# Date 2008-01-16 Time 06:13:52 PST -0800 (1200492832.68 s)
#phil __OFF__

Command line arguments: "../1063.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31641
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1063

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.6339, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.02102
Completeness in resolution range: 0.977885
Completeness with d_max=infinity: 0.974771

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   2.0210

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.02102
Completeness in resolution range: 0.977885
Completeness with d_max=infinity: 0.974771

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.3239 [2101/2125]  1892   209   9.9%
  bin  2:  4.3239 -  3.4451 [2029/2048]  1826   203  10.0%
  bin  3:  3.4451 -  3.0135 [1993/2012]  1790   203  10.2%
  bin  4:  3.0135 -  2.7397 [1966/1996]  1772   194   9.9%
  bin  5:  2.7397 -  2.5443 [1963/1982]  1767   196  10.0%
  bin  6:  2.5443 -  2.3949 [1952/1977]  1756   196  10.0%
  bin  7:  2.3949 -  2.2754 [1969/1997]  1772   197  10.0%
  bin  8:  2.2754 -  2.1767 [1927/1963]  1735   192  10.0%
  bin  9:  2.1767 -  2.0931 [1917/1959]  1728   189   9.9%
  bin 10:  2.0931 -  2.0210 [1772/1973]  1592   180  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1063/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:
        1.56 -     2.23: 5
        2.23 -     2.90: 1315
        2.90 -     3.56: 4368
        3.56 -     4.23: 8999
        4.23 -     4.90: 13074
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.561 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.155 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.155 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27756 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_1063/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1063/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.63395 87.2539 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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4030   r_free= 0.3920   ksol= 0.00   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.190968                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8223 0.99   1372  153 0.3134 0.3141      6.4173      6.3586|
|  2:  4.8223 -  3.8481 0.99   1312  145 0.3259 0.3267        6.65      6.6749|
|  3:  3.8481 -  3.3677 0.99   1288  144 0.3501 0.3344      6.5365      6.4851|
|  4:  3.3677 -  3.0625 0.99   1278  143 0.3932 0.3755      6.4374      6.3708|
|  5:  3.0625 -  2.8445 0.99   1270  140 0.4173 0.3940      6.2711      6.2688|
|  6:  2.8445 -  2.6778 0.99   1277  140 0.4320 0.4203      6.2087      6.1573|
|  7:  2.6778 -  2.5443 0.99   1250  140 0.4370 0.4112      6.1508      6.0852|
|  8:  2.5443 -  2.4340 0.98   1263  140 0.4473 0.4018      6.1293      6.1113|
|  9:  2.4340 -  2.3407 0.98   1256  138 0.4482 0.4513      6.0619      6.1141|
| 10:  2.3407 -  2.2602 0.99   1237  138 0.4648 0.4312      6.0723      6.0328|
| 11:  2.2602 -  2.1897 0.98   1249  142 0.4654 0.4467      6.0041       6.037|
| 12:  2.1897 -  2.1273 0.97   1242  134 0.4710 0.4665      5.9522      5.9825|
| 13:  2.1273 -  2.0714 1.00   1233  141 0.4708 0.4825      5.8622       5.849|
| 14:  2.0714 -  2.0210 0.86   1103  121 0.4743 0.4932      5.8059      5.7588|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8223  1372   153  0.77  28.32   0.84     0.79      50382.59|
|  2:  4.8223 -  3.8481  1312   145  0.79  26.88   0.93     0.86      65458.44|
|  3:  3.8481 -  3.3677  1288   144  0.74  32.07   0.94     0.85      68666.01|
|  4:  3.3677 -  3.0625  1278   143  0.68  37.29   0.92     0.81      62392.28|
|  5:  3.0625 -  2.8445  1270   140  0.60  43.91   0.92     0.76      52826.87|
|  6:  2.8445 -  2.6778  1277   140  0.59  45.23   0.93     0.74      46942.85|
|  7:  2.6778 -  2.5443  1250   140  0.56  46.90   0.93     0.73      43116.84|
|  8:  2.5443 -  2.4340  1263   140  0.56  47.51   0.94     0.74      40949.58|
|  9:  2.4340 -  2.3407  1256   138  0.55  48.06   0.94     0.73      38293.59|
| 10:  2.3407 -  2.2602  1237   138  0.53  49.97   0.96     0.72      36220.33|
| 11:  2.2602 -  2.1897  1249   142  0.51  51.56   0.95     0.71      35099.85|
| 12:  2.1897 -  2.1273  1242   134  0.49  53.33   0.94     0.69      34265.80|
| 13:  2.1273 -  2.0714  1233   141  0.45  56.37   0.93     0.64      31307.70|
| 14:  2.0714 -  2.0210  1103   121  0.42  58.45   0.94     0.55      26379.56|
|alpha:            min =        0.55 max =            0.86 mean =         0.74|
|beta:             min =    26379.56 max =        68666.01 mean =     45538.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.96 mean =        44.36|
|phase err.(test): min =        0.00 max =           89.97 mean =        44.44|
|-----------------------------------------------------------------------------|

============================== 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 = 9.268564              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.267   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.300058              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.373   (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 |  1.561 -  1.895:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.895 -  2.229:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.229 -  2.563:       17 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.563 -  2.897:     1298 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.897 -  3.231:     1867 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.231 -  3.564:     2501 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.564 -  3.898:     4595 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.898 -  4.232:     4404 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.232 -  4.566:     5931 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.566 -  4.900:     7143 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.561 |       0.164 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4030   r_free= 0.3920   ksol= 0.00   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.190968                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3945   r_free= 0.3842   ksol= 0.30   Bsol= 80.00   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,2.43,-0.11,0.00,-0.00,-0.00); trace/3= 0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.179372                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.351312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.251   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.703865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.156   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3945      final r-factor (work) = 0.2347          |
| start r-factor (free) = 0.3842      final r-factor (free) = 0.2570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9736 = 8.35 * 0.50 * 6.1810 + 1.00 * 0.1640                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.9424 = 8.35 * 0.50 * 5.9499 + 1.00 * 0.0978                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2347      final r-factor (work) = 0.2155          |
| start r-factor (free) = 0.2570      final r-factor (free) = 0.2609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1944 = 0.70 * 1.00 * 5.9499 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0379 = 0.70 * 1.00 * 5.6899 + 1.00 * 0.0330                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.47   17.10    None  None   None       |
|    all(noH): 2823   0      0.00    68.47   17.10    None  None   None       |
|    Sol.    : 438    0      3.91    68.47   39.16    None  None   None       |
|    Mac.    : 2385   0      0.00    60.91   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.847:  479   |   5:    34.237 -  41.084:  106        |
|      1:     6.847 -  13.695: 1069   |   6:    41.084 -  47.931:  102        |
|      2:    13.695 -  20.542:  540   |   7:    47.931 -  54.779:   79        |
|      3:    20.542 -  27.389:  268   |   8:    54.779 -  61.626:   57        |
