# Date 2008-01-16 Time 04:35:59 PST -0800 (1200486959.53 s)
#phil __OFF__

Command line arguments: "../379.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23657
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 379

-------------------------------------------------------------------------------
  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: (69.5475, 45.9914, 86.39, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.96237
Completeness in resolution range: 0.959822
Completeness with d_max=infinity: 0.956868

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8842
                             d_min =   1.9624

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: (69.5475, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.96237
Completeness in resolution range: 0.959822
Completeness with d_max=infinity: 0.956868

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8847 -  4.1991 [2147/2171]  1929   218  10.2%
  bin  2:  4.1991 -  3.3454 [2051/2071]  1849   202   9.8%
  bin  3:  3.3454 -  2.9262 [2039/2058]  1833   206  10.1%
  bin  4:  2.9262 -  2.6603 [2006/2036]  1807   199   9.9%
  bin  5:  2.6603 -  2.4705 [2010/2029]  1811   199   9.9%
  bin  6:  2.4705 -  2.3255 [1976/2001]  1774   202  10.2%
  bin  7:  2.3255 -  2.2094 [1992/2020]  1793   199  10.0%
  bin  8:  2.2094 -  2.1135 [1972/2008]  1778   194   9.8%
  bin  9:  2.1135 -  2.0323 [1966/2008]  1772   194   9.9%
  bin 10:  2.0323 -  1.9624 [1430/2007]  1284   146  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_379/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.69 -     2.33: 31
        2.33 -     2.97: 1812
        2.97 -     3.61: 4643
        3.61 -     4.26: 9358
        4.26 -     4.90: 12894
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.687 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.928 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28733 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_379/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_379/model_refine_001.geo

CPU time processing inputs: 9.38


============================ 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 = 69.5475 45.9914 86.39 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: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3983   r_free= 0.3882   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.206680                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.6835 0.99   1394  154 0.3336 0.3262      6.4806      6.4625|
|  2:  4.6835 -  3.7368 0.99   1336  151 0.3267 0.2997      6.6745      6.5908|
|  3:  3.7368 -  3.2702 0.99   1311  143 0.3652 0.3314      6.5963      6.6205|
|  4:  3.2702 -  2.9738 0.99   1304  149 0.3727 0.3748      6.4315      6.4694|
|  5:  2.9738 -  2.7621 0.99   1302  145 0.4270 0.3740      6.2964      6.2492|
|  6:  2.7621 -  2.6001 0.99   1295  141 0.4183 0.4567      6.2064      6.1443|
|  7:  2.6001 -  2.4705 0.99   1287  141 0.4259 0.4213      6.1557      6.1076|
|  8:  2.4705 -  2.3634 0.98   1271  144 0.4437 0.4690      6.1378      6.1616|
|  9:  2.3634 -  2.2728 0.98   1268  140 0.4314 0.4459      6.0636      6.1062|
| 10:  2.2728 -  2.1946 1.00   1296  144 0.4378 0.4332      6.0437      6.0296|
| 11:  2.1946 -  2.1262 0.97   1255  137 0.4303 0.4423      5.9675      6.0252|
| 12:  2.1262 -  2.0656 0.98   1250  144 0.4474 0.4148      5.9403       5.925|
| 13:  2.0656 -  2.0113 0.99   1301  135 0.4470 0.4228      5.8231      5.8013|
| 14:  2.0113 -  1.9624 0.60    760   91 0.4890 0.4431      5.8786      5.7359|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.6835  1394   154  0.75  30.18   0.85     0.79      57541.34|
|  2:  4.6835 -  3.7368  1336   151  0.78  27.97   0.95     0.89      73900.57|
|  3:  3.7368 -  3.2702  1311   143  0.71  34.49   0.97     0.89      77204.38|
|  4:  3.2702 -  2.9738  1304   149  0.65  39.37   0.97     0.84      71135.15|
|  5:  2.9738 -  2.7621  1302   145  0.57  46.01   0.94     0.78      56998.83|
|  6:  2.7621 -  2.6001  1295   141  0.57  46.71   0.94     0.76      50422.03|
|  7:  2.6001 -  2.4705  1287   141  0.54  48.78   0.98     0.74      47417.72|
|  8:  2.4705 -  2.3634  1271   144  0.52  50.63   0.96     0.72      45135.02|
|  9:  2.3634 -  2.2728  1268   140  0.52  50.59   0.98     0.73      41655.75|
| 10:  2.2728 -  2.1946  1296   144  0.52  50.57   1.00     0.73      36948.72|
| 11:  2.1946 -  2.1262  1255   137  0.51  51.36   1.01     0.76      35362.73|
| 12:  2.1262 -  2.0656  1250   144  0.52  50.63   1.02     0.76      31241.75|
| 13:  2.0656 -  2.0113  1301   135  0.50  52.31   0.99     0.76      26706.28|
| 14:  2.0113 -  1.9624   760    91  0.54  49.02   1.02     0.75      21665.05|
|alpha:            min =        0.72 max =            0.89 mean =         0.78|
|beta:             min =    21665.05 max =        77204.38 mean =     49130.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.60|
|phase err.(test): min =        0.00 max =           89.83 mean =        44.49|
|-----------------------------------------------------------------------------|

