A  46 " =    0.852
peak=    3.160 closest distance to " CB  ARG A 259 " =    1.926
peak=    3.160 closest distance to " N   GLU A  44 " =    2.284
peak=    3.157 closest distance to " O   HOH Z  48 " =    1.520
peak=    3.151 closest distance to " O   HOH Z 367 " =    1.954
peak=    3.151 closest distance to " O   HOH Z 358 " =    1.304
peak=    3.148 closest distance to " O   HOH Z 383 " =    2.113
peak=    3.142 closest distance to " CB  ARG A  79 " =    0.880
peak=    3.141 closest distance to " CB  GLU A 277 " =    0.742
peak=    3.137 closest distance to " CB  VAL A 257 " =    0.849
peak=    3.136 closest distance to " O   HOH Z 435 " =    1.693
peak=    3.133 closest distance to " O   HOH Z 313 " =    1.923
peak=    3.127 closest distance to " CB  ILE A 120 " =    1.432
peak=    3.125 closest distance to " O   HOH Z 426 " =    1.353
peak=    3.123 closest distance to " ND1 HIS A  81 " =    1.601
peak=    3.123 closest distance to " O   HOH Z   9 " =    2.303
peak=    3.121 closest distance to " CB  PRO A 243 " =    1.369
peak=    3.120 closest distance to " CA  ASN A 249 " =    1.410
peak=    3.114 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.110 closest distance to " CA  ALA A  84 " =    1.226
peak=    3.098 closest distance to " CB  SER A  97 " =    1.330
peak=    3.091 closest distance to " O   HOH Z 145 " =    2.757
peak=    3.091 closest distance to " CB  ALA A  43 " =    0.891
peak=    3.088 closest distance to " O   HOH Z 409 " =    3.156
peak=    3.085 closest distance to " O   HOH Z  88 " =    3.114
peak=    3.081 closest distance to " CB  GLN A 103 " =    0.943
peak=    3.075 closest distance to " O   HOH Z 344 " =    3.276
peak=    3.070 closest distance to " OG  SER A  28 " =    1.576
peak=    3.069 closest distance to " ND2 ASN A 249 " =    0.855
peak=    3.055 closest distance to " OG BSER A 134 " =    2.877
peak=    3.041 closest distance to " CB  SER A  62 " =    1.029
peak=    3.027 closest distance to " N   VAL A 126 " =    1.706

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 235         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 5.214
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 231 from: 235
   mapped sites are within: 0.708 - 5.214

peak=   -4.713 closest distance to " O   HOH Z 266 " =    5.214
peak=   -4.564 closest distance to " CD  GLN A  58 " =    1.013
peak=   -4.395 closest distance to " CD  GLN A 223 " =    1.422
peak=   -4.212 closest distance to " O   HOH Z   5 " =    1.586
peak=   -4.128 closest distance to " CD1 PHE A  59 " =    1.972
peak=   -4.120 closest distance to " O   HOH Z 166 " =    1.822
peak=   -4.092 closest distance to " ND2 ASN A  45 " =    1.873
peak=   -4.091 closest distance to " CD  GLN A  88 " =    0.978
peak=   -4.067 closest distance to " OXT GLY A 302 " =    3.027
peak=   -4.063 closest distance to " O   HOH Z 290 " =    1.029
peak=   -4.057 closest distance to " O   HOH Z 150 " =    0.931
peak=   -4.049 closest distance to " O   HOH Z 377 " =    0.963
peak=   -4.041 closest distance to " CG1 VAL A 112 " =    2.641
peak=   -3.955 closest distance to " CB  PRO A 243 " =    2.731
peak=   -3.942 closest distance to " O   HOH Z  15 " =    1.473
peak=   -3.941 closest distance to " O   PRO A 198 " =    1.378
peak=   -3.918 closest distance to " CH2 TRP A 179 " =    1.200
peak=   -3.917 closest distance to " CD2 LEU A 237 " =    2.687
peak=   -3.916 closest distance to " CG  ARG A 269 " =    2.323
