# Date 2008-01-16 Time 04:38:56 PST -0800 (1200487136.26 s)
#phil __OFF__

Command line arguments: "../404.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8144
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 404

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.98041
Completeness in resolution range: 0.961471
Completeness with d_max=infinity: 0.958507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             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: (69.5475, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.98041
Completeness in resolution range: 0.961471
Completeness with d_max=infinity: 0.958507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.2373 [2143/2167]  1924   219  10.2%
  bin  2:  4.2373 -  3.3760 [2050/2070]  1848   202   9.9%
  bin  3:  3.3760 -  2.9530 [2032/2051]  1834   198   9.7%
  bin  4:  2.9530 -  2.6847 [1994/2024]  1789   205  10.3%
  bin  5:  2.6847 -  2.4932 [2003/2022]  1802   201  10.0%
  bin  6:  2.4932 -  2.3468 [1997/2022]  1796   201  10.1%
  bin  7:  2.3468 -  2.2297 [1982/2010]  1785   197   9.9%
  bin  8:  2.2297 -  2.1329 [1955/1991]  1760   195  10.0%
  bin  9:  2.1329 -  2.0510 [1960/2002]  1766   194   9.9%
  bin 10:  2.0510 -  1.9804 [1473/2015]  1326   147  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_404/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:
        1.51 -     2.19: 10
        2.19 -     2.87: 1200
        2.87 -     3.54: 4458
        3.54 -     4.22: 9243
        4.22 -     4.90: 13515
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.510 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.888 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.942 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.957 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28421 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_404/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_404/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.4607 87.68585 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 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3723   r_free= 0.3685   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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: 6.140923                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.7259 0.99   1394  152 0.2982 0.2898      6.4057      6.3066|
|  2:  4.7259 -  3.7709 0.99   1329  154 0.2821 0.2981      6.5114      6.5314|
|  3:  3.7709 -  3.3001 0.99   1307  143 0.3269 0.3068      6.4676      6.4693|
|  4:  3.3001 -  3.0010 0.99   1304  140 0.3538 0.3952      6.3499      6.4487|
|  5:  3.0010 -  2.7874 0.99   1292  147 0.3889 0.3123      6.2061      6.0755|
|  6:  2.7874 -  2.6240 0.99   1300  145 0.3866 0.4342      6.1143       6.096|
|  7:  2.6240 -  2.4932 0.99   1271  144 0.3902 0.3455      6.0924      5.9875|
|  8:  2.4932 -  2.3852 0.98   1270  136 0.4269 0.4266      6.0894       6.105|
|  9:  2.3852 -  2.2937 0.98   1282  148 0.4177 0.4293      6.0194      6.0525|
| 10:  2.2937 -  2.2148 1.00   1275  139 0.4440 0.4093       6.035      5.9345|
| 11:  2.2148 -  2.1457 0.97   1267  134 0.4423 0.4679      5.9686      5.9936|
| 12:  2.1457 -  2.0846 0.98   1247  145 0.4543 0.3912      5.9113      5.9123|
| 13:  2.0846 -  2.0298 1.00   1271  138 0.4401 0.4556      5.8158      5.7821|
| 14:  2.0298 -  1.9804 0.63    821   94 0.4385 0.4380      5.8062      5.6919|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.7259  1394   152  0.80  25.06   0.86     0.82      40234.59|
|  2:  4.7259 -  3.7709  1329   154  0.82  23.93   0.97     0.91      55296.02|
|  3:  3.7709 -  3.3001  1307   143  0.77  29.11   0.98     0.93      58102.74|
|  4:  3.3001 -  3.0010  1304   140  0.72  33.55   0.97     0.89      52327.06|
|  5:  3.0010 -  2.7874  1292   147  0.67  38.28   0.97     0.85      40811.77|
|  6:  2.7874 -  2.6240  1300   145  0.66  39.11   0.96     0.83      35915.33|
|  7:  2.6240 -  2.4932  1271   144  0.65  40.22   0.99     0.83      33779.48|
|  8:  2.4932 -  2.3852  1270   136  0.63  41.93   0.96     0.81      32675.11|
|  9:  2.3852 -  2.2937  1282   148  0.62  42.77   1.00     0.82      31381.30|
| 10:  2.2937 -  2.2148  1275   139  0.60  44.28   1.00     0.82      29626.53|
| 11:  2.2148 -  2.1457  1267   134  0.58  45.50   0.98     0.86      29972.14|
| 12:  2.1457 -  2.0846  1247   145  0.56  47.46   1.00     0.84      28140.84|
| 13:  2.0846 -  2.0298  1271   138  0.55  48.55   0.99     0.79      25202.05|
| 14:  2.0298 -  1.9804   821    94  0.54  48.88   1.03     0.71      20603.11|
|alpha:            min =        0.71 max =            0.93 mean =         0.84|
|beta:             min =    20603.11 max =        58102.74 mean =     37301.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.93 mean =        38.75|
|phase err.(test): min =        0.00 max =           89.76 mean =        38.67|
|-----------------------------------------------------------------------------|

============================== 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 = 4.162148              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.279   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.838474              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.939   (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 |  1.510 -  1.849:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.849 -  2.188:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.188 -  2.527:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.527 -  2.866:     1156 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.866 -  3.205:     1922 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.205 -  3.544:     2536 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.544 -  3.883:     4645 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.883 -  4.222:     4598 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.222 -  4.561:     6173 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.561 -  4.900:     7342 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.510 |       0.279 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    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 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3723   r_free= 0.3685   ksol= 0.00   Bsol= 0.00   scale= 0.953    |
|                                                                             |
| 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: 6.140923                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3604   r_free= 0.3555   ksol= 0.33   Bsol= 38.62   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-0.17,2.09,-0.00,0.00,0.00); trace/3= -0.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.127604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.423889              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.062   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.471514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.739   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3604      final r-factor (work) = 0.2192          |
| start r-factor (free) = 0.3555      final r-factor (free) = 0.2485          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6499 = 3.42 * 0.50 * 6.1224 + 1.00 * 0.1687                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1091 = 3.42 * 0.50 * 5.8595 + 1.00 * 0.0780                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2192      final r-factor (work) = 0.1992          |
| start r-factor (free) = 0.2485      final r-factor (free) = 0.2581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7689 = 0.47 * 1.00 * 5.8595 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6625 = 0.47 * 1.00 * 5.6241 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.53   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    75.53   17.37    None  None   None       |
|    Sol.    : 438    0      3.54    75.53   39.76    None  None   None       |
|    Mac.    : 2385   0      0.00    68.74   13.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.553:  506   |   5:    37.767 -  45.320:  104        |
|      1:     7.553 -  15.107: 1230   |   6:    45.320 -  52.874:  100        |