|      4:    27.389 -  34.237:  115   |   9:    61.626 -  68.473:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2155 r_free = 0.2609             target_work(ml) = 5.694         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2152 r_free = 0.2601             target_work(ml) = 5.693         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2152   r_free= 0.2601   ksol= 0.30   Bsol= 80.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,2.43,-0.11,0.00,-0.00,-0.00); trace/3= 0.43                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.693303                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2131   r_free= 0.2579   ksol= 0.33   Bsol= 80.45   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.36,-1.01,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.690639                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.402320              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.859   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.393099              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2131      final r-factor (work) = 0.1557          |
| start r-factor (free) = 0.2579      final r-factor (free) = 0.1922          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7931 = 3.40 * 0.50 * 5.6992 + 1.00 * 0.0978                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5261 = 3.40 * 0.50 * 5.5612 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1557      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.1922      final r-factor (free) = 0.1806          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2054 = 0.39 * 1.00 * 5.5612 + 1.00 * 0.0193                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1680 = 0.39 * 1.00 * 5.3619 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.23   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    77.23   17.20    None  None   None       |
|    Sol.    : 438    0      5.29    77.23   40.87    None  None   None       |
|    Mac.    : 2385   0      0.00    73.65   12.85    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 -   7.723:  579   |   5:    38.613 -  46.335:   88        |
|      1:     7.723 -  15.445: 1290   |   6:    46.335 -  54.058:   96        |
|      2:    15.445 -  23.168:  400   |   7:    54.058 -  61.781:   83        |
|      3:    23.168 -  30.890:  140   |   8:    61.781 -  69.503:   33        |
|      4:    30.890 -  38.613:  105   |   9:    69.503 -  77.226:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1421 r_free = 0.1806             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1806             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1806   ksol= 0.33   Bsol= 80.45   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.36,-1.01,-0.00,-0.00,-0.00); trace/3= -1.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.330062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1418   r_free= 0.1802   ksol= 0.33   Bsol= 75.23   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.11,-0.69,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.327954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.295128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.408  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.067249              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.828   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1802      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8983 = 3.30 * 0.50 * 5.3610 + 1.00 * 0.0657                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7408 = 3.30 * 0.50 * 5.2580 + 1.00 * 0.0780                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1667      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6236 = 1.07 * 1.00 * 5.2580 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5575 = 1.07 * 1.00 * 5.1967 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.17   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    90.17   17.24    None  None   None       |
|    Sol.    : 438    0      0.00    87.46   42.21    None  None   None       |
|    Mac.    : 2385   0      0.00    90.17   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.018:  903   |   5:    45.087 -  54.105:   97        |
|      1:     9.018 -  18.035: 1182   |   6:    54.105 -  63.122:   75        |
|      2:    18.035 -  27.052:  263   |   7:    63.122 -  72.140:   50        |
|      3:    27.052 -  36.070:  124   |   8:    72.140 -  81.157:   15        |
|      4:    36.070 -  45.087:  107   |   9:    81.157 -  90.175:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1653             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1652             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1652   ksol= 0.33   Bsol= 75.23   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.11,-0.69,-0.00,-0.00,-0.00); trace/3= -1.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.189860                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1652   ksol= 0.32   Bsol= 69.29   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.17,-0.41,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.189623                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.436934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.959  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.235747              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4104 = 2.44 * 0.50 * 5.1970 + 1.00 * 0.0780                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3855 = 2.44 * 0.50 * 5.1833 + 1.00 * 0.0698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2332 = 0.24 * 1.00 * 5.1833 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2307 = 0.24 * 1.00 * 5.1824 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    87.46   16.40    None  None   None       |
|    all(noH): 2823   0      0.55    87.46   16.40    None  None   None       |
|    Sol.    : 438    0      1.86    85.75   38.97    None  None   None       |
|    Mac.    : 2385   0      0.55    87.46   12.25    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:     0.549 -   9.240:  987   |   5:    44.004 -  52.695:   89        |
|      1:     9.240 -  17.931: 1128   |   6:    52.695 -  61.386:   70        |
|      2:    17.931 -  26.622:  247   |   7:    61.386 -  70.077:   30        |
|      3:    26.622 -  35.313:  138   |   8:    70.077 -  78.768:    7        |
|      4:    35.313 -  44.004:  122   |   9:    78.768 -  87.459:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1622             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1622             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1622   ksol= 0.32   Bsol= 69.29   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.17,-0.41,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1618   ksol= 0.32   Bsol= 65.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.17,-0.41,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.177257                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.971923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.519  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.122524              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.951  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1792 = 1.97 * 0.50 * 5.1822 + 1.00 * 0.0698                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1685 = 1.97 * 0.50 * 5.1750 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6430 = 0.12 * 1.00 * 5.1750 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6424 = 0.12 * 1.00 * 5.1863 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    81.02   15.67    None  None   None       |
|    all(noH): 2823   0      1.29    81.02   15.67    None  None   None       |
|    Sol.    : 438    0      4.27    81.02   35.97    None  None   None       |
|    Mac.    : 2385   0      1.29    80.87   11.94    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:     1.293 -   9.266: 1011   |   5:    41.156 -  49.129:   91        |
|      1:     9.266 -  17.238: 1094   |   6:    49.129 -  57.102:   66        |
|      2:    17.238 -  25.211:  261   |   7:    57.102 -  65.074:   22        |
|      3:    25.211 -  33.184:  136   |   8:    65.074 -  73.047:    7        |
