# Date 2008-01-16 Time 04:32:16 PST -0800 (1200486736.26 s)
#phil __OFF__

Command line arguments: "../356.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4194
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 356

-------------------------------------------------------------------------------
  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: (69.1963, 48.1033, 85.9581, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.97069
Completeness in resolution range: 0.940468
Completeness with d_max=infinity: 0.937632

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0230
                             d_min =   1.9707

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: (69.1963, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.97069
Completeness in resolution range: 0.940468
Completeness with d_max=infinity: 0.937632

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0234 -  4.2174 [2196/2225]  1973   223  10.2%
  bin  2:  4.2174 -  3.3598 [2094/2117]  1886   208   9.9%
  bin  3:  3.3598 -  2.9387 [2067/2092]  1861   206  10.0%
  bin  4:  2.9387 -  2.6716 [2041/2058]  1839   202   9.9%
  bin  5:  2.6716 -  2.4810 [2044/2087]  1834   210  10.3%
  bin  6:  2.4810 -  2.3353 [2039/2067]  1847   192   9.4%
  bin  7:  2.3353 -  2.2188 [2013/2049]  1804   209  10.4%
  bin  8:  2.2188 -  2.1225 [2015/2057]  1820   195   9.7%
  bin  9:  2.1225 -  2.0410 [1984/2041]  1784   200  10.1%
  bin 10:  2.0410 -  1.9707 [1096/2036]   982   114  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_356/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:
        1.49 -     2.17: 18
        2.17 -     2.85: 1117
        2.85 -     3.54: 4438
        3.54 -     4.22: 9220
        4.22 -     4.90: 13488
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.489 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.653 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.673 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.701 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28276 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_356/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_356/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 69.19625 48.10325 85.95805 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: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4456   r_free= 0.4322   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.263188                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.7041 0.99   1420  159 0.3654 0.4042      6.5537      6.6088|
|  2:  4.7041 -  3.7529 0.99   1365  151 0.3924 0.3883      6.8117      6.7957|
|  3:  3.7529 -  3.2842 0.99   1353  149 0.4158 0.3853      6.6511      6.6477|
|  4:  3.2842 -  2.9865 0.99   1314  143 0.4288 0.3771       6.488      6.3658|
|  5:  2.9865 -  2.7739 0.99   1329  150 0.4791 0.4322      6.3493      6.3499|
|  6:  2.7739 -  2.6112 0.99   1317  145 0.4759 0.4431       6.266      6.0985|
|  7:  2.6112 -  2.4810 0.98   1295  152 0.4825 0.4216      6.2308      6.1282|
|  8:  2.4810 -  2.3735 0.98   1334  138 0.4773 0.4966      6.1541      6.2115|
|  9:  2.3735 -  2.2824 0.99   1287  143 0.5057 0.4731       6.111      6.1009|
| 10:  2.2824 -  2.2039 0.98   1305  144 0.4794 0.4944      6.0829      6.0958|
| 11:  2.2039 -  2.1352 0.97   1289  146 0.4883 0.4948      6.0112      6.0157|
| 12:  2.1352 -  2.0743 0.98   1283  148 0.4848 0.4616      5.9312      5.9544|
| 13:  2.0743 -  2.0199 0.92   1216  133 0.4758 0.4784      5.8452      5.8202|
| 14:  2.0199 -  1.9707 0.40    523   58 0.4855 0.5193      5.8386      5.6935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0234 -  4.7041  1420   159  0.66  37.36   0.83     0.69      81234.58|
|  2:  4.7041 -  3.7529  1365   151  0.71  33.95   0.91     0.80      98864.96|
|  3:  3.7529 -  3.2842  1353   149  0.65  39.60   0.92     0.84      96543.37|
|  4:  3.2842 -  2.9865  1314   143  0.62  42.42   0.92     0.81      76081.36|
|  5:  2.9865 -  2.7739  1329   150  0.54  48.51   0.89     0.75      62014.02|
|  6:  2.7739 -  2.6112  1317   145  0.53  49.47   0.91     0.70      52796.68|
|  7:  2.6112 -  2.4810  1295   152  0.50  51.73   0.91     0.68      51347.81|
|  8:  2.4810 -  2.3735  1334   138  0.47  54.36   0.91     0.65      48963.88|
|  9:  2.3735 -  2.2824  1287   143  0.45  56.08   0.93     0.66      46684.62|
| 10:  2.2824 -  2.2039  1305   144  0.46  55.49   0.95     0.65      41723.10|
| 11:  2.2039 -  2.1352  1289   146  0.47  54.91   0.95     0.70      38295.72|
| 12:  2.1352 -  2.0743  1283   148  0.45  56.42   0.96     0.68      35672.16|
| 13:  2.0743 -  2.0199  1216   133  0.42  58.69   0.97     0.63      32084.29|
| 14:  2.0199 -  1.9707   523    58  0.36  63.09   0.97     0.49      28372.85|
|alpha:            min =        0.49 max =            0.84 mean =         0.70|
|beta:             min =    28372.85 max =        98864.96 mean =     58319.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           90.00 mean =        49.35|
|phase err.(test): min =        0.00 max =           89.91 mean =        49.23|
|-----------------------------------------------------------------------------|

============================== 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 = 6.845814              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.658   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.476694              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.342   (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 |  1.489 -  1.830:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.830 -  2.171:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.171 -  2.512:       24 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.512 -  2.854:     1093 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.854 -  3.195:     1961 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.195 -  3.536:     2477 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.536 -  3.877:     4648 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.877 -  4.218:     4572 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.218 -  4.559:     6107 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7381 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.489 |       0.412 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    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: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4456   r_free= 0.4322   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.263188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4358   r_free= 0.4192   ksol= 0.30   Bsol= 25.70   scale= 0.932   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,5.22,-1.79,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.251666                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.238760              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.234   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.829734              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.090   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4358      final r-factor (work) = 0.3563          |
| start r-factor (free) = 0.4192      final r-factor (free) = 0.3815          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6836 = 6.24 * 0.50 * 6.2529 + 1.00 * 0.1785                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2715 = 6.24 * 0.50 * 6.1404 + 1.00 * 0.1172                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3563      final r-factor (work) = 0.3278          |
| start r-factor (free) = 0.3815      final r-factor (free) = 0.3848          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1008 = 0.83 * 1.00 * 6.1404 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0535 = 0.83 * 1.00 * 6.0716 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.06   18.56    None  None   None       |
|    all(noH): 2823   0      0.00    94.06   18.56    None  None   None       |
|    Sol.    : 438    0      0.00    94.06   35.53    None  None   None       |
|    Mac.    : 2385   0      0.00    75.27   15.44    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 -   9.406:  843   |   5:    47.029 -  56.435:   82        |
|      1:     9.406 -  18.812:  924   |   6:    56.435 -  65.841:   48        |
|      2:    18.812 -  28.218:  489   |   7:    65.841 -  75.247:   18        |
|      3:    28.218 -  37.623:  272   |   8:    75.247 -  84.652:    4        |
