# Date 2008-01-16 Time 04:51:26 PST -0800 (1200487886.64 s)
#phil __OFF__

Command line arguments: "../493.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15436
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 493

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.7567, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.95331
Completeness in resolution range: 0.928829
Completeness with d_max=infinity: 0.926106

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9533

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.95331
Completeness in resolution range: 0.928829
Completeness with d_max=infinity: 0.926106

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1809 [2211/2236]  1988   223  10.1%
  bin  2:  4.1809 -  3.3304 [2137/2157]  1928   209   9.8%
  bin  3:  3.3304 -  2.9129 [2096/2115]  1887   209  10.0%
  bin  4:  2.9129 -  2.6481 [2085/2115]  1867   218  10.5%
  bin  5:  2.6481 -  2.4592 [2075/2094]  1869   206   9.9%
  bin  6:  2.4592 -  2.3148 [2056/2081]  1856   200   9.7%
  bin  7:  2.3148 -  2.1992 [2040/2068]  1831   209  10.2%
  bin  8:  2.1992 -  2.1038 [2045/2081]  1835   210  10.3%
  bin  9:  2.1038 -  2.0230 [2004/2078]  1817   187   9.3%
  bin 10:  2.0230 -  1.9533 [ 840/2065]   752    88  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_493/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.37 -     2.08: 22
        2.08 -     2.78: 652
        2.78 -     3.49: 4558
        3.49 -     4.19: 9392
        4.19 -     4.90: 13875
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.375 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.655 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.706 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28494 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_493/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_493/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.75675 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4712   r_free= 0.4748   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.287894                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6637 0.99   1434  157 0.3854 0.3805      6.6122      6.5811|
|  2:  4.6637 -  3.7202 0.99   1389  157 0.4138 0.4269      6.8261      6.8031|
|  3:  3.7202 -  3.2554 0.99   1358  150 0.4456 0.4269      6.6876      6.6793|
|  4:  3.2554 -  2.9603 0.99   1343  150 0.4731 0.4911      6.5426      6.5475|
|  5:  2.9603 -  2.7495 0.99   1345  149 0.5049 0.4913       6.354      6.3972|
|  6:  2.7495 -  2.5882 0.99   1339  148 0.4965 0.5069      6.2708      6.1823|
|  7:  2.5882 -  2.4592 0.99   1331  154 0.4983 0.5165      6.2291      6.1665|
|  8:  2.4592 -  2.3526 0.98   1318  148 0.5253 0.5241      6.1692      6.1707|
|  9:  2.3526 -  2.2623 0.98   1310  138 0.5044 0.5573      6.1194      6.1868|
| 10:  2.2623 -  2.1845 1.00   1336  149 0.5211 0.5513      6.0727      6.1131|
| 11:  2.1845 -  2.1164 0.98   1312  148 0.5087 0.4779      6.0218      6.0062|
| 12:  2.1164 -  2.0561 0.98   1298  140 0.5053 0.4843       5.938      5.9499|
| 13:  2.0561 -  2.0021 0.88   1169  133 0.5064 0.4858      5.8815      5.7822|
| 14:  2.0021 -  1.9533 0.26    348   38 0.5297 0.5013      5.8789      5.8914|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6637  1434   157  0.72  32.39   0.81     0.78      67859.24|
|  2:  4.6637 -  3.7202  1389   157  0.68  37.09   0.89     0.79     117896.92|
|  3:  3.7202 -  3.2554  1358   150  0.54  48.61   0.91     0.73     130197.44|
|  4:  3.2554 -  2.9603  1343   150  0.43  57.35   0.90     0.61     121238.60|
|  5:  2.9603 -  2.7495  1345   149  0.38  61.04   0.86     0.56      86206.07|
|  6:  2.7495 -  2.5882  1339   148  0.37  62.00   0.90     0.53      72432.54|
|  7:  2.5882 -  2.4592  1331   154  0.38  61.63   0.91     0.52      63488.14|
|  8:  2.4592 -  2.3526  1318   148  0.34  64.34   0.90     0.50      59567.67|
|  9:  2.3526 -  2.2623  1310   138  0.32  65.73   0.93     0.48      56596.31|
| 10:  2.2623 -  2.1845  1336   149  0.32  66.25   0.92     0.48      50805.31|
| 11:  2.1845 -  2.1164  1312   148  0.31  66.49   0.95     0.50      49661.79|
| 12:  2.1164 -  2.0561  1298   140  0.34  64.79   0.95     0.54      42519.97|
| 13:  2.0561 -  2.0021  1169   133  0.35  63.65   0.95     0.59      35966.24|
| 14:  2.0021 -  1.9533   348    38  0.46  55.42   1.00     0.64      25505.72|
|alpha:            min =        0.48 max =            0.79 mean =         0.59|
|beta:             min =    25505.72 max =       130197.44 mean =     73166.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.43|
|phase err.(test): min =        0.00 max =           89.86 mean =        57.92|
|-----------------------------------------------------------------------------|

============================== 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 = 17.683998             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.523   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.892073              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.457   (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 |  1.375 -  1.727:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.727 -  2.080:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.080 -  2.432:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.432 -  2.785:      617 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.785 -  3.137:     2159 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.137 -  3.490:     2399 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.490 -  3.842:     4546 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.842 -  4.195:     4846 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.195 -  4.547:     6253 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.547 -  4.900:     7622 |
|-----------------------------------------------------------------------------|
|-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 |   4.108    4.900  1.375 |       0.667 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4712   r_free= 0.4748   ksol= 0.00   Bsol= 0.00   scale= 0.888    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.287894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4653   ksol= 0.36   Bsol= 50.00   scale= 0.921   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,1.83,2.53,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.282204                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.604155             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.438   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.297016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.230   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4602      final r-factor (work) = 0.3756          |
| start r-factor (free) = 0.4653      final r-factor (free) = 0.4209          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.8857 = 13.60 * 0.50 * 6.2762 + 1.00 * 0.1947                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.2058 = 13.60 * 0.50 * 6.1821 + 1.00 * 0.1546                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3756      final r-factor (work) = 0.3458          |
| start r-factor (free) = 0.4209      final r-factor (free) = 0.4295          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0244 = 1.30 * 1.00 * 6.1821 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9476 = 1.30 * 1.00 * 6.1117 + 1.00 * 0.0207                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.89   18.29    None  None   None       |
|    all(noH): 2823   0      0.00    80.89   18.29    None  None   None       |
|    Sol.    : 438    0      0.00    80.89   34.24    None  None   None       |
|    Mac.    : 2385   0      0.00    71.49   15.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.089:  638   |   5:    40.444 -  48.533:  101        |
|      1:     8.089 -  16.178:  846   |   6:    48.533 -  56.622:   67        |
|      2:    16.178 -  24.267:  598   |   7:    56.622 -  64.711:   24        |
|      3:    24.267 -  32.355:  334   |   8:    64.711 -  72.800:   15        |
|      4:    32.355 -  40.444:  197   |   9:    72.800 -  80.888:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3458 r_free = 0.4295             target_work(ml) = 6.117         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3453 r_free = 0.4297             target_work(ml) = 6.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3453   r_free= 0.4297   ksol= 0.36   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,1.83,2.53,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.117056                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3449   r_free= 0.4267   ksol= 0.36   Bsol= 74.85   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.54,1.23,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.118835                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.735075             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.358  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.677978              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.124  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3449      final r-factor (work) = 0.2845          |