peak=   -3.902 closest distance to " CD  ARG A 156 " =    2.110
peak=   -3.858 closest distance to " OG  SER A  97 " =    2.299
peak=   -3.853 closest distance to " CE2 TYR A  30 " =    2.744
peak=   -3.838 closest distance to " CG2 ILE A  20 " =    3.050
peak=   -3.827 closest distance to " O   HOH Z 348 " =    2.436
peak=   -3.822 closest distance to " O   VAL A  67 " =    2.668
peak=   -3.819 closest distance to " O   HOH Z  13 " =    1.862
peak=   -3.808 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.789 closest distance to " O   HOH Z 308 " =    1.536
peak=   -3.780 closest distance to " CD1 LEU A 101 " =    2.485
peak=   -3.772 closest distance to " CB  ALA A 291 " =    2.452
peak=   -3.771 closest distance to " O   HOH Z   6 " =    1.435
peak=   -3.745 closest distance to " CD1 LEU A 167 " =    2.055
peak=   -3.742 closest distance to " O   HOH Z  58 " =    1.188
peak=   -3.735 closest distance to " C   ASN A 285 " =    2.413
peak=   -3.727 closest distance to " C   SER A 206 " =    1.402
peak=   -3.725 closest distance to " O   HOH Z 252 " =    4.038
peak=   -3.724 closest distance to " O   HOH Z  49 " =    1.009
peak=   -3.720 closest distance to " C   HIS A 108 " =    1.106
peak=   -3.699 closest distance to " NE2 GLN A 223 " =    1.087
peak=   -3.692 closest distance to " CD  ARG A  14 " =    3.361
peak=   -3.676 closest distance to " O   HOH Z 351 " =    1.545
peak=   -3.674 closest distance to " O   HOH Z 407 " =    0.889
peak=   -3.672 closest distance to " O   PRO A 163 " =    2.165
peak=   -3.651 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.648 closest distance to " CA  GLY A  98 " =    2.227
peak=   -3.646 closest distance to " O   HOH Z 283 " =    2.046
peak=   -3.644 closest distance to " OE1 GLN A 223 " =    2.367
peak=   -3.635 closest distance to " C   THR A 279 " =    1.087
peak=   -3.632 closest distance to " NE2 GLN A 103 " =    1.783
peak=   -3.631 closest distance to " NH2 ARG A  79 " =    2.057
peak=   -3.627 closest distance to " O   ILE A 109 " =    2.636
peak=   -3.586 closest distance to " O   HOH Z   7 " =    1.366
peak=   -3.582 closest distance to " CG2 ILE A  49 " =    2.731
peak=   -3.571 closest distance to " CB  ALA A  10 " =    2.076
peak=   -3.567 closest distance to " O   HOH Z 109 " =    3.571
peak=   -3.567 closest distance to " O   ALA A  10 " =    1.811
peak=   -3.562 closest distance to " O   ALA A  34 " =    2.056
peak=   -3.561 closest distance to " O   HOH Z 234 " =    4.321
peak=   -3.560 closest distance to " C   ALA A 158 " =    1.406
peak=   -3.555 closest distance to " O   HOH Z 197 " =    1.961
peak=   -3.554 closest distance to " CD1 PHE A 130 " =    2.367
peak=   -3.550 closest distance to " O   HOH Z 418 " =    1.284
peak=   -3.544 closest distance to " CB  ALA A 291 " =    2.438
peak=   -3.537 closest distance to " OG BSER A 210 " =    1.327
peak=   -3.524 closest distance to " CZ  TYR A 169 " =    1.831
peak=   -3.510 closest distance to " ND2 ASN A  45 " =    1.125
peak=   -3.507 closest distance to " O   HOH Z 394 " =    1.542
peak=   -3.507 closest distance to " O   TRP A  92 " =    1.993
peak=   -3.505 closest distance to " O   HOH Z 185 " =    2.562
peak=   -3.505 closest distance to " CB  ALA A 131 " =    2.383
peak=   -3.495 closest distance to " CE2 PHE A  61 " =    2.569
peak=   -3.491 closest distance to " O   HOH Z 133 " =    1.575
peak=   -3.489 closest distance to " CD1 TRP A 179 " =    0.965
