# Date 2008-01-16 Time 05:08:44 PST -0800 (1200488924.33 s)
#phil __OFF__

Command line arguments: "../615.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27394
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 615

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.7567, 88.5498, 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: (70.25, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.95366
Completeness in resolution range: 0.920449
Completeness with d_max=infinity: 0.917818

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9537

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.95366
Completeness in resolution range: 0.920449
Completeness with d_max=infinity: 0.917818

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.1820 [2236/2262]  2011   225  10.1%
  bin  2:  4.1820 -  3.3311 [2148/2168]  1938   210   9.8%
  bin  3:  3.3311 -  2.9135 [2118/2137]  1905   213  10.1%
  bin  4:  2.9135 -  2.6487 [2099/2129]  1879   220  10.5%
  bin  5:  2.6487 -  2.4597 [2094/2113]  1885   209  10.0%
  bin  6:  2.4597 -  2.3152 [2078/2103]  1873   205   9.9%
  bin  7:  2.3152 -  2.1996 [2062/2090]  1861   201   9.7%
  bin  8:  2.1996 -  2.1041 [2076/2112]  1862   214  10.3%
  bin  9:  2.1041 -  2.0233 [1967/2086]  1780   187   9.5%
  bin 10:  2.0233 -  1.9537 [ 711/2082]   636    75  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_615/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: 0.13 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:
        1.48 -     2.16: 27
        2.16 -     2.85: 1111
        2.85 -     3.53: 4448
        3.53 -     4.22: 9273
        4.22 -     4.90: 13490
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.481 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.562 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.629 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 104 "  1.681 3.040 -x+1,y+1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  ... (remaining 28344 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_615/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_615/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.75675 88.54975 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: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4835   r_free= 0.4869   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.299217                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6652 0.99   1445  159 0.4016 0.3952      6.6392      6.6082|
|  2:  4.6652 -  3.7211 0.99   1395  159 0.4330 0.4405      6.8494      6.8467|
|  3:  3.7211 -  3.2562 0.99   1383  151 0.4575 0.4428      6.6969      6.6781|
|  4:  3.2562 -  2.9609 0.99   1360  154 0.4878 0.5097      6.5476      6.5434|
|  5:  2.9609 -  2.7500 0.99   1357  150 0.5184 0.5117      6.3722      6.4024|
|  6:  2.7500 -  2.5887 0.99   1352  143 0.5134 0.5384        6.28      6.2066|
|  7:  2.5887 -  2.4597 0.99   1326  161 0.5108 0.5247       6.235      6.2001|
|  8:  2.4597 -  2.3530 0.98   1340  146 0.5302 0.5298      6.1685      6.1397|
|  9:  2.3530 -  2.2627 0.98   1311  140 0.5142 0.5401      6.1219       6.232|
| 10:  2.2627 -  2.1849 1.00   1371  150 0.5220 0.5347      6.0706       6.087|
| 11:  2.1849 -  2.1168 0.98   1305  151 0.5145 0.5068      6.0157      6.0267|
| 12:  2.1168 -  2.0564 0.98   1325  137 0.5157 0.5085      5.9379      5.9222|
| 13:  2.0564 -  2.0024 0.81   1085  126 0.5167 0.4981      5.8931      5.7971|
| 14:  2.0024 -  1.9537 0.21    275   32 0.5260 0.4886      5.8489      5.8294|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.6652  1445   159  0.71  33.86   0.80     0.76      73529.80|
|  2:  4.6652 -  3.7211  1395   159  0.65  39.64   0.88     0.75     131272.59|
|  3:  3.7211 -  3.2562  1383   151  0.49  52.55   0.90     0.67     145005.91|
|  4:  3.2562 -  2.9609  1360   154  0.36  63.09   0.88     0.52     136322.13|
|  5:  2.9609 -  2.7500  1357   150  0.31  66.59   0.85     0.46      96631.13|
|  6:  2.7500 -  2.5887  1352   143  0.29  67.94   0.88     0.43      81615.76|
|  7:  2.5887 -  2.4597  1326   161  0.31  66.48   0.91     0.44      69122.17|
|  8:  2.4597 -  2.3530  1340   146  0.29  68.47   0.89     0.43      64164.05|
|  9:  2.3530 -  2.2627  1311   140  0.27  69.54   0.90     0.41      59766.89|
| 10:  2.2627 -  2.1849  1371   150  0.27  69.80   0.91     0.41      53569.22|
| 11:  2.1849 -  2.1168  1305   151  0.28  68.84   0.95     0.45      51005.02|
| 12:  2.1168 -  2.0564  1325   137  0.31  67.12   0.92     0.50      43869.23|
| 13:  2.0564 -  2.0024  1085   126  0.32  66.07   0.94     0.54      37785.33|
| 14:  2.0024 -  1.9537   275    32  0.40  60.14   1.01     0.58      28552.42|
|alpha:            min =        0.41 max =            0.76 mean =         0.52|
|beta:             min =    28552.42 max =       145005.91 mean =     80530.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.98 mean =        61.19|
|phase err.(test): min =        0.00 max =           89.88 mean =        61.59|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 24.798913             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.673   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.791268              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.791   (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 |  1.481 -  1.823:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.823 -  2.165:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.165 -  2.507:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.507 -  2.849:     1072 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.849 -  3.190:     1990 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.190 -  3.532:     2458 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.532 -  3.874:     4647 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.874 -  4.216:     4626 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.216 -  4.558:     6140 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7350 |
|-----------------------------------------------------------------------------|
|-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 |        0.195 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.481 |       0.664 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    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: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4835   r_free= 0.4869   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.299217                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4723   r_free= 0.4798   ksol= 0.33   Bsol= 33.38   scale= 0.909   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.54,1.19,3.53,0.00,0.00,0.00); trace/3= 0.39                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.293792                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.035919             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.551   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.579791              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.457   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4723      final r-factor (work) = 0.3910          |
| start r-factor (free) = 0.4798      final r-factor (free) = 0.4412          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.0506 = 19.04 * 0.50 * 6.2887 + 1.00 * 0.1954                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.2404 = 19.04 * 0.50 * 6.2059 + 1.00 * 0.1728                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3910      final r-factor (work) = 0.3619          |
| start r-factor (free) = 0.4412      final r-factor (free) = 0.4500          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8102 = 1.58 * 1.00 * 6.2059 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7200 = 1.58 * 1.00 * 6.1395 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.74   18.57    None  None   None       |
|    all(noH): 2823   0      0.00    79.74   18.57    None  None   None       |
|    Sol.    : 438    0      0.00    79.74   34.11    None  None   None       |
|    Mac.    : 2385   0      0.00    70.98   15.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.974:  614   |   5:    39.870 -  47.844:  116        |
|      1:     7.974 -  15.948:  813   |   6:    47.844 -  55.817:   73        |
|      2:    15.948 -  23.922:  614   |   7:    55.817 -  63.791:   22        |
|      3:    23.922 -  31.896:  348   |   8:    63.791 -  71.765:   14        |