| start r-factor (free) = 0.4267      final r-factor (free) = 0.3635          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.0846 = 12.74 * 0.50 * 6.1138 + 1.00 * 0.1546                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.6965 = 12.74 * 0.50 * 6.0582 + 1.00 * 0.1209                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2845      final r-factor (work) = 0.2654          |
| start r-factor (free) = 0.3635      final r-factor (free) = 0.3481          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1305 = 0.68 * 1.00 * 6.0582 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0378 = 0.68 * 1.00 * 5.9362 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.93   18.35    None  None   None       |
|    all(noH): 2823   0      0.00    86.93   18.35    None  None   None       |
|    Sol.    : 438    0      1.26    86.93   37.65    None  None   None       |
|    Mac.    : 2385   0      0.00    75.62   14.80    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 -   8.693:  736   |   5:    43.463 -  52.156:  100        |
|      1:     8.693 -  17.385:  969   |   6:    52.156 -  60.849:   62        |
|      2:    17.385 -  26.078:  492   |   7:    60.849 -  69.541:   22        |
|      3:    26.078 -  34.771:  271   |   8:    69.541 -  78.234:   11        |
|      4:    34.771 -  43.463:  156   |   9:    78.234 -  86.927:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2654 r_free = 0.3481             target_work(ml) = 5.918         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2653 r_free = 0.3477             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2653   r_free= 0.3477   ksol= 0.36   Bsol= 74.85   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.54,1.23,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.917388                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2655   r_free= 0.3464   ksol= 0.34   Bsol= 78.02   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,-0.44,0.70,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.915261                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.708496              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.540   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.812806              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.905  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2655      final r-factor (work) = 0.2046          |
| start r-factor (free) = 0.3464      final r-factor (free) = 0.2694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9674 = 8.71 * 0.50 * 5.9359 + 1.00 * 0.1209                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.4477 = 8.71 * 0.50 * 5.8241 + 1.00 * 0.0882                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2046      final r-factor (work) = 0.1807          |
| start r-factor (free) = 0.2694      final r-factor (free) = 0.2456          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7469 = 0.81 * 1.00 * 5.8241 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5817 = 0.81 * 1.00 * 5.6202 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.65   18.45    None  None   None       |
|    all(noH): 2823   0      0.00    99.65   18.45    None  None   None       |
|    Sol.    : 438    0      5.01    99.65   45.21    None  None   None       |
|    Mac.    : 2385   0      0.00    87.17   13.54    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 -   9.965: 1046   |   5:    49.827 -  59.792:  100        |
|      1:     9.965 -  19.931: 1005   |   6:    59.792 -  69.757:   76        |
|      2:    19.931 -  29.896:  280   |   7:    69.757 -  79.723:   28        |
|      3:    29.896 -  39.861:  141   |   8:    79.723 -  89.688:   10        |
|      4:    39.861 -  49.827:  136   |   9:    89.688 -  99.653:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1807 r_free = 0.2456             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1806 r_free = 0.2451             target_work(ml) = 5.573         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1806   r_free= 0.2451   ksol= 0.34   Bsol= 78.02   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,-0.44,0.70,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.573324                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1800   r_free= 0.2450   ksol= 0.35   Bsol= 80.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.73,0.02,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.572222                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.285523              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.503  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.277611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.647  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1800      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.2450      final r-factor (free) = 0.2010          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1365 = 4.29 * 0.50 * 5.6228 + 1.00 * 0.0882                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8389 = 4.29 * 0.50 * 5.4948 + 1.00 * 0.0649                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1471      final r-factor (work) = 0.1396          |
| start r-factor (free) = 0.2010      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5389 = 0.28 * 1.00 * 5.4948 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5679 = 0.28 * 1.00 * 5.3637 + 1.00 * 0.0789                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.75   17.85    None  None   None       |
|    all(noH): 2823   0      0.00    99.75   17.85    None  None   None       |
|    Sol.    : 438    0      4.30    99.75   44.62    None  None   None       |
|    Mac.    : 2385   0      0.00    87.27   12.93    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 -   9.975: 1110   |   5:    49.873 -  59.848:   98        |
|      1:     9.975 -  19.949: 1020   |   6:    59.848 -  69.822:   76        |
|      2:    19.949 -  29.924:  231   |   7:    69.822 -  79.797:   26        |
|      3:    29.924 -  39.898:  129   |   8:    79.797 -  89.771:   10        |
|      4:    39.898 -  49.873:  122   |   9:    89.771 -  99.746:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1396 r_free = 0.1897             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1394 r_free = 0.1895             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1895   ksol= 0.35   Bsol= 80.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.73,0.02,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.330488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1396   r_free= 0.1892   ksol= 0.32   Bsol= 59.67   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.18,-0.08,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.328694                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.996119              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.670  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.540644              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.361   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1396      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1892      final r-factor (free) = 0.1760          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4179 = 2.00 * 0.50 * 5.3634 + 1.00 * 0.0649                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3463 = 2.00 * 0.50 * 5.3042 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.1760      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2024 = 1.54 * 1.00 * 5.3042 + 1.00 * 0.0305                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1035 = 1.54 * 1.00 * 5.2519 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    108.86  17.93    None  None   None       |
|    all(noH): 2823   0      0.49    108.86  17.93    None  None   None       |
|    Sol.    : 438    0      2.83    108.86  46.40    None  None   None       |
|    Mac.    : 2385   0      0.49    98.54   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.493 -  11.330: 1412   |   5:    54.677 -  65.513:   86        |
|      1:    11.330 -  22.167:  826   |   6:    65.513 -  76.350:   64        |
|      2:    22.167 -  33.003:  192   |   7:    76.350 -  87.187:   30        |
|      3:    33.003 -  43.840:  103   |   8:    87.187 -  98.023:    9        |