============================== 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 = 8.926113              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.347   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.278787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.135   (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 |  1.687 -  2.008:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.008 -  2.330:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.330 -  2.651:       82 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.651 -  2.972:     1730 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.972 -  3.293:     1942 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.293 -  3.615:     2701 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.615 -  3.936:     4820 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.936 -  4.257:     4538 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.257 -  4.579:     5832 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.579 -  4.900:     7062 |
|-----------------------------------------------------------------------------|
|-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 |        0.174 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.687 |       0.383 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    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: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3983   r_free= 0.3882   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.206680                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3845   r_free= 0.3757   ksol= 0.34   Bsol= 27.88   scale= 0.959   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,3.38,-1.81,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.191792                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.571912              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.222   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.705363              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.036   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3845      final r-factor (work) = 0.2694          |
| start r-factor (free) = 0.3757      final r-factor (free) = 0.3033          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6134 = 7.57 * 0.50 * 6.1911 + 1.00 * 0.1743                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8257 = 7.57 * 0.50 * 5.9969 + 1.00 * 0.1219                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2694      final r-factor (work) = 0.2443          |
| start r-factor (free) = 0.3033      final r-factor (free) = 0.3165          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2359 = 0.71 * 1.00 * 5.9969 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1268 = 0.71 * 1.00 * 5.8318 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.46   17.68    None  None   None       |
|    all(noH): 2823   0      0.00    92.46   17.68    None  None   None       |
|    Sol.    : 438    0      4.93    92.46   39.22    None  None   None       |
|    Mac.    : 2385   0      0.00    76.38   13.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.246:  843   |   5:    46.230 -  55.476:  107        |
|      1:     9.246 -  18.492: 1080   |   6:    55.476 -  64.722:   49        |
|      2:    18.492 -  27.738:  393   |   7:    64.722 -  73.968:   18        |
|      3:    27.738 -  36.984:  191   |   8:    73.968 -  83.214:    1        |
|      4:    36.984 -  46.230:  140   |   9:    83.214 -  92.460:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2443 r_free = 0.3165             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2440 r_free = 0.3165             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2440   r_free= 0.3165   ksol= 0.34   Bsol= 27.88   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,3.38,-1.81,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.846533                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2419   r_free= 0.3118   ksol= 0.33   Bsol= 42.76   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-0.09,-1.01,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.836379                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.394994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.278   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.197906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.509  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2419      final r-factor (work) = 0.1850          |
| start r-factor (free) = 0.3118      final r-factor (free) = 0.2360          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0171 = 3.39 * 0.50 * 5.8293 + 1.00 * 0.1219                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7910 = 3.39 * 0.50 * 5.7278 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1850      final r-factor (work) = 0.1718          |
| start r-factor (free) = 0.2360      final r-factor (free) = 0.2195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1468 = 0.20 * 1.00 * 5.7278 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1055 = 0.20 * 1.00 * 5.5474 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    86.93   17.01    None  None   None       |
|    all(noH): 2823   0      1.08    86.93   17.01    None  None   None       |
|    Sol.    : 438    0      6.06    86.93   38.10    None  None   None       |
|    Mac.    : 2385   0      1.08    77.87   13.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.080 -   9.665:  887   |   5:    44.005 -  52.590:  124        |
|      1:     9.665 -  18.250: 1148   |   6:    52.590 -  61.174:   47        |
|      2:    18.250 -  26.835:  312   |   7:    61.174 -  69.759:   16        |
|      3:    26.835 -  35.420:  148   |   8:    69.759 -  78.344:    2        |
|      4:    35.420 -  44.005:  138   |   9:    78.344 -  86.929:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1718 r_free = 0.2195             target_work(ml) = 5.516         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1717 r_free = 0.2193             target_work(ml) = 5.515         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1717   r_free= 0.2193   ksol= 0.33   Bsol= 42.76   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-0.09,-1.01,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.515394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1710   r_free= 0.2182   ksol= 0.32   Bsol= 42.76   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.61,-0.97,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.509960                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.574185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.188   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243872              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.576  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1352          |
| start r-factor (free) = 0.2182      final r-factor (free) = 0.1816          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2063 = 2.57 * 0.50 * 5.5463 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0016 = 2.57 * 0.50 * 5.3974 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1816      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3238 = 0.24 * 1.00 * 5.3974 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2927 = 0.24 * 1.00 * 5.2689 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    83.96   16.98    None  None   None       |
|    all(noH): 2823   0      1.01    83.96   16.98    None  None   None       |
|    Sol.    : 438    0      4.21    83.96   39.64    None  None   None       |
|    Mac.    : 2385   0      1.01    78.86   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.012 -   9.307:  850   |   5:    42.485 -  50.780:  120        |
|      1:     9.307 -  17.601: 1210   |   6:    50.780 -  59.075:   76        |
|      2:    17.601 -  25.896:  276   |   7:    59.075 -  67.369:   35        |
|      3:    25.896 -  34.191:  133   |   8:    67.369 -  75.664:   10        |
|      4:    34.191 -  42.485:  110   |   9:    75.664 -  83.959:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1276 r_free = 0.1748             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1275 r_free = 0.1748             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1275   r_free= 0.1748   ksol= 0.32   Bsol= 42.76   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.61,-0.97,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249482                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1745   ksol= 0.32   Bsol= 42.76   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.36,-1.15,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.248006                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.960755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.260  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.627  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8578 = 2.96 * 0.50 * 5.2710 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7600 = 2.96 * 0.50 * 5.2011 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2890 = 0.25 * 1.00 * 5.2011 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2762 = 0.25 * 1.00 * 5.1495 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.73    83.37   16.82    None  None   None       |
