# Date 2008-01-16 Time 04:31:36 PST -0800 (1200486696.28 s)
#phil __OFF__

Command line arguments: "../350.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3630
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 350

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.8686, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.9709
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.919197

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0027
                             d_min =   1.9709

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.9709
Completeness in resolution range: 0.921965
Completeness with d_max=infinity: 0.919197

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0031 -  4.2177 [2229/2257]  2003   226  10.1%
  bin  2:  4.2177 -  3.3601 [2141/2164]  1926   215  10.0%
  bin  3:  3.3601 -  2.9390 [2112/2137]  1905   207   9.8%
  bin  4:  2.9390 -  2.6719 [2092/2108]  1883   209  10.0%
  bin  5:  2.6719 -  2.4813 [2077/2121]  1863   214  10.3%
  bin  6:  2.4813 -  2.3356 [2072/2100]  1868   204   9.8%
  bin  7:  2.3356 -  2.2190 [2052/2088]  1854   198   9.6%
  bin  8:  2.2190 -  2.1227 [2071/2113]  1862   209  10.1%
  bin  9:  2.1227 -  2.0412 [2038/2085]  1836   202   9.9%
  bin 10:  2.0412 -  1.9709 [ 705/2074]   630    75  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_350/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 18
        2.20 -     2.87: 1232
        2.87 -     3.55: 4387
        3.55 -     4.22: 9113
        4.22 -     4.90: 13268
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.524 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.627 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.646 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.739 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.744 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28013 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_350/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_350/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.8686 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: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4726   r_free= 0.4689   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.279462                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.7044 0.99   1453  160 0.3669 0.3768      6.5503      6.5573|
|  2:  4.7044 -  3.7533 0.99   1400  155 0.4115 0.4403      6.8156       6.861|
|  3:  3.7533 -  3.2845 0.99   1361  151 0.4550 0.4324      6.6697      6.6223|
|  4:  3.2845 -  2.9868 0.99   1366  146 0.4634 0.4383      6.4916      6.4748|
|  5:  2.9868 -  2.7741 0.98   1331  154 0.5017 0.4689      6.3596      6.3785|
|  6:  2.7741 -  2.6115 0.99   1349  151 0.5047 0.5352      6.2723      6.1865|
|  7:  2.6115 -  2.4813 0.98   1320  154 0.5022 0.4503      6.2185      6.1358|
|  8:  2.4813 -  2.3737 0.99   1338  140 0.5262 0.5016      6.1722      6.1509|
|  9:  2.3737 -  2.2827 0.99   1338  146 0.5203 0.4932      6.1141      6.1834|
| 10:  2.2827 -  2.2042 0.98   1331  146 0.5244 0.5283      6.0915      6.1017|
| 11:  2.2042 -  2.1354 0.97   1292  157 0.5315 0.5236      6.0181      6.0058|
| 12:  2.1354 -  2.0746 0.99   1331  146 0.5272 0.5414      5.9397      5.9427|
| 13:  2.0746 -  2.0201 0.84   1148  117 0.5243 0.5803      5.8653      5.8563|
| 14:  2.0201 -  1.9709 0.21    272   36 0.4998 0.4482      5.9078      5.7348|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.7044  1453   160  0.70  34.02   0.82     0.73      69740.56|
|  2:  4.7044 -  3.7533  1400   155  0.70  35.40   0.91     0.79     105205.70|
|  3:  3.7533 -  3.2845  1361   151  0.60  44.12   0.87     0.77     111266.16|
|  4:  3.2845 -  2.9868  1366   146  0.51  51.31   0.89     0.68      97296.70|
|  5:  2.9868 -  2.7741  1331   154  0.44  56.60   0.87     0.61      76568.61|
|  6:  2.7741 -  2.6115  1349   151  0.42  58.65   0.88     0.57      66075.68|
|  7:  2.6115 -  2.4813  1320   154  0.41  58.70   0.91     0.56      60023.09|
|  8:  2.4813 -  2.3737  1338   140  0.40  60.27   0.89     0.56      54363.49|
|  9:  2.3737 -  2.2827  1338   146  0.39  60.55   0.89     0.58      51557.36|
| 10:  2.2827 -  2.2042  1331   146  0.38  61.30   0.91     0.55      46583.40|
| 11:  2.2042 -  2.1354  1292   157  0.31  66.63   0.90     0.49      48231.26|
| 12:  2.1354 -  2.0746  1331   146  0.25  71.51   0.91     0.40      46447.16|
| 13:  2.0746 -  2.0201  1148   117  0.22  73.54   0.89     0.36      41869.94|
| 14:  2.0201 -  1.9709   272    36  0.31  66.47   1.00     0.41      30675.75|
|alpha:            min =        0.36 max =            0.79 mean =         0.59|
|beta:             min =    30675.75 max =       111266.16 mean =     67357.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.05|
|phase err.(test): min =        0.00 max =           89.80 mean =        56.22|
|-----------------------------------------------------------------------------|

============================== 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 = 12.063536             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.230   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.338260              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.838   (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 |  1.524 -  1.862:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.862 -  2.199:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.199 -  2.537:       36 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.537 -  2.875:     1196 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.875 -  3.212:     1883 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.212 -  3.550:     2504 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.550 -  3.887:     4639 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.887 -  4.225:     4474 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.225 -  4.562:     6033 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.562 -  4.900:     7235 |
|-----------------------------------------------------------------------------|
|-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 |        0.182 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.524 |       0.437 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4726   r_free= 0.4689   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.279462                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4651   r_free= 0.4585   ksol= 0.30   Bsol= 30.23   scale= 0.930   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,3.19,2.68,0.00,0.00,0.00); trace/3= 1.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.274195                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.015297             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.719   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.222057              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.458   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4651      final r-factor (work) = 0.3470          |
| start r-factor (free) = 0.4585      final r-factor (free) = 0.3737          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.5878 = 10.02 * 0.50 * 6.2717 + 1.00 * 0.1815                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8899 = 10.02 * 0.50 * 6.1414 + 1.00 * 0.1358                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3470      final r-factor (work) = 0.3124          |
| start r-factor (free) = 0.3737      final r-factor (free) = 0.3820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5111 = 1.22 * 1.00 * 6.1414 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3763 = 1.22 * 1.00 * 6.0196 + 1.00 * 0.0200                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.10  19.22    None  None   None       |
|    all(noH): 2823   0      0.00    104.10  19.22    None  None   None       |
|    Sol.    : 438    0      0.00    104.10  39.92    None  None   None       |
|    Mac.    : 2385   0      0.00    92.82   15.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.410:  964   |   5:    52.048 -  62.457:   78        |
|      1:    10.410 -  20.819:  921   |   6:    62.457 -  72.867:   35        |
|      2:    20.819 -  31.229:  426   |   7:    72.867 -  83.276:   24        |
|      3:    31.229 -  41.638:  235   |   8:    83.276 -  93.686:    8        |