|      4:    43.840 -  54.677:   99   |   9:    98.023 - 108.860:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1265 r_free = 0.1754             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1265 r_free = 0.1755             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1755   ksol= 0.32   Bsol= 59.67   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.18,-0.08,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.249384                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6637 0.99   1434  157 0.1000 0.1334      5.3988      5.6328|
|  2:  4.6637 -  3.7202 0.99   1389  157 0.0907 0.1189      5.4848      5.6937|
|  3:  3.7202 -  3.2554 0.99   1358  150 0.1216 0.1540      5.5736      5.8418|
|  4:  3.2554 -  2.9603 0.99   1343  150 0.1459 0.1987      5.5837      5.7738|
|  5:  2.9603 -  2.7495 0.99   1345  149 0.1574 0.1988      5.4659      5.6713|
|  6:  2.7495 -  2.5882 0.99   1339  148 0.1441 0.2220      5.3203      5.5725|
|  7:  2.5882 -  2.4592 0.99   1331  154 0.1437 0.1867      5.2825      5.4375|
|  8:  2.4592 -  2.3526 0.98   1318  148 0.1421 0.1912      5.2089      5.4434|
|  9:  2.3526 -  2.2623 0.98   1310  138 0.1329 0.2008      5.1336      5.3942|
| 10:  2.2623 -  2.1845 1.00   1336  149 0.1238 0.1726      5.0158      5.2332|
| 11:  2.1845 -  2.1164 0.98   1312  148 0.1254 0.2068      5.0192      5.4171|
| 12:  2.1164 -  2.0561 0.98   1298  140 0.1292 0.1981      4.9697      5.2334|
| 13:  2.0561 -  2.0021 0.88   1169  133 0.1179 0.1685      4.8324      5.0109|
| 14:  2.0021 -  1.9533 0.26    348   38 0.1057 0.1798         4.7      5.0045|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6637  1434   157  0.94   9.39   0.97     0.94       7369.26|
|  2:  4.6637 -  3.7202  1389   157  0.95   8.24   1.02     1.01       9739.66|
|  3:  3.7202 -  3.2554  1358   150  0.92  13.11   1.04     1.04      12548.75|
|  4:  3.2554 -  2.9603  1343   150  0.89  16.68   1.02     1.00      13385.37|
|  5:  2.9603 -  2.7495  1345   149  0.88  18.33   0.99     0.98      10965.17|
|  6:  2.7495 -  2.5882  1339   148  0.87  18.81   0.98     0.95       8699.55|
|  7:  2.5882 -  2.4592  1331   154  0.88  18.41   1.00     0.96       7978.08|
|  8:  2.4592 -  2.3526  1318   148  0.88  18.31   1.00     0.96       6985.85|
|  9:  2.3526 -  2.2623  1310   138  0.89  17.79   1.00     0.94       6095.17|
| 10:  2.2623 -  2.1845  1336   149  0.89  17.23   1.00     0.97       5060.57|
| 11:  2.1845 -  2.1164  1312   148  0.89  17.67   0.98     0.93       4970.85|
| 12:  2.1164 -  2.0561  1298   140  0.89  17.87   1.01     1.01       4807.04|
| 13:  2.0561 -  2.0021  1169   133  0.89  18.01   0.99     0.97       3798.69|
| 14:  2.0021 -  1.9533   348    38  0.94  12.68   0.99     0.95       2618.70|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2618.70 max =        13385.37 mean =      7838.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.98|
|phase err.(test): min =        0.00 max =           89.65 mean =        15.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1754   ksol= 0.32   Bsol= 59.66   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.15,-0.01,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.249372                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1754   ksol= 0.32   Bsol= 59.66   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.15,-0.01,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.249372                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6637 0.99   1434  157 0.1001 0.1334      5.3992      5.6334|
|  2:  4.6637 -  3.7202 0.99   1389  157 0.0907 0.1190      5.4851      5.6937|
|  3:  3.7202 -  3.2554 0.99   1358  150 0.1216 0.1540      5.5737       5.842|
|  4:  3.2554 -  2.9603 0.99   1343  150 0.1460 0.1987      5.5837      5.7739|
|  5:  2.9603 -  2.7495 0.99   1345  149 0.1573 0.1988      5.4657      5.6711|
|  6:  2.7495 -  2.5882 0.99   1339  148 0.1441 0.2219      5.3201      5.5725|
|  7:  2.5882 -  2.4592 0.99   1331  154 0.1437 0.1867      5.2824      5.4377|
|  8:  2.4592 -  2.3526 0.98   1318  148 0.1421 0.1911       5.209      5.4433|
|  9:  2.3526 -  2.2623 0.98   1310  138 0.1328 0.2008      5.1338      5.3943|
| 10:  2.2623 -  2.1845 1.00   1336  149 0.1237 0.1726      5.0157      5.2334|
| 11:  2.1845 -  2.1164 0.98   1312  148 0.1253 0.2068      5.0192      5.4174|
| 12:  2.1164 -  2.0561 0.98   1298  140 0.1292 0.1980      4.9697      5.2332|
| 13:  2.0561 -  2.0021 0.88   1169  133 0.1179 0.1683      4.8319      5.0097|
| 14:  2.0021 -  1.9533 0.26    348   38 0.1057 0.1797       4.699      5.0035|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6637  1434   157  0.94   9.40   0.97     0.94       7375.05|
|  2:  4.6637 -  3.7202  1389   157  0.95   8.25   1.02     1.01       9745.31|
|  3:  3.7202 -  3.2554  1358   150  0.92  13.12   1.04     1.04      12556.22|
|  4:  3.2554 -  2.9603  1343   150  0.89  16.68   1.03     1.00      13386.15|
|  5:  2.9603 -  2.7495  1345   149  0.88  18.33   1.00     0.98      10961.68|
|  6:  2.7495 -  2.5882  1339   148  0.87  18.81   0.99     0.95       8694.74|
|  7:  2.5882 -  2.4592  1331   154  0.88  18.40   1.00     0.96       7976.63|
|  8:  2.4592 -  2.3526  1318   148  0.88  18.31   1.00     0.96       6986.72|
|  9:  2.3526 -  2.2623  1310   138  0.89  17.79   1.00     0.95       6098.77|
| 10:  2.2623 -  2.1845  1336   149  0.89  17.24   1.00     0.98       5061.62|
| 11:  2.1845 -  2.1164  1312   148  0.89  17.68   0.99     0.93       4973.08|
| 12:  2.1164 -  2.0561  1298   140  0.89  17.87   1.02     1.01       4806.49|
| 13:  2.0561 -  2.0021  1169   133  0.89  17.99   1.00     0.97       3793.39|
| 14:  2.0021 -  1.9533   348    38  0.94  12.65   0.99     0.96       2610.81|
|alpha:            min =        0.93 max =            1.04 mean =         0.98|
|beta:             min =     2610.81 max =        13386.15 mean =      7839.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.98|
|phase err.(test): min =        0.00 max =           89.65 mean =        15.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.661)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    108.84  17.92    None  None   None       |
|    all(noH): 2823   0      0.48    108.84  17.92    None  None   None       |
|    Sol.    : 438    0      2.81    108.84  46.38    None  None   None       |
|    Mac.    : 2385   0      0.48    98.52   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.478 -  11.315: 1412   |   5:    54.661 -  65.498:   86        |
|      1:    11.315 -  22.151:  826   |   6:    65.498 -  76.335:   64        |
|      2:    22.151 -  32.988:  192   |   7:    76.335 -  87.171:   30        |
|      3:    32.988 -  43.825:  103   |   8:    87.171 -  98.008:    9        |
|      4:    43.825 -  54.661:   99   |   9:    98.008 - 108.845:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.551 - 4.382
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 341
   mapped sites are within: 0.725 - 4.382

peak=    7.660 closest distance to " O   HOH Z 390 " =    1.246
peak=    7.612 closest distance to " O   HOH Z 385 " =    1.968
peak=    6.319 closest distance to " O   HOH Z 245 " =    1.222
peak=    6.087 closest distance to " O   HOH Z 422 " =    1.341
peak=    5.797 closest distance to " O   HOH Z 222 " =    1.425
peak=    5.753 closest distance to " O   HOH Z  65 " =    1.554
peak=    5.612 closest distance to " O   HOH Z 142 " =    1.873
peak=    5.590 closest distance to " O   HOH Z 417 " =    2.748
peak=    5.570 closest distance to " O   HOH Z   7 " =    2.013
peak=    5.543 closest distance to " NE2 GLN A  11 " =    1.344
peak=    5.538 closest distance to " O   HOH Z  29 " =    1.712
peak=    5.525 closest distance to " O   HOH Z 431 " =    1.618
peak=    5.479 closest distance to " O   HOH Z 105 " =    1.314
peak=    5.455 closest distance to " O   HOH Z 287 " =    2.067
peak=    5.439 closest distance to " O   HOH Z  77 " =    1.142
peak=    5.322 closest distance to " O   HOH Z  69 " =    2.016
peak=    5.151 closest distance to " CG  PRO A  54 " =    1.447
peak=    5.062 closest distance to " O   HOH Z 130 " =    1.075
peak=    5.004 closest distance to " O   HOH Z 403 " =    1.842
peak=    5.000 closest distance to " O   HOH Z 278 " =    1.230
peak=    4.950 closest distance to " O   HOH Z  63 " =    2.103
peak=    4.940 closest distance to " O   HOH Z 423 " =    2.278
peak=    4.847 closest distance to " O   HOH Z 380 " =    2.243
peak=    4.748 closest distance to " O   HOH Z 418 " =    1.140
peak=    4.702 closest distance to " O   HOH Z  49 " =    1.342
peak=    4.691 closest distance to " CB  PRO A  54 " =    1.142
peak=    4.674 closest distance to " O   HOH Z 359 " =    1.623
peak=    4.650 closest distance to " O   HOH Z   9 " =    1.987
peak=    4.636 closest distance to " O   HOH Z 427 " =    2.050
peak=    4.598 closest distance to " O   HOH Z 427 " =    1.238