|    all(noH): 2823   0      0.73    83.37   16.82    None  None   None       |
|    Sol.    : 438    0      4.03    83.37   39.21    None  None   None       |
|    Mac.    : 2385   0      0.73    81.85   12.70    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:     0.733 -   8.997:  778   |   5:    42.052 -  50.316:  101        |
|      1:     8.997 -  17.261: 1279   |   6:    50.316 -  58.580:   85        |
|      2:    17.261 -  25.525:  283   |   7:    58.580 -  66.844:   33        |
|      3:    25.525 -  33.789:  134   |   8:    66.844 -  75.108:   10        |
|      4:    33.789 -  42.052:  115   |   9:    75.108 -  83.372:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1583             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1582             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1582   ksol= 0.32   Bsol= 42.76   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.36,-1.15,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1582   ksol= 0.32   Bsol= 43.44   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.42,-1.05,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.141485                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.431243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.200  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7454 = 1.43 * 0.50 * 5.1494 + 1.00 * 0.0604                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7301 = 1.43 * 0.50 * 5.1462 + 1.00 * 0.0474                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2716 = 0.25 * 1.00 * 5.1462 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2702 = 0.25 * 1.00 * 5.1401 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.77    83.04   16.69    None  None   None       |
|    all(noH): 2823   0      0.77    83.04   16.69    None  None   None       |
|    Sol.    : 438    0      5.37    83.04   38.97    None  None   None       |
|    Mac.    : 2385   0      0.77    82.73   12.60    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:     0.770 -   8.997:  806   |   5:    41.903 -  50.130:   95        |
|      1:     8.997 -  17.223: 1261   |   6:    50.130 -  58.356:   85        |
|      2:    17.223 -  25.450:  278   |   7:    58.356 -  66.583:   34        |
|      3:    25.450 -  33.677:  133   |   8:    66.583 -  74.809:    9        |
|      4:    33.677 -  41.903:  116   |   9:    74.809 -  83.036:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1566             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1566             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1566   ksol= 0.32   Bsol= 43.44   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.42,-1.05,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139331                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.6835 0.99   1394  154 0.0996 0.1207      5.3682      5.5168|
|  2:  4.6835 -  3.7368 0.99   1336  151 0.0861 0.1162      5.4447      5.6378|
|  3:  3.7368 -  3.2702 0.99   1311  143 0.1088 0.1499      5.4963      5.8397|
|  4:  3.2702 -  2.9738 0.99   1304  149 0.1236 0.1656      5.4503      5.5946|
|  5:  2.9738 -  2.7621 0.99   1302  145 0.1339 0.1746      5.3309      5.5466|
|  6:  2.7621 -  2.6001 0.99   1295  141 0.1202 0.1949      5.1964      5.4703|
|  7:  2.6001 -  2.4705 0.99   1287  141 0.1282 0.1548      5.1683      5.3222|
|  8:  2.4705 -  2.3634 0.98   1271  144 0.1178 0.1674      5.0659       5.307|
|  9:  2.3634 -  2.2728 0.98   1268  140 0.1160 0.1653      5.0224      5.2386|
| 10:  2.2728 -  2.1946 1.00   1296  144 0.1117 0.1703      4.9416      5.1876|
| 11:  2.1946 -  2.1262 0.97   1255  137 0.1126 0.1745      4.9198      5.2765|
| 12:  2.1262 -  2.0656 0.98   1250  144 0.1115 0.1723       4.865      5.1851|
| 13:  2.0656 -  2.0113 0.99   1301  135 0.1115 0.1777      4.7695      5.0482|
| 14:  2.0113 -  1.9624 0.60    760   91 0.0981 0.1522      4.6607      4.8317|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.6835  1394   154  0.94   8.65   0.98     0.96       6481.03|
|  2:  4.6835 -  3.7368  1336   151  0.96   7.65   1.02     1.01       8856.19|
|  3:  3.7368 -  3.2702  1311   143  0.93  11.36   1.03     1.03      10557.60|
|  4:  3.2702 -  2.9738  1304   149  0.92  13.41   1.01     0.99       9934.59|
|  5:  2.9738 -  2.7621  1302   145  0.90  15.37   1.00     0.98       8105.36|
|  6:  2.7621 -  2.6001  1295   141  0.90  15.65   0.98     0.96       6702.00|
|  7:  2.6001 -  2.4705  1287   141  0.90  15.73   0.99     0.96       6119.87|
|  8:  2.4705 -  2.3634  1271   144  0.91  14.89   1.00     0.97       5125.86|
|  9:  2.3634 -  2.2728  1268   140  0.92  14.62   1.01     0.98       4822.18|
| 10:  2.2728 -  2.1946  1296   144  0.90  15.43   1.01     0.97       4224.85|
| 11:  2.1946 -  2.1262  1255   137  0.90  15.72   1.00     0.96       4144.53|
| 12:  2.1262 -  2.0656  1250   144  0.91  15.16   1.02     1.01       3846.10|
| 13:  2.0656 -  2.0113  1301   135  0.91  15.82   1.01     0.99       3213.07|
| 14:  2.0113 -  1.9624   760    91  0.93  13.33   1.00     0.97       2545.64|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2545.64 max =        10557.60 mean =      6182.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.73|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1566   ksol= 0.32   Bsol= 43.41   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.37,-0.90,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1566   ksol= 0.32   Bsol= 43.41   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.37,-0.90,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139236                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.6835 0.99   1394  154 0.0996 0.1209      5.3688      5.5177|
|  2:  4.6835 -  3.7368 0.99   1336  151 0.0862 0.1162      5.4451      5.6378|
|  3:  3.7368 -  3.2702 0.99   1311  143 0.1088 0.1499      5.4964      5.8399|
|  4:  3.2702 -  2.9738 0.99   1304  149 0.1236 0.1657      5.4503      5.5945|
|  5:  2.9738 -  2.7621 0.99   1302  145 0.1339 0.1745      5.3307      5.5462|
|  6:  2.7621 -  2.6001 0.99   1295  141 0.1201 0.1946       5.196      5.4694|
|  7:  2.6001 -  2.4705 0.99   1287  141 0.1283 0.1548      5.1682      5.3225|
|  8:  2.4705 -  2.3634 0.98   1271  144 0.1179 0.1674      5.0659      5.3066|
|  9:  2.3634 -  2.2728 0.98   1268  140 0.1161 0.1650      5.0225       5.238|
| 10:  2.2728 -  2.1946 1.00   1296  144 0.1116 0.1705      4.9415      5.1888|
| 11:  2.1946 -  2.1262 0.97   1255  137 0.1126 0.1745      4.9199      5.2766|
| 12:  2.1262 -  2.0656 0.98   1250  144 0.1114 0.1723      4.8649      5.1855|
| 13:  2.0656 -  2.0113 0.99   1301  135 0.1115 0.1774      4.7689      5.0464|
| 14:  2.0113 -  1.9624 0.60    760   91 0.0981 0.1520      4.6592      4.8301|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8847 -  4.6835  1394   154  0.94   8.65   0.99     0.96       6489.75|
|  2:  4.6835 -  3.7368  1336   151  0.95   7.66   1.03     1.02       8863.82|
|  3:  3.7368 -  3.2702  1311   143  0.93  11.36   1.03     1.03      10559.77|
|  4:  3.2702 -  2.9738  1304   149  0.92  13.41   1.01     0.99       9931.85|
|  5:  2.9738 -  2.7621  1302   145  0.90  15.36   1.01     0.99       8096.55|
|  6:  2.7621 -  2.6001  1295   141  0.90  15.65   0.99     0.96       6696.36|
|  7:  2.6001 -  2.4705  1287   141  0.90  15.73   1.00     0.96       6116.24|
|  8:  2.4705 -  2.3634  1271   144  0.91  14.89   1.00     0.98       5123.13|
|  9:  2.3634 -  2.2728  1268   140  0.92  14.62   1.01     0.98       4821.62|
| 10:  2.2728 -  2.1946  1296   144  0.90  15.43   1.01     0.98       4226.45|
| 11:  2.1946 -  2.1262  1255   137  0.90  15.73   1.00     0.96       4148.29|
| 12:  2.1262 -  2.0656  1250   144  0.91  15.17   1.02     1.01       3846.99|
| 13:  2.0656 -  2.0113  1301   135  0.91  15.81   1.01     1.00       3207.41|
| 14:  2.0113 -  1.9624   760    91  0.93  13.29   1.00     0.97       2534.40|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2534.40 max =        10559.77 mean =      6181.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.73|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.517)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    83.01   16.67    None  None   None       |
|    all(noH): 2823   0      0.74    83.01   16.67    None  None   None       |
|    Sol.    : 438    0      5.34    83.01   38.94    None  None   None       |
|    Mac.    : 2385   0      0.74    82.71   12.58    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:     0.744 -   8.971:  806   |   5:    41.877 -  50.104:   95        |
|      1:     8.971 -  17.197: 1261   |   6:    50.104 -  58.330:   85        |
|      2:    17.197 -  25.424:  278   |   7:    58.330 -  66.557:   34        |
|      3:    25.424 -  33.651:  133   |   8:    66.557 -  74.783:    9        |
|      4:    33.651 -  41.877:  116   |   9:    74.783 -  83.010:    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)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 4.667
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 310
   mapped sites are within: 0.705 - 4.667