|      4:    41.638 -  52.048:  130   |   9:    93.686 - 104.095:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3124 r_free = 0.3820             target_work(ml) = 6.025         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3121 r_free = 0.3817             target_work(ml) = 6.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3121   r_free= 0.3817   ksol= 0.30   Bsol= 30.23   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,3.19,2.68,0.00,0.00,0.00); trace/3= 1.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.024962                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3108   r_free= 0.3787   ksol= 0.32   Bsol= 55.81   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,1.31,1.05,0.00,0.00,0.00); trace/3= 0.10                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.022658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.440871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.397   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.358910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.499  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3108      final r-factor (work) = 0.2424          |
| start r-factor (free) = 0.3787      final r-factor (free) = 0.2967          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5206 = 6.44 * 0.50 * 6.0193 + 1.00 * 0.1358                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1983 = 6.44 * 0.50 * 5.9341 + 1.00 * 0.0879                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2424      final r-factor (work) = 0.2285          |
| start r-factor (free) = 0.2967      final r-factor (free) = 0.2845          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1498 = 0.36 * 1.00 * 5.9341 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1372 = 0.36 * 1.00 * 5.7815 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.18  18.91    None  None   None       |
|    all(noH): 2823   0      0.00    103.18  18.91    None  None   None       |
|    Sol.    : 438    0      2.67    103.18  39.93    None  None   None       |
|    Mac.    : 2385   0      0.00    90.07   15.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.319:  923   |   5:    51.592 -  61.911:   70        |
|      1:    10.319 -  20.637: 1037   |   6:    61.911 -  72.229:   30        |
|      2:    20.637 -  30.955:  388   |   7:    72.229 -  82.548:   22        |
|      3:    30.955 -  41.274:  206   |   8:    82.548 -  92.866:    9        |
|      4:    41.274 -  51.592:  136   |   9:    92.866 - 103.185:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2285 r_free = 0.2845             target_work(ml) = 5.765         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2283 r_free = 0.2842             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2283   r_free= 0.2842   ksol= 0.32   Bsol= 55.81   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,1.31,1.05,0.00,0.00,0.00); trace/3= 0.10                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.764197                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2279   r_free= 0.2844   ksol= 0.32   Bsol= 66.04   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,0.11,0.26,0.00,0.00,0.00); trace/3= -0.70                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.764290                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.892639              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.721  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.598267              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.202   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2279      final r-factor (work) = 0.1710          |
| start r-factor (free) = 0.2844      final r-factor (free) = 0.2186          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0140 = 6.89 * 0.50 * 5.7818 + 1.00 * 0.0879                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5638 = 6.89 * 0.50 * 5.6526 + 1.00 * 0.0831                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1491          |
| start r-factor (free) = 0.2186      final r-factor (free) = 0.2024          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0580 = 1.60 * 1.00 * 5.6526 + 1.00 * 0.0236                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7106 = 1.60 * 1.00 * 5.4415 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.14  18.87    None  None   None       |
|    all(noH): 2823   0      0.00    104.14  18.87    None  None   None       |
|    Sol.    : 438    0      4.95    104.14  45.96    None  None   None       |
|    Mac.    : 2385   0      0.00    91.86   13.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.414: 1058   |   5:    52.070 -  62.484:  101        |
|      1:    10.414 -  20.828: 1072   |   6:    62.484 -  72.898:   61        |
|      2:    20.828 -  31.242:  246   |   7:    72.898 -  83.312:   35        |
|      3:    31.242 -  41.656:  126   |   8:    83.312 -  93.727:   16        |
|      4:    41.656 -  52.070:  106   |   9:    93.727 - 104.141:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1491 r_free = 0.2024             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1490 r_free = 0.2026             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.2026   ksol= 0.32   Bsol= 66.04   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,0.11,0.26,0.00,0.00,0.00); trace/3= -0.70                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.399111                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1489   r_free= 0.2024   ksol= 0.34   Bsol= 79.50   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.08,-0.48,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.400579                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.928601              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.829  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298733              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.048  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1489      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.2024      final r-factor (free) = 0.1836          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0603 = 2.93 * 0.50 * 5.4478 + 1.00 * 0.0831                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9081 = 2.93 * 0.50 * 5.3555 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.1836      final r-factor (free) = 0.1764          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6134 = 0.30 * 1.00 * 5.3555 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5928 = 0.30 * 1.00 * 5.2954 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    102.46  18.04    None  None   None       |
|    all(noH): 2823   0      0.76    102.46  18.04    None  None   None       |
|    Sol.    : 438    0      5.50    102.46  43.89    None  None   None       |
|    Mac.    : 2385   0      0.76    92.19   13.29    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:     0.765 -  10.934: 1210   |   5:    51.614 -  61.784:   89        |
|      1:    10.934 -  21.104:  995   |   6:    61.784 -  71.953:   52        |
|      2:    21.104 -  31.274:  196   |   7:    71.953 -  82.123:   35        |
|      3:    31.274 -  41.444:  122   |   8:    82.123 -  92.293:    9        |
|      4:    41.444 -  51.614:  113   |   9:    92.293 - 102.463:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1295 r_free = 0.1764             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1764             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1764   ksol= 0.34   Bsol= 79.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.08,-0.48,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.273021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1764   ksol= 0.33   Bsol= 71.17   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.51,-0.62,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.272873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.545506              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.233  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.698911              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.646  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1764      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4531 = 3.55 * 0.50 * 5.2952 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3682 = 3.55 * 0.50 * 5.2409 + 1.00 * 0.0774                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1675      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.1555 = 2.70 * 1.00 * 5.2409 + 1.00 * 0.0107                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0562 = 2.70 * 1.00 * 5.2035 + 1.00 * 0.0124                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.21  18.08    None  None   None       |