peak=    4.578 closest distance to " O   HOH Z  63 " =    1.783
peak=    4.541 closest distance to " O   HOH Z 145 " =    1.632
peak=    4.540 closest distance to " CG  PRO A  90 " =    1.444
peak=    4.522 closest distance to " O   HOH Z  39 " =    1.300
peak=    4.516 closest distance to " O   HOH Z 425 " =    1.408
peak=    4.495 closest distance to " O   HOH Z 158 " =    1.253
peak=    4.481 closest distance to " O   ASP A 286 " =    2.552
peak=    4.474 closest distance to " O   HOH Z 232 " =    2.222
peak=    4.429 closest distance to " CB  SER A 216 " =    1.046
peak=    4.429 closest distance to " O   HOH Z  66 " =    1.075
peak=    4.413 closest distance to " CB  GLN A 223 " =    1.544
peak=    4.408 closest distance to " O   HOH Z 375 " =    1.064
peak=    4.392 closest distance to " O   HOH Z 316 " =    3.074
peak=    4.326 closest distance to " CG2 VAL A 257 " =    0.856
peak=    4.326 closest distance to " CB  ARG A 275 " =    1.056
peak=    4.278 closest distance to " NH1AARG A 145 " =    1.218
peak=    4.269 closest distance to " O   HOH Z  30 " =    1.800
peak=    4.264 closest distance to " CG  PRO A 280 " =    1.033
peak=    4.258 closest distance to " CG  TRP A 179 " =    2.191
peak=    4.227 closest distance to " O   HOH Z 272 " =    1.888
peak=    4.214 closest distance to " CG  PRO A 213 " =    1.264
peak=    4.211 closest distance to " CA  TYR A  30 " =    1.070
peak=    4.210 closest distance to " CG  PRO A 198 " =    1.251
peak=    4.209 closest distance to " CB  ALA A 114 " =    0.897
peak=    4.204 closest distance to " O   HOH Z  78 " =    1.710
peak=    4.197 closest distance to " O   HOH Z 298 " =    1.870
peak=    4.192 closest distance to " O   HOH Z 124 " =    1.443
peak=    4.177 closest distance to " CZ3 TRP A 266 " =    1.240
peak=    4.155 closest distance to " O   HOH Z 415 " =    1.047
peak=    4.144 closest distance to " O   PRO A 198 " =    1.293
peak=    4.144 closest distance to " O   HOH Z 392 " =    1.309
peak=    4.133 closest distance to " O   HOH Z 424 " =    1.202
peak=    4.118 closest distance to " O   HOH Z 368 " =    3.585
peak=    4.092 closest distance to " O   HOH Z 225 " =    1.788
peak=    4.088 closest distance to " O   HOH Z 293 " =    1.519
peak=    4.053 closest distance to " O   HOH Z 276 " =    1.299
peak=    4.044 closest distance to " O  BHOH Z  74 " =    1.370
peak=    4.033 closest distance to " CB  SER A  63 " =    1.310
peak=    4.024 closest distance to " ND2 ASN A  60 " =    3.008
peak=    4.015 closest distance to " CE3 TRP A 150 " =    1.067
peak=    4.001 closest distance to " CE  LYS A 119 " =    1.244
peak=    3.989 closest distance to " CD  GLN A  77 " =    1.330
peak=    3.986 closest distance to " CB  ASN A 148 " =    1.441
peak=    3.980 closest distance to " CD  ARG A  66 " =    2.333
peak=    3.979 closest distance to " O   HOH Z  43 " =    1.287
peak=    3.954 closest distance to " CB  ASN A  39 " =    0.923
peak=    3.953 closest distance to " NH2 ARG A  56 " =    2.045
peak=    3.947 closest distance to " CG  GLN A  58 " =    1.095
peak=    3.937 closest distance to " O   HOH Z 295 " =    1.121
peak=    3.914 closest distance to " O   HOH Z 365 " =    1.493
peak=    3.886 closest distance to " CB  TRP A 266 " =    1.112
peak=    3.873 closest distance to " NZ  LYS A 117 " =    2.935
peak=    3.870 closest distance to " N   GLU A   2 " =    1.438
peak=    3.870 closest distance to " CE3 TRP A 274 " =    1.413
peak=    3.865 closest distance to " CB  GLU A 277 " =    3.586
peak=    3.851 closest distance to " O   HOH Z  46 " =    1.057
peak=    3.851 closest distance to " O   HOH Z 211 " =    1.014
peak=    3.846 closest distance to " O   HOH Z 365 " =    2.435
peak=    3.844 closest distance to " O   HOH Z 437 " =    1.951
peak=    3.841 closest distance to " O   HOH Z 258 " =    2.144
peak=    3.839 closest distance to " O   HOH Z 327 " =    1.743
peak=    3.836 closest distance to " CB  LYS A 117 " =    1.221
peak=    3.834 closest distance to " O   HOH Z 414 " =    1.394
peak=    3.831 closest distance to " O   HOH Z 371 " =    1.789
peak=    3.819 closest distance to " CB  SER A 273 " =    0.957
peak=    3.818 closest distance to " CG  LYS A  76 " =    1.732
peak=    3.808 closest distance to " CB  SER A 276 " =    1.315
peak=    3.806 closest distance to " O   HOH Z 405 " =    1.577
peak=    3.800 closest distance to " O   HOH Z 282 " =    1.876
peak=    3.799 closest distance to " CB  THR A  31 " =    1.641
peak=    3.787 closest distance to " O   HOH Z  76 " =    1.254
peak=    3.785 closest distance to " N   GLN A 278 " =    1.187
peak=    3.785 closest distance to " O   HOH Z  88 " =    3.570
peak=    3.777 closest distance to " CB  GLU A 128 " =    1.079
peak=    3.760 closest distance to " ND2 ASN A 249 " =    0.802
peak=    3.759 closest distance to " O   HOH Z 244 " =    1.497
peak=    3.750 closest distance to " N   TYR A  15 " =    1.172
peak=    3.732 closest distance to " O   HOH Z  40 " =    2.209
peak=    3.731 closest distance to " O   HOH Z  67 " =    1.343
peak=    3.728 closest distance to " O   HOH Z 143 " =    1.183
peak=    3.727 closest distance to " ND2BASN A 224 " =    0.905
peak=    3.725 closest distance to " CA  ALA A 160 " =    1.037
peak=    3.722 closest distance to " O   HOH Z 236 " =    1.437
peak=    3.721 closest distance to " CB  ARG A 190 " =    1.687
peak=    3.716 closest distance to " O   HOH Z  11 " =    1.025
peak=    3.700 closest distance to " CG2 ILE A 120 " =    1.070
peak=    3.687 closest distance to " CB  GLN A 183 " =    1.225
peak=    3.681 closest distance to " O   HOH Z 153 " =    3.561
peak=    3.673 closest distance to " CB  SER A  99 " =    0.864
peak=    3.664 closest distance to " O   HOH Z 201 " =    1.674
peak=    3.662 closest distance to " CB  ASN A 215 " =    1.068
peak=    3.660 closest distance to " CA  VAL A 125 " =    1.178
peak=    3.655 closest distance to " OG BSER A 164 " =    2.229
peak=    3.653 closest distance to " O   HOH Z 193 " =    1.622
peak=    3.644 closest distance to " CB  VAL A 202 " =    1.622
peak=    3.638 closest distance to " O   HOH Z 434 " =    1.503
peak=    3.637 closest distance to " O   HOH Z 415 " =    1.676
peak=    3.628 closest distance to " NZ  LYS A 119 " =    2.484
peak=    3.627 closest distance to " CB  ASP A 124 " =    0.853
peak=    3.625 closest distance to " CB  TRP A 179 " =    1.436
peak=    3.625 closest distance to " CA  GLY A 267 " =    1.144
peak=    3.623 closest distance to " CA  ALA A  51 " =    1.046
peak=    3.622 closest distance to " O   HOH Z 215 " =    1.541
peak=    3.618 closest distance to " O   HOH Z   2 " =    1.643
peak=    3.612 closest distance to " O   HOH Z 411 " =    3.849
peak=    3.607 closest distance to " O   HOH Z 362 " =    1.460
peak=    3.603 closest distance to " O   HOH Z 112 " =    1.168
peak=    3.602 closest distance to " O   HOH Z 214 " =    2.439
peak=    3.602 closest distance to " O   HOH Z   7 " =    2.881
peak=    3.590 closest distance to " CZ  PHE A 218 " =    1.147
peak=    3.588 closest distance to " CB  ASN A 110 " =    1.060
peak=    3.580 closest distance to " CB  PRO A  90 " =    1.097
peak=    3.574 closest distance to " NE1 TRP A 274 " =    1.044
peak=    3.572 closest distance to " CB  PHE A 130 " =    0.999
peak=    3.562 closest distance to " O   HOH Z  51 " =    1.724
peak=    3.555 closest distance to " O   HOH Z 425 " =    1.962
peak=    3.554 closest distance to " CZ  PHE A  38 " =    1.246
peak=    3.553 closest distance to " CA  ARG A 102 " =    1.123
peak=    3.550 closest distance to " CB  ALA A 114 " =    1.255
peak=    3.546 closest distance to " O   HOH Z  68 " =    1.997
peak=    3.535 closest distance to " O   HOH Z  26 " =    1.460
peak=    3.519 closest distance to " O   HOH Z 156 " =    3.147
peak=    3.517 closest distance to " CB  SER A 210 " =    0.836
peak=    3.517 closest distance to " O   HOH Z 361 " =    1.339
peak=    3.514 closest distance to " O   HOH Z 357 " =    2.072
peak=    3.512 closest distance to " CG  GLN A  11 " =    2.174
peak=    3.512 closest distance to " CE  LYS A  76 " =    0.905
peak=    3.511 closest distance to " CG2 ILE A  20 " =    1.543
peak=    3.509 closest distance to " CG2 THR A 221 " =    1.231
peak=    3.507 closest distance to " O   HOH Z 203 " =    1.787
peak=    3.504 closest distance to " O   HOH Z   6 " =    1.657
peak=    3.496 closest distance to " CA  ARG A 195 " =    1.306
peak=    3.494 closest distance to " CE AMET A  47 " =    1.457
peak=    3.492 closest distance to " O   HOH Z 222 " =    2.384
peak=    3.488 closest distance to " CB  ASN A 142 " =    0.994
peak=    3.486 closest distance to " CB  SER A 212 " =    1.415
peak=    3.486 closest distance to " O   HOH Z 394 " =    1.628
peak=    3.485 closest distance to " CB  SER A   3 " =    1.416