peak=    6.327 closest distance to " NE2 GLN A  11 " =    1.272
peak=    6.145 closest distance to " O   HOH Z 144 " =    1.933
peak=    5.827 closest distance to " O   HOH Z 126 " =    2.036
peak=    5.619 closest distance to " CG  PRO A  54 " =    1.346
peak=    5.378 closest distance to " NH2 ARG A  56 " =    2.054
peak=    5.278 closest distance to " O   HOH Z 423 " =    1.739
peak=    5.267 closest distance to " CB  ARG A 275 " =    0.950
peak=    5.187 closest distance to " O   HOH Z 417 " =    1.689
peak=    5.128 closest distance to " O   HOH Z 287 " =    1.933
peak=    5.067 closest distance to " CB  PRO A  54 " =    1.027
peak=    5.013 closest distance to " O   HOH Z 427 " =    2.208
peak=    4.893 closest distance to " O   HOH Z  63 " =    1.595
peak=    4.863 closest distance to " O   HOH Z  78 " =    1.623
peak=    4.773 closest distance to " O   HOH Z   9 " =    1.348
peak=    4.769 closest distance to " CB  SER A  63 " =    1.220
peak=    4.731 closest distance to " CG  PRO A  90 " =    1.207
peak=    4.729 closest distance to " CG  PRO A 213 " =    1.315
peak=    4.729 closest distance to " CG2 VAL A 257 " =    0.891
peak=    4.728 closest distance to " CB  GLN A 223 " =    1.491
peak=    4.675 closest distance to " O   HOH Z 232 " =    2.308
peak=    4.651 closest distance to " O   HOH Z 375 " =    1.101
peak=    4.624 closest distance to " O   HOH Z 236 " =    1.446
peak=    4.605 closest distance to " O   HOH Z 112 " =    1.287
peak=    4.595 closest distance to " O   HOH Z 371 " =    2.211
peak=    4.543 closest distance to " O   HOH Z  65 " =    0.984
peak=    4.541 closest distance to " O   HOH Z 298 " =    1.907
peak=    4.529 closest distance to " O   HOH Z 209 " =    2.202
peak=    4.437 closest distance to " CG  PRO A 198 " =    1.245
peak=    4.408 closest distance to " CB  ASN A 148 " =    1.376
peak=    4.349 closest distance to " O   HOH Z   1 " =    1.753
peak=    4.342 closest distance to " O   HOH Z 380 " =    1.766
peak=    4.334 closest distance to " CG  TRP A 179 " =    2.178
peak=    4.327 closest distance to " ND2 ASN A 187 " =    1.630
peak=    4.249 closest distance to " CA  TYR A  30 " =    0.977
peak=    4.236 closest distance to " CB  GLN A 183 " =    1.155
peak=    4.223 closest distance to " O   HOH Z 371 " =    1.985
peak=    4.202 closest distance to " CG  PRO A 243 " =    1.135
peak=    4.189 closest distance to " O   HOH Z 193 " =    1.804
peak=    4.185 closest distance to " CB  SER A   3 " =    1.273
peak=    4.181 closest distance to " O   HOH Z 272 " =    1.789
peak=    4.174 closest distance to " CB  GLU A 128 " =    0.974
peak=    4.154 closest distance to " O   HOH Z 427 " =    1.170
peak=    4.138 closest distance to " O   HOH Z 419 " =    2.510
peak=    4.125 closest distance to " CB  ARG A 190 " =    1.684
peak=    4.110 closest distance to " CB  ASN A 187 " =    1.228
peak=    4.106 closest distance to " CB  VAL A 265 " =    1.269
peak=    4.105 closest distance to " CB  ARG A  79 " =    1.316
peak=    4.087 closest distance to " CD  ARG A 159 " =    0.801
peak=    4.081 closest distance to " O   SER A  87 " =    2.295
peak=    4.070 closest distance to " O   HOH Z 316 " =    3.046
peak=    4.040 closest distance to " O   HOH Z 158 " =    2.801
peak=    4.030 closest distance to " O   HOH Z  44 " =    1.793
peak=    4.014 closest distance to " OG BSER A 164 " =    2.252
peak=    4.002 closest distance to " CB  GLU A 152 " =    1.292
peak=    4.001 closest distance to " O   HOH Z   2 " =    1.637
peak=    3.977 closest distance to " O   HOH Z 146 " =    1.689
peak=    3.977 closest distance to " O   HOH Z 128 " =    2.021
peak=    3.949 closest distance to " O   HOH Z 365 " =    2.710
peak=    3.939 closest distance to " O   HOH Z 425 " =    1.374
peak=    3.938 closest distance to " NZ  LYS A 117 " =    3.019
peak=    3.935 closest distance to " O   HOH Z 352 " =    1.785
peak=    3.934 closest distance to " CG  ARG A  66 " =    2.426
peak=    3.934 closest distance to " O   HOH Z 144 " =    2.168
peak=    3.922 closest distance to " O   HOH Z 250 " =    1.526
peak=    3.908 closest distance to " CB  SER A 216 " =    0.771
peak=    3.902 closest distance to " O   HOH Z 368 " =    3.553
peak=    3.902 closest distance to " CB  ARG A 139 " =    1.027
peak=    3.887 closest distance to " O   HOH Z 346 " =    1.700
peak=    3.855 closest distance to " O   HOH Z 234 " =    3.646
peak=    3.849 closest distance to " O   HOH Z   1 " =    1.809
peak=    3.847 closest distance to " O   HOH Z  61 " =    1.485
peak=    3.846 closest distance to " O   HOH Z 362 " =    2.111
peak=    3.846 closest distance to " CB  ILE A 120 " =    1.275
peak=    3.843 closest distance to " O   HOH Z 403 " =    1.361
peak=    3.818 closest distance to " O   HOH Z 128 " =    2.005
peak=    3.810 closest distance to " O   HOH Z 425 " =    1.972
peak=    3.805 closest distance to " O   HOH Z 132 " =    2.366
peak=    3.800 closest distance to " CB  GLU A 277 " =    3.473
peak=    3.799 closest distance to " CB  TYR A 169 " =    0.785
peak=    3.795 closest distance to " NZ  LYS A 119 " =    2.507
peak=    3.795 closest distance to " O   HOH Z 327 " =    1.674
peak=    3.793 closest distance to " O   HOH Z  61 " =    1.648
peak=    3.779 closest distance to " OG BSER A  99 " =    2.327
peak=    3.779 closest distance to " O   HOH Z  97 " =    2.018
peak=    3.770 closest distance to " CE  LYS A  76 " =    0.845
peak=    3.765 closest distance to " O   HOH Z   9 " =    1.940
peak=    3.747 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.741 closest distance to " O   HOH Z 405 " =    1.420
peak=    3.736 closest distance to " CB  LEU A 228 " =    1.078
peak=    3.732 closest distance to " CB  TRP A 266 " =    1.072
peak=    3.730 closest distance to " O   HOH Z  66 " =    2.233
peak=    3.729 closest distance to " O   HOH Z 214 " =    2.275
peak=    3.714 closest distance to " O   HOH Z 245 " =    1.337
peak=    3.711 closest distance to " O   HOH Z 344 " =    3.140
peak=    3.702 closest distance to " CA  ASN A 215 " =    1.101
peak=    3.700 closest distance to " CB  THR A  31 " =    1.616
peak=    3.700 closest distance to " CB  THR A 157 " =    1.118
peak=    3.684 closest distance to " NH1BARG A 145 " =    1.338
peak=    3.683 closest distance to " O   HOH Z   3 " =    1.899
peak=    3.678 closest distance to " CA  ALA A 299 " =    0.908
peak=    3.674 closest distance to " CZ  PHE A 218 " =    1.071
peak=    3.671 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.662 closest distance to " NH1AARG A 145 " =    1.193
peak=    3.659 closest distance to " O   HOH Z 394 " =    1.644
peak=    3.659 closest distance to " CG1BVAL A  72 " =    1.367
peak=    3.658 closest distance to " O   HOH Z 286 " =    2.296
peak=    3.643 closest distance to " O   HOH Z 389 " =    1.696
peak=    3.642 closest distance to " CB  ALA A 114 " =    1.056
peak=    3.640 closest distance to " O   HOH Z 257 " =    2.101
peak=    3.632 closest distance to " O   HOH Z   7 " =    1.373
peak=    3.624 closest distance to " O   HOH Z  88 " =    2.628
peak=    3.621 closest distance to " ND1 HIS A  86 " =    1.803
peak=    3.619 closest distance to " CA  ALA A  84 " =    1.278
peak=    3.605 closest distance to " O   HOH Z 175 " =    2.067
peak=    3.605 closest distance to " CD  ARG A 138 " =    0.705
peak=    3.590 closest distance to " CB  SER A  26 " =    1.645
peak=    3.589 closest distance to " C   PRO A 198 " =    1.464
peak=    3.588 closest distance to " O   HOH Z  44 " =    2.896
peak=    3.588 closest distance to " O  BHOH Z  74 " =    1.329
peak=    3.585 closest distance to " O   HOH Z 390 " =    2.303
peak=    3.583 closest distance to " OD1 ASN A  69 " =    2.527
peak=    3.581 closest distance to " O   HOH Z 222 " =    2.390
peak=    3.577 closest distance to " CB  SER A 212 " =    1.213
peak=    3.569 closest distance to " N   GLN A 278 " =    1.170
peak=    3.565 closest distance to " O   HOH Z 437 " =    1.927
peak=    3.560 closest distance to " CB  SER A  62 " =    1.196
peak=    3.555 closest distance to " N   GLU A   2 " =    1.376
peak=    3.552 closest distance to " O   HOH Z 130 " =    2.296
peak=    3.550 closest distance to " O   HOH Z 213 " =    2.002
peak=    3.549 closest distance to " OD1BASN A 224 " =    2.189
peak=    3.543 closest distance to " O   HOH Z 109 " =    2.413
peak=    3.541 closest distance to " O   HOH Z 124 " =    1.305
peak=    3.539 closest distance to " CB  LYS A 117 " =    1.228
peak=    3.533 closest distance to " O   HOH Z 305 " =    3.536
peak=    3.528 closest distance to " CG2 ILE A 120 " =    1.127
peak=    3.520 closest distance to " O   HOH Z 116 " =    2.740
peak=    3.514 closest distance to " CB  TRP A 179 " =    1.298
peak=    3.513 closest distance to " O   HOH Z 291 " =    1.502
peak=    3.510 closest distance to " O   HOH Z 357 " =    1.911
peak=    3.509 closest distance to " NH2AARG A 190 " =    1.746
peak=    3.506 closest distance to " O   HOH Z  59 " =    2.073
peak=    3.505 closest distance to " O   HOH Z 422 " =    2.574
peak=    3.503 closest distance to " O   HOH Z 371 " =    3.024
peak=    3.484 closest distance to " O   HOH Z  10 " =    1.810
peak=    3.484 closest distance to " O   HOH Z 345 " =    3.262
peak=    3.482 closest distance to " O   HOH Z 368 " =    1.871
peak=    3.469 closest distance to " O   HOH Z 139 " =    1.129
peak=    3.467 closest distance to " O   HOH Z  21 " =    1.698
peak=    3.466 closest distance to " N   ARG A 156 " =    1.330
peak=    3.465 closest distance to " OG  SER A  62 " =    2.929
peak=    3.463 closest distance to " CD2 LEU A 297 " =    0.994
peak=    3.462 closest distance to " CG  MET A 113 " =    0.961