|    all(noH): 2823   0      0.00    105.21  18.08    None  None   None       |
|    Sol.    : 438    0      0.00    105.21  44.77    None  None   None       |
|    Mac.    : 2385   0      0.48    101.87  13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.521: 1154   |   5:    52.603 -  63.124:   85        |
|      1:    10.521 -  21.041: 1052   |   6:    63.124 -  73.644:   52        |
|      2:    21.041 -  31.562:  204   |   7:    73.644 -  84.165:   37        |
|      3:    31.562 -  42.083:  116   |   8:    84.165 -  94.686:   12        |
|      4:    42.083 -  52.603:  105   |   9:    94.686 - 105.206:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1680             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1681             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1681   ksol= 0.33   Bsol= 71.17   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.51,-0.62,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204976                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.7044 0.99   1453  160 0.0965 0.1318      5.3928      5.6079|
|  2:  4.7044 -  3.7533 0.99   1400  155 0.0818 0.1022      5.4148      5.5948|
|  3:  3.7533 -  3.2845 0.99   1361  151 0.1098 0.1561      5.4881      5.8712|
|  4:  3.2845 -  2.9868 0.99   1366  146 0.1337 0.1775      5.5045       5.678|
|  5:  2.9868 -  2.7741 0.98   1331  154 0.1426 0.1840         5.4      5.5808|
|  6:  2.7741 -  2.6115 0.99   1349  151 0.1367 0.2220      5.2958      5.5678|
|  7:  2.6115 -  2.4813 0.98   1320  154 0.1357 0.1754       5.245      5.4306|
|  8:  2.4813 -  2.3737 0.99   1338  140 0.1288 0.1910      5.1728      5.3754|
|  9:  2.3737 -  2.2827 0.99   1338  146 0.1244 0.1964      5.0854      5.3928|
| 10:  2.2827 -  2.2042 0.98   1331  146 0.1207 0.1881      5.0162       5.245|
| 11:  2.2042 -  2.1354 0.97   1292  157 0.1212 0.1882      4.9548      5.2825|
| 12:  2.1354 -  2.0746 0.99   1331  146 0.1164 0.1600      4.8787      5.0841|
| 13:  2.0746 -  2.0201 0.84   1148  117 0.1142 0.1994      4.8017      5.1107|
| 14:  2.0201 -  1.9709 0.21    272   36 0.1012 0.1547      4.7592      4.9303|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.7044  1453   160  0.94   9.57   0.97     0.94       7657.04|
|  2:  4.7044 -  3.7533  1400   155  0.95   8.18   1.01     1.00       9171.81|
|  3:  3.7533 -  3.2845  1361   151  0.93  11.68   1.02     1.02      10662.06|
|  4:  3.2845 -  2.9868  1366   146  0.90  15.53   1.01     1.00      11654.32|
|  5:  2.9868 -  2.7741  1331   154  0.89  17.63   1.00     0.98      10042.84|
|  6:  2.7741 -  2.6115  1349   151  0.88  18.56   0.98     0.95       8635.08|
|  7:  2.6115 -  2.4813  1320   154  0.89  17.53   0.99     0.96       7538.67|
|  8:  2.4813 -  2.3737  1338   140  0.89  17.84   0.99     0.95       6806.25|
|  9:  2.3737 -  2.2827  1338   146  0.89  17.42   0.98     0.93       5659.28|
| 10:  2.2827 -  2.2042  1331   146  0.89  17.47   0.98     0.95       5144.25|
| 11:  2.2042 -  2.1354  1292   157  0.89  17.07   0.98     0.93       4562.55|
| 12:  2.1354 -  2.0746  1331   146  0.90  16.60   0.99     0.99       4058.05|
| 13:  2.0746 -  2.0201  1148   117  0.89  17.13   0.97     0.96       3543.47|
| 14:  2.0201 -  1.9709   272    36  0.91  15.51   0.95     0.90       3137.38|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3137.38 max =        11654.32 mean =      7323.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.46|
|phase err.(test): min =        0.00 max =           89.63 mean =        14.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1679   ksol= 0.33   Bsol= 69.05   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-1.52,-0.51,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204202                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1679   ksol= 0.33   Bsol= 69.05   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-1.52,-0.51,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204202                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.7044 0.99   1453  160 0.0965 0.1310      5.3807      5.5937|
|  2:  4.7044 -  3.7533 0.99   1400  155 0.0826 0.1013      5.4163      5.6002|
|  3:  3.7533 -  3.2845 0.99   1361  151 0.1102 0.1556      5.4902      5.8667|
|  4:  3.2845 -  2.9868 0.99   1366  146 0.1342 0.1775      5.5049      5.6781|
|  5:  2.9868 -  2.7741 0.98   1331  154 0.1428 0.1845      5.3988      5.5796|
|  6:  2.7741 -  2.6115 0.99   1349  151 0.1365 0.2217      5.2945      5.5666|
|  7:  2.6115 -  2.4813 0.98   1320  154 0.1357 0.1758      5.2454      5.4316|
|  8:  2.4813 -  2.3737 0.99   1338  140 0.1287 0.1908      5.1731      5.3755|
|  9:  2.3737 -  2.2827 0.99   1338  146 0.1242 0.1965      5.0852      5.3936|
| 10:  2.2827 -  2.2042 0.98   1331  146 0.1206 0.1883      5.0162      5.2456|
| 11:  2.2042 -  2.1354 0.97   1292  157 0.1212 0.1882      4.9547      5.2822|
| 12:  2.1354 -  2.0746 0.99   1331  146 0.1164 0.1603       4.879      5.0846|
| 13:  2.0746 -  2.0201 0.84   1148  117 0.1144 0.1992      4.8019      5.1088|
| 14:  2.0201 -  1.9709 0.21    272   36 0.1011 0.1545      4.7604      4.9322|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.7044  1453   160  0.94   9.40   0.96     0.93       7368.44|
|  2:  4.7044 -  3.7533  1400   155  0.95   8.12   1.01     1.00       9059.43|
|  3:  3.7533 -  3.2845  1361   151  0.93  11.71   1.03     1.02      10712.27|
|  4:  3.2845 -  2.9868  1366   146  0.90  15.51   1.01     1.00      11638.84|
|  5:  2.9868 -  2.7741  1331   154  0.89  17.60   1.00     0.98       9999.14|
|  6:  2.7741 -  2.6115  1349   151  0.88  18.51   0.98     0.95       8606.26|
|  7:  2.6115 -  2.4813  1320   154  0.89  17.54   0.99     0.96       7550.17|
|  8:  2.4813 -  2.3737  1338   140  0.89  17.86   1.00     0.95       6819.17|
|  9:  2.3737 -  2.2827  1338   146  0.89  17.44   0.99     0.93       5670.56|
| 10:  2.2827 -  2.2042  1331   146  0.89  17.48   0.99     0.95       5146.70|
| 11:  2.2042 -  2.1354  1292   157  0.89  17.07   0.98     0.94       4563.37|
| 12:  2.1354 -  2.0746  1331   146  0.90  16.61   1.00     0.99       4062.08|
| 13:  2.0746 -  2.0201  1148   117  0.89  17.14   0.98     0.96       3542.80|
| 14:  2.0201 -  1.9709   272    36  0.91  15.52   0.96     0.91       3135.35|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3135.35 max =        11638.84 mean =      7290.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.44|
|phase err.(test): min =        0.00 max =           89.29 mean =        14.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.21  18.08    None  None   None       |
|    all(noH): 2823   0      0.00    105.21  18.08    None  None   None       |
|    Sol.    : 438    0      0.00    105.21  44.77    None  None   None       |
|    Mac.    : 2385   0      0.48    101.87  13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.524: 1154   |   5:    52.606 -  63.127:   85        |
|      1:    10.524 -  21.044: 1052   |   6:    63.127 -  73.647:   52        |
|      2:    21.044 -  31.565:  204   |   7:    73.647 -  84.168:   37        |
|      3:    31.565 -  42.086:  116   |   8:    84.168 -  94.689:   12        |
|      4:    42.086 -  52.606:  105   |   9:    94.689 - 105.209:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.719 - 5.236
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 302
   mapped sites are within: 0.719 - 5.236

peak=    6.042 closest distance to " O   HOH Z 210 " =    1.299
peak=    5.672 closest distance to " O   HOH Z 117 " =    1.246
peak=    5.400 closest distance to " O  BHOH Z  74 " =    1.084
peak=    5.361 closest distance to " O   HOH Z 403 " =    2.024
peak=    5.314 closest distance to " O   HOH Z  49 " =    1.491
peak=    5.238 closest distance to " O   HOH Z 113 " =    1.871
peak=    5.225 closest distance to " O   HOH Z  65 " =    1.151
peak=    5.140 closest distance to " O   HOH Z 255 " =    1.023
peak=    5.043 closest distance to " O   HOH Z 248 " =    1.415
peak=    4.955 closest distance to " CG  PRO A  54 " =    1.339
peak=    4.793 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.783 closest distance to " CD2 TRP A 179 " =    1.335
peak=    4.676 closest distance to " O   HOH Z  43 " =    2.277
peak=    4.648 closest distance to " CB  GLN A 183 " =    1.288
peak=    4.628 closest distance to " CB  SER A  63 " =    1.151
peak=    4.600 closest distance to " O   HOH Z 369 " =    2.403