|      4:    37.623 -  47.029:  139   |   9:    84.652 -  94.058:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3278 r_free = 0.3848             target_work(ml) = 6.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3274 r_free = 0.3849             target_work(ml) = 6.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3274   r_free= 0.3849   ksol= 0.30   Bsol= 25.70   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,5.22,-1.79,0.00,-0.00,-0.00); trace/3= 0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.071900                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3266   r_free= 0.3832   ksol= 0.28   Bsol= 33.89   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,3.21,-0.69,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.072798                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.941889              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.264   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.668944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.159  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3266      final r-factor (work) = 0.2598          |
| start r-factor (free) = 0.3832      final r-factor (free) = 0.3144          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.3045 = 9.94 * 0.50 * 6.0727 + 1.00 * 0.1172                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8001 = 9.94 * 0.50 * 5.9718 + 1.00 * 0.1147                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2598      final r-factor (work) = 0.2392          |
| start r-factor (free) = 0.3144      final r-factor (free) = 0.3014          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0103 = 0.67 * 1.00 * 5.9718 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9169 = 0.67 * 1.00 * 5.8352 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.23   18.12    None  None   None       |
|    all(noH): 2823   0      0.00    92.23   18.12    None  None   None       |
|    Sol.    : 438    0      1.94    92.23   37.85    None  None   None       |
|    Mac.    : 2385   0      0.00    85.08   14.49    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 -   9.223:  914   |   5:    46.114 -  55.336:  104        |
|      1:     9.223 -  18.445:  951   |   6:    55.336 -  64.559:   57        |
|      2:    18.445 -  27.668:  395   |   7:    64.559 -  73.782:   23        |
|      3:    27.668 -  36.891:  232   |   8:    73.782 -  83.004:   13        |
|      4:    36.891 -  46.114:  127   |   9:    83.004 -  92.227:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2392 r_free = 0.3014             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2390 r_free = 0.3012             target_work(ml) = 5.820         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2390   r_free= 0.3012   ksol= 0.28   Bsol= 33.89   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,3.21,-0.69,0.00,-0.00,-0.00); trace/3= 0.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.820333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2383   r_free= 0.3004   ksol= 0.32   Bsol= 52.44   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,1.61,-0.41,0.00,-0.00,-0.00); trace/3= -0.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.819519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.345850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.048  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.301139              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.852  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2383      final r-factor (work) = 0.1832          |
| start r-factor (free) = 0.3004      final r-factor (free) = 0.2347          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6291 = 6.35 * 0.50 * 5.8351 + 1.00 * 0.1147                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2164 = 6.35 * 0.50 * 5.7163 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1832      final r-factor (work) = 0.1625          |
| start r-factor (free) = 0.2347      final r-factor (free) = 0.2165          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1677 = 2.30 * 1.00 * 5.7163 + 1.00 * 0.0136                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6986 = 2.30 * 1.00 * 5.5116 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.04  18.42    None  None   None       |
|    all(noH): 2823   0      0.00    108.04  18.42    None  None   None       |
|    Sol.    : 438    0      5.09    107.90  44.81    None  None   None       |
|    Mac.    : 2385   0      0.00    108.04  13.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.804: 1266   |   5:    54.020 -  64.824:   91        |
|      1:    10.804 -  21.608:  882   |   6:    64.824 -  75.628:   56        |
|      2:    21.608 -  32.412:  220   |   7:    75.628 -  86.433:   25        |
|      3:    32.412 -  43.216:  144   |   8:    86.433 -  97.237:   15        |
|      4:    43.216 -  54.020:  117   |   9:    97.237 - 108.041:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1625 r_free = 0.2165             target_work(ml) = 5.473         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1624 r_free = 0.2167             target_work(ml) = 5.473         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1624   r_free= 0.2167   ksol= 0.32   Bsol= 52.44   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,1.61,-0.41,0.00,-0.00,-0.00); trace/3= -0.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.473176                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1624   r_free= 0.2156   ksol= 0.33   Bsol= 64.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,0.29,-0.61,0.00,-0.00,-0.00); trace/3= -0.78                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.471923                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.081470              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.861   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663288              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.626  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1624      final r-factor (work) = 0.1353          |
| start r-factor (free) = 0.2156      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3347 = 4.08 * 0.50 * 5.5157 + 1.00 * 0.0787                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0828 = 4.08 * 0.50 * 5.3950 + 1.00 * 0.0730                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1353      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1899      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5939 = 0.66 * 1.00 * 5.3950 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5243 = 0.66 * 1.00 * 5.2944 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.11  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    112.11  17.56    None  None   None       |
|    Sol.    : 438    0      0.00    108.82  44.06    None  None   None       |
|    Mac.    : 2385   0      0.39    112.11  12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.211: 1411   |   5:    56.057 -  67.268:   91        |
|      1:    11.211 -  22.423:  844   |   6:    67.268 -  78.480:   33        |
|      2:    22.423 -  33.634:  171   |   7:    78.480 -  89.691:   26        |
|      3:    33.634 -  44.846:  134   |   8:    89.691 - 100.902:    8        |
|      4:    44.846 -  56.057:  100   |   9:   100.902 - 112.114:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1269 r_free = 0.1769             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1267 r_free = 0.1765             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1765   ksol= 0.33   Bsol= 64.23   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,0.29,-0.61,0.00,-0.00,-0.00); trace/3= -0.78                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.255172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1768   ksol= 0.33   Bsol= 62.95   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-0.24,-0.51,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.256643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.602457              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.320  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.796107              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.875  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1768      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6110 = 3.60 * 0.50 * 5.2953 + 1.00 * 0.0730                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4873 = 3.60 * 0.50 * 5.2266 + 1.00 * 0.0730                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1735 = 0.80 * 1.00 * 5.2266 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1435 = 0.80 * 1.00 * 5.1898 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.06  17.11    None  None   None       |
|    all(noH): 2823   0      0.00    115.06  17.11    None  None   None       |
|    Sol.    : 438    0      0.92    111.76  43.06    None  None   None       |
|    Mac.    : 2385   0      0.00    115.06  12.34    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 -  11.506: 1535   |   5:    57.531 -  69.037:   79        |
|      1:    11.506 -  23.012:  757   |   6:    69.037 -  80.543:   33        |