peak=    3.457 closest distance to " O   HOH Z 386 " =    2.990
peak=    3.452 closest distance to " CE1 TYR A 186 " =    1.340
peak=    3.451 closest distance to " O   HOH Z  40 " =    2.157
peak=    3.442 closest distance to " CG  LEU A 167 " =    1.223
peak=    3.437 closest distance to " O   HOH Z 128 " =    1.961
peak=    3.436 closest distance to " N   PHE A 130 " =    1.201
peak=    3.432 closest distance to " CB  ASN A 142 " =    0.972
peak=    3.430 closest distance to " CG1 ILE A 151 " =    1.011
peak=    3.429 closest distance to " CA  SER A  87 " =    1.032
peak=    3.427 closest distance to " O   HOH Z 391 " =    2.832
peak=    3.421 closest distance to " O   HOH Z 336 " =    1.930
peak=    3.419 closest distance to " CB  LEU A 300 " =    0.938
peak=    3.417 closest distance to " O   HOH Z 392 " =    1.222
peak=    3.416 closest distance to " O   HOH Z 166 " =    1.480
peak=    3.415 closest distance to " ND2 ASN A 249 " =    0.808
peak=    3.414 closest distance to " CB  ALA A 114 " =    1.379
peak=    3.412 closest distance to " O   HOH Z 426 " =    1.950
peak=    3.412 closest distance to " O   ASN A  74 " =    1.449
peak=    3.411 closest distance to " CA  ASN A 127 " =    0.978
peak=    3.407 closest distance to " O   HOH Z 189 " =    2.217
peak=    3.406 closest distance to " O   HOH Z  93 " =    2.132
peak=    3.404 closest distance to " CG2 THR A 221 " =    1.223
peak=    3.396 closest distance to " O   HOH Z  90 " =    2.095
peak=    3.387 closest distance to " O   HOH Z 244 " =    1.694
peak=    3.384 closest distance to " O   HOH Z 423 " =    1.831
peak=    3.382 closest distance to " CA  ARG A 195 " =    1.305
peak=    3.382 closest distance to " CG2BVAL A  41 " =    0.751
peak=    3.379 closest distance to " O   HOH Z 359 " =    1.432
peak=    3.370 closest distance to " O   HOH Z  30 " =    1.780
peak=    3.368 closest distance to " CE  LYS A 119 " =    1.219
peak=    3.365 closest distance to " O   HOH Z 283 " =    2.415
peak=    3.364 closest distance to " CB  VAL A 202 " =    1.604
peak=    3.363 closest distance to " CB  ALA A  21 " =    1.922
peak=    3.362 closest distance to " CA  PHE A 283 " =    1.182
peak=    3.361 closest distance to " O   HOH Z 261 " =    2.410
peak=    3.357 closest distance to " O   HOH Z 172 " =    2.563
peak=    3.347 closest distance to " CD BLYS A 290 " =    1.177
peak=    3.344 closest distance to " CD2 TRP A 179 " =    1.266
peak=    3.341 closest distance to " NE2 GLN A  73 " =    3.634
peak=    3.337 closest distance to " N   SER A  97 " =    0.873
peak=    3.335 closest distance to " NE  ARG A  56 " =    3.412
peak=    3.334 closest distance to " O   HOH Z   6 " =    1.906
peak=    3.333 closest distance to " CB  SER A 276 " =    1.232
peak=    3.333 closest distance to " O   PRO A 198 " =    1.260
peak=    3.332 closest distance to " CD1 ILE A 263 " =    1.365
peak=    3.330 closest distance to " NE2 GLN A 278 " =    3.409
peak=    3.329 closest distance to " O   HOH Z 411 " =    3.764
peak=    3.325 closest distance to " O   HOH Z 329 " =    3.775
peak=    3.324 closest distance to " CB  MET A 188 " =    1.666
peak=    3.323 closest distance to " O   HOH Z  94 " =    1.925
peak=    3.317 closest distance to " O   HOH Z  85 " =    2.239
peak=    3.315 closest distance to " NH2BARG A 145 " =    1.892
peak=    3.311 closest distance to " O   HOH Z 272 " =    2.021
peak=    3.309 closest distance to " CB  PRO A 243 " =    1.175
peak=    3.309 closest distance to " O   ARG A 145 " =    1.681
peak=    3.301 closest distance to " O   HOH Z 421 " =    2.174
peak=    3.297 closest distance to " CD  PRO A 243 " =    1.651
peak=    3.293 closest distance to " O   HOH Z 302 " =    1.528
peak=    3.292 closest distance to " CA  THR A 264 " =    0.804
peak=    3.280 closest distance to " N   ALA A   1 " =    1.076
peak=    3.278 closest distance to " CB  ALA A  34 " =    1.146
peak=    3.274 closest distance to " O   HOH Z  88 " =    2.583
peak=    3.270 closest distance to " CB  ASN A 215 " =    1.038
peak=    3.264 closest distance to " O   HOH Z  59 " =    1.417
peak=    3.264 closest distance to " CB  SER A  99 " =    1.050
peak=    3.261 closest distance to " CA  ILE A 234 " =    0.955
peak=    3.260 closest distance to " O   PRO A  90 " =    1.691
peak=    3.257 closest distance to " OE2 GLU A  53 " =    2.065
peak=    3.257 closest distance to " CB  ASP A 124 " =    0.887
peak=    3.252 closest distance to " O   HOH Z 126 " =    1.442
peak=    3.251 closest distance to " N   ALA A   1 " =    2.262
peak=    3.251 closest distance to " O   HOH Z 419 " =    1.616
peak=    3.250 closest distance to " O   HOH Z  89 " =    2.119
peak=    3.250 closest distance to " N   ASN A  39 " =    1.143
peak=    3.249 closest distance to " CB  LYS A 290 " =    1.098
peak=    3.249 closest distance to " NH2BARG A 190 " =    1.471
peak=    3.246 closest distance to " O   HOH Z  32 " =    1.829
peak=    3.238 closest distance to " CB  ALA A   1 " =    4.667
peak=    3.232 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.231 closest distance to " CB  GLN A  88 " =    1.216
peak=    3.231 closest distance to " CG  GLU A 277 " =    1.996
peak=    3.230 closest distance to " O   HOH Z 193 " =    1.968
peak=    3.230 closest distance to " O   HOH Z 407 " =    2.141
peak=    3.225 closest distance to " N   ASN A 127 " =    1.387
peak=    3.222 closest distance to " CA  ALA A 233 " =    0.943
peak=    3.221 closest distance to " CB  LEU A 143 " =    1.081
peak=    3.221 closest distance to " O   HOH Z 153 " =    3.688
peak=    3.217 closest distance to " CA  MET A 105 " =    0.859
peak=    3.217 closest distance to " O   HOH Z 151 " =    1.459
peak=    3.212 closest distance to " CB  TYR A 116 " =    0.925
peak=    3.205 closest distance to " O   HOH Z 227 " =    1.851
peak=    3.201 closest distance to " NH1 ARG A  14 " =    1.043
peak=    3.199 closest distance to " NZ  LYS A 117 " =    1.308
peak=    3.195 closest distance to " CB  ARG A 219 " =    0.872
peak=    3.192 closest distance to " CG AARG A 275 " =    1.085
peak=    3.191 closest distance to " O   HOH Z 193 " =    1.657
peak=    3.191 closest distance to " O   HOH Z 373 " =    1.495
peak=    3.191 closest distance to " O   HOH Z 248 " =    1.584
peak=    3.190 closest distance to " N   ASP A 162 " =    1.119
peak=    3.188 closest distance to " CA  ARG A 102 " =    1.142
peak=    3.185 closest distance to " N   CYS A 260 " =    0.722
peak=    3.175 closest distance to " O   HOH Z  88 " =    3.664
peak=    3.175 closest distance to " O   HOH Z 325 " =    3.618
peak=    3.175 closest distance to " CA  GLY A 302 " =    1.035
peak=    3.175 closest distance to " CB  ASP A 140 " =    0.792
peak=    3.174 closest distance to " O   HOH Z 417 " =    1.951
peak=    3.170 closest distance to " O   HOH Z  17 " =    1.874
peak=    3.165 closest distance to " N   ALA A   1 " =    2.762
peak=    3.165 closest distance to " CG2 VAL A 197 " =    1.022
peak=    3.161 closest distance to " NE2 GLN A  58 " =    3.880
peak=    3.161 closest distance to " CG2 THR A 294 " =    1.670
peak=    3.158 closest distance to " CG BARG A 102 " =    1.805
peak=    3.158 closest distance to " CB  HIS A 108 " =    0.777
peak=    3.151 closest distance to " CA  ALA A  51 " =    0.954
peak=    3.147 closest distance to " CG2 THR A 220 " =    0.921
peak=    3.146 closest distance to " CA  ASN A 217 " =    1.097
peak=    3.133 closest distance to " O  BHOH Z 338 " =    2.373
peak=    3.128 closest distance to " O   HOH Z 406 " =    1.616
peak=    3.128 closest distance to " CE AMET A  47 " =    1.286
peak=    3.127 closest distance to " O   HOH Z 290 " =    1.139
peak=    3.127 closest distance to " CB  ARG A 138 " =    0.794
peak=    3.123 closest distance to " O   HOH Z 403 " =    1.539
peak=    3.123 closest distance to " O   HOH Z 145 " =    1.255
peak=    3.121 closest distance to " O   HOH Z 434 " =    1.193
peak=    3.121 closest distance to " O   HOH Z 183 " =    1.378
peak=    3.119 closest distance to " O   PHE A 192 " =    1.475
peak=    3.115 closest distance to " O   HOH Z 214 " =    3.730
peak=    3.114 closest distance to " O   HOH Z 153 " =    1.719
peak=    3.112 closest distance to " CG  GLN A 278 " =    1.292
peak=    3.109 closest distance to " CA  ILE A 263 " =    1.063
peak=    3.092 closest distance to " O   HOH Z 189 " =    2.385
peak=    3.085 closest distance to " O   HOH Z 298 " =    2.508
peak=    3.074 closest distance to " O   HOH Z  43 " =    2.245
peak=    3.074 closest distance to " O   HOH Z 173 " =    2.044
peak=    3.073 closest distance to " O   HOH Z 125 " =    2.332
peak=    3.073 closest distance to " O   ALA A   1 " =    1.453
peak=    3.069 closest distance to " O   GLY A 147 " =    1.388
peak=    3.067 closest distance to " CE3 TRP A 274 " =    1.298
peak=    3.064 closest distance to " OG BSER A 134 " =    3.181
peak=    3.063 closest distance to " O   HOH Z 130 " =    3.445
peak=    3.062 closest distance to " O   HOH Z  47 " =    1.802
peak=    3.061 closest distance to " O   HOH Z 180 " =    2.180
peak=    3.058 closest distance to " O   HOH Z 266 " =    3.321
peak=    3.055 closest distance to " CG  LYS A  76 " =    0.935
peak=    3.040 closest distance to " O   HOH Z 383 " =    1.738
peak=    3.040 closest distance to " CA  ALA A 158 " =    1.133
peak=    3.037 closest distance to " O   GLY A 302 " =    2.107
peak=    3.032 closest distance to " CA  LYS A 290 " =    1.406
peak=    3.022 closest distance to " N   HIS A  86 " =    1.216
peak=    3.017 closest distance to " NE AARG A 275 " =    1.690
peak=    3.016 closest distance to " O   HOH Z 389 " =    1.894
peak=    3.014 closest distance to " CD1 LEU A 261 " =    1.192