|      4:    31.896 -  39.870:  206   |   9:    71.765 -  79.739:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3619 r_free = 0.4500             target_work(ml) = 6.143         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3612 r_free = 0.4511             target_work(ml) = 6.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3612   r_free= 0.4511   ksol= 0.33   Bsol= 33.38   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.54,1.19,3.53,0.00,0.00,0.00); trace/3= 0.39                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.143073                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3604   r_free= 0.4498   ksol= 0.35   Bsol= 66.92   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.29,2.09,0.00,0.00,0.00); trace/3= 0.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.146169                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.971969             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.002  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.779123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.939  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3604      final r-factor (work) = 0.2967          |
| start r-factor (free) = 0.4498      final r-factor (free) = 0.3832          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.3705 = 17.97 * 0.50 * 6.1426 + 1.00 * 0.1728                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.8619 = 17.97 * 0.50 * 6.0907 + 1.00 * 0.1310                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2967      final r-factor (work) = 0.2755          |
| start r-factor (free) = 0.3832      final r-factor (free) = 0.3649          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7657 = 0.78 * 1.00 * 6.0907 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6664 = 0.78 * 1.00 * 5.9717 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.97   18.09    None  None   None       |
|    all(noH): 2823   0      0.00    82.97   18.09    None  None   None       |
|    Sol.    : 438    0      0.00    82.97   36.09    None  None   None       |
|    Mac.    : 2385   0      0.00    71.80   14.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.297:  679   |   5:    41.483 -  49.779:  107        |
|      1:     8.297 -  16.593:  913   |   6:    49.779 -  58.076:   62        |
|      2:    16.593 -  24.890:  565   |   7:    58.076 -  66.373:   19        |
|      3:    24.890 -  33.186:  288   |   8:    66.373 -  74.669:   11        |
|      4:    33.186 -  41.483:  177   |   9:    74.669 -  82.966:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2755 r_free = 0.3649             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2754 r_free = 0.3650             target_work(ml) = 5.951         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2754   r_free= 0.3650   ksol= 0.35   Bsol= 66.92   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.29,2.09,0.00,0.00,0.00); trace/3= 0.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.950893                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2756   r_free= 0.3633   ksol= 0.35   Bsol= 74.86   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.32,1.48,-0.00,0.00,0.00); trace/3= 0.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.947491                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.639482              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.262628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.242  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2756      final r-factor (work) = 0.2293          |
| start r-factor (free) = 0.3633      final r-factor (free) = 0.3053          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9696 = 5.64 * 0.50 * 5.9717 + 1.00 * 0.1310                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6682 = 5.64 * 0.50 * 5.8873 + 1.00 * 0.0675                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2293      final r-factor (work) = 0.2090          |
| start r-factor (free) = 0.3053      final r-factor (free) = 0.2921          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3346 = 2.26 * 1.00 * 5.8873 + 1.00 * 0.0137                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0211 = 2.26 * 1.00 * 5.7461 + 1.00 * 0.0197                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.84  19.52    None  None   None       |
|    all(noH): 2823   0      0.00    106.84  19.52    None  None   None       |
|    Sol.    : 438    0      1.78    106.84  48.27    None  None   None       |
|    Mac.    : 2385   0      0.00    101.25  14.24    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 -  10.684: 1156   |   5:    53.418 -  64.102:   90        |
|      1:    10.684 -  21.367:  862   |   6:    64.102 -  74.786:   68        |
|      2:    21.367 -  32.051:  298   |   7:    74.786 -  85.469:   39        |
|      3:    32.051 -  42.735:  171   |   8:    85.469 -  96.153:   15        |
|      4:    42.735 -  53.418:  116   |   9:    96.153 - 106.837:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2090 r_free = 0.2921             target_work(ml) = 5.725         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2090 r_free = 0.2920             target_work(ml) = 5.724         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2090   r_free= 0.2920   ksol= 0.35   Bsol= 74.86   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.32,1.48,-0.00,0.00,0.00); trace/3= 0.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.724126                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2091   r_free= 0.2921   ksol= 0.34   Bsol= 74.86   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-1.11,0.89,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.723302                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.397628              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.924  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.277866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.151  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2091      final r-factor (work) = 0.1754          |
| start r-factor (free) = 0.2921      final r-factor (free) = 0.2400          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8298 = 3.40 * 0.50 * 5.7466 + 1.00 * 0.0675                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6646 = 3.40 * 0.50 * 5.6546 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1754      final r-factor (work) = 0.1649          |
| start r-factor (free) = 0.2400      final r-factor (free) = 0.2187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5909 = 0.28 * 1.00 * 5.6546 + 1.00 * 0.0197                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5472 = 0.28 * 1.00 * 5.5283 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    97.40   17.87    None  None   None       |
|    all(noH): 2823   0      1.12    97.40   17.87    None  None   None       |
|    Sol.    : 438    0      4.75    97.09   45.18    None  None   None       |
|    Mac.    : 2385   0      1.12    97.40   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.123 -  10.751: 1282   |   5:    49.262 -  58.889:   89        |
|      1:    10.751 -  20.379:  878   |   6:    58.889 -  68.517:   72        |
|      2:    20.379 -  30.006:  208   |   7:    68.517 -  78.144:   27        |
|      3:    30.006 -  39.634:  124   |   8:    78.144 -  87.772:   16        |
|      4:    39.634 -  49.262:  114   |   9:    87.772 -  97.400:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1649 r_free = 0.2187             target_work(ml) = 5.480         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1648 r_free = 0.2183             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1648   r_free= 0.2183   ksol= 0.34   Bsol= 74.86   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-1.11,0.89,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.478892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1647   r_free= 0.2175   ksol= 0.33   Bsol= 61.40   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-1.79,0.55,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.477322                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.422397              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.281  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.562143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.304  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1353          |
| start r-factor (free) = 0.2175      final r-factor (free) = 0.1853          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2822 = 4.42 * 0.50 * 5.5281 + 1.00 * 0.0585                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0114 = 4.42 * 0.50 * 5.3985 + 1.00 * 0.0742                              |
|-----------------------------------------------------------------------------|
| 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) = 0.1290          |
| start r-factor (free) = 0.1853      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0457 = 0.56 * 1.00 * 5.3985 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9832 = 0.56 * 1.00 * 5.2865 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.72   17.57    None  None   None       |
|    all(noH): 2823   0      0.00    96.72   17.57    None  None   None       |
|    Sol.    : 438    0      5.06    95.70   45.59    None  None   None       |
|    Mac.    : 2385   0      0.00    96.72   12.43    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 -   9.672: 1112   |   5:    48.358 -  58.030:   95        |