|      2:    23.012 -  34.518:  172   |   7:    80.543 -  92.049:   17        |
|      3:    34.518 -  46.025:  114   |   8:    92.049 - 103.555:    6        |
|      4:    46.025 -  57.531:  106   |   9:   103.555 - 115.061:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1659             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1659             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1659   ksol= 0.33   Bsol= 62.95   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-0.24,-0.51,-0.00,-0.00,-0.00); trace/3= -0.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183466                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.7041 0.99   1420  159 0.0954 0.1347      5.3723      5.5957|
|  2:  4.7041 -  3.7529 0.99   1365  151 0.0825 0.1069      5.4317      5.6331|
|  3:  3.7529 -  3.2842 0.99   1353  149 0.1084 0.1603      5.4843      5.8599|
|  4:  3.2842 -  2.9865 0.99   1314  143 0.1281 0.1718      5.4849      5.6663|
|  5:  2.9865 -  2.7739 0.99   1329  150 0.1368 0.1821      5.3606      5.5561|
|  6:  2.7739 -  2.6112 0.99   1317  145 0.1354 0.2126        5.29      5.5185|
|  7:  2.6112 -  2.4810 0.98   1295  152 0.1292 0.1689      5.2018       5.421|
|  8:  2.4810 -  2.3735 0.98   1334  138 0.1241 0.1734       5.134      5.3576|
|  9:  2.3735 -  2.2824 0.99   1287  143 0.1201 0.1916      5.0526      5.3702|
| 10:  2.2824 -  2.2039 0.98   1305  144 0.1215 0.1795      5.0352      5.2421|
| 11:  2.2039 -  2.1352 0.97   1289  146 0.1182 0.1931      4.9514      5.2652|
| 12:  2.1352 -  2.0743 0.98   1283  148 0.1190 0.1644      4.8923      5.1248|
| 13:  2.0743 -  2.0199 0.92   1216  133 0.1139 0.1832       4.801      5.0982|
| 14:  2.0199 -  1.9707 0.40    523   58 0.1068 0.1949       4.717      4.9953|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0234 -  4.7041  1420   159  0.93   9.72   0.97     0.95       7679.98|
|  2:  4.7041 -  3.7529  1365   151  0.95   8.41   1.02     1.01       9593.16|
|  3:  3.7529 -  3.2842  1353   149  0.93  11.79   1.03     1.02      10833.28|
|  4:  3.2842 -  2.9865  1314   143  0.91  14.79   1.02     1.00      11158.51|
|  5:  2.9865 -  2.7739  1329   150  0.89  17.27   1.01     0.98       9339.24|
|  6:  2.7739 -  2.6112  1317   145  0.89  17.75   0.98     0.95       8220.62|
|  7:  2.6112 -  2.4810  1295   152  0.90  16.61   0.99     0.95       6807.48|
|  8:  2.4810 -  2.3735  1334   138  0.89  16.83   1.00     0.97       6301.97|
|  9:  2.3735 -  2.2824  1287   143  0.89  16.96   0.99     0.95       5389.99|
| 10:  2.2824 -  2.2039  1305   144  0.89  17.28   0.99     0.96       5262.95|
| 11:  2.2039 -  2.1352  1289   146  0.89  16.88   0.99     0.96       4579.54|
| 12:  2.1352 -  2.0743  1283   148  0.90  16.24   0.99     0.97       4031.82|
| 13:  2.0743 -  2.0199  1216   133  0.90  16.67   0.99     0.98       3498.52|
| 14:  2.0199 -  1.9707   523    58  0.90  16.34   0.97     0.93       2980.14|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2980.14 max =        11158.51 mean =      7060.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.13|
|phase err.(test): min =        0.00 max =           89.60 mean =        14.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1658   ksol= 0.33   Bsol= 61.40   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-0.32,-0.37,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183481                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1658   ksol= 0.33   Bsol= 61.40   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-0.32,-0.37,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.183481                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.7041 0.99   1420  159 0.0953 0.1347      5.3718      5.5956|
|  2:  4.7041 -  3.7529 0.99   1365  151 0.0825 0.1069      5.4315      5.6331|
|  3:  3.7529 -  3.2842 0.99   1353  149 0.1084 0.1604      5.4845      5.8605|
|  4:  3.2842 -  2.9865 0.99   1314  143 0.1282 0.1718      5.4852      5.6662|
|  5:  2.9865 -  2.7739 0.99   1329  150 0.1369 0.1821      5.3605      5.5556|
|  6:  2.7739 -  2.6112 0.99   1317  145 0.1353 0.2121      5.2894      5.5174|
|  7:  2.6112 -  2.4810 0.98   1295  152 0.1292 0.1689      5.2016      5.4206|
|  8:  2.4810 -  2.3735 0.98   1334  138 0.1239 0.1735      5.1341      5.3584|
|  9:  2.3735 -  2.2824 0.99   1287  143 0.1200 0.1915      5.0528      5.3707|
| 10:  2.2824 -  2.2039 0.98   1305  144 0.1214 0.1799      5.0354      5.2437|
| 11:  2.2039 -  2.1352 0.97   1289  146 0.1182 0.1931      4.9515      5.2648|
| 12:  2.1352 -  2.0743 0.98   1283  148 0.1191 0.1648      4.8929       5.126|
| 13:  2.0743 -  2.0199 0.92   1216  133 0.1140 0.1829      4.8014      5.0968|
| 14:  2.0199 -  1.9707 0.40    523   58 0.1067 0.1950      4.7162      4.9951|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0234 -  4.7041  1420   159  0.93   9.71   0.97     0.95       7669.62|
|  2:  4.7041 -  3.7529  1365   151  0.95   8.41   1.02     1.01       9587.41|
|  3:  3.7529 -  3.2842  1353   149  0.93  11.79   1.03     1.02      10836.70|
|  4:  3.2842 -  2.9865  1314   143  0.91  14.80   1.02     1.01      11164.88|
|  5:  2.9865 -  2.7739  1329   150  0.89  17.25   1.01     0.99       9324.45|
|  6:  2.7739 -  2.6112  1317   145  0.89  17.73   0.98     0.95       8207.81|
|  7:  2.6112 -  2.4810  1295   152  0.90  16.60   0.99     0.95       6800.54|
|  8:  2.4810 -  2.3735  1334   138  0.89  16.84   1.01     0.97       6307.97|
|  9:  2.3735 -  2.2824  1287   143  0.89  16.97   1.00     0.95       5401.10|
| 10:  2.2824 -  2.2039  1305   144  0.89  17.30   1.00     0.96       5268.81|
| 11:  2.2039 -  2.1352  1289   146  0.89  16.90   1.00     0.96       4583.30|
| 12:  2.1352 -  2.0743  1283   148  0.90  16.25   1.00     0.98       4038.51|
| 13:  2.0743 -  2.0199  1216   133  0.90  16.66   0.99     0.99       3497.15|
| 14:  2.0199 -  1.9707   523    58  0.90  16.32   0.97     0.94       2969.90|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2969.90 max =        11164.88 mean =      7059.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.13|
|phase err.(test): min =        0.00 max =           89.55 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.06  17.11    None  None   None       |
|    all(noH): 2823   0      0.00    115.06  17.11    None  None   None       |
|    Sol.    : 438    0      0.92    111.76  43.06    None  None   None       |
|    Mac.    : 2385   0      0.00    115.06  12.35    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:     0.003 -  11.509: 1535   |   5:    57.534 -  69.040:   79        |
|      1:    11.509 -  23.015:  757   |   6:    69.040 -  80.546:   33        |
|      2:    23.015 -  34.521:  172   |   7:    80.546 -  92.052:   17        |
|      3:    34.521 -  46.028:  114   |   8:    92.052 - 103.558:    6        |
|      4:    46.028 -  57.534:  106   |   9:   103.558 - 115.064:    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)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.621 - 5.026
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 322
   mapped sites are within: 0.711 - 5.026

peak=    6.092 closest distance to " O   HOH Z 210 " =    1.244
peak=    5.263 closest distance to " CB  SER A  63 " =    1.127
peak=    5.164 closest distance to " O   HOH Z 113 " =    2.218
peak=    5.019 closest distance to " CA  TYR A  30 " =    0.918
peak=    4.914 closest distance to " CG  PRO A  54 " =    1.254
peak=    4.901 closest distance to " O   HOH Z 154 " =    1.908
peak=    4.835 closest distance to " O   HOH Z 134 " =    1.888
peak=    4.797 closest distance to " CB  ARG A 275 " =    0.868
peak=    4.775 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.759 closest distance to " O   HOH Z  43 " =    1.804
peak=    4.728 closest distance to " C   PRO A 198 " =    1.501
peak=    4.716 closest distance to " O   HOH Z 403 " =    1.922
peak=    4.697 closest distance to " CB  GLN A 223 " =    1.432
peak=    4.674 closest distance to " O   HOH Z 433 " =    1.771
peak=    4.622 closest distance to " O   HOH Z 357 " =    2.104
peak=    4.604 closest distance to " O   HOH Z  80 " =    1.952
peak=    4.579 closest distance to " O   HOH Z 209 " =    2.351
peak=    4.569 closest distance to " O   HOH Z  15 " =    2.196
peak=    4.534 closest distance to " CG1 ILE A  33 " =    1.211
peak=    4.528 closest distance to " O   GLY A  23 " =    2.441
peak=    4.500 closest distance to " O   HOH Z 120 " =    1.008
peak=    4.486 closest distance to " O   HOH Z 402 " =    1.579
peak=    4.477 closest distance to " O   HOH Z 124 " =    1.332
peak=    4.385 closest distance to " O   HOH Z 234 " =    3.704
peak=    4.375 closest distance to " CD2 TRP A 179 " =    1.401
peak=    4.375 closest distance to " O   HOH Z 406 " =    1.625