|      2:    15.107 -  22.660:  486   |   7:    52.874 -  60.427:   66        |
|      3:    22.660 -  30.214:  183   |   8:    60.427 -  67.981:   28        |
|      4:    30.214 -  37.767:  112   |   9:    67.981 -  75.534:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1992 r_free = 0.2581             target_work(ml) = 5.641         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1991 r_free = 0.2579             target_work(ml) = 5.641         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1991   r_free= 0.2579   ksol= 0.33   Bsol= 38.62   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-0.17,2.09,-0.00,0.00,0.00); trace/3= -0.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.640796                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1974   r_free= 0.2559   ksol= 0.33   Bsol= 58.86   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.87,-0.05,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.638702                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.057485              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.073   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.160527              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.283  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1974      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2559      final r-factor (free) = 0.1955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8764 = 2.06 * 0.50 * 5.6367 + 1.00 * 0.0778                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7309 = 2.06 * 0.50 * 5.5190 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1475      final r-factor (work) = 0.1411          |
| start r-factor (free) = 0.1955      final r-factor (free) = 0.1841          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8965 = 0.16 * 1.00 * 5.5190 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8668 = 0.16 * 1.00 * 5.3540 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.59    72.08   16.89    None  None   None       |
|    all(noH): 2823   0      0.59    72.08   16.89    None  None   None       |
|    Sol.    : 438    0      6.00    72.08   38.39    None  None   None       |
|    Mac.    : 2385   0      0.59    71.92   12.94    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:     0.586 -   7.735:  449   |   5:    36.331 -  43.480:  110        |
|      1:     7.735 -  14.884: 1374   |   6:    43.480 -  50.629:  100        |
|      2:    14.884 -  22.033:  429   |   7:    50.629 -  57.778:   61        |
|      3:    22.033 -  29.182:  147   |   8:    57.778 -  64.927:   28        |
|      4:    29.182 -  36.331:  114   |   9:    64.927 -  72.076:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1411 r_free = 0.1841             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1409 r_free = 0.1840             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1840   ksol= 0.33   Bsol= 58.86   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.87,-0.05,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.322185                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1843   ksol= 0.34   Bsol= 58.86   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.29,-0.47,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.321030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.217596              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.834  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.891864              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.640  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1843      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6660 = 3.22 * 0.50 * 5.3535 + 1.00 * 0.0533                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4917 = 3.22 * 0.50 * 5.2380 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6789 = 0.89 * 1.00 * 5.2380 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6044 = 0.89 * 1.00 * 5.1522 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.28    82.09   17.25    None  None   None       |
|    all(noH): 2823   0      0.28    82.09   17.25    None  None   None       |
|    Sol.    : 438    0      1.45    77.63   40.84    None  None   None       |
|    Mac.    : 2385   0      0.28    82.09   12.92    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:     0.282 -   8.462:  677   |   5:    41.185 -  49.365:  103        |
|      1:     8.462 -  16.643: 1318   |   6:    49.365 -  57.546:   82        |
|      2:    16.643 -  24.823:  319   |   7:    57.546 -  65.726:   61        |
|      3:    24.823 -  33.004:  132   |   8:    65.726 -  73.907:   24        |
|      4:    33.004 -  41.185:   98   |   9:    73.907 -  82.088:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1579             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1578             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1578   ksol= 0.34   Bsol= 58.86   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.29,-0.47,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1580   ksol= 0.34   Bsol= 58.86   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.35,-0.56,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145016                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.381157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.516  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.461499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.590  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1989 = 2.38 * 0.50 * 5.1522 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1732 = 2.38 * 0.50 * 5.1346 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1093          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3789 = 0.46 * 1.00 * 5.1346 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3746 = 0.46 * 1.00 * 5.1255 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    83.68   17.01    None  None   None       |
|    all(noH): 2823   0      0.70    83.68   17.01    None  None   None       |
|    Sol.    : 438    0      1.27    77.22   40.22    None  None   None       |
|    Mac.    : 2385   0      0.70    83.68   12.74    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:     0.701 -   8.998:  834   |   5:    42.189 -  50.486:  103        |
|      1:     8.998 -  17.296: 1222   |   6:    50.486 -  58.784:   82        |
|      2:    17.296 -  25.594:  282   |   7:    58.784 -  67.081:   43        |
|      3:    25.594 -  33.891:  123   |   8:    67.081 -  75.379:   22        |
|      4:    33.891 -  42.189:  105   |   9:    75.379 -  83.677:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1093 r_free = 0.1552             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1552             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1552   ksol= 0.34   Bsol= 58.86   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.35,-0.56,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125870                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1552   ksol= 0.32   Bsol= 52.95   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.22,-0.44,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.589176              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.661  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.253168              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.937  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6958 = 2.59 * 0.50 * 5.1258 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6907 = 2.59 * 0.50 * 5.1183 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.0148 = 6.25 * 1.00 * 5.1183 + 1.00 * 0.0091                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.0044 = 6.25 * 1.00 * 5.1165 + 1.00 * 0.0103                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.11   16.99    None  None   None       |
|    all(noH): 2823   0      0.00    93.11   16.99    None  None   None       |
|    Sol.    : 438    0      3.18    82.00   40.53    None  None   None       |
|    Mac.    : 2385   0      0.00    93.11   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.311:  970   |   5:    46.554 -  55.864:   89        |
|      1:     9.311 -  18.621: 1159   |   6:    55.864 -  65.175:   67        |