|      1:     9.672 -  19.343: 1035   |   6:    58.030 -  67.702:   76        |
|      2:    19.343 -  29.015:  227   |   7:    67.702 -  77.373:   38        |
|      3:    29.015 -  38.687:  111   |   8:    77.373 -  87.045:   17        |
|      4:    38.687 -  48.358:  100   |   9:    87.045 -  96.717:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1792             target_work(ml) = 5.272         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1289 r_free = 0.1792             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1792   ksol= 0.33   Bsol= 61.40   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-1.79,0.55,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.271497                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6652 0.99   1445  159 0.0932 0.1399      5.3919      5.6641|
|  2:  4.6652 -  3.7211 0.99   1395  159 0.0884 0.1238      5.4929      5.7438|
|  3:  3.7211 -  3.2562 0.99   1383  151 0.1243 0.1708      5.5961      5.8987|
|  4:  3.2562 -  2.9609 0.99   1360  154 0.1537 0.2018      5.6208      5.7903|
|  5:  2.9609 -  2.7500 0.99   1357  150 0.1602 0.2044      5.4986      5.7203|
|  6:  2.7500 -  2.5887 0.99   1352  143 0.1505 0.2261      5.3588      5.6003|
|  7:  2.5887 -  2.4597 0.99   1326  161 0.1461 0.1943      5.2957      5.4705|
|  8:  2.4597 -  2.3530 0.98   1340  146 0.1506 0.1981      5.2494      5.4718|
|  9:  2.3530 -  2.2627 0.98   1311  140 0.1433 0.1995      5.1712      5.4194|
| 10:  2.2627 -  2.1849 1.00   1371  150 0.1277 0.1716      5.0427      5.2205|
| 11:  2.1849 -  2.1168 0.98   1305  151 0.1267 0.2082      5.0181       5.429|
| 12:  2.1168 -  2.0564 0.98   1325  137 0.1309 0.1868      4.9409      5.1633|
| 13:  2.0564 -  2.0024 0.81   1085  126 0.1180 0.1577      4.8365      4.9965|
| 14:  2.0024 -  1.9537 0.21    275   32 0.1085 0.1924      4.7266      5.1137|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.6652  1445   159  0.93  10.14   0.97     0.94       8399.76|
|  2:  4.6652 -  3.7211  1395   159  0.95   8.99   1.03     1.01      10702.40|
|  3:  3.7211 -  3.2562  1383   151  0.92  13.78   1.05     1.04      13411.10|
|  4:  3.2562 -  2.9609  1360   154  0.88  18.16   1.02     0.99      14879.99|
|  5:  2.9609 -  2.7500  1357   150  0.87  19.71   1.00     0.97      12120.14|
|  6:  2.7500 -  2.5887  1352   143  0.87  19.94   0.99     0.95       9566.65|
|  7:  2.5887 -  2.4597  1326   161  0.87  18.98   1.01     0.97       8282.01|
|  8:  2.4597 -  2.3530  1340   146  0.87  19.38   1.01     0.96       7553.42|
|  9:  2.3530 -  2.2627  1311   140  0.87  19.26   1.01     0.96       6635.72|
| 10:  2.2627 -  2.1849  1371   150  0.88  18.33   1.01     0.98       5446.62|
| 11:  2.1849 -  2.1168  1305   151  0.89  17.84   1.00     0.94       5033.47|
| 12:  2.1168 -  2.0564  1325   137  0.88  18.11   1.02     1.01       4526.17|
| 13:  2.0564 -  2.0024  1085   126  0.89  18.08   1.01     0.99       3824.96|
| 14:  2.0024 -  1.9537   275    32  0.93  13.35   1.00     0.97       2880.01|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     2880.01 max =        14879.99 mean =      8508.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.83|
|phase err.(test): min =        0.00 max =           88.31 mean =        16.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1788   ksol= 0.33   Bsol= 61.41   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.05,0.29,-0.00,0.00,0.00); trace/3= -1.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.271534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1788   ksol= 0.33   Bsol= 61.41   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.05,0.29,-0.00,0.00,0.00); trace/3= -1.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.271534                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6652 0.99   1445  159 0.0967 0.1363      5.3906      5.6425|
|  2:  4.6652 -  3.7211 0.99   1395  159 0.0896 0.1242      5.4942      5.7478|
|  3:  3.7211 -  3.2562 0.99   1383  151 0.1249 0.1705      5.5991      5.8971|
|  4:  3.2562 -  2.9609 0.99   1360  154 0.1541 0.2018      5.6217      5.7897|
|  5:  2.9609 -  2.7500 0.99   1357  150 0.1604 0.2047      5.4988      5.7204|
|  6:  2.7500 -  2.5887 0.99   1352  143 0.1508 0.2260      5.3584      5.5983|
|  7:  2.5887 -  2.4597 0.99   1326  161 0.1463 0.1945      5.2954      5.4706|
|  8:  2.4597 -  2.3530 0.98   1340  146 0.1503 0.1981      5.2479      5.4711|
|  9:  2.3530 -  2.2627 0.98   1311  140 0.1432 0.1996      5.1707      5.4192|
| 10:  2.2627 -  2.1849 1.00   1371  150 0.1277 0.1717      5.0424      5.2217|
| 11:  2.1849 -  2.1168 0.98   1305  151 0.1266 0.2081      5.0177       5.428|
| 12:  2.1168 -  2.0564 0.98   1325  137 0.1309 0.1869      4.9411      5.1636|
| 13:  2.0564 -  2.0024 0.81   1085  126 0.1180 0.1577      4.8363      4.9963|
| 14:  2.0024 -  1.9537 0.21    275   32 0.1085 0.1921      4.7261      5.1119|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.6652  1445   159  0.93   9.95   0.97     0.94       8098.60|
|  2:  4.6652 -  3.7211  1395   159  0.95   8.92   1.02     1.01      10559.70|
|  3:  3.7211 -  3.2562  1383   151  0.92  13.80   1.04     1.04      13445.63|
|  4:  3.2562 -  2.9609  1360   154  0.88  18.17   1.02     0.99      14888.44|
|  5:  2.9609 -  2.7500  1357   150  0.87  19.70   0.99     0.97      12100.13|
|  6:  2.7500 -  2.5887  1352   143  0.87  19.90   0.98     0.94       9552.00|
|  7:  2.5887 -  2.4597  1326   161  0.87  18.95   1.00     0.96       8265.62|
|  8:  2.4597 -  2.3530  1340   146  0.87  19.36   1.00     0.95       7536.80|
|  9:  2.3530 -  2.2627  1311   140  0.87  19.26   1.00     0.95       6638.46|
| 10:  2.2627 -  2.1849  1371   150  0.88  18.34   1.00     0.97       5449.47|
| 11:  2.1849 -  2.1168  1305   151  0.89  17.84   0.99     0.93       5036.57|
| 12:  2.1168 -  2.0564  1325   137  0.88  18.11   1.01     1.00       4527.12|
| 13:  2.0564 -  2.0024  1085   126  0.89  18.06   0.99     0.98       3821.44|
| 14:  2.0024 -  1.9537   275    32  0.93  13.32   0.98     0.96       2874.05|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2874.05 max =        14888.44 mean =      8471.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.80|
|phase err.(test): min =        0.00 max =           88.31 mean =        16.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.762)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.72   17.57    None  None   None       |
|    all(noH): 2823   0      0.00    96.72   17.57    None  None   None       |
|    Sol.    : 438    0      5.06    95.70   45.59    None  None   None       |
|    Mac.    : 2385   0      0.00    96.72   12.43    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 -   9.675: 1112   |   5:    48.361 -  58.033:   95        |
|      1:     9.675 -  19.346: 1035   |   6:    58.033 -  67.705:   76        |
|      2:    19.346 -  29.018:  227   |   7:    67.705 -  77.376:   38        |
|      3:    29.018 -  38.690:  111   |   8:    77.376 -  87.048:   17        |
|      4:    38.690 -  48.361:  100   |   9:    87.048 -  96.720:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 353         
Filter by distance & map next to the model:
   mapped sites are within: 0.581 - 4.421
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 353
   mapped sites are within: 0.711 - 4.421

peak=    8.619 closest distance to " O   HOH Z 390 " =    1.280
peak=    7.502 closest distance to " O   HOH Z 387 " =    2.058
peak=    7.243 closest distance to " O   HOH Z 381 " =    1.186
peak=    6.223 closest distance to " O   HOH Z 245 " =    1.202
peak=    6.057 closest distance to " O   HOH Z 431 " =    1.985
peak=    6.017 closest distance to " O   HOH Z  77 " =    1.223
peak=    5.856 closest distance to " O   HOH Z 222 " =    1.668
peak=    5.842 closest distance to " O   HOH Z 105 " =    1.299
peak=    5.722 closest distance to " O   HOH Z 424 " =    2.008
peak=    5.608 closest distance to " O   HOH Z  29 " =    1.862
peak=    5.520 closest distance to " O   HOH Z 417 " =    2.922
peak=    5.451 closest distance to " NE2 GLN A  11 " =    1.327
peak=    5.372 closest distance to " O   HOH Z  65 " =    1.819
peak=    5.360 closest distance to " O   HOH Z 287 " =    2.058
peak=    5.345 closest distance to " O   HOH Z 422 " =    1.219
peak=    5.335 closest distance to " O   HOH Z 418 " =    1.441
peak=    5.266 closest distance to " O   HOH Z  66 " =    1.132
peak=    5.196 closest distance to " O   HOH Z  69 " =    2.205
peak=    5.143 closest distance to " O   HOH Z 126 " =    2.062
peak=    5.134 closest distance to " O   HOH Z 243 " =    2.577
peak=    5.018 closest distance to " O   HOH Z 278 " =    1.410
peak=    5.001 closest distance to " O   HOH Z 403 " =    1.872
peak=    4.970 closest distance to " O   HOH Z 142 " =    1.846
peak=    4.965 closest distance to " CG  PRO A  54 " =    1.422
peak=    4.945 closest distance to " O   HOH Z 103 " =    1.109