peak=   -3.485 closest distance to " OE1 GLN A  88 " =    0.727
peak=   -3.484 closest distance to " O   HOH Z 109 " =    3.328
peak=   -3.484 closest distance to " O   HOH Z 422 " =    1.279
peak=   -3.476 closest distance to " O   ALA A   1 " =    2.020
peak=   -3.473 closest distance to " N   GLN A  58 " =    1.451
peak=   -3.470 closest distance to " CD  PRO A 213 " =    2.199
peak=   -3.469 closest distance to " OD1 ASP A 191 " =    1.586
peak=   -3.463 closest distance to " CD2 LEU A 300 " =    2.895
peak=   -3.449 closest distance to " O   SER A 276 " =    1.779
peak=   -3.447 closest distance to " CG2 ILE A 263 " =    2.241
peak=   -3.443 closest distance to " O   HOH Z 331 " =    1.152
peak=   -3.432 closest distance to " CD2 PHE A  61 " =    2.155
peak=   -3.429 closest distance to " O   SER A 210 " =    1.886
peak=   -3.425 closest distance to " CB  SER A 210 " =    1.117
peak=   -3.425 closest distance to " O   HOH Z 136 " =    2.219
peak=   -3.419 closest distance to " CE BMET A  47 " =    1.790
peak=   -3.415 closest distance to " CA  VAL A 197 " =    0.982
peak=   -3.414 closest distance to " NH2 ARG A  79 " =    1.754
peak=   -3.412 closest distance to " O   HOH Z 149 " =    1.838
peak=   -3.410 closest distance to " CD2 HIS A 115 " =    1.046
peak=   -3.410 closest distance to " CG  GLU A  53 " =    1.428
peak=   -3.408 closest distance to " CD  ARG A 139 " =    1.064
peak=   -3.403 closest distance to " NE2 GLN A 194 " =    2.036
peak=   -3.401 closest distance to " O   HOH Z  71 " =    1.708
peak=   -3.400 closest distance to " O   HOH Z 392 " =    1.222
peak=   -3.397 closest distance to " O   HOH Z 200 " =    1.213
peak=   -3.393 closest distance to " O   HOH Z 421 " =    3.923
peak=   -3.391 closest distance to " OG BSER A 210 " =    2.389
peak=   -3.387 closest distance to " O   HOH Z 388 " =    1.927
peak=   -3.384 closest distance to " O   VAL A 189 " =    2.562
peak=   -3.376 closest distance to " C   GLN A  11 " =    1.251
peak=   -3.376 closest distance to " O   HOH Z  52 " =    1.724
peak=   -3.375 closest distance to " O   HOH Z 422 " =    1.429
peak=   -3.370 closest distance to " CD2 TYR A 293 " =    1.825
peak=   -3.369 closest distance to " NH2 ARG A 159 " =    2.371
peak=   -3.365 closest distance to " O   ASP A 171 " =    0.966
peak=   -3.357 closest distance to " CA  GLY A 241 " =    2.382
peak=   -3.356 closest distance to " CB  TRP A  85 " =    2.502
peak=   -3.355 closest distance to " O   HOH Z 366 " =    1.942
peak=   -3.355 closest distance to " CG  PRO A 243 " =    1.638
peak=   -3.353 closest distance to " CG2AVAL A  41 " =    2.866
peak=   -3.352 closest distance to " CG  ASP A 132 " =    2.401
peak=   -3.352 closest distance to " CG1 VAL A 197 " =    2.310
peak=   -3.351 closest distance to " O   HOH Z 313 " =    1.427
peak=   -3.350 closest distance to " CG2 VAL A 189 " =    2.209
peak=   -3.339 closest distance to " CD1 LEU A  25 " =    2.541
peak=   -3.336 closest distance to " CH2 TRP A 150 " =    1.154
peak=   -3.335 closest distance to " CD  GLN A  73 " =    0.758
peak=   -3.333 closest distance to " O   HOH Z 114 " =    3.851
peak=   -3.332 closest distance to " CB  PHE A 192 " =    1.963
peak=   -3.332 closest distance to " O   HOH Z 377 " =    2.087
peak=   -3.332 closest distance to " O   HOH Z  37 " =    1.906
peak=   -3.329 closest distance to " CZ  PHE A 155 " =    1.297
peak=   -3.328 closest distance to " O   SER A 271 " =    2.099
peak=   -3.325 closest distance to " CD  ARG A 139 " =    1.449