|      2:    18.621 -  27.932:  242   |   7:    65.175 -  74.486:   27        |
|      3:    27.932 -  37.243:  136   |   8:    74.486 -  83.796:   18        |
|      4:    37.243 -  46.554:  113   |   9:    83.796 -  93.107:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1070 r_free = 0.1562             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1069 r_free = 0.1562             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1562   ksol= 0.32   Bsol= 52.95   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.22,-0.44,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120050                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.7259 0.99   1394  152 0.0955 0.1257      5.3686      5.5205|
|  2:  4.7259 -  3.7709 0.99   1329  154 0.0820 0.1095      5.4128      5.6184|
|  3:  3.7709 -  3.3001 0.99   1307  143 0.1014 0.1511      5.4499      5.8503|
|  4:  3.3001 -  3.0010 0.99   1304  140 0.1155 0.1646      5.4235      5.6007|
|  5:  3.0010 -  2.7874 0.99   1292  147 0.1244 0.1680      5.2956      5.5441|
|  6:  2.7874 -  2.6240 0.99   1300  145 0.1164 0.1936      5.1937      5.4865|
|  7:  2.6240 -  2.4932 0.99   1271  144 0.1227 0.1579      5.1534      5.3049|
|  8:  2.4932 -  2.3852 0.98   1270  136 0.1090 0.1583      5.0407      5.3073|
|  9:  2.3852 -  2.2937 0.98   1282  148 0.1109 0.1826      4.9969      5.3052|
| 10:  2.2937 -  2.2148 1.00   1275  139 0.1074 0.1677      4.9258      5.1757|
| 11:  2.2148 -  2.1457 0.97   1267  134 0.1071 0.1736      4.9215      5.2328|
| 12:  2.1457 -  2.0846 0.98   1247  145 0.1124 0.1677      4.8763      5.2384|
| 13:  2.0846 -  2.0298 1.00   1271  138 0.1050 0.1759      4.7679      5.0394|
| 14:  2.0298 -  1.9804 0.63    821   94 0.0915 0.1682      4.6109      4.8902|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.7259  1394   152  0.94   9.27   0.98     0.94       7103.53|
|  2:  4.7259 -  3.7709  1329   154  0.95   7.80   1.02     1.01       9001.19|
|  3:  3.7709 -  3.3001  1307   143  0.94  10.92   1.03     1.02       9978.15|
|  4:  3.3001 -  3.0010  1304   140  0.92  13.17   1.01     0.99       9966.23|
|  5:  3.0010 -  2.7874  1292   147  0.90  15.41   1.00     0.97       8054.16|
|  6:  2.7874 -  2.6240  1300   145  0.90  16.22   0.98     0.96       7112.18|
|  7:  2.6240 -  2.4932  1271   144  0.91  15.57   0.98     0.95       6173.38|
|  8:  2.4932 -  2.3852  1270   136  0.91  14.59   0.99     0.97       5134.89|
|  9:  2.3852 -  2.2937  1282   148  0.91  14.70   1.00     0.95       4720.68|
| 10:  2.2937 -  2.2148  1275   139  0.90  15.76   1.00     0.97       4251.36|
| 11:  2.2148 -  2.1457  1267   134  0.90  15.84   0.99     0.95       4343.15|
| 12:  2.1457 -  2.0846  1247   145  0.90  16.11   1.00     0.99       4036.65|
| 13:  2.0846 -  2.0298  1271   138  0.91  15.32   0.98     0.96       3274.69|
| 14:  2.0298 -  1.9804   821    94  0.92  13.58   0.97     0.94       2389.32|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2389.32 max =         9978.15 mean =      6242.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.83 mean =        13.83|
|phase err.(test): min =        0.00 max =           88.98 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1561   ksol= 0.32   Bsol= 52.96   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.03,-0.26,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1561   ksol= 0.32   Bsol= 52.96   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.03,-0.26,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120071                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.7259 0.99   1394  152 0.0954 0.1258      5.3683      5.5205|
|  2:  4.7259 -  3.7709 0.99   1329  154 0.0821 0.1096      5.4134      5.6186|
|  3:  3.7709 -  3.3001 0.99   1307  143 0.1015 0.1511      5.4502      5.8507|
|  4:  3.3001 -  3.0010 0.99   1304  140 0.1155 0.1645      5.4235      5.6006|
|  5:  3.0010 -  2.7874 0.99   1292  147 0.1244 0.1679      5.2954      5.5435|
|  6:  2.7874 -  2.6240 0.99   1300  145 0.1164 0.1936      5.1935      5.4864|
|  7:  2.6240 -  2.4932 0.99   1271  144 0.1227 0.1579      5.1534      5.3049|
|  8:  2.4932 -  2.3852 0.98   1270  136 0.1090 0.1582      5.0408      5.3072|
|  9:  2.3852 -  2.2937 0.98   1282  148 0.1109 0.1825       4.997      5.3053|
| 10:  2.2937 -  2.2148 1.00   1275  139 0.1074 0.1677      4.9259      5.1758|
| 11:  2.2148 -  2.1457 0.97   1267  134 0.1071 0.1736      4.9215      5.2326|
| 12:  2.1457 -  2.0846 0.98   1247  145 0.1124 0.1676      4.8762       5.238|
| 13:  2.0846 -  2.0298 1.00   1271  138 0.1049 0.1761      4.7678      5.0397|
| 14:  2.0298 -  1.9804 0.63    821   94 0.0915 0.1681      4.6109      4.8898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.7259  1394   152  0.94   9.26   0.98     0.94       7097.04|
|  2:  4.7259 -  3.7709  1329   154  0.95   7.80   1.02     1.01       9003.92|
|  3:  3.7709 -  3.3001  1307   143  0.94  10.93   1.03     1.02       9983.11|
|  4:  3.3001 -  3.0010  1304   140  0.92  13.17   1.02     1.00       9964.93|
|  5:  3.0010 -  2.7874  1292   147  0.90  15.41   1.01     0.98       8051.54|
|  6:  2.7874 -  2.6240  1300   145  0.90  16.22   0.99     0.96       7108.75|
|  7:  2.6240 -  2.4932  1271   144  0.91  15.57   0.99     0.96       6173.00|
|  8:  2.4932 -  2.3852  1270   136  0.91  14.59   1.00     0.97       5135.39|
|  9:  2.3852 -  2.2937  1282   148  0.91  14.70   1.00     0.96       4721.90|
| 10:  2.2937 -  2.2148  1275   139  0.90  15.76   1.01     0.97       4251.53|
| 11:  2.2148 -  2.1457  1267   134  0.90  15.84   1.00     0.96       4342.74|
| 12:  2.1457 -  2.0846  1247   145  0.90  16.11   1.01     1.00       4036.27|
| 13:  2.0846 -  2.0298  1271   138  0.91  15.32   1.00     0.97       3273.59|
| 14:  2.0298 -  1.9804   821    94  0.92  13.57   0.98     0.95       2388.30|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2388.30 max =         9983.11 mean =      6241.90|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.83|
|phase err.(test): min =        0.00 max =           89.00 mean =        13.42|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.11   16.99    None  None   None       |
|    all(noH): 2823   0      0.00    93.11   16.99    None  None   None       |
|    Sol.    : 438    0      3.18    82.01   40.53    None  None   None       |
|    Mac.    : 2385   0      0.00    93.11   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.314:  970   |   5:    46.557 -  55.867:   89        |
|      1:     9.314 -  18.624: 1159   |   6:    55.867 -  65.178:   67        |
|      2:    18.624 -  27.935:  242   |   7:    65.178 -  74.489:   27        |
|      3:    27.935 -  37.246:  136   |   8:    74.489 -  83.799:   18        |
|      4:    37.246 -  46.557:  113   |   9:    83.799 -  93.110:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 280         
Filter by distance & map next to the model:
   mapped sites are within: 0.426 - 5.487
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 280
   mapped sites are within: 0.703 - 5.487

peak=    5.919 closest distance to " NE2 GLN A  11 " =    1.157
peak=    5.768 closest distance to " O   HOH Z 142 " =    1.865
peak=    5.580 closest distance to " NH2 ARG A  56 " =    2.183
peak=    5.347 closest distance to " CG  PRO A  54 " =    1.267
peak=    5.013 closest distance to " CB  ARG A 275 " =    0.937
peak=    4.819 closest distance to " O   HOH Z 126 " =    1.906
peak=    4.730 closest distance to " CB  GLN A 223 " =    1.472
peak=    4.717 closest distance to " CG  PRO A 213 " =    1.203
peak=    4.679 closest distance to " CB  ARG A  79 " =    1.461
peak=    4.670 closest distance to " O   HOH Z 369 " =    2.264
peak=    4.661 closest distance to " O   HOH Z  78 " =    1.831
peak=    4.652 closest distance to " CB  GLN A 183 " =    1.221
peak=    4.620 closest distance to " O   HOH Z 427 " =    2.903
peak=    4.563 closest distance to " O   HOH Z 287 " =    2.273
peak=    4.520 closest distance to " CB  ARG A 190 " =    1.664
peak=    4.470 closest distance to " O   HOH Z 232 " =    2.354
peak=    4.447 closest distance to " O   HOH Z  15 " =    2.171
peak=    4.443 closest distance to " CB  PRO A  54 " =    0.935