|      4:    33.184 -  41.156:  131   |   9:    73.047 -  81.019:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1624             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1624             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1624   ksol= 0.32   Bsol= 65.00   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-1.17,-0.41,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186461                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8223 0.99   1372  153 0.1042 0.1304      5.4253      5.5435|
|  2:  4.8223 -  3.8481 0.99   1312  145 0.0909 0.1135      5.4795      5.6801|
|  3:  3.8481 -  3.3677 0.99   1288  144 0.1070 0.1501      5.5055      5.8509|
|  4:  3.3677 -  3.0625 0.99   1278  143 0.1270 0.1576      5.4911      5.6247|
|  5:  3.0625 -  2.8445 0.99   1270  140 0.1427 0.1818       5.396      5.5851|
|  6:  2.8445 -  2.6778 0.99   1277  140 0.1312 0.1986       5.281      5.5181|
|  7:  2.6778 -  2.5443 0.99   1250  140 0.1344 0.1819      5.2231      5.4396|
|  8:  2.5443 -  2.4340 0.98   1263  140 0.1246 0.1777      5.1384       5.411|
|  9:  2.4340 -  2.3407 0.98   1256  138 0.1214 0.1740      5.0695      5.2955|
| 10:  2.3407 -  2.2602 0.99   1237  138 0.1224 0.1911      5.0325      5.2794|
| 11:  2.2602 -  2.1897 0.98   1249  142 0.1233 0.1789      4.9854      5.2607|
| 12:  2.1897 -  2.1273 0.97   1242  134 0.1213 0.1742      4.9446      5.2416|
| 13:  2.1273 -  2.0714 1.00   1233  141 0.1178 0.1722      4.8265      5.1002|
| 14:  2.0714 -  2.0210 0.86   1103  121 0.1105 0.1798      4.6862      4.9687|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8223  1372   153  0.94   9.65   0.96     0.94       7850.28|
|  2:  4.8223 -  3.8481  1312   145  0.95   8.40   0.99     0.97       9547.68|
|  3:  3.8481 -  3.3677  1288   144  0.93  11.40   1.00     0.99      10991.30|
|  4:  3.3677 -  3.0625  1278   143  0.92  13.89   0.99     0.97      10789.80|
|  5:  3.0625 -  2.8445  1270   140  0.89  16.67   0.98     0.95       9255.88|
|  6:  2.8445 -  2.6778  1277   140  0.89  16.72   0.98     0.95       7880.70|
|  7:  2.6778 -  2.5443  1250   140  0.89  16.74   0.98     0.95       6911.30|
|  8:  2.5443 -  2.4340  1263   140  0.91  15.68   0.98     0.95       5950.86|
|  9:  2.4340 -  2.3407  1256   138  0.90  15.87   0.99     0.95       5325.17|
| 10:  2.3407 -  2.2602  1237   138  0.90  16.33   0.99     0.94       4877.40|
| 11:  2.2602 -  2.1897  1249   142  0.90  16.58   0.98     0.93       4532.82|
| 12:  2.1897 -  2.1273  1242   134  0.91  15.68   0.99     0.98       4314.46|
| 13:  2.1273 -  2.0714  1233   141  0.91  15.68   0.98     0.97       3479.05|
| 14:  2.0714 -  2.0210  1103   121  0.91  14.62   0.95     0.91       2502.85|
|alpha:            min =        0.91 max =            0.99 mean =         0.95|
|beta:             min =     2502.85 max =        10991.30 mean =      6807.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.74 mean =        14.50|
|phase err.(test): min =        0.00 max =           89.23 mean =        13.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1623   ksol= 0.32   Bsol= 58.85   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-1.13,-0.36,-0.00,-0.00,-0.00); trace/3= -1.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186585                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1623   ksol= 0.32   Bsol= 58.85   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-1.13,-0.36,-0.00,-0.00,-0.00); trace/3= -1.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186585                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8223 0.99   1372  153 0.1040 0.1302      5.4226      5.5406|
|  2:  4.8223 -  3.8481 0.99   1312  145 0.0903 0.1129      5.4753      5.6751|
|  3:  3.8481 -  3.3677 0.99   1288  144 0.1069 0.1501      5.5038       5.851|
|  4:  3.3677 -  3.0625 0.99   1278  143 0.1271 0.1575      5.4922       5.625|
|  5:  3.0625 -  2.8445 0.99   1270  140 0.1429 0.1823      5.3981      5.5872|
|  6:  2.8445 -  2.6778 0.99   1277  140 0.1313 0.1987      5.2826      5.5193|
|  7:  2.6778 -  2.5443 0.99   1250  140 0.1345 0.1821      5.2245      5.4412|
|  8:  2.5443 -  2.4340 0.98   1263  140 0.1249 0.1778      5.1395      5.4118|
|  9:  2.4340 -  2.3407 0.98   1256  138 0.1215 0.1738      5.0701      5.2957|
| 10:  2.3407 -  2.2602 0.99   1237  138 0.1224 0.1913      5.0333      5.2807|
| 11:  2.2602 -  2.1897 0.98   1249  142 0.1234 0.1790      4.9861      5.2612|
| 12:  2.1897 -  2.1273 0.97   1242  134 0.1213 0.1744      4.9451      5.2425|
| 13:  2.1273 -  2.0714 1.00   1233  141 0.1178 0.1724      4.8269      5.1006|
| 14:  2.0714 -  2.0210 0.86   1103  121 0.1105 0.1799      4.6868      4.9692|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8223  1372   153  0.94   9.62   0.96     0.94       7788.95|
|  2:  4.8223 -  3.8481  1312   145  0.95   8.36   0.99     0.97       9480.90|
|  3:  3.8481 -  3.3677  1288   144  0.93  11.35   1.00     0.99      10943.29|
|  4:  3.3677 -  3.0625  1278   143  0.92  13.90   0.99     0.97      10808.43|
|  5:  3.0625 -  2.8445  1270   140  0.89  16.69   0.98     0.95       9286.41|
|  6:  2.8445 -  2.6778  1277   140  0.89  16.75   0.97     0.95       7910.44|
|  7:  2.6778 -  2.5443  1250   140  0.89  16.76   0.98     0.95       6929.57|
|  8:  2.5443 -  2.4340  1263   140  0.91  15.69   0.98     0.95       5961.91|
|  9:  2.4340 -  2.3407  1256   138  0.90  15.88   0.99     0.95       5331.89|
| 10:  2.3407 -  2.2602  1237   138  0.90  16.34   0.99     0.94       4884.78|
| 11:  2.2602 -  2.1897  1249   142  0.90  16.60   0.98     0.93       4540.12|
| 12:  2.1897 -  2.1273  1242   134  0.91  15.69   0.99     0.97       4320.48|
| 13:  2.1273 -  2.0714  1233   141  0.91  15.69   0.98     0.97       3483.60|
| 14:  2.0714 -  2.0210  1103   121  0.91  14.63   0.95     0.91       2506.08|
|alpha:            min =        0.91 max =            0.99 mean =         0.95|
|beta:             min =     2506.08 max =        10943.29 mean =      6804.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.51|
|phase err.(test): min =        0.00 max =           89.32 mean =        13.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.25    80.97   15.62    None  None   None       |
|    all(noH): 2823   0      1.25    80.97   15.62    None  None   None       |
|    Sol.    : 438    0      4.23    80.97   35.93    None  None   None       |
|    Mac.    : 2385   0      1.25    80.83   11.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.248 -   9.220: 1011   |   5:    41.111 -  49.083:   91        |
|      1:     9.220 -  17.193: 1094   |   6:    49.083 -  57.056:   66        |
|      2:    17.193 -  25.166:  261   |   7:    57.056 -  65.029:   22        |
|      3:    25.166 -  33.138:  136   |   8:    65.029 -  73.001:    7        |
|      4:    33.138 -  41.111:  131   |   9:    73.001 -  80.974:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.431 - 4.860
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 301
   mapped sites are within: 0.702 - 4.860

peak=    5.744 closest distance to " O   HOH Z 111 " =    2.283
peak=    5.485 closest distance to " CB  GLN A 223 " =    1.412
peak=    5.081 closest distance to " CG  PRO A  54 " =    1.373
peak=    4.897 closest distance to " CB  SER A  63 " =    1.259
peak=    4.825 closest distance to " CZ  PHE A 218 " =    1.078
peak=    4.809 closest distance to " CB  ARG A 190 " =    1.679
peak=    4.694 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.690 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.526 closest distance to " CG  PRO A 198 " =    1.319
peak=    4.497 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.474 closest distance to " C   PRO A 198 " =    1.519
peak=    4.435 closest distance to " CB  LEU A 228 " =    1.037
peak=    4.418 closest distance to " O   HOH Z 298 " =    1.968
peak=    4.403 closest distance to " O   HOH Z 234 " =    3.954
peak=    4.382 closest distance to " CB  ARG A  79 " =    1.332
peak=    4.363 closest distance to " CB  GLU A 152 " =    1.187
peak=    4.360 closest distance to " CB  ASN A 148 " =    1.428
peak=    4.342 closest distance to " CB  PRO A  54 " =    0.951
peak=    4.341 closest distance to " O   HOH Z 369 " =    2.029
peak=    4.321 closest distance to " O   HOH Z 232 " =    2.301
peak=    4.291 closest distance to " CB  ASN A  39 " =    0.882
