# Date 2008-01-16 Time 06:15:54 PST -0800 (1200492954.99 s)
#phil __OFF__

Command line arguments: "../1072.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11035
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1072

-------------------------------------------------------------------------------
  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, 47.8686, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00124
Completeness in resolution range: 0.955375
Completeness with d_max=infinity: 0.952402

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   2.0012

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, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00124
Completeness in resolution range: 0.955375
Completeness with d_max=infinity: 0.952402

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2822 [2151/2179]  1939   212   9.9%
  bin  2:  4.2822 -  3.4116 [2063/2082]  1854   209  10.1%
  bin  3:  3.4116 -  2.9841 [2044/2064]  1840   204  10.0%
  bin  4:  2.9841 -  2.7130 [2032/2057]  1835   197   9.7%
  bin  5:  2.7130 -  2.5195 [2014/2033]  1808   206  10.2%
  bin  6:  2.5195 -  2.3715 [1998/2043]  1799   199  10.0%
  bin  7:  2.3715 -  2.2532 [1971/2005]  1771   200  10.1%
  bin  8:  2.2532 -  2.1554 [1992/2027]  1791   201  10.1%
  bin  9:  2.1554 -  2.0726 [1995/2024]  1802   193   9.7%
  bin 10:  2.0726 -  2.0012 [1329/1990]  1191   138  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1072/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.43 -     2.12: 6
        2.12 -     2.82: 808
        2.82 -     3.51: 4381
        3.51 -     4.21: 9143
        4.21 -     4.90: 13501
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.425 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 206 " - " O   HOH Z 342 "  1.816 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.939 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27834 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_1072/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1072/model_refine_001.geo

CPU time processing inputs: 9.58


============================ 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 47.8686 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4096   r_free= 0.3928   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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: 6.216499                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7761 0.99   1393  154 0.3292 0.3478      6.4648      6.4245|
|  2:  4.7761 -  3.8108 0.99   1359  148 0.3424 0.3518      6.7302      6.7136|
|  3:  3.8108 -  3.3349 0.99   1307  153 0.3729 0.3295      6.5764      6.5007|
|  4:  3.3349 -  3.0327 0.99   1327  142 0.3951 0.3665      6.4462      6.3565|
|  5:  3.0327 -  2.8168 0.99   1303  146 0.4271 0.4323      6.3097      6.3646|
|  6:  2.8168 -  2.6516 0.98   1283  143 0.4402 0.3926      6.2127      6.1066|
|  7:  2.6516 -  2.5195 0.99   1304  142 0.4437 0.3860       6.191      6.0901|
|  8:  2.5195 -  2.4102 0.98   1272  147 0.4586 0.4253      6.1232      6.1061|
|  9:  2.4102 -  2.3178 0.98   1296  141 0.4627 0.4649      6.0734      6.1384|
| 10:  2.3178 -  2.2381 0.98   1274  138 0.4556 0.4266       6.053       6.021|
| 11:  2.2381 -  2.1683 0.99   1267  146 0.4661 0.4273      6.0207      5.9984|
| 12:  2.1683 -  2.1065 0.98   1275  138 0.4614 0.4637      5.9365      5.9653|
| 13:  2.1065 -  2.0512 0.97   1260  140 0.4594 0.4369      5.8434      5.8097|
| 14:  2.0512 -  2.0012 0.56    710   81 0.4412 0.4458      5.7727      5.7494|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7761  1393   154  0.74  30.76   0.84     0.77      58255.13|
|  2:  4.7761 -  3.8108  1359   148  0.78  28.23   0.93     0.84      72254.43|
|  3:  3.8108 -  3.3349  1307   153  0.71  34.63   0.92     0.85      75576.36|
|  4:  3.3349 -  3.0327  1327   142  0.66  38.94   0.92     0.81      67156.97|
|  5:  3.0327 -  2.8168  1303   146  0.58  45.11   0.92     0.76      56122.58|
|  6:  2.8168 -  2.6516  1283   143  0.58  45.53   0.91     0.75      46331.58|
|  7:  2.6516 -  2.5195  1304   142  0.58  45.47   0.93     0.74      42267.43|
|  8:  2.5195 -  2.4102  1272   147  0.54  49.21   0.94     0.73      41218.57|
|  9:  2.4102 -  2.3178  1296   141  0.51  51.10   0.92     0.70      40749.34|
| 10:  2.3178 -  2.2381  1274   138  0.50  51.88   0.95     0.70      38582.15|