peak=    4.363 closest distance to " O   HOH Z  63 " =    2.277
peak=    4.342 closest distance to " O   HOH Z 154 " =    2.198
peak=    4.340 closest distance to " O   HOH Z 130 " =    2.541
peak=    4.335 closest distance to " O   HOH Z 389 " =    2.054
peak=    4.324 closest distance to " O   HOH Z  97 " =    1.938
peak=    4.315 closest distance to " CB  ARG A  79 " =    1.424
peak=    4.312 closest distance to " NE2 GLN A  11 " =    1.035
peak=    4.292 closest distance to " CG  PRO A 213 " =    1.240
peak=    4.275 closest distance to " O   HOH Z  44 " =    2.032
peak=    4.264 closest distance to " O   HOH Z   7 " =    1.013
peak=    4.252 closest distance to " O   HOH Z 334 " =    1.607
peak=    4.246 closest distance to " O   SER A  87 " =    2.220
peak=    4.237 closest distance to " NZ  LYS A 117 " =    2.906
peak=    4.225 closest distance to " O   HOH Z 126 " =    1.621
peak=    4.213 closest distance to " CA  ALA A  51 " =    1.008
peak=    4.200 closest distance to " O   HOH Z 102 " =    1.349
peak=    4.198 closest distance to " O   HOH Z 130 " =    1.172
peak=    4.173 closest distance to " O   HOH Z  39 " =    1.862
peak=    4.160 closest distance to " O   HOH Z 189 " =    2.174
peak=    4.145 closest distance to " O   HOH Z  20 " =    1.554
peak=    4.142 closest distance to " O   HOH Z 352 " =    1.865
peak=    4.129 closest distance to " CG  PRO A 198 " =    1.224
peak=    4.124 closest distance to " O   HOH Z 245 " =    1.382
peak=    4.104 closest distance to " CB  PRO A  54 " =    0.839
peak=    4.092 closest distance to " O   HOH Z 414 " =    1.860
peak=    4.078 closest distance to " CG  PRO A 280 " =    0.746
peak=    4.071 closest distance to " CB  TRP A 179 " =    1.179
peak=    4.069 closest distance to " O   HOH Z  49 " =    1.273
peak=    4.042 closest distance to " O   HOH Z 425 " =    1.412
peak=    4.039 closest distance to " O   HOH Z 428 " =    1.094
peak=    4.035 closest distance to " O   HOH Z 141 " =    1.755
peak=    4.033 closest distance to " CG  PRO A  90 " =    1.168
peak=    4.029 closest distance to " CD  LYS A 166 " =    1.468
peak=    4.027 closest distance to " O   HOH Z 142 " =    1.407
peak=    4.021 closest distance to " NH2BARG A 145 " =    2.091
peak=    4.019 closest distance to " O   HOH Z 369 " =    2.395
peak=    4.012 closest distance to " O   HOH Z 361 " =    3.249
peak=    3.996 closest distance to " CG  ARG A  66 " =    0.997
peak=    3.996 closest distance to " CB  SER A 141 " =    1.039
peak=    3.979 closest distance to " O   HOH Z 247 " =    1.428
peak=    3.971 closest distance to " O   HOH Z 214 " =    1.385
peak=    3.969 closest distance to " CB  ARG A 190 " =    1.764
peak=    3.966 closest distance to " CD  ARG A 269 " =    0.958
peak=    3.956 closest distance to " O   ALA A 165 " =    1.271
peak=    3.953 closest distance to " O   HOH Z 298 " =    1.937
peak=    3.941 closest distance to " O   HOH Z 437 " =    1.934
peak=    3.937 closest distance to " CZ  PHE A  38 " =    1.368
peak=    3.931 closest distance to " O   HOH Z 336 " =    1.820
peak=    3.924 closest distance to " O   HOH Z 163 " =    1.449
peak=    3.917 closest distance to " O   HOH Z 128 " =    2.271
peak=    3.911 closest distance to " O   HOH Z 431 " =    1.158
peak=    3.910 closest distance to " CB  GLU A 277 " =    3.696
peak=    3.895 closest distance to " CA  ASN A 176 " =    1.488
peak=    3.891 closest distance to " O   HOH Z 232 " =    2.360
peak=    3.890 closest distance to " O   HOH Z 279 " =    2.041
peak=    3.878 closest distance to " C   ILE A 106 " =    1.809
peak=    3.873 closest distance to " CG2BVAL A  41 " =    0.943
peak=    3.866 closest distance to " CB  ASN A 285 " =    0.960
peak=    3.863 closest distance to " O   HOH Z 345 " =    2.555
peak=    3.862 closest distance to " CB  GLU A 128 " =    1.176
peak=    3.856 closest distance to " O   HOH Z 150 " =    1.745
peak=    3.856 closest distance to " O   HOH Z 412 " =    3.627
peak=    3.847 closest distance to " O   HOH Z  61 " =    1.540
peak=    3.840 closest distance to " O   HOH Z 193 " =    1.645
peak=    3.814 closest distance to " CB  SER A   3 " =    1.282
peak=    3.809 closest distance to " CB  GLU A 152 " =    1.101
peak=    3.809 closest distance to " CG2 VAL A 197 " =    1.168
peak=    3.799 closest distance to " O   HOH Z 132 " =    2.153
peak=    3.798 closest distance to " O   ALA A 158 " =    1.197
peak=    3.790 closest distance to " O   HOH Z 128 " =    2.025
peak=    3.785 closest distance to " O   ASN A  74 " =    1.843
peak=    3.782 closest distance to " O   HOH Z 403 " =    1.492
peak=    3.775 closest distance to " O   HOH Z 345 " =    1.826
peak=    3.767 closest distance to " O   HOH Z 132 " =    1.160
peak=    3.765 closest distance to " O   HOH Z 371 " =    3.246
peak=    3.761 closest distance to " O   HOH Z 386 " =    2.275
peak=    3.751 closest distance to " O   HOH Z 132 " =    2.649
peak=    3.746 closest distance to " O   HOH Z 423 " =    1.854
peak=    3.734 closest distance to " CA  LEU A  83 " =    1.302
peak=    3.727 closest distance to " O   HOH Z 250 " =    1.784
peak=    3.723 closest distance to " O   HOH Z 227 " =    1.764
peak=    3.715 closest distance to " CB  SER A  26 " =    1.774
peak=    3.713 closest distance to " CE  LYS A 119 " =    1.119
peak=    3.709 closest distance to " O   HOH Z 374 " =    2.655
peak=    3.709 closest distance to " CD  PRO A  54 " =    1.093
peak=    3.705 closest distance to " N   ASN A  39 " =    1.298
peak=    3.704 closest distance to " O   HOH Z   6 " =    2.210
peak=    3.703 closest distance to " O   HOH Z  40 " =    1.823
peak=    3.701 closest distance to " OG  SER A  62 " =    2.934
peak=    3.681 closest distance to " O   HOH Z   9 " =    2.397
peak=    3.680 closest distance to " O   HOH Z 196 " =    1.277
peak=    3.679 closest distance to " O   HOH Z 380 " =    1.853
peak=    3.673 closest distance to " O   HOH Z 417 " =    2.987
peak=    3.671 closest distance to " O   HOH Z 258 " =    2.265
peak=    3.666 closest distance to " CD  ARG A 195 " =    0.996
peak=    3.659 closest distance to " O   HOH Z 346 " =    1.612
peak=    3.655 closest distance to " O   HOH Z  68 " =    2.023
peak=    3.652 closest distance to " CB  TRP A 266 " =    1.073
peak=    3.647 closest distance to " CA  ALA A  21 " =    1.404
peak=    3.644 closest distance to " CB  VAL A 202 " =    1.500
peak=    3.639 closest distance to " O   HOH Z  78 " =    1.600
peak=    3.636 closest distance to " CD  ARG A 159 " =    0.851
peak=    3.625 closest distance to " O   HOH Z 173 " =    2.186
peak=    3.624 closest distance to " O   HOH Z 365 " =    1.387
peak=    3.621 closest distance to " O   HOH Z 271 " =    2.656
peak=    3.618 closest distance to " CB  ASN A 148 " =    1.382
peak=    3.616 closest distance to " O   HOH Z 438 " =    2.416
peak=    3.614 closest distance to " CB  SER A  62 " =    0.775
peak=    3.605 closest distance to " O   HOH Z 185 " =    1.719
peak=    3.605 closest distance to " O   HOH Z 316 " =    2.837
peak=    3.603 closest distance to " CG AARG A 275 " =    1.129
peak=    3.590 closest distance to " ND2 ASN A 187 " =    1.551
peak=    3.580 closest distance to " O   HOH Z 265 " =    1.999
peak=    3.574 closest distance to " O   HOH Z 358 " =    2.075
peak=    3.572 closest distance to " O   HOH Z  30 " =    1.243
peak=    3.571 closest distance to " CA  ALA A 160 " =    0.893
peak=    3.568 closest distance to " CG2 ILE A  20 " =    1.434
peak=    3.562 closest distance to " O   HOH Z 327 " =    1.721
peak=    3.559 closest distance to " OG BSER A 164 " =    2.351
peak=    3.552 closest distance to " CG2 THR A 220 " =    0.812
peak=    3.544 closest distance to " NH2AARG A 275 " =    3.513
peak=    3.537 closest distance to " O   HOH Z 339 " =    1.229
peak=    3.537 closest distance to " CB  THR A  52 " =    0.984
peak=    3.532 closest distance to " NH2AARG A 145 " =    2.282
peak=    3.529 closest distance to " O   HOH Z  21 " =    1.791
peak=    3.526 closest distance to " O   HOH Z  48 " =    1.741
peak=    3.524 closest distance to " O   HOH Z 126 " =    1.834
peak=    3.522 closest distance to " CA  GLU A 152 " =    0.920
peak=    3.516 closest distance to " O   HOH Z 421 " =    2.050
peak=    3.511 closest distance to " O   HOH Z 130 " =    2.373
peak=    3.500 closest distance to " O   HOH Z  88 " =    3.525
peak=    3.499 closest distance to " O   HOH Z  35 " =    2.097
peak=    3.493 closest distance to " O   HOH Z 303 " =    2.249
peak=    3.486 closest distance to " CA  GLY A 196 " =    1.173
peak=    3.483 closest distance to " O   HOH Z 147 " =    1.804
peak=    3.478 closest distance to " O   HOH Z 368 " =    2.010
peak=    3.471 closest distance to " NE2 GLN A  77 " =    3.203
peak=    3.469 closest distance to " CD  GLN A 194 " =    1.617