peak=    4.410 closest distance to " C   PRO A 198 " =    1.441
peak=    4.368 closest distance to " ND2 ASN A 187 " =    1.414
peak=    4.337 closest distance to " O   HOH Z 158 " =    3.098
peak=    4.281 closest distance to " CB  VAL A 265 " =    1.258
peak=    4.271 closest distance to " O   HOH Z 303 " =    2.150
peak=    4.254 closest distance to " O   HOH Z  61 " =    1.644
peak=    4.225 closest distance to " O   SER A  87 " =    2.155
peak=    4.215 closest distance to " O   HOH Z 298 " =    1.843
peak=    4.201 closest distance to " CZ  PHE A 218 " =    1.051
peak=    4.181 closest distance to " CD2 TRP A 179 " =    1.318
peak=    4.169 closest distance to " CA  TYR A  30 " =    0.920
peak=    4.164 closest distance to " O   HOH Z 133 " =    2.770
peak=    4.158 closest distance to " CD  ARG A 159 " =    0.703
peak=    4.146 closest distance to " O   HOH Z 250 " =    1.488
peak=    4.118 closest distance to " CG2 VAL A 257 " =    0.826
peak=    4.114 closest distance to " CB  SER A  63 " =    1.165
peak=    4.071 closest distance to " CB  ASN A 148 " =    1.427
peak=    4.057 closest distance to " O   HOH Z 406 " =    1.626
peak=    4.051 closest distance to " OD1 ASN A  69 " =    2.568
peak=    4.047 closest distance to " CB  GLU A 152 " =    1.257
peak=    4.013 closest distance to " O   HOH Z 359 " =    1.559
peak=    4.010 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.989 closest distance to " O   HOH Z 272 " =    1.802
peak=    3.985 closest distance to " O   HOH Z 189 " =    2.805
peak=    3.985 closest distance to " O   HOH Z 265 " =    2.154
peak=    3.984 closest distance to " O   HOH Z 346 " =    1.629
peak=    3.976 closest distance to " OG ASER A 258 " =    3.069
peak=    3.969 closest distance to " CA  ASN A 215 " =    1.129
peak=    3.959 closest distance to " O   HOH Z 353 " =    2.615
peak=    3.941 closest distance to " O   HOH Z 419 " =    2.184
peak=    3.940 closest distance to " O   HOH Z 371 " =    1.835
peak=    3.938 closest distance to " CB  VAL A 202 " =    1.623
peak=    3.935 closest distance to " NZ  LYS A 117 " =    3.160
peak=    3.918 closest distance to " O   HOH Z 327 " =    1.552
peak=    3.911 closest distance to " O   HOH Z 203 " =    1.747
peak=    3.906 closest distance to " O   HOH Z 313 " =    1.975
peak=    3.895 closest distance to " CB  TRP A 266 " =    1.105
peak=    3.890 closest distance to " CG  PRO A 198 " =    1.226
peak=    3.880 closest distance to " CB  ASP A 140 " =    1.019
peak=    3.879 closest distance to " CG  ARG A  66 " =    2.551
peak=    3.879 closest distance to " CB  GLU A 277 " =    3.604
peak=    3.870 closest distance to " CB  TYR A 169 " =    0.824
peak=    3.860 closest distance to " O   HOH Z 402 " =    1.371
peak=    3.858 closest distance to " OG BSER A 164 " =    2.270
peak=    3.849 closest distance to " O   HOH Z 209 " =    2.258
peak=    3.845 closest distance to " O   HOH Z 180 " =    2.242
peak=    3.843 closest distance to " CB  SER A 212 " =    1.110
peak=    3.842 closest distance to " O   HOH Z   1 " =    2.017
peak=    3.840 closest distance to " N   TYR A 116 " =    1.516
peak=    3.821 closest distance to " O   HOH Z 234 " =    3.623
peak=    3.812 closest distance to " O   HOH Z  40 " =    1.648
peak=    3.809 closest distance to " CB  LEU A 228 " =    1.131
peak=    3.809 closest distance to " O   HOH Z  63 " =    1.983
peak=    3.798 closest distance to " CG  PRO A  90 " =    1.159
peak=    3.786 closest distance to " ND2 ASN A 249 " =    0.842
peak=    3.717 closest distance to " O   HOH Z  61 " =    1.471
peak=    3.714 closest distance to " O   HOH Z 193 " =    1.746
peak=    3.711 closest distance to " CG  PRO A 243 " =    1.045
peak=    3.702 closest distance to " O   HOH Z 368 " =    3.584
peak=    3.700 closest distance to " O   HOH Z 425 " =    2.042
peak=    3.698 closest distance to " CB  THR A  31 " =    1.643
peak=    3.697 closest distance to " CB  SER A   3 " =    1.320
peak=    3.683 closest distance to " O   HOH Z 392 " =    3.044
peak=    3.679 closest distance to " O   HOH Z 248 " =    1.504
peak=    3.669 closest distance to " CG2 ILE A 120 " =    1.150
peak=    3.665 closest distance to " O   ASN A  74 " =    1.437
peak=    3.665 closest distance to " O   HOH Z 365 " =    2.769
peak=    3.653 closest distance to " O   HOH Z 403 " =    1.519
peak=    3.652 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.648 closest distance to " O   HOH Z  53 " =    2.506
peak=    3.631 closest distance to " CB  SER A  26 " =    1.728
peak=    3.623 closest distance to " CB  GLU A  46 " =    1.011
peak=    3.618 closest distance to " O   HOH Z 172 " =    3.205
peak=    3.615 closest distance to " O   HOH Z 423 " =    1.919
peak=    3.615 closest distance to " O   HOH Z  59 " =    1.684
peak=    3.614 closest distance to " CB  PRO A  90 " =    1.135
peak=    3.613 closest distance to " O   HOH Z 285 " =    2.277
peak=    3.610 closest distance to " O   HOH Z 126 " =    1.536
peak=    3.609 closest distance to " O   HOH Z 389 " =    1.808
peak=    3.609 closest distance to " CB  LYS A 117 " =    1.223
peak=    3.608 closest distance to " CB  ASN A  39 " =    0.910
peak=    3.605 closest distance to " O   HOH Z 394 " =    3.855
peak=    3.597 closest distance to " O   HOH Z 368 " =    2.132
peak=    3.589 closest distance to " CB  ARG A 139 " =    1.015
peak=    3.588 closest distance to " O   HOH Z  44 " =    1.767
peak=    3.583 closest distance to " O   HOH Z 132 " =    2.455
peak=    3.578 closest distance to " O   HOH Z 193 " =    2.036
peak=    3.577 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.576 closest distance to " O   HOH Z 417 " =    3.501
peak=    3.576 closest distance to " N   ASN A  39 " =    1.271
peak=    3.568 closest distance to " NH1AARG A 145 " =    1.211
peak=    3.563 closest distance to " O   HOH Z 336 " =    1.754
peak=    3.561 closest distance to " NH2BARG A 145 " =    2.084
peak=    3.560 closest distance to " CB  GLN A  88 " =    1.179
peak=    3.560 closest distance to " CD2 LEU A 297 " =    0.922
peak=    3.549 closest distance to " O   HOH Z   1 " =    1.684
peak=    3.541 closest distance to " CD  ARG A  66 " =    2.485
peak=    3.526 closest distance to " O   HOH Z  10 " =    1.795
peak=    3.525 closest distance to " O   HOH Z   3 " =    1.994
peak=    3.522 closest distance to " O   HOH Z 214 " =    2.201
peak=    3.517 closest distance to " O   HOH Z  66 " =    2.114
peak=    3.516 closest distance to " O   HOH Z 128 " =    2.095
peak=    3.515 closest distance to " CA  ARG A  36 " =    1.001
peak=    3.513 closest distance to " CG  LEU A 167 " =    1.303
peak=    3.510 closest distance to " O   HOH Z 261 " =    1.689
peak=    3.506 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.499 closest distance to " O   HOH Z  44 " =    2.858
peak=    3.496 closest distance to " CA  SER A  87 " =    1.043
peak=    3.491 closest distance to " CG  MET A 185 " =    1.170
peak=    3.490 closest distance to " CB  ASN A 215 " =    1.118
peak=    3.488 closest distance to " N   PHE A 130 " =    1.299
peak=    3.482 closest distance to " O   HOH Z 337 " =    3.578
peak=    3.479 closest distance to " O   HOH Z 411 " =    3.824
peak=    3.478 closest distance to " O   HOH Z 291 " =    1.502
peak=    3.471 closest distance to " O   HOH Z 380 " =    1.678
peak=    3.469 closest distance to " CB  ALA A 114 " =    1.314
peak=    3.467 closest distance to " O  BHOH Z 338 " =    2.302
peak=    3.463 closest distance to " CB  ASN A 187 " =    1.390
peak=    3.459 closest distance to " CA  THR A 221 " =    1.051
peak=    3.459 closest distance to " O   HOH Z 371 " =    2.931
peak=    3.454 closest distance to " O   HOH Z 128 " =    2.122
peak=    3.450 closest distance to " O   HOH Z 245 " =    1.317
peak=    3.447 closest distance to " CG2 ILE A  20 " =    1.453
peak=    3.441 closest distance to " CD  ARG A 269 " =    0.914
peak=    3.438 closest distance to " CB  GLN A  89 " =    1.420
peak=    3.435 closest distance to " O   HOH Z 257 " =    2.207
peak=    3.429 closest distance to " CB  ASN A 142 " =    1.032
peak=    3.429 closest distance to " O   HOH Z 261 " =    2.039
peak=    3.429 closest distance to " O   HOH Z  97 " =    2.590