peak=    4.252 closest distance to " CG  PRO A 243 " =    1.100
peak=    4.249 closest distance to " CB  TRP A 266 " =    0.927
peak=    4.239 closest distance to " NH2 ARG A 156 " =    1.223
peak=    4.221 closest distance to " CA  TYR A  30 " =    0.927
peak=    4.217 closest distance to " O   HOH Z  21 " =    1.852
peak=    4.214 closest distance to " O   HOH Z 189 " =    2.722
peak=    4.195 closest distance to " O   HOH Z 368 " =    2.144
peak=    4.191 closest distance to " O   HOH Z 126 " =    1.901
peak=    4.190 closest distance to " CB  TYR A 169 " =    0.769
peak=    4.189 closest distance to " O   HOH Z  40 " =    1.860
peak=    4.172 closest distance to " CB  GLU A  46 " =    0.960
peak=    4.169 closest distance to " CB  VAL A 202 " =    1.543
peak=    4.133 closest distance to " CB  GLU A 128 " =    1.039
peak=    4.102 closest distance to " CD1 LEU A 300 " =    1.250
peak=    4.090 closest distance to " ND2 ASN A 187 " =    1.519
peak=    4.076 closest distance to " O   HOH Z  15 " =    2.032
peak=    4.075 closest distance to " O   HOH Z 303 " =    2.160
peak=    4.074 closest distance to " CB  GLU A 277 " =    3.731
peak=    4.066 closest distance to " CB  ASP A 124 " =    0.743
peak=    4.050 closest distance to " CA  ALA A  51 " =    0.909
peak=    4.049 closest distance to " O   HOH Z 265 " =    2.212
peak=    4.014 closest distance to " CB  ALA A 104 " =    0.704
peak=    4.003 closest distance to " CD  LYS A 166 " =    1.302
peak=    4.002 closest distance to " CA  ASP A 191 " =    0.806
peak=    3.977 closest distance to " O   HOH Z 236 " =    1.973
peak=    3.954 closest distance to " O   HOH Z 403 " =    1.709
peak=    3.951 closest distance to " CA  SER A  87 " =    1.057
peak=    3.951 closest distance to " CG2 VAL A 257 " =    0.911
peak=    3.943 closest distance to " O   HOH Z  63 " =    1.849
peak=    3.940 closest distance to " CB  ASN A 187 " =    1.132
peak=    3.925 closest distance to " CD  ARG A 269 " =    0.911
peak=    3.916 closest distance to " O   HOH Z 214 " =    2.063
peak=    3.895 closest distance to " O   HOH Z  19 " =    2.074
peak=    3.873 closest distance to " O   HOH Z 423 " =    1.931
peak=    3.866 closest distance to " CZ  PHE A 192 " =    0.994
peak=    3.856 closest distance to " CB  ILE A 120 " =    1.190
peak=    3.853 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.845 closest distance to " O   HOH Z 147 " =    1.834
peak=    3.833 closest distance to " O   MET A 105 " =    1.917
peak=    3.825 closest distance to " CG1 VAL A 153 " =    0.990
peak=    3.811 closest distance to " CB  ASP A 140 " =    0.907
peak=    3.804 closest distance to " O   HOH Z 158 " =    3.124
peak=    3.796 closest distance to " O   HOH Z 261 " =    1.877
peak=    3.793 closest distance to " CA  THR A 221 " =    0.885
peak=    3.782 closest distance to " CB  VAL A 265 " =    1.286
peak=    3.772 closest distance to " O   HOH Z 406 " =    1.688
peak=    3.772 closest distance to " CA  ARG A 195 " =    1.186
peak=    3.767 closest distance to " CD1 LEU A  96 " =    0.720
peak=    3.765 closest distance to " O   HOH Z 133 " =    2.352
peak=    3.762 closest distance to " CB  SER A   3 " =    1.403
peak=    3.758 closest distance to " O   HOH Z 193 " =    2.073
peak=    3.750 closest distance to " O   HOH Z  67 " =    1.929
peak=    3.750 closest distance to " O   HOH Z 368 " =    3.643
peak=    3.732 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.723 closest distance to " O   SER A  87 " =    2.233
peak=    3.723 closest distance to " CA  THR A 264 " =    0.876
peak=    3.719 closest distance to " CB  ALA A 291 " =    1.101
peak=    3.713 closest distance to " CE  LYS A  76 " =    0.884
peak=    3.705 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.701 closest distance to " N   GLY A  98 " =    1.161
peak=    3.696 closest distance to " NE2 GLN A  11 " =    1.081
peak=    3.696 closest distance to " O   HOH Z 213 " =    1.869
peak=    3.693 closest distance to " O   HOH Z  61 " =    1.648
peak=    3.685 closest distance to " O   HOH Z 421 " =    1.650
peak=    3.684 closest distance to " O   HOH Z 346 " =    1.526
peak=    3.680 closest distance to " O   HOH Z  44 " =    2.077
peak=    3.668 closest distance to " O   HOH Z 402 " =    1.504
peak=    3.664 closest distance to " CB  GLN A 103 " =    0.869
peak=    3.663 closest distance to " O   HOH Z 148 " =    3.313
peak=    3.662 closest distance to " CB  PRO A 198 " =    0.966
peak=    3.662 closest distance to " CG2 THR A 221 " =    0.933
peak=    3.662 closest distance to " O   HOH Z 294 " =    1.557
peak=    3.641 closest distance to " CA  ARG A  36 " =    1.145
peak=    3.637 closest distance to " CA  GLY A 241 " =    0.818
peak=    3.620 closest distance to " O   HOH Z  43 " =    1.893
peak=    3.611 closest distance to " CA  ASP A 162 " =    1.015
peak=    3.611 closest distance to " CD2 LEU A 297 " =    0.886
peak=    3.610 closest distance to " CD1 ILE A 106 " =    0.901
peak=    3.608 closest distance to " OD1 ASN A  69 " =    2.541
peak=    3.607 closest distance to " NH1AARG A 145 " =    1.424
peak=    3.602 closest distance to " O   HOH Z 285 " =    2.696
peak=    3.595 closest distance to " N   ASN A  39 " =    1.228
peak=    3.591 closest distance to " O   HOH Z  10 " =    1.805
peak=    3.588 closest distance to " O   HOH Z  48 " =    1.838
peak=    3.583 closest distance to " CB  LEU A  83 " =    0.762
peak=    3.582 closest distance to " CB  ASN A 142 " =    0.987
peak=    3.581 closest distance to " O   THR A 251 " =    1.178
peak=    3.580 closest distance to " O   HOH Z  40 " =    1.701
peak=    3.580 closest distance to " CG2 ILE A 120 " =    1.087
peak=    3.570 closest distance to " CB  MET A  40 " =    0.795
peak=    3.569 closest distance to " CZ  PHE A  38 " =    1.243
peak=    3.568 closest distance to " O   HOH Z 432 " =    1.749
peak=    3.560 closest distance to " O   ALA A 165 " =    1.431
peak=    3.556 closest distance to " O   HOH Z  66 " =    2.188
peak=    3.555 closest distance to " CG2BVAL A  41 " =    0.888
peak=    3.549 closest distance to " CG AARG A 275 " =    1.172
peak=    3.545 closest distance to " CG BARG A 275 " =    1.391
peak=    3.540 closest distance to " O   HOH Z  80 " =    1.723
peak=    3.537 closest distance to " O   HOH Z 412 " =    3.765
peak=    3.521 closest distance to " CB  GLN A  88 " =    1.201
peak=    3.520 closest distance to " O   HOH Z 291 " =    1.567
peak=    3.519 closest distance to " OD2 ASP A 298 " =    3.926
peak=    3.518 closest distance to " ND2 ASN A 249 " =    1.999
peak=    3.517 closest distance to " CA  ASN A 215 " =    1.137
peak=    3.504 closest distance to " CA  ALA A  84 " =    1.293
peak=    3.490 closest distance to " O   HOH Z 280 " =    2.949
peak=    3.488 closest distance to " O   HOH Z 180 " =    2.104
peak=    3.485 closest distance to " N   ASN A 127 " =    1.194
peak=    3.483 closest distance to " O   HOH Z  78 " =    1.688
peak=    3.479 closest distance to " O   HOH Z 383 " =    2.121
peak=    3.478 closest distance to " CG2AVAL A  72 " =    1.775
peak=    3.477 closest distance to " O   HOH Z 134 " =    1.480
peak=    3.475 closest distance to " CD  ARG A  66 " =    2.417
peak=    3.475 closest distance to " O   HOH Z  97 " =    2.044
peak=    3.475 closest distance to " CD ALYS A 290 " =    1.019
peak=    3.474 closest distance to " CA  GLU A 152 " =    0.931
peak=    3.472 closest distance to " O   HOH Z 271 " =    2.986
peak=    3.470 closest distance to " CD  ARG A 219 " =    1.090
peak=    3.465 closest distance to " O   PRO A 213 " =    1.564
peak=    3.463 closest distance to " O   HOH Z 193 " =    2.151
peak=    3.460 closest distance to " CG  MET A 185 " =    1.176
peak=    3.460 closest distance to " O   HOH Z 426 " =    1.592
peak=    3.456 closest distance to " O   HOH Z 197 " =    2.710
peak=    3.451 closest distance to " O   HOH Z 141 " =    1.723
peak=    3.440 closest distance to " O   HOH Z 146 " =    2.321
peak=    3.440 closest distance to " O   HOH Z 128 " =    2.223
peak=    3.440 closest distance to " CB  MET A  47 " =    0.940
peak=    3.439 closest distance to " O   HOH Z 425 " =    1.377
peak=    3.437 closest distance to " CE1 TYR A 186 " =    1.426
peak=    3.434 closest distance to " O   HOH Z 427 " =    3.119