peak=    3.469 closest distance to " O   HOH Z 250 " =    1.411
peak=    3.467 closest distance to " CA  ASP A 162 " =    1.135
peak=    3.464 closest distance to " O   HOH Z 109 " =    1.382
peak=    3.464 closest distance to " O  BHOH Z  74 " =    1.415
peak=    3.462 closest distance to " CB  PRO A  54 " =    1.310
peak=    3.461 closest distance to " CB  LEU A 228 " =    1.189
peak=    3.459 closest distance to " O   HOH Z 236 " =    1.335
peak=    3.451 closest distance to " O   HOH Z 365 " =    2.553
peak=    3.445 closest distance to " O   HOH Z 418 " =    1.695
peak=    3.443 closest distance to " O   HOH Z 408 " =    2.014
peak=    3.442 closest distance to " O   HOH Z 208 " =    1.532
peak=    3.441 closest distance to " O   HOH Z  47 " =    2.186
peak=    3.441 closest distance to " CG2 THR A 221 " =    1.142
peak=    3.438 closest distance to " O   HOH Z 435 " =    1.733
peak=    3.437 closest distance to " O   HOH Z  66 " =    2.070
peak=    3.424 closest distance to " CG1BVAL A  72 " =    1.809
peak=    3.416 closest distance to " O   HOH Z  11 " =    1.313
peak=    3.415 closest distance to " CB  ALA A   9 " =    1.614
peak=    3.414 closest distance to " O   HOH Z 423 " =    3.262
peak=    3.414 closest distance to " O   HOH Z 272 " =    1.886
peak=    3.409 closest distance to " CG  PRO A 243 " =    1.161
peak=    3.407 closest distance to " CB  PHE A  16 " =    1.222
peak=    3.391 closest distance to " O   ASP A 124 " =    1.791
peak=    3.391 closest distance to " O   HOH Z 156 " =    2.607
peak=    3.390 closest distance to " O   HOH Z 284 " =    2.891
peak=    3.386 closest distance to " CB  MET A 105 " =    1.175
peak=    3.386 closest distance to " O   HOH Z 282 " =    2.102
peak=    3.385 closest distance to " O   HOH Z 394 " =    1.683
peak=    3.378 closest distance to " CA  ALA A 158 " =    1.230
peak=    3.378 closest distance to " O   HOH Z 162 " =    1.329
peak=    3.378 closest distance to " O   HOH Z 189 " =    2.627
peak=    3.368 closest distance to " CB  TYR A 169 " =    0.809
peak=    3.364 closest distance to " CA  ARG A  36 " =    1.035
peak=    3.364 closest distance to " CG  GLN A  58 " =    2.411
peak=    3.353 closest distance to " O   HOH Z 162 " =    1.958
peak=    3.352 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.346 closest distance to " O   HOH Z  64 " =    2.110
peak=    3.345 closest distance to " CE  LYS A  76 " =    0.805
peak=    3.345 closest distance to " OG1 THR A 221 " =    1.313
peak=    3.342 closest distance to " NH2AARG A 275 " =    2.878
peak=    3.335 closest distance to " CA  ARG A 195 " =    1.133
peak=    3.332 closest distance to " CB  ALA A 100 " =    1.293
peak=    3.331 closest distance to " CB  ARG A 139 " =    0.967
peak=    3.330 closest distance to " O   GLY A  91 " =    1.159
peak=    3.326 closest distance to " CD  LYS A 119 " =    1.849
peak=    3.318 closest distance to " O   THR A 251 " =    1.177
peak=    3.317 closest distance to " CA  ALA A 100 " =    1.197
peak=    3.314 closest distance to " O   HOH Z 281 " =    4.410
peak=    3.313 closest distance to " O   HOH Z 313 " =    1.831
peak=    3.311 closest distance to " NZ  LYS A  48 " =    1.237
peak=    3.306 closest distance to " CD2 LEU A 255 " =    1.163
peak=    3.296 closest distance to " OH  TYR A 116 " =    1.178
peak=    3.295 closest distance to " CB  MET A  40 " =    0.899
peak=    3.295 closest distance to " O   HOH Z 419 " =    1.667
peak=    3.291 closest distance to " O   HOH Z 427 " =    3.069
peak=    3.287 closest distance to " O   HOH Z 261 " =    1.955
peak=    3.282 closest distance to " CD2 LEU A 297 " =    0.815
peak=    3.282 closest distance to " OE1 GLN A  11 " =    1.969
peak=    3.280 closest distance to " CB  ASP A 140 " =    0.926
peak=    3.278 closest distance to " ND1 HIS A  81 " =    1.470
peak=    3.278 closest distance to " CA  VAL A 125 " =    1.264
peak=    3.274 closest distance to " CB  ALA A  71 " =    1.359
peak=    3.272 closest distance to " N   VAL A 125 " =    1.518
peak=    3.271 closest distance to " CE1 HIS A 108 " =    1.088
peak=    3.270 closest distance to " O   HOH Z  95 " =    1.407
peak=    3.270 closest distance to " O   HOH Z 272 " =    1.165
peak=    3.270 closest distance to " O   HOH Z 291 " =    1.418
peak=    3.268 closest distance to " CA  THR A 221 " =    1.621
peak=    3.265 closest distance to " CG2 ILE A 120 " =    1.235
peak=    3.263 closest distance to " CG2 THR A  29 " =    1.343
peak=    3.262 closest distance to " CB  TYR A 247 " =    0.974
peak=    3.261 closest distance to " NZ  LYS A 117 " =    1.391
peak=    3.261 closest distance to " CB  ASN A  39 " =    0.860
peak=    3.256 closest distance to " N   TRP A 150 " =    1.081
peak=    3.256 closest distance to " O   HOH Z 412 " =    3.642
peak=    3.253 closest distance to " CA  CYS A 260 " =    1.844
peak=    3.250 closest distance to " CA  ARG A  66 " =    1.098
peak=    3.248 closest distance to " O   HOH Z 295 " =    1.492
peak=    3.245 closest distance to " O   HOH Z 355 " =    1.859
peak=    3.242 closest distance to " O   HOH Z 393 " =    3.288
peak=    3.242 closest distance to " CA  ASP A 191 " =    0.946
peak=    3.241 closest distance to " O   HOH Z 146 " =    1.137
peak=    3.238 closest distance to " CD  PRO A 213 " =    1.223
peak=    3.234 closest distance to " OD1 ASN A  69 " =    2.478
peak=    3.234 closest distance to " CA  LYS A 166 " =    1.410
peak=    3.233 closest distance to " O   SER A  26 " =    1.624
peak=    3.233 closest distance to " O   HOH Z 344 " =    2.969
peak=    3.232 closest distance to " O   HOH Z 325 " =    3.916
peak=    3.231 closest distance to " O   HOH Z 298 " =    2.245
peak=    3.229 closest distance to " O   HOH Z 407 " =    1.305
peak=    3.225 closest distance to " O   HOH Z 402 " =    2.749
peak=    3.222 closest distance to " O   HOH Z 435 " =    1.901
peak=    3.219 closest distance to " CB  SER A 273 " =    0.822
peak=    3.206 closest distance to " O   HOH Z 123 " =    2.114
peak=    3.205 closest distance to " O   HOH Z 427 " =    2.881
peak=    3.205 closest distance to " N   CYS A 260 " =    0.817
peak=    3.204 closest distance to " OG  SER A 245 " =    1.473
peak=    3.202 closest distance to " CG2AVAL A 121 " =    2.110
peak=    3.195 closest distance to " O   HOH Z  46 " =    1.439
peak=    3.193 closest distance to " O   HOH Z 214 " =    2.501
peak=    3.186 closest distance to " CG2BVAL A  72 " =    1.538
peak=    3.186 closest distance to " CA  ASP A 191 " =    1.204
peak=    3.186 closest distance to " N   SER A 164 " =    1.039
peak=    3.180 closest distance to " O   ILE A  33 " =    1.259
peak=    3.180 closest distance to " O   HOH Z 145 " =    2.629
peak=    3.179 closest distance to " O   HOH Z 240 " =    2.324
peak=    3.179 closest distance to " CD1 LEU A 228 " =    1.673
peak=    3.178 closest distance to " OD2 ASP A 298 " =    4.040
peak=    3.175 closest distance to " O   HOH Z  88 " =    3.169
peak=    3.173 closest distance to " CA  ASP A 149 " =    1.213
peak=    3.173 closest distance to " O   HOH Z 419 " =    2.555
peak=    3.170 closest distance to " O   HOH Z 109 " =    1.845
peak=    3.167 closest distance to " O   HOH Z 118 " =    0.830
peak=    3.164 closest distance to " OH  TYR A  30 " =    1.278
peak=    3.163 closest distance to " CA  SER A  32 " =    1.579
peak=    3.163 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.163 closest distance to " CB  LEU A   5 " =    1.130
peak=    3.162 closest distance to " CB  PRO A 198 " =    1.074
peak=    3.161 closest distance to " OE1 GLN A  73 " =    1.138
peak=    3.157 closest distance to " O   HOH Z 426 " =    1.398
peak=    3.156 closest distance to " CA  SER A  12 " =    1.629
peak=    3.156 closest distance to " CB  PRO A 280 " =    1.166
peak=    3.154 closest distance to " CZ3 TRP A  85 " =    0.983
peak=    3.154 closest distance to " O   HOH Z 395 " =    1.470
peak=    3.153 closest distance to " CB  ASP A 253 " =    1.002
peak=    3.149 closest distance to " O   HOH Z  22 " =    2.856
peak=    3.149 closest distance to " CA  VAL A  41 " =    0.842
peak=    3.149 closest distance to " CA  LYS A 117 " =    1.313
peak=    3.147 closest distance to " O   HOH Z 114 " =    1.077
peak=    3.141 closest distance to " CD1 LEU A 300 " =    1.163
peak=    3.134 closest distance to " OE1 GLN A  58 " =    3.166
peak=    3.132 closest distance to " NZ  LYS A 166 " =    2.952
peak=    3.130 closest distance to " CB  ALA A 248 " =    1.335
peak=    3.128 closest distance to " O   HOH Z 298 " =    4.328
peak=    3.124 closest distance to " OG BSER A 210 " =    1.169
peak=    3.124 closest distance to " O   HOH Z 234 " =    1.900
peak=    3.122 closest distance to " O   HOH Z 298 " =    5.026
peak=    3.121 closest distance to " CB  PHE A 283 " =    0.711
peak=    3.118 closest distance to " O   HOH Z 152 " =    1.725