| 11:  2.2381 -  2.1683  1267   146  0.51  51.55   0.95     0.71      35444.51|
| 12:  2.1683 -  2.1065  1275   138  0.51  51.62   0.96     0.74      32541.42|
| 13:  2.1065 -  2.0512  1260   140  0.49  52.73   0.93     0.71      27827.89|
| 14:  2.0512 -  2.0012   710    81  0.51  51.59   0.96     0.67      22425.77|
|alpha:            min =        0.67 max =            0.85 mean =         0.75|
|beta:             min =    22425.77 max =        75576.36 mean =     48026.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.46|
|phase err.(test): min =        0.00 max =           89.92 mean =        44.38|
|-----------------------------------------------------------------------------|

============================== 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 = 5.390524              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.563   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.381711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.974   (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 |  1.425 -  1.773:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.773 -  2.120:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.120 -  2.468:       11 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.468 -  2.815:      797 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.815 -  3.163:     2013 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.163 -  3.510:     2368 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.510 -  3.858:     4521 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.858 -  4.205:     4622 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.205 -  4.552:     6123 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.552 -  4.900:     7378 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.425 |       0.215 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    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: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4096   r_free= 0.3928   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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: 6.216499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3983   r_free= 0.3826   ksol= 0.30   Bsol= 50.00   scale= 0.948   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,4.74,-1.90,0.00,-0.00,-0.00); trace/3= 0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.203992                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.782393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.696062              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.861   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3983      final r-factor (work) = 0.3031          |
| start r-factor (free) = 0.3826      final r-factor (free) = 0.3273          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9997 = 4.78 * 0.50 * 6.2030 + 1.00 * 0.1671                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5369 = 4.78 * 0.50 * 6.0376 + 1.00 * 0.0999                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3031      final r-factor (work) = 0.2775          |
| start r-factor (free) = 0.3273      final r-factor (free) = 0.3340          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2086 = 0.70 * 1.00 * 6.0376 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1461 = 0.70 * 1.00 * 5.9370 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.06   17.46    None  None   None       |
|    all(noH): 2823   0      0.00    95.06   17.46    None  None   None       |
|    Sol.    : 438    0      2.01    95.06   37.49    None  None   None       |
|    Mac.    : 2385   0      0.00    81.21   13.78    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 -   9.506:  949   |   5:    47.531 -  57.037:   89        |
|      1:     9.506 -  19.012:  997   |   6:    57.037 -  66.543:   51        |
|      2:    19.012 -  28.518:  397   |   7:    66.543 -  76.049:   19        |
|      3:    28.518 -  38.025:  202   |   8:    76.049 -  85.555:    6        |