peak=    4.555 closest distance to " CB  GLN A 223 " =    1.444
peak=    4.502 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.464 closest distance to " CB  ARG A 190 " =    1.752
peak=    4.449 closest distance to " CA  ARG A  36 " =    1.086
peak=    4.328 closest distance to " O   HOH Z  63 " =    1.902
peak=    4.303 closest distance to " CG  GLN A  58 " =    0.948
peak=    4.272 closest distance to " CG  PRO A 280 " =    0.781
peak=    4.252 closest distance to " O   HOH Z 402 " =    1.511
peak=    4.248 closest distance to " CG  ARG A  66 " =    2.618
peak=    4.234 closest distance to " O   HOH Z 232 " =    2.305
peak=    4.215 closest distance to " O   HOH Z 394 " =    1.618
peak=    4.192 closest distance to " CG  PRO A  90 " =    1.191
peak=    4.184 closest distance to " O   SER A  87 " =    2.263
peak=    4.181 closest distance to " O   HOH Z 261 " =    2.343
peak=    4.151 closest distance to " CB  GLU A 277 " =    3.753
peak=    4.148 closest distance to " CA  ALA A  51 " =    0.988
peak=    4.144 closest distance to " CA  ARG A 195 " =    1.204
peak=    4.141 closest distance to " O   HOH Z 189 " =    2.768
peak=    4.104 closest distance to " O   HOH Z 346 " =    1.593
peak=    4.093 closest distance to " CB  ASN A 285 " =    0.951
peak=    4.078 closest distance to " O   HOH Z 134 " =    1.626
peak=    4.075 closest distance to " O   HOH Z 368 " =    2.081
peak=    4.066 closest distance to " O   HOH Z 423 " =    1.914
peak=    4.062 closest distance to " CB  GLU A 152 " =    1.104
peak=    4.054 closest distance to " O   HOH Z 234 " =    3.674
peak=    4.048 closest distance to " O   HOH Z  40 " =    1.940
peak=    4.031 closest distance to " CZ3 TRP A 266 " =    1.072
peak=    4.024 closest distance to " O   HOH Z 425 " =    1.447
peak=    4.020 closest distance to " O   ALA A 165 " =    1.336
peak=    4.011 closest distance to " CG2BVAL A  41 " =    0.864
peak=    3.998 closest distance to " O   HOH Z 251 " =    1.613
peak=    3.997 closest distance to " O   HOH Z 214 " =    1.326
peak=    3.994 closest distance to " O   HOH Z 417 " =    2.668
peak=    3.967 closest distance to " CD  LYS A 166 " =    1.485
peak=    3.956 closest distance to " NZ  LYS A 117 " =    2.906
peak=    3.955 closest distance to " O   HOH Z 412 " =    3.656
peak=    3.954 closest distance to " O   HOH Z  80 " =    1.911
peak=    3.947 closest distance to " O   HOH Z 361 " =    3.479
peak=    3.934 closest distance to " O   HOH Z 142 " =    1.457
peak=    3.921 closest distance to " CB  TRP A 179 " =    1.301
peak=    3.918 closest distance to " CB  ARG A  79 " =    1.556
peak=    3.917 closest distance to " CB  PRO A  54 " =    0.937
peak=    3.911 closest distance to " O   PRO A 198 " =    1.531
peak=    3.887 closest distance to " O   HOH Z 209 " =    2.282
peak=    3.883 closest distance to " CB  SER A  26 " =    1.781
peak=    3.865 closest distance to " CB  SER A 141 " =    1.095
peak=    3.861 closest distance to " O   HOH Z 345 " =    1.651
peak=    3.855 closest distance to " CZ  PHE A  38 " =    1.210
peak=    3.848 closest distance to " CB  THR A  52 " =    0.820
peak=    3.844 closest distance to " O   HOH Z 433 " =    1.432
peak=    3.842 closest distance to " N   CYS A 260 " =    0.943
peak=    3.842 closest distance to " O   HOH Z 406 " =    1.541
peak=    3.840 closest distance to " O   HOH Z  44 " =    2.207
peak=    3.835 closest distance to " O   HOH Z  59 " =    2.403
peak=    3.834 closest distance to " O   HOH Z  15 " =    2.253
peak=    3.824 closest distance to " CZ  PHE A 218 " =    1.181
peak=    3.820 closest distance to " CB  GLU A 128 " =    1.063
peak=    3.820 closest distance to " CG  PRO A 213 " =    1.223
peak=    3.817 closest distance to " ND2 ASN A 187 " =    1.538
peak=    3.800 closest distance to " O   HOH Z 365 " =    2.534
peak=    3.789 closest distance to " CG1 ILE A  33 " =    1.210
peak=    3.788 closest distance to " O   HOH Z 298 " =    1.857
peak=    3.786 closest distance to " CD  PRO A  54 " =    0.963
peak=    3.782 closest distance to " O   HOH Z 227 " =    1.650
peak=    3.777 closest distance to " O   HOH Z 280 " =    3.002
peak=    3.775 closest distance to " O   HOH Z 213 " =    1.784
peak=    3.771 closest distance to " O   HOH Z 193 " =    1.370
peak=    3.770 closest distance to " N   ASN A  39 " =    1.287
peak=    3.766 closest distance to " O   HOH Z 389 " =    1.955
peak=    3.761 closest distance to " CB  ASN A 148 " =    1.433
peak=    3.761 closest distance to " NE2 GLN A  11 " =    1.152
peak=    3.754 closest distance to " O   HOH Z 404 " =    1.512
peak=    3.752 closest distance to " CA  TYR A 116 " =    1.284
peak=    3.750 closest distance to " OE1 GLN A  55 " =    1.552
peak=    3.747 closest distance to " O   HOH Z 128 " =    1.479
peak=    3.745 closest distance to " CA  ALA A 160 " =    0.873
peak=    3.745 closest distance to " CD  LYS A  76 " =    1.886
peak=    3.724 closest distance to " CB  VAL A 202 " =    1.460
peak=    3.721 closest distance to " O   HOH Z 250 " =    1.342
peak=    3.720 closest distance to " O   HOH Z  68 " =    1.863
peak=    3.718 closest distance to " CE  LYS A  76 " =    0.850
peak=    3.717 closest distance to " O   HOH Z 336 " =    2.036
peak=    3.715 closest distance to " CB  TYR A 169 " =    0.783
peak=    3.710 closest distance to " O   HOH Z 132 " =    2.545
peak=    3.705 closest distance to " CD  ARG A 269 " =    1.005
peak=    3.703 closest distance to " CG2 VAL A 197 " =    1.126
peak=    3.701 closest distance to " O   HOH Z 102 " =    1.390
peak=    3.683 closest distance to " O   HOH Z 393 " =    3.246
peak=    3.679 closest distance to " CG1 ILE A  20 " =    1.243
peak=    3.677 closest distance to " O   HOH Z 298 " =    4.229
peak=    3.670 closest distance to " CA  ALA A 295 " =    1.046
peak=    3.667 closest distance to " O   HOH Z 299 " =    4.302
peak=    3.666 closest distance to " O   HOH Z 132 " =    2.626
peak=    3.658 closest distance to " O   HOH Z 291 " =    1.443
peak=    3.656 closest distance to " CA  VAL A 125 " =    1.282
peak=    3.656 closest distance to " O   HOH Z 285 " =    2.563
peak=    3.649 closest distance to " O   HOH Z 316 " =    2.966
peak=    3.644 closest distance to " CB  ASN A 142 " =    1.178
peak=    3.637 closest distance to " CD1 LEU A  96 " =    0.788
peak=    3.626 closest distance to " O   HOH Z 287 " =    1.653
peak=    3.605 closest distance to " O   HOH Z 427 " =    2.842
peak=    3.605 closest distance to " CG  PRO A 243 " =    1.088
peak=    3.600 closest distance to " O   HOH Z 422 " =    2.792
peak=    3.576 closest distance to " O   HOH Z 176 " =    1.521
peak=    3.572 closest distance to " NH2BARG A 145 " =    2.151
peak=    3.568 closest distance to " O   HOH Z  35 " =    2.344
peak=    3.566 closest distance to " O   ASP A 124 " =    1.678
peak=    3.560 closest distance to " O   HOH Z 394 " =    3.800
peak=    3.556 closest distance to " O   HOH Z 185 " =    1.763
peak=    3.555 closest distance to " O   HOH Z 126 " =    1.555
peak=    3.555 closest distance to " CA  SER A  32 " =    1.671
peak=    3.551 closest distance to " OG BSER A 164 " =    2.196
peak=    3.547 closest distance to " O   HOH Z 214 " =    3.094
peak=    3.546 closest distance to " CA  ASN A 176 " =    1.595
peak=    3.546 closest distance to " O   HOH Z 265 " =    2.011
peak=    3.543 closest distance to " O   HOH Z 124 " =    1.151
peak=    3.542 closest distance to " CB  SER A  62 " =    0.937
peak=    3.541 closest distance to " O   HOH Z 286 " =    2.161
peak=    3.531 closest distance to " O   HOH Z 132 " =    1.050
peak=    3.531 closest distance to " CG  GLN A  11 " =    1.397
peak=    3.530 closest distance to " CA  ALA A 100 " =    1.002
peak=    3.526 closest distance to " O   HOH Z 193 " =    1.797
peak=    3.524 closest distance to " NZ  LYS A  48 " =    1.182
peak=    3.515 closest distance to " O   HOH Z 359 " =    1.723
peak=    3.514 closest distance to " CB  PHE A 204 " =    0.867
peak=    3.513 closest distance to " O   HOH Z  20 " =    1.339
peak=    3.499 closest distance to " OH  TYR A 116 " =    1.191
peak=    3.497 closest distance to " CD  ARG A 195 " =    0.903
peak=    3.496 closest distance to " NE2 GLN A  77 " =    3.185
peak=    3.496 closest distance to " O   HOH Z 285 " =    1.887
peak=    3.491 closest distance to " O   HOH Z 126 " =    1.954
peak=    3.484 closest distance to " O   HOH Z 414 " =    1.664
peak=    3.476 closest distance to " CA  ASP A 162 " =    1.119
peak=    3.474 closest distance to " O   HOH Z  78 " =    1.636