peak=    4.889 closest distance to " O   HOH Z 359 " =    1.885
peak=    4.755 closest distance to " O   HOH Z 145 " =    1.823
peak=    4.682 closest distance to " O   HOH Z 293 " =    1.503
peak=    4.676 closest distance to " O   HOH Z 427 " =    2.062
peak=    4.672 closest distance to " CG  PRO A  90 " =    1.590
peak=    4.659 closest distance to " O   HOH Z 130 " =    1.046
peak=    4.598 closest distance to " O   HOH Z 380 " =    2.275
peak=    4.578 closest distance to " O   HOH Z  63 " =    1.742
peak=    4.556 closest distance to " O   HOH Z   9 " =    2.051
peak=    4.547 closest distance to " O   HOH Z  67 " =    1.382
peak=    4.515 closest distance to " O   HOH Z 295 " =    1.203
peak=    4.515 closest distance to " CB  GLN A 223 " =    1.523
peak=    4.504 closest distance to " O   HOH Z 427 " =    1.331
peak=    4.438 closest distance to " O   HOH Z 415 " =    1.057
peak=    4.434 closest distance to " O   HOH Z 298 " =    1.991
peak=    4.411 closest distance to " CB  ARG A 275 " =    0.995
peak=    4.405 closest distance to " CB  PRO A  54 " =    1.132
peak=    4.401 closest distance to " O   HOH Z 423 " =    2.370
peak=    4.401 closest distance to " O   HOH Z  11 " =    1.190
peak=    4.395 closest distance to " O   HOH Z 296 " =    1.132
peak=    4.377 closest distance to " CB  SER A 216 " =    1.112
peak=    4.358 closest distance to " O   HOH Z 181 " =    1.460
peak=    4.350 closest distance to " CZ3 TRP A 266 " =    1.121
peak=    4.278 closest distance to " O   HOH Z 316 " =    3.087
peak=    4.277 closest distance to " O   HOH Z 158 " =    1.334
peak=    4.274 closest distance to " CA  VAL A 125 " =    1.090
peak=    4.231 closest distance to " O   HOH Z 424 " =    1.286
peak=    4.231 closest distance to " O   HOH Z  97 " =    1.389
peak=    4.228 closest distance to " O   HOH Z  39 " =    1.233
peak=    4.215 closest distance to " O   HOH Z 232 " =    2.239
peak=    4.208 closest distance to " O   HOH Z  92 " =    1.407
peak=    4.207 closest distance to " CB  SER A  63 " =    1.357
peak=    4.196 closest distance to " O   HOH Z 119 " =    1.505
peak=    4.189 closest distance to " O   HOH Z  91 " =    2.511
peak=    4.154 closest distance to " CG  GLN A  58 " =    1.096
peak=    4.137 closest distance to " NH1AARG A 145 " =    1.150
peak=    4.133 closest distance to " CD  GLN A  77 " =    1.323
peak=    4.128 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.101 closest distance to " CB  GLU A 277 " =    3.611
peak=    4.094 closest distance to " O   HOH Z  30 " =    1.883
peak=    4.091 closest distance to " O   HOH Z 207 " =    1.099
peak=    4.076 closest distance to " O   HOH Z 147 " =    1.159
peak=    4.068 closest distance to " O   HOH Z 124 " =    1.436
peak=    4.065 closest distance to " O   HOH Z  49 " =    1.464
peak=    4.062 closest distance to " CB  SER A  99 " =    0.893
peak=    4.044 closest distance to " NH2 ARG A  56 " =    2.048
peak=    4.035 closest distance to " CA  TYR A  30 " =    1.194
peak=    4.033 closest distance to " CA  ALA A  51 " =    1.026
peak=    4.006 closest distance to " O   HOH Z  76 " =    1.522
peak=    3.996 closest distance to " O   HOH Z 258 " =    2.068
peak=    3.994 closest distance to " O   HOH Z 405 " =    1.687
peak=    3.987 closest distance to " O   HOH Z 225 " =    1.753
peak=    3.967 closest distance to " CG  LYS A  76 " =    1.852
peak=    3.965 closest distance to " O   HOH Z 112 " =    1.149
peak=    3.945 closest distance to " NZ  LYS A 117 " =    2.973
peak=    3.934 closest distance to " OG ASER A 212 " =    1.470
peak=    3.934 closest distance to " O   HOH Z 100 " =    0.991
peak=    3.929 closest distance to " CG  TRP A 179 " =    2.240
peak=    3.925 closest distance to " ND2BASN A 224 " =    0.951
peak=    3.923 closest distance to " N   CYS A 260 " =    0.921
peak=    3.899 closest distance to " O   HOH Z 126 " =    1.493
peak=    3.894 closest distance to " CB  ASN A  39 " =    0.881
peak=    3.891 closest distance to " O   HOH Z 371 " =    1.698
peak=    3.885 closest distance to " O   HOH Z 139 " =    1.000
peak=    3.881 closest distance to " O   HOH Z 368 " =    3.518
peak=    3.876 closest distance to " CB  ASP A 140 " =    1.038
peak=    3.873 closest distance to " O   HOH Z 282 " =    1.751
peak=    3.864 closest distance to " O   HOH Z  43 " =    1.291
peak=    3.861 closest distance to " ND2 ASN A  60 " =    2.923
peak=    3.860 closest distance to " O   HOH Z 425 " =    1.446
peak=    3.859 closest distance to " O   HOH Z 211 " =    1.269
peak=    3.856 closest distance to " CE  LYS A 119 " =    1.316
peak=    3.850 closest distance to " CG2 VAL A 257 " =    0.896
peak=    3.848 closest distance to " O   HOH Z  46 " =    1.144
peak=    3.841 closest distance to " CB  SER A 276 " =    1.190
peak=    3.839 closest distance to " CG1 ILE A 120 " =    1.411
peak=    3.836 closest distance to " O   PRO A 198 " =    1.398
peak=    3.820 closest distance to " CB  PRO A  90 " =    1.107
peak=    3.800 closest distance to " O   HOH Z  51 " =    1.944
peak=    3.799 closest distance to " O   HOH Z 147 " =    1.451
peak=    3.796 closest distance to " N   TYR A  15 " =    1.141
peak=    3.790 closest distance to " O   HOH Z 180 " =    2.232
peak=    3.784 closest distance to " O   HOH Z   7 " =    2.572
peak=    3.779 closest distance to " O   HOH Z 133 " =    0.795
peak=    3.777 closest distance to " O   HOH Z 434 " =    1.606
peak=    3.766 closest distance to " CB  ALA A  43 " =    0.845
peak=    3.761 closest distance to " CE3 TRP A 150 " =    1.116
peak=    3.760 closest distance to " CE  MET A  93 " =    1.364
peak=    3.757 closest distance to " O   HOH Z 327 " =    1.839
peak=    3.751 closest distance to " O   HOH Z 132 " =    0.921
peak=    3.748 closest distance to " CB  ASP A 124 " =    0.881
peak=    3.746 closest distance to " O   HOH Z   6 " =    1.829
peak=    3.740 closest distance to " CD2 TRP A 179 " =    1.370
peak=    3.738 closest distance to " O   HOH Z 104 " =    1.699
peak=    3.734 closest distance to " CE3 TRP A 274 " =    1.422
peak=    3.733 closest distance to " O   HOH Z 244 " =    1.606
peak=    3.730 closest distance to " O   HOH Z 358 " =    1.150
peak=    3.726 closest distance to " CG  GLN A  89 " =    1.523
peak=    3.723 closest distance to " CA  ALA A 129 " =    1.209
peak=    3.720 closest distance to " O   HOH Z  40 " =    2.218
peak=    3.712 closest distance to " N   ALA A   1 " =    1.479
peak=    3.710 closest distance to " O   HOH Z 353 " =    1.931
peak=    3.708 closest distance to " O   HOH Z 215 " =    1.758
peak=    3.706 closest distance to " O   HOH Z 214 " =    2.462
peak=    3.696 closest distance to " O   HOH Z 410 " =    1.528
peak=    3.696 closest distance to " O   HOH Z 217 " =    1.252
peak=    3.689 closest distance to " CD  ARG A 159 " =    0.832
peak=    3.688 closest distance to " NH2AARG A 145 " =    1.162
peak=    3.686 closest distance to " N   GLN A 278 " =    1.306
peak=    3.685 closest distance to " O   HOH Z 392 " =    1.339
peak=    3.675 closest distance to " O   HOH Z  78 " =    1.834
peak=    3.672 closest distance to " O   HOH Z 280 " =    1.579
peak=    3.668 closest distance to " O   HOH Z 365 " =    2.484
peak=    3.667 closest distance to " CB  ARG A 190 " =    1.653
peak=    3.653 closest distance to " O   HOH Z 423 " =    1.902
peak=    3.649 closest distance to " CB  ALA A 114 " =    0.854
peak=    3.646 closest distance to " O   ALA A 165 " =    1.491
peak=    3.643 closest distance to " O   HOH Z 375 " =    1.025
peak=    3.642 closest distance to " O   HOH Z 259 " =    2.145
peak=    3.635 closest distance to " NZ  LYS A 119 " =    2.364
peak=    3.630 closest distance to " O   HOH Z 357 " =    2.142
peak=    3.624 closest distance to " O   HOH Z  40 " =    1.817
peak=    3.623 closest distance to " CD  ARG A  66 " =    2.348
peak=    3.623 closest distance to " CG2 THR A 221 " =    1.204
peak=    3.619 closest distance to " O   HOH Z 374 " =    1.303
peak=    3.617 closest distance to " O   HOH Z 411 " =    3.753
peak=    3.603 closest distance to " O   HOH Z 414 " =    1.347
peak=    3.601 closest distance to " CG AARG A 275 " =    1.309
peak=    3.598 closest distance to " O   HOH Z  88 " =    3.264
peak=    3.592 closest distance to " CG  PRO A 198 " =    1.253
peak=    3.592 closest distance to " O   HOH Z  71 " =    1.459
peak=    3.591 closest distance to " O   HOH Z 143 " =    1.290
peak=    3.590 closest distance to " OE2 GLU A  53 " =    2.086
peak=    3.589 closest distance to " O   HOH Z 153 " =    3.568
peak=    3.584 closest distance to " O   HOH Z 222 " =    2.184
peak=    3.576 closest distance to " O   HOH Z 201 " =    1.740
peak=    3.575 closest distance to " CB  TRP A 179 " =    1.464
peak=    3.570 closest distance to " O   HOH Z 406 " =    1.532
peak=    3.568 closest distance to " CB  GLU A 128 " =    1.049
peak=    3.566 closest distance to " O   HOH Z 155 " =    1.790
peak=    3.559 closest distance to " CG  LEU A 167 " =    1.329