peak=    3.483 closest distance to " CG2 ILE A 239 " =    0.951
peak=    3.481 closest distance to " O   HOH Z 378 " =    0.970
peak=    3.479 closest distance to " O   HOH Z  61 " =    1.595
peak=    3.476 closest distance to " O   HOH Z  91 " =    2.429
peak=    3.471 closest distance to " CA  LEU A 282 " =    1.195
peak=    3.470 closest distance to " CG  LEU A 167 " =    1.319
peak=    3.469 closest distance to " CD2 TRP A 179 " =    1.368
peak=    3.468 closest distance to " O   HOH Z   1 " =    1.720
peak=    3.468 closest distance to " O   HOH Z 290 " =    1.087
peak=    3.466 closest distance to " O   HOH Z 146 " =    1.568
peak=    3.461 closest distance to " O   HOH Z 393 " =    1.243
peak=    3.459 closest distance to " O   HOH Z 390 " =    2.363
peak=    3.457 closest distance to " CA  ARG A  36 " =    1.079
peak=    3.457 closest distance to " CG  PRO A 243 " =    1.091
peak=    3.452 closest distance to " CG  GLN A  89 " =    1.570
peak=    3.451 closest distance to " O   HOH Z 358 " =    1.151
peak=    3.448 closest distance to " CB  ARG A  79 " =    1.219
peak=    3.444 closest distance to " O   HOH Z 406 " =    1.475
peak=    3.439 closest distance to " O   HOH Z 261 " =    2.009
peak=    3.438 closest distance to " CB  LEU A 300 " =    0.866
peak=    3.438 closest distance to " CG  GLU A 277 " =    1.897
peak=    3.435 closest distance to " O   HOH Z 345 " =    1.981
peak=    3.432 closest distance to " CD  LYS A 166 " =    1.562
peak=    3.432 closest distance to " O   HOH Z  27 " =    0.873
peak=    3.428 closest distance to " CB  ALA A  43 " =    0.886
peak=    3.428 closest distance to " O   HOH Z  44 " =    1.918
peak=    3.427 closest distance to " CA  ASN A 127 " =    1.157
peak=    3.425 closest distance to " CB  GLU A  46 " =    1.157
peak=    3.424 closest distance to " O   HOH Z 117 " =    1.217
peak=    3.423 closest distance to " O   HOH Z 368 " =    1.755
peak=    3.414 closest distance to " CG AARG A 275 " =    1.200
peak=    3.411 closest distance to " O   HOH Z  90 " =    2.134
peak=    3.407 closest distance to " O   HOH Z 181 " =    2.367
peak=    3.405 closest distance to " O   HOH Z  92 " =    1.266
peak=    3.404 closest distance to " N   ALA A   1 " =    1.592
peak=    3.404 closest distance to " O   HOH Z 157 " =    1.619
peak=    3.400 closest distance to " CA  TYR A 116 " =    1.416
peak=    3.400 closest distance to " CD  ARG A 159 " =    0.780
peak=    3.396 closest distance to " CA  ALA A 160 " =    1.357
peak=    3.395 closest distance to " CG2 VAL A 197 " =    1.147
peak=    3.391 closest distance to " CB  ALA A 248 " =    1.044
peak=    3.384 closest distance to " O   HOH Z 198 " =    1.411
peak=    3.383 closest distance to " O   HOH Z 180 " =    2.278
peak=    3.382 closest distance to " NE2 GLN A  73 " =    1.564
peak=    3.377 closest distance to " O   HOH Z  61 " =    1.647
peak=    3.372 closest distance to " O   HOH Z  59 " =    1.789
peak=    3.371 closest distance to " NH2AARG A 190 " =    1.794
peak=    3.370 closest distance to " CD  ARG A  66 " =    1.947
peak=    3.364 closest distance to " O   HOH Z 371 " =    2.062
peak=    3.361 closest distance to " CA  PHE A 283 " =    1.296
peak=    3.360 closest distance to " OE2 GLU A  53 " =    1.937
peak=    3.359 closest distance to " O   HOH Z 128 " =    2.000
peak=    3.358 closest distance to " N   THR A  42 " =    1.404
peak=    3.357 closest distance to " O   HOH Z 369 " =    1.753
peak=    3.356 closest distance to " OG  SER A  26 " =    1.538
peak=    3.350 closest distance to " O   HOH Z 122 " =    2.116
peak=    3.350 closest distance to " CG1 ILE A 120 " =    1.475
peak=    3.349 closest distance to " O   HOH Z 410 " =    1.619
peak=    3.341 closest distance to " O   HOH Z 119 " =    4.249
peak=    3.340 closest distance to " CB  TYR A 116 " =    1.152
peak=    3.338 closest distance to " O   HOH Z 103 " =    1.033
peak=    3.334 closest distance to " NZ BLYS A 290 " =    0.905
peak=    3.334 closest distance to " NZ  LYS A 117 " =    1.263
peak=    3.333 closest distance to " CB  MET A  40 " =    0.725
peak=    3.328 closest distance to " CB  VAL A 265 " =    1.323
peak=    3.327 closest distance to " O   HOH Z 172 " =    1.924
peak=    3.322 closest distance to " O   HOH Z 207 " =    2.415
peak=    3.321 closest distance to " O   HOH Z 344 " =    3.028
peak=    3.320 closest distance to " CG  LYS A 119 " =    1.054
peak=    3.319 closest distance to " CG  ARG A 159 " =    0.740
peak=    3.317 closest distance to " CA  ALA A 291 " =    0.936
peak=    3.316 closest distance to " CB  THR A 157 " =    1.110
peak=    3.313 closest distance to " CB  PHE A 225 " =    1.371
peak=    3.313 closest distance to " O   ALA A 165 " =    1.412
peak=    3.313 closest distance to " N   LYS A  76 " =    1.404
peak=    3.312 closest distance to " O   HOH Z 386 " =    2.766
peak=    3.311 closest distance to " O   HOH Z  44 " =    2.948
peak=    3.309 closest distance to " N   VAL A  72 " =    1.432
peak=    3.304 closest distance to " CB  TYR A  30 " =    1.542
peak=    3.304 closest distance to " O   HOH Z 234 " =    3.558
peak=    3.303 closest distance to " O   HOH Z 423 " =    1.845
peak=    3.302 closest distance to " O   TYR A 116 " =    1.328
peak=    3.297 closest distance to " O   HOH Z 280 " =    1.459
peak=    3.297 closest distance to " CA  SER A  87 " =    1.098
peak=    3.293 closest distance to " O   HOH Z 431 " =    1.555
peak=    3.293 closest distance to " CA  ARG A 159 " =    1.308
peak=    3.293 closest distance to " OG BSER A  99 " =    2.356
peak=    3.288 closest distance to " N   ALA A   1 " =    2.980
peak=    3.285 closest distance to " O   HOH Z 126 " =    1.380
peak=    3.276 closest distance to " CA  ALA A 129 " =    1.207
peak=    3.275 closest distance to " O   HOH Z 424 " =    3.256
peak=    3.273 closest distance to " CB  GLN A  88 " =    1.299
peak=    3.267 closest distance to " CB  GLU A 152 " =    1.243
peak=    3.266 closest distance to " O   ASN A 142 " =    1.031
peak=    3.263 closest distance to " O   HOH Z 132 " =    3.837
peak=    3.260 closest distance to " ND1 HIS A  86 " =    1.876
peak=    3.258 closest distance to " CA  ILE A 234 " =    1.082
peak=    3.257 closest distance to " O   HOH Z 394 " =    3.744
peak=    3.256 closest distance to " ND1 HIS A  81 " =    1.682
peak=    3.255 closest distance to " O   HOH Z 383 " =    2.317
peak=    3.252 closest distance to " O   HOH Z  88 " =    2.710
peak=    3.249 closest distance to " O   HOH Z  48 " =    1.673
peak=    3.245 closest distance to " O   HOH Z 353 " =    1.832
peak=    3.243 closest distance to " O   HOH Z 362 " =    1.947
peak=    3.243 closest distance to " O   HOH Z  90 " =    4.094
peak=    3.237 closest distance to " CA  MET A 105 " =    0.962
peak=    3.236 closest distance to " O   HOH Z  58 " =    1.751
peak=    3.233 closest distance to " O   HOH Z 106 " =    3.982
peak=    3.225 closest distance to " CA  ARG A 156 " =    1.053
peak=    3.224 closest distance to " O   HOH Z 285 " =    2.400
peak=    3.219 closest distance to " O   HOH Z 119 " =    1.507
peak=    3.216 closest distance to " O   HOH Z 194 " =    2.448
peak=    3.215 closest distance to " O   HOH Z 292 " =    2.787
peak=    3.214 closest distance to " O   HOH Z 219 " =    3.651
peak=    3.214 closest distance to " CE3 TRP A  85 " =    1.021
peak=    3.212 closest distance to " NH1 ARG A  14 " =    0.908
peak=    3.205 closest distance to " O   HOH Z 299 " =    3.041
peak=    3.198 closest distance to " O   HOH Z  22 " =    1.528
peak=    3.197 closest distance to " O   MET A 105 " =    1.768
peak=    3.196 closest distance to " O   HOH Z 250 " =    1.298
peak=    3.194 closest distance to " CB  LEU A 237 " =    0.758
peak=    3.191 closest distance to " OE1 GLU A   2 " =    1.394
peak=    3.183 closest distance to " CB  TRP A 274 " =    1.077
peak=    3.180 closest distance to " NH2AARG A 145 " =    1.171
peak=    3.180 closest distance to " CG2 VAL A 232 " =    1.019
peak=    3.175 closest distance to " O   HOH Z 303 " =    2.859
peak=    3.174 closest distance to " O   LEU A 228 " =    2.031
peak=    3.171 closest distance to " CG2 THR A 178 " =    0.989
peak=    3.170 closest distance to " O   HOH Z 127 " =    0.950
peak=    3.170 closest distance to " OD1 ASP A 238 " =    0.923
peak=    3.163 closest distance to " N   VAL A 296 " =    1.772
peak=    3.155 closest distance to " ND2 ASN A 187 " =    1.611
peak=    3.154 closest distance to " CG  LEU A 101 " =    1.064
peak=    3.154 closest distance to " O   HOH Z 193 " =    1.624
peak=    3.153 closest distance to " O   HOH Z  83 " =    1.163
peak=    3.151 closest distance to " CB  LEU A 228 " =    1.147
peak=    3.148 closest distance to " CB  LYS A 290 " =    0.945
peak=    3.145 closest distance to " O   HOH Z 298 " =    4.382
peak=    3.145 closest distance to " CA  THR A 264 " =    0.739