|      4:    38.025 -  47.531:  112   |   9:    85.555 -  95.061:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2775 r_free = 0.3340             target_work(ml) = 5.939         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2772 r_free = 0.3339             target_work(ml) = 5.939         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2772   r_free= 0.3339   ksol= 0.30   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,4.74,-1.90,0.00,-0.00,-0.00); trace/3= 0.63                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.938746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2761   r_free= 0.3323   ksol= 0.32   Bsol= 66.37   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,2.14,-0.87,0.00,-0.00,-0.00); trace/3= 0.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.938115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.034885              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.870   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.519516              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.263  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2761      final r-factor (work) = 0.2097          |
| start r-factor (free) = 0.3323      final r-factor (free) = 0.2523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0459 = 5.03 * 0.50 * 5.9370 + 1.00 * 0.0999                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7380 = 5.03 * 0.50 * 5.8228 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2097      final r-factor (work) = 0.1914          |
| start r-factor (free) = 0.2523      final r-factor (free) = 0.2392          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0385 = 0.52 * 1.00 * 5.8228 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9433 = 0.52 * 1.00 * 5.6341 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.12   17.47    None  None   None       |
|    all(noH): 2823   0      0.00    95.12   17.47    None  None   None       |
|    Sol.    : 438    0      2.40    95.12   40.84    None  None   None       |
|    Mac.    : 2385   0      0.00    91.26   13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.512: 1049   |   5:    47.560 -  57.072:  101        |
|      1:     9.512 -  19.024: 1001   |   6:    57.072 -  66.584:   57        |
|      2:    19.024 -  28.536:  300   |   7:    66.584 -  76.096:   26        |
|      3:    28.536 -  38.048:  153   |   8:    76.096 -  85.608:   18        |
|      4:    38.048 -  47.560:  115   |   9:    85.608 -  95.120:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1914 r_free = 0.2392             target_work(ml) = 5.611         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1912 r_free = 0.2389             target_work(ml) = 5.611         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1912   r_free= 0.2389   ksol= 0.32   Bsol= 66.37   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,2.14,-0.87,0.00,-0.00,-0.00); trace/3= 0.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.610757                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1911   r_free= 0.2383   ksol= 0.32   Bsol= 71.78   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,0.50,-0.64,0.00,-0.00,-0.00); trace/3= -0.46                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.609564                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.145382              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.977  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.830   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1911      final r-factor (work) = 0.1469          |
| start r-factor (free) = 0.2383      final r-factor (free) = 0.1898          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7590 = 4.15 * 0.50 * 5.6347 + 1.00 * 0.0801                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4556 = 4.15 * 0.50 * 5.4926 + 1.00 * 0.0711                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1469      final r-factor (work) = 0.1361          |
| start r-factor (free) = 0.1898      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9321 = 0.35 * 1.00 * 5.4926 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8658 = 0.35 * 1.00 * 5.3340 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    93.64   16.84    None  None   None       |
|    all(noH): 2823   0      1.09    93.64   16.84    None  None   None       |
|    Sol.    : 438    0      1.72    92.34   41.29    None  None   None       |
|    Mac.    : 2385   0      1.09    93.64   12.35    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:     1.088 -  10.343: 1269   |   5:    47.364 -  56.619:   88        |