peak=   -3.322 closest distance to " O   HOH Z 275 " =    1.536
peak=   -3.317 closest distance to " O   HOH Z 146 " =    1.513
peak=   -3.316 closest distance to " NH2 ARG A  66 " =    1.658
peak=   -3.310 closest distance to " O   HOH Z 198 " =    1.328
peak=   -3.309 closest distance to " CB  ALA A 248 " =    2.443
peak=   -3.301 closest distance to " O   HOH Z 403 " =    1.024
peak=   -3.301 closest distance to " N   ALA A  43 " =    2.745
peak=   -3.300 closest distance to " SD  MET A 105 " =    2.463
peak=   -3.298 closest distance to " CB  ASP A 162 " =    2.519
peak=   -3.298 closest distance to " O   HOH Z 298 " =    2.855
peak=   -3.297 closest distance to " O   GLY A 118 " =    2.303
peak=   -3.295 closest distance to " O   HOH Z  78 " =    1.764
peak=   -3.295 closest distance to " O   VAL A 174 " =    2.102
peak=   -3.294 closest distance to " O   HOH Z 236 " =    1.817
peak=   -3.293 closest distance to " OH  TYR A 247 " =    2.269
peak=   -3.293 closest distance to " CG  LEU A  83 " =    2.094
peak=   -3.288 closest distance to " O   HOH Z 171 " =    2.305
peak=   -3.286 closest distance to " OG1 THR A  82 " =    1.281
peak=   -3.282 closest distance to " CG  MET A 105 " =    0.821
peak=   -3.281 closest distance to " OD2 ASP A 171 " =    1.929
peak=   -3.278 closest distance to " CB  PHE A  16 " =    2.523
peak=   -3.278 closest distance to " CA  SER A 276 " =    1.490
peak=   -3.277 closest distance to " O   PHE A 218 " =    1.413
peak=   -3.275 closest distance to " O   HOH Z 126 " =    1.885
peak=   -3.272 closest distance to " O   HOH Z 301 " =    2.453
peak=   -3.259 closest distance to " O   HOH Z 118 " =    1.388
peak=   -3.249 closest distance to " NH2 ARG A  66 " =    3.994
peak=   -3.249 closest distance to " O   HOH Z 210 " =    1.279
peak=   -3.248 closest distance to " O   HOH Z 193 " =    2.409
peak=   -3.247 closest distance to " OG  SER A  63 " =    1.010
peak=   -3.247 closest distance to " NH2BARG A 145 " =    2.533
peak=   -3.244 closest distance to " O   HOH Z 196 " =    2.116
peak=   -3.244 closest distance to " O   HOH Z 117 " =    4.613
peak=   -3.243 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.240 closest distance to " CA  GLY A 203 " =    2.354
peak=   -3.239 closest distance to " N   ALA A 226 " =    2.116
peak=   -3.239 closest distance to " CA  GLY A 241 " =    3.244
peak=   -3.237 closest distance to " CD1 ILE A 263 " =    2.036
peak=   -3.232 closest distance to " O   HOH Z 396 " =    2.097
peak=   -3.231 closest distance to " OE2 GLU A 277 " =    2.830
peak=   -3.227 closest distance to " O   HOH Z 165 " =    1.905
peak=   -3.224 closest distance to " O   HOH Z 128 " =    4.308
peak=   -3.224 closest distance to " O   HOH Z 109 " =    1.305
peak=   -3.223 closest distance to " O   HOH Z  19 " =    2.321
peak=   -3.216 closest distance to " CG  PHE A 225 " =    1.322
peak=   -3.205 closest distance to " CA  GLY A 133 " =    2.387
peak=   -3.204 closest distance to " ND2 ASN A 301 " =    2.032
peak=   -3.203 closest distance to " CD1 ILE A 151 " =    2.334
peak=   -3.202 closest distance to " CB  CYS A 254 " =    2.522
peak=   -3.201 closest distance to " ND2 ASN A  69 " =    1.444
peak=   -3.193 closest distance to " O   HOH Z  56 " =    1.452
peak=   -3.191 closest distance to " O   HOH Z 292 " =    4.729
peak=   -3.190 closest distance to " ND2 ASN A  60 " =    1.443
peak=   -3.190 closest distance to " O   SER A  26 " =    1.571