peak=    3.425 closest distance to " O   HOH Z 213 " =    1.886
peak=    3.420 closest distance to " CG2 THR A 221 " =    1.070
peak=    3.409 closest distance to " O   HOH Z  97 " =    2.005
peak=    3.409 closest distance to " CB  TYR A 116 " =    0.786
peak=    3.403 closest distance to " O   HOH Z 422 " =    2.613
peak=    3.400 closest distance to " O   HOH Z  88 " =    2.550
peak=    3.398 closest distance to " CB  TRP A 179 " =    1.388
peak=    3.394 closest distance to " CA  ALA A 233 " =    0.983
peak=    3.392 closest distance to " CA  ALA A 158 " =    1.274
peak=    3.388 closest distance to " O   HOH Z 147 " =    1.782
peak=    3.373 closest distance to " NE2 GLN A  77 " =    3.116
peak=    3.371 closest distance to " O   HOH Z 305 " =    3.471
peak=    3.371 closest distance to " O   HOH Z  90 " =    2.197
peak=    3.368 closest distance to " CA  VAL A 125 " =    1.157
peak=    3.368 closest distance to " O   HOH Z 173 " =    1.859
peak=    3.365 closest distance to " O   HOH Z 325 " =    2.421
peak=    3.362 closest distance to " ND1 HIS A  86 " =    1.838
peak=    3.355 closest distance to " CG2AVAL A  72 " =    1.640
peak=    3.354 closest distance to " CA  PHE A 283 " =    1.324
peak=    3.353 closest distance to " CB  GLU A 128 " =    0.961
peak=    3.352 closest distance to " O   HOH Z 357 " =    1.985
peak=    3.352 closest distance to " O   HOH Z 280 " =    3.007
peak=    3.352 closest distance to " O   HOH Z 344 " =    3.237
peak=    3.351 closest distance to " O   HOH Z 329 " =    4.076
peak=    3.349 closest distance to " CG2 VAL A 197 " =    1.112
peak=    3.345 closest distance to " CG1 ILE A  33 " =    1.214
peak=    3.344 closest distance to " O   HOH Z 391 " =    2.852
peak=    3.343 closest distance to " CA  ASN A 217 " =    1.171
peak=    3.339 closest distance to " O   HOH Z 290 " =    0.852
peak=    3.339 closest distance to " O   HOH Z  40 " =    1.976
peak=    3.337 closest distance to " CA  MET A  40 " =    1.199
peak=    3.333 closest distance to " CA  ALA A 291 " =    0.768
peak=    3.333 closest distance to " CG1 VAL A 153 " =    1.004
peak=    3.330 closest distance to " O   HOH Z 294 " =    1.442
peak=    3.329 closest distance to " CD1 ILE A 106 " =    0.809
peak=    3.328 closest distance to " CB  ALA A   1 " =    4.821
peak=    3.323 closest distance to " C   PHE A  59 " =    0.961
peak=    3.321 closest distance to " CD BLYS A 290 " =    1.193
peak=    3.320 closest distance to " O   HOH Z 148 " =    3.443
peak=    3.319 closest distance to " CD  LYS A 166 " =    1.226
peak=    3.316 closest distance to " O   HOH Z 233 " =    1.967
peak=    3.313 closest distance to " CA  ARG A 159 " =    1.264
peak=    3.311 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.311 closest distance to " NE2 GLN A  73 " =    3.848
peak=    3.310 closest distance to " OD2 ASP A 286 " =    3.258
peak=    3.307 closest distance to " CE1 TYR A 186 " =    1.348
peak=    3.306 closest distance to " O   HOH Z 193 " =    1.664
peak=    3.302 closest distance to " O   HOH Z  88 " =    2.442
peak=    3.300 closest distance to " CA  TYR A 116 " =    1.299
peak=    3.294 closest distance to " CA  ASN A 127 " =    1.141
peak=    3.293 closest distance to " CB  PHE A 204 " =    0.785
peak=    3.289 closest distance to " CB  ILE A 120 " =    1.375
peak=    3.286 closest distance to " CB  MET A  47 " =    1.279
peak=    3.286 closest distance to " OG  SER A  22 " =    2.659
peak=    3.283 closest distance to " O   HOH Z 116 " =    1.703
peak=    3.278 closest distance to " O   HOH Z 227 " =    1.876
peak=    3.276 closest distance to " CD  LYS A  76 " =    1.822
peak=    3.276 closest distance to " O   HOH Z 116 " =    2.979
peak=    3.269 closest distance to " CA  THR A 264 " =    0.919
peak=    3.268 closest distance to " CA  ASP A 162 " =    1.060
peak=    3.267 closest distance to " O   HOH Z  21 " =    1.766
peak=    3.265 closest distance to " O   HOH Z 345 " =    3.307
peak=    3.265 closest distance to " O   HOH Z 426 " =    1.950
peak=    3.258 closest distance to " N   ASP A 162 " =    1.120
peak=    3.256 closest distance to " OG BSER A  99 " =    2.340
peak=    3.252 closest distance to " CD1 ILE A 263 " =    1.347
peak=    3.251 closest distance to " CB  SER A 273 " =    0.822
peak=    3.249 closest distance to " CZ  PHE A  38 " =    1.269
peak=    3.249 closest distance to " CB  ALA A  34 " =    1.058
peak=    3.247 closest distance to " O   HOH Z 421 " =    1.981
peak=    3.247 closest distance to " O   HOH Z 403 " =    1.564
peak=    3.243 closest distance to " CB  SER A  62 " =    1.328
peak=    3.242 closest distance to " O   HOH Z 287 " =    2.302
peak=    3.235 closest distance to " N   ASN A 127 " =    1.296
peak=    3.235 closest distance to " O   THR A 220 " =    1.298
peak=    3.234 closest distance to " OD2 ASP A 286 " =    2.819
peak=    3.232 closest distance to " O   HOH Z 286 " =    2.356
peak=    3.229 closest distance to " O   HOH Z 188 " =    1.829
peak=    3.229 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.226 closest distance to " CA  GLU A  46 " =    0.906
peak=    3.222 closest distance to " CG1 VAL A 189 " =    1.905
peak=    3.215 closest distance to " O   HOH Z 299 " =    4.280
peak=    3.202 closest distance to " O   HOH Z  43 " =    1.899
peak=    3.194 closest distance to " O   HOH Z 340 " =    2.114
peak=    3.193 closest distance to " NE2 HIS A 207 " =    1.271
peak=    3.191 closest distance to " O   ALA A   1 " =    1.637
peak=    3.190 closest distance to " CA  MET A 105 " =    0.994
peak=    3.190 closest distance to " O   HOH Z 266 " =    3.492
peak=    3.185 closest distance to " NZ  LYS A  48 " =    1.135
peak=    3.185 closest distance to " O   HOH Z 409 " =    2.593
peak=    3.184 closest distance to " OE2 GLU A  53 " =    2.006
peak=    3.171 closest distance to " CD  ARG A 195 " =    3.452
peak=    3.168 closest distance to " O   HOH Z  80 " =    2.111
peak=    3.165 closest distance to " CA  ALA A  84 " =    1.288
peak=    3.163 closest distance to " OD1BASN A 224 " =    2.300
peak=    3.162 closest distance to " O   HOH Z   6 " =    2.069
peak=    3.159 closest distance to " O   HOH Z 185 " =    1.856
peak=    3.156 closest distance to " CB  LEU A 300 " =    0.912
peak=    3.154 closest distance to " NH1 ARG A 138 " =    1.146
peak=    3.154 closest distance to " CB  MET A  47 " =    1.193
peak=    3.145 closest distance to " CG1 ILE A  49 " =    1.415
peak=    3.143 closest distance to " CG  LYS A  76 " =    0.923
peak=    3.142 closest distance to " CE AMET A  47 " =    1.444
peak=    3.142 closest distance to " CA  SER A  32 " =    1.637
peak=    3.140 closest distance to " CD1 LEU A  96 " =    0.718
peak=    3.137 closest distance to " O   HOH Z  28 " =    1.801
peak=    3.137 closest distance to " CB  THR A  52 " =    0.802
peak=    3.132 closest distance to " O   HOH Z 298 " =    2.492
peak=    3.132 closest distance to " O   HOH Z 109 " =    2.534
peak=    3.130 closest distance to " CA  SER A 146 " =    1.756
peak=    3.128 closest distance to " O   HOH Z 175 " =    2.144
peak=    3.122 closest distance to " O   HOH Z 227 " =    2.055
peak=    3.120 closest distance to " CA  PRO A 280 " =    1.305
peak=    3.119 closest distance to " O   HOH Z 407 " =    2.343
peak=    3.115 closest distance to " O   HOH Z 433 " =    1.841
peak=    3.114 closest distance to " OG BSER A 134 " =    3.130
peak=    3.110 closest distance to " O   HOH Z 234 " =    2.231
peak=    3.099 closest distance to " CB  HIS A 108 " =    0.800
peak=    3.098 closest distance to " O   HOH Z 361 " =    3.113
peak=    3.081 closest distance to " CD1 LEU A 261 " =    1.169
peak=    3.077 closest distance to " O   HOH Z 271 " =    2.221
peak=    3.067 closest distance to " CB  ALA A 291 " =    1.322
peak=    3.048 closest distance to " CA  ALA A 233 " =    1.655
peak=    3.046 closest distance to " N   GLU A   2 " =    1.548
peak=    3.044 closest distance to " O   HOH Z 172 " =    5.487
peak=    3.041 closest distance to " CA  ALA A 299 " =    0.902
peak=    3.029 closest distance to " CA  ALA A 233 " =    1.004

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.772 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 219