|      1:    10.343 -  19.598:  917   |   6:    56.619 -  65.874:   70        |
|      2:    19.598 -  28.853:  191   |   7:    65.874 -  75.130:   28        |
|      3:    28.853 -  38.109:  135   |   8:    75.130 -  84.385:    9        |
|      4:    38.109 -  47.364:  108   |   9:    84.385 -  93.640:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1361 r_free = 0.1792             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1360 r_free = 0.1791             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1360   r_free= 0.1791   ksol= 0.32   Bsol= 71.78   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,0.50,-0.64,0.00,-0.00,-0.00); trace/3= -0.46                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302455                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1792   ksol= 0.33   Bsol= 71.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.43,-0.55,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.303916                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.831528              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.278  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.367  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6247 = 2.83 * 0.50 * 5.3353 + 1.00 * 0.0711                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5151 = 2.83 * 0.50 * 5.2571 + 1.00 * 0.0723                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5138 = 0.67 * 1.00 * 5.2571 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4829 = 0.67 * 1.00 * 5.2094 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.29   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    99.29   16.66    None  None   None       |
|    Sol.    : 438    0      1.94    98.89   41.65    None  None   None       |
|    Mac.    : 2385   0      0.00    99.29   12.07    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 -   9.929: 1239   |   5:    49.644 -  59.572:   98        |
|      1:     9.929 -  19.858:  976   |   6:    59.572 -  69.501:   52        |
|      2:    19.858 -  29.786:  190   |   7:    69.501 -  79.430:   23        |
|      3:    29.786 -  39.715:  127   |   8:    79.430 -  89.359:    9        |
|      4:    39.715 -  49.644:  103   |   9:    89.359 -  99.287:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1674             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1193 r_free = 0.1673             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1673   ksol= 0.33   Bsol= 71.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.43,-0.55,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206320                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1673   ksol= 0.33   Bsol= 69.01   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.57,-0.34,-0.00,-0.00,-0.00); trace/3= -0.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206176                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.770196              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.239  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6831 = 1.77 * 0.50 * 5.2093 + 1.00 * 0.0723                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6685 = 1.77 * 0.50 * 5.2098 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5368 = 0.29 * 1.00 * 5.2098 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5358 = 0.29 * 1.00 * 5.2093 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.92   16.31    None  None   None       |
|    all(noH): 2823   0      0.00    98.92   16.31    None  None   None       |
|    Sol.    : 438    0      3.76    98.04   40.83    None  None   None       |
|    Mac.    : 2385   0      0.00    98.92   11.80    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 -   9.892: 1282   |   5:    49.458 -  59.350:   86        |
|      1:     9.892 -  19.783:  942   |   6:    59.350 -  69.242:   51        |
|      2:    19.783 -  29.675:  193   |   7:    69.242 -  79.133:   20        |
|      3:    29.675 -  39.567:  123   |   8:    79.133 -  89.025:   10        |