peak=   -3.189 closest distance to " O   HOH Z   7 " =    1.715
peak=   -3.188 closest distance to " CA  TRP A 274 " =    1.387
peak=   -3.186 closest distance to " O   GLY A  75 " =    2.019
peak=   -3.185 closest distance to " OD2 ASP A  50 " =    2.195
peak=   -3.183 closest distance to " O   ALA A  34 " =    2.484
peak=   -3.181 closest distance to " O   HOH Z 157 " =    3.693
peak=   -3.174 closest distance to " O   HOH Z  60 " =    1.732
peak=   -3.172 closest distance to " O   HOH Z  48 " =    0.994
peak=   -3.172 closest distance to " CG2 THR A 221 " =    2.300
peak=   -3.171 closest distance to " CE  MET A 105 " =    2.332
peak=   -3.170 closest distance to " O   HOH Z  88 " =    2.536
peak=   -3.170 closest distance to " ND2 ASN A  60 " =    1.855
peak=   -3.163 closest distance to " O   HOH Z 111 " =    1.540
peak=   -3.160 closest distance to " CB  ALA A  43 " =    2.606
peak=   -3.160 closest distance to " CG1 VAL A  78 " =    2.719
peak=   -3.156 closest distance to " O   THR A  18 " =    1.470
peak=   -3.153 closest distance to " CE  MET A  93 " =    1.284
peak=   -3.152 closest distance to " CD1 ILE A 106 " =    2.151
peak=   -3.152 closest distance to " N   ARG A 138 " =    1.877
peak=   -3.151 closest distance to " O   HOH Z 409 " =    4.977
peak=   -3.150 closest distance to " CD2 PHE A  59 " =    2.468
peak=   -3.147 closest distance to " CG2BVAL A  41 " =    1.333
peak=   -3.145 closest distance to " O   HOH Z 318 " =    1.499
peak=   -3.140 closest distance to " ND2 ASN A 249 " =    2.233
peak=   -3.133 closest distance to " O   HOH Z 134 " =    2.117
peak=   -3.130 closest distance to " CZ  ARG A 259 " =    0.708
peak=   -3.125 closest distance to " O   HOH Z 222 " =    1.178
peak=   -3.119 closest distance to " O   HOH Z 183 " =    1.877
peak=   -3.119 closest distance to " NE2 GLN A  58 " =    2.749
peak=   -3.118 closest distance to " O   HOH Z 423 " =    2.187
peak=   -3.118 closest distance to " O  BHOH Z 338 " =    1.235
peak=   -3.116 closest distance to " O   HOH Z 264 " =    1.876
peak=   -3.115 closest distance to " N   ALA A 242 " =    1.893
peak=   -3.112 closest distance to " SG BCYS A 201 " =    0.923
peak=   -3.107 closest distance to " O   HOH Z 372 " =    2.598
peak=   -3.103 closest distance to " CE  MET A 105 " =    2.104
peak=   -3.096 closest distance to " O   HOH Z 128 " =    2.431
peak=   -3.094 closest distance to " CE3 TRP A 274 " =    2.466
peak=   -3.087 closest distance to " N   SER A   3 " =    2.332
peak=   -3.081 closest distance to " O   GLN A 240 " =    2.614
peak=   -3.074 closest distance to " C   ARG A  79 " =    2.669
peak=   -3.073 closest distance to " O   HOH Z 323 " =    1.448
peak=   -3.069 closest distance to " O   HOH Z 424 " =    3.011
peak=   -3.068 closest distance to " CD  ARG A 195 " =    5.066
peak=   -3.067 closest distance to " CG  ASP A  65 " =    1.300
peak=   -3.064 closest distance to " O   HOH Z  91 " =    2.267
peak=   -3.061 closest distance to " CB  ARG A 219 " =    2.333
peak=   -3.060 closest distance to " OG  SER A  87 " =    1.720
peak=   -3.053 closest distance to " O   HOH Z 259 " =    1.935

================= 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    :  0.4166 0.3983   6.236638e+00   6.194308e+00
   1_bss:  0.4033 0.3837   6.222202e+00   6.177385e+00
   1_xyz:  0.3410 0.3636   6.093512e+00   6.128660e+00
   1_adp:  0.3156 0.3728   6.045664e+00   6.138254e+00