peak=    3.468 closest distance to " CB  ARG A  79 " =    0.950
peak=    3.467 closest distance to " O   HOH Z 327 " =    1.667
peak=    3.466 closest distance to " O   HOH Z  21 " =    1.799
peak=    3.466 closest distance to " O   HOH Z 189 " =    2.575
peak=    3.466 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.466 closest distance to " O   HOH Z 325 " =    2.091
peak=    3.463 closest distance to " CB  TRP A 266 " =    1.075
peak=    3.460 closest distance to " O   HOH Z 180 " =    2.204
peak=    3.449 closest distance to " CG1BVAL A  72 " =    1.938
peak=    3.449 closest distance to " OG  SER A 135 " =    1.302
peak=    3.448 closest distance to " O   TYR A 116 " =    1.445
peak=    3.447 closest distance to " OD1 ASN A  69 " =    2.428
peak=    3.446 closest distance to " O   THR A 220 " =    1.106
peak=    3.445 closest distance to " O   HOH Z 357 " =    2.087
peak=    3.433 closest distance to " O   HOH Z 199 " =    1.629
peak=    3.433 closest distance to " N   HIS A 108 " =    1.719
peak=    3.431 closest distance to " O   HOH Z 146 " =    2.142
peak=    3.431 closest distance to " CB  PHE A  16 " =    1.149
peak=    3.424 closest distance to " CA  GLU A 152 " =    0.873
peak=    3.423 closest distance to " O   HOH Z  63 " =    2.051
peak=    3.421 closest distance to " CB  LEU A  83 " =    0.791
peak=    3.419 closest distance to " CB  GLU A  46 " =    1.038
peak=    3.419 closest distance to " CG  PRO A 198 " =    1.220
peak=    3.417 closest distance to " CB  VAL A 265 " =    1.174
peak=    3.416 closest distance to " N   TYR A 116 " =    1.656
peak=    3.412 closest distance to " OE1 GLN A  11 " =    2.046
peak=    3.404 closest distance to " CA  ALA A 158 " =    1.350
peak=    3.401 closest distance to " O   HOH Z  85 " =    1.274
peak=    3.397 closest distance to " O   ASN A  74 " =    1.704
peak=    3.397 closest distance to " CB  THR A  31 " =    1.626
peak=    3.397 closest distance to " NH2 ARG A 156 " =    1.138
peak=    3.392 closest distance to " CB  ASP A 124 " =    0.725
peak=    3.389 closest distance to " O   HOH Z 214 " =    2.132
peak=    3.387 closest distance to " CD  ARG A 159 " =    0.800
peak=    3.382 closest distance to " O   HOH Z 313 " =    1.493
peak=    3.374 closest distance to " O   HOH Z 303 " =    2.295
peak=    3.374 closest distance to " CG2 ILE A 120 " =    1.260
peak=    3.373 closest distance to " NH1AARG A 145 " =    1.455
peak=    3.371 closest distance to " O   HOH Z 200 " =    2.884
peak=    3.370 closest distance to " O   HOH Z 299 " =    4.150
peak=    3.367 closest distance to " O   HOH Z 380 " =    1.776
peak=    3.367 closest distance to " CE  LYS A 119 " =    1.160
peak=    3.366 closest distance to " O   HOH Z 130 " =    2.307
peak=    3.360 closest distance to " O   HOH Z 352 " =    1.708
peak=    3.359 closest distance to " ND2 ASN A 249 " =    0.915
peak=    3.351 closest distance to " N   ASP A 162 " =    1.257
peak=    3.349 closest distance to " O   HOH Z 247 " =    1.382
peak=    3.349 closest distance to " O   LEU A 228 " =    1.866
peak=    3.346 closest distance to " O   HOH Z 361 " =    2.597
peak=    3.346 closest distance to " CG AARG A 275 " =    1.366
peak=    3.344 closest distance to " O   HOH Z 279 " =    2.107
peak=    3.339 closest distance to " CB  MET A 105 " =    1.148
peak=    3.339 closest distance to " OE1 GLN A 223 " =    2.262
peak=    3.337 closest distance to " O   HOH Z 258 " =    2.054
peak=    3.334 closest distance to " CD2 LEU A 297 " =    0.939
peak=    3.333 closest distance to " CB  ALA A 248 " =    1.407
peak=    3.332 closest distance to " O   HOH Z  48 " =    1.745
peak=    3.332 closest distance to " O   HOH Z 147 " =    1.634
peak=    3.330 closest distance to " O   HOH Z 126 " =    1.583
peak=    3.330 closest distance to " O   HOH Z 227 " =    1.737
peak=    3.329 closest distance to " OE1 GLU A   2 " =    1.806
peak=    3.328 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.327 closest distance to " CD  GLN A 194 " =    1.589
peak=    3.324 closest distance to " CG2BVAL A 121 " =    0.880
peak=    3.319 closest distance to " O   ASP A 191 " =    1.596
peak=    3.317 closest distance to " O   HOH Z  83 " =    1.620
peak=    3.316 closest distance to " CA  SER A  87 " =    1.097
peak=    3.313 closest distance to " O   HOH Z 371 " =    2.808
peak=    3.308 closest distance to " O   HOH Z 245 " =    1.313
peak=    3.303 closest distance to " CB  PRO A  90 " =    1.180
peak=    3.302 closest distance to " CB  ALA A   9 " =    1.723
peak=    3.298 closest distance to " O   HOH Z 313 " =    1.931
peak=    3.298 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.298 closest distance to " O   HOH Z 271 " =    2.657
peak=    3.295 closest distance to " O   HOH Z 150 " =    1.229
peak=    3.294 closest distance to " CB  SER A   3 " =    1.317
peak=    3.291 closest distance to " O   HOH Z 418 " =    1.268
peak=    3.291 closest distance to " O   HOH Z  47 " =    2.312
peak=    3.283 closest distance to " CB  MET A  47 " =    1.046
peak=    3.281 closest distance to " O   HOH Z 272 " =    1.838
peak=    3.276 closest distance to " CD  LYS A 119 " =    1.747
peak=    3.276 closest distance to " CG2 ILE A 234 " =    1.177
peak=    3.273 closest distance to " CE1 HIS A  81 " =    1.506
peak=    3.270 closest distance to " O   HOH Z 154 " =    3.094
peak=    3.263 closest distance to " O   HOH Z  19 " =    1.459
peak=    3.262 closest distance to " CB  PRO A 243 " =    1.369
peak=    3.259 closest distance to " O   ALA A 242 " =    1.328
peak=    3.257 closest distance to " O   HOH Z 391 " =    3.082
peak=    3.254 closest distance to " O   HOH Z  54 " =    1.136
peak=    3.251 closest distance to " O   HOH Z 139 " =    4.773
peak=    3.251 closest distance to " O   HOH Z 298 " =    2.272
peak=    3.250 closest distance to " O   HOH Z 193 " =    1.778
peak=    3.250 closest distance to " O   HOH Z 158 " =    3.088
peak=    3.250 closest distance to " CE3 TRP A 150 " =    1.098
peak=    3.250 closest distance to " CG2 ILE A  20 " =    1.387
peak=    3.245 closest distance to " O   HOH Z  30 " =    0.955
peak=    3.239 closest distance to " O   ALA A 158 " =    1.189
peak=    3.238 closest distance to " CB  ASP A 140 " =    1.063
peak=    3.238 closest distance to " O   HOH Z  88 " =    3.177
peak=    3.235 closest distance to " O   HOH Z 203 " =    1.002
peak=    3.232 closest distance to " O   HOH Z 240 " =    2.533
peak=    3.229 closest distance to " CB  ALA A  71 " =    1.377
peak=    3.226 closest distance to " O   HOH Z 409 " =    3.296
peak=    3.224 closest distance to " O   HOH Z 116 " =    1.223
peak=    3.216 closest distance to " CB  ALA A 114 " =    0.758
peak=    3.213 closest distance to " CG2 THR A 220 " =    0.844
peak=    3.208 closest distance to " OG BSER A 258 " =    3.053
peak=    3.201 closest distance to " CB  ASN A 110 " =    1.094
peak=    3.194 closest distance to " OG  SER A  28 " =    1.530
peak=    3.189 closest distance to " O   GLY A  91 " =    1.222
peak=    3.189 closest distance to " N   THR A  52 " =    1.181
peak=    3.188 closest distance to " O   HOH Z 365 " =    2.776
peak=    3.186 closest distance to " O  BHOH Z 338 " =    2.180
peak=    3.180 closest distance to " NE2 GLN A  58 " =    4.737
peak=    3.177 closest distance to " CD1 LEU A 228 " =    1.566
peak=    3.173 closest distance to " O   THR A 182 " =    1.496
peak=    3.171 closest distance to " CA  GLU A  46 " =    1.049
peak=    3.170 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.167 closest distance to " O   HOH Z 128 " =    2.238
peak=    3.166 closest distance to " O   HOH Z  39 " =    1.057
peak=    3.164 closest distance to " CD2 TYR A 186 " =    1.048
peak=    3.164 closest distance to " CA  MET A 188 " =    1.013
peak=    3.161 closest distance to " CG  LEU A 167 " =    1.152
peak=    3.155 closest distance to " CA  MET A 105 " =    1.124
peak=    3.152 closest distance to " O   HOH Z 366 " =    2.420
peak=    3.151 closest distance to " O   HOH Z 334 " =    1.453
peak=    3.149 closest distance to " O   HOH Z 244 " =    1.667
peak=    3.149 closest distance to " CG  MET A 185 " =    1.147
peak=    3.148 closest distance to " CB  LYS A 289 " =    1.030
peak=    3.137 closest distance to " O   HOH Z 420 " =    5.236
peak=    3.136 closest distance to " OG  SER A 245 " =    1.576
peak=    3.131 closest distance to " CA  ASP A 140 " =    1.396
peak=    3.131 closest distance to " O   HOH Z  80 " =    1.707
peak=    3.128 closest distance to " OD1 ASN A 301 " =    1.706