peak=    3.114 closest distance to " O   HOH Z  63 " =    2.057
peak=    3.114 closest distance to " O   HOH Z 339 " =    2.170
peak=    3.113 closest distance to " CG  MET A 185 " =    1.149
peak=    3.110 closest distance to " CA  SER A  87 " =    1.006
peak=    3.110 closest distance to " CG  GLN A  11 " =    1.371
peak=    3.102 closest distance to " O   HOH Z 111 " =    1.772
peak=    3.101 closest distance to " O   HOH Z 109 " =    2.751
peak=    3.101 closest distance to " O   TRP A 274 " =    1.804
peak=    3.097 closest distance to " CG2 THR A  42 " =    0.902
peak=    3.086 closest distance to " CA  ALA A 299 " =    1.092
peak=    3.079 closest distance to " CG  MET A  40 " =    2.254
peak=    3.074 closest distance to " O   HOH Z 353 " =    2.834
peak=    3.065 closest distance to " CA  ALA A 295 " =    1.111
peak=    3.063 closest distance to " O   HOH Z 261 " =    1.791

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 230         
Filter by distance & map next to the model:
   mapped sites are within: 0.797 - 5.993
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 230 from: 230
   mapped sites are within: 0.797 - 5.993

peak=   -4.712 closest distance to " O   HOH Z 266 " =    4.673
peak=   -4.542 closest distance to " OXT GLY A 302 " =    2.926
peak=   -4.326 closest distance to " O   VAL A  67 " =    2.969
peak=   -4.316 closest distance to " C   HIS A 108 " =    1.109
peak=   -4.220 closest distance to " O   HOH Z 165 " =    1.923
peak=   -4.218 closest distance to " O   PHE A 218 " =    1.401
peak=   -4.218 closest distance to " O   PRO A 163 " =    2.086
peak=   -4.208 closest distance to " OG  SER A  97 " =    2.213
peak=   -4.191 closest distance to " O   VAL A  67 " =    2.875
peak=   -4.183 closest distance to " O   HOH Z 377 " =    2.100
peak=   -4.152 closest distance to " CG2 ILE A  49 " =    2.762
peak=   -4.120 closest distance to " O   ALA A  34 " =    2.329
peak=   -4.116 closest distance to " CD  GLN A  58 " =    1.262
peak=   -4.056 closest distance to " CD1 PHE A  59 " =    1.972
peak=   -4.044 closest distance to " O   HOH Z  13 " =    1.806
peak=   -4.035 closest distance to " CD1 LEU A 101 " =    2.460
peak=   -3.988 closest distance to " NE2 GLN A 223 " =    1.208
peak=   -3.942 closest distance to " O   HOH Z 196 " =    1.920
peak=   -3.938 closest distance to " C   THR A 279 " =    1.189
peak=   -3.911 closest distance to " CD  ARG A 156 " =    2.062
peak=   -3.910 closest distance to " CA  SER A 276 " =    1.484
peak=   -3.899 closest distance to " SG  CYS A 254 " =    3.372
peak=   -3.884 closest distance to " O   HOH Z 422 " =    1.474
peak=   -3.877 closest distance to " CD  GLN A 223 " =    1.436
peak=   -3.853 closest distance to " CB  PHE A 208 " =    2.348
peak=   -3.832 closest distance to " CE2 TYR A  30 " =    2.631
peak=   -3.823 closest distance to " CG  GLU A  53 " =    1.328
peak=   -3.794 closest distance to " O   PRO A 198 " =    1.376
peak=   -3.775 closest distance to " O   HOH Z  10 " =    1.544
peak=   -3.774 closest distance to " CB  LEU A 167 " =    2.153
peak=   -3.744 closest distance to " O   HOH Z 234 " =    4.032
peak=   -3.739 closest distance to " O   VAL A 174 " =    2.148
peak=   -3.739 closest distance to " CG2 VAL A 189 " =    2.185
peak=   -3.724 closest distance to " OG BSER A 210 " =    1.220
peak=   -3.724 closest distance to " CH2 TRP A 179 " =    1.255
peak=   -3.720 closest distance to " CD2 LEU A 237 " =    2.472
peak=   -3.711 closest distance to " O   ALA A   1 " =    2.155
peak=   -3.690 closest distance to " O   HOH Z   7 " =    1.147
peak=   -3.687 closest distance to " CZ  TYR A 169 " =    1.914
peak=   -3.682 closest distance to " O   HOH Z 196 " =    1.805
peak=   -3.674 closest distance to " O   HOH Z 423 " =    2.293
peak=   -3.661 closest distance to " O   HOH Z  71 " =    1.958
peak=   -3.659 closest distance to " OG BSER A 134 " =    1.425
peak=   -3.646 closest distance to " O   TRP A  92 " =    1.986
peak=   -3.629 closest distance to " ND2 ASN A  69 " =    1.535
peak=   -3.613 closest distance to " O   HOH Z 145 " =    2.252
peak=   -3.601 closest distance to " C   SER A 206 " =    1.535
peak=   -3.598 closest distance to " NH2 ARG A  66 " =    1.578
peak=   -3.598 closest distance to " CG  PRO A 243 " =    1.673
peak=   -3.592 closest distance to " CD  ARG A 195 " =    5.082
peak=   -3.590 closest distance to " O   HOH Z  56 " =    1.220
peak=   -3.588 closest distance to " O   HOH Z 109 " =    3.294
peak=   -3.585 closest distance to " ND2 ASN A  45 " =    1.103
peak=   -3.583 closest distance to " OD1 ASP A 191 " =    1.791
peak=   -3.583 closest distance to " O   HOH Z 196 " =    2.008
peak=   -3.582 closest distance to " O   HOH Z 283 " =    1.886
peak=   -3.582 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.570 closest distance to " O   HOH Z 197 " =    1.930
peak=   -3.564 closest distance to " O   ASN A 187 " =    1.591
peak=   -3.564 closest distance to " O   HOH Z 290 " =    1.061
peak=   -3.561 closest distance to " O   HOH Z 418 " =    1.333
peak=   -3.556 closest distance to " O   ALA A 161 " =    1.770
peak=   -3.552 closest distance to " OG BSER A 210 " =    2.412
peak=   -3.549 closest distance to " CG  MET A 105 " =    0.870
peak=   -3.545 closest distance to " CD2 LEU A 237 " =    2.515
peak=   -3.538 closest distance to " O   HOH Z 426 " =    1.700
peak=   -3.532 closest distance to " CB  ALA A 184 " =    2.350
peak=   -3.521 closest distance to " NH2 ARG A  79 " =    2.081
peak=   -3.521 closest distance to " CB  ALA A 248 " =    2.206
peak=   -3.508 closest distance to " CG2 THR A 182 " =    2.234
peak=   -3.507 closest distance to " NE2 GLN A  88 " =    1.796
peak=   -3.504 closest distance to " O   HOH Z 171 " =    2.288
peak=   -3.504 closest distance to " O   HOH Z 353 " =    2.250
peak=   -3.489 closest distance to " CG1 VAL A  78 " =    2.766
peak=   -3.472 closest distance to " C   ALA A 158 " =    1.310
peak=   -3.470 closest distance to " CA  GLY A 203 " =    2.274
peak=   -3.467 closest distance to " CB  ALA A  43 " =    2.432
peak=   -3.467 closest distance to " O   HOH Z  78 " =    1.783
peak=   -3.457 closest distance to " CD2 LEU A 237 " =    2.305
peak=   -3.454 closest distance to " CD  GLN A  58 " =    1.075
peak=   -3.451 closest distance to " O   HOH Z 351 " =    1.497
peak=   -3.451 closest distance to " ND2 ASN A 187 " =    1.522
peak=   -3.449 closest distance to " O   HOH Z  38 " =    1.761
peak=   -3.448 closest distance to " O   HOH Z  15 " =    1.499
peak=   -3.447 closest distance to " O   HOH Z   6 " =    1.690
peak=   -3.446 closest distance to " O   HOH Z 120 " =    0.855
peak=   -3.445 closest distance to " CB  ALA A 161 " =    2.503
peak=   -3.435 closest distance to " CG  ARG A 219 " =    2.458
peak=   -3.424 closest distance to " O   HOH Z 392 " =    1.173
peak=   -3.422 closest distance to " O   HOH Z  52 " =    1.838
peak=   -3.421 closest distance to " O   HOH Z 185 " =    2.285
peak=   -3.416 closest distance to " CG  PHE A 225 " =    1.368
peak=   -3.411 closest distance to " CB  ALA A 100 " =    1.752
peak=   -3.409 closest distance to " CD1 TRP A 179 " =    1.212
peak=   -3.404 closest distance to " CA  VAL A 197 " =    0.988
peak=   -3.403 closest distance to " O   SER A 210 " =    1.852
peak=   -3.401 closest distance to " O  BHOH Z 338 " =    1.104
peak=   -3.396 closest distance to " O   HOH Z 119 " =    2.129
peak=   -3.395 closest distance to " CB  SER A 210 " =    1.283
peak=   -3.387 closest distance to " O   HOH Z 136 " =    2.022
peak=   -3.385 closest distance to " O   HOH Z 120 " =    1.385
peak=   -3.380 closest distance to " O   HOH Z 372 " =    2.431
peak=   -3.374 closest distance to " CD2 PHE A  59 " =    2.356
peak=   -3.368 closest distance to " CA  GLY A 133 " =    2.018
peak=   -3.367 closest distance to " O   HOH Z 396 " =    1.675
peak=   -3.366 closest distance to " O   HOH Z 150 " =    1.136
peak=   -3.363 closest distance to " CB  ALA A 291 " =    2.370
peak=   -3.356 closest distance to " O   HOH Z 174 " =    2.198
peak=   -3.355 closest distance to " OG  SER A   3 " =    1.789
peak=   -3.350 closest distance to " CD2 TYR A 293 " =    1.759
peak=   -3.345 closest distance to " O   HOH Z 176 " =    1.754
peak=   -3.341 closest distance to " O   HOH Z 361 " =    3.443
peak=   -3.335 closest distance to " CH2 TRP A 150 " =    1.035
peak=   -3.328 closest distance to " O   HOH Z 388 " =    1.987
peak=   -3.327 closest distance to " CG1 VAL A  78 " =    2.833
peak=   -3.325 closest distance to " O   HOH Z 109 " =    5.899
peak=   -3.321 closest distance to " OD1 ASN A 148 " =    1.602
peak=   -3.317 closest distance to " CZ3 TRP A 274 " =    2.317
peak=   -3.317 closest distance to " OE1 GLN A 223 " =    2.127
peak=   -3.306 closest distance to " CG1 VAL A 112 " =    2.590