   1_occ:  0.3153 0.3724   6.044926e+00   6.138039e+00
   2_bss:  0.3143 0.3708   6.046637e+00   6.139919e+00
   2_xyz:  0.2496 0.2972   5.828996e+00   5.963868e+00
   2_adp:  0.2283 0.2866   5.775091e+00   5.938012e+00
   2_occ:  0.2281 0.2865   5.774508e+00   5.937970e+00
   3_bss:  0.2274 0.2844   5.773037e+00   5.935997e+00
   3_xyz:  0.1687 0.2171   5.495013e+00   5.697464e+00
   3_adp:  0.1555 0.2026   5.423275e+00   5.633134e+00
   3_occ:  0.1552 0.2023   5.422093e+00   5.632100e+00
   4_bss:  0.1553 0.2018   5.422099e+00   5.630511e+00
   4_xyz:  0.1428 0.1909   5.358777e+00   5.574239e+00
   4_adp:  0.1321 0.1832   5.295051e+00   5.524515e+00
   4_occ:  0.1320 0.1832   5.294480e+00   5.524197e+00
   5_bss:  0.1320 0.1832   5.293987e+00   5.524157e+00
   5_xyz:  0.1224 0.1724   5.231304e+00   5.474218e+00
   5_adp:  0.1227 0.1671   5.219178e+00   5.446150e+00
   5_occ:  0.1226 0.1672   5.218725e+00   5.446185e+00
   5_bss:  0.1227 0.1670   5.218416e+00   5.444567e+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:  0.297  41.109  -3.418   5.953  -1.427   0.000  -0.000  -0.000
   1_xyz:  0.297  41.109  -3.418   5.953  -1.427   0.000  -0.000  -0.000
   1_adp:  0.297  41.109  -3.418   5.953  -1.427   0.000  -0.000  -0.000
   1_occ:  0.297  41.109  -3.418   5.953  -1.427   0.000  -0.000  -0.000
   2_bss:  0.287  54.177  -1.805   3.525  -0.364   0.000  -0.000  -0.000
   2_xyz:  0.287  54.177  -1.805   3.525  -0.364   0.000  -0.000  -0.000
   2_adp:  0.287  54.177  -1.805   3.525  -0.364   0.000  -0.000  -0.000
   2_occ:  0.287  54.177  -1.805   3.525  -0.364   0.000  -0.000  -0.000
   3_bss:  0.318  70.251  -1.056   1.760   0.150   0.000   0.000   0.000
   3_xyz:  0.318  70.251  -1.056   1.760   0.150   0.000   0.000   0.000
   3_adp:  0.318  70.251  -1.056   1.760   0.150   0.000   0.000   0.000
   3_occ:  0.318  70.251  -1.056   1.760   0.150   0.000   0.000   0.000
   4_bss:  0.327  69.356  -1.141   0.574   0.106   0.000   0.000   0.000
   4_xyz:  0.327  69.356  -1.141   0.574   0.106   0.000   0.000   0.000
   4_adp:  0.327  69.356  -1.141   0.574   0.106   0.000   0.000   0.000
   4_occ:  0.327  69.356  -1.141   0.574   0.106   0.000   0.000   0.000
   5_bss:  0.329  74.920  -1.174   0.117   0.162   0.000   0.000   0.000
   5_xyz:  0.329  74.920  -1.174   0.117   0.162   0.000   0.000   0.000
   5_adp:  0.329  74.920  -1.174   0.117   0.162   0.000   0.000   0.000
   5_occ:  0.329  74.920  -1.174   0.117   0.162   0.000   0.000   0.000
   5_bss:  0.324  68.819  -1.189  -0.121   0.224  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.696 0.5889  0.7457    49795.337
   1_bss:  44.003 0.5959  0.7613    46633.816
   1_xyz:  41.280 0.6276  0.7940    39880.531
   1_adp:  41.635 0.6232  0.7783    40633.953
   1_occ:  41.659 0.6228  0.7768    40597.423
   2_bss:  41.346 0.6268  0.7883    40472.213
   2_xyz:  31.668 0.7383  0.9099    23965.404
   2_adp:  30.253 0.7544  0.9022    22262.875
   2_occ:  30.241 0.7545  0.9020    22243.299
   3_bss:  30.015 0.7571  0.9023    22035.438
   3_xyz:  21.732 0.8438  0.9720    12163.550
   3_adp:  19.783 0.8635  0.9786    10650.629
   3_occ:  19.758 0.8637  0.9788    10638.344
   4_bss:  19.672 0.8646  0.9656    10569.964
   4_xyz:  18.074 0.8801  0.9708     9304.998
   4_adp:  16.984 0.8898  0.9633     8424.813
   4_occ:  16.969 0.8899  0.9632     8415.339
   5_bss:  16.958 0.8900  0.9588     8412.672
   5_xyz:  15.870 0.8994  0.9645     7559.007
   5_adp:  15.236 0.9050  0.9608     7217.430