peak=    3.434 closest distance to " CA  ILE A 106 " =    0.808
peak=    3.433 closest distance to " O   HOH Z 171 " =    3.878
peak=    3.428 closest distance to " NH2 ARG A  79 " =    1.326
peak=    3.423 closest distance to " CG2 THR A 220 " =    0.834
peak=    3.423 closest distance to " CB  ALA A 242 " =    0.727
peak=    3.419 closest distance to " CB  ASP A 298 " =    1.232
peak=    3.419 closest distance to " NE2 GLN A  77 " =    3.546
peak=    3.415 closest distance to " O   TRP A 274 " =    1.849
peak=    3.409 closest distance to " CB  SER A 141 " =    0.995
peak=    3.403 closest distance to " CB  ALA A   9 " =    1.597
peak=    3.403 closest distance to " O   HOH Z 135 " =    1.767
peak=    3.399 closest distance to " OD1 ASN A 217 " =    1.663
peak=    3.399 closest distance to " O   HOH Z   1 " =    2.428
peak=    3.397 closest distance to " CA  ALA A 295 " =    1.140
peak=    3.396 closest distance to " CB  PHE A 204 " =    0.864
peak=    3.392 closest distance to " OE1 GLN A  11 " =    2.029
peak=    3.388 closest distance to " O   HOH Z 163 " =    2.028
peak=    3.387 closest distance to " CB  ALA A   1 " =    4.860
peak=    3.385 closest distance to " CG  LEU A 167 " =    1.222
peak=    3.385 closest distance to " O  BHOH Z 338 " =    2.385
peak=    3.380 closest distance to " O   HOH Z  98 " =    1.802
peak=    3.379 closest distance to " CA  GLN A 223 " =    0.870
peak=    3.379 closest distance to " CB  TRP A 179 " =    1.526
peak=    3.374 closest distance to " CB  TYR A 169 " =    0.702
peak=    3.374 closest distance to " O   HOH Z 250 " =    1.433
peak=    3.367 closest distance to " OG BSER A 134 " =    2.834
peak=    3.357 closest distance to " CA  ALA A 233 " =    1.500
peak=    3.353 closest distance to " O   HOH Z 316 " =    3.160
peak=    3.352 closest distance to " O   HOH Z 285 " =    1.724
peak=    3.349 closest distance to " CG2 VAL A 197 " =    1.129
peak=    3.349 closest distance to " CD2 TRP A 179 " =    1.304
peak=    3.349 closest distance to " CA  ALA A  21 " =    1.190
peak=    3.348 closest distance to " CB  PRO A 243 " =    1.605
peak=    3.345 closest distance to " O   HOH Z 367 " =    2.334
peak=    3.344 closest distance to " O   HOH Z 248 " =    1.709
peak=    3.343 closest distance to " CG  GLU A  37 " =    0.884
peak=    3.341 closest distance to " CB  ALA A 100 " =    1.308
peak=    3.340 closest distance to " CA  ASN A 217 " =    1.355
peak=    3.331 closest distance to " O   HOH Z 163 " =    1.714
peak=    3.330 closest distance to " CA  ALA A 160 " =    1.012
peak=    3.327 closest distance to " CG  LYS A  76 " =    1.043
peak=    3.323 closest distance to " O   HOH Z 234 " =    1.814
peak=    3.317 closest distance to " O   HOH Z 250 " =    1.496
peak=    3.315 closest distance to " CA  GLU A  46 " =    0.919
peak=    3.314 closest distance to " CB  GLN A  89 " =    1.107
peak=    3.314 closest distance to " CG2 ILE A  20 " =    1.273
peak=    3.313 closest distance to " CA  ILE A  33 " =    1.630
peak=    3.313 closest distance to " CA  ASP A 124 " =    0.760
peak=    3.311 closest distance to " OG  SER A 245 " =    1.689
peak=    3.311 closest distance to " OG  SER A  28 " =    1.521
peak=    3.310 closest distance to " CB  TYR A 116 " =    0.852
peak=    3.310 closest distance to " CB  SER A 216 " =    0.759
peak=    3.299 closest distance to " O   HOH Z  88 " =    1.695
peak=    3.295 closest distance to " N   CYS A 260 " =    0.753
peak=    3.291 closest distance to " O   HOH Z 344 " =    3.204
peak=    3.291 closest distance to " O   HOH Z 203 " =    1.833
peak=    3.284 closest distance to " O   HOH Z 272 " =    1.884
peak=    3.283 closest distance to " CB  ALA A 248 " =    1.200
peak=    3.281 closest distance to " O   ASN A  74 " =    1.578
peak=    3.278 closest distance to " O   HOH Z 109 " =    2.783
peak=    3.276 closest distance to " O   HOH Z  97 " =    2.297
peak=    3.264 closest distance to " NH2BARG A 145 " =    2.130
peak=    3.259 closest distance to " CA  ALA A 154 " =    1.001
peak=    3.255 closest distance to " CA  MET A 105 " =    0.954
peak=    3.252 closest distance to " CB  SER A  26 " =    1.764
peak=    3.251 closest distance to " O   HOH Z  88 " =    3.594
peak=    3.251 closest distance to " CB  HIS A 108 " =    0.771
peak=    3.247 closest distance to " O   HOH Z  49 " =    2.481
peak=    3.245 closest distance to " CB  SER A 212 " =    1.238
peak=    3.244 closest distance to " O   HOH Z 185 " =    1.888
peak=    3.244 closest distance to " O   TYR A 116 " =    1.304
peak=    3.242 closest distance to " CB  PRO A  90 " =    1.163
peak=    3.238 closest distance to " O   HOH Z 353 " =    2.671
peak=    3.237 closest distance to " O   ASP A 124 " =    1.189
peak=    3.234 closest distance to " CE2 TYR A  30 " =    0.749
peak=    3.233 closest distance to " O   HOH Z 313 " =    1.729
peak=    3.227 closest distance to " CA  TYR A 116 " =    1.469
peak=    3.226 closest distance to " O   HOH Z   4 " =    1.836
peak=    3.225 closest distance to " O   HOH Z 371 " =    2.952
peak=    3.223 closest distance to " N   ARG A 190 " =    1.023
peak=    3.223 closest distance to " O   HOH Z 417 " =    3.286
peak=    3.219 closest distance to " CB  ALA A 248 " =    1.035
peak=    3.215 closest distance to " ND2 ASN A 249 " =    0.852
peak=    3.213 closest distance to " CG  GLU A 277 " =    2.277
peak=    3.210 closest distance to " CA  LEU A 282 " =    1.027
peak=    3.210 closest distance to " CG  ARG A 159 " =    0.961
peak=    3.204 closest distance to " OG BSER A 164 " =    2.489
peak=    3.203 closest distance to " O   HOH Z 325 " =    2.324
peak=    3.202 closest distance to " O   HOH Z 329 " =    3.893
peak=    3.201 closest distance to " O   HOH Z 403 " =    1.393
peak=    3.197 closest distance to " CB  ALA A 114 " =    1.102
peak=    3.193 closest distance to " O   HOH Z  90 " =    2.141
peak=    3.192 closest distance to " CB  ALA A  34 " =    0.712
peak=    3.186 closest distance to " OH  TYR A  30 " =    1.149
peak=    3.185 closest distance to " O   HOH Z 359 " =    1.564
peak=    3.185 closest distance to " CG  ARG A 138 " =    1.112
peak=    3.184 closest distance to " CA  GLN A  88 " =    1.294
peak=    3.184 closest distance to " O   HOH Z 246 " =    1.479
peak=    3.183 closest distance to " N   VAL A 126 " =    1.455
peak=    3.182 closest distance to " CH2 TRP A  70 " =    0.927
peak=    3.178 closest distance to " CZ2 TRP A 179 " =    1.794
peak=    3.177 closest distance to " O   HOH Z 227 " =    1.734
peak=    3.177 closest distance to " CB  SER A 210 " =    0.846
peak=    3.177 closest distance to " ND2 ASN A 110 " =    1.517
peak=    3.176 closest distance to " O   HOH Z 387 " =    2.824
peak=    3.175 closest distance to " ND1 HIS A  81 " =    1.701
peak=    3.166 closest distance to " OD1 ASP A 231 " =    1.883
peak=    3.166 closest distance to " O   HOH Z 188 " =    2.235
peak=    3.163 closest distance to " N   ARG A 156 " =    1.513
peak=    3.161 closest distance to " CG  PHE A 204 " =    0.922
peak=    3.160 closest distance to " O   HOH Z 126 " =    1.619
peak=    3.159 closest distance to " O   HOH Z 299 " =    4.587
peak=    3.159 closest distance to " O   THR A 220 " =    1.127
peak=    3.158 closest distance to " O   HOH Z 295 " =    1.491
peak=    3.158 closest distance to " O   ASN A 209 " =    1.332
peak=    3.155 closest distance to " CA  GLN A  11 " =    1.312
peak=    3.155 closest distance to " O   HOH Z 121 " =    3.808
peak=    3.155 closest distance to " N   PHE A 130 " =    1.199
peak=    3.153 closest distance to " O   HOH Z 273 " =    2.806
peak=    3.147 closest distance to " C   SER A  32 " =    1.042
peak=    3.142 closest distance to " O   ALA A 158 " =    1.265
peak=    3.140 closest distance to " O   HOH Z 394 " =    1.850
peak=    3.135 closest distance to " O   HOH Z 116 " =    1.847
peak=    3.134 closest distance to " O   HOH Z 173 " =    2.088
peak=    3.128 closest distance to " NZ  LYS A 117 " =    3.370
peak=    3.126 closest distance to " CB  LYS A 193 " =    0.941
peak=    3.111 closest distance to " CB  MET A 113 " =    1.868
peak=    3.108 closest distance to " CA  GLY A 267 " =    0.987
peak=    3.106 closest distance to " O   HOH Z  78 " =    2.133