peak=    3.555 closest distance to " NZ  LYS A 166 " =    1.096
peak=    3.553 closest distance to " O   HOH Z 272 " =    1.866
peak=    3.551 closest distance to " O   HOH Z 368 " =    1.755
peak=    3.547 closest distance to " O   HOH Z  44 " =    1.947
peak=    3.542 closest distance to " O   HOH Z 437 " =    2.026
peak=    3.530 closest distance to " O   HOH Z 363 " =    1.131
peak=    3.520 closest distance to " O   HOH Z  61 " =    1.659
peak=    3.516 closest distance to " O   HOH Z 361 " =    1.413
peak=    3.511 closest distance to " CG  PRO A 280 " =    1.008
peak=    3.498 closest distance to " O  BHOH Z  74 " =    1.312
peak=    3.494 closest distance to " O   HOH Z 286 " =    1.810
peak=    3.487 closest distance to " CB  THR A  31 " =    1.533
peak=    3.482 closest distance to " O   HOH Z 219 " =    3.892
peak=    3.479 closest distance to " O   HOH Z 276 " =    1.205
peak=    3.478 closest distance to " CB  PHE A 130 " =    0.963
peak=    3.478 closest distance to " CB  TRP A 266 " =    1.051
peak=    3.474 closest distance to " O   HOH Z   2 " =    1.856
peak=    3.470 closest distance to " O   HOH Z 426 " =    1.082
peak=    3.469 closest distance to " CB  ALA A 248 " =    1.096
peak=    3.469 closest distance to " O   HOH Z 371 " =    3.455
peak=    3.465 closest distance to " O   HOH Z 424 " =    3.352
peak=    3.463 closest distance to " O   HOH Z  57 " =    1.204
peak=    3.450 closest distance to " NE1 TRP A 274 " =    1.081
peak=    3.449 closest distance to " O   HOH Z  26 " =    1.422
peak=    3.447 closest distance to " CG2 VAL A 197 " =    1.193
peak=    3.446 closest distance to " O   HOH Z 362 " =    1.966
peak=    3.439 closest distance to " O   VAL A  72 " =    0.952
peak=    3.436 closest distance to " CA  ASN A  74 " =    1.261
peak=    3.435 closest distance to " CD  ARG A  66 " =    2.336
peak=    3.434 closest distance to " CA  PHE A 283 " =    1.314
peak=    3.427 closest distance to " NH2AARG A 190 " =    1.922
peak=    3.425 closest distance to " CA  TYR A 116 " =    1.438
peak=    3.424 closest distance to " O   HOH Z 157 " =    1.631
peak=    3.423 closest distance to " CG2 ILE A  20 " =    1.624
peak=    3.419 closest distance to " O   HOH Z 248 " =    1.712
peak=    3.418 closest distance to " CB  GLU A 152 " =    1.143
peak=    3.418 closest distance to " CB  ASN A 142 " =    1.011
peak=    3.418 closest distance to " CA  ALA A 160 " =    1.062
peak=    3.412 closest distance to " O   ASN A 142 " =    1.052
peak=    3.411 closest distance to " O   HOH Z 127 " =    0.962
peak=    3.408 closest distance to " O   HOH Z 265 " =    2.095
peak=    3.403 closest distance to " CB  SER A   3 " =    1.475
peak=    3.401 closest distance to " O   HOH Z 394 " =    1.655
peak=    3.399 closest distance to " O   HOH Z  68 " =    2.013
peak=    3.399 closest distance to " O   HOH Z 193 " =    1.565
peak=    3.397 closest distance to " CZ  PHE A  38 " =    1.362
peak=    3.397 closest distance to " CG  GLN A  11 " =    2.232
peak=    3.391 closest distance to " CA  ARG A 195 " =    1.311
peak=    3.386 closest distance to " CB  VAL A 265 " =    1.356
peak=    3.386 closest distance to " CA  ARG A 159 " =    1.218
peak=    3.380 closest distance to " O   HOH Z 193 " =    1.597
peak=    3.379 closest distance to " O   HOH Z 116 " =    3.054
peak=    3.370 closest distance to " O   HOH Z 369 " =    1.770
peak=    3.368 closest distance to " CA  ASN A 127 " =    1.113
peak=    3.368 closest distance to " NH2 ARG A  56 " =    1.032
peak=    3.368 closest distance to " O   HOH Z 425 " =    2.238
peak=    3.356 closest distance to " CG  LYS A 119 " =    0.963
peak=    3.352 closest distance to " CG2 ILE A 239 " =    0.908
peak=    3.352 closest distance to " CB  ASP A 191 " =    1.294
peak=    3.350 closest distance to " N   PHE A 130 " =    1.281
peak=    3.350 closest distance to " CD  ARG A 195 " =    3.565
peak=    3.348 closest distance to " CA  LEU A 282 " =    0.958
peak=    3.346 closest distance to " OG BSER A  99 " =    2.305
peak=    3.346 closest distance to " O   HOH Z 128 " =    2.067
peak=    3.343 closest distance to " CB  MET A  40 " =    0.864
peak=    3.342 closest distance to " CG  ARG A 159 " =    0.840
peak=    3.341 closest distance to " O   HOH Z 235 " =    1.733
peak=    3.339 closest distance to " O   HOH Z  58 " =    1.711
peak=    3.330 closest distance to " CA  ALA A 291 " =    0.912
peak=    3.323 closest distance to " O   HOH Z  17 " =    2.042
peak=    3.321 closest distance to " CB  ARG A 190 " =    1.108
peak=    3.319 closest distance to " O   HOH Z 365 " =    1.499
peak=    3.318 closest distance to " O   HOH Z 328 " =    1.543
peak=    3.318 closest distance to " CB  LYS A 117 " =    1.210
peak=    3.317 closest distance to " O   HOH Z 383 " =    2.576
peak=    3.311 closest distance to " O   HOH Z 240 " =    2.054
peak=    3.308 closest distance to " O   HOH Z 220 " =    1.380
peak=    3.304 closest distance to " CG  PRO A 213 " =    1.226
peak=    3.304 closest distance to " CB  ALA A   1 " =    1.105
peak=    3.303 closest distance to " N   GLU A   2 " =    1.390
peak=    3.298 closest distance to " NE2 HIS A 207 " =    1.044
peak=    3.298 closest distance to " CB  GLN A 183 " =    1.211
peak=    3.296 closest distance to " O   HOH Z 158 " =    2.554
peak=    3.294 closest distance to " ND2 ASN A 249 " =    1.927
peak=    3.293 closest distance to " O   HOH Z 189 " =    3.098
peak=    3.293 closest distance to " O   HOH Z 146 " =    1.567
peak=    3.286 closest distance to " CA  SER A  87 " =    1.046
peak=    3.285 closest distance to " N   SER A  97 " =    0.809
peak=    3.284 closest distance to " CB  LEU A 300 " =    0.993
peak=    3.278 closest distance to " O   HOH Z  61 " =    1.746
peak=    3.276 closest distance to " O   HOH Z 291 " =    1.563
peak=    3.274 closest distance to " O   HOH Z  47 " =    2.069
peak=    3.273 closest distance to " CB  ASN A 110 " =    1.060
peak=    3.272 closest distance to " N   ASP A 162 " =    1.093
peak=    3.271 closest distance to " CB  VAL A 202 " =    1.653
peak=    3.270 closest distance to " NH2 ARG A 219 " =    1.737
peak=    3.270 closest distance to " NZ BLYS A 290 " =    0.977
peak=    3.268 closest distance to " O   HOH Z 273 " =    1.296
peak=    3.266 closest distance to " ND2 ASN A 187 " =    1.767
peak=    3.265 closest distance to " CB  TRP A 150 " =    0.932
peak=    3.251 closest distance to " O   HOH Z 430 " =    1.976
peak=    3.250 closest distance to " CA  GLY A 196 " =    0.883
peak=    3.244 closest distance to " CB  ARG A  79 " =    1.239
peak=    3.243 closest distance to " ND2 ASN A 249 " =    0.799
peak=    3.242 closest distance to " O   HOH Z 213 " =    2.069
peak=    3.238 closest distance to " O   ALA A  71 " =    1.287
peak=    3.238 closest distance to " CG2 ILE A 234 " =    0.919
peak=    3.236 closest distance to " CA  ILE A 234 " =    1.063
peak=    3.235 closest distance to " O   HOH Z 239 " =    1.528
peak=    3.233 closest distance to " O   LEU A 228 " =    1.987
peak=    3.231 closest distance to " O   HOH Z 236 " =    1.496
peak=    3.230 closest distance to " O   HOH Z  60 " =    1.370
peak=    3.229 closest distance to " CA  SER A  95 " =    0.925
peak=    3.229 closest distance to " CA  ILE A 106 " =    0.711
peak=    3.228 closest distance to " NZ  LYS A 117 " =    1.306
peak=    3.225 closest distance to " CB  SER A 210 " =    0.887
peak=    3.224 closest distance to " CB  TYR A 116 " =    1.150
peak=    3.224 closest distance to " O   HOH Z 283 " =    2.228
peak=    3.222 closest distance to " N   GLN A  77 " =    1.598
peak=    3.216 closest distance to " N   ALA A 256 " =    0.980
peak=    3.215 closest distance to " CA  MET A 105 " =    0.899
peak=    3.212 closest distance to " CA  GLY A  35 " =    0.942
peak=    3.211 closest distance to " O   HOH Z  44 " =    2.883
peak=    3.208 closest distance to " CB  ALA A 242 " =    1.204
peak=    3.207 closest distance to " O   HOH Z 350 " =    1.503
peak=    3.204 closest distance to " C   GLU A 277 " =    1.413
peak=    3.203 closest distance to " CE3 TRP A  85 " =    1.111
peak=    3.201 closest distance to " O   MET A 105 " =    1.645
peak=    3.199 closest distance to " O   HOH Z 345 " =    1.961
peak=    3.197 closest distance to " OD2 ASP A 286 " =    2.590
peak=    3.193 closest distance to " CB  ASN A 285 " =    0.913
peak=    3.192 closest distance to " CA  LEU A  83 " =    1.720
peak=    3.185 closest distance to " CB  ASN A 215 " =    1.079
peak=    3.185 closest distance to " OG BSER A 164 " =    2.395
peak=    3.184 closest distance to " CG2BVAL A 121 " =    0.888
peak=    3.182 closest distance to " C   GLN A  73 " =    1.101
peak=    3.182 closest distance to " NE2 GLN A 278 " =    3.449
peak=    3.181 closest distance to " CB  GLN A  88 " =    1.310
peak=    3.176 closest distance to " O   HOH Z 119 " =    4.185
peak=    3.174 closest distance to " CB  PRO A 163 " =    4.156
peak=    3.172 closest distance to " O   HOH Z 116 " =    1.177