   mapped sites are within: 0.772 - 5.939

peak=   -4.826 closest distance to " O   HOH Z 377 " =    2.163
peak=   -4.635 closest distance to " OG BSER A 134 " =    1.312
peak=   -4.508 closest distance to " CB  PRO A 243 " =    2.663
peak=   -4.437 closest distance to " CD  ARG A  14 " =    3.404
peak=   -4.423 closest distance to " O   HOH Z 266 " =    5.284
peak=   -4.398 closest distance to " C   HIS A 108 " =    1.114
peak=   -4.342 closest distance to " CG  GLN A  58 " =    1.077
peak=   -4.286 closest distance to " CD  ARG A 156 " =    2.080
peak=   -4.285 closest distance to " CE  MET A 105 " =    2.498
peak=   -4.278 closest distance to " O   HOH Z 231 " =    2.287
peak=   -4.276 closest distance to " O   VAL A  67 " =    2.625
peak=   -4.240 closest distance to " CG  GLN A 223 " =    1.965
peak=   -4.186 closest distance to " O   PRO A 198 " =    1.297
peak=   -4.184 closest distance to " CD2 PHE A 192 " =    1.981
peak=   -3.996 closest distance to " CB  ALA A  43 " =    2.549
peak=   -3.996 closest distance to " CG1 VAL A  67 " =    2.903
peak=   -3.994 closest distance to " CG1 VAL A 112 " =    2.829
peak=   -3.954 closest distance to " O   HOH Z 198 " =    1.743
peak=   -3.941 closest distance to " OD1 ASP A 171 " =    1.621
peak=   -3.937 closest distance to " CB  ALA A 248 " =    2.282
peak=   -3.865 closest distance to " CZ3 TRP A 179 " =    1.200
peak=   -3.849 closest distance to " O   HOH Z 351 " =    1.508
peak=   -3.848 closest distance to " CB  ASN A  39 " =    2.332
peak=   -3.848 closest distance to " OD2 ASP A 191 " =    1.384
peak=   -3.847 closest distance to " CE BMET A  47 " =    1.296
peak=   -3.817 closest distance to " O   HOH Z 372 " =    2.321
peak=   -3.808 closest distance to " CD1 LEU A 255 " =    2.814
peak=   -3.786 closest distance to " ND2 ASN A  45 " =    1.837
peak=   -3.783 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -3.779 closest distance to " O   HOH Z 389 " =    1.955
peak=   -3.779 closest distance to " ND2 ASN A 249 " =    2.372
peak=   -3.775 closest distance to " CB  ALA A 291 " =    2.160
peak=   -3.771 closest distance to " O   HOH Z 185 " =    2.354
peak=   -3.761 closest distance to " CE2 PHE A 218 " =    2.404
peak=   -3.755 closest distance to " O   HOH Z 407 " =    2.935
peak=   -3.755 closest distance to " CD1 PHE A  59 " =    2.066
peak=   -3.738 closest distance to " OXT GLY A 302 " =    2.919
peak=   -3.737 closest distance to " CB  ALA A 291 " =    2.213
peak=   -3.694 closest distance to " O   HOH Z 348 " =    2.222
peak=   -3.680 closest distance to " O   HOH Z 313 " =    1.820
peak=   -3.674 closest distance to " CG1 VAL A 112 " =    2.607
peak=   -3.673 closest distance to " N   ALA A  43 " =    2.614
peak=   -3.654 closest distance to " O   HOH Z 290 " =    1.271
peak=   -3.652 closest distance to " O   HOH Z  73 " =    2.343
peak=   -3.643 closest distance to " CD2 TYR A 247 " =    2.465
peak=   -3.637 closest distance to " N   ALA A 248 " =    1.664
peak=   -3.636 closest distance to " CB  ALA A 161 " =    2.461
peak=   -3.606 closest distance to " O   VAL A 189 " =    2.617
peak=   -3.604 closest distance to " O   HOH Z  38 " =    1.711
peak=   -3.601 closest distance to " O   HOH Z 395 " =    5.123
peak=   -3.596 closest distance to " CG2 ILE A 263 " =    2.238
peak=   -3.593 closest distance to " OD1 ASN A 148 " =    1.508
peak=   -3.580 closest distance to " O   HOH Z 394 " =    1.465
peak=   -3.578 closest distance to " O   HOH Z  44 " =    2.279
peak=   -3.576 closest distance to " O   SER A 135 " =    1.423
peak=   -3.572 closest distance to " O   HOH Z 429 " =    1.971
peak=   -3.564 closest distance to " O   HOH Z 102 " =    1.610
peak=   -3.560 closest distance to " N   THR A 157 " =    1.538
peak=   -3.556 closest distance to " O   SER A 210 " =    1.989
peak=   -3.555 closest distance to " NH2BARG A 275 " =    1.876
peak=   -3.549 closest distance to " CD2 PHE A  61 " =    2.028
peak=   -3.549 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.548 closest distance to " O   HOH Z 298 " =    1.304
peak=   -3.547 closest distance to " CB  TYR A  15 " =    2.267
peak=   -3.544 closest distance to " ND2 ASN A 187 " =    1.487
peak=   -3.531 closest distance to " O   HOH Z  60 " =    2.241
peak=   -3.523 closest distance to " O   HOH Z 196 " =    2.225
peak=   -3.511 closest distance to " O   HOH Z 114 " =    2.996
peak=   -3.508 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.508 closest distance to " CZ  PHE A  59 " =    1.529
peak=   -3.499 closest distance to " CB  TRP A  85 " =    2.524
peak=   -3.493 closest distance to " OD2 ASP A 171 " =    2.375
peak=   -3.490 closest distance to " O   HOH Z 211 " =    1.561
peak=   -3.490 closest distance to " O   PRO A 198 " =    1.315
peak=   -3.489 closest distance to " CD2 TYR A 293 " =    1.857
peak=   -3.486 closest distance to " O   VAL A 189 " =    1.712
peak=   -3.483 closest distance to " CZ  TYR A 169 " =    1.740
peak=   -3.481 closest distance to " O   HOH Z  13 " =    1.802
peak=   -3.473 closest distance to " CG  PHE A 283 " =    2.656
peak=   -3.466 closest distance to " O   ALA A 161 " =    1.713
peak=   -3.460 closest distance to " CD2 LEU A 237 " =    2.752
peak=   -3.458 closest distance to " NE  ARG A 156 " =    1.925
peak=   -3.447 closest distance to " O   PHE A 218 " =    1.511
peak=   -3.446 closest distance to " O   HOH Z  11 " =    1.739
peak=   -3.442 closest distance to " CD1 LEU A 101 " =    2.209
peak=   -3.440 closest distance to " ND2 ASN A  45 " =    1.232
peak=   -3.439 closest distance to " O   HOH Z 131 " =    4.101
peak=   -3.437 closest distance to " O   SER A  95 " =    1.503
peak=   -3.433 closest distance to " O   ALA A  10 " =    1.622
peak=   -3.431 closest distance to " CA  GLY A 241 " =    3.114
peak=   -3.422 closest distance to " O   HOH Z 165 " =    2.133
peak=   -3.421 closest distance to " OE2 GLU A 152 " =    1.260
peak=   -3.412 closest distance to " CB  ALA A   7 " =    2.175
peak=   -3.411 closest distance to " O   HOH Z 123 " =    2.489
peak=   -3.408 closest distance to " CG2 THR A  18 " =    2.822
peak=   -3.404 closest distance to " O   PRO A 163 " =    2.000
peak=   -3.397 closest distance to " CG  ARG A 269 " =    2.319
peak=   -3.393 closest distance to " O   ALA A 292 " =    2.085
peak=   -3.389 closest distance to " O   HOH Z  63 " =    1.745
peak=   -3.389 closest distance to " CG1 VAL A 250 " =    2.576
peak=   -3.388 closest distance to " CD2 PHE A 225 " =    1.180
peak=   -3.384 closest distance to " OG  SER A  97 " =    2.187
peak=   -3.369 closest distance to " CA  GLY A  98 " =    1.855
peak=   -3.367 closest distance to " O   HOH Z 316 " =    1.742
peak=   -3.366 closest distance to " CB  ASP A 132 " =    2.388
peak=   -3.363 closest distance to " O   HOH Z  10 " =    1.444
peak=   -3.362 closest distance to " O   HOH Z 369 " =    2.328
peak=   -3.362 closest distance to " O   HOH Z 166 " =    1.996
peak=   -3.355 closest distance to " CA  GLY A 241 " =    2.254
peak=   -3.345 closest distance to " CG2 THR A 221 " =    2.659
peak=   -3.342 closest distance to " O   HOH Z   6 " =    1.462
peak=   -3.341 closest distance to " CB  ASP A 132 " =    2.259
peak=   -3.339 closest distance to " O   HOH Z 359 " =    3.184
peak=   -3.337 closest distance to " OD1 ASN A 187 " =    1.620
peak=   -3.334 closest distance to " O   HOH Z 103 " =    1.693
peak=   -3.329 closest distance to " O   HOH Z 362 " =    5.939
peak=   -3.329 closest distance to " N   MET A 188 " =    1.916
peak=   -3.328 closest distance to " O   ALA A 180 " =    1.040
peak=   -3.324 closest distance to " OG BSER A 134 " =    1.763
peak=   -3.319 closest distance to " OE1 GLN A 183 " =    1.587
peak=   -3.319 closest distance to " O   TRP A  70 " =    1.439
peak=   -3.318 closest distance to " CB  GLN A  11 " =    1.842
peak=   -3.318 closest distance to " O   HOH Z 253 " =    3.893
peak=   -3.316 closest distance to " CA  GLY A  57 " =    2.235
peak=   -3.313 closest distance to " O   HOH Z 243 " =    2.008
peak=   -3.308 closest distance to " O   GLU A 152 " =    1.431
peak=   -3.299 closest distance to " CA  GLY A 203 " =    2.332
peak=   -3.296 closest distance to " CG  LEU A  83 " =    1.927