peak=    3.126 closest distance to " O   HOH Z 421 " =    1.998
peak=    3.121 closest distance to " CA  ALA A 248 " =    1.187
peak=    3.120 closest distance to " O   HOH Z 353 " =    2.793
peak=    3.115 closest distance to " O   HOH Z  63 " =    2.214
peak=    3.105 closest distance to " N   TYR A 247 " =    1.238
peak=    3.098 closest distance to " CA  LEU A  83 " =    1.410
peak=    3.098 closest distance to " CB  ALA A  10 " =    1.214
peak=    3.093 closest distance to " CA  ALA A 291 " =    0.783
peak=    3.089 closest distance to " CG  ARG A 138 " =    1.281
peak=    3.080 closest distance to " OG1 THR A 264 " =    0.759
peak=    3.072 closest distance to " CA  ALA A 299 " =    1.108
peak=    3.069 closest distance to " CA  LEU A 101 " =    1.529
peak=    3.064 closest distance to " CB  ARG A 269 " =    0.719
peak=    3.045 closest distance to " CD  ARG A  66 " =    2.516
peak=    3.027 closest distance to " O   HOH Z 109 " =    1.498
peak=    3.023 closest distance to " O   ASP A 200 " =    1.611
peak=    3.009 closest distance to " NE2 GLN A  58 " =    3.244

                           ----------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: 0.990 - 5.992
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 216
   mapped sites are within: 0.990 - 5.992

peak=   -4.595 closest distance to " CD  ARG A  14 " =    3.473
peak=   -4.507 closest distance to " CG2 ILE A  49 " =    2.785
peak=   -4.390 closest distance to " O   HOH Z 266 " =    5.450
peak=   -4.343 closest distance to " O   VAL A  67 " =    2.889
peak=   -4.333 closest distance to " CD2 LEU A 237 " =    2.715
peak=   -4.288 closest distance to " O   PRO A 198 " =    1.380
peak=   -4.283 closest distance to " CD  GLN A  58 " =    1.011
peak=   -4.273 closest distance to " O   HOH Z 377 " =    2.135
peak=   -4.246 closest distance to " CD2 TYR A 293 " =    1.878
peak=   -4.163 closest distance to " CD1 LEU A 101 " =    2.418
peak=   -4.134 closest distance to " O   HOH Z 422 " =    1.230
peak=   -4.106 closest distance to " CD  GLN A 223 " =    1.465
peak=   -4.074 closest distance to " CG2 ILE A  20 " =    3.053
peak=   -4.003 closest distance to " CA  ASP A 298 " =    1.050
peak=   -4.000 closest distance to " OG BSER A 134 " =    1.440
peak=   -3.957 closest distance to " O   HOH Z 166 " =    1.473
peak=   -3.956 closest distance to " CD  GLN A  58 " =    0.990
peak=   -3.947 closest distance to " CD  ARG A 156 " =    2.108
peak=   -3.930 closest distance to " CB  ALA A  43 " =    2.553
peak=   -3.928 closest distance to " O   HOH Z 438 " =    3.009
peak=   -3.925 closest distance to " CD1 PHE A  59 " =    2.090
peak=   -3.916 closest distance to " CE3 TRP A 150 " =    2.298
peak=   -3.901 closest distance to " O   HOH Z 366 " =    1.597
peak=   -3.874 closest distance to " C   HIS A 108 " =    1.123
peak=   -3.861 closest distance to " CD1 LEU A  25 " =    2.548
peak=   -3.848 closest distance to " O   HOH Z  13 " =    1.865
peak=   -3.840 closest distance to " CZ  TYR A 169 " =    1.900
peak=   -3.839 closest distance to " O   HOH Z 165 " =    1.862
peak=   -3.818 closest distance to " NE2 GLN A 223 " =    1.225
peak=   -3.812 closest distance to " O   ALA A  34 " =    2.357
peak=   -3.810 closest distance to " CG  GLN A  11 " =    1.554
peak=   -3.808 closest distance to " ND2 ASN A  45 " =    2.068
peak=   -3.783 closest distance to " O   HOH Z 214 " =    2.736
peak=   -3.754 closest distance to " O   HOH Z 102 " =    1.604
peak=   -3.750 closest distance to " OG  SER A  97 " =    2.189
peak=   -3.750 closest distance to " O   HOH Z 193 " =    1.206
peak=   -3.747 closest distance to " O   HOH Z   5 " =    1.696
peak=   -3.746 closest distance to " O   SER A 210 " =    1.794
peak=   -3.723 closest distance to " CB  PRO A 243 " =    2.743
peak=   -3.702 closest distance to " O   PHE A 218 " =    1.488
peak=   -3.696 closest distance to " CD2 PHE A  61 " =    2.142
peak=   -3.694 closest distance to " CG  GLN A  58 " =    1.221
peak=   -3.688 closest distance to " O   HOH Z 150 " =    1.920
peak=   -3.680 closest distance to " CD  LYS A 289 " =    2.315
peak=   -3.679 closest distance to " O   HOH Z 191 " =    5.992
peak=   -3.676 closest distance to " ND2BASN A 224 " =    1.847
peak=   -3.670 closest distance to " C   THR A 279 " =    1.204
peak=   -3.648 closest distance to " CG  GLU A  53 " =    1.514
peak=   -3.638 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.637 closest distance to " O   HOH Z 196 " =    2.044
peak=   -3.635 closest distance to " CE2 TYR A  30 " =    2.779
peak=   -3.623 closest distance to " O   HOH Z 252 " =    3.609
peak=   -3.601 closest distance to " NH2 ARG A  79 " =    2.154
peak=   -3.594 closest distance to " NE2 GLN A 194 " =    2.039
peak=   -3.591 closest distance to " OD1 ASP A 191 " =    1.588
peak=   -3.589 closest distance to " O   TRP A  92 " =    2.060
peak=   -3.587 closest distance to " CG  PRO A 243 " =    1.677
peak=   -3.584 closest distance to " CG2 VAL A 189 " =    2.182
peak=   -3.580 closest distance to " O   HOH Z 285 " =    1.331
peak=   -3.579 closest distance to " CG1AVAL A  41 " =    2.606
peak=   -3.578 closest distance to " O   HOH Z 185 " =    2.471
peak=   -3.571 closest distance to " O   HOH Z 198 " =    1.600
peak=   -3.570 closest distance to " O   HOH Z 150 " =    1.135
peak=   -3.565 closest distance to " CZ  PHE A  38 " =    2.252
peak=   -3.560 closest distance to " OG1 THR A 157 " =    2.983
peak=   -3.560 closest distance to " O   HOH Z  56 " =    1.267
peak=   -3.551 closest distance to " OG BSER A 134 " =    4.103
peak=   -3.549 closest distance to " O   HOH Z 174 " =    2.405
peak=   -3.541 closest distance to " CA  GLY A 241 " =    3.191
peak=   -3.538 closest distance to " CB  TRP A  85 " =    2.544
peak=   -3.537 closest distance to " CB  ALA A 161 " =    2.581
peak=   -3.534 closest distance to " C   ASN A 285 " =    2.151
peak=   -3.520 closest distance to " O   HOH Z   6 " =    1.578
peak=   -3.517 closest distance to " CB  ALA A  10 " =    2.251
peak=   -3.517 closest distance to " CH2 TRP A 179 " =    1.281
peak=   -3.507 closest distance to " OD1 ASP A 171 " =    1.552
peak=   -3.505 closest distance to " O   HOH Z 145 " =    2.841
peak=   -3.494 closest distance to " O   HOH Z 283 " =    2.326
peak=   -3.488 closest distance to " ND2 ASN A 249 " =    2.205
peak=   -3.479 closest distance to " OE1 GLN A 223 " =    2.339
peak=   -3.476 closest distance to " CB  PRO A 213 " =    2.087
peak=   -3.476 closest distance to " N   SER A 276 " =    1.466
peak=   -3.475 closest distance to " O   PRO A 163 " =    2.117
peak=   -3.459 closest distance to " CD1 ILE A 106 " =    2.205
peak=   -3.450 closest distance to " O   HOH Z 166 " =    1.728
peak=   -3.448 closest distance to " O   SER A   3 " =    1.070
peak=   -3.442 closest distance to " O   HOH Z 351 " =    1.580
peak=   -3.439 closest distance to " O   HOH Z 348 " =    2.173
peak=   -3.435 closest distance to " O   HOH Z 196 " =    1.696
peak=   -3.432 closest distance to " CG1 VAL A 112 " =    2.572
peak=   -3.415 closest distance to " O   SER A 276 " =    1.658
peak=   -3.414 closest distance to " CA  SER A  62 " =    2.743
peak=   -3.408 closest distance to " CG  GLN A 103 " =    2.528
peak=   -3.408 closest distance to " CG  LEU A  83 " =    2.117
peak=   -3.405 closest distance to " CA  GLY A 241 " =    2.338
peak=   -3.404 closest distance to " CH2 TRP A 150 " =    1.163
peak=   -3.403 closest distance to " O   HOH Z 394 " =    1.718
peak=   -3.398 closest distance to " CG  ARG A 269 " =    2.249
peak=   -3.397 closest distance to " O   HOH Z 154 " =    1.608
peak=   -3.392 closest distance to " O   HOH Z 156 " =    3.510
peak=   -3.390 closest distance to " NE2 GLN A  94 " =    1.781
peak=   -3.384 closest distance to " O   HOH Z 407 " =    1.616
peak=   -3.384 closest distance to " O   HOH Z 264 " =    1.747
peak=   -3.374 closest distance to " N   ALA A  43 " =    2.794
peak=   -3.369 closest distance to " CD2 HIS A 207 " =    2.314
peak=   -3.367 closest distance to " O   VAL A 257 " =    1.432
peak=   -3.367 closest distance to " O   HOH Z 110 " =    1.389
peak=   -3.364 closest distance to " O   HOH Z 106 " =    1.869
peak=   -3.362 closest distance to " O   HOH Z 418 " =    1.252
peak=   -3.356 closest distance to " O   HOH Z 252 " =    3.889
peak=   -3.352 closest distance to " O   VAL A 174 " =    2.159
peak=   -3.351 closest distance to " O   HOH Z   7 " =    1.774
peak=   -3.348 closest distance to " CG2 THR A 182 " =    2.219
peak=   -3.342 closest distance to " CG  ASP A 286 " =    1.495