|      4:    39.567 -  49.458:  110   |   9:    89.025 -  98.917:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1661             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1662             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1662   ksol= 0.33   Bsol= 69.01   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.57,-0.34,-0.00,-0.00,-0.00); trace/3= -0.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206549                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7761 0.99   1393  154 0.1020 0.1323       5.407      5.5457|
|  2:  4.7761 -  3.8108 0.99   1359  148 0.0881 0.1067      5.4454      5.6071|
|  3:  3.8108 -  3.3349 0.99   1307  153 0.1073 0.1526      5.4843       5.858|
|  4:  3.3349 -  3.0327 0.99   1327  142 0.1317 0.1715      5.5164       5.678|
|  5:  3.0327 -  2.8168 0.99   1303  146 0.1454 0.1858      5.4193      5.5833|
|  6:  2.8168 -  2.6516 0.98   1283  143 0.1375 0.2090       5.304       5.545|
|  7:  2.6516 -  2.5195 0.99   1304  142 0.1329 0.1749      5.2249      5.4181|
|  8:  2.5195 -  2.4102 0.98   1272  147 0.1286 0.1766      5.1408      5.3649|
|  9:  2.4102 -  2.3178 0.98   1296  141 0.1270 0.1935      5.1007      5.3866|
| 10:  2.3178 -  2.2381 0.98   1274  138 0.1256 0.1850      5.0406      5.2681|
| 11:  2.2381 -  2.1683 0.99   1267  146 0.1243 0.1805      4.9931      5.2919|
| 12:  2.1683 -  2.1065 0.98   1275  138 0.1196 0.1774      4.9379       5.186|
| 13:  2.1065 -  2.0512 0.97   1260  140 0.1267 0.1906      4.8657      5.1526|
| 14:  2.0512 -  2.0012 0.56    710   81 0.1170 0.1840      4.7421       4.989|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7761  1393   154  0.94   9.24   0.96     0.93       7341.57|
|  2:  4.7761 -  3.8108  1359   148  0.95   8.03   1.00     0.98       8822.71|
|  3:  3.8108 -  3.3349  1307   153  0.93  11.47   1.01     1.00      10572.65|
|  4:  3.3349 -  3.0327  1327   142  0.91  14.93   1.00     0.97      11500.17|
|  5:  3.0327 -  2.8168  1303   146  0.88  17.69   0.99     0.97       9951.71|
|  6:  2.8168 -  2.6516  1283   143  0.89  17.43   0.98     0.95       8363.88|
|  7:  2.6516 -  2.5195  1304   142  0.90  16.22   0.98     0.95       6831.02|
|  8:  2.5195 -  2.4102  1272   147  0.89  16.79   0.98     0.95       6145.51|
|  9:  2.4102 -  2.3178  1296   141  0.90  16.35   0.98     0.93       5492.96|
| 10:  2.3178 -  2.2381  1274   138  0.89  17.02   0.98     0.93       5070.54|
| 11:  2.2381 -  2.1683  1267   146  0.89  16.99   0.97     0.93       4644.74|
| 12:  2.1683 -  2.1065  1275   138  0.91  16.01   0.98     0.95       4395.02|
| 13:  2.1065 -  2.0512  1260   140  0.89  17.60   0.97     0.97       3893.98|
| 14:  2.0512 -  2.0012   710    81  0.90  16.48   0.95     0.91       2961.05|
|alpha:            min =        0.91 max =            1.00 mean =         0.95|
|beta:             min =     2961.05 max =        11500.17 mean =      7021.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.04|
|phase err.(test): min =        0.00 max =           89.90 mean =        14.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1661   ksol= 0.32   Bsol= 69.01   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.57,-0.16,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1661   ksol= 0.32   Bsol= 69.01   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.57,-0.16,-0.00,-0.00,-0.00); trace/3= -0.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206619                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7761 0.99   1393  154 0.1020 0.1322      5.4067      5.5464|
|  2:  4.7761 -  3.8108 0.99   1359  148 0.0882 0.1068      5.4463      5.6079|
|  3:  3.8108 -  3.3349 0.99   1307  153 0.1074 0.1526      5.4849      5.8584|
|  4:  3.3349 -  3.0327 0.99   1327  142 0.1317 0.1715      5.5164       5.678|
|  5:  3.0327 -  2.8168 0.99   1303  146 0.1454 0.1859      5.4191      5.5835|
|  6:  2.8168 -  2.6516 0.98   1283  143 0.1374 0.2084      5.3037      5.5436|
|  7:  2.6516 -  2.5195 0.99   1304  142 0.1329 0.1753      5.2247      5.4187|
|  8:  2.5195 -  2.4102 0.98   1272  147 0.1285 0.1765      5.1407      5.3641|
|  9:  2.4102 -  2.3178 0.98   1296  141 0.1269 0.1935      5.1007      5.3866|
| 10:  2.3178 -  2.2381 0.98   1274  138 0.1256 0.1853       5.041      5.2694|
| 11:  2.2381 -  2.1683 0.99   1267  146 0.1243 0.1806      4.9933      5.2919|
| 12:  2.1683 -  2.1065 0.98   1275  138 0.1196 0.1777      4.9382      5.1881|
| 13:  2.1065 -  2.0512 0.97   1260  140 0.1268 0.1905      4.8658      5.1523|