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.684 - 5.924
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.753 - 5.924

peak=   -4.478 closest distance to " O   HOH Z 290 " =    1.052
peak=   -4.405 closest distance to " CD  ARG A 156 " =    2.066
peak=   -4.355 closest distance to " O   PRO A 198 " =    1.190
peak=   -4.311 closest distance to " CB  PRO A 243 " =    2.597
peak=   -4.270 closest distance to " C   HIS A 108 " =    1.195
peak=   -4.265 closest distance to " CD1 LEU A 255 " =    2.847
peak=   -4.231 closest distance to " O   HOH Z 377 " =    1.886
peak=   -4.148 closest distance to " CG  GLN A  58 " =    1.014
peak=   -4.115 closest distance to " O   HOH Z 185 " =    2.100
peak=   -4.109 closest distance to " O   HOH Z 351 " =    1.562
peak=   -4.103 closest distance to " O   VAL A  67 " =    2.547
peak=   -4.096 closest distance to " O   HOH Z  65 " =    1.103
peak=   -4.024 closest distance to " CB  ALA A 248 " =    2.085
peak=   -4.018 closest distance to " O   HOH Z 266 " =    4.818
peak=   -4.008 closest distance to " CA  GLY A  98 " =    1.724
peak=   -4.002 closest distance to " CG1 VAL A 112 " =    2.951
peak=   -3.954 closest distance to " SG  CYS A 254 " =    3.368
peak=   -3.942 closest distance to " O   HOH Z 372 " =    2.530
peak=   -3.929 closest distance to " CB  ALA A 291 " =    2.143
peak=   -3.918 closest distance to " OD2 ASP A 191 " =    1.387
peak=   -3.915 closest distance to " O   HOH Z 389 " =    1.988
peak=   -3.904 closest distance to " O   SER A 135 " =    1.420
peak=   -3.875 closest distance to " CG  PHE A 283 " =    2.610
peak=   -3.856 closest distance to " CG  GLN A 223 " =    1.484
peak=   -3.845 closest distance to " OG BSER A 134 " =    1.382
peak=   -3.821 closest distance to " CA  VAL A  67 " =    2.946
peak=   -3.814 closest distance to " O   HOH Z 231 " =    2.010
peak=   -3.811 closest distance to " N   GLN A  58 " =    1.739
peak=   -3.801 closest distance to " N   THR A 157 " =    1.450
peak=   -3.796 closest distance to " O   HOH Z 198 " =    1.639
peak=   -3.782 closest distance to " CB  PHE A 192 " =    1.870
peak=   -3.775 closest distance to " CZ  PHE A  59 " =    1.386
peak=   -3.770 closest distance to " O   HOH Z 317 " =    1.409
peak=   -3.755 closest distance to " O   SER A  95 " =    1.425
peak=   -3.733 closest distance to " O   HOH Z 298 " =    2.446
peak=   -3.730 closest distance to " O   PRO A 243 " =    2.516
peak=   -3.723 closest distance to " O   HOH Z 407 " =    2.925
peak=   -3.720 closest distance to " CB  ASN A  39 " =    2.317
peak=   -3.710 closest distance to " O   HOH Z 377 " =    0.898
peak=   -3.705 closest distance to " O   SER A  22 " =    2.512
peak=   -3.688 closest distance to " CE  MET A 105 " =    2.376
peak=   -3.685 closest distance to " O   HOH Z  90 " =    2.373
peak=   -3.678 closest distance to " ND2 ASN A  45 " =    1.083
peak=   -3.667 closest distance to " CB  ALA A  43 " =    2.267
peak=   -3.648 closest distance to " OG  SER A   3 " =    1.633
peak=   -3.647 closest distance to " OE1 GLN A  88 " =    1.129
peak=   -3.634 closest distance to " O   VAL A 189 " =    2.531
peak=   -3.627 closest distance to " OD2 ASP A 171 " =    2.056
peak=   -3.616 closest distance to " O   HOH Z 313 " =    1.715
peak=   -3.616 closest distance to " ND2 ASN A  45 " =    1.885
peak=   -3.606 closest distance to " O   HOH Z  13 " =    1.662
peak=   -3.601 closest distance to " CD2 TYR A 293 " =    1.849
peak=   -3.593 closest distance to " O   HOH Z  52 " =    1.341
peak=   -3.592 closest distance to " CE  LYS A  76 " =    2.770
peak=   -3.582 closest distance to " O   ALA A 161 " =    1.598
peak=   -3.560 closest distance to " CD1 LEU A 101 " =    2.178
peak=   -3.557 closest distance to " CZ2 TRP A 274 " =    0.960
peak=   -3.554 closest distance to " OD1 ASN A 148 " =    1.561
peak=   -3.552 closest distance to " NH1AARG A 275 " =    1.870
peak=   -3.548 closest distance to " CZ3 TRP A 179 " =    1.280
peak=   -3.543 closest distance to " O   HOH Z 250 " =    1.326
peak=   -3.534 closest distance to " O   HOH Z 140 " =    1.462
peak=   -3.533 closest distance to " O   HOH Z 298 " =    1.116
peak=   -3.529 closest distance to " O   HOH Z  60 " =    1.747
peak=   -3.524 closest distance to " O   ARG A 145 " =    1.452
peak=   -3.523 closest distance to " O   HOH Z  24 " =    1.209
peak=   -3.520 closest distance to " N   ALA A  43 " =    2.488
peak=   -3.520 closest distance to " CA  GLY A  57 " =    2.108
peak=   -3.515 closest distance to " OD1 ASP A 191 " =    1.888
peak=   -3.509 closest distance to " O   ALA A  10 " =    1.704
peak=   -3.499 closest distance to " O   HOH Z 427 " =    1.877
peak=   -3.493 closest distance to " CG  ASP A 231 " =    0.753
peak=   -3.492 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.481 closest distance to " O   HOH Z 131 " =    4.069
peak=   -3.478 closest distance to " O   HOH Z 211 " =    1.557
peak=   -3.476 closest distance to " CE3 TRP A 274 " =    2.335
peak=   -3.474 closest distance to " CA  GLY A 133 " =    1.988
peak=   -3.449 closest distance to " C   ALA A 114 " =    2.169
peak=   -3.447 closest distance to " O   HOH Z 166 " =    1.225
peak=   -3.441 closest distance to " ND2 ASN A 252 " =    1.787
peak=   -3.437 closest distance to " CG1 VAL A 268 " =    2.382
peak=   -3.422 closest distance to " NE2 GLN A 278 " =    1.638
peak=   -3.421 closest distance to " OE1 GLN A 183 " =    1.495
peak=   -3.421 closest distance to " CD2 LEU A 237 " =    2.831
peak=   -3.420 closest distance to " ND2 ASN A  45 " =    1.269
peak=   -3.420 closest distance to " O   HOH Z  15 " =    1.534
peak=   -3.420 closest distance to " CG  MET A 105 " =    0.940
peak=   -3.407 closest distance to " CG1 VAL A 230 " =    2.025
peak=   -3.405 closest distance to " O   ASN A 127 " =    1.598
peak=   -3.400 closest distance to " O   ILE A  49 " =    1.673
peak=   -3.400 closest distance to " CG1 VAL A 268 " =    2.850
peak=   -3.397 closest distance to " O   HOH Z  63 " =    2.243
peak=   -3.396 closest distance to " O   HOH Z 409 " =    5.924
peak=   -3.386 closest distance to " O   ALA A   1 " =    1.608
peak=   -3.382 closest distance to " CE2 TYR A  30 " =    2.706
peak=   -3.381 closest distance to " O   HOH Z  60 " =    2.349
peak=   -3.379 closest distance to " O   HOH Z  37 " =    1.720
peak=   -3.378 closest distance to " C   ALA A 158 " =    1.637
peak=   -3.378 closest distance to " O   ALA A 180 " =    1.114
peak=   -3.376 closest distance to " OG  SER A  87 " =    1.312
peak=   -3.370 closest distance to " N   GLN A 122 " =    1.350