peak=   -3.303 closest distance to " CD  GLN A  88 " =    1.065
peak=   -3.302 closest distance to " O   TYR A  15 " =    1.735
peak=   -3.300 closest distance to " O   HOH Z 252 " =    3.187
peak=   -3.296 closest distance to " OG1 THR A  82 " =    1.447
peak=   -3.295 closest distance to " O   HOH Z 198 " =    1.949
peak=   -3.291 closest distance to " CG2 ILE A 263 " =    2.297
peak=   -3.290 closest distance to " OD2 ASP A 171 " =    1.807
peak=   -3.289 closest distance to " C   ASN A 285 " =    2.245
peak=   -3.289 closest distance to " CG  ASP A 132 " =    2.353
peak=   -3.287 closest distance to " O   HOH Z  90 " =    2.240
peak=   -3.286 closest distance to " CB  ASP A 162 " =    2.660
peak=   -3.281 closest distance to " O   HOH Z 114 " =    3.509
peak=   -3.278 closest distance to " O   HOH Z 397 " =    1.147
peak=   -3.277 closest distance to " CB  ALA A 131 " =    2.303
peak=   -3.274 closest distance to " O   HOH Z 151 " =    1.363
peak=   -3.273 closest distance to " O   HOH Z 133 " =    1.904
peak=   -3.268 closest distance to " CB  PRO A 213 " =    1.582
peak=   -3.265 closest distance to " NE1 TRP A 123 " =    1.273
peak=   -3.264 closest distance to " ND2 ASN A  45 " =    1.726
peak=   -3.263 closest distance to " O   SER A   3 " =    1.109
peak=   -3.263 closest distance to " CD  ARG A 139 " =    1.568
peak=   -3.262 closest distance to " O   HOH Z 126 " =    1.974
peak=   -3.262 closest distance to " CG2 THR A   4 " =    1.827
peak=   -3.258 closest distance to " O   HOH Z 377 " =    1.257
peak=   -3.249 closest distance to " CB  ASP A 132 " =    2.394
peak=   -3.249 closest distance to " CG  ASP A 231 " =    0.797
peak=   -3.248 closest distance to " OD2 ASP A 171 " =    2.303
peak=   -3.248 closest distance to " CG2AVAL A  41 " =    2.936
peak=   -3.241 closest distance to " O   HOH Z 210 " =    0.953
peak=   -3.239 closest distance to " CB  ALA A 291 " =    2.248
peak=   -3.239 closest distance to " O   HOH Z 394 " =    1.580
peak=   -3.232 closest distance to " N   ALA A 226 " =    1.906
peak=   -3.228 closest distance to " NE2 GLN A 103 " =    1.529
peak=   -3.228 closest distance to " O   HOH Z 407 " =    1.350
peak=   -3.223 closest distance to " CB  SER A 146 " =    2.140
peak=   -3.216 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.212 closest distance to " O   HOH Z 191 " =    5.993
peak=   -3.211 closest distance to " NH1 ARG A 195 " =    2.590
peak=   -3.211 closest distance to " OG  SER A  26 " =    1.382
peak=   -3.211 closest distance to " CD1 LEU A  25 " =    2.525
peak=   -3.210 closest distance to " NH2BARG A 275 " =    1.738
peak=   -3.206 closest distance to " NH1 ARG A  66 " =    3.289
peak=   -3.203 closest distance to " OD1 ASN A 301 " =    1.993
peak=   -3.198 closest distance to " O   LEU A 282 " =    2.231
peak=   -3.197 closest distance to " OD1 ASP A 298 " =    2.020
peak=   -3.197 closest distance to " OD1 ASN A  39 " =    2.229
peak=   -3.193 closest distance to " O   HOH Z 252 " =    3.973
peak=   -3.192 closest distance to " ND2BASN A 224 " =    1.932
peak=   -3.189 closest distance to " O   GLY A  80 " =    2.548
peak=   -3.189 closest distance to " O   HOH Z 345 " =    2.844
peak=   -3.188 closest distance to " O   HOH Z 150 " =    2.250
peak=   -3.187 closest distance to " CB  TRP A  85 " =    2.484
peak=   -3.183 closest distance to " O   SER A 135 " =    1.652
peak=   -3.183 closest distance to " CZ  PHE A  38 " =    1.985
peak=   -3.182 closest distance to " O   GLU A 152 " =    1.494
peak=   -3.181 closest distance to " CD2 HIS A 207 " =    2.371
peak=   -3.179 closest distance to " C   GLY A  80 " =    2.592
peak=   -3.176 closest distance to " O   VAL A 125 " =    2.203
peak=   -3.175 closest distance to " N   ALA A 248 " =    1.803
peak=   -3.171 closest distance to " CG1 VAL A 112 " =    2.581
peak=   -3.170 closest distance to " O   HOH Z 149 " =    1.448
peak=   -3.167 closest distance to " ND2 ASN A  39 " =    1.159
peak=   -3.165 closest distance to " CG  ARG A 259 " =    2.354
peak=   -3.165 closest distance to " CG1 VAL A 197 " =    2.115
peak=   -3.164 closest distance to " OE2 GLU A   2 " =    1.649
peak=   -3.164 closest distance to " CB  ALA A   9 " =    2.567
peak=   -3.162 closest distance to " O   SER A  26 " =    1.490
peak=   -3.156 closest distance to " CA  GLU A   2 " =    2.505
peak=   -3.156 closest distance to " CD1 ILE A 106 " =    2.116
peak=   -3.151 closest distance to " O   HOH Z  37 " =    1.431
peak=   -3.148 closest distance to " ND2 ASN A  45 " =    1.222
peak=   -3.148 closest distance to " O   HOH Z 258 " =    2.072
peak=   -3.145 closest distance to " O   HOH Z 215 " =    3.758
peak=   -3.145 closest distance to " O   HOH Z 139 " =    3.319
peak=   -3.145 closest distance to " CE1 TYR A 247 " =    2.433
peak=   -3.145 closest distance to " NH2 ARG A  66 " =    5.653
peak=   -3.144 closest distance to " O   HOH Z 166 " =    1.396
peak=   -3.143 closest distance to " O   GLY A 196 " =    0.995
peak=   -3.141 closest distance to " CG1 VAL A  78 " =    2.516
peak=   -3.140 closest distance to " CG1AVAL A  41 " =    2.584
peak=   -3.137 closest distance to " O   ALA A  10 " =    1.764
peak=   -3.134 closest distance to " CG  GLN A  11 " =    1.634
peak=   -3.130 closest distance to " O   SER A 273 " =    1.341
peak=   -3.125 closest distance to " OXT GLY A 302 " =    3.284
peak=   -3.124 closest distance to " OG BSER A 134 " =    1.812
peak=   -3.123 closest distance to " OE1 GLN A 183 " =    1.523
peak=   -3.118 closest distance to " O   HOH Z 422 " =    1.394
peak=   -3.113 closest distance to " C   ASN A 148 " =    1.698
peak=   -3.112 closest distance to " NH1 ARG A 195 " =    2.313
peak=   -3.111 closest distance to " O   HOH Z 428 " =    1.145
peak=   -3.106 closest distance to " O   HOH Z 384 " =    1.846
peak=   -3.103 closest distance to " N   ARG A 138 " =    1.656
peak=   -3.100 closest distance to " ND2 ASN A  60 " =    1.558
peak=   -3.098 closest distance to " O   HOH Z 196 " =    1.738
peak=   -3.096 closest distance to " CE  MET A 105 " =    2.393
peak=   -3.094 closest distance to " NZ  LYS A 117 " =    1.948
peak=   -3.092 closest distance to " N   THR A  52 " =    1.652
peak=   -3.089 closest distance to " O   HOH Z  64 " =    1.774
peak=   -3.089 closest distance to " CG  ARG A 269 " =    2.591
peak=   -3.087 closest distance to " N   ARG A 159 " =    1.585
peak=   -3.085 closest distance to " O   HOH Z  79 " =    1.739
peak=   -3.084 closest distance to " CE  MET A  93 " =    1.271
peak=   -3.077 closest distance to " O   SER A 276 " =    1.700
peak=   -3.072 closest distance to " CD1 LEU A 228 " =    2.201
peak=   -3.069 closest distance to " O   HOH Z 166 " =    1.457
peak=   -3.069 closest distance to " OH  TYR A 169 " =    0.971
peak=   -3.060 closest distance to " O   HOH Z 200 " =    1.339
peak=   -3.053 closest distance to " CG  PHE A 283 " =    2.850
peak=   -3.024 closest distance to " CA  GLY A 241 " =    2.303
peak=   -3.006 closest distance to " O   HOH Z 120 " =    2.260

================= 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    :  0.4456 0.4322   6.263188e+00   6.236490e+00
   1_bss:  0.4358 0.4192   6.251666e+00   6.223456e+00
   1_xyz:  0.3563 0.3815   6.123858e+00   6.159826e+00
   1_adp:  0.3278 0.3848   6.072657e+00   6.166362e+00
   1_occ:  0.3274 0.3849   6.071900e+00   6.166296e+00
   2_bss:  0.3266 0.3832   6.072798e+00   6.166666e+00
   2_xyz:  0.2598 0.3144   5.870399e+00   6.013946e+00
   2_adp:  0.2392 0.3014   5.821154e+00   5.986588e+00
   2_occ:  0.2390 0.3012   5.820333e+00   5.986378e+00
   3_bss:  0.2383 0.3004   5.819519e+00   5.985048e+00
   3_xyz:  0.1832 0.2347   5.566189e+00   5.758594e+00
   3_adp:  0.1625 0.2165   5.473381e+00   5.687332e+00
   3_occ:  0.1624 0.2167   5.473176e+00   5.687464e+00
   4_bss:  0.1624 0.2156   5.471923e+00   5.684062e+00
   4_xyz:  0.1353 0.1899   5.319438e+00   5.556871e+00
   4_adp:  0.1269 0.1769   5.256218e+00   5.492217e+00
   4_occ:  0.1267 0.1765   5.255172e+00   5.491584e+00
   5_bss:  0.1272 0.1768   5.256643e+00   5.491755e+00
   5_xyz:  0.1176 0.1683   5.196761e+00   5.442103e+00
   5_adp:  0.1156 0.1659   5.183838e+00   5.430776e+00
   5_occ:  0.1155 0.1659   5.183466e+00   5.430540e+00
   5_bss:  0.1155 0.1658   5.183481e+00   5.430607e+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:  0.298  25.704  -2.021   5.222  -1.793   0.000  -0.000  -0.000
   1_xyz:  0.298  25.704  -2.021   5.222  -1.793   0.000  -0.000  -0.000
   1_adp:  0.298  25.704  -2.021   5.222  -1.793   0.000  -0.000  -0.000
   1_occ:  0.298  25.704  -2.021   5.222  -1.793   0.000  -0.000  -0.000
   2_bss:  0.277  33.890  -1.956   3.212  -0.686   0.000  -0.000  -0.000
   2_xyz:  0.277  33.890  -1.956   3.212  -0.686   0.000  -0.000  -0.000