peak=    3.172 closest distance to " O   HOH Z 145 " =    1.728
peak=    3.169 closest distance to " O   HOH Z 368 " =    4.421
peak=    3.166 closest distance to " O   HOH Z 106 " =    4.067
peak=    3.163 closest distance to " N   VAL A  72 " =    1.660
peak=    3.163 closest distance to " O   HOH Z  48 " =    1.720
peak=    3.161 closest distance to " CG2 THR A 294 " =    1.346
peak=    3.156 closest distance to " O   HOH Z  59 " =    1.921
peak=    3.154 closest distance to " O   HOH Z 425 " =    1.987
peak=    3.152 closest distance to " O   HOH Z 379 " =    1.585
peak=    3.152 closest distance to " O   HOH Z 175 " =    3.558
peak=    3.151 closest distance to " O   HOH Z 154 " =    2.243
peak=    3.145 closest distance to " O   HOH Z 203 " =    1.734
peak=    3.145 closest distance to " CA  PRO A  54 " =    1.284
peak=    3.140 closest distance to " O   HOH Z 216 " =    3.848
peak=    3.137 closest distance to " CD  LYS A 166 " =    1.587
peak=    3.137 closest distance to " O   HOH Z  42 " =    1.450
peak=    3.136 closest distance to " CB  ARG A 138 " =    0.952
peak=    3.134 closest distance to " O   HOH Z 296 " =    1.138
peak=    3.129 closest distance to " CB  ALA A 242 " =    0.812
peak=    3.128 closest distance to " CD  ARG A 138 " =    0.846
peak=    3.125 closest distance to " CD1 ILE A  33 " =    1.809
peak=    3.121 closest distance to " CB  SER A 245 " =    3.252
peak=    3.121 closest distance to " NE AARG A 145 " =    1.068
peak=    3.120 closest distance to " CA  ALA A 160 " =    1.356
peak=    3.119 closest distance to " N   ARG A 159 " =    1.093
peak=    3.119 closest distance to " CB  ASP A 200 " =    0.947
peak=    3.115 closest distance to " OE2 GLU A  44 " =    1.096
peak=    3.110 closest distance to " O   HOH Z 193 " =    2.377
peak=    3.103 closest distance to " CB  SER A  97 " =    0.785
peak=    3.099 closest distance to " CG2 VAL A 232 " =    1.394
peak=    3.094 closest distance to " O   HOH Z 422 " =    2.043
peak=    3.087 closest distance to " CB  ASN A 142 " =    1.446
peak=    3.085 closest distance to " O   HOH Z 413 " =    1.635
peak=    3.084 closest distance to " CB  ALA A 233 " =    1.114
peak=    3.077 closest distance to " O   HOH Z 194 " =    2.303
peak=    3.074 closest distance to " O   HOH Z 128 " =    1.950
peak=    3.068 closest distance to " O   HOH Z  80 " =    2.331
peak=    3.067 closest distance to " CB  TYR A  30 " =    1.696
peak=    3.054 closest distance to " O   GLN A  55 " =    1.782
peak=    3.052 closest distance to " CA  ASN A 217 " =    1.329
peak=    3.050 closest distance to " O   HOH Z 234 " =    3.546
peak=    3.049 closest distance to " CB  ARG A 156 " =    1.091
peak=    3.033 closest distance to " O   HOH Z 130 " =    1.930

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.576 - 5.933
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 212
   mapped sites are within: 0.707 - 5.933

peak=   -4.557 closest distance to " O   PRO A 198 " =    1.145
peak=   -4.496 closest distance to " O   HOH Z 385 " =    1.308
peak=   -4.375 closest distance to " O   HOH Z  60 " =    1.752
peak=   -4.341 closest distance to " CD  ARG A  14 " =    3.200
peak=   -4.251 closest distance to " O   HOH Z 103 " =    0.707
peak=   -4.239 closest distance to " O   HOH Z 313 " =    1.225
peak=   -4.198 closest distance to " O   HOH Z 100 " =    1.026
peak=   -4.182 closest distance to " O   HOH Z 231 " =    0.779
peak=   -4.150 closest distance to " O   ALA A  10 " =    1.606
peak=   -4.104 closest distance to " O   HOH Z  28 " =    1.270
peak=   -4.097 closest distance to " CG2 ILE A  49 " =    2.849
peak=   -4.076 closest distance to " CB  ALA A  43 " =    2.482
peak=   -4.065 closest distance to " O   SER A  22 " =    2.649
peak=   -4.046 closest distance to " O   HOH Z 219 " =    3.867
peak=   -3.986 closest distance to " O   HOH Z  24 " =    0.896
peak=   -3.943 closest distance to " CG  MET A 105 " =    0.948
peak=   -3.919 closest distance to " O   HOH Z 242 " =    1.458
peak=   -3.911 closest distance to " O   HOH Z 105 " =    2.017
peak=   -3.905 closest distance to " CB  PRO A 243 " =    2.626
peak=   -3.870 closest distance to " O   HOH Z 415 " =    0.956
peak=   -3.861 closest distance to " CG  TRP A 266 " =    1.778
peak=   -3.856 closest distance to " CB  ALA A 291 " =    2.136
peak=   -3.838 closest distance to " O   HOH Z  69 " =    1.432
peak=   -3.837 closest distance to " CZ  PHE A  59 " =    1.515
peak=   -3.824 closest distance to " CD2 TYR A 293 " =    1.896
peak=   -3.819 closest distance to " O   HOH Z 216 " =    1.358
peak=   -3.818 closest distance to " CZ3 TRP A 179 " =    1.327
peak=   -3.812 closest distance to " O   HOH Z 111 " =    1.769
peak=   -3.806 closest distance to " CB  ASP A 171 " =    2.205
peak=   -3.798 closest distance to " O   HOH Z 412 " =    3.851
peak=   -3.790 closest distance to " NH2 ARG A 219 " =    1.983
peak=   -3.789 closest distance to " CD1 TRP A 179 " =    1.244
peak=   -3.774 closest distance to " NE2 GLN A  55 " =    1.103
peak=   -3.765 closest distance to " CA  GLY A  98 " =    1.726
peak=   -3.761 closest distance to " CG1BVAL A  41 " =    2.791
peak=   -3.760 closest distance to " CA  GLY A 241 " =    2.272
peak=   -3.736 closest distance to " OG  SER A 245 " =    1.555
peak=   -3.733 closest distance to " CG  ARG A 219 " =    2.487
peak=   -3.709 closest distance to " N   THR A 157 " =    1.563
peak=   -3.696 closest distance to " OG  SER A  97 " =    2.133
peak=   -3.677 closest distance to " CB  GLN A  55 " =    1.272
peak=   -3.666 closest distance to " O   HOH Z 275 " =    1.811
peak=   -3.666 closest distance to " O   HOH Z  71 " =    1.119
peak=   -3.653 closest distance to " O   HOH Z 377 " =    1.994
peak=   -3.634 closest distance to " N   ARG A 159 " =    2.053
peak=   -3.628 closest distance to " OE1 GLU A  44 " =    1.904
peak=   -3.616 closest distance to " O   HOH Z 198 " =    1.277
peak=   -3.608 closest distance to " O   HOH Z  49 " =    1.291
peak=   -3.598 closest distance to " CA  GLY A 133 " =    1.932
peak=   -3.574 closest distance to " O   HOH Z 276 " =    1.187
peak=   -3.571 closest distance to " O   PRO A 163 " =    1.685
peak=   -3.564 closest distance to " O   HOH Z 389 " =    1.072
peak=   -3.559 closest distance to " O   GLU A 152 " =    1.496
peak=   -3.558 closest distance to " OG BSER A 134 " =    1.652
peak=   -3.556 closest distance to " CD1 LEU A 101 " =    2.246
peak=   -3.553 closest distance to " O   HOH Z  39 " =    0.821
peak=   -3.542 closest distance to " O   HOH Z 426 " =    1.585
peak=   -3.535 closest distance to " CD  LYS A 166 " =    2.581
peak=   -3.534 closest distance to " O   HOH Z 298 " =    2.508
peak=   -3.528 closest distance to " CA  ASP A  27 " =    2.479
peak=   -3.523 closest distance to " O   ASP A 191 " =    1.924
peak=   -3.516 closest distance to " C   HIS A 108 " =    1.186
peak=   -3.513 closest distance to " CD  PRO A 213 " =    2.143
peak=   -3.510 closest distance to " C   VAL A  72 " =    0.926
peak=   -3.510 closest distance to " OD2 ASP A 272 " =    1.548
peak=   -3.509 closest distance to " CA  HIS A 207 " =    1.232
peak=   -3.502 closest distance to " CD2 PHE A  61 " =    2.143
peak=   -3.486 closest distance to " CG1 VAL A 125 " =    2.325
peak=   -3.481 closest distance to " NE2 GLN A 194 " =    1.898
peak=   -3.469 closest distance to " O   HOH Z 238 " =    0.996
peak=   -3.467 closest distance to " N   ALA A   1 " =    1.618
peak=   -3.456 closest distance to " CG  ARG A 259 " =    2.368
peak=   -3.456 closest distance to " O   HOH Z 266 " =    5.251
peak=   -3.454 closest distance to " O   HOH Z 100 " =    1.324
peak=   -3.454 closest distance to " NE2 GLN A  58 " =    3.459
peak=   -3.452 closest distance to " CZ2 TRP A 274 " =    1.000
peak=   -3.443 closest distance to " CB  PRO A  54 " =    2.291
peak=   -3.442 closest distance to " CD  GLU A 277 " =    1.059
peak=   -3.439 closest distance to " O   HOH Z 163 " =    1.878
peak=   -3.435 closest distance to " CG2 ILE A 151 " =    2.519
peak=   -3.425 closest distance to " O   HOH Z 414 " =    1.232
peak=   -3.423 closest distance to " CE2 TYR A  30 " =    2.477
peak=   -3.417 closest distance to " O   HOH Z 357 " =    1.759
peak=   -3.411 closest distance to " O   HOH Z 323 " =    2.016
peak=   -3.407 closest distance to " O   HOH Z 438 " =    0.932
peak=   -3.402 closest distance to " CG  ARG A 219 " =    2.340
peak=   -3.402 closest distance to " CG2 ILE A  20 " =    2.662
peak=   -3.400 closest distance to " CB  ALA A   9 " =    2.427
peak=   -3.391 closest distance to " CB  ASN A  45 " =    2.045
peak=   -3.389 closest distance to " O   LYS A  76 " =    1.924
peak=   -3.386 closest distance to " CE3 TRP A 274 " =    2.182
peak=   -3.382 closest distance to " OE1 GLU A 277 " =    2.172
peak=   -3.381 closest distance to " O   HOH Z 250 " =    1.029
peak=   -3.379 closest distance to " O   GLY A  80 " =    2.632
peak=   -3.376 closest distance to " N   GLN A  58 " =    1.356