peak=   -3.366 closest distance to " CZ  TYR A 169 " =    1.717
peak=   -3.361 closest distance to " O   HOH Z 282 " =    0.940
peak=   -3.360 closest distance to " CD2 PHE A 225 " =    1.146
peak=   -3.357 closest distance to " O   HOH Z 152 " =    4.870
peak=   -3.356 closest distance to " O   HOH Z  43 " =    1.832
peak=   -3.350 closest distance to " O   HOH Z 385 " =    1.955
peak=   -3.347 closest distance to " CB  ASP A 132 " =    2.350
peak=   -3.346 closest distance to " CE BMET A  47 " =    1.176
peak=   -3.345 closest distance to " O   HOH Z 384 " =    2.957
peak=   -3.343 closest distance to " O   HOH Z 102 " =    1.489
peak=   -3.336 closest distance to " O   PHE A 218 " =    1.440
peak=   -3.335 closest distance to " O   HOH Z  11 " =    1.796
peak=   -3.333 closest distance to " O   HOH Z 134 " =    3.830
peak=   -3.331 closest distance to " N   MET A 188 " =    1.931
peak=   -3.328 closest distance to " ND2 ASN A 249 " =    2.414
peak=   -3.327 closest distance to " CB  ALA A 248 " =    2.321
peak=   -3.327 closest distance to " CE2 PHE A 218 " =    2.341
peak=   -3.324 closest distance to " CA  GLY A 203 " =    2.253
peak=   -3.321 closest distance to " CG2 VAL A 296 " =    1.957
peak=   -3.318 closest distance to " N   SER A 212 " =    1.896
peak=   -3.312 closest distance to " ND2 ASN A 187 " =    1.482
peak=   -3.310 closest distance to " OD1 ASP A 171 " =    1.554
peak=   -3.309 closest distance to " O   ASP A 162 " =    2.145
peak=   -3.307 closest distance to " OG  SER A  97 " =    2.169
peak=   -3.306 closest distance to " CB  GLN A  55 " =    1.321
peak=   -3.302 closest distance to " CB  ALA A 291 " =    2.196
peak=   -3.298 closest distance to " O   HOH Z 288 " =    1.366
peak=   -3.296 closest distance to " ND2 ASN A  60 " =    4.109
peak=   -3.294 closest distance to " O   HOH Z  28 " =    1.856
peak=   -3.293 closest distance to " CB  TYR A  15 " =    2.170
peak=   -3.287 closest distance to " O   HOH Z 191 " =    5.470
peak=   -3.287 closest distance to " O   TRP A  70 " =    1.404
peak=   -3.285 closest distance to " CB  ASP A  27 " =    2.290
peak=   -3.283 closest distance to " CB  CYS A 254 " =    2.234
peak=   -3.278 closest distance to " CD  ARG A 139 " =    1.524
peak=   -3.277 closest distance to " C   LEU A 143 " =    1.051
peak=   -3.276 closest distance to " O   VAL A 197 " =    1.604
peak=   -3.275 closest distance to " CE3 TRP A 123 " =    1.374
peak=   -3.274 closest distance to " OE2 GLU A 152 " =    1.029
peak=   -3.270 closest distance to " NE  ARG A  36 " =    1.927
peak=   -3.269 closest distance to " O   HOH Z 213 " =    1.386
peak=   -3.267 closest distance to " O   HOH Z 165 " =    2.294
peak=   -3.266 closest distance to " O   HOH Z 345 " =    1.945
peak=   -3.263 closest distance to " NH2 ARG A  79 " =    2.145
peak=   -3.262 closest distance to " O   HOH Z   9 " =    1.689
peak=   -3.262 closest distance to " O   HOH Z 432 " =    3.668
peak=   -3.261 closest distance to " CD  GLU A 277 " =    1.174
peak=   -3.256 closest distance to " CG1 VAL A 197 " =    2.140
peak=   -3.255 closest distance to " O   LEU A 101 " =    2.260
peak=   -3.254 closest distance to " O   HOH Z 348 " =    2.257
peak=   -3.252 closest distance to " O   MET A  40 " =    2.783
peak=   -3.252 closest distance to " CB  PRO A 163 " =    2.469
peak=   -3.246 closest distance to " CB  ALA A   7 " =    2.002
peak=   -3.245 closest distance to " OG  SER A  63 " =    1.159
peak=   -3.241 closest distance to " O   HOH Z   1 " =    1.449
peak=   -3.240 closest distance to " CB  CYS A 201 " =    2.453
peak=   -3.239 closest distance to " CG  PRO A 243 " =    1.597
peak=   -3.238 closest distance to " O   HOH Z 134 " =    3.213
peak=   -3.235 closest distance to " C   ASN A 285 " =    2.184
peak=   -3.234 closest distance to " OXT GLY A 302 " =    2.973
peak=   -3.234 closest distance to " N   ALA A 248 " =    1.524
peak=   -3.233 closest distance to " CA  GLY A 241 " =    2.186
peak=   -3.233 closest distance to " OG BSER A 134 " =    1.595
peak=   -3.232 closest distance to " O   HOH Z  51 " =    1.022
peak=   -3.231 closest distance to " CG2 ILE A 151 " =    2.561
peak=   -3.226 closest distance to " O   GLN A 240 " =    2.013
peak=   -3.223 closest distance to " ND2BASN A 224 " =    1.749
peak=   -3.221 closest distance to " OG  SER A  87 " =    1.677
peak=   -3.206 closest distance to " OD1 ASP A 200 " =    1.368
peak=   -3.205 closest distance to " CG  ARG A 139 " =    2.176
peak=   -3.204 closest distance to " OG  SER A 245 " =    1.284
peak=   -3.203 closest distance to " O   HOH Z 339 " =    1.788
peak=   -3.200 closest distance to " CD1 TRP A 179 " =    1.037
peak=   -3.199 closest distance to " N   GLN A  58 " =    1.263
peak=   -3.195 closest distance to " CD2 LEU A 237 " =    2.300
peak=   -3.190 closest distance to " O   HOH Z 438 " =    1.244
peak=   -3.182 closest distance to " O   SER A 146 " =    1.115
peak=   -3.181 closest distance to " CD1 PHE A  59 " =    2.026
peak=   -3.181 closest distance to " CB  ALA A 114 " =    2.550
peak=   -3.181 closest distance to " OE1 GLU A 277 " =    2.204
peak=   -3.180 closest distance to " O   ALA A  51 " =    1.246
peak=   -3.175 closest distance to " CB  TRP A  85 " =    2.311
peak=   -3.174 closest distance to " CG2 THR A 178 " =    2.152
peak=   -3.169 closest distance to " ND2 ASN A 285 " =    2.071
peak=   -3.168 closest distance to " O   HOH Z 369 " =    2.219
peak=   -3.163 closest distance to " C   MET A 188 " =    1.591
peak=   -3.161 closest distance to " ND2 ASN A  39 " =    1.358
peak=   -3.134 closest distance to " O   HOH Z 390 " =    2.501
peak=   -3.134 closest distance to " O   GLY A  80 " =    2.423
peak=   -3.127 closest distance to " O   HOH Z 137 " =    1.390
peak=   -3.123 closest distance to " O   PRO A 163 " =    1.235
peak=   -3.120 closest distance to " O   GLU A 152 " =    1.437
peak=   -3.112 closest distance to " O   HOH Z 158 " =    2.004
peak=   -3.109 closest distance to " CG2 ILE A 263 " =    2.319
peak=   -3.107 closest distance to " O   HOH Z 256 " =    1.388
peak=   -3.104 closest distance to " O   HOH Z 292 " =    1.520
peak=   -3.095 closest distance to " OG  SER A  97 " =    1.557
peak=   -3.072 closest distance to " O   HOH Z 337 " =    1.685
peak=   -3.065 closest distance to " OG  SER A 206 " =    1.726
peak=   -3.064 closest distance to " CE1 PHE A  59 " =    2.046
peak=   -3.040 closest distance to " CE  MET A 105 " =    2.259
peak=   -3.032 closest distance to " O   HOH Z 111 " =    2.383
peak=   -3.013 closest distance to " O   ALA A 180 " =    0.975

================= 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    :  0.3983 0.3882   6.206680e+00   6.191420e+00
   1_bss:  0.3845 0.3757   6.191792e+00   6.170167e+00
   1_xyz:  0.2694 0.3033   5.895063e+00   5.975789e+00
   1_adp:  0.2443 0.3165   5.847202e+00   6.006175e+00
   1_occ:  0.2440 0.3165   5.846533e+00   6.005785e+00
   2_bss:  0.2419 0.3118   5.836379e+00   5.995497e+00
   2_xyz:  0.1850 0.2360   5.581670e+00   5.769808e+00
   2_adp:  0.1718 0.2195   5.516321e+00   5.709381e+00
   2_occ:  0.1717 0.2193   5.515394e+00   5.708644e+00
   3_bss:  0.1710 0.2182   5.509960e+00   5.702318e+00
   3_xyz:  0.1352 0.1816   5.296716e+00   5.516756e+00
   3_adp:  0.1276 0.1748   5.249850e+00   5.477211e+00
   3_occ:  0.1275 0.1748   5.249482e+00   5.476804e+00
   4_bss:  0.1277 0.1745   5.248006e+00   5.474056e+00
   4_xyz:  0.1143 0.1609   5.157001e+00   5.398471e+00
   4_adp:  0.1122 0.1583   5.141958e+00   5.384188e+00
   4_occ:  0.1121 0.1582   5.141765e+00   5.384091e+00
   5_bss:  0.1121 0.1582   5.141485e+00   5.383718e+00
   5_xyz:  0.1130 0.1571   5.142533e+00   5.377042e+00
   5_adp:  0.1124 0.1566   5.139506e+00   5.375785e+00
   5_occ:  0.1124 0.1566   5.139331e+00   5.375672e+00
   5_bss:  0.1123 0.1566   5.139236e+00   5.375521e+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:  0.337  27.879  -2.469   3.375  -1.808   0.000  -0.000  -0.000
   1_xyz:  0.337  27.879  -2.469   3.375  -1.808   0.000  -0.000  -0.000
   1_adp:  0.337  27.879  -2.469   3.375  -1.808   0.000  -0.000  -0.000
   1_occ:  0.337  27.879  -2.469   3.375  -1.808   0.000  -0.000  -0.000
   2_bss:  0.326  42.758  -2.259  -0.088  -1.007  -0.000  -0.000  -0.000
   2_xyz:  0.326  42.758  -2.259  -0.088  -1.007  -0.000  -0.000  -0.000
   2_adp:  0.326  42.758  -2.259  -0.088  -1.007  -0.000  -0.000  -0.000
   2_occ:  0.326  42.758  -2.259  -0.088  -1.007  -0.000  -0.000  -0.000
   3_bss:  0.323  42.758  -2.505  -1.606  -0.974  -0.000  -0.000  -0.000
   3_xyz:  0.323  42.758  -2.505  -1.606  -0.974  -0.000  -0.000  -0.000
   3_adp:  0.323  42.758  -2.505  -1.606  -0.974  -0.000  -0.000  -0.000
   3_occ:  0.323  42.758  -2.505  -1.606  -0.974  -0.000  -0.000  -0.000
   4_bss:  0.317  42.758  -2.744  -2.361  -1.155  -0.000  -0.000  -0.000
   4_xyz:  0.317  42.758  -2.744  -2.361  -1.155  -0.000  -0.000  -0.000
   4_adp:  0.317  42.758  -2.744  -2.361  -1.155  -0.000  -0.000  -0.000
   4_occ:  0.317  42.758  -2.744  -2.361  -1.155  -0.000  -0.000  -0.000
   5_bss:  0.319  43.438  -2.671  -2.424  -1.050  -0.000  -0.000  -0.000
   5_xyz:  0.319  43.438  -2.671  -2.424  -1.050  -0.000  -0.000  -0.000
   5_adp:  0.319  43.438  -2.671  -2.424  -1.050  -0.000  -0.000  -0.000
   5_occ:  0.319  43.438  -2.671  -2.424  -1.050  -0.000  -0.000  -0.000
   5_bss:  0.319  43.412  -2.535  -2.371  -0.895  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.588 0.5896  0.7813    49132.734
   1_bss:  43.534 0.6007  0.7849    45598.134
   1_xyz:  31.068 0.7472  0.9385    24915.219
   1_adp:  32.785 0.7269  0.9164    27141.963
   1_occ:  32.799 0.7267  0.9156    27114.520
   2_bss:  31.964 0.7358  0.9027    25947.072
   2_xyz:  23.226 0.8293  0.9841    14390.035
   2_adp:  21.032 0.8523  0.9977    12497.937
   2_occ:  21.015 0.8524  0.9975    12457.097
   3_bss:  20.788 0.8544  0.9784    12201.570
   3_xyz:  16.841 0.8905  0.9961     8291.151
   3_adp:  15.931 0.8989  0.9938     7736.604
   3_occ:  15.926 0.8989  0.9936     7721.456
   4_bss:  15.845 0.8995  0.9801     7659.080
   4_xyz:  14.275 0.9124  0.9876     6498.572
   4_adp:  13.951 0.9152  0.9857     6335.622
   4_occ:  13.948 0.9152  0.9857     6328.595
   5_bss:  13.941 0.9153  0.9872     6325.968
   5_xyz:  13.748 0.9171  0.9863     6212.500
   5_adp:  13.693 0.9176  0.9821     6185.960
   5_occ:  13.691 0.9176  0.9820     6182.892
   5_bss:  13.688 0.9176  0.9853     6182.095
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7429e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7429e-01
   1_xyz:   1.493  0.012  0.099 15.451  0.007  4.104   1.2187e-01
   1_adp:   1.493  0.012  0.099 15.451  0.007  4.104   1.2187e-01
   1_occ:   1.493  0.012  0.099 15.451  0.007  4.104   1.2187e-01
   2_bss:   1.493  0.012  0.099 15.451  0.007  4.104   1.2187e-01
   2_xyz:   1.063  0.008  0.075 14.395  0.004  4.113   6.8119e-02
   2_adp:   1.063  0.008  0.075 14.395  0.004  4.113   6.8119e-02
   2_occ:   1.063  0.008  0.075 14.395  0.004  4.113   6.8119e-02
   3_bss:   1.063  0.008  0.075 14.395  0.004  4.113   6.8119e-02
   3_xyz:   0.966  0.006  0.069 14.606  0.004  4.108   5.4699e-02
   3_adp:   0.966  0.006  0.069 14.606  0.004  4.108   5.4699e-02
   3_occ:   0.966  0.006  0.069 14.606  0.004  4.108   5.4699e-02
   4_bss:   0.966  0.006  0.069 14.606  0.004  4.108   5.4699e-02
   4_xyz:   1.006  0.007  0.073 14.743  0.004  4.111   6.0383e-02
   4_adp:   1.006  0.007  0.073 14.743  0.004  4.111   6.0383e-02
   4_occ:   1.006  0.007  0.073 14.743  0.004  4.111   6.0383e-02
   5_bss:   1.006  0.007  0.073 14.743  0.004  4.111   6.0383e-02
   5_xyz:   0.863  0.005  0.065 14.376  0.004  4.108   4.7354e-02
   5_adp:   0.863  0.005  0.065 14.376  0.004  4.108   4.7354e-02
   5_occ:   0.863  0.005  0.065 14.376  0.004  4.108   4.7354e-02
   5_bss:   0.863  0.005  0.065 14.376  0.004  4.108   4.7354e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.687   2.3835e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.687   2.3835e-01
   1_xyz:   8.917  0.065  0.341 82.283  0.056  2.080   9.8396e-02
   1_adp:   8.917  0.065  0.341 82.283  0.056  2.080   9.8396e-02
   1_occ:   8.917  0.065  0.341 82.283  0.056  2.080   9.8396e-02
   2_bss:   8.917  0.065  0.341 82.283  0.056  2.080   9.8396e-02
   2_xyz:   6.907  0.042  0.232 81.449  0.034  2.343   1.4155e-01
   2_adp:   6.907  0.042  0.232 81.449  0.034  2.343   1.4155e-01
   2_occ:   6.907  0.042  0.232 81.449  0.034  2.343   1.4155e-01
   3_bss:   6.907  0.042  0.232 81.449  0.034  2.343   1.4155e-01
   3_xyz:   6.576  0.046  0.208 83.342  0.031  2.346   3.7774e-02
   3_adp:   6.576  0.046  0.208 83.342  0.031  2.346   3.7774e-02
   3_occ:   6.576  0.046  0.208 83.342  0.031  2.346   3.7774e-02
   4_bss:   6.576  0.046  0.208 83.342  0.031  2.346   3.7774e-02
   4_xyz:   6.866  0.045  0.235 84.457  0.037  2.290   4.7646e-02
   4_adp:   6.866  0.045  0.235 84.457  0.037  2.290   4.7646e-02
   4_occ:   6.866  0.045  0.235 84.457  0.037  2.290   4.7646e-02
   5_bss:   6.866  0.045  0.235 84.457  0.037  2.290   4.7646e-02
   5_xyz:   6.346  0.042  0.198 84.699  0.036  2.369   3.2634e-02
   5_adp:   6.346  0.042  0.198 84.699  0.036  2.369   3.2634e-02
   5_occ:   6.346  0.042  0.198 84.699  0.036  2.369   3.2634e-02
   5_bss:   6.346  0.042  0.198 84.699  0.036  2.369   3.2634e-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:  92.46   0.00  17.68  76.38   0.00  13.73  92.46   4.93  39.22
   1_occ:  92.46   0.00  17.68  76.38   0.00  13.73  92.46   4.93  39.22
   2_bss:  92.46   0.00  17.68  76.38   0.00  13.73  92.46   4.93  39.22
   2_xyz:  92.46   0.00  17.68  76.38   0.00  13.73  92.46   4.93  39.22
   2_adp:  86.93   1.08  17.01  77.87   1.08  13.14  86.93   6.06  38.10
   2_occ:  86.93   1.08  17.01  77.87   1.08  13.14  86.93   6.06  38.10
   3_bss:  86.93   1.08  17.01  77.87   1.08  13.14  86.93   6.06  38.10
   3_xyz:  86.93   1.08  17.01  77.87   1.08  13.14  86.93   6.06  38.10
   3_adp:  83.96   1.01  16.98  78.86   1.01  12.82  83.96   4.21  39.64
   3_occ:  83.96   1.01  16.98  78.86   1.01  12.82  83.96   4.21  39.64
   4_bss:  83.96   1.01  16.98  78.86   1.01  12.82  83.96   4.21  39.64
   4_xyz:  83.96   1.01  16.98  78.86   1.01  12.82  83.96   4.21  39.64
   4_adp:  83.37   0.73  16.82  81.85   0.73  12.70  83.37   4.03  39.21
   4_occ:  83.37   0.73  16.82  81.85   0.73  12.70  83.37   4.03  39.21
   5_bss:  83.37   0.73  16.82  81.85   0.73  12.70  83.37   4.03  39.21
   5_xyz:  83.37   0.73  16.82  81.85   0.73  12.70  83.37   4.03  39.21
   5_adp:  83.04   0.77  16.69  82.73   0.77  12.60  83.04   5.37  38.97
   5_occ:  83.04   0.77  16.69  82.73   0.77  12.60  83.04   5.37  38.97
   5_bss:  83.01   0.74  16.67  82.71   0.74  12.58  83.01   5.34  38.94
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.643    0.020    0.408
   1_adp:    1.643    0.020    0.408
   1_occ:    1.643    0.020    0.408
   2_bss:    1.643    0.020    0.408
   2_xyz:    1.303    0.039    0.496
   2_adp:    1.303    0.039    0.496
   2_occ:    1.303    0.039    0.496
   3_bss:    1.303    0.039    0.496
   3_xyz:    1.258    0.062    0.593
   3_adp:    1.258    0.062    0.593
   3_occ:    1.258    0.062    0.593
   4_bss:    1.258    0.062    0.593
   4_xyz:    1.256    0.062    0.623
   4_adp:    1.256    0.062    0.623
   4_occ:    1.256    0.062    0.623
   5_bss:    1.256    0.062    0.623
   5_xyz:    1.303    0.094    0.632
   5_adp:    1.303    0.094    0.632
   5_occ:    1.303    0.094    0.632
   5_bss:    1.303    0.094    0.632
------------------------------------------------------------------------

CPU time actual refinement: 345.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_379/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_379/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_379/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_379/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_379/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.87 
  Macro-tasks:
    bulk solvent and scale       = 39.28  
    individual site refinement   = 147.97 
    weights calculation          = 30.09  
    collect and process          = 6.64   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 224.11 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 109.93 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 121.07 
    fmodel                         = 6.69   
    r_factors                      = 0.18   
    phase_errors                   = 10.54  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 260.09 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.757 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    678 calls, 109.57 s
gradients_fft:          623 calls, 106.45 s

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

# Date 2008-01-16 Time 04:41:58 PST -0800 (1200487318.64 s)
Start R-work = 0.3983, R-free = 0.3882 (no bulk solvent and anisotropic scale)
Final R-work = 0.1371, R-free = 0.1761 (no bulk solvent and anisotropic scale)

Start R-work = 0.3845, R-free = 0.3757
Final R-work = 0.1123, R-free = 0.1566