   5_occ:  15.237 0.9051  0.9608     7217.323
   5_bss:  15.228 0.9050  0.9574     7179.132
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6588e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6588e-01
   1_xyz:   1.332  0.010  0.082 15.541  0.005  4.113   9.8044e-02
   1_adp:   1.332  0.010  0.082 15.541  0.005  4.113   9.8044e-02
   1_occ:   1.332  0.010  0.082 15.541  0.005  4.113   9.8044e-02
   2_bss:   1.332  0.010  0.082 15.541  0.005  4.113   9.8044e-02
   2_xyz:   1.450  0.011  0.092 15.268  0.006  4.115   1.1326e-01
   2_adp:   1.450  0.011  0.092 15.268  0.006  4.115   1.1326e-01
   2_occ:   1.450  0.011  0.092 15.268  0.006  4.115   1.1326e-01
   3_bss:   1.450  0.011  0.092 15.268  0.006  4.115   1.1326e-01
   3_xyz:   1.234  0.012  0.087 15.084  0.005  4.135   9.1481e-02
   3_adp:   1.234  0.012  0.087 15.084  0.005  4.135   9.1481e-02
   3_occ:   1.234  0.012  0.087 15.084  0.005  4.135   9.1481e-02
   4_bss:   1.234  0.012  0.087 15.084  0.005  4.135   9.1481e-02
   4_xyz:   1.024  0.008  0.074 14.541  0.004  4.124   6.2530e-02
   4_adp:   1.024  0.008  0.074 14.541  0.004  4.124   6.2530e-02
   4_occ:   1.024  0.008  0.074 14.541  0.004  4.124   6.2530e-02
   5_bss:   1.024  0.008  0.074 14.541  0.004  4.124   6.2530e-02
   5_xyz:   1.081  0.009  0.079 14.649  0.004  4.130   6.9068e-02
   5_adp:   1.081  0.009  0.079 14.649  0.004  4.130   6.9068e-02
   5_occ:   1.081  0.009  0.079 14.649  0.004  4.130   6.9068e-02
   5_bss:   1.081  0.009  0.079 14.649  0.004  4.130   6.9068e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.718   2.4421e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.718   2.4421e-01
   1_xyz:   8.647  0.066  0.411 85.639  0.036  2.157   1.4785e-01
   1_adp:   8.647  0.066  0.411 85.639  0.036  2.157   1.4785e-01
   1_occ:   8.647  0.066  0.411 85.639  0.036  2.157   1.4785e-01
   2_bss:   8.647  0.066  0.411 85.639  0.036  2.157   1.4785e-01
   2_xyz:   8.604  0.070  0.319 89.059  0.059  2.220   1.9102e-01
   2_adp:   8.604  0.070  0.319 89.059  0.059  2.220   1.9102e-01
   2_occ:   8.604  0.070  0.319 89.059  0.059  2.220   1.9102e-01
   3_bss:   8.604  0.070  0.319 89.059  0.059  2.220   1.9102e-01
   3_xyz:   8.105  0.070  0.265 89.633  0.037  2.063   8.9526e-02
   3_adp:   8.105  0.070  0.265 89.633  0.037  2.063   8.9526e-02
   3_occ:   8.105  0.070  0.265 89.633  0.037  2.063   8.9526e-02
   4_bss:   8.105  0.070  0.265 89.633  0.037  2.063   8.9526e-02
   4_xyz:   7.336  0.054  0.246 81.119  0.039  2.347   7.7087e-02
   4_adp:   7.336  0.054  0.246 81.119  0.039  2.347   7.7087e-02
   4_occ:   7.336  0.054  0.246 81.119  0.039  2.347   7.7087e-02
   5_bss:   7.336  0.054  0.246 81.119  0.039  2.347   7.7087e-02
   5_xyz:   8.163  0.050  0.251 80.789  0.044  2.319   7.1314e-02
   5_adp:   8.163  0.050  0.251 80.789  0.044  2.319   7.1314e-02
   5_occ:   8.163  0.050  0.251 80.789  0.044  2.319   7.1314e-02
   5_bss:   8.163  0.050  0.251 80.789  0.044  2.319   7.1314e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  84.48   0.00  17.52  74.12   0.00  14.37  84.48   2.23  34.71
   1_occ:  84.48   0.00  17.52  74.12   0.00  14.37  84.48   2.23  34.71
   2_bss:  84.48   0.00  17.52  74.12   0.00  14.37  84.48   2.23  34.71
   2_xyz:  84.48   0.00  17.52  74.12   0.00  14.37  84.48   2.23  34.71
   2_adp:  96.66   0.00  17.88  96.66   0.00  13.85  90.58   0.46  39.87
   2_occ:  96.66   0.00  17.88  96.66   0.00  13.85  90.58   0.46  39.87