peak=   -3.369 closest distance to " O   HOH Z 181 " =    2.165
peak=   -3.361 closest distance to " O   HOH Z 251 " =    0.883
peak=   -3.354 closest distance to " NH2BARG A 102 " =    0.943
peak=   -3.352 closest distance to " CB  PHE A 130 " =    1.159
peak=   -3.348 closest distance to " OE2 GLU A 152 " =    1.333
peak=   -3.347 closest distance to " N   ASN A 127 " =    1.346
peak=   -3.345 closest distance to " CD  ARG A 156 " =    2.032
peak=   -3.345 closest distance to " CB  ASN A  39 " =    2.262
peak=   -3.344 closest distance to " O   GLN A 240 " =    3.147
peak=   -3.343 closest distance to " O   HOH Z 181 " =    1.429
peak=   -3.333 closest distance to " O   ILE A  49 " =    1.622
peak=   -3.333 closest distance to " O   HOH Z 129 " =    3.674
peak=   -3.331 closest distance to " O   SER A   3 " =    2.240
peak=   -3.329 closest distance to " CA  GLY A 203 " =    2.430
peak=   -3.322 closest distance to " O   HOH Z   5 " =    1.278
peak=   -3.321 closest distance to " OG  SER A  63 " =    1.429
peak=   -3.312 closest distance to " NE2 GLN A 223 " =    1.680
peak=   -3.305 closest distance to " O   HOH Z 143 " =    1.342
peak=   -3.298 closest distance to " CB  ALA A 227 " =    2.411
peak=   -3.296 closest distance to " O   HOH Z 428 " =    2.330
peak=   -3.295 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.293 closest distance to " O   HOH Z 359 " =    3.300
peak=   -3.289 closest distance to " O   HOH Z 181 " =    1.692
peak=   -3.289 closest distance to " CG2BVAL A  41 " =    2.670
peak=   -3.286 closest distance to " O   HOH Z 381 " =    1.167
peak=   -3.284 closest distance to " O   HOH Z  25 " =    1.353
peak=   -3.284 closest distance to " NZ  LYS A 166 " =    1.293
peak=   -3.276 closest distance to " O   HOH Z  67 " =    1.499
peak=   -3.274 closest distance to " O   HOH Z 324 " =    0.826
peak=   -3.274 closest distance to " O   HOH Z 139 " =    3.257
peak=   -3.273 closest distance to " CD2 TYR A 116 " =    2.140
peak=   -3.270 closest distance to " NE2 GLN A  77 " =    1.611
peak=   -3.263 closest distance to " CG2 VAL A 189 " =    1.832
peak=   -3.262 closest distance to " CG1 VAL A 265 " =    2.391
peak=   -3.254 closest distance to " CB  TRP A  85 " =    2.510
peak=   -3.254 closest distance to " O   HOH Z 100 " =    1.603
peak=   -3.253 closest distance to " O   HOH Z  60 " =    1.279
peak=   -3.245 closest distance to " OG  SER A  87 " =    1.753
peak=   -3.242 closest distance to " O   HOH Z 268 " =    2.881
peak=   -3.235 closest distance to " CA  ASN A 110 " =    0.960
peak=   -3.234 closest distance to " O   HOH Z 280 " =    0.744
peak=   -3.234 closest distance to " CB  TYR A  68 " =    1.163
peak=   -3.232 closest distance to " O   HOH Z 348 " =    1.865
peak=   -3.232 closest distance to " N   LYS A 166 " =    1.889
peak=   -3.231 closest distance to " O   HOH Z  35 " =    2.956
peak=   -3.227 closest distance to " O   HOH Z  88 " =    2.109
peak=   -3.226 closest distance to " O   HOH Z 389 " =    2.279
peak=   -3.225 closest distance to " CE1 TYR A 293 " =    2.139
peak=   -3.220 closest distance to " O   HOH Z 372 " =    2.656
peak=   -3.218 closest distance to " O   HOH Z 231 " =    1.964
peak=   -3.215 closest distance to " O   HOH Z 140 " =    1.023
peak=   -3.214 closest distance to " O   HOH Z 215 " =    1.593
peak=   -3.202 closest distance to " CB  ALA A 114 " =    2.449
peak=   -3.200 closest distance to " O   HOH Z  73 " =    2.087
peak=   -3.200 closest distance to " CE BMET A  47 " =    1.364
peak=   -3.199 closest distance to " O   HOH Z 390 " =    1.257
peak=   -3.197 closest distance to " O   HOH Z 212 " =    0.859
peak=   -3.195 closest distance to " O   HOH Z 286 " =    1.616
peak=   -3.190 closest distance to " O   HOH Z 337 " =    1.455
peak=   -3.189 closest distance to " ND2 ASN A  39 " =    1.374
peak=   -3.188 closest distance to " N   GLY A 196 " =    1.686
peak=   -3.187 closest distance to " O   HOH Z 353 " =    4.145
peak=   -3.183 closest distance to " O   HOH Z 283 " =    5.933
peak=   -3.183 closest distance to " O   HOH Z   1 " =    1.175
peak=   -3.182 closest distance to " C   ALA A 158 " =    1.605
peak=   -3.182 closest distance to " NE  ARG A  36 " =    1.950
peak=   -3.180 closest distance to " CD2 HIS A 207 " =    1.426
peak=   -3.179 closest distance to " O   HOH Z 147 " =    1.956
peak=   -3.178 closest distance to " CG2 VAL A 232 " =    2.023
peak=   -3.175 closest distance to " CB  ASP A 132 " =    2.593
peak=   -3.168 closest distance to " CG2 THR A 221 " =    2.279
peak=   -3.166 closest distance to " N   ASP A 171 " =    2.521
peak=   -3.165 closest distance to " ND2 ASN A 209 " =    1.857
peak=   -3.160 closest distance to " O   HOH Z 275 " =    1.582
peak=   -3.160 closest distance to " CG  GLU A 128 " =    1.715
peak=   -3.160 closest distance to " CD  GLN A  88 " =    0.959
peak=   -3.159 closest distance to " CG2BVAL A  72 " =    1.760
peak=   -3.154 closest distance to " O   ALA A  84 " =    1.626
peak=   -3.153 closest distance to " O   HOH Z 105 " =    0.964
peak=   -3.144 closest distance to " O   ALA A  34 " =    2.568
peak=   -3.143 closest distance to " C   GLU A   2 " =    1.802
peak=   -3.142 closest distance to " O   LEU A 167 " =    1.764
peak=   -3.141 closest distance to " O   HOH Z 397 " =    1.214
peak=   -3.138 closest distance to " NH2 ARG A  79 " =    2.352
peak=   -3.137 closest distance to " CE  LYS A  76 " =    2.942
peak=   -3.136 closest distance to " OG BSER A 210 " =    2.224
peak=   -3.134 closest distance to " CB  ALA A 100 " =    1.874
peak=   -3.133 closest distance to " OE1 GLN A 183 " =    1.648
peak=   -3.133 closest distance to " O   ASN A 170 " =    2.041
peak=   -3.131 closest distance to " CB  ASP A 132 " =    2.533
peak=   -3.129 closest distance to " O   HOH Z 401 " =    1.292
peak=   -3.121 closest distance to " O   HOH Z 128 " =    2.624
peak=   -3.119 closest distance to " O   HOH Z 139 " =    1.078
peak=   -3.112 closest distance to " CB  ALA A 248 " =    1.990
peak=   -3.110 closest distance to " C   ASN A 301 " =    1.386
peak=   -3.103 closest distance to " NE2 GLN A 278 " =    1.478
peak=   -3.098 closest distance to " O   HOH Z 166 " =    1.820
peak=   -3.097 closest distance to " ND2 ASN A 285 " =    2.153
peak=   -3.096 closest distance to " CG1 VAL A 197 " =    2.191
peak=   -3.095 closest distance to " CG2 VAL A 112 " =    2.736
peak=   -3.094 closest distance to " O   HOH Z 359 " =    1.582
peak=   -3.093 closest distance to " O   HOH Z 185 " =    1.999
peak=   -3.093 closest distance to " O   HOH Z 351 " =    1.715
peak=   -3.090 closest distance to " C   LEU A 222 " =    0.938
peak=   -3.087 closest distance to " O   HOH Z  56 " =    1.797
peak=   -3.085 closest distance to " CD  ARG A 139 " =    1.610
peak=   -3.081 closest distance to " O   HOH Z  22 " =    2.791
peak=   -3.073 closest distance to " CZ  PHE A  38 " =    2.356
peak=   -3.069 closest distance to " O   HOH Z 134 " =    4.054
peak=   -3.061 closest distance to " O   HOH Z 377 " =    1.214
peak=   -3.061 closest distance to " O   HOH Z 244 " =    1.805
peak=   -3.055 closest distance to " O   HOH Z  29 " =    2.095
peak=   -3.048 closest distance to " CD1 TYR A 247 " =    2.798
peak=   -3.046 closest distance to " O   ARG A 145 " =    1.270
peak=   -3.020 closest distance to " CB  ASP A 132 " =    2.236

================= 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    :  0.4835 0.4869   6.299217e+00   6.289843e+00
   1_bss:  0.4723 0.4798   6.293792e+00   6.282982e+00
   1_xyz:  0.3910 0.4412   6.172786e+00   6.238158e+00
   1_adp:  0.3619 0.4500   6.142822e+00   6.245799e+00
   1_occ:  0.3612 0.4511   6.143073e+00   6.246461e+00
   2_bss:  0.3604 0.4498   6.146169e+00   6.247680e+00
   2_xyz:  0.2967 0.3832   5.993276e+00   6.145237e+00
   2_adp:  0.2755 0.3649   5.951346e+00   6.116489e+00
   2_occ:  0.2754 0.3650   5.950893e+00   6.116355e+00
   3_bss:  0.2756 0.3633   5.947491e+00   6.113130e+00
   3_xyz:  0.2293 0.3053   5.786273e+00   5.975573e+00
   3_adp:  0.2090 0.2921   5.724603e+00   5.938255e+00
   3_occ:  0.2090 0.2920   5.724126e+00   5.937577e+00
   4_bss:  0.2091 0.2921   5.723302e+00   5.937465e+00
   4_xyz:  0.1754 0.2400   5.545541e+00   5.782674e+00
   4_adp:  0.1649 0.2187   5.480246e+00   5.699529e+00
   4_occ:  0.1648 0.2183   5.478892e+00   5.697812e+00
   5_bss:  0.1647 0.2175   5.477322e+00   5.695919e+00
   5_xyz:  0.1353 0.1853   5.307443e+00   5.541105e+00
   5_adp:  0.1290 0.1792   5.271688e+00   5.511668e+00
   5_occ:  0.1289 0.1792   5.271497e+00   5.511441e+00
   5_bss:  0.1296 0.1788   5.271534e+00   5.509642e+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:  0.326  33.377  -3.542   1.190   3.527   0.000   0.000   0.000
   1_xyz:  0.326  33.377  -3.542   1.190   3.527   0.000   0.000   0.000
   1_adp:  0.326  33.377  -3.542   1.190   3.527   0.000   0.000   0.000
   1_occ:  0.326  33.377  -3.542   1.190   3.527   0.000   0.000   0.000
   2_bss:  0.354  66.922  -1.005   0.293   2.089   0.000   0.000   0.000