peak=    3.140 closest distance to " O   HOH Z 411 " =    3.143
peak=    3.137 closest distance to " CB  HIS A 108 " =    0.867
peak=    3.136 closest distance to " CB  ARG A 138 " =    0.927
peak=    3.134 closest distance to " O   HOH Z 389 " =    1.902
peak=    3.132 closest distance to " CB  ASP A 140 " =    1.058
peak=    3.131 closest distance to " O   HOH Z 387 " =    2.531
peak=    3.125 closest distance to " CB  ASP A 272 " =    1.073
peak=    3.123 closest distance to " NE2 HIS A 207 " =    1.080
peak=    3.122 closest distance to " N   CYS A 260 " =    0.895
peak=    3.117 closest distance to " N   ASP A 162 " =    1.119
peak=    3.116 closest distance to " NZ  LYS A 119 " =    1.950
peak=    3.115 closest distance to " O   HOH Z 356 " =    2.383
peak=    3.114 closest distance to " NH1BARG A 145 " =    1.236
peak=    3.107 closest distance to " N   ILE A  33 " =    1.051
peak=    3.106 closest distance to " CB  SER A  97 " =    0.759
peak=    3.088 closest distance to " O   HOH Z 288 " =    1.896
peak=    3.088 closest distance to " CB  TYR A  30 " =    1.286
peak=    3.080 closest distance to " O   HOH Z  11 " =    1.612
peak=    3.073 closest distance to " O   HOH Z 248 " =    1.624
peak=    3.072 closest distance to " O   GLN A 278 " =    1.390
peak=    3.069 closest distance to " CA  LEU A  83 " =    1.685
peak=    3.068 closest distance to " CB  ALA A 242 " =    1.289
peak=    3.067 closest distance to " CA  ASN A  74 " =    1.252
peak=    3.065 closest distance to " CG1 ILE A  49 " =    1.465
peak=    3.060 closest distance to " O   HOH Z 392 " =    1.684
peak=    3.059 closest distance to " O   HOH Z 158 " =    2.707
peak=    3.058 closest distance to " O   HOH Z 128 " =    2.180
peak=    3.057 closest distance to " CD  ARG A 138 " =    0.733
peak=    3.043 closest distance to " CD1 ILE A  33 " =    1.731
peak=    3.023 closest distance to " OE2 GLU A  53 " =    1.855
peak=    3.022 closest distance to " O   HOH Z 303 " =    2.321

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.954
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 216
   mapped sites are within: 0.794 - 5.954

peak=   -4.656 closest distance to " O   HOH Z 385 " =    1.331
peak=   -4.616 closest distance to " CG2 ILE A  49 " =    2.734
peak=   -4.422 closest distance to " N   THR A 157 " =    1.539
peak=   -4.380 closest distance to " O   PRO A 198 " =    1.093
peak=   -4.296 closest distance to " O   HOH Z  60 " =    1.712
peak=   -4.255 closest distance to " O   HOH Z 313 " =    1.270
peak=   -4.254 closest distance to " O   HOH Z 131 " =    3.921
peak=   -4.254 closest distance to " SG  CYS A 254 " =    3.429
peak=   -4.167 closest distance to " O   ALA A  10 " =    1.548
peak=   -4.157 closest distance to " O   HOH Z 415 " =    1.039
peak=   -4.105 closest distance to " O   HOH Z  28 " =    1.271
peak=   -4.018 closest distance to " O   SER A  22 " =    2.642
peak=   -4.006 closest distance to " O   SER A 135 " =    1.437
peak=   -3.993 closest distance to " CA  GLY A  98 " =    1.724
peak=   -3.991 closest distance to " CZ2 TRP A 274 " =    0.898
peak=   -3.990 closest distance to " O   HOH Z 425 " =    0.917
peak=   -3.941 closest distance to " O   GLU A 152 " =    1.362
peak=   -3.933 closest distance to " O   HOH Z  69 " =    1.522
peak=   -3.928 closest distance to " CZ  PHE A  59 " =    1.368
peak=   -3.917 closest distance to " O   HOH Z 351 " =    1.627
peak=   -3.904 closest distance to " OG  SER A  32 " =    0.995
peak=   -3.904 closest distance to " CB  GLN A  55 " =    1.149
peak=   -3.903 closest distance to " O   HOH Z  39 " =    1.047
peak=   -3.882 closest distance to " O   HOH Z  24 " =    0.956
peak=   -3.849 closest distance to " CG2 THR A  18 " =    2.830
peak=   -3.838 closest distance to " CB  ALA A  43 " =    2.349
peak=   -3.830 closest distance to " O   HOH Z 276 " =    1.246
peak=   -3.815 closest distance to " CA  GLY A 241 " =    2.210
peak=   -3.808 closest distance to " CD2 TYR A 293 " =    1.791
peak=   -3.792 closest distance to " OG BSER A 134 " =    1.510
peak=   -3.788 closest distance to " O   HOH Z 105 " =    1.946
peak=   -3.783 closest distance to " CA  GLY A 203 " =    2.398
peak=   -3.777 closest distance to " O   HOH Z 377 " =    1.917
peak=   -3.754 closest distance to " OG  SER A  97 " =    2.135
peak=   -3.744 closest distance to " O   HOH Z 111 " =    1.975
peak=   -3.738 closest distance to " O   HOH Z 100 " =    1.138
peak=   -3.733 closest distance to " OE1 GLN A 223 " =    2.401
peak=   -3.718 closest distance to " O   HOH Z 231 " =    1.052
peak=   -3.716 closest distance to " N   ALA A   1 " =    1.698
peak=   -3.708 closest distance to " NH2 ARG A 219 " =    1.954
peak=   -3.707 closest distance to " O   HOH Z 266 " =    4.998
peak=   -3.705 closest distance to " CA  ASP A  27 " =    2.438
peak=   -3.687 closest distance to " O   ASP A 191 " =    1.806
peak=   -3.683 closest distance to " CE2 TYR A  30 " =    2.591
peak=   -3.678 closest distance to " O   HOH Z 385 " =    1.738
peak=   -3.674 closest distance to " ND2 ASN A 249 " =    2.134
peak=   -3.669 closest distance to " CB  PRO A 243 " =    2.625
peak=   -3.646 closest distance to " CG  MET A 105 " =    0.984
peak=   -3.641 closest distance to " NE2 GLN A 223 " =    1.745
peak=   -3.630 closest distance to " CA  HIS A 207 " =    1.192
peak=   -3.623 closest distance to " CB  ALA A 291 " =    2.172
peak=   -3.617 closest distance to " CE BMET A  47 " =    1.200
peak=   -3.610 closest distance to " CB  ALA A 158 " =    1.655
peak=   -3.608 closest distance to " ND2 ASN A 285 " =    1.991
peak=   -3.608 closest distance to " O   PRO A 163 " =    1.440
peak=   -3.606 closest distance to " N   GLN A  58 " =    1.317
peak=   -3.600 closest distance to " OD2 ASP A 171 " =    2.096
peak=   -3.598 closest distance to " O   HOH Z 185 " =    1.972
peak=   -3.588 closest distance to " O   HOH Z 298 " =    2.590
peak=   -3.586 closest distance to " O   PRO A 243 " =    2.591
peak=   -3.585 closest distance to " O   HOH Z 412 " =    3.649
peak=   -3.578 closest distance to " O   ARG A 145 " =    1.238
peak=   -3.578 closest distance to " O   HOH Z 211 " =    0.960
peak=   -3.567 closest distance to " O   HOH Z  56 " =    1.994
peak=   -3.564 closest distance to " CA  GLY A 133 " =    1.977
peak=   -3.550 closest distance to " CE3 TRP A 274 " =    2.256
peak=   -3.549 closest distance to " CZ3 TRP A 179 " =    1.348
peak=   -3.544 closest distance to " CD1 LEU A 101 " =    2.206
peak=   -3.544 closest distance to " OG  SER A 245 " =    1.550
peak=   -3.538 closest distance to " O   ILE A  49 " =    1.683
peak=   -3.532 closest distance to " N   ALA A  43 " =    2.709
peak=   -3.524 closest distance to " OE1 GLU A 277 " =    2.155
peak=   -3.517 closest distance to " O   HOH Z 357 " =    1.806
peak=   -3.506 closest distance to " CD  LYS A 166 " =    2.575
peak=   -3.505 closest distance to " OG  SER A  87 " =    1.700
peak=   -3.496 closest distance to " CD  ARG A 156 " =    2.002
peak=   -3.495 closest distance to " O   HOH Z 105 " =    1.625
peak=   -3.489 closest distance to " CD2 TYR A 116 " =    2.104
peak=   -3.479 closest distance to " O   HOH Z 374 " =    1.833
peak=   -3.468 closest distance to " OG  SER A  63 " =    1.388
peak=   -3.466 closest distance to " C   HIS A 108 " =    1.243
peak=   -3.459 closest distance to " OE2 GLU A 152 " =    1.258
peak=   -3.459 closest distance to " O   HOH Z 198 " =    1.513
peak=   -3.458 closest distance to " O   TRP A  70 " =    1.328
peak=   -3.454 closest distance to " O   HOH Z 129 " =    3.610
peak=   -3.449 closest distance to " O   HOH Z 428 " =    2.308
peak=   -3.447 closest distance to " O   HOH Z 340 " =    2.045
peak=   -3.442 closest distance to " O   HOH Z 389 " =    1.029
peak=   -3.439 closest distance to " CD2 PHE A  61 " =    1.988
peak=   -3.423 closest distance to " N   LYS A 166 " =    1.849
peak=   -3.422 closest distance to " O   GLY A  80 " =    2.479
peak=   -3.418 closest distance to " CD1 ILE A  49 " =    1.545
peak=   -3.414 closest distance to " O   PHE A 218 " =    1.446
peak=   -3.406 closest distance to " O   HOH Z 231 " =    1.867
peak=   -3.403 closest distance to " OG  SER A   3 " =    1.626
peak=   -3.403 closest distance to " OE1 GLU A  44 " =    1.946
peak=   -3.399 closest distance to " O   HOH Z  22 " =    2.939
peak=   -3.398 closest distance to " CG  GLN A  58 " =    1.160
peak=   -3.393 closest distance to " NE2 GLN A  77 " =    1.546
peak=   -3.390 closest distance to " O   HOH Z 100 " =    0.905
peak=   -3.386 closest distance to " CD1 TRP A 179 " =    1.203
peak=   -3.372 closest distance to " O   HOH Z 372 " =    2.557
peak=   -3.367 closest distance to " ND2 ASN A 187 " =    1.452
peak=   -3.365 closest distance to " O   HOH Z 278 " =    1.524