peak=    3.100 closest distance to " CB  GLU A 236 " =    0.952
peak=    3.093 closest distance to " CG2 ILE A 234 " =    0.809
peak=    3.087 closest distance to " O   HOH Z  59 " =    2.437
peak=    3.074 closest distance to " O   HOH Z 298 " =    2.500
peak=    3.063 closest distance to " O   HOH Z 175 " =    3.668
peak=    3.062 closest distance to " CG1 ILE A  49 " =    1.546
peak=    3.052 closest distance to " O   HOH Z 419 " =    1.779
peak=    3.050 closest distance to " CD1AILE A 234 " =    0.858
peak=    3.043 closest distance to " NH2AARG A 275 " =    3.565
peak=    3.037 closest distance to " O   HOH Z 391 " =    2.933
peak=    3.036 closest distance to " O   HOH Z 365 " =    2.900
peak=    3.009 closest distance to " O   GLN A 278 " =    1.557

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.260 - 5.540
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 212
   mapped sites are within: 0.725 - 5.540

peak=   -4.690 closest distance to " O   HOH Z 290 " =    1.039
peak=   -4.674 closest distance to " CD  GLN A  58 " =    0.844
peak=   -4.513 closest distance to " CG1 VAL A 112 " =    2.610
peak=   -4.274 closest distance to " O   HOH Z 266 " =    5.250
peak=   -4.246 closest distance to " O   VAL A  67 " =    2.636
peak=   -4.241 closest distance to " CD  ARG A 156 " =    2.091
peak=   -4.142 closest distance to " CB  PRO A 243 " =    2.671
peak=   -4.128 closest distance to " CH2 TRP A 179 " =    1.179
peak=   -4.110 closest distance to " O   HOH Z 394 " =    1.496
peak=   -4.108 closest distance to " CG1 VAL A 250 " =    2.767
peak=   -4.083 closest distance to " O   HOH Z  10 " =    1.622
peak=   -4.067 closest distance to " O   PRO A 198 " =    1.276
peak=   -4.026 closest distance to " OG  SER A  97 " =    2.302
peak=   -4.006 closest distance to " CD2 TYR A 293 " =    2.029
peak=   -4.003 closest distance to " CE2 TYR A  30 " =    2.797
peak=   -3.984 closest distance to " CD  GLN A 223 " =    0.776
peak=   -3.967 closest distance to " CA  GLY A 241 " =    3.181
peak=   -3.956 closest distance to " O   HOH Z 231 " =    2.321
peak=   -3.953 closest distance to " O   HOH Z 196 " =    2.100
peak=   -3.936 closest distance to " CD2 PHE A  61 " =    2.539
peak=   -3.923 closest distance to " O   HOH Z 114 " =    1.229
peak=   -3.879 closest distance to " CD  GLN A 223 " =    1.456
peak=   -3.876 closest distance to " N   ALA A  43 " =    2.494
peak=   -3.849 closest distance to " CB  ALA A 161 " =    2.613
peak=   -3.841 closest distance to " C   HIS A 108 " =    1.089
peak=   -3.794 closest distance to " OD1 ASN A 148 " =    1.477
peak=   -3.792 closest distance to " O   HOH Z 241 " =    1.123
peak=   -3.776 closest distance to " O   HOH Z  73 " =    2.289
peak=   -3.771 closest distance to " NE2 GLN A  88 " =    0.929
peak=   -3.768 closest distance to " CG1 VAL A 265 " =    2.352
peak=   -3.762 closest distance to " O   HOH Z 185 " =    2.496
peak=   -3.751 closest distance to " CD  ARG A  14 " =    3.296
peak=   -3.746 closest distance to " OXT GLY A 302 " =    2.979
peak=   -3.737 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.729 closest distance to " NH2AARG A 275 " =    5.474
peak=   -3.725 closest distance to " C   ASN A 285 " =    2.447
peak=   -3.720 closest distance to " CG  ARG A  66 " =    2.439
peak=   -3.719 closest distance to " CD1 LEU A 101 " =    2.502
peak=   -3.714 closest distance to " O   HOH Z 166 " =    1.785
peak=   -3.661 closest distance to " ND2 ASN A  45 " =    1.886
peak=   -3.655 closest distance to " C   SER A 206 " =    1.486
peak=   -3.654 closest distance to " NE2 GLN A 103 " =    1.865
peak=   -3.648 closest distance to " O   VAL A 189 " =    2.648
peak=   -3.637 closest distance to " O   HOH Z 372 " =    2.492
peak=   -3.625 closest distance to " CD1 ILE A 151 " =    2.441
peak=   -3.620 closest distance to " CG  ASP A 231 " =    0.757
peak=   -3.608 closest distance to " O   HOH Z  52 " =    1.644
peak=   -3.608 closest distance to " O   ALA A  10 " =    1.706
peak=   -3.606 closest distance to " O   VAL A  67 " =    2.893
peak=   -3.590 closest distance to " CD1 PHE A  59 " =    1.987
peak=   -3.563 closest distance to " O   HOH Z 351 " =    1.519
peak=   -3.554 closest distance to " CD2 LEU A 300 " =    2.898
peak=   -3.550 closest distance to " CB  ASN A  39 " =    2.265
peak=   -3.539 closest distance to " N   ALA A 226 " =    2.142
peak=   -3.535 closest distance to " CG  MET A 105 " =    0.952
peak=   -3.527 closest distance to " O   HOH Z 377 " =    1.108
peak=   -3.526 closest distance to " NH2 ARG A 159 " =    2.318
peak=   -3.519 closest distance to " O   HOH Z 114 " =    3.624
peak=   -3.518 closest distance to " N   ASP A 171 " =    2.405
peak=   -3.513 closest distance to " O   HOH Z 234 " =    4.502
peak=   -3.512 closest distance to " CA  GLY A 241 " =    2.363
peak=   -3.490 closest distance to " O   HOH Z 426 " =    1.669
peak=   -3.484 closest distance to " CB  ASP A 132 " =    2.380
peak=   -3.480 closest distance to " O   HOH Z 211 " =    1.603
peak=   -3.476 closest distance to " O   HOH Z 176 " =    0.725
peak=   -3.471 closest distance to " O   HOH Z 313 " =    1.107
peak=   -3.471 closest distance to " O   HOH Z 353 " =    2.199
peak=   -3.468 closest distance to " CB  PHE A 192 " =    2.035
peak=   -3.465 closest distance to " CD1 LEU A   5 " =    2.601
peak=   -3.464 closest distance to " CE3 TRP A 150 " =    2.108
peak=   -3.462 closest distance to " O   HOH Z  38 " =    1.255
peak=   -3.451 closest distance to " O   HOH Z 393 " =    1.333
peak=   -3.442 closest distance to " O   TYR A 247 " =    2.862
peak=   -3.435 closest distance to " CG  ARG A 269 " =    2.427
peak=   -3.433 closest distance to " ND2 ASN A  45 " =    1.074
peak=   -3.433 closest distance to " CG1 VAL A 112 " =    2.848
peak=   -3.431 closest distance to " CG  GLU A  53 " =    1.549
peak=   -3.431 closest distance to " C   ALA A 158 " =    1.420
peak=   -3.428 closest distance to " CG1 VAL A 112 " =    2.865
peak=   -3.423 closest distance to " O   HOH Z 210 " =    0.733
peak=   -3.421 closest distance to " O   HOH Z 264 " =    1.776
peak=   -3.420 closest distance to " N   THR A  52 " =    1.718
peak=   -3.420 closest distance to " CA  ASP A 298 " =    1.114
peak=   -3.413 closest distance to " O   HOH Z 193 " =    2.155
peak=   -3.410 closest distance to " O   HOH Z 351 " =    1.450
peak=   -3.404 closest distance to " CG2 ILE A  20 " =    2.902
peak=   -3.398 closest distance to " SG ACYS A 201 " =    2.305
peak=   -3.396 closest distance to " CB  ALA A 291 " =    2.146
peak=   -3.396 closest distance to " CD1 ILE A 239 " =    2.057
peak=   -3.385 closest distance to " CZ3 TRP A 274 " =    0.949
peak=   -3.380 closest distance to " CD  ARG A  79 " =    1.131
peak=   -3.378 closest distance to " C   LEU A 143 " =    1.121
peak=   -3.377 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.376 closest distance to " O   HOH Z 198 " =    0.780
peak=   -3.374 closest distance to " CB  PHE A 208 " =    2.307
peak=   -3.365 closest distance to " O   GLY A 211 " =    1.424
peak=   -3.365 closest distance to " CG  LYS A 166 " =    2.076
peak=   -3.364 closest distance to " CG  GLU A 277 " =    1.154
peak=   -3.364 closest distance to " N   SER A 212 " =    2.023
peak=   -3.363 closest distance to " CE BMET A  47 " =    2.144
peak=   -3.359 closest distance to " CD  GLU A 152 " =    0.848
peak=   -3.352 closest distance to " N   SER A   3 " =    2.017
peak=   -3.349 closest distance to " CB  ALA A  43 " =    2.624
peak=   -3.349 closest distance to " O   ALA A   7 " =    1.545
peak=   -3.348 closest distance to " O   HOH Z 232 " =    1.660
peak=   -3.337 closest distance to " NE2 GLN A 194 " =    1.905
peak=   -3.330 closest distance to " C   MET A 188 " =    1.450
peak=   -3.329 closest distance to " O   HOH Z 111 " =    2.063
peak=   -3.329 closest distance to " CA  GLY A 241 " =    2.862
peak=   -3.324 closest distance to " O   VAL A 153 " =    2.240
peak=   -3.323 closest distance to " ND2 ASN A  60 " =    1.298
peak=   -3.322 closest distance to " NH2 ARG A  66 " =    2.029
peak=   -3.320 closest distance to " CG1 VAL A 125 " =    1.939
peak=   -3.320 closest distance to " O   ALA A  34 " =    2.705