   2_adp:  0.277  33.890  -1.956   3.212  -0.686   0.000  -0.000  -0.000
   2_occ:  0.277  33.890  -1.956   3.212  -0.686   0.000  -0.000  -0.000
   3_bss:  0.317  52.440  -1.602   1.606  -0.409   0.000  -0.000  -0.000
   3_xyz:  0.317  52.440  -1.602   1.606  -0.409   0.000  -0.000  -0.000
   3_adp:  0.317  52.440  -1.602   1.606  -0.409   0.000  -0.000  -0.000
   3_occ:  0.317  52.440  -1.602   1.606  -0.409   0.000  -0.000  -0.000
   4_bss:  0.327  64.228  -2.013   0.293  -0.614   0.000  -0.000  -0.000
   4_xyz:  0.327  64.228  -2.013   0.293  -0.614   0.000  -0.000  -0.000
   4_adp:  0.327  64.228  -2.013   0.293  -0.614   0.000  -0.000  -0.000
   4_occ:  0.327  64.228  -2.013   0.293  -0.614   0.000  -0.000  -0.000
   5_bss:  0.330  62.953  -2.079  -0.239  -0.515  -0.000  -0.000  -0.000
   5_xyz:  0.330  62.953  -2.079  -0.239  -0.515  -0.000  -0.000  -0.000
   5_adp:  0.330  62.953  -2.079  -0.239  -0.515  -0.000  -0.000  -0.000
   5_occ:  0.330  62.953  -2.079  -0.239  -0.515  -0.000  -0.000  -0.000
   5_bss:  0.327  61.399  -1.960  -0.321  -0.366  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.334 0.5312  0.7045    58311.976
   1_bss:  48.179 0.5444  0.7326    54790.911
   1_xyz:  43.672 0.5982  0.7874    43874.930
   1_adp:  43.726 0.5975  0.7905    44250.805
   1_occ:  43.705 0.5976  0.7887    44062.494
   2_bss:  43.425 0.6011  0.7891    43754.535
   2_xyz:  34.373 0.7068  0.9080    27553.858
   2_adp:  32.614 0.7276  0.9087    25547.231
   2_occ:  32.590 0.7279  0.9086    25505.335
   3_bss:  32.410 0.7300  0.9033    25322.961
   3_xyz:  23.496 0.8263  0.9848    14070.503
   3_adp:  21.130 0.8507  0.9863    12100.482
   3_occ:  21.130 0.8507  0.9865    12112.276
   4_bss:  20.962 0.8521  0.9659    11919.840
   4_xyz:  18.022 0.8796  0.9801     9022.042
   4_adp:  16.464 0.8940  0.9774     7986.143
   4_occ:  16.440 0.8943  0.9776     7972.881
   5_bss:  16.429 0.8944  0.9722     7971.667
   5_xyz:  15.343 0.9038  0.9775     7183.833
   5_adp:  15.081 0.9061  0.9713     7064.600
   5_occ:  15.074 0.9062  0.9713     7059.242
   5_bss:  15.074 0.9062  0.9738     7058.175
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7852e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7852e-01
   1_xyz:   1.468  0.011  0.086 15.525  0.005  4.109   1.1718e-01
   1_adp:   1.468  0.011  0.086 15.525  0.005  4.109   1.1718e-01
   1_occ:   1.468  0.011  0.086 15.525  0.005  4.109   1.1718e-01
   2_bss:   1.468  0.011  0.086 15.525  0.005  4.109   1.1718e-01
   2_xyz:   1.497  0.011  0.096 15.604  0.006  4.106   1.1474e-01
   2_adp:   1.497  0.011  0.096 15.604  0.006  4.106   1.1474e-01
   2_occ:   1.497  0.011  0.096 15.604  0.006  4.106   1.1474e-01
   3_bss:   1.497  0.011  0.096 15.604  0.006  4.106   1.1474e-01
   3_xyz:   1.125  0.009  0.070 14.852  0.005  4.122   7.8888e-02
   3_adp:   1.125  0.009  0.070 14.852  0.005  4.122   7.8888e-02
   3_occ:   1.125  0.009  0.070 14.852  0.005  4.122   7.8888e-02
   4_bss:   1.125  0.009  0.070 14.852  0.005  4.122   7.8888e-02
   4_xyz:   1.138  0.009  0.078 14.806  0.004  4.124   7.3004e-02
   4_adp:   1.138  0.009  0.078 14.806  0.004  4.124   7.3004e-02
   4_occ:   1.138  0.009  0.078 14.806  0.004  4.124   7.3004e-02
   5_bss:   1.138  0.009  0.078 14.806  0.004  4.124   7.3004e-02
   5_xyz:   1.130  0.009  0.081 14.803  0.005  4.112   7.2989e-02
   5_adp:   1.130  0.009  0.081 14.803  0.005  4.112   7.2989e-02
   5_occ:   1.130  0.009  0.081 14.803  0.005  4.112   7.2989e-02
   5_bss:   1.130  0.009  0.081 14.803  0.005  4.112   7.2989e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.489   2.4183e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.489   2.4183e-01
   1_xyz:   8.953  0.077  0.464 89.707  0.034  1.806   1.8507e-01
   1_adp:   8.953  0.077  0.464 89.707  0.034  1.806   1.8507e-01
   1_occ:   8.953  0.077  0.464 89.707  0.034  1.806   1.8507e-01
   2_bss:   8.953  0.077  0.464 89.707  0.034  1.806   1.8507e-01
   2_xyz:   8.936  0.065  0.367 84.016  0.028  2.131   9.1693e-02
   2_adp:   8.936  0.065  0.367 84.016  0.028  2.131   9.1693e-02
   2_occ:   8.936  0.065  0.367 84.016  0.028  2.131   9.1693e-02
   3_bss:   8.936  0.065  0.367 84.016  0.028  2.131   9.1693e-02
   3_xyz:   7.387  0.045  0.231 85.088  0.046  2.239   1.4559e-01
   3_adp:   7.387  0.045  0.231 85.088  0.046  2.239   1.4559e-01
   3_occ:   7.387  0.045  0.231 85.088  0.046  2.239   1.4559e-01
   4_bss:   7.387  0.045  0.231 85.088  0.046  2.239   1.4559e-01
   4_xyz:   7.830  0.063  0.228 81.372  0.035  2.305   6.7026e-02
   4_adp:   7.830  0.063  0.228 81.372  0.035  2.305   6.7026e-02
   4_occ:   7.830  0.063  0.228 81.372  0.035  2.305   6.7026e-02
   5_bss:   7.830  0.063  0.228 81.372  0.035  2.305   6.7026e-02
   5_xyz:   8.207  0.049  0.307 81.046  0.038  2.276   6.4509e-02
   5_adp:   8.207  0.049  0.307 81.046  0.038  2.276   6.4509e-02
   5_occ:   8.207  0.049  0.307 81.046  0.038  2.276   6.4509e-02
   5_bss:   8.207  0.049  0.307 81.046  0.038  2.276   6.4509e-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:  94.06   0.00  18.56  75.27   0.00  15.44  94.06   0.00  35.53
   1_occ:  94.06   0.00  18.56  75.27   0.00  15.44  94.06   0.00  35.53
   2_bss:  94.06   0.00  18.56  75.27   0.00  15.44  94.06   0.00  35.53
   2_xyz:  94.06   0.00  18.56  75.27   0.00  15.44  94.06   0.00  35.53
   2_adp:  92.23   0.00  18.12  85.08   0.00  14.49  92.23   1.94  37.85
   2_occ:  92.23   0.00  18.12  85.08   0.00  14.49  92.23   1.94  37.85
   3_bss:  92.23   0.00  18.12  85.08   0.00  14.49  92.23   1.94  37.85
   3_xyz:  92.23   0.00  18.12  85.08   0.00  14.49  92.23   1.94  37.85
   3_adp: 108.04   0.00  18.42 108.04   0.00  13.57 107.90   5.09  44.81
   3_occ: 108.04   0.00  18.42 108.04   0.00  13.57 107.90   5.09  44.81
   4_bss: 108.04   0.00  18.42 108.04   0.00  13.57 107.90   5.09  44.81
   4_xyz: 108.04   0.00  18.42 108.04   0.00  13.57 107.90   5.09  44.81
   4_adp: 112.11   0.00  17.56 112.11   0.39  12.69 108.82   0.00  44.06
   4_occ: 112.11   0.00  17.56 112.11   0.39  12.69 108.82   0.00  44.06
   5_bss: 112.11   0.00  17.56 112.11   0.39  12.69 108.82   0.00  44.06
   5_xyz: 112.11   0.00  17.56 112.11   0.39  12.69 108.82   0.00  44.06
   5_adp: 115.06   0.00  17.11 115.06   0.00  12.34 111.76   0.92  43.06
   5_occ: 115.06   0.00  17.11 115.06   0.00  12.34 111.76   0.92  43.06
   5_bss: 115.06   0.00  17.11 115.06   0.00  12.35 111.76   0.92  43.06
------------------------------------------------------------------------
 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:    1.822    0.011    0.302
   1_adp:    1.822    0.011    0.302
   1_occ:    1.822    0.011    0.302
   2_bss:    1.822    0.011    0.302
   2_xyz:    1.580    0.066    0.555
   2_adp:    1.580    0.066    0.555
   2_occ:    1.580    0.066    0.555
   3_bss:    1.580    0.066    0.555
   3_xyz:    1.519    0.079    0.706
   3_adp:    1.519    0.079    0.706
   3_occ:    1.519    0.079    0.706
   4_bss:    1.519    0.079    0.706
   4_xyz:    1.549    0.114    0.782
   4_adp:    1.549    0.114    0.782
   4_occ:    1.549    0.114    0.782
   5_bss:    1.549    0.114    0.782
   5_xyz:    1.577    0.095    0.805
   5_adp:    1.577    0.095    0.805
   5_occ:    1.577    0.095    0.805
   5_bss:    1.577    0.095    0.805
------------------------------------------------------------------------

CPU time actual refinement: 333.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_356/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_356/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_356/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_356/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_356/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.33 
  Macro-tasks:
    bulk solvent and scale       = 40.70  
    individual site refinement   = 134.18 
    weights calculation          = 30.86  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 212.50 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 105.50 
    alpha_beta                      = 8.58   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 113.28 
    fmodel                         = 6.69   
    r_factors                      = 0.15   
    phase_errors                   = 10.62  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 248.70 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.803 micro seconds
Total CPU time: 5.78 minutes
from_scatterers_fft:    624 calls, 105.21 s
gradients_fft:          569 calls, 100.88 s

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

# Date 2008-01-16 Time 04:38:02 PST -0800 (1200487082.99 s)
Start R-work = 0.4456, R-free = 0.4322 (no bulk solvent and anisotropic scale)
Final R-work = 0.1344, R-free = 0.1812 (no bulk solvent and anisotropic scale)

Start R-work = 0.4358, R-free = 0.4192
Final R-work = 0.1155, R-free = 0.1658