peak=   -3.292 closest distance to " CD2 HIS A 207 " =    2.249
peak=   -3.290 closest distance to " N   THR A  52 " =    1.757
peak=   -3.289 closest distance to " O   ALA A 180 " =    1.224
peak=   -3.288 closest distance to " O   HOH Z 357 " =    2.115
peak=   -3.287 closest distance to " CE3 TRP A 274 " =    2.316
peak=   -3.287 closest distance to " O   HOH Z 348 " =    1.886
peak=   -3.279 closest distance to " O   HOH Z 281 " =    2.716
peak=   -3.273 closest distance to " OH  TYR A 172 " =    1.842
peak=   -3.271 closest distance to " CA  GLY A 133 " =    2.016
peak=   -3.270 closest distance to " ND2 ASN A  60 " =    4.101
peak=   -3.268 closest distance to " NH2AARG A 275 " =    5.222
peak=   -3.264 closest distance to " O   ALA A  51 " =    1.245
peak=   -3.264 closest distance to " CB  ASP A 286 " =    2.182
peak=   -3.258 closest distance to " CE2 PHE A  61 " =    2.594
peak=   -3.255 closest distance to " O   HOH Z 292 " =    4.606
peak=   -3.248 closest distance to " O   HOH Z  43 " =    1.686
peak=   -3.246 closest distance to " NE  ARG A  36 " =    1.941
peak=   -3.240 closest distance to " CG1 VAL A 197 " =    2.149
peak=   -3.236 closest distance to " O   HOH Z 174 " =    2.570
peak=   -3.234 closest distance to " CB  ASP A 286 " =    1.712
peak=   -3.234 closest distance to " CG  TRP A 266 " =    1.942
peak=   -3.232 closest distance to " O   HOH Z  71 " =    2.199
peak=   -3.231 closest distance to " CG2 ILE A  49 " =    2.821
peak=   -3.225 closest distance to " O   HOH Z 139 " =    2.988
peak=   -3.220 closest distance to " ND2 ASN A  69 " =    1.766
peak=   -3.218 closest distance to " O   HOH Z 174 " =    4.194
peak=   -3.217 closest distance to " O   HOH Z 140 " =    1.752
peak=   -3.215 closest distance to " O   HOH Z 421 " =    3.107
peak=   -3.215 closest distance to " CG1 VAL A 197 " =    2.289
peak=   -3.213 closest distance to " O   VAL A 174 " =    2.209
peak=   -3.213 closest distance to " O   HOH Z 295 " =    1.529
peak=   -3.212 closest distance to " O   HOH Z 244 " =    1.958
peak=   -3.209 closest distance to " O   HOH Z 200 " =    2.825
peak=   -3.207 closest distance to " O   GLN A 240 " =    1.973
peak=   -3.204 closest distance to " NE2 GLN A 278 " =    1.648
peak=   -3.203 closest distance to " ND2 ASN A  60 " =    1.403
peak=   -3.203 closest distance to " O   HOH Z 318 " =    1.939
peak=   -3.190 closest distance to " CZ2 TRP A 274 " =    0.947
peak=   -3.186 closest distance to " OD2 ASP A  50 " =    1.657
peak=   -3.180 closest distance to " O   LYS A  76 " =    1.755
peak=   -3.178 closest distance to " CG1 VAL A 230 " =    2.055
peak=   -3.173 closest distance to " OE1 GLN A 223 " =    2.025
peak=   -3.171 closest distance to " O   HOH Z  52 " =    1.323
peak=   -3.167 closest distance to " OG  SER A  87 " =    1.359
peak=   -3.167 closest distance to " CA  GLY A 241 " =    2.857
peak=   -3.167 closest distance to " CB  SER A 210 " =    1.171
peak=   -3.157 closest distance to " C   ALA A 158 " =    1.473
peak=   -3.157 closest distance to " NE2 GLN A 194 " =    1.813
peak=   -3.153 closest distance to " O   ASN A 252 " =    1.355
peak=   -3.152 closest distance to " O   HOH Z 353 " =    2.234
peak=   -3.152 closest distance to " CG  MET A 105 " =    0.975
peak=   -3.152 closest distance to " OXT GLY A 302 " =    3.501
peak=   -3.150 closest distance to " O   HOH Z 191 " =    5.608
peak=   -3.148 closest distance to " O   SER A  22 " =    2.457
peak=   -3.138 closest distance to " N   SER A 276 " =    1.267
peak=   -3.137 closest distance to " CD  GLN A  77 " =    1.517
peak=   -3.136 closest distance to " CB  PRO A 163 " =    2.476
peak=   -3.133 closest distance to " CG  ASP A 231 " =    0.772
peak=   -3.132 closest distance to " O   ARG A 145 " =    1.501
peak=   -3.129 closest distance to " O   HOH Z 134 " =    3.329
peak=   -3.127 closest distance to " CG1 VAL A 125 " =    1.890
peak=   -3.125 closest distance to " CB  PHE A  16 " =    2.565
peak=   -3.124 closest distance to " OG  SER A  63 " =    1.281
peak=   -3.123 closest distance to " O   SER A 276 " =    1.696
peak=   -3.120 closest distance to " O   HOH Z 346 " =    1.733
peak=   -3.110 closest distance to " CG1 VAL A 268 " =    2.427
peak=   -3.109 closest distance to " NE2 GLN A  88 " =    1.876
peak=   -3.106 closest distance to " OE1 GLN A  88 " =    1.125
peak=   -3.105 closest distance to " CA  GLY A 133 " =    2.277
peak=   -3.104 closest distance to " O   HOH Z 256 " =    1.403
peak=   -3.101 closest distance to " CB  ALA A 100 " =    2.229
peak=   -3.093 closest distance to " O   HOH Z 189 " =    2.010
peak=   -3.087 closest distance to " O   HOH Z 218 " =    3.918
peak=   -3.082 closest distance to " C   ASP A 272 " =    2.271
peak=   -3.079 closest distance to " O   ALA A  34 " =    2.367
peak=   -3.078 closest distance to " O   HOH Z 216 " =    1.454
peak=   -3.073 closest distance to " NH1 ARG A 195 " =    2.678
peak=   -3.069 closest distance to " CG2 THR A 178 " =    2.191
peak=   -3.069 closest distance to " OD1AASN A 224 " =    1.774
peak=   -3.068 closest distance to " CA  SER A 135 " =    1.322
peak=   -3.066 closest distance to " O   HOH Z 283 " =    5.569
peak=   -3.066 closest distance to " O   HOH Z 216 " =    1.551
peak=   -3.063 closest distance to " CG2 VAL A 189 " =    1.965
peak=   -3.056 closest distance to " C   MET A 188 " =    1.415
peak=   -3.047 closest distance to " O   HOH Z 166 " =    1.483
peak=   -3.043 closest distance to " O   HOH Z 412 " =    4.068
peak=   -3.033 closest distance to " C   GLN A  58 " =    1.960
peak=   -3.023 closest distance to " OD1 ASP A 200 " =    1.575
peak=   -3.019 closest distance to " CD2 LEU A 143 " =    2.691
peak=   -3.011 closest distance to " C   ALA A 114 " =    2.265
peak=   -3.000 closest distance to " O   HOH Z 350 " =    1.858

================= 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    :  0.3723 0.3685   6.140923e+00   6.113279e+00
   1_bss:  0.3604 0.3555   6.127604e+00   6.092167e+00
   1_xyz:  0.2192 0.2485   5.691897e+00   5.777648e+00
   1_adp:  0.1992 0.2581   5.641183e+00   5.819981e+00
   1_occ:  0.1991 0.2579   5.640796e+00   5.820079e+00
   2_bss:  0.1974 0.2559   5.638702e+00   5.817387e+00
   2_xyz:  0.1475 0.1955   5.373258e+00   5.579300e+00
   2_adp:  0.1411 0.1841   5.322921e+00   5.518451e+00
   2_occ:  0.1409 0.1840   5.322185e+00   5.518170e+00
   3_bss:  0.1409 0.1843   5.321030e+00   5.516740e+00
   3_xyz:  0.1175 0.1597   5.172374e+00   5.398584e+00
   3_adp:  0.1130 0.1579   5.144986e+00   5.384394e+00
   3_occ:  0.1130 0.1578   5.144734e+00   5.384222e+00
   4_bss:  0.1131 0.1580   5.145016e+00   5.383649e+00
   4_xyz:  0.1100 0.1557   5.128800e+00   5.376329e+00
   4_adp:  0.1093 0.1552   5.125828e+00   5.374679e+00
   4_occ:  0.1092 0.1552   5.125870e+00   5.374946e+00
   5_bss:  0.1091 0.1552   5.125785e+00   5.375163e+00
   5_xyz:  0.1073 0.1554   5.119303e+00   5.376937e+00
   5_adp:  0.1070 0.1562   5.119937e+00   5.380885e+00
   5_occ:  0.1069 0.1562   5.120050e+00   5.381193e+00
   5_bss:  0.1068 0.1561   5.120071e+00   5.381148e+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:  0.328  38.617  -2.331  -0.167   2.093  -0.000   0.000   0.000
   1_xyz:  0.328  38.617  -2.331  -0.167   2.093  -0.000   0.000   0.000
   1_adp:  0.328  38.617  -2.331  -0.167   2.093  -0.000   0.000   0.000
   1_occ:  0.328  38.617  -2.331  -0.167   2.093  -0.000   0.000   0.000
   2_bss:  0.334  58.862  -2.977  -1.866  -0.053  -0.000  -0.000  -0.000
   2_xyz:  0.334  58.862  -2.977  -1.866  -0.053  -0.000  -0.000  -0.000
   2_adp:  0.334  58.862  -2.977  -1.866  -0.053  -0.000  -0.000  -0.000
   2_occ:  0.334  58.862  -2.977  -1.866  -0.053  -0.000  -0.000  -0.000
   3_bss:  0.336  58.862  -2.932  -2.289  -0.469  -0.000  -0.000  -0.000
   3_xyz:  0.336  58.862  -2.932  -2.289  -0.469  -0.000  -0.000  -0.000
   3_adp:  0.336  58.862  -2.932  -2.289  -0.469  -0.000  -0.000  -0.000
   3_occ:  0.336  58.862  -2.932  -2.289  -0.469  -0.000  -0.000  -0.000
   4_bss:  0.336  58.862  -2.822  -2.345  -0.563  -0.000  -0.000  -0.000
   4_xyz:  0.336  58.862  -2.822  -2.345  -0.563  -0.000  -0.000  -0.000
   4_adp:  0.336  58.862  -2.822  -2.345  -0.563  -0.000  -0.000  -0.000