peak=   -3.319 closest distance to " O   HOH Z   6 " =    1.384
peak=   -3.315 closest distance to " CD1 PHE A  16 " =    2.622
peak=   -3.315 closest distance to " N   THR A  18 " =    1.349
peak=   -3.315 closest distance to " O   HOH Z 113 " =    2.509
peak=   -3.297 closest distance to " OD1 ASP A 171 " =    1.596
peak=   -3.297 closest distance to " O   HOH Z  60 " =    2.366
peak=   -3.295 closest distance to " O   HOH Z 174 " =    3.948
peak=   -3.294 closest distance to " CB  PRO A 163 " =    2.550
peak=   -3.292 closest distance to " O   HOH Z 128 " =    2.572
peak=   -3.288 closest distance to " O   HOH Z 377 " =    1.971
peak=   -3.286 closest distance to " N   THR A 157 " =    1.674
peak=   -3.284 closest distance to " O   HOH Z  19 " =    2.199
peak=   -3.283 closest distance to " O   HOH Z  71 " =    1.582
peak=   -3.280 closest distance to " CZ  PHE A 155 " =    1.154
peak=   -3.279 closest distance to " CG  LEU A  83 " =    1.995
peak=   -3.275 closest distance to " O   HOH Z 198 " =    1.077
peak=   -3.274 closest distance to " CG2 VAL A 189 " =    2.197
peak=   -3.270 closest distance to " OG BSER A 134 " =    2.030
peak=   -3.268 closest distance to " NE1 TRP A 266 " =    2.423
peak=   -3.265 closest distance to " CG  TRP A 266 " =    1.883
peak=   -3.260 closest distance to " OG BSER A 210 " =    2.219
peak=   -3.258 closest distance to " O   HOH Z 275 " =    1.861
peak=   -3.258 closest distance to " CD1 TRP A 179 " =    0.892
peak=   -3.258 closest distance to " O   PRO A 163 " =    2.195
peak=   -3.254 closest distance to " OG BSER A 134 " =    1.364
peak=   -3.248 closest distance to " O   HOH Z 298 " =    2.596
peak=   -3.246 closest distance to " CD1 LEU A 101 " =    2.629
peak=   -3.244 closest distance to " O   HOH Z 177 " =    1.754
peak=   -3.238 closest distance to " O   GLY A 196 " =    1.231
peak=   -3.236 closest distance to " CA  GLY A 203 " =    2.427
peak=   -3.232 closest distance to " CZ  TYR A 169 " =    1.790
peak=   -3.231 closest distance to " CG2 ILE A  49 " =    2.748
peak=   -3.230 closest distance to " O   ARG A  24 " =    2.190
peak=   -3.226 closest distance to " O   HOH Z 368 " =    1.772
peak=   -3.226 closest distance to " CB  ALA A  10 " =    2.246
peak=   -3.223 closest distance to " OD1 ASP A 191 " =    1.540
peak=   -3.221 closest distance to " O   HOH Z  37 " =    1.886
peak=   -3.220 closest distance to " C   THR A 279 " =    1.169
peak=   -3.220 closest distance to " OD2 ASP A  50 " =    2.177
peak=   -3.217 closest distance to " O   HOH Z 283 " =    5.540
peak=   -3.215 closest distance to " CB  ALA A 248 " =    2.481
peak=   -3.211 closest distance to " C   GLY A 262 " =    2.022
peak=   -3.210 closest distance to " O   HOH Z 421 " =    3.423
peak=   -3.208 closest distance to " O   HOH Z 435 " =    2.711
peak=   -3.207 closest distance to " O   HOH Z 150 " =    1.030
peak=   -3.207 closest distance to " N   GLY A  23 " =    2.254
peak=   -3.201 closest distance to " O   HOH Z 389 " =    1.980
peak=   -3.201 closest distance to " O   HOH Z 311 " =    3.804
peak=   -3.199 closest distance to " O   SER A 271 " =    2.214
peak=   -3.191 closest distance to " NH1 ARG A 195 " =    2.555
peak=   -3.190 closest distance to " CH2 TRP A 177 " =    2.145
peak=   -3.187 closest distance to " O   HOH Z 407 " =    3.559
peak=   -3.185 closest distance to " ND2 ASN A  69 " =    1.702
peak=   -3.181 closest distance to " O   SER A  95 " =    1.783
peak=   -3.180 closest distance to " C   GLY A  13 " =    0.903
peak=   -3.176 closest distance to " CG1 VAL A 197 " =    2.291
peak=   -3.172 closest distance to " O   HOH Z 275 " =    1.587
peak=   -3.168 closest distance to " O   HOH Z 106 " =    2.003
peak=   -3.168 closest distance to " NH2 ARG A  79 " =    2.027
peak=   -3.163 closest distance to " ND2 ASN A 187 " =    1.600
peak=   -3.161 closest distance to " CD1 LEU A 228 " =    2.433
peak=   -3.161 closest distance to " CD  PRO A 213 " =    2.229
peak=   -3.159 closest distance to " O   HOH Z  13 " =    1.535
peak=   -3.155 closest distance to " OE1 GLN A  55 " =    0.791
peak=   -3.155 closest distance to " O   HOH Z 236 " =    1.333
peak=   -3.155 closest distance to " N   GLN A  58 " =    1.789
peak=   -3.149 closest distance to " CZ  PHE A  38 " =    2.001
peak=   -3.137 closest distance to " O   HOH Z 326 " =    5.033
peak=   -3.128 closest distance to " O   HOH Z 357 " =    2.233
peak=   -3.128 closest distance to " O   HOH Z 323 " =    1.313
peak=   -3.126 closest distance to " CB  CYS A 254 " =    2.476
peak=   -3.125 closest distance to " C   ASN A 187 " =    1.926
peak=   -3.122 closest distance to " OE1 GLN A  88 " =    1.232
peak=   -3.117 closest distance to " O   HOH Z 396 " =    2.099
peak=   -3.113 closest distance to " CB  TRP A  85 " =    2.543
peak=   -3.107 closest distance to " O   HOH Z 134 " =    2.494
peak=   -3.101 closest distance to " O   HOH Z 139 " =    4.949
peak=   -3.099 closest distance to " O   HOH Z 166 " =    1.733
peak=   -3.098 closest distance to " CG2 VAL A 112 " =    2.651
peak=   -3.096 closest distance to " N   VAL A 232 " =    2.445
peak=   -3.094 closest distance to " ND2 ASN A  60 " =    4.097
peak=   -3.094 closest distance to " OD2 ASP A 171 " =    1.953
peak=   -3.090 closest distance to " CG1 VAL A  67 " =    2.992
peak=   -3.089 closest distance to " OE2 GLU A 277 " =    2.987
peak=   -3.085 closest distance to " CB  ALA A 248 " =    2.192
peak=   -3.081 closest distance to " CG  PHE A 283 " =    2.691
peak=   -3.079 closest distance to " CE3 TRP A  70 " =    1.925
peak=   -3.064 closest distance to " CH2 TRP A 150 " =    1.185
peak=   -3.048 closest distance to " OH  TYR A 247 " =    1.845
peak=   -3.031 closest distance to " CG2BVAL A  41 " =    1.794
peak=   -3.027 closest distance to " CG  PRO A 163 " =    2.377
peak=   -3.026 closest distance to " CG  GLN A  11 " =    1.525

================= 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    :  0.4030 0.3920   6.190968e+00   6.171246e+00
   1_bss:  0.3945 0.3842   6.179372e+00   6.155961e+00
   1_xyz:  0.2347 0.2570   5.750965e+00   5.828324e+00
   1_adp:  0.2155 0.2609   5.694378e+00   5.846126e+00
   1_occ:  0.2152 0.2601   5.693303e+00   5.845459e+00
   2_bss:  0.2131 0.2579   5.690639e+00   5.841728e+00
   2_xyz:  0.1557 0.1922   5.407024e+00   5.590687e+00
   2_adp:  0.1421 0.1806   5.330818e+00   5.527351e+00
   2_occ:  0.1419 0.1806   5.330062e+00   5.527156e+00
   3_bss:  0.1418 0.1802   5.327954e+00   5.523995e+00
   3_xyz:  0.1213 0.1667   5.210952e+00   5.443395e+00
   3_adp:  0.1179 0.1653   5.189916e+00   5.430434e+00
   3_occ:  0.1179 0.1652   5.189860e+00   5.430555e+00
   4_bss:  0.1178 0.1652   5.189623e+00   5.430409e+00
   4_xyz:  0.1160 0.1642   5.180385e+00   5.424863e+00
   4_adp:  0.1165 0.1622   5.177765e+00   5.417632e+00
   4_occ:  0.1164 0.1622   5.177701e+00   5.418112e+00
   5_bss:  0.1165 0.1618   5.177257e+00   5.416440e+00
   5_xyz:  0.1158 0.1621   5.177600e+00   5.419639e+00
   5_adp:  0.1179 0.1624   5.186680e+00   5.421653e+00
   5_occ:  0.1179 0.1624   5.186461e+00   5.421757e+00
   5_bss:  0.1179 0.1623   5.186585e+00   5.421855e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  80.000  -1.034   2.428  -0.106   0.000  -0.000  -0.000
   1_xyz:  0.300  80.000  -1.034   2.428  -0.106   0.000  -0.000  -0.000
   1_adp:  0.300  80.000  -1.034   2.428  -0.106   0.000  -0.000  -0.000
   1_occ:  0.300  80.000  -1.034   2.428  -0.106   0.000  -0.000  -0.000
   2_bss:  0.331  80.447  -1.983  -0.362  -1.011  -0.000  -0.000  -0.000
   2_xyz:  0.331  80.447  -1.983  -0.362  -1.011  -0.000  -0.000  -0.000
   2_adp:  0.331  80.447  -1.983  -0.362  -1.011  -0.000  -0.000  -0.000
   2_occ:  0.331  80.447  -1.983  -0.362  -1.011  -0.000  -0.000  -0.000
   3_bss:  0.331  75.227  -1.940  -1.113  -0.685  -0.000  -0.000  -0.000
   3_xyz:  0.331  75.227  -1.940  -1.113  -0.685  -0.000  -0.000  -0.000
   3_adp:  0.331  75.227  -1.940  -1.113  -0.685  -0.000  -0.000  -0.000
   3_occ:  0.331  75.227  -1.940  -1.113  -0.685  -0.000  -0.000  -0.000