peak=   -3.341 closest distance to " O   HOH Z 211 " =    1.359
peak=   -3.339 closest distance to " CG2 THR A  18 " =    2.836
peak=   -3.337 closest distance to " O   HOH Z  71 " =    2.677
peak=   -3.335 closest distance to " CB  ALA A 184 " =    2.369
peak=   -3.334 closest distance to " CD  ARG A 195 " =    5.265
peak=   -3.332 closest distance to " NE2 GLN A  88 " =    1.905
peak=   -3.332 closest distance to " O   HOH Z 433 " =    1.038
peak=   -3.332 closest distance to " O   HOH Z 287 " =    1.860
peak=   -3.330 closest distance to " CG  ASP A 132 " =    2.347
peak=   -3.328 closest distance to " O   HOH Z  15 " =    1.534
peak=   -3.328 closest distance to " CG1 VAL A 265 " =    2.709
peak=   -3.321 closest distance to " CD1 ILE A 151 " =    2.472
peak=   -3.318 closest distance to " O   HOH Z   6 " =    1.657
peak=   -3.316 closest distance to " O   HOH Z   1 " =    4.426
peak=   -3.315 closest distance to " O   HOH Z 423 " =    2.438
peak=   -3.315 closest distance to " O   HOH Z  91 " =    2.074
peak=   -3.312 closest distance to " N   ALA A 248 " =    2.441
peak=   -3.308 closest distance to " CD2 TYR A 247 " =    2.457
peak=   -3.306 closest distance to " OE2 GLU A 152 " =    1.447
peak=   -3.306 closest distance to " CG1 VAL A 112 " =    2.636
peak=   -3.302 closest distance to " OD1 ASN A 301 " =    1.881
peak=   -3.300 closest distance to " NE2 GLN A  88 " =    1.071
peak=   -3.299 closest distance to " O   ILE A 234 " =    1.286
peak=   -3.298 closest distance to " CB  PRO A 213 " =    1.744
peak=   -3.294 closest distance to " O   HOH Z 250 " =    1.804
peak=   -3.292 closest distance to " CB  ALA A 248 " =    2.236
peak=   -3.291 closest distance to " CG  PHE A 283 " =    2.640
peak=   -3.287 closest distance to " ND2 ASN A  69 " =    1.849
peak=   -3.286 closest distance to " O   ALA A   1 " =    2.083
peak=   -3.283 closest distance to " CE BMET A  47 " =    1.701
peak=   -3.283 closest distance to " OD1 ASN A 148 " =    1.412
peak=   -3.279 closest distance to " O   HOH Z  88 " =    2.083
peak=   -3.269 closest distance to " CD2 PHE A 225 " =    1.300
peak=   -3.267 closest distance to " CG1 VAL A 189 " =    2.636
peak=   -3.265 closest distance to " O   HOH Z 131 " =    4.193
peak=   -3.264 closest distance to " O   HOH Z 171 " =    2.435
peak=   -3.263 closest distance to " O   GLN A  11 " =    1.309
peak=   -3.262 closest distance to " O   SER A 271 " =    2.001
peak=   -3.252 closest distance to " CB  GLU A 277 " =    1.379
peak=   -3.240 closest distance to " O   HOH Z 435 " =    2.329
peak=   -3.239 closest distance to " CE1 PHE A 218 " =    2.669
peak=   -3.238 closest distance to " O   HOH Z  63 " =    1.227
peak=   -3.236 closest distance to " O   HOH Z 149 " =    2.067
peak=   -3.233 closest distance to " O   GLU A 152 " =    1.419
peak=   -3.232 closest distance to " ND2 ASN A  45 " =    1.277
peak=   -3.230 closest distance to " O   HOH Z 197 " =    1.981
peak=   -3.229 closest distance to " O   HOH Z 345 " =    2.747
peak=   -3.226 closest distance to " O   GLY A  80 " =    2.680
peak=   -3.226 closest distance to " O   HOH Z 200 " =    1.347
peak=   -3.224 closest distance to " C   LEU A 143 " =    1.085
peak=   -3.222 closest distance to " O   HOH Z 134 " =    2.772
peak=   -3.211 closest distance to " O   ALA A  10 " =    1.857
peak=   -3.210 closest distance to " OG BSER A 210 " =    1.331
peak=   -3.210 closest distance to " O   HOH Z 244 " =    1.314
peak=   -3.204 closest distance to " CG2 ILE A 263 " =    2.235
peak=   -3.202 closest distance to " O   HOH Z 123 " =    2.420
peak=   -3.201 closest distance to " CD1 ILE A 109 " =    2.849
peak=   -3.199 closest distance to " O   HOH Z 148 " =    3.789
peak=   -3.196 closest distance to " O   HOH Z 234 " =    4.134
peak=   -3.196 closest distance to " O   HOH Z 407 " =    3.072
peak=   -3.191 closest distance to " O   HOH Z  78 " =    1.884
peak=   -3.188 closest distance to " O   TYR A 186 " =    1.749
peak=   -3.185 closest distance to " CG1 VAL A  78 " =    2.596
peak=   -3.183 closest distance to " O   HOH Z 126 " =    1.896
peak=   -3.181 closest distance to " O   HOH Z 210 " =    1.872
peak=   -3.177 closest distance to " C   SER A 206 " =    1.498
peak=   -3.176 closest distance to " CA  GLY A 241 " =    2.835
peak=   -3.173 closest distance to " CA  GLY A 133 " =    2.116
peak=   -3.170 closest distance to " O   HOH Z 109 " =    3.606
peak=   -3.163 closest distance to " CB  HIS A  86 " =    1.177
peak=   -3.162 closest distance to " O   SER A 273 " =    1.240
peak=   -3.160 closest distance to " O   HOH Z 115 " =    1.809
peak=   -3.156 closest distance to " ND2 ASN A 187 " =    1.706
peak=   -3.154 closest distance to " CZ3 TRP A 274 " =    2.289
peak=   -3.154 closest distance to " NH2 ARG A  66 " =    2.107
peak=   -3.152 closest distance to " O   HOH Z 392 " =    1.557
peak=   -3.150 closest distance to " O   HOH Z 113 " =    2.062
peak=   -3.148 closest distance to " N   ALA A 226 " =    1.899
peak=   -3.147 closest distance to " NE  ARG A  66 " =    4.550
peak=   -3.139 closest distance to " CA  LYS A 289 " =    2.240
peak=   -3.137 closest distance to " CB  ALA A 291 " =    2.413
peak=   -3.137 closest distance to " O   ASN A 301 " =    1.371
peak=   -3.135 closest distance to " O   HOH Z 259 " =    1.931
peak=   -3.132 closest distance to " CA  ASN A 110 " =    1.026
peak=   -3.131 closest distance to " OE1 GLN A 223 " =    2.186
peak=   -3.130 closest distance to " O   HOH Z 377 " =    1.831
peak=   -3.127 closest distance to " O   HOH Z  40 " =    2.408
peak=   -3.121 closest distance to " CD  PRO A 243 " =    1.984
peak=   -3.115 closest distance to " OXT GLY A 302 " =    3.141
peak=   -3.114 closest distance to " CD1 ILE A 263 " =    1.977
peak=   -3.108 closest distance to " O   HOH Z  11 " =    1.727
peak=   -3.108 closest distance to " O   HOH Z 198 " =    1.586
peak=   -3.106 closest distance to " CB  SER A  62 " =    5.582
peak=   -3.101 closest distance to " CD1 TRP A  70 " =    1.037
peak=   -3.095 closest distance to " O   HOH Z 278 " =    1.327
peak=   -3.093 closest distance to " O   HOH Z  38 " =    1.753
peak=   -3.079 closest distance to " O   HOH Z 105 " =    2.282
peak=   -3.069 closest distance to " OD2 ASP A 270 " =    1.077
peak=   -3.063 closest distance to " CB  ALA A   9 " =    2.469
peak=   -3.057 closest distance to " O   ILE A 263 " =    2.237
peak=   -3.048 closest distance to " O   HOH Z 426 " =    1.734

================= 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    :  0.4726 0.4689   6.279462e+00   6.266583e+00
   1_bss:  0.4651 0.4585   6.274195e+00   6.258698e+00
   1_xyz:  0.3470 0.3737   6.075565e+00   6.133483e+00
   1_adp:  0.3124 0.3820   6.025429e+00   6.148422e+00
   1_occ:  0.3121 0.3817   6.024962e+00   6.148957e+00
   2_bss:  0.3108 0.3787   6.022658e+00   6.147060e+00
   2_xyz:  0.2424 0.2967   5.805354e+00   5.968154e+00
   2_adp:  0.2285 0.2845   5.764754e+00   5.937210e+00
   2_occ:  0.2283 0.2842   5.764197e+00   5.937139e+00
   3_bss:  0.2279 0.2844   5.764290e+00   5.936712e+00
   3_xyz:  0.1710 0.2186   5.505589e+00   5.708561e+00
   3_adp:  0.1491 0.2024   5.399268e+00   5.629149e+00
   3_occ:  0.1490 0.2026   5.399111e+00   5.629128e+00
   4_bss:  0.1489 0.2024   5.400579e+00   5.628695e+00
   4_xyz:  0.1329 0.1836   5.304528e+00   5.540676e+00
   4_adp:  0.1295 0.1764   5.273616e+00   5.499669e+00
   4_occ:  0.1294 0.1764   5.273021e+00   5.498950e+00
   5_bss:  0.1293 0.1764   5.272873e+00   5.498891e+00
   5_xyz:  0.1199 0.1675   5.212035e+00   5.447327e+00
   5_adp:  0.1179 0.1680   5.205120e+00   5.446185e+00
   5_occ:  0.1178 0.1681   5.204976e+00   5.446271e+00
   5_bss:  0.1178 0.1679   5.204202e+00   5.445137e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  30.228  -2.351   3.193   2.683   0.000   0.000   0.000
   1_xyz:  0.300  30.228  -2.351   3.193   2.683   0.000   0.000   0.000
   1_adp:  0.300  30.228  -2.351   3.193   2.683   0.000   0.000   0.000
   1_occ:  0.300  30.228  -2.351   3.193   2.683   0.000   0.000   0.000
   2_bss:  0.315  55.814  -2.057   1.305   1.052   0.000   0.000   0.000
   2_xyz:  0.315  55.814  -2.057   1.305   1.052   0.000   0.000   0.000
   2_adp:  0.315  55.814  -2.057   1.305   1.052   0.000   0.000   0.000
   2_occ:  0.315  55.814  -2.057   1.305   1.052   0.000   0.000   0.000
   3_bss:  0.325  66.039  -2.493   0.115   0.263   0.000   0.000   0.000
   3_xyz:  0.325  66.039  -2.493   0.115   0.263   0.000   0.000   0.000