   2_xyz:  0.354  66.922  -1.005   0.293   2.089   0.000   0.000   0.000
   2_adp:  0.354  66.922  -1.005   0.293   2.089   0.000   0.000   0.000
   2_occ:  0.354  66.922  -1.005   0.293   2.089   0.000   0.000   0.000
   3_bss:  0.351  74.863  -0.830  -0.321   1.476  -0.000   0.000   0.000
   3_xyz:  0.351  74.863  -0.830  -0.321   1.476  -0.000   0.000   0.000
   3_adp:  0.351  74.863  -0.830  -0.321   1.476  -0.000   0.000   0.000
   3_occ:  0.351  74.863  -0.830  -0.321   1.476  -0.000   0.000   0.000
   4_bss:  0.338  74.863  -1.325  -1.108   0.892  -0.000   0.000   0.000
   4_xyz:  0.338  74.863  -1.325  -1.108   0.892  -0.000   0.000   0.000
   4_adp:  0.338  74.863  -1.325  -1.108   0.892  -0.000   0.000   0.000
   4_occ:  0.338  74.863  -1.325  -1.108   0.892  -0.000   0.000   0.000
   5_bss:  0.326  61.404  -1.649  -1.785   0.548  -0.000   0.000   0.000
   5_xyz:  0.326  61.404  -1.649  -1.785   0.548  -0.000   0.000   0.000
   5_adp:  0.326  61.404  -1.649  -1.785   0.548  -0.000   0.000   0.000
   5_occ:  0.326  61.404  -1.649  -1.785   0.548  -0.000   0.000   0.000
   5_bss:  0.326  61.407  -1.891  -2.050   0.287  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.226 0.3779  0.5248    80538.342
   1_bss:  59.762 0.3960  0.5626    77681.982
   1_xyz:  52.855 0.4835  0.6727    62062.857
   1_adp:  53.524 0.4747  0.6656    63652.560
   1_occ:  53.676 0.4727  0.6621    63886.509
   2_bss:  53.574 0.4740  0.6680    63994.395
   2_xyz:  42.725 0.6082  0.8404    42099.831
   2_adp:  39.981 0.6419  0.8647    38423.153
   2_occ:  39.953 0.6423  0.8652    38386.456
   3_bss:  39.735 0.6445  0.8565    37782.368
   3_xyz:  31.665 0.7381  0.9455    25198.586
   3_adp:  29.886 0.7579  0.9401    22638.248
   3_occ:  29.877 0.7580  0.9400    22607.005
   4_bss:  29.838 0.7584  0.9202    22568.718
   4_xyz:  24.157 0.8185  0.9681    15059.570
   4_adp:  21.357 0.8481  0.9807    12626.647
   4_occ:  21.303 0.8486  0.9809    12565.967
   5_bss:  21.234 0.8491  0.9655    12471.869
   5_xyz:  17.544 0.8841  0.9834     9000.396
   5_adp:  16.765 0.8916  0.9788     8518.161
   5_occ:  16.760 0.8917  0.9787     8509.240
   5_bss:  16.733 0.8918  0.9704     8471.869
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9538e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9538e-01
   1_xyz:   1.753  0.013  0.121 16.728  0.008  4.099   1.7283e-01
   1_adp:   1.753  0.013  0.121 16.728  0.008  4.099   1.7283e-01
   1_occ:   1.753  0.013  0.121 16.728  0.008  4.099   1.7283e-01
   2_bss:   1.753  0.013  0.121 16.728  0.008  4.099   1.7283e-01
   2_xyz:   1.473  0.012  0.104 16.438  0.006  4.111   1.3100e-01
   2_adp:   1.473  0.012  0.104 16.438  0.006  4.111   1.3100e-01
   2_occ:   1.473  0.012  0.104 16.438  0.006  4.111   1.3100e-01
   3_bss:   1.473  0.012  0.104 16.438  0.006  4.111   1.3100e-01
   3_xyz:   1.057  0.008  0.074 14.960  0.004  4.117   6.7483e-02
   3_adp:   1.057  0.008  0.074 14.960  0.004  4.117   6.7483e-02
   3_occ:   1.057  0.008  0.074 14.960  0.004  4.117   6.7483e-02
   4_bss:   1.057  0.008  0.074 14.960  0.004  4.117   6.7483e-02
   4_xyz:   1.003  0.007  0.073 14.388  0.004  4.125   5.8517e-02
   4_adp:   1.003  0.007  0.073 14.388  0.004  4.125   5.8517e-02
   4_occ:   1.003  0.007  0.073 14.388  0.004  4.125   5.8517e-02
   5_bss:   1.003  0.007  0.073 14.388  0.004  4.125   5.8517e-02
   5_xyz:   1.128  0.009  0.081 14.749  0.004  4.121   7.4249e-02
   5_adp:   1.128  0.009  0.081 14.749  0.004  4.121   7.4249e-02
   5_occ:   1.128  0.009  0.081 14.749  0.004  4.121   7.4249e-02
   5_bss:   1.128  0.009  0.081 14.749  0.004  4.121   7.4249e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.481   2.4216e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.481   2.4216e-01
   1_xyz:  10.283  0.065  0.437 79.108  0.055  1.937   1.1524e-01
   1_adp:  10.283  0.065  0.437 79.108  0.055  1.937   1.1524e-01
   1_occ:  10.283  0.065  0.437 79.108  0.055  1.937   1.1524e-01
   2_bss:  10.283  0.065  0.437 79.108  0.055  1.937   1.1524e-01
   2_xyz:  12.145  0.067  0.384 89.328  0.034  1.946   1.8325e-01
   2_adp:  12.145  0.067  0.384 89.328  0.034  1.946   1.8325e-01
   2_occ:  12.145  0.067  0.384 89.328  0.034  1.946   1.8325e-01
   3_bss:  12.145  0.067  0.384 89.328  0.034  1.946   1.8325e-01
   3_xyz:   7.412  0.063  0.265 84.154  0.038  2.328   5.6224e-02
   3_adp:   7.412  0.063  0.265 84.154  0.038  2.328   5.6224e-02
   3_occ:   7.412  0.063  0.265 84.154  0.038  2.328   5.6224e-02
   4_bss:   7.412  0.063  0.265 84.154  0.038  2.328   5.6224e-02
   4_xyz:   6.403  0.041  0.212 86.343  0.043  2.379   5.5140e-02
   4_adp:   6.403  0.041  0.212 86.343  0.043  2.379   5.5140e-02
   4_occ:   6.403  0.041  0.212 86.343  0.043  2.379   5.5140e-02
   5_bss:   6.403  0.041  0.212 86.343  0.043  2.379   5.5140e-02
   5_xyz:   6.782  0.057  0.273 87.058  0.029  2.328   6.7947e-02
   5_adp:   6.782  0.057  0.273 87.058  0.029  2.328   6.7947e-02
   5_occ:   6.782  0.057  0.273 87.058  0.029  2.328   6.7947e-02
   5_bss:   6.782  0.057  0.273 87.058  0.029  2.328   6.7947e-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:  79.74   0.00  18.57  70.98   0.00  15.72  79.74   0.00  34.11
   1_occ:  79.74   0.00  18.57  70.98   0.00  15.72  79.74   0.00  34.11
   2_bss:  79.74   0.00  18.57  70.98   0.00  15.72  79.74   0.00  34.11
   2_xyz:  79.74   0.00  18.57  70.98   0.00  15.72  79.74   0.00  34.11
   2_adp:  82.97   0.00  18.09  71.80   0.00  14.79  82.97   0.00  36.09
   2_occ:  82.97   0.00  18.09  71.80   0.00  14.79  82.97   0.00  36.09
   3_bss:  82.97   0.00  18.09  71.80   0.00  14.79  82.97   0.00  36.09
   3_xyz:  82.97   0.00  18.09  71.80   0.00  14.79  82.97   0.00  36.09
   3_adp: 106.84   0.00  19.52 101.25   0.00  14.24 106.84   1.78  48.27
   3_occ: 106.84   0.00  19.52 101.25   0.00  14.24 106.84   1.78  48.27
   4_bss: 106.84   0.00  19.52 101.25   0.00  14.24 106.84   1.78  48.27
   4_xyz: 106.84   0.00  19.52 101.25   0.00  14.24 106.84   1.78  48.27
   4_adp:  97.40   1.12  17.87  97.40   1.12  12.85  97.09   4.75  45.18
   4_occ:  97.40   1.12  17.87  97.40   1.12  12.85  97.09   4.75  45.18
   5_bss:  97.40   1.12  17.87  97.40   1.12  12.85  97.09   4.75  45.18
   5_xyz:  97.40   1.12  17.87  97.40   1.12  12.85  97.09   4.75  45.18
   5_adp:  96.72   0.00  17.57  96.72   0.00  12.43  95.70   5.06  45.59
   5_occ:  96.72   0.00  17.57  96.72   0.00  12.43  95.70   5.06  45.59
   5_bss:  96.72   0.00  17.57  96.72   0.00  12.43  95.70   5.06  45.59
------------------------------------------------------------------------
 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:    1.983    0.022    0.422
   1_adp:    1.983    0.022    0.422
   1_occ:    1.983    0.022    0.422
   2_bss:    1.983    0.022    0.422
   2_xyz:    1.726    0.022    0.653
   2_adp:    1.726    0.022    0.653
   2_occ:    1.726    0.022    0.653
   3_bss:    1.726    0.022    0.653
   3_xyz:    1.688    0.034    0.769
   3_adp:    1.688    0.034    0.769
   3_occ:    1.688    0.034    0.769
   4_bss:    1.688    0.034    0.769
   4_xyz:    1.716    0.102    0.850
   4_adp:    1.716    0.102    0.850
   4_occ:    1.716    0.102    0.850
   5_bss:    1.716    0.102    0.850
   5_xyz:    1.809    0.072    0.910
   5_adp:    1.809    0.072    0.910
   5_occ:    1.809    0.072    0.910
   5_bss:    1.809    0.072    0.910
------------------------------------------------------------------------

CPU time actual refinement: 322.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_615/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_615/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_615/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_615/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_615/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.63 
  Macro-tasks:
    bulk solvent and scale       = 36.82  
    individual site refinement   = 134.72 
    weights calculation          = 30.95  
    collect and process          = 6.45   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 209.05 
  Micro-tasks:
    mask                            = 2.95   
    f_calc                          = 101.34 
    alpha_beta                      = 8.50   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 110.21 
    fmodel                         = 6.35   
    r_factors                      = 0.17   
    phase_errors                   = 10.24  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 241.23 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.653 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    603 calls, 100.93 s
gradients_fft:          548 calls,  97.53 s

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

# Date 2008-01-16 Time 05:14:20 PST -0800 (1200489260.85 s)
Start R-work = 0.4835, R-free = 0.4869 (no bulk solvent and anisotropic scale)
Final R-work = 0.1495, R-free = 0.1958 (no bulk solvent and anisotropic scale)

Start R-work = 0.4723, R-free = 0.4798
Final R-work = 0.1296, R-free = 0.1788