| 14:  2.0512 -  2.0012 0.56    710   81 0.1171 0.1836      4.7416      4.9867|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7761  1393   154  0.94   9.25   0.96     0.93       7348.55|
|  2:  4.7761 -  3.8108  1359   148  0.95   8.04   1.00     0.98       8837.15|
|  3:  3.8108 -  3.3349  1307   153  0.93  11.49   1.01     1.00      10591.24|
|  4:  3.3349 -  3.0327  1327   142  0.91  14.93   1.00     0.97      11502.52|
|  5:  3.0327 -  2.8168  1303   146  0.88  17.68   0.99     0.97       9941.43|
|  6:  2.8168 -  2.6516  1283   143  0.89  17.41   0.98     0.96       8354.53|
|  7:  2.6516 -  2.5195  1304   142  0.90  16.21   0.99     0.96       6826.40|
|  8:  2.5195 -  2.4102  1272   147  0.89  16.80   0.98     0.95       6147.56|
|  9:  2.4102 -  2.3178  1296   141  0.90  16.36   0.99     0.93       5496.20|
| 10:  2.3178 -  2.2381  1274   138  0.89  17.03   0.98     0.94       5075.67|
| 11:  2.2381 -  2.1683  1267   146  0.89  17.01   0.98     0.93       4650.50|
| 12:  2.1683 -  2.1065  1275   138  0.91  16.03   0.98     0.96       4401.28|
| 13:  2.1065 -  2.0512  1260   140  0.89  17.60   0.98     0.97       3893.17|
| 14:  2.0512 -  2.0012   710    81  0.90  16.47   0.96     0.91       2955.81|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2955.81 max =        11502.52 mean =      7024.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.05|
|phase err.(test): min =        0.00 max =           89.83 mean =        14.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.92   16.31    None  None   None       |
|    all(noH): 2823   0      0.00    98.92   16.31    None  None   None       |
|    Sol.    : 438    0      3.76    98.04   40.84    None  None   None       |
|    Mac.    : 2385   0      0.00    98.92   11.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.895: 1282   |   5:    49.461 -  59.353:   86        |
|      1:     9.895 -  19.786:  942   |   6:    59.353 -  69.245:   51        |
|      2:    19.786 -  29.678:  193   |   7:    69.245 -  79.136:   20        |
|      3:    29.678 -  39.570:  123   |   8:    79.136 -  89.028:   10        |
|      4:    39.570 -  49.461:  110   |   9:    89.028 -  98.919:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.620 - 4.750
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 326
   mapped sites are within: 0.708 - 4.750

peak=    5.986 closest distance to " O   HOH Z 111 " =    2.147
peak=    5.914 closest distance to " CB  GLN A 223 " =    1.384
peak=    5.624 closest distance to " O   HOH Z 210 " =    1.141
peak=    5.403 closest distance to " CG  PRO A  54 " =    1.360
peak=    5.261 closest distance to " CB  SER A  63 " =    1.328
peak=    5.166 closest distance to " CG  PRO A 280 " =    0.835
peak=    5.059 closest distance to " O   HOH Z 232 " =    2.342
peak=    5.010 closest distance to " CG  PRO A 198 " =    1.227
peak=    4.834 closest distance to " O   PRO A 198 " =    1.574
peak=    4.773 closest distance to " CG  PRO A 213 " =    1.268
peak=    4.767 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.704 closest distance to " CB  GLU A 128 " =    1.094
peak=    4.696 closest distance to " O   HOH Z 134 " =    1.709
peak=    4.629 closest distance to " CB  ARG A 190 " =    1.738
peak=    4.601 closest distance to " CB  ARG A 275 " =    0.877
peak=    4.574 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.433 closest distance to " O   HOH Z 369 " =    2.191
peak=    4.426 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.421 closest distance to " CZ  PHE A 218 " =    1.092
peak=    4.321 closest distance to " CD  ARG A 269 " =    0.951
peak=    4.293 closest distance to " NH2 ARG A 156 " =    1.202
peak=    4.266 closest distance to " CB  TRP A 266 " =    0.970
peak=    4.263 closest distance to " O   HOH Z 298 " =    2.027
peak=    4.263 closest distance to " O   HOH Z 234 " =    3.871
peak=    4.227 closest distance to " CG  PRO A 243 " =    1.168
peak=    4.214 closest distance to " O   HOH Z 133 " =    2.409
peak=    4.175 closest distance to " O   HOH Z  44 " =    2.234
peak=    4.143 closest distance to " CB  LEU A 228 " =    1.061
peak=    4.115 closest distance to " CA  PRO A  54 " =    1.367
peak=    4.113 closest distance to " O   HOH Z 189 " =    2.627
peak=    4.112 closest distance to " CB  VAL A 202 " =    1.525
peak=    4.110 closest distance to " O   HOH Z 271 " =    2.786
peak=    4.102 closest distance to " O   HOH Z  15