   4_occ:  0.336  58.862  -2.822  -2.345  -0.563  -0.000  -0.000  -0.000
   5_bss:  0.324  52.954  -2.617  -2.222  -0.442  -0.000  -0.000  -0.000
   5_xyz:  0.324  52.954  -2.617  -2.222  -0.442  -0.000  -0.000  -0.000
   5_adp:  0.324  52.954  -2.617  -2.222  -0.442  -0.000  -0.000  -0.000
   5_occ:  0.324  52.954  -2.617  -2.222  -0.442  -0.000  -0.000  -0.000
   5_bss:  0.321  52.956  -2.392  -2.029  -0.256  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.742 0.6600  0.8390    37300.148
   1_bss:  37.320 0.6745  0.8556    33927.373
   1_xyz:  23.338 0.8297  0.9997    14925.992
   1_adp:  24.743 0.8145  0.9874    16380.000
   1_occ:  24.773 0.8141  0.9863    16364.920
   2_bss:  24.570 0.8162  0.9385    16199.605
   2_xyz:  18.236 0.8780  0.9811     9400.578
   2_adp:  16.669 0.8928  0.9838     8389.027
   2_occ:  16.662 0.8929  0.9837     8376.277
   3_bss:  16.609 0.8934  0.9746     8337.297
   3_xyz:  14.318 0.9119  0.9842     6497.058
   3_adp:  13.970 0.9150  0.9789     6304.832
   3_occ:  13.965 0.9150  0.9788     6300.609
   4_bss:  13.967 0.9150  0.9784     6307.610
   4_xyz:  13.681 0.9177  0.9790     6182.765
   4_adp:  13.627 0.9183  0.9730     6159.608
   4_occ:  13.632 0.9182  0.9729     6159.557
   5_bss:  13.637 0.9182  0.9781     6158.368
   5_xyz:  13.698 0.9176  0.9784     6211.213
   5_adp:  13.783 0.9169  0.9704     6240.868
   5_occ:  13.786 0.9169  0.9703     6242.198
   5_bss:  13.787 0.9169  0.9775     6241.645
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6872e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6872e-01
   1_xyz:   1.167  0.008  0.077 15.314  0.005  4.109   7.8044e-02
   1_adp:   1.167  0.008  0.077 15.314  0.005  4.109   7.8044e-02
   1_occ:   1.167  0.008  0.077 15.314  0.005  4.109   7.8044e-02
   2_bss:   1.167  0.008  0.077 15.314  0.005  4.109   7.8044e-02
   2_xyz:   0.961  0.006  0.071 14.632  0.004  4.111   5.3285e-02
   2_adp:   0.961  0.006  0.071 14.632  0.004  4.111   5.3285e-02
   2_occ:   0.961  0.006  0.071 14.632  0.004  4.111   5.3285e-02
   3_bss:   0.961  0.006  0.071 14.632  0.004  4.111   5.3285e-02
   3_xyz:   1.042  0.008  0.079 14.962  0.004  4.115   6.4803e-02
   3_adp:   1.042  0.008  0.079 14.962  0.004  4.115   6.4803e-02
   3_occ:   1.042  0.008  0.079 14.962  0.004  4.115   6.4803e-02
   4_bss:   1.042  0.008  0.079 14.962  0.004  4.115   6.4803e-02
   4_xyz:   1.002  0.007  0.077 14.732  0.004  4.118   6.0106e-02
   4_adp:   1.002  0.007  0.077 14.732  0.004  4.118   6.0106e-02
   4_occ:   1.002  0.007  0.077 14.732  0.004  4.118   6.0106e-02
   5_bss:   1.002  0.007  0.077 14.732  0.004  4.118   6.0106e-02
   5_xyz:   1.037  0.008  0.079 14.778  0.004  4.120   6.4537e-02
   5_adp:   1.037  0.008  0.079 14.778  0.004  4.120   6.4537e-02
   5_occ:   1.037  0.008  0.079 14.778  0.004  4.120   6.4537e-02
   5_bss:   1.037  0.008  0.079 14.778  0.004  4.120   6.4537e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.510   2.4032e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.510   2.4032e-01
   1_xyz:   8.500  0.051  0.307 83.336  0.040  2.068   8.0372e-02
   1_adp:   8.500  0.051  0.307 83.336  0.040  2.068   8.0372e-02
   1_occ:   8.500  0.051  0.307 83.336  0.040  2.068   8.0372e-02
   2_bss:   8.500  0.051  0.307 83.336  0.040  2.068   8.0372e-02
   2_xyz:   6.410  0.049  0.224 81.875  0.043  2.396   3.9474e-02
   2_adp:   6.410  0.049  0.224 81.875  0.043  2.396   3.9474e-02
   2_occ:   6.410  0.049  0.224 81.875  0.043  2.396   3.9474e-02
   3_bss:   6.410  0.049  0.224 81.875  0.043  2.396   3.9474e-02
   3_xyz:   6.588  0.051  0.271 83.704  0.033  2.316   5.0832e-02
   3_adp:   6.588  0.051  0.271 83.704  0.033  2.316   5.0832e-02
   3_occ:   6.588  0.051  0.271 83.704  0.033  2.316   5.0832e-02
   4_bss:   6.588  0.051  0.271 83.704  0.033  2.316   5.0832e-02
   4_xyz:   6.329  0.047  0.253 83.217  0.040  2.340   4.3153e-02
   4_adp:   6.329  0.047  0.253 83.217  0.040  2.340   4.3153e-02
   4_occ:   6.329  0.047  0.253 83.217  0.040  2.340   4.3153e-02
   5_bss:   6.329  0.047  0.253 83.217  0.040  2.340   4.3153e-02
   5_xyz:   6.373  0.054  0.271 83.714  0.035  2.291   5.3047e-02
   5_adp:   6.373  0.054  0.271 83.714  0.035  2.291   5.3047e-02
   5_occ:   6.373  0.054  0.271 83.714  0.035  2.291   5.3047e-02
   5_bss:   6.373  0.054  0.271 83.714  0.035  2.291   5.3047e-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:  75.53   0.00  17.37  68.74   0.00  13.26  75.53   3.54  39.76
   1_occ:  75.53   0.00  17.37  68.74   0.00  13.26  75.53   3.54  39.76
   2_bss:  75.53   0.00  17.37  68.74   0.00  13.26  75.53   3.54  39.76
   2_xyz:  75.53   0.00  17.37  68.74   0.00  13.26  75.53   3.54  39.76
   2_adp:  72.08   0.59  16.89  71.92   0.59  12.94  72.08   6.00  38.39
   2_occ:  72.08   0.59  16.89  71.92   0.59  12.94  72.08   6.00  38.39
   3_bss:  72.08   0.59  16.89  71.92   0.59  12.94  72.08   6.00  38.39
   3_xyz:  72.08   0.59  16.89  71.92   0.59  12.94  72.08   6.00  38.39
   3_adp:  82.09   0.28  17.25  82.09   0.28  12.92  77.63   1.45  40.84
   3_occ:  82.09   0.28  17.25  82.09   0.28  12.92  77.63   1.45  40.84
   4_bss:  82.09   0.28  17.25  82.09   0.28  12.92  77.63   1.45  40.84
   4_xyz:  82.09   0.28  17.25  82.09   0.28  12.92  77.63   1.45  40.84
   4_adp:  83.68   0.70  17.01  83.68   0.70  12.74  77.22   1.27  40.22
   4_occ:  83.68   0.70  17.01  83.68   0.70  12.74  77.22   1.27  40.22
   5_bss:  83.68   0.70  17.01  83.68   0.70  12.74  77.22   1.27  40.22
   5_xyz:  83.68   0.70  17.01  83.68   0.70  12.74  77.22   1.27  40.22
   5_adp:  93.11   0.00  16.99  93.11   0.00  12.67  82.00   3.18  40.53
   5_occ:  93.11   0.00  16.99  93.11   0.00  12.67  82.00   3.18  40.53
   5_bss:  93.11   0.00  16.99  93.11   0.00  12.67  82.01   3.18  40.53
------------------------------------------------------------------------
 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:    1.734    0.016    0.315
   1_adp:    1.734    0.016    0.315
   1_occ:    1.734    0.016    0.315
   2_bss:    1.734    0.016    0.315
   2_xyz:    1.256    0.033    0.398
   2_adp:    1.256    0.033    0.398
   2_occ:    1.256    0.033    0.398
   3_bss:    1.256    0.033    0.398
   3_xyz:    1.179    0.036    0.465
   3_adp:    1.179    0.036    0.465
   3_occ:    1.179    0.036    0.465
   4_bss:    1.179    0.036    0.465
   4_xyz:    1.413    0.021    0.481
   4_adp:    1.413    0.021    0.481
   4_occ:    1.413    0.021    0.481
   5_bss:    1.413    0.021    0.481
   5_xyz:    1.456    0.067    0.491
   5_adp:    1.456    0.067    0.491
   5_occ:    1.456    0.067    0.491
   5_bss:    1.456    0.067    0.491
------------------------------------------------------------------------

CPU time actual refinement: 323.27


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_404/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_404/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_404/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_404/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_404/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.11 
  Macro-tasks:
    bulk solvent and scale       = 36.05  
    individual site refinement   = 133.07 
    weights calculation          = 29.52  
    collect and process          = 6.68   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 205.44 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 102.68 
    alpha_beta                      = 8.01   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 111.28 
    fmodel                         = 6.73   
    r_factors                      = 0.24   
    phase_errors                   = 11.23  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 243.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.600 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    639 calls, 102.31 s
gradients_fft:          584 calls,  97.87 s

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

# Date 2008-01-16 Time 04:44:33 PST -0800 (1200487473.10 s)
Start R-work = 0.3723, R-free = 0.3685 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1749 (no bulk solvent and anisotropic scale)

Start R-work = 0.3604, R-free = 0.3555
Final R-work = 0.1068, R-free = 0.1561