   3_adp:  0.325  66.039  -2.493   0.115   0.263   0.000   0.000   0.000
   3_occ:  0.325  66.039  -2.493   0.115   0.263   0.000   0.000   0.000
   4_bss:  0.339  79.503  -2.981  -1.084  -0.475  -0.000  -0.000  -0.000
   4_xyz:  0.339  79.503  -2.981  -1.084  -0.475  -0.000  -0.000  -0.000
   4_adp:  0.339  79.503  -2.981  -1.084  -0.475  -0.000  -0.000  -0.000
   4_occ:  0.339  79.503  -2.981  -1.084  -0.475  -0.000  -0.000  -0.000
   5_bss:  0.334  71.166  -3.058  -1.507  -0.619  -0.000  -0.000  -0.000
   5_xyz:  0.334  71.166  -3.058  -1.507  -0.619  -0.000  -0.000  -0.000
   5_adp:  0.334  71.166  -3.058  -1.507  -0.619  -0.000  -0.000  -0.000
   5_occ:  0.334  71.166  -3.058  -1.507  -0.619  -0.000  -0.000  -0.000
   5_bss:  0.328  69.045  -2.894  -1.518  -0.510  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.064 0.4443  0.5921    67348.644
   1_bss:  55.094 0.4551  0.6321    64448.411
   1_xyz:  41.566 0.6239  0.8419    40342.084
   1_adp:  42.646 0.6102  0.8314    42319.817
   1_occ:  42.650 0.6101  0.8304    42306.600
   2_bss:  42.269 0.6147  0.8092    41706.033
   2_xyz:  31.453 0.7406  0.9400    24169.288
   2_adp:  29.707 0.7608  0.9543    22226.718
   2_occ:  29.718 0.7606  0.9539    22216.036
   3_bss:  29.630 0.7617  0.9290    22167.739
   3_xyz:  21.700 0.8442  0.9935    12388.758
   3_adp:  19.543 0.8655  0.9961    10578.074
   3_occ:  19.545 0.8655  0.9962    10582.691
   4_bss:  19.507 0.8659  0.9693    10586.067
   4_xyz:  17.421 0.8854  0.9753     8717.743
   4_adp:  16.481 0.8942  0.9722     8145.322
   4_occ:  16.471 0.8942  0.9722     8136.230
   5_bss:  16.468 0.8942  0.9653     8132.839
   5_xyz:  15.422 0.9032  0.9710     7323.659
   5_adp:  15.413 0.9034  0.9636     7326.211
   5_occ:  15.413 0.9034  0.9634     7322.646
   5_bss:  15.394 0.9035  0.9664     7290.292
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8154e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8154e-01
   1_xyz:   1.623  0.012  0.098 15.449  0.006  4.111   1.3581e-01
   1_adp:   1.623  0.012  0.098 15.449  0.006  4.111   1.3581e-01
   1_occ:   1.623  0.012  0.098 15.449  0.006  4.111   1.3581e-01
   2_bss:   1.623  0.012  0.098 15.449  0.006  4.111   1.3581e-01
   2_xyz:   1.331  0.009  0.090 14.582  0.005  4.110   8.7895e-02
   2_adp:   1.331  0.009  0.090 14.582  0.005  4.110   8.7895e-02
   2_occ:   1.331  0.009  0.090 14.582  0.005  4.110   8.7895e-02
   3_bss:   1.331  0.009  0.090 14.582  0.005  4.110   8.7895e-02
   3_xyz:   1.222  0.010  0.081 14.701  0.004  4.125   8.3140e-02
   3_adp:   1.222  0.010  0.081 14.701  0.004  4.125   8.3140e-02
   3_occ:   1.222  0.010  0.081 14.701  0.004  4.125   8.3140e-02
   4_bss:   1.222  0.010  0.081 14.701  0.004  4.125   8.3140e-02
   4_xyz:   1.086  0.008  0.078 14.481  0.004  4.115   6.6063e-02
   4_adp:   1.086  0.008  0.078 14.481  0.004  4.115   6.6063e-02
   4_occ:   1.086  0.008  0.078 14.481  0.004  4.115   6.6063e-02
   5_bss:   1.086  0.008  0.078 14.481  0.004  4.115   6.6063e-02
   5_xyz:   1.156  0.011  0.083 14.654  0.004  4.113   7.7419e-02
   5_adp:   1.156  0.011  0.083 14.654  0.004  4.113   7.7419e-02
   5_occ:   1.156  0.011  0.083 14.654  0.004  4.113   7.7419e-02
   5_bss:   1.156  0.011  0.083 14.654  0.004  4.113   7.7419e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.524   2.4371e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.524   2.4371e-01
   1_xyz:   9.381  0.070  0.360 82.281  0.027  1.911   1.1879e-01
   1_adp:   9.381  0.070  0.360 82.281  0.027  1.911   1.1879e-01
   1_occ:   9.381  0.070  0.360 82.281  0.027  1.911   1.1879e-01
   2_bss:   9.381  0.070  0.360 82.281  0.027  1.911   1.1879e-01
   2_xyz:   7.806  0.043  0.307 85.406  0.031  2.233   6.8946e-02
   2_adp:   7.806  0.043  0.307 85.406  0.031  2.233   6.8946e-02
   2_occ:   7.806  0.043  0.307 85.406  0.031  2.233   6.8946e-02
   3_bss:   7.806  0.043  0.307 85.406  0.031  2.233   6.8946e-02
   3_xyz:   7.712  0.060  0.281 81.106  0.033  2.179   6.5587e-02
   3_adp:   7.712  0.060  0.281 81.106  0.033  2.179   6.5587e-02
   3_occ:   7.712  0.060  0.281 81.106  0.033  2.179   6.5587e-02
   4_bss:   7.712  0.060  0.281 81.106  0.033  2.179   6.5587e-02
   4_xyz:   7.382  0.044  0.249 83.240  0.035  2.310   4.8783e-02
   4_adp:   7.382  0.044  0.249 83.240  0.035  2.310   4.8783e-02
   4_occ:   7.382  0.044  0.249 83.240  0.035  2.310   4.8783e-02
   5_bss:   7.382  0.044  0.249 83.240  0.035  2.310   4.8783e-02
   5_xyz:   8.477  0.049  0.297 82.306  0.030  2.250   5.8416e-02
   5_adp:   8.477  0.049  0.297 82.306  0.030  2.250   5.8416e-02
   5_occ:   8.477  0.049  0.297 82.306  0.030  2.250   5.8416e-02
   5_bss:   8.477  0.049  0.297 82.306  0.030  2.250   5.8416e-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: 104.10   0.00  19.22  92.82   0.00  15.42 104.10   0.00  39.92
   1_occ: 104.10   0.00  19.22  92.82   0.00  15.42 104.10   0.00  39.92
   2_bss: 104.10   0.00  19.22  92.82   0.00  15.42 104.10   0.00  39.92
   2_xyz: 104.10   0.00  19.22  92.82   0.00  15.42 104.10   0.00  39.92
   2_adp: 103.18   0.00  18.91  90.07   0.00  15.04 103.18   2.67  39.93
   2_occ: 103.18   0.00  18.91  90.07   0.00  15.04 103.18   2.67  39.93
   3_bss: 103.18   0.00  18.91  90.07   0.00  15.04 103.18   2.67  39.93
   3_xyz: 103.18   0.00  18.91  90.07   0.00  15.04 103.18   2.67  39.93
   3_adp: 104.14   0.00  18.87  91.86   0.00  13.89 104.14   4.95  45.96
   3_occ: 104.14   0.00  18.87  91.86   0.00  13.89 104.14   4.95  45.96
   4_bss: 104.14   0.00  18.87  91.86   0.00  13.89 104.14   4.95  45.96
   4_xyz: 104.14   0.00  18.87  91.86   0.00  13.89 104.14   4.95  45.96
   4_adp: 102.46   0.76  18.04  92.19   0.76  13.29 102.46   5.50  43.89
   4_occ: 102.46   0.76  18.04  92.19   0.76  13.29 102.46   5.50  43.89
   5_bss: 102.46   0.76  18.04  92.19   0.76  13.29 102.46   5.50  43.89
   5_xyz: 102.46   0.76  18.04  92.19   0.76  13.29 102.46   5.50  43.89
   5_adp: 105.21   0.00  18.08 101.87   0.48  13.17 105.21   0.00  44.77
   5_occ: 105.21   0.00  18.08 101.87   0.48  13.17 105.21   0.00  44.77
   5_bss: 105.21   0.00  18.08 101.87   0.48  13.18 105.21   0.00  44.77
------------------------------------------------------------------------
 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:    2.065    0.019    0.407
   1_adp:    2.065    0.019    0.407
   1_occ:    2.065    0.019    0.407
   2_bss:    2.065    0.019    0.407
   2_xyz:    1.672    0.054    0.565
   2_adp:    1.672    0.054    0.565
   2_occ:    1.672    0.054    0.565
   3_bss:    1.672    0.054    0.565
   3_xyz:    1.555    0.072    0.721
   3_adp:    1.555    0.072    0.721
   3_occ:    1.555    0.072    0.721
   4_bss:    1.555    0.072    0.721
   4_xyz:    1.531    0.071    0.763
   4_adp:    1.531    0.071    0.763
   4_occ:    1.531    0.071    0.763
   5_bss:    1.531    0.071    0.763
   5_xyz:    1.491    0.073    0.788
   5_adp:    1.491    0.073    0.788
   5_occ:    1.491    0.073    0.788
   5_bss:    1.491    0.073    0.788
------------------------------------------------------------------------

CPU time actual refinement: 356.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_350/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_350/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_350/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_350/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_350/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.17 
  Macro-tasks:
    bulk solvent and scale       = 47.51  
    individual site refinement   = 148.51 
    weights calculation          = 30.20  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 232.96 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 111.93 
    alpha_beta                      = 8.16   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.66 
    fmodel                         = 7.64   
    r_factors                      = 0.26   
    phase_errors                   = 10.57  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 264.10 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.002 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    650 calls, 111.57 s
gradients_fft:          595 calls, 108.15 s

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

# Date 2008-01-16 Time 04:37:45 PST -0800 (1200487065.62 s)
Start R-work = 0.4726, R-free = 0.4689 (no bulk solvent and anisotropic scale)
Final R-work = 0.1403, R-free = 0.1856 (no bulk solvent and anisotropic scale)

Start R-work = 0.4651, R-free = 0.4585
Final R-work = 0.1178, R-free = 0.1679