peak=   -3.364 closest distance to " CZ  PHE A  38 " =    2.355
peak=   -3.363 closest distance to " O   HOH Z 348 " =    1.865
peak=   -3.355 closest distance to " CB  ALA A   9 " =    2.370
peak=   -3.347 closest distance to " CG2 VAL A 189 " =    1.875
peak=   -3.346 closest distance to " CD  GLU A 236 " =    1.133
peak=   -3.344 closest distance to " CB  ASN A  39 " =    2.195
peak=   -3.342 closest distance to " O   HOH Z 102 " =    1.588
peak=   -3.335 closest distance to " O   HOH Z 275 " =    1.753
peak=   -3.325 closest distance to " O   ALA A  34 " =    2.441
peak=   -3.324 closest distance to " O   HOH Z 166 " =    1.959
peak=   -3.324 closest distance to " CB  TRP A  85 " =    2.395
peak=   -3.322 closest distance to " OE1 GLN A 183 " =    1.679
peak=   -3.319 closest distance to " O   HOH Z 244 " =    1.687
peak=   -3.310 closest distance to " CG2 ILE A  20 " =    2.744
peak=   -3.310 closest distance to " NE  ARG A  36 " =    1.935
peak=   -3.307 closest distance to " O   HOH Z 181 " =    1.499
peak=   -3.305 closest distance to " NE2 GLN A  55 " =    1.177
peak=   -3.302 closest distance to " O   HOH Z 147 " =    0.998
peak=   -3.298 closest distance to " CG  TRP A 266 " =    1.887
peak=   -3.298 closest distance to " O   HOH Z 282 " =    4.689
peak=   -3.296 closest distance to " CG  GLU A 128 " =    1.547
peak=   -3.294 closest distance to " O   HOH Z 286 " =    1.731
peak=   -3.294 closest distance to " O   HOH Z 123 " =    2.579
peak=   -3.293 closest distance to " O   HOH Z 323 " =    2.097
peak=   -3.293 closest distance to " O   HOH Z  88 " =    2.226
peak=   -3.286 closest distance to " CA  ASP A 298 " =    1.169
peak=   -3.284 closest distance to " ND2 ASN A  60 " =    4.021
peak=   -3.283 closest distance to " O   ILE A 120 " =    1.717
peak=   -3.277 closest distance to " CG  PHE A 283 " =    2.761
peak=   -3.276 closest distance to " O   HOH Z 337 " =    1.747
peak=   -3.275 closest distance to " CB  ASP A 132 " =    2.392
peak=   -3.268 closest distance to " CG BMET A  47 " =    3.186
peak=   -3.266 closest distance to " C   VAL A 257 " =    1.140
peak=   -3.265 closest distance to " CD  PRO A 213 " =    2.116
peak=   -3.265 closest distance to " O   HOH Z   5 " =    1.334
peak=   -3.265 closest distance to " CG2 THR A 178 " =    2.021
peak=   -3.260 closest distance to " CB  PRO A  54 " =    2.362
peak=   -3.259 closest distance to " O   HOH Z 429 " =    1.989
peak=   -3.256 closest distance to " N   GLN A 223 " =    2.089
peak=   -3.255 closest distance to " CG  LEU A  83 " =    2.179
peak=   -3.254 closest distance to " O   HOH Z  67 " =    1.531
peak=   -3.244 closest distance to " CZ  PHE A 130 " =    0.955
peak=   -3.244 closest distance to " O   HOH Z 250 " =    1.163
peak=   -3.243 closest distance to " O   HOH Z 407 " =    3.035
peak=   -3.236 closest distance to " O   HOH Z 201 " =    1.903
peak=   -3.233 closest distance to " O   HOH Z 152 " =    4.243
peak=   -3.233 closest distance to " O   HOH Z 412 " =    5.710
peak=   -3.233 closest distance to " CA  ASN A 127 " =    1.312
peak=   -3.226 closest distance to " O   HOH Z 358 " =    3.636
peak=   -3.225 closest distance to " O   HOH Z 414 " =    1.408
peak=   -3.225 closest distance to " OD1 ASN A 301 " =    1.663
peak=   -3.223 closest distance to " CD2 PHE A 225 " =    1.015
peak=   -3.223 closest distance to " CB  ALA A 100 " =    1.836
peak=   -3.222 closest distance to " O   HOH Z  49 " =    1.224
peak=   -3.216 closest distance to " C   LEU A 222 " =    0.912
peak=   -3.207 closest distance to " CG1 VAL A 112 " =    2.657
peak=   -3.205 closest distance to " O   HOH Z 128 " =    2.521
peak=   -3.204 closest distance to " O   LYS A 289 " =    2.891
peak=   -3.203 closest distance to " CB  GLN A  11 " =    1.678
peak=   -3.202 closest distance to " CB  ASP A 132 " =    2.538
peak=   -3.201 closest distance to " O   HOH Z  73 " =    2.185
peak=   -3.201 closest distance to " O   HOH Z 438 " =    0.969
peak=   -3.197 closest distance to " NE2 GLN A 122 " =    1.083
peak=   -3.196 closest distance to " OD2 ASP A 191 " =    1.418
peak=   -3.192 closest distance to " O   HOH Z 368 " =    2.495
peak=   -3.191 closest distance to " SG BCYS A 201 " =    2.240
peak=   -3.188 closest distance to " O   HOH Z 126 " =    1.533
peak=   -3.186 closest distance to " O   HOH Z  11 " =    1.713
peak=   -3.184 closest distance to " O   HOH Z 324 " =    0.794
peak=   -3.183 closest distance to " O   HOH Z 288 " =    1.376
peak=   -3.179 closest distance to " O   HOH Z 197 " =    3.544
peak=   -3.178 closest distance to " N   VAL A 232 " =    2.137
peak=   -3.177 closest distance to " O   HOH Z 392 " =    1.209
peak=   -3.175 closest distance to " O   HOH Z 251 " =    0.989
peak=   -3.174 closest distance to " CG1 VAL A 265 " =    2.334
peak=   -3.171 closest distance to " CG  ARG A 269 " =    2.619
peak=   -3.165 closest distance to " O   HOH Z  71 " =    2.823
peak=   -3.161 closest distance to " O   HOH Z 283 " =    5.954
peak=   -3.157 closest distance to " CG1 VAL A 197 " =    2.417
peak=   -3.157 closest distance to " CG  GLN A 240 " =    2.271
peak=   -3.153 closest distance to " C   ASN A 301 " =    1.355
peak=   -3.145 closest distance to " CG2 ILE A 151 " =    2.581
peak=   -3.143 closest distance to " CB  ALA A  10 " =    2.329
peak=   -3.141 closest distance to " CG  ARG A 219 " =    2.269
peak=   -3.137 closest distance to " CD  ARG A 139 " =    1.688
peak=   -3.137 closest distance to " CD2 LEU A 237 " =    2.856
peak=   -3.137 closest distance to " CD2 TYR A 293 " =    2.129
peak=   -3.135 closest distance to " OD2 ASP A  27 " =    1.519
peak=   -3.133 closest distance to " OE1 GLN A 223 " =    2.052
peak=   -3.132 closest distance to " OE1 GLN A  88 " =    1.003
peak=   -3.128 closest distance to " CB  ASN A  45 " =    2.055
peak=   -3.125 closest distance to " C   GLU A   2 " =    1.763
peak=   -3.124 closest distance to " O   HOH Z 390 " =    2.311
peak=   -3.122 closest distance to " O   HOH Z 212 " =    0.983
peak=   -3.121 closest distance to " O   HOH Z 368 " =    1.635
peak=   -3.117 closest distance to " O   HOH Z   1 " =    1.162
peak=   -3.114 closest distance to " O   VAL A 125 " =    2.129
peak=   -3.112 closest distance to " O   HOH Z 427 " =    1.909
peak=   -3.108 closest distance to " O   ILE A 106 " =    1.893
peak=   -3.101 closest distance to " O   LEU A 261 " =    1.326
peak=   -3.100 closest distance to " NH2AARG A 275 " =    5.305
peak=   -3.099 closest distance to " CG1 VAL A  78 " =    2.521
peak=   -3.092 closest distance to " CG2BVAL A  41 " =    2.558
peak=   -3.089 closest distance to " C   SER A 276 " =    1.483
peak=   -3.088 closest distance to " O   HOH Z  71 " =    2.499
peak=   -3.073 closest distance to " CD2 PHE A 130 " =    2.986
peak=   -3.062 closest distance to " O   HOH Z 221 " =    2.037
peak=   -3.060 closest distance to " O   ALA A 137 " =    1.011
peak=   -3.034 closest distance to " O   PRO A 163 " =    1.045
peak=   -3.031 closest distance to " OD1 ASP A 171 " =    1.630

================= 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    :  0.4712 0.4748   6.287894e+00   6.276590e+00
   1_bss:  0.4602 0.4653   6.282204e+00   6.267817e+00
   1_xyz:  0.3756 0.4209   6.149716e+00   6.216989e+00
   1_adp:  0.3458 0.4295   6.116785e+00   6.227303e+00
   1_occ:  0.3453 0.4297   6.117056e+00   6.228091e+00
   2_bss:  0.3449 0.4267   6.118835e+00   6.229529e+00
   2_xyz:  0.2845 0.3635   5.960151e+00   6.115292e+00
   2_adp:  0.2654 0.3481   5.917993e+00   6.085328e+00
   2_occ:  0.2653 0.3477   5.917388e+00   6.084840e+00
   3_bss:  0.2655 0.3464   5.915261e+00   6.083363e+00
   3_xyz:  0.2046 0.2694   5.676413e+00   5.881206e+00
   3_adp:  0.1807 0.2456   5.574052e+00   5.798935e+00
   3_occ:  0.1806 0.2451   5.573324e+00   5.797746e+00
   4_bss:  0.1800 0.2450   5.572222e+00   5.796708e+00
   4_xyz:  0.1471 0.2010   5.382969e+00   5.620990e+00
   4_adp:  0.1396 0.1897   5.331365e+00   5.564892e+00
   4_occ:  0.1394 0.1895   5.330488e+00   5.563522e+00
   5_bss:  0.1396 0.1892   5.328694e+00   5.560831e+00
   5_xyz:  0.1307 0.1760   5.267017e+00   5.494233e+00
   5_adp:  0.1265 0.1754   5.249412e+00   5.486619e+00
   5_occ:  0.1265 0.1755   5.249384e+00   5.486734e+00
   5_bss:  0.1265 0.1754   5.249372e+00   5.486725e+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:  0.358  50.000  -3.354   1.827   2.530   0.000   0.000   0.000
   1_xyz:  0.358  50.000  -3.354   1.827   2.530   0.000   0.000   0.000
   1_adp:  0.358  50.000  -3.354   1.827   2.530   0.000   0.000   0.000
   1_occ:  0.358  50.000  -3.354   1.827   2.530   0.000   0.000   0.000
   2_bss:  0.362  74.855  -1.437   0.535   1.232   0.000   0.000   0.000
   2_xyz:  0.362  74.855  -1.437   0.535   1.232   0.000   0.000   0.000
   2_adp:  0.362  74.855  -1.437   0.535   1.232   0.000   0.000   0.000