   3_bss:  96.66   0.00  17.88  96.66   0.00  13.85  90.58   0.46  39.87
   3_xyz:  96.66   0.00  17.88  96.66   0.00  13.85  90.58   0.46  39.87
   3_adp:  96.63   0.00  17.47  96.63   0.00  13.26  90.57   3.56  40.37
   3_occ:  96.63   0.00  17.47  96.63   0.00  13.26  90.57   3.56  40.37
   4_bss:  96.63   0.00  17.47  96.63   0.00  13.26  90.57   3.56  40.37
   4_xyz:  96.63   0.00  17.47  96.63   0.00  13.26  90.57   3.56  40.37
   4_adp: 113.46   0.00  17.21 113.46   0.00  12.36 105.89   0.00  43.66
   4_occ: 113.46   0.00  17.21 113.46   0.00  12.36 105.89   0.00  43.66
   5_bss: 113.46   0.00  17.21 113.46   0.00  12.36 105.89   0.00  43.66
   5_xyz: 113.46   0.00  17.21 113.46   0.00  12.36 105.89   0.00  43.66
   5_adp: 104.09   0.85  16.09 104.09   0.85  11.71  98.86   2.47  39.95
   5_occ: 104.09   0.85  16.09 104.09   0.85  11.71  98.86   2.47  39.95
   5_bss: 104.06   0.82  16.06 104.06   0.82  11.68  98.83   2.45  39.92
------------------------------------------------------------------------
 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:    1.551    0.014    0.274
   1_adp:    1.551    0.014    0.274
   1_occ:    1.551    0.014    0.274
   2_bss:    1.551    0.014    0.274
   2_xyz:    1.535    0.029    0.524
   2_adp:    1.535    0.029    0.524
   2_occ:    1.535    0.029    0.524
   3_bss:    1.535    0.029    0.524
   3_xyz:    1.567    0.082    0.689
   3_adp:    1.567    0.082    0.689
   3_occ:    1.567    0.082    0.689
   4_bss:    1.567    0.082    0.689
   4_xyz:    1.523    0.100    0.724
   4_adp:    1.523    0.100    0.724
   4_occ:    1.523    0.100    0.724
   5_bss:    1.523    0.100    0.724
   5_xyz:    1.545    0.118    0.752
   5_adp:    1.545    0.118    0.752
   5_occ:    1.545    0.118    0.752
   5_bss:    1.545    0.118    0.752
------------------------------------------------------------------------

CPU time actual refinement: 323.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_842/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/noshake/run_842/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_842/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_842/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_842/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.76 
  Macro-tasks:
    bulk solvent and scale       = 37.93  
    individual site refinement   = 129.46 
    weights calculation          = 29.42  
    collect and process          = 6.58   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 203.49 
  Micro-tasks:
    mask                            = 2.33   
    f_calc                          = 103.26 
    alpha_beta                      = 8.43   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 111.05 
    fmodel                         = 6.34   
    r_factors                      = 0.13   
    phase_errors                   = 10.82  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 243.80 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.673 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    635 calls, 102.93 s
gradients_fft:          580 calls,  98.53 s

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

# Date 2008-01-16 Time 05:47:28 PST -0800 (1200491248.98 s)
Start R-work = 0.4166, R-free = 0.3983 (no bulk solvent and anisotropic scale)
Final R-work = 0.1389, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.4033, R-free = 0.3837
Final R-work = 0.1227, R-free = 0.1670