   4_bss:  0.323  69.287  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   4_xyz:  0.323  69.287  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   4_adp:  0.323  69.287  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   4_occ:  0.323  69.287  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   5_bss:  0.319  64.998  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   5_xyz:  0.319  64.998  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   5_adp:  0.319  64.998  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   5_occ:  0.319  64.998  -1.676  -1.173  -0.410  -0.000  -0.000  -0.000
   5_bss:  0.316  58.851  -1.630  -1.127  -0.365  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.367 0.5912  0.7392    45538.177
   1_bss:  43.615 0.5989  0.7643    43256.758
   1_xyz:  25.633 0.8059  0.9750    17077.496
   1_adp:  26.224 0.7991  0.9638    17760.013
   1_occ:  26.209 0.7992  0.9633    17708.145
   2_bss:  26.040 0.8009  0.9155    17500.346
   2_xyz:  18.659 0.8740  0.9670     9590.583
   2_adp:  16.976 0.8899  0.9644     8417.481
   2_occ:  16.960 0.8900  0.9644     8410.841
   3_bss:  16.888 0.8906  0.9607     8333.279
   3_xyz:  15.135 0.9055  0.9694     7016.389
   3_adp:  14.770 0.9088  0.9616     6861.543
   3_occ:  14.770 0.9088  0.9615     6861.099
   4_bss:  14.767 0.9089  0.9671     6858.519
   4_xyz:  14.590 0.9106  0.9674     6774.191
   4_adp:  14.388 0.9123  0.9606     6725.039
   4_occ:  14.395 0.9123  0.9604     6730.182
   5_bss:  14.390 0.9123  0.9603     6697.944
   5_xyz:  14.454 0.9118  0.9603     6742.164
   5_adp:  14.447 0.9120  0.9549     6806.758
   5_occ:  14.448 0.9119  0.9548     6807.048
   5_bss:  14.451 0.9119  0.9548     6804.043
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6398e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6398e-01
   1_xyz:   1.373  0.012  0.084 15.366  0.005  4.120   9.7787e-02
   1_adp:   1.373  0.012  0.084 15.366  0.005  4.120   9.7787e-02
   1_occ:   1.373  0.012  0.084 15.366  0.005  4.120   9.7787e-02
   2_bss:   1.373  0.012  0.084 15.366  0.005  4.120   9.7787e-02
   2_xyz:   1.071  0.008  0.076 14.802  0.004  4.141   6.5664e-02
   2_adp:   1.071  0.008  0.076 14.802  0.004  4.141   6.5664e-02
   2_occ:   1.071  0.008  0.076 14.802  0.004  4.141   6.5664e-02
   3_bss:   1.071  0.008  0.076 14.802  0.004  4.141   6.5664e-02
   3_xyz:   1.129  0.011  0.083 15.009  0.004  4.117   7.8010e-02
   3_adp:   1.129  0.011  0.083 15.009  0.004  4.117   7.8010e-02
   3_occ:   1.129  0.011  0.083 15.009  0.004  4.117   7.8010e-02
   4_bss:   1.129  0.011  0.083 15.009  0.004  4.117   7.8010e-02
   4_xyz:   1.064  0.010  0.080 14.851  0.004  4.121   6.9761e-02
   4_adp:   1.064  0.010  0.080 14.851  0.004  4.121   6.9761e-02
   4_occ:   1.064  0.010  0.080 14.851  0.004  4.121   6.9761e-02
   5_bss:   1.064  0.010  0.080 14.851  0.004  4.121   6.9761e-02
   5_xyz:   1.042  0.009  0.079 14.741  0.003  4.123   6.6107e-02
   5_adp:   1.042  0.009  0.079 14.741  0.003  4.123   6.6107e-02
   5_occ:   1.042  0.009  0.079 14.741  0.003  4.123   6.6107e-02
   5_bss:   1.042  0.009  0.079 14.741  0.003  4.123   6.6107e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.561   2.4468e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.561   2.4468e-01
   1_xyz:   8.929  0.087  0.271 86.936  0.041  2.136   9.4434e-02
   1_adp:   8.929  0.087  0.271 86.936  0.041  2.136   9.4434e-02
   1_occ:   8.929  0.087  0.271 86.936  0.041  2.136   9.4434e-02
   2_bss:   8.929  0.087  0.271 86.936  0.041  2.136   9.4434e-02
   2_xyz:   7.695  0.047  0.229 85.094  0.048  2.294   7.2373e-02
   2_adp:   7.695  0.047  0.229 85.094  0.048  2.294   7.2373e-02
   2_occ:   7.695  0.047  0.229 85.094  0.048  2.294   7.2373e-02
   3_bss:   7.695  0.047  0.229 85.094  0.048  2.294   7.2373e-02
   3_xyz:   7.998  0.050  0.263 83.776  0.043  2.304   6.8207e-02
   3_adp:   7.998  0.050  0.263 83.776  0.043  2.304   6.8207e-02
   3_occ:   7.998  0.050  0.263 83.776  0.043  2.304   6.8207e-02
   4_bss:   7.998  0.050  0.263 83.776  0.043  2.304   6.8207e-02
   4_xyz:   7.703  0.046  0.263 81.656  0.040  2.376   4.9693e-02
   4_adp:   7.703  0.046  0.263 81.656  0.040  2.376   4.9693e-02
   4_occ:   7.703  0.046  0.263 81.656  0.040  2.376   4.9693e-02
   5_bss:   7.703  0.046  0.263 81.656  0.040  2.376   4.9693e-02
   5_xyz:   7.640  0.045  0.246 82.474  0.036  2.382   4.1463e-02
   5_adp:   7.640  0.045  0.246 82.474  0.036  2.382   4.1463e-02
   5_occ:   7.640  0.045  0.246 82.474  0.036  2.382   4.1463e-02
   5_bss:   7.640  0.045  0.246 82.474  0.036  2.382   4.1463e-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:  68.47   0.00  17.10  60.91   0.00  13.05  68.47   3.91  39.16
   1_occ:  68.47   0.00  17.10  60.91   0.00  13.05  68.47   3.91  39.16
   2_bss:  68.47   0.00  17.10  60.91   0.00  13.05  68.47   3.91  39.16
   2_xyz:  68.47   0.00  17.10  60.91   0.00  13.05  68.47   3.91  39.16
   2_adp:  77.23   0.00  17.20  73.65   0.00  12.85  77.23   5.29  40.87
   2_occ:  77.23   0.00  17.20  73.65   0.00  12.85  77.23   5.29  40.87
   3_bss:  77.23   0.00  17.20  73.65   0.00  12.85  77.23   5.29  40.87
   3_xyz:  77.23   0.00  17.20  73.65   0.00  12.85  77.23   5.29  40.87
   3_adp:  90.17   0.00  17.24  90.17   0.00  12.65  87.46   0.00  42.21
   3_occ:  90.17   0.00  17.24  90.17   0.00  12.65  87.46   0.00  42.21
   4_bss:  90.17   0.00  17.24  90.17   0.00  12.65  87.46   0.00  42.21
   4_xyz:  90.17   0.00  17.24  90.17   0.00  12.65  87.46   0.00  42.21
   4_adp:  87.46   0.55  16.40  87.46   0.55  12.25  85.75   1.86  38.97
   4_occ:  87.46   0.55  16.40  87.46   0.55  12.25  85.75   1.86  38.97
   5_bss:  87.46   0.55  16.40  87.46   0.55  12.25  85.75   1.86  38.97
   5_xyz:  87.46   0.55  16.40  87.46   0.55  12.25  85.75   1.86  38.97
   5_adp:  81.02   1.29  15.67  80.87   1.29  11.94  81.02   4.27  35.97
   5_occ:  81.02   1.29  15.67  80.87   1.29  11.94  81.02   4.27  35.97
   5_bss:  80.97   1.25  15.62  80.83   1.25  11.89  80.97   4.23  35.93
------------------------------------------------------------------------
 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:    1.298    0.015    0.430
   1_adp:    1.298    0.015    0.430
   1_occ:    1.298    0.015    0.430
   2_bss:    1.298    0.015    0.430
   2_xyz:    0.981    0.047    0.508
   2_adp:    0.981    0.047    0.508
   2_occ:    0.981    0.047    0.508
   3_bss:    0.981    0.047    0.508
   3_xyz:    1.053    0.064    0.565
   3_adp:    1.053    0.064    0.565
   3_occ:    1.053    0.064    0.565
   4_bss:    1.053    0.064    0.565
   4_xyz:    1.114    0.092    0.581
   4_adp:    1.114    0.092    0.581
   4_occ:    1.114    0.092    0.581
   5_bss:    1.114    0.092    0.581
   5_xyz:    1.210    0.080    0.591
   5_adp:    1.210    0.080    0.591
   5_occ:    1.210    0.080    0.591
   5_bss:    1.210    0.080    0.591
------------------------------------------------------------------------

CPU time actual refinement: 336.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1063/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_1063/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1063/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1063/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1063/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.75 
  Macro-tasks:
    bulk solvent and scale       = 54.98  
    individual site refinement   = 127.53 
    weights calculation          = 28.95  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 218.21 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 100.83 
    alpha_beta                      = 8.26   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 109.42 
    fmodel                         = 8.92   
    r_factors                      = 0.39   
    phase_errors                   = 11.05  
    foms                           = 0.35   
    TOTAL for micro-tasks          = 242.19 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.786 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    640 calls, 100.50 s
gradients_fft:          585 calls,  96.53 s

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

# Date 2008-01-16 Time 06:19:41 PST -0800 (1200493181.90 s)
Start R-work = 0.4030, R-free = 0.3920 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1794 (no bulk solvent and anisotropic scale)

Start R-work = 0.3945, R-free = 0.3842
Final R-work = 0.1179, R-free = 0.1623