   2_occ:  0.362  74.855  -1.437   0.535   1.232   0.000   0.000   0.000
   3_bss:  0.342  78.016  -1.433  -0.439   0.699  -0.000   0.000   0.000
   3_xyz:  0.342  78.016  -1.433  -0.439   0.699  -0.000   0.000   0.000
   3_adp:  0.342  78.016  -1.433  -0.439   0.699  -0.000   0.000   0.000
   3_occ:  0.342  78.016  -1.433  -0.439   0.699  -0.000   0.000   0.000
   4_bss:  0.346  80.000  -2.065  -1.726   0.023  -0.000   0.000   0.000
   4_xyz:  0.346  80.000  -2.065  -1.726   0.023  -0.000   0.000   0.000
   4_adp:  0.346  80.000  -2.065  -1.726   0.023  -0.000   0.000   0.000
   4_occ:  0.346  80.000  -2.065  -1.726   0.023  -0.000   0.000   0.000
   5_bss:  0.323  59.672  -2.257  -2.180  -0.076  -0.000  -0.000  -0.000
   5_xyz:  0.323  59.672  -2.257  -2.180  -0.076  -0.000  -0.000  -0.000
   5_adp:  0.323  59.672  -2.257  -2.180  -0.076  -0.000  -0.000  -0.000
   5_occ:  0.323  59.672  -2.257  -2.180  -0.076  -0.000  -0.000  -0.000
   5_bss:  0.323  59.656  -2.153  -2.153  -0.006  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.483 0.4265  0.5882    73173.993
   1_bss:  56.288 0.4408  0.6191    70533.020
   1_xyz:  49.414 0.5269  0.7252    55706.519
   1_adp:  50.374 0.5144  0.7146    57915.120
   1_occ:  50.521 0.5126  0.7112    58154.941
   2_bss:  50.356 0.5146  0.7100    57908.062
   2_xyz:  39.604 0.6462  0.8757    37456.785
   2_adp:  37.341 0.6735  0.8937    34376.578
   2_occ:  37.301 0.6740  0.8944    34322.541
   3_bss:  37.143 0.6756  0.8804    33979.269
   3_xyz:  27.403 0.7847  0.9745    19185.302
   3_adp:  24.470 0.8161  0.9796    15761.281
   3_occ:  24.443 0.8163  0.9794    15721.615
   4_bss:  24.393 0.8168  0.9504    15692.240
   4_xyz:  19.412 0.8665  0.9807    10425.786
   4_adp:  17.887 0.8815  0.9825     9350.536
   4_occ:  17.859 0.8817  0.9824     9316.858
   5_bss:  17.809 0.8820  0.9735     9229.139
   5_xyz:  16.181 0.8967  0.9800     7940.097
   5_adp:  15.931 0.8992  0.9737     7836.810
   5_occ:  15.935 0.8992  0.9735     7839.308
   5_bss:  15.935 0.8992  0.9753     7840.147
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.9473e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.9473e-01
   1_xyz:   1.664  0.013  0.117 16.408  0.007  4.099   1.5457e-01
   1_adp:   1.664  0.013  0.117 16.408  0.007  4.099   1.5457e-01
   1_occ:   1.664  0.013  0.117 16.408  0.007  4.099   1.5457e-01
   2_bss:   1.664  0.013  0.117 16.408  0.007  4.099   1.5457e-01
   2_xyz:   1.452  0.011  0.100 15.805  0.006  4.109   1.2087e-01
   2_adp:   1.452  0.011  0.100 15.805  0.006  4.109   1.2087e-01
   2_occ:   1.452  0.011  0.100 15.805  0.006  4.109   1.2087e-01
   3_bss:   1.452  0.011  0.100 15.805  0.006  4.109   1.2087e-01
   3_xyz:   1.252  0.010  0.087 15.252  0.005  4.106   8.8156e-02
   3_adp:   1.252  0.010  0.087 15.252  0.005  4.106   8.8156e-02
   3_occ:   1.252  0.010  0.087 15.252  0.005  4.106   8.8156e-02
   4_bss:   1.252  0.010  0.087 15.252  0.005  4.106   8.8156e-02
   4_xyz:   1.066  0.007  0.075 14.625  0.004  4.116   6.4918e-02
   4_adp:   1.066  0.007  0.075 14.625  0.004  4.116   6.4918e-02
   4_occ:   1.066  0.007  0.075 14.625  0.004  4.116   6.4918e-02
   5_bss:   1.066  0.007  0.075 14.625  0.004  4.116   6.4918e-02
   5_xyz:   0.928  0.006  0.069 14.248  0.003  4.110   5.2375e-02
   5_adp:   0.928  0.006  0.069 14.248  0.003  4.110   5.2375e-02
   5_occ:   0.928  0.006  0.069 14.248  0.003  4.110   5.2375e-02
   5_bss:   0.928  0.006  0.069 14.248  0.003  4.110   5.2375e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.375   2.4118e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.375   2.4118e-01
   1_xyz:   9.788  0.073  0.424 79.091  0.050  1.981   1.2197e-01
   1_adp:   9.788  0.073  0.424 79.091  0.050  1.981   1.2197e-01
   1_occ:   9.788  0.073  0.424 79.091  0.050  1.981   1.2197e-01
   2_bss:   9.788  0.073  0.424 79.091  0.050  1.981   1.2197e-01
   2_xyz:  10.670  0.096  0.360 83.292  0.035  2.041   1.6570e-01
   2_adp:  10.670  0.096  0.360 83.292  0.035  2.041   1.6570e-01
   2_occ:  10.670  0.096  0.360 83.292  0.035  2.041   1.6570e-01
   3_bss:  10.670  0.096  0.360 83.292  0.035  2.041   1.6570e-01
   3_xyz:   7.593  0.065  0.278 81.188  0.040  2.268   7.8995e-02
   3_adp:   7.593  0.065  0.278 81.188  0.040  2.268   7.8995e-02
   3_occ:   7.593  0.065  0.278 81.188  0.040  2.268   7.8995e-02
   4_bss:   7.593  0.065  0.278 81.188  0.040  2.268   7.8995e-02
   4_xyz:   7.127  0.053  0.231 84.004  0.037  2.323   5.4638e-02
   4_adp:   7.127  0.053  0.231 84.004  0.037  2.323   5.4638e-02
   4_occ:   7.127  0.053  0.231 84.004  0.037  2.323   5.4638e-02
   5_bss:   7.127  0.053  0.231 84.004  0.037  2.323   5.4638e-02
   5_xyz:   7.046  0.043  0.211 80.467  0.029  2.402   3.4034e-02
   5_adp:   7.046  0.043  0.211 80.467  0.029  2.402   3.4034e-02
   5_occ:   7.046  0.043  0.211 80.467  0.029  2.402   3.4034e-02
   5_bss:   7.046  0.043  0.211 80.467  0.029  2.402   3.4034e-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:  80.89   0.00  18.29  71.49   0.00  15.36  80.89   0.00  34.24
   1_occ:  80.89   0.00  18.29  71.49   0.00  15.36  80.89   0.00  34.24
   2_bss:  80.89   0.00  18.29  71.49   0.00  15.36  80.89   0.00  34.24
   2_xyz:  80.89   0.00  18.29  71.49   0.00  15.36  80.89   0.00  34.24
   2_adp:  86.93   0.00  18.35  75.62   0.00  14.80  86.93   1.26  37.65
   2_occ:  86.93   0.00  18.35  75.62   0.00  14.80  86.93   1.26  37.65
   3_bss:  86.93   0.00  18.35  75.62   0.00  14.80  86.93   1.26  37.65
   3_xyz:  86.93   0.00  18.35  75.62   0.00  14.80  86.93   1.26  37.65
   3_adp:  99.65   0.00  18.45  87.17   0.00  13.54  99.65   5.01  45.21
   3_occ:  99.65   0.00  18.45  87.17   0.00  13.54  99.65   5.01  45.21
   4_bss:  99.65   0.00  18.45  87.17   0.00  13.54  99.65   5.01  45.21
   4_xyz:  99.65   0.00  18.45  87.17   0.00  13.54  99.65   5.01  45.21
   4_adp:  99.75   0.00  17.85  87.27   0.00  12.93  99.75   4.30  44.62
   4_occ:  99.75   0.00  17.85  87.27   0.00  12.93  99.75   4.30  44.62
   5_bss:  99.75   0.00  17.85  87.27   0.00  12.93  99.75   4.30  44.62
   5_xyz:  99.75   0.00  17.85  87.27   0.00  12.93  99.75   4.30  44.62
   5_adp: 108.86   0.49  17.93  98.54   0.49  12.71 108.86   2.83  46.40
   5_occ: 108.86   0.49  17.93  98.54   0.49  12.71 108.86   2.83  46.40
   5_bss: 108.84   0.48  17.92  98.52   0.48  12.69 108.84   2.81  46.38
------------------------------------------------------------------------
 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:    2.437    0.013    0.399
   1_adp:    2.437    0.013    0.399
   1_occ:    2.437    0.013    0.399
   2_bss:    2.437    0.013    0.399
   2_xyz:    2.023    0.033    0.596
   2_adp:    2.023    0.033    0.596
   2_occ:    2.023    0.033    0.596
   3_bss:    2.023    0.033    0.596
   3_xyz:    1.883    0.054    0.773
   3_adp:    1.883    0.054    0.773
   3_occ:    1.883    0.054    0.773
   4_bss:    1.883    0.054    0.773
   4_xyz:    1.718    0.087    0.837
   4_adp:    1.718    0.087    0.837
   4_occ:    1.718    0.087    0.837
   5_bss:    1.718    0.087    0.837
   5_xyz:    1.762    0.096    0.861
   5_adp:    1.762    0.096    0.861
   5_occ:    1.762    0.096    0.861
   5_bss:    1.762    0.096    0.861
------------------------------------------------------------------------

CPU time actual refinement: 343.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_493/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_493/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_493/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_493/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_493/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.36 
  Macro-tasks:
    bulk solvent and scale       = 49.79  
    individual site refinement   = 138.20 
    weights calculation          = 29.45  
    collect and process          = 6.42   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.99 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 105.46 
    alpha_beta                      = 8.32   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 113.94 
    fmodel                         = 7.97   
    r_factors                      = 0.24   
    phase_errors                   = 10.29  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 250.12 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.862 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    636 calls, 105.18 s
gradients_fft:          581 calls, 100.98 s

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

# Date 2008-01-16 Time 04:57:23 PST -0800 (1200488243.36 s)
Start R-work = 0.4712, R-free = 0.4748 (no bulk solvent and anisotropic scale)
Final R-work = 0.1471, R-free = 0.1910 (no bulk solvent and anisotropic scale)

Start R-work = 0.4602, R-free = 0.4653
Final R-work = 0.1265, R-free = 0.1754