# Date 2008-01-16 Time 06:05:33 PST -0800 (1200492333.34 s)
#phil __OFF__

Command line arguments: "../1004.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26262
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1004

-------------------------------------------------------------------------------
  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: (71.3037, 46.4607, 85.5261, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98037
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959822

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9804

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: (71.3037, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98037
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959822

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2382 [2132/2157]  1922   210   9.8%
  bin  2:  4.2382 -  3.3763 [2059/2079]  1852   207  10.1%
  bin  3:  3.3763 -  2.9531 [2021/2040]  1816   205  10.1%
  bin  4:  2.9531 -  2.6848 [2007/2037]  1808   199   9.9%
  bin  5:  2.6848 -  2.4932 [2007/2026]  1812   195   9.7%
  bin  6:  2.4932 -  2.3468 [1987/2012]  1779   208  10.5%
  bin  7:  2.3468 -  2.2297 [1973/2001]  1775   198  10.0%
  bin  8:  2.2297 -  2.1329 [1968/2004]  1773   195   9.9%
  bin  9:  2.1329 -  2.0510 [1961/2003]  1767   194   9.9%
  bin 10:  2.0510 -  1.9804 [1474/1988]  1326   148  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1004/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:
        1.81 -     2.42: 22
        2.42 -     3.04: 2202
        3.04 -     3.66: 4712
        3.66 -     4.28: 9085
        4.28 -     4.90: 12330
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.068 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.102 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.183 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28346 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_1004/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1004/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.4607 85.5261 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: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3670   r_free= 0.3671   ksol= 0.00   Bsol= 0.00   scale= 0.956    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.125291                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7273 0.99   1390  155 0.3049 0.3031      6.3922      6.3505|
|  2:  4.7273 -  3.7714 0.99   1335  146 0.2934 0.2812      6.5435       6.501|
|  3:  3.7714 -  3.3004 0.99   1312  144 0.3183 0.2831      6.4189      6.4957|
|  4:  3.3004 -  3.0012 0.99   1300  153 0.3372 0.3826      6.3249      6.3325|
|  5:  3.0012 -  2.7875 0.99   1295  140 0.3821 0.3916      6.1975      6.2195|
|  6:  2.7875 -  2.6241 0.99   1288  140 0.3823 0.4057      6.1217      6.1144|
|  7:  2.6241 -  2.4932 0.99   1290  138 0.3982 0.3703      6.1078      6.1107|
|  8:  2.4932 -  2.3851 0.98   1256  150 0.4145 0.3874      6.0529       6.002|
|  9:  2.3851 -  2.2937 0.98   1273  144 0.4015 0.3884      5.9915      5.9897|
| 10:  2.2937 -  2.2148 1.00   1276  139 0.4125 0.4607      5.9843      6.0216|
| 11:  2.2148 -  2.1457 0.98   1273  136 0.4352 0.4122      5.9572      5.9566|
| 12:  2.1457 -  2.0845 0.98   1254  141 0.4354 0.4630       5.896      5.9583|
| 13:  2.0845 -  2.0298 1.00   1257  138 0.4299 0.4203      5.8004      5.7231|
| 14:  2.0298 -  1.9804 0.64    831   95 0.4498 0.4436      5.7776      5.7353|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7273  1390   155  0.78  26.83   0.86     0.81      45448.24|
|  2:  4.7273 -  3.7714  1335   146  0.82  24.53   0.96     0.90      55876.27|
|  3:  3.7714 -  3.3004  1312   144  0.76  30.19   0.99     0.92      59327.61|
|  4:  3.3004 -  3.0012  1300   153  0.71  34.62   0.98     0.89      55778.52|
|  5:  3.0012 -  2.7875  1295   140  0.63  40.94   0.95     0.83      47678.29|
|  6:  2.7875 -  2.6241  1288   140  0.64  41.05   0.98     0.84      41398.21|
|  7:  2.6241 -  2.4932  1290   138  0.64  40.44   0.98     0.84      36112.38|
|  8:  2.4932 -  2.3851  1256   150  0.63  41.55   0.97     0.86      32786.00|
|  9:  2.3851 -  2.2937  1273   144  0.63  41.59   1.00     0.84      30615.49|
| 10:  2.2937 -  2.2148  1276   139  0.60  43.96   1.02     0.84      30798.22|
| 11:  2.2148 -  2.1457  1273   136  0.58  46.18   1.02     0.82      30121.37|
| 12:  2.1457 -  2.0845  1254   141  0.57  46.77   1.00     0.81      27804.61|
| 13:  2.0845 -  2.0298  1257   138  0.55  48.17   1.00     0.80      23848.80|
| 14:  2.0298 -  1.9804   831    95  0.57  47.00   1.00     0.79      19999.08|
|alpha:            min =        0.79 max =            0.92 mean =         0.84|
|beta:             min =    19999.08 max =        59327.61 mean =     39082.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.65|
|phase err.(work): min =        0.00 max =           89.98 mean =        39.19|
|phase err.(test): min =        0.00 max =           89.78 mean =        39.34|
|-----------------------------------------------------------------------------|

============================== 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 = 7.407394              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.197   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.025274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.196   (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 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      205 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1997 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1866 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2846 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4669 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4416 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5625 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6705 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.184 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    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: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3670   r_free= 0.3671   ksol= 0.00   Bsol= 0.00   scale= 0.956    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.125291                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3563   r_free= 0.3575   ksol= 0.32   Bsol= 36.28   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.11,-0.47,-0.68,-0.00,-0.00,-0.00); trace/3= -0.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.112321                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.408106              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.446   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.498151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.993   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3563      final r-factor (work) = 0.1875          |
| start r-factor (free) = 0.3575      final r-factor (free) = 0.2130          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7513 = 6.41 * 0.50 * 6.1137 + 1.00 * 0.1626                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7758 = 6.41 * 0.50 * 5.8376 + 1.00 * 0.0718                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1875      final r-factor (work) = 0.1748          |
| start r-factor (free) = 0.2130      final r-factor (free) = 0.2189          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9143 = 0.50 * 1.00 * 5.8376 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7706 = 0.50 * 1.00 * 5.4975 + 1.00 * 0.0320                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.36   16.59    None  None   None       |
|    all(noH): 2823   0      0.00    62.36   16.59    None  None   None       |
|    Sol.    : 438    0      6.03    62.36   37.89    None  None   None       |
|    Mac.    : 2385   0      0.00    55.26   12.68    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 -   6.237:  240   |   5:    31.182 -  37.419:  100        |
|      1:     6.237 -  12.473: 1183   |   6:    37.419 -  43.655:  106        |
|      2:    12.473 -  18.710:  707   |   7:    43.655 -  49.892:   69        |
|      3:    18.710 -  24.946:  213   |   8:    49.892 -  56.128:   57        |
|      4:    24.946 -  31.182:  116   |   9:    56.128 -  62.365:   32        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1748 r_free = 0.2189             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1743 r_free = 0.2190             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1743   r_free= 0.2190   ksol= 0.32   Bsol= 36.28   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.11,-0.47,-0.68,-0.00,-0.00,-0.00); trace/3= -0.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.508519                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1728   r_free= 0.2164   ksol= 0.33   Bsol= 52.50   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.51,-1.82,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.506611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.970109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.005   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297416              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.266   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1728      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.2164      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5169 = 1.97 * 0.50 * 5.5277 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3716 = 1.97 * 0.50 * 5.4023 + 1.00 * 0.0500                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1356      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1768      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7442 = 0.30 * 1.00 * 5.4023 + 1.00 * 0.1375                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5720 = 0.30 * 1.00 * 5.2582 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.44    71.02   17.09    None  None   None       |
|    all(noH): 2823   0      1.44    71.02   17.09    None  None   None       |
|    Sol.    : 438    0      6.17    71.02   39.45    None  None   None       |
|    Mac.    : 2385   0      1.44    69.10   12.99    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:     1.444 -   8.402:  588   |   5:    36.234 -  43.192:   95        |
|      1:     8.402 -  15.360: 1285   |   6:    43.192 -  50.150:   99        |
|      2:    15.360 -  22.318:  381   |   7:    50.150 -  57.108:   74        |
|      3:    22.318 -  29.276:  143   |   8:    57.108 -  64.066:   43        |
|      4:    29.276 -  36.234:  100   |   9:    64.066 -  71.024:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1687             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1270 r_free = 0.1688             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1688   ksol= 0.33   Bsol= 52.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.51,-1.82,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.233710                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1685   ksol= 0.33   Bsol= 52.50   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.68,-1.73,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.233239                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.683691              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.239  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.194993              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.077  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1271      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4763 = 1.68 * 0.50 * 5.2578 + 1.00 * 0.0500                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4238 = 1.68 * 0.50 * 5.1930 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2136 = 1.19 * 1.00 * 5.1930 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1647 = 1.19 * 1.00 * 5.1507 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.21    87.53   17.43    None  None   None       |
|    all(noH): 2823   0      0.21    87.53   17.43    None  None   None       |
|    Sol.    : 438    0      4.01    85.23   41.02    None  None   None       |
|    Mac.    : 2385   0      0.21    87.53   13.09    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:     0.208 -   8.940:  750   |   5:    43.867 -  52.599:  108        |
|      1:     8.940 -  17.672: 1301   |   6:    52.599 -  61.331:   71        |
|      2:    17.672 -  26.404:  293   |   7:    61.331 -  70.063:   35        |
|      3:    26.404 -  35.135:  126   |   8:    70.063 -  78.795:   18        |
|      4:    35.135 -  43.867:  111   |   9:    78.795 -  87.526:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1578             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1578             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1578   ksol= 0.33   Bsol= 52.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.68,-1.73,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1577   ksol= 0.32   Bsol= 52.50   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.63,-1.66,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.980758              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.449  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.516694              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.480  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1529 = 1.98 * 0.50 * 5.1503 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1406 = 1.98 * 0.50 * 5.1345 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6626 = 0.52 * 1.00 * 5.1345 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6599 = 0.52 * 1.00 * 5.1301 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    91.33   17.14    None  None   None       |
|    all(noH): 2823   0      0.66    91.33   17.14    None  None   None       |
|    Sol.    : 438    0      5.00    85.70   40.04    None  None   None       |
|    Mac.    : 2385   0      0.66    91.33   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.661 -   9.728:  976   |   5:    45.995 -  55.061:   97        |
|      1:     9.728 -  18.795: 1154   |   6:    55.061 -  64.128:   56        |
|      2:    18.795 -  27.861:  238   |   7:    64.128 -  73.195:   21        |
|      3:    27.861 -  36.928:  143   |   8:    73.195 -  82.262:   10        |
|      4:    36.928 -  45.995:  120   |   9:    82.262 -  91.328:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1568             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1568             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1568   ksol= 0.32   Bsol= 52.50   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.63,-1.66,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.129944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1568   ksol= 0.32   Bsol= 52.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.49,-1.47,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130026                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.340224              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.017  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205554              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4935 = 1.34 * 0.50 * 5.1306 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4901 = 1.34 * 0.50 * 5.1375 + 1.00 * 0.0475                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0652 = 0.21 * 1.00 * 5.1375 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0653 = 0.21 * 1.00 * 5.1448 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    89.11   16.64    None  None   None       |
|    all(noH): 2823   0      1.53    89.11   16.64    None  None   None       |
|    Sol.    : 438    0      6.37    82.87   38.06    None  None   None       |
|    Mac.    : 2385   0      1.53    89.11   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.527 -  10.285: 1129   |   5:    45.318 -  54.076:   93        |
|      1:    10.285 -  19.043: 1037   |   6:    54.076 -  62.834:   48        |
|      2:    19.043 -  27.801:  220   |   7:    62.834 -  71.592:   15        |
|      3:    27.801 -  36.560:  137   |   8:    71.592 -  80.350:    8        |
|      4:    36.560 -  45.318:  129   |   9:    80.350 -  89.108:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1566             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1566             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1566   ksol= 0.32   Bsol= 52.50   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.49,-1.47,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142464                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7273 0.99   1390  155 0.1001 0.1295      5.3877      5.5249|
|  2:  4.7273 -  3.7714 0.99   1335  146 0.0881 0.1103      5.4507      5.6289|
|  3:  3.7714 -  3.3004 0.99   1312  144 0.1060 0.1514      5.4745      5.8498|
|  4:  3.3004 -  3.0012 0.99   1300  153 0.1204 0.1579      5.4628       5.588|
|  5:  3.0012 -  2.7875 0.99   1295  140 0.1351 0.1828      5.3298      5.5684|
|  6:  2.7875 -  2.6241 0.99   1288  140 0.1200 0.1669      5.2039      5.4105|
|  7:  2.6241 -  2.4932 0.99   1290  138 0.1256 0.1561      5.1684      5.3503|
|  8:  2.4932 -  2.3851 0.98   1256  150 0.1161 0.1798      5.0281      5.3698|
|  9:  2.3851 -  2.2937 0.98   1273  144 0.1148 0.1634      5.0129      5.2791|
| 10:  2.2937 -  2.2148 1.00   1276  139 0.1118 0.1777       4.939      5.2472|
| 11:  2.2148 -  2.1457 0.98   1273  136 0.1152 0.1749      4.9629       5.274|
| 12:  2.1457 -  2.0845 0.98   1254  141 0.1113 0.1591      4.8759      5.1098|
| 13:  2.0845 -  2.0298 1.00   1257  138 0.1171 0.1822      4.7936      5.1068|
| 14:  2.0298 -  1.9804 0.64    831   95 0.1069 0.1608      4.6731      4.8886|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7273  1390   155  0.94   8.87   0.98     0.95       6915.44|
|  2:  4.7273 -  3.7714  1335   146  0.95   8.00   1.01     1.00       8985.20|
|  3:  3.7714 -  3.3004  1312   144  0.94  11.17   1.02     1.02      10266.74|
|  4:  3.3004 -  3.0012  1300   153  0.92  13.44   1.00     0.98      10307.35|
|  5:  3.0012 -  2.7875  1295   140  0.90  16.06   0.99     0.97       8283.73|
|  6:  2.7875 -  2.6241  1288   140  0.91  15.41   0.99     0.96       6927.55|
|  7:  2.6241 -  2.4932  1290   138  0.91  15.35   0.99     0.97       6189.23|
|  8:  2.4932 -  2.3851  1256   150  0.91  14.62   0.98     0.96       4724.01|
|  9:  2.3851 -  2.2937  1273   144  0.92  14.43   1.00     0.97       4658.59|
| 10:  2.2937 -  2.2148  1276   139  0.91  14.96   1.00     0.97       4114.04|
| 11:  2.2148 -  2.1457  1273   136  0.90  16.10   0.99     0.94       4425.54|
| 12:  2.1457 -  2.0845  1254   141  0.91  14.91   1.01     1.00       3936.06|
| 13:  2.0845 -  2.0298  1257   138  0.90  16.16   0.99     0.98       3328.09|
| 14:  2.0298 -  1.9804   831    95  0.92  14.40   0.98     0.94       2537.53|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2537.53 max =        10307.35 mean =      6244.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.63 mean =        13.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1566   ksol= 0.32   Bsol= 52.44   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.37,-1.33,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1566   ksol= 0.32   Bsol= 52.44   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.37,-1.33,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142518                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7273 0.99   1390  155 0.1001 0.1295      5.3882      5.5254|
|  2:  4.7273 -  3.7714 0.99   1335  146 0.0881 0.1103      5.4507      5.6287|
|  3:  3.7714 -  3.3004 0.99   1312  144 0.1060 0.1514      5.4744      5.8497|
|  4:  3.3004 -  3.0012 0.99   1300  153 0.1204 0.1579      5.4628       5.588|
|  5:  3.0012 -  2.7875 0.99   1295  140 0.1351 0.1828      5.3299      5.5685|
|  6:  2.7875 -  2.6241 0.99   1288  140 0.1200 0.1668      5.2039      5.4102|
|  7:  2.6241 -  2.4932 0.99   1290  138 0.1256 0.1560      5.1682        5.35|
|  8:  2.4932 -  2.3851 0.98   1256  150 0.1161 0.1798       5.028        5.37|
|  9:  2.3851 -  2.2937 0.98   1273  144 0.1148 0.1634       5.013      5.2789|
| 10:  2.2937 -  2.2148 1.00   1276  139 0.1118 0.1777       4.939      5.2473|
| 11:  2.2148 -  2.1457 0.98   1273  136 0.1152 0.1750      4.9631      5.2743|
| 12:  2.1457 -  2.0845 0.98   1254  141 0.1114 0.1592      4.8762        5.11|
| 13:  2.0845 -  2.0298 1.00   1257  138 0.1171 0.1823      4.7936       5.107|
| 14:  2.0298 -  1.9804 0.64    831   95 0.1070 0.1608      4.6731      4.8884|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7273  1390   155  0.94   8.88   0.98     0.95       6922.81|
|  2:  4.7273 -  3.7714  1335   146  0.95   8.00   1.01     1.00       8987.51|
|  3:  3.7714 -  3.3004  1312   144  0.94  11.16   1.02     1.02      10263.04|
|  4:  3.3004 -  3.0012  1300   153  0.92  13.44   1.00     0.98      10308.37|
|  5:  3.0012 -  2.7875  1295   140  0.90  16.06   0.99     0.97       8282.82|
|  6:  2.7875 -  2.6241  1288   140  0.91  15.41   0.99     0.96       6926.60|
|  7:  2.6241 -  2.4932  1290   138  0.91  15.35   1.00     0.97       6187.36|
|  8:  2.4932 -  2.3851  1256   150  0.91  14.62   0.99     0.96       4722.89|
|  9:  2.3851 -  2.2937  1273   144  0.92  14.43   1.00     0.98       4657.46|
| 10:  2.2937 -  2.2148  1276   139  0.91  14.96   1.00     0.97       4113.79|
| 11:  2.2148 -  2.1457  1273   136  0.90  16.11   0.99     0.94       4426.52|
| 12:  2.1457 -  2.0845  1254   141  0.91  14.92   1.01     1.00       3938.57|
| 13:  2.0845 -  2.0298  1257   138  0.90  16.16   1.00     0.99       3328.80|
| 14:  2.0298 -  1.9804   831    95  0.92  14.41   0.98     0.94       2537.49|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2537.49 max =        10308.37 mean =      6244.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.65 mean =        13.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    89.05   16.59    None  None   None       |
|    all(noH): 2823   0      1.47    89.05   16.59    None  None   None       |
|    Sol.    : 438    0      6.31    82.82   38.01    None  None   None       |
|    Mac.    : 2385   0      1.47    89.05   12.65    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:     1.473 -  10.231: 1129   |   5:    45.263 -  54.021:   93        |
|      1:    10.231 -  18.989: 1037   |   6:    54.021 -  62.780:   48        |
|      2:    18.989 -  27.747:  220   |   7:    62.780 -  71.538:   15        |
|      3:    27.747 -  36.505:  137   |   8:    71.538 -  80.296:    8        |
|      4:    36.505 -  45.263:  129   |   9:    80.296 -  89.054:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.673 - 4.544
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 313
   mapped sites are within: 0.723 - 4.544

peak=    5.781 closest distance to " CG  PRO A  54 " =    1.333
peak=    5.512 closest distance to " NE2 GLN A  11 " =    1.205
peak=    5.439 closest distance to " CG  PRO A 213 " =    1.259
peak=    5.346 closest distance to " O   HOH Z 126 " =    1.976
peak=    5.273 closest distance to " CB  GLN A 223 " =    1.413
peak=    5.259 closest distance to " NH2 ARG A  56 " =    2.149
peak=    5.135 closest distance to " CB  SER A  63 " =    1.263
peak=    5.108 closest distance to " CG  PRO A  90 " =    1.110
peak=    5.046 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.020 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.985 closest distance to " O   HOH Z 232 " =    2.270
peak=    4.755 closest distance to " CB  GLU A 128 " =    1.035
peak=    4.739 closest distance to " O   HOH Z 144 " =    1.781
peak=    4.739 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.679 closest distance to " C   PRO A 198 " =    1.519
peak=    4.671 closest distance to " O   HOH Z  78 " =    1.928
peak=    4.604 closest distance to " CB  LEU A 228 " =    1.075
peak=    4.584 closest distance to " ND2 ASN A 187 " =    1.523
peak=    4.543 closest distance to " CB  GLN A 183 " =    1.190
peak=    4.482 closest distance to " CG2 VAL A 257 " =    1.018
peak=    4.475 closest distance to " CG  PRO A 280 " =    0.829
peak=    4.457 closest distance to " CB  ASN A 187 " =    1.351
peak=    4.443 closest distance to " O   HOH Z 236 " =    2.003
peak=    4.419 closest distance to " CG  PRO A 243 " =    1.075
peak=    4.409 closest distance to " CB  ASN A 148 " =    1.331
peak=    4.374 closest distance to " CB  SER A 216 " =    0.834
peak=    4.361 closest distance to " O   HOH Z 369 " =    2.005
peak=    4.356 closest distance to " CA  TYR A  30 " =    0.964
peak=    4.354 closest distance to " O   HOH Z 298 " =    1.938
peak=    4.312 closest distance to " O   HOH Z 132 " =    2.440
peak=    4.289 closest distance to " O   HOH Z 423 " =    1.539
peak=    4.281 closest distance to " CB  GLU A 152 " =    1.242
peak=    4.274 closest distance to " O   HOH Z 193 " =    1.870
peak=    4.272 closest distance to " O   HOH Z  15 " =    2.297
peak=    4.224 closest distance to " O   HOH Z 234 " =    3.794
peak=    4.178 closest distance to " CB  SER A   3 " =    1.414
peak=    4.168 closest distance to " O   HOH Z 427 " =    2.805
peak=    4.162 closest distance to " OD1 ASN A  69 " =    2.598
peak=    4.159 closest distance to " O   HOH Z 316 " =    3.097
peak=    4.127 closest distance to " CB  TRP A 266 " =    0.952
peak=    4.089 closest distance to " CD  ARG A 159 " =    0.777
peak=    4.081 closest distance to " CA  THR A 264 " =    0.863
peak=    4.075 closest distance to " NH1AARG A 145 " =    1.148
peak=    4.049 closest distance to " CB  ARG A  79 " =    1.334
peak=    4.002 closest distance to " O   HOH Z 193 " =    1.718
peak=    3.960 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.947 closest distance to " CD1 LEU A 300 " =    1.240
peak=    3.941 closest distance to " O   HOH Z 425 " =    1.302
peak=    3.940 closest distance to " O   HOH Z 189 " =    2.331
peak=    3.934 closest distance to " CA  ASN A 215 " =    1.246
peak=    3.929 closest distance to " O   HOH Z   1 " =    1.874
peak=    3.927 closest distance to " O   HOH Z 214 " =    2.012
peak=    3.924 closest distance to " O   HOH Z  21 " =    1.736
peak=    3.919 closest distance to " CD BLYS A 290 " =    1.134
peak=    3.913 closest distance to " O   HOH Z 346 " =    1.636
peak=    3.912 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.902 closest distance to " ND1 HIS A  86 " =    1.724
peak=    3.897 closest distance to " O   HOH Z 217 " =    3.148
peak=    3.888 closest distance to " O   HOH Z   9 " =    2.029
peak=    3.888 closest distance to " O   HOH Z 303 " =    2.216
peak=    3.872 closest distance to " O   HOH Z 437 " =    1.619
peak=    3.869 closest distance to " O   HOH Z  40 " =    1.928
peak=    3.868 closest distance to " O   HOH Z 261 " =    1.854
peak=    3.849 closest distance to " O   HOH Z  10 " =    1.834
peak=    3.826 closest distance to " O   HOH Z 352 " =    1.772
peak=    3.822 closest distance to " O   HOH Z 344 " =    3.157
peak=    3.816 closest distance to " O   HOH Z 368 " =    1.868
peak=    3.790 closest distance to " CG1 ILE A  33 " =    1.284
peak=    3.782 closest distance to " CB  ASN A  39 " =    0.906
peak=    3.778 closest distance to " CG2 THR A 221 " =    1.005
peak=    3.775 closest distance to " CB  VAL A 265 " =    1.278
peak=    3.773 closest distance to " CB  SER A 212 " =    1.130
peak=    3.771 closest distance to " O   HOH Z 219 " =    2.218
peak=    3.758 closest distance to " CZ  PHE A 218 " =    1.031
peak=    3.754 closest distance to " CB  TRP A 179 " =    1.383
peak=    3.752 closest distance to " CB  ASN A 148 " =    1.889
peak=    3.751 closest distance to " O   HOH Z 158 " =    2.905
peak=    3.747 closest distance to " CB  ASP A 124 " =    0.738
peak=    3.745 closest distance to " N   PHE A 130 " =    1.255
peak=    3.745 closest distance to " CD2 LEU A 255 " =    1.596
peak=    3.732 closest distance to " CA  MET A  40 " =    1.109
peak=    3.729 closest distance to " O   HOH Z 389 " =    1.874
peak=    3.724 closest distance to " CB  ARG A 190 " =    1.688
peak=    3.722 closest distance to " CB  MET A  47 " =    1.032
peak=    3.718 closest distance to " CG  LEU A 167 " =    1.190
peak=    3.717 closest distance to " O   HOH Z  61 " =    1.525
peak=    3.717 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.713 closest distance to " CD  ARG A  66 " =    2.243
peak=    3.707 closest distance to " O   HOH Z 133 " =    1.683
peak=    3.706 closest distance to " O   HOH Z 250 " =    1.429
peak=    3.702 closest distance to " OD1BASN A 224 " =    2.304
peak=    3.695 closest distance to " CA  SER A  87 " =    0.973
peak=    3.688 closest distance to " O   HOH Z 411 " =    3.801
peak=    3.687 closest distance to " CB  LEU A 143 " =    1.102
peak=    3.677 closest distance to " O   HOH Z 135 " =    1.717
peak=    3.676 closest distance to " CB  MET A  40 " =    0.767
peak=    3.660 closest distance to " O   HOH Z 419 " =    2.030
peak=    3.657 closest distance to " O   HOH Z 368 " =    3.565
peak=    3.656 closest distance to " O   HOH Z  66 " =    2.196
peak=    3.652 closest distance to " O   HOH Z  61 " =    1.633
peak=    3.652 closest distance to " NH2BARG A 145 " =    2.083
peak=    3.651 closest distance to " N   ARG A 156 " =    1.275
peak=    3.650 closest distance to " O   HOH Z 180 " =    2.092
peak=    3.643 closest distance to " O   HOH Z 213 " =    1.857
peak=    3.638 closest distance to " N   ASN A  39 " =    1.302
peak=    3.632 closest distance to " O   HOH Z 207 " =    1.777
peak=    3.624 closest distance to " O   HOH Z  64 " =    2.221
peak=    3.596 closest distance to " CD  ARG A 219 " =    1.078
peak=    3.595 closest distance to " N   GLN A 278 " =    1.013
peak=    3.590 closest distance to " O   HOH Z  40 " =    2.223
peak=    3.589 closest distance to " O   HOH Z 193 " =    2.004
peak=    3.585 closest distance to " CZ  PHE A 208 " =    1.150
peak=    3.578 closest distance to " NH2 ARG A 156 " =    1.199
peak=    3.577 closest distance to " CB  ALA A 291 " =    1.375
peak=    3.572 closest distance to " CD  ARG A 269 " =    0.930
peak=    3.567 closest distance to " O   HOH Z 272 " =    1.847
peak=    3.563 closest distance to " CB  VAL A 202 " =    1.651
peak=    3.563 closest distance to " O   HOH Z   1 " =    1.806
peak=    3.562 closest distance to " CB  ASN A 142 " =    0.947
peak=    3.556 closest distance to " CZ  PHE A 192 " =    0.862
peak=    3.550 closest distance to " O   HOH Z 426 " =    1.747
peak=    3.549 closest distance to " O   HOH Z 371 " =    1.758
peak=    3.532 closest distance to " CG  ARG A 159 " =    0.909
peak=    3.511 closest distance to " CG  MET A 113 " =    1.229
peak=    3.510 closest distance to " O   HOH Z 133 " =    2.498
peak=    3.502 closest distance to " CB  ILE A 234 " =    0.984
peak=    3.501 closest distance to " CB  THR A 157 " =    1.113
peak=    3.499 closest distance to " O   MET A 105 " =    1.771
peak=    3.496 closest distance to " O   SER A  87 " =    2.268
peak=    3.491 closest distance to " O   HOH Z  59 " =    1.785
peak=    3.488 closest distance to " OG  SER A 206 " =    1.304
peak=    3.486 closest distance to " O   HOH Z 423 " =    2.542
peak=    3.484 closest distance to " O   HOH Z 409 " =    2.632
peak=    3.481 closest distance to " CB  ALA A  34 " =    1.115
peak=    3.477 closest distance to " O   HOH Z 407 " =    2.247
peak=    3.476 closest distance to " O   HOH Z 386 " =    3.103
peak=    3.472 closest distance to " O   HOH Z 236 " =    1.549
peak=    3.466 closest distance to " CD  LYS A 166 " =    1.266
peak=    3.464 closest distance to " CB  ALA A 248 " =    0.948
peak=    3.464 closest distance to " O   HOH Z  58 " =    1.578
peak=    3.463 closest distance to " CB  ASP A 171 " =    0.783
peak=    3.460 closest distance to " CA  ALA A 154 " =    0.993
peak=    3.458 closest distance to " O   HOH Z 128 " =    2.174
peak=    3.458 closest distance to " CA  THR A 221 " =    0.947
peak=    3.457 closest distance to " CA  ALA A  51 " =    0.940
peak=    3.453 closest distance to " O   HOH Z 261 " =    2.121
peak=    3.452 closest distance to " O   HOH Z 327 " =    1.755
peak=    3.449 closest distance to " CZ3 TRP A 123 " =    1.263
peak=    3.448 closest distance to " O   HOH Z  88 " =    3.403
peak=    3.441 closest distance to " CA  LYS A 290 " =    1.306
peak=    3.441 closest distance to " O   HOH Z 265 " =    2.320
peak=    3.438 closest distance to " CB  ALA A   1 " =    4.544
peak=    3.437 closest distance to " O   HOH Z 425 " =    2.029
peak=    3.433 closest distance to " O   HOH Z 271 " =    2.300
peak=    3.431 closest distance to " O   TYR A 116 " =    1.336
peak=    3.425 closest distance to " CB  GLU A 236 " =    1.214
peak=    3.424 closest distance to " O   HOH Z 234 " =    1.742
peak=    3.415 closest distance to " O   THR A 251 " =    1.146
peak=    3.415 closest distance to " O   HOH Z 402 " =    1.445
peak=    3.411 closest distance to " CD2 TRP A 179 " =    1.316
peak=    3.409 closest distance to " CA  ALA A 233 " =    1.273
peak=    3.398 closest distance to " CB  SER A  62 " =    1.255
peak=    3.397 closest distance to " OG  SER A  22 " =    2.774
peak=    3.396 closest distance to " CB  TYR A 116 " =    0.882
peak=    3.395 closest distance to " O  BHOH Z  74 " =    1.320
peak=    3.391 closest distance to " N   ASN A 127 " =    1.272
peak=    3.384 closest distance to " CB  PRO A 198 " =    0.877
peak=    3.384 closest distance to " O   HOH Z  44 " =    3.129
peak=    3.384 closest distance to " CA  ARG A 195 " =    1.278
peak=    3.383 closest distance to " CB  ARG A 139 " =    0.947
peak=    3.383 closest distance to " OG  SER A  97 " =    3.498
peak=    3.379 closest distance to " O   HOH Z 280 " =    3.084
peak=    3.378 closest distance to " O   THR A 220 " =    1.386
peak=    3.374 closest distance to " CB  SER A 210 " =    0.748
peak=    3.374 closest distance to " NH2AARG A 190 " =    1.699
peak=    3.371 closest distance to " CG1 VAL A 153 " =    0.948
peak=    3.369 closest distance to " O   HOH Z 209 " =    2.297
peak=    3.361 closest distance to " CB  PHE A  16 " =    1.003
peak=    3.361 closest distance to " CG1 ILE A 151 " =    1.015
peak=    3.360 closest distance to " CB  ASP A 132 " =    3.955
peak=    3.360 closest distance to " CA  ILE A 234 " =    0.987
peak=    3.356 closest distance to " O   HOH Z 371 " =    2.850
peak=    3.354 closest distance to " O   HOH Z 353 " =    2.685
peak=    3.351 closest distance to " O   GLY A  57 " =    2.585
peak=    3.350 closest distance to " O   HOH Z 227 " =    1.638
peak=    3.350 closest distance to " O   HOH Z 403 " =    1.653
peak=    3.347 closest distance to " NH1 ARG A  14 " =    1.034
peak=    3.345 closest distance to " O   HOH Z  97 " =    1.954
peak=    3.344 closest distance to " NE2 GLN A  73 " =    3.735
peak=    3.338 closest distance to " CG1 VAL A 189 " =    2.003
peak=    3.337 closest distance to " CB  ILE A 120 " =    1.175
peak=    3.336 closest distance to " CB  ASP A 140 " =    0.801
peak=    3.336 closest distance to " O   HOH Z 291 " =    1.933
peak=    3.335 closest distance to " O   HOH Z 295 " =    1.516
peak=    3.334 closest distance to " CA  GLN A 223 " =    0.974
peak=    3.333 closest distance to " O   HOH Z  44 " =    1.617
peak=    3.332 closest distance to " CD1 ILE A 106 " =    0.796
peak=    3.328 closest distance to " O   HOH Z 147 " =    1.727
peak=    3.326 closest distance to " CG  GLN A 144 " =    0.957
peak=    3.318 closest distance to " O   HOH Z 134 " =    1.327
peak=    3.317 closest distance to " O   ASN A 209 " =    1.373
peak=    3.313 closest distance to " O   HOH Z 273 " =    2.725
peak=    3.311 closest distance to " CG1BVAL A  72 " =    1.545
peak=    3.301 closest distance to " O   HOH Z 345 " =    3.542
peak=    3.300 closest distance to " CD  PRO A 243 " =    1.693
peak=    3.299 closest distance to " CB  ALA A 248 " =    1.319
peak=    3.298 closest distance to " O   HOH Z 172 " =    3.259
peak=    3.297 closest distance to " CA  ALA A 158 " =    1.153
peak=    3.293 closest distance to " NH2AARG A 190 " =    1.218
peak=    3.291 closest distance to " NZ ALYS A 290 " =    1.132
peak=    3.283 closest distance to " O   HOH Z 302 " =    1.806
peak=    3.283 closest distance to " O   HOH Z 238 " =    3.652
peak=    3.282 closest distance to " CA  ALA A 291 " =    0.980
peak=    3.280 closest distance to " O   HOH Z 227 " =    2.065
peak=    3.280 closest distance to " N   SER A 134 " =    1.332
peak=    3.277 closest distance to " OG BSER A 164 " =    2.411
peak=    3.277 closest distance to " O   HOH Z 211 " =    2.709
peak=    3.271 closest distance to " O   HOH Z 305 " =    3.636
peak=    3.270 closest distance to " CD  GLN A 240 " =    1.640
peak=    3.270 closest distance to " O   HOH Z 154 " =    2.055
peak=    3.269 closest distance to " CB  GLU A 277 " =    3.589
peak=    3.267 closest distance to " O   HOH Z   3 " =    1.844
peak=    3.265 closest distance to " O   HOH Z 359 " =    4.041
peak=    3.263 closest distance to " O   HOH Z 291 " =    1.697
peak=    3.262 closest distance to " CA  ASP A 191 " =    0.723
peak=    3.261 closest distance to " O   HOH Z 286 " =    2.273
peak=    3.256 closest distance to " O   HOH Z 108 " =    2.178
peak=    3.246 closest distance to " O   HOH Z 391 " =    2.966
peak=    3.246 closest distance to " O   HOH Z 285 " =    2.928
peak=    3.244 closest distance to " O   HOH Z 163 " =    1.835
peak=    3.243 closest distance to " NZ  LYS A  76 " =    1.396
peak=    3.242 closest distance to " NE AARG A 275 " =    1.354
peak=    3.242 closest distance to " O   HOH Z 213 " =    1.946
peak=    3.238 closest distance to " O   HOH Z 217 " =    1.492
peak=    3.237 closest distance to " O   HOH Z 109 " =    2.659
peak=    3.237 closest distance to " O   HOH Z 188 " =    2.025
peak=    3.236 closest distance to " O   ALA A 165 " =    1.378
peak=    3.234 closest distance to " OD1 ASP A 238 " =    0.989
peak=    3.233 closest distance to " CA  ARG A 102 " =    1.189
peak=    3.230 closest distance to " CA  GLY A 267 " =    1.230
peak=    3.228 closest distance to " O   HOH Z   1 " =    2.184
peak=    3.227 closest distance to " N   TYR A  15 " =    0.729
peak=    3.227 closest distance to " OD1 ASN A 217 " =    1.579
peak=    3.221 closest distance to " CB  GLU A 152 " =    1.408
peak=    3.221 closest distance to " CG BARG A 275 " =    1.507
peak=    3.221 closest distance to " OG1 THR A 246 " =    3.271
peak=    3.220 closest distance to " CB  LEU A 255 " =    0.781
peak=    3.219 closest distance to " O   HOH Z  43 " =    1.796
peak=    3.219 closest distance to " O   HOH Z 379 " =    3.420
peak=    3.218 closest distance to " O   HOH Z 345 " =    1.632
peak=    3.218 closest distance to " CB  HIS A 108 " =    0.803
peak=    3.212 closest distance to " CG2 ILE A 120 " =    1.177
peak=    3.210 closest distance to " O   HOH Z 435 " =    1.975
peak=    3.208 closest distance to " O   HOH Z  49 " =    2.073
peak=    3.208 closest distance to " O   HOH Z 153 " =    1.682
peak=    3.202 closest distance to " CB  ARG A 145 " =    0.869
peak=    3.200 closest distance to " O   HOH Z 108 " =    1.235
peak=    3.199 closest distance to " CB  ALA A 242 " =    0.863
peak=    3.198 closest distance to " O   HOH Z  88 " =    2.802
peak=    3.195 closest distance to " CB  ALA A 184 " =    0.928
peak=    3.191 closest distance to " O   HOH Z 329 " =    3.664
peak=    3.189 closest distance to " CA  LEU A 282 " =    1.053
peak=    3.186 closest distance to " CD  ARG A  14 " =    1.342
peak=    3.185 closest distance to " CG  GLU A 277 " =    2.210
peak=    3.184 closest distance to " OH  TYR A 186 " =    1.078
peak=    3.180 closest distance to " CA  ARG A  36 " =    1.116
peak=    3.175 closest distance to " O   HOH Z 247 " =    1.294
peak=    3.175 closest distance to " O   HOH Z 263 " =    1.623
peak=    3.169 closest distance to " CE BLYS A 290 " =    1.122
peak=    3.167 closest distance to " CB  ASN A 224 " =    1.066
peak=    3.167 closest distance to " O   HOH Z  64 " =    2.175
peak=    3.164 closest distance to " O   HOH Z 128 " =    2.181
peak=    3.160 closest distance to " O   HOH Z   2 " =    1.551
peak=    3.153 closest distance to " CG  LYS A  76 " =    0.986
peak=    3.151 closest distance to " NH1 ARG A 138 " =    1.088
peak=    3.150 closest distance to " O   HOH Z 130 " =    3.819
peak=    3.148 closest distance to " O   HOH Z 162 " =    2.081
peak=    3.147 closest distance to " NH1BARG A 145 " =    1.098
peak=    3.147 closest distance to " CB  SER A 276 " =    1.207
peak=    3.145 closest distance to " CG  GLN A 278 " =    1.295
peak=    3.142 closest distance to " O   HOH Z 366 " =    2.972
peak=    3.142 closest distance to " O   HOH Z 340 " =    2.233
peak=    3.141 closest distance to " CB  TRP A 179 " =    1.716
peak=    3.141 closest distance to " N   SER A 135 " =    1.286
peak=    3.139 closest distance to " CD  LYS A 119 " =    1.220
peak=    3.136 closest distance to " N   ASN A 252 " =    1.391
peak=    3.135 closest distance to " O   HOH Z 148 " =    3.328
peak=    3.128 closest distance to " O   HOH Z 285 " =    1.741
peak=    3.125 closest distance to " CG  MET A 185 " =    1.018
peak=    3.119 closest distance to " O   HOH Z 411 " =    1.858
peak=    3.117 closest distance to " CB  ARG A 138 " =    1.013
peak=    3.115 closest distance to " ND1 HIS A  81 " =    1.655
peak=    3.114 closest distance to " CB  LYS A 117 " =    1.206
peak=    3.112 closest distance to " O  BHOH Z 338 " =    2.468
peak=    3.105 closest distance to " O   HOH Z 406 " =    1.661
peak=    3.105 closest distance to " O   HOH Z 216 " =    2.641
peak=    3.103 closest distance to " CB  PHE A 283 " =    0.812
peak=    3.093 closest distance to " O   HOH Z 183 " =    1.402
peak=    3.090 closest distance to " CA  ASP A 140 " =    1.200
peak=    3.089 closest distance to " CG BARG A 102 " =    1.839
peak=    3.086 closest distance to " O   THR A 294 " =    1.049
peak=    3.080 closest distance to " CA  ALA A  84 " =    1.408
peak=    3.076 closest distance to " CA  PHE A 283 " =    1.115
peak=    3.070 closest distance to " CB  ALA A 114 " =    0.867
peak=    3.051 closest distance to " O   ALA A 158 " =    1.311
peak=    3.040 closest distance to " CB  TRP A 150 " =    1.451
peak=    3.038 closest distance to " O   HOH Z 171 " =    2.168
peak=    3.036 closest distance to " O   HOH Z 245 " =    1.297
peak=    3.006 closest distance to " O   HOH Z 175 " =    2.111

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.714 - 5.537
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 191
   mapped sites are within: 0.714 - 5.537

peak=   -4.789 closest distance to " CB  PRO A 243 " =    2.587
peak=   -4.696 closest distance to " O   HOH Z 290 " =    1.111
peak=   -4.398 closest distance to " O   HOH Z 377 " =    1.961
peak=   -4.360 closest distance to " CG  GLN A 223 " =    1.767
peak=   -4.345 closest distance to " O   HOH Z 266 " =    4.799
peak=   -4.225 closest distance to " CD  ARG A 156 " =    1.997
peak=   -4.201 closest distance to " O   HOH Z 389 " =    1.909
peak=   -4.083 closest distance to " O   HOH Z 231 " =    2.068
peak=   -4.081 closest distance to " O   PRO A 198 " =    1.256
peak=   -4.058 closest distance to " O   HOH Z 351 " =    1.494
peak=   -4.058 closest distance to " O   HOH Z 435 " =    2.825
peak=   -4.054 closest distance to " CZ3 TRP A 179 " =    1.140
peak=   -4.047 closest distance to " ND2 ASN A  45 " =    1.304
peak=   -4.042 closest distance to " O   VAL A  67 " =    2.602
peak=   -4.032 closest distance to " N   ALA A  43 " =    2.524
peak=   -4.015 closest distance to " CD  ARG A  14 " =    3.390
peak=   -4.013 closest distance to " O   HOH Z 372 " =    2.438
peak=   -3.950 closest distance to " CE2 TYR A  30 " =    2.847
peak=   -3.946 closest distance to " CG  PHE A 283 " =    2.783
peak=   -3.907 closest distance to " CG  MET A 105 " =    0.978
peak=   -3.888 closest distance to " CD1 PHE A  59 " =    1.822
peak=   -3.856 closest distance to " CG BMET A  47 " =    3.007
peak=   -3.816 closest distance to " O   TYR A 247 " =    2.840
peak=   -3.812 closest distance to " C   ALA A 158 " =    1.397
peak=   -3.811 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.794 closest distance to " C   HIS A 108 " =    1.112
peak=   -3.787 closest distance to " O   HOH Z  52 " =    1.197
peak=   -3.784 closest distance to " O   ILE A 109 " =    2.619
peak=   -3.783 closest distance to " O   HOH Z  60 " =    2.564
peak=   -3.779 closest distance to " CG  ASP A 231 " =    0.744
peak=   -3.775 closest distance to " O   HOH Z 126 " =    1.872
peak=   -3.771 closest distance to " O   HOH Z  43 " =    1.576
peak=   -3.749 closest distance to " N   ASP A 286 " =    2.509
peak=   -3.746 closest distance to " O   HOH Z 353 " =    2.123
peak=   -3.736 closest distance to " O   HOH Z 377 " =    0.773
peak=   -3.726 closest distance to " O   HOH Z 198 " =    2.061
peak=   -3.719 closest distance to " O   VAL A 189 " =    2.496
peak=   -3.706 closest distance to " OD1 ASP A 191 " =    1.693
peak=   -3.704 closest distance to " O   HOH Z  38 " =    1.544
peak=   -3.703 closest distance to " CZ  PHE A  59 " =    1.545
peak=   -3.702 closest distance to " CZ  TYR A 169 " =    1.669
peak=   -3.702 closest distance to " O   GLY A 211 " =    1.331
peak=   -3.696 closest distance to " O   HOH Z 313 " =    1.895
peak=   -3.687 closest distance to " CB  CYS A 254 " =    2.152
peak=   -3.679 closest distance to " O   PRO A 163 " =    1.970
peak=   -3.677 closest distance to " CA  GLY A  98 " =    1.943
peak=   -3.669 closest distance to " N   GLN A  58 " =    1.832
peak=   -3.666 closest distance to " CD1 LEU A 228 " =    2.318
peak=   -3.661 closest distance to " CD  ARG A 195 " =    5.140
peak=   -3.649 closest distance to " O   HOH Z 185 " =    2.236
peak=   -3.649 closest distance to " CA  GLY A 203 " =    2.214
peak=   -3.646 closest distance to " O   HOH Z 407 " =    3.240
peak=   -3.644 closest distance to " O   HOH Z 118 " =    3.008
peak=   -3.641 closest distance to " OG BSER A 134 " =    1.203
peak=   -3.635 closest distance to " N   THR A 157 " =    1.539
peak=   -3.630 closest distance to " CB  ASN A  39 " =    2.236
peak=   -3.619 closest distance to " N   SER A 212 " =    1.760
peak=   -3.619 closest distance to " CD1 LEU A 101 " =    2.337
peak=   -3.611 closest distance to " OD1 ASN A 187 " =    1.608
peak=   -3.607 closest distance to " NH2AARG A 275 " =    5.537
peak=   -3.603 closest distance to " CB  ALA A  43 " =    2.511
peak=   -3.583 closest distance to " O   HOH Z 388 " =    2.007
peak=   -3.577 closest distance to " O   HOH Z 211 " =    1.576
peak=   -3.570 closest distance to " CG  ARG A 269 " =    2.595
peak=   -3.562 closest distance to " O   HOH Z  93 " =    2.459
peak=   -3.561 closest distance to " OE1 GLN A  88 " =    1.140
peak=   -3.551 closest distance to " CA  ASP A  27 " =    2.439
peak=   -3.541 closest distance to " C   LEU A 143 " =    1.363
peak=   -3.535 closest distance to " O   ALA A 180 " =    1.251
peak=   -3.527 closest distance to " O   ALA A 161 " =    1.518
peak=   -3.525 closest distance to " CB  PRO A 163 " =    2.593
peak=   -3.518 closest distance to " O   HOH Z 184 " =    1.850
peak=   -3.500 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.493 closest distance to " CE  MET A 105 " =    2.247
peak=   -3.489 closest distance to " NH1 ARG A 195 " =    2.580
peak=   -3.474 closest distance to " CA  GLY A 241 " =    2.256
peak=   -3.474 closest distance to " CG1 VAL A 197 " =    2.243
peak=   -3.472 closest distance to " CE2 PHE A 218 " =    2.481
peak=   -3.463 closest distance to " CG  GLN A  88 " =    0.875
peak=   -3.454 closest distance to " O   HOH Z 282 " =    1.028
peak=   -3.453 closest distance to " CB  PHE A 192 " =    1.921
peak=   -3.427 closest distance to " CD1 ILE A 263 " =    3.015
peak=   -3.420 closest distance to " OD1 ASN A 148 " =    1.655
peak=   -3.418 closest distance to " CZ BARG A 275 " =    1.835
peak=   -3.411 closest distance to " OXT GLY A 302 " =    2.844
peak=   -3.411 closest distance to " CB  TYR A  15 " =    2.117
peak=   -3.409 closest distance to " O   HOH Z 298 " =    1.160
peak=   -3.407 closest distance to " C   LEU A 222 " =    0.714
peak=   -3.405 closest distance to " CB  ALA A 248 " =    2.025
peak=   -3.403 closest distance to " NH2 ARG A 159 " =    2.401
peak=   -3.392 closest distance to " OG BSER A 134 " =    1.652
peak=   -3.390 closest distance to " O   HOH Z  10 " =    1.489
peak=   -3.388 closest distance to " O   HOH Z 222 " =    1.117
peak=   -3.386 closest distance to " CG2 ILE A 263 " =    2.342
peak=   -3.380 closest distance to " NH1AARG A 275 " =    1.822
peak=   -3.380 closest distance to " OG  SER A  87 " =    1.377
peak=   -3.375 closest distance to " ND2 ASN A 249 " =    2.253
peak=   -3.375 closest distance to " CE2 TYR A 116 " =    3.161
peak=   -3.365 closest distance to " O   HOH Z 281 " =    2.696
peak=   -3.360 closest distance to " O   GLY A 196 " =    1.151
peak=   -3.358 closest distance to " O   HOH Z  51 " =    1.135
peak=   -3.356 closest distance to " O   VAL A  67 " =    2.517
peak=   -3.353 closest distance to " SG ACYS A 201 " =    2.031
peak=   -3.336 closest distance to " SD BMET A  47 " =    0.944
peak=   -3.334 closest distance to " O   TRP A  70 " =    1.459
peak=   -3.323 closest distance to " CG  GLU A 152 " =    0.784
peak=   -3.320 closest distance to " OXT GLY A 302 " =    3.393
peak=   -3.319 closest distance to " CD  ARG A 139 " =    1.574
peak=   -3.314 closest distance to " NH2 ARG A  79 " =    1.851
peak=   -3.312 closest distance to " CG1 VAL A 250 " =    2.644
peak=   -3.311 closest distance to " O   GLY A 203 " =    2.410
peak=   -3.310 closest distance to " O   HOH Z 102 " =    1.672
peak=   -3.307 closest distance to " O   HOH Z 417 " =    2.465
peak=   -3.306 closest distance to " O   HOH Z  24 " =    1.451
peak=   -3.304 closest distance to " CG  TRP A 266 " =    1.750
peak=   -3.303 closest distance to " CB  CYS A 201 " =    2.589
peak=   -3.300 closest distance to " CB  TRP A  85 " =    2.369
peak=   -3.298 closest distance to " O   PRO A 198 " =    1.277
peak=   -3.295 closest distance to " O   HOH Z  11 " =    1.888
peak=   -3.294 closest distance to " CB  ALA A   9 " =    2.560
peak=   -3.288 closest distance to " CD2 LEU A 300 " =    2.829
peak=   -3.287 closest distance to " CB  ASP A 132 " =    2.298
peak=   -3.273 closest distance to " O   HOH Z  47 " =    1.597
peak=   -3.268 closest distance to " CD1 TRP A 179 " =    0.888
peak=   -3.265 closest distance to " CD  LYS A 289 " =    2.454
peak=   -3.264 closest distance to " O   HOH Z 198 " =    1.442
peak=   -3.260 closest distance to " O   HOH Z  13 " =    1.429
peak=   -3.260 closest distance to " O   HOH Z  63 " =    1.515
peak=   -3.258 closest distance to " O   HOH Z 426 " =    1.625
peak=   -3.255 closest distance to " O   SER A  22 " =    2.456
peak=   -3.251 closest distance to " OD2 ASP A 200 " =    1.435
peak=   -3.250 closest distance to " CA  GLY A 241 " =    3.019
peak=   -3.243 closest distance to " OD1 ASP A 171 " =    1.579
peak=   -3.240 closest distance to " O   HOH Z 359 " =    3.252
peak=   -3.239 closest distance to " NE2 GLN A  88 " =    1.954
peak=   -3.236 closest distance to " NH2 ARG A  79 " =    1.589
peak=   -3.228 closest distance to " CE  LYS A  76 " =    2.708
peak=   -3.226 closest distance to " CD1 LEU A   5 " =    2.542
peak=   -3.226 closest distance to " O   HOH Z 423 " =    1.203
peak=   -3.224 closest distance to " CD  GLN A  58 " =    1.039
peak=   -3.223 closest distance to " CB  ALA A 248 " =    2.462
peak=   -3.222 closest distance to " O   HOH Z 394 " =    1.430
peak=   -3.220 closest distance to " CE BMET A  47 " =    1.785
peak=   -3.219 closest distance to " O   HOH Z 298 " =    2.512
peak=   -3.217 closest distance to " CD2 TYR A 293 " =    2.037
peak=   -3.217 closest distance to " O   HOH Z 324 " =    2.190
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    1.759
peak=   -3.208 closest distance to " O   SER A  62 " =    2.126
peak=   -3.199 closest distance to " O   HOH Z 111 " =    2.196
peak=   -3.196 closest distance to " O   SER A 135 " =    1.440
peak=   -3.193 closest distance to " CE1 TYR A 169 " =    2.514
peak=   -3.191 closest distance to " O   HOH Z 311 " =    3.585
peak=   -3.191 closest distance to " CD2 PHE A  61 " =    1.947
peak=   -3.189 closest distance to " C   MET A 188 " =    1.485
peak=   -3.186 closest distance to " CZ  ARG A 259 " =    0.876
peak=   -3.184 closest distance to " O   PHE A 218 " =    1.484
peak=   -3.179 closest distance to " O   HOH Z 137 " =    1.593
peak=   -3.178 closest distance to " O   HOH Z  73 " =    2.142
peak=   -3.177 closest distance to " O   HOH Z 176 " =    0.840
peak=   -3.171 closest distance to " O   GLN A 240 " =    2.121
peak=   -3.171 closest distance to " CD1 LEU A 297 " =    2.531
peak=   -3.170 closest distance to " O   HOH Z  98 " =    2.294
peak=   -3.166 closest distance to " OH  TYR A 169 " =    1.007
peak=   -3.165 closest distance to " O   HOH Z 322 " =    1.456
peak=   -3.161 closest distance to " NE  ARG A  36 " =    1.959
peak=   -3.160 closest distance to " O   HOH Z 191 " =    5.505
peak=   -3.159 closest distance to " O   HOH Z 417 " =    2.630
peak=   -3.158 closest distance to " O   HOH Z 241 " =    1.279
peak=   -3.153 closest distance to " CG1 VAL A 112 " =    2.613
peak=   -3.149 closest distance to " OG  SER A  62 " =    1.592
peak=   -3.147 closest distance to " CD1 ILE A 239 " =    2.005
peak=   -3.147 closest distance to " O   HOH Z  28 " =    2.133
peak=   -3.146 closest distance to " O   HOH Z 309 " =    2.427
peak=   -3.146 closest distance to " CG  LEU A  83 " =    1.813
peak=   -3.135 closest distance to " CG  GLU A 277 " =    1.151
peak=   -3.133 closest distance to " OD1 ASN A 301 " =    1.848
peak=   -3.132 closest distance to " CB  ASP A 286 " =    2.062
peak=   -3.130 closest distance to " CE3 TRP A 150 " =    2.075
peak=   -3.129 closest distance to " N   GLN A 122 " =    1.503
peak=   -3.120 closest distance to " CE3 TRP A 123 " =    1.325
peak=   -3.114 closest distance to " N   THR A 235 " =    1.276
peak=   -3.100 closest distance to " O   HOH Z 207 " =    2.164
peak=   -3.097 closest distance to " CE3 TRP A 274 " =    2.430
peak=   -3.090 closest distance to " N   ALA A 226 " =    2.162
peak=   -3.089 closest distance to " O   HOH Z 252 " =    4.281
peak=   -3.075 closest distance to " O   HOH Z 390 " =    2.414
peak=   -3.068 closest distance to " CD1 ILE A 239 " =    2.410
peak=   -3.067 closest distance to " OG1 THR A 246 " =    1.442
peak=   -3.038 closest distance to " O   HOH Z 263 " =    5.141
peak=   -3.019 closest distance to " O   HOH Z 171 " =    1.584

================= 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    :  0.3670 0.3671   6.125291e+00   6.121712e+00
   1_bss:  0.3563 0.3575   6.112321e+00   6.101681e+00
   1_xyz:  0.1875 0.2130   5.552689e+00   5.661591e+00
   1_adp:  0.1748 0.2189   5.510392e+00   5.692442e+00
   1_occ:  0.1743 0.2190   5.508519e+00   5.691446e+00
   2_bss:  0.1728 0.2164   5.506611e+00   5.687690e+00
   2_xyz:  0.1356 0.1768   5.289526e+00   5.499863e+00
   2_adp:  0.1271 0.1687   5.233854e+00   5.455315e+00
   2_occ:  0.1270 0.1688   5.233710e+00   5.455700e+00
   3_bss:  0.1271 0.1685   5.233239e+00   5.454713e+00
   3_xyz:  0.1163 0.1580   5.161871e+00   5.393972e+00
   3_adp:  0.1138 0.1578   5.149261e+00   5.389195e+00
   3_occ:  0.1137 0.1578   5.149329e+00   5.389586e+00
   4_bss:  0.1137 0.1577   5.148873e+00   5.389336e+00
   4_xyz:  0.1100 0.1574   5.131685e+00   5.384568e+00
   4_adp:  0.1097 0.1568   5.129856e+00   5.383050e+00
   4_occ:  0.1096 0.1568   5.129944e+00   5.383434e+00
   5_bss:  0.1096 0.1568   5.130026e+00   5.383467e+00
   5_xyz:  0.1113 0.1576   5.141164e+00   5.389544e+00
   5_adp:  0.1122 0.1566   5.142451e+00   5.386610e+00
   5_occ:  0.1121 0.1566   5.142464e+00   5.386847e+00
   5_bss:  0.1121 0.1566   5.142518e+00   5.386860e+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:  0.322  36.279  -0.112  -0.466  -0.677  -0.000  -0.000  -0.000
   1_xyz:  0.322  36.279  -0.112  -0.466  -0.677  -0.000  -0.000  -0.000
   1_adp:  0.322  36.279  -0.112  -0.466  -0.677  -0.000  -0.000  -0.000
   1_occ:  0.322  36.279  -0.112  -0.466  -0.677  -0.000  -0.000  -0.000
   2_bss:  0.335  52.496  -1.955  -2.514  -1.818  -0.000  -0.000  -0.000
   2_xyz:  0.335  52.496  -1.955  -2.514  -1.818  -0.000  -0.000  -0.000
   2_adp:  0.335  52.496  -1.955  -2.514  -1.818  -0.000  -0.000  -0.000
   2_occ:  0.335  52.496  -1.955  -2.514  -1.818  -0.000  -0.000  -0.000
   3_bss:  0.335  52.496  -2.235  -2.681  -1.733  -0.000  -0.000  -0.000
   3_xyz:  0.335  52.496  -2.235  -2.681  -1.733  -0.000  -0.000  -0.000
   3_adp:  0.335  52.496  -2.235  -2.681  -1.733  -0.000  -0.000  -0.000
   3_occ:  0.335  52.496  -2.235  -2.681  -1.733  -0.000  -0.000  -0.000
   4_bss:  0.324  52.496  -2.196  -2.626  -1.659  -0.000  -0.000  -0.000
   4_xyz:  0.324  52.496  -2.196  -2.626  -1.659  -0.000  -0.000  -0.000
   4_adp:  0.324  52.496  -2.196  -2.626  -1.659  -0.000  -0.000  -0.000
   4_occ:  0.324  52.496  -2.196  -2.626  -1.659  -0.000  -0.000  -0.000
   5_bss:  0.324  52.496  -2.059  -2.488  -1.475  -0.000  -0.000  -0.000
   5_xyz:  0.324  52.496  -2.059  -2.488  -1.475  -0.000  -0.000  -0.000
   5_adp:  0.324  52.496  -2.059  -2.488  -1.475  -0.000  -0.000  -0.000
   5_occ:  0.324  52.496  -2.059  -2.488  -1.475  -0.000  -0.000  -0.000
   5_bss:  0.325  52.441  -1.964  -2.369  -1.333  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  39.209 0.6546  0.8431    39081.952
   1_bss:  38.118 0.6656  0.8464    36082.169
   1_xyz:  19.916 0.8643  1.0172    11585.702
   1_adp:  20.827 0.8551  1.0110    12367.598
   1_occ:  20.816 0.8551  1.0108    12315.878
   2_bss:  20.681 0.8563  0.9529    12182.329
   2_xyz:  16.158 0.8970  0.9781     7892.883
   2_adp:  15.125 0.9060  0.9818     7242.664
   2_occ:  15.130 0.9060  0.9815     7243.418
   3_bss:  15.104 0.9062  0.9773     7209.525
   3_xyz:  13.977 0.9151  0.9803     6352.409
   3_adp:  13.873 0.9162  0.9754     6288.386
   3_occ:  13.877 0.9162  0.9753     6292.269
   4_bss:  13.869 0.9162  0.9772     6283.706
   4_xyz:  13.760 0.9171  0.9775     6199.153
   4_adp:  13.720 0.9174  0.9726     6181.598
   4_occ:  13.726 0.9174  0.9725     6184.091
   5_bss:  13.728 0.9174  0.9779     6185.126
   5_xyz:  13.820 0.9167  0.9771     6269.579
   5_adp:  13.731 0.9175  0.9730     6243.705
   5_occ:  13.735 0.9174  0.9730     6244.201
   5_bss:  13.736 0.9174  0.9753     6244.604
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6260e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6260e-01
   1_xyz:   1.115  0.008  0.076 15.107  0.005  4.111   7.1777e-02
   1_adp:   1.115  0.008  0.076 15.107  0.005  4.111   7.1777e-02
   1_occ:   1.115  0.008  0.076 15.107  0.005  4.111   7.1777e-02
   2_bss:   1.115  0.008  0.076 15.107  0.005  4.111   7.1777e-02
   2_xyz:   0.918  0.005  0.068 14.243  0.004  4.119   5.0034e-02
   2_adp:   0.918  0.005  0.068 14.243  0.004  4.119   5.0034e-02
   2_occ:   0.918  0.005  0.068 14.243  0.004  4.119   5.0034e-02
   3_bss:   0.918  0.005  0.068 14.243  0.004  4.119   5.0034e-02
   3_xyz:   0.934  0.006  0.071 14.291  0.004  4.121   5.2129e-02
   3_adp:   0.934  0.006  0.071 14.291  0.004  4.121   5.2129e-02
   3_occ:   0.934  0.006  0.071 14.291  0.004  4.121   5.2129e-02
   4_bss:   0.934  0.006  0.071 14.291  0.004  4.121   5.2129e-02
   4_xyz:   0.958  0.007  0.072 14.437  0.004  4.124   5.5426e-02
   4_adp:   0.958  0.007  0.072 14.437  0.004  4.124   5.5426e-02
   4_occ:   0.958  0.007  0.072 14.437  0.004  4.124   5.5426e-02
   5_bss:   0.958  0.007  0.072 14.437  0.004  4.124   5.5426e-02
   5_xyz:   0.874  0.005  0.067 14.157  0.003  4.123   4.7452e-02
   5_adp:   0.874  0.005  0.067 14.157  0.003  4.123   4.7452e-02
   5_occ:   0.874  0.005  0.067 14.157  0.003  4.123   4.7452e-02
   5_bss:   0.874  0.005  0.067 14.157  0.003  4.123   4.7452e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4054e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4054e-01
   1_xyz:   8.469  0.067  0.364 86.044  0.048  2.278   8.4567e-02
   1_adp:   8.469  0.067  0.364 86.044  0.048  2.278   8.4567e-02
   1_occ:   8.469  0.067  0.364 86.044  0.048  2.278   8.4567e-02
   2_bss:   8.469  0.067  0.364 86.044  0.048  2.278   8.4567e-02
   2_xyz:   8.147  0.032  0.198 82.551  0.035  2.358   3.8785e-02
   2_adp:   8.147  0.032  0.198 82.551  0.035  2.358   3.8785e-02
   2_occ:   8.147  0.032  0.198 82.551  0.035  2.358   3.8785e-02
   3_bss:   8.147  0.032  0.198 82.551  0.035  2.358   3.8785e-02
   3_xyz:   7.965  0.045  0.212 85.431  0.032  2.323   3.4414e-02
   3_adp:   7.965  0.045  0.212 85.431  0.032  2.323   3.4414e-02
   3_occ:   7.965  0.045  0.212 85.431  0.032  2.323   3.4414e-02
   4_bss:   7.965  0.045  0.212 85.431  0.032  2.323   3.4414e-02
   4_xyz:   7.627  0.043  0.219 83.683  0.035  2.299   4.4919e-02
   4_adp:   7.627  0.043  0.219 83.683  0.035  2.299   4.4919e-02
   4_occ:   7.627  0.043  0.219 83.683  0.035  2.299   4.4919e-02
   5_bss:   7.627  0.043  0.219 83.683  0.035  2.299   4.4919e-02
   5_xyz:   7.531  0.042  0.205 83.955  0.029  2.370   2.8276e-02
   5_adp:   7.531  0.042  0.205 83.955  0.029  2.370   2.8276e-02
   5_occ:   7.531  0.042  0.205 83.955  0.029  2.370   2.8276e-02
   5_bss:   7.531  0.042  0.205 83.955  0.029  2.370   2.8276e-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:  62.36   0.00  16.59  55.26   0.00  12.68  62.36   6.03  37.89
   1_occ:  62.36   0.00  16.59  55.26   0.00  12.68  62.36   6.03  37.89
   2_bss:  62.36   0.00  16.59  55.26   0.00  12.68  62.36   6.03  37.89
   2_xyz:  62.36   0.00  16.59  55.26   0.00  12.68  62.36   6.03  37.89
   2_adp:  71.02   1.44  17.09  69.10   1.44  12.99  71.02   6.17  39.45
   2_occ:  71.02   1.44  17.09  69.10   1.44  12.99  71.02   6.17  39.45
   3_bss:  71.02   1.44  17.09  69.10   1.44  12.99  71.02   6.17  39.45
   3_xyz:  71.02   1.44  17.09  69.10   1.44  12.99  71.02   6.17  39.45
   3_adp:  87.53   0.21  17.43  87.53   0.21  13.09  85.23   4.01  41.02
   3_occ:  87.53   0.21  17.43  87.53   0.21  13.09  85.23   4.01  41.02
   4_bss:  87.53   0.21  17.43  87.53   0.21  13.09  85.23   4.01  41.02
   4_xyz:  87.53   0.21  17.43  87.53   0.21  13.09  85.23   4.01  41.02
   4_adp:  91.33   0.66  17.14  91.33   0.66  12.93  85.70   5.00  40.04
   4_occ:  91.33   0.66  17.14  91.33   0.66  12.93  85.70   5.00  40.04
   5_bss:  91.33   0.66  17.14  91.33   0.66  12.93  85.70   5.00  40.04
   5_xyz:  91.33   0.66  17.14  91.33   0.66  12.93  85.70   5.00  40.04
   5_adp:  89.11   1.53  16.64  89.11   1.53  12.71  82.87   6.37  38.06
   5_occ:  89.11   1.53  16.64  89.11   1.53  12.71  82.87   6.37  38.06
   5_bss:  89.05   1.47  16.59  89.05   1.47  12.65  82.82   6.31  38.01
------------------------------------------------------------------------
 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:    1.154    0.014    0.364
   1_adp:    1.154    0.014    0.364
   1_occ:    1.154    0.014    0.364
   2_bss:    1.154    0.014    0.364
   2_xyz:    0.828    0.015    0.414
   2_adp:    0.828    0.015    0.414
   2_occ:    0.828    0.015    0.414
   3_bss:    0.828    0.015    0.414
   3_xyz:    0.869    0.023    0.457
   3_adp:    0.869    0.023    0.457
   3_occ:    0.869    0.023    0.457
   4_bss:    0.869    0.023    0.457
   4_xyz:    0.890    0.038    0.470
   4_adp:    0.890    0.038    0.470
   4_occ:    0.890    0.038    0.470
   5_bss:    0.890    0.038    0.470
   5_xyz:    0.977    0.042    0.474
   5_adp:    0.977    0.042    0.474
   5_occ:    0.977    0.042    0.474
   5_bss:    0.977    0.042    0.474
------------------------------------------------------------------------

CPU time actual refinement: 336.31


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1004/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_1004/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1004/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1004/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1004/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.15 
  Macro-tasks:
    bulk solvent and scale       = 36.74  
    individual site refinement   = 143.53 
    weights calculation          = 30.36  
    collect and process          = 6.67   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.43 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 109.16 
    alpha_beta                      = 8.05   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 118.05 
    fmodel                         = 6.84   
    r_factors                      = 0.17   
    phase_errors                   = 11.24  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 256.08 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.754 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    634 calls, 108.72 s
gradients_fft:          579 calls, 104.33 s

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

# Date 2008-01-16 Time 06:11:22 PST -0800 (1200492682.88 s)
Start R-work = 0.3670, R-free = 0.3671 (no bulk solvent and anisotropic scale)
Final R-work = 0.1360, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.3563, R-free = 0.3575
Final R-work = 0.1121, R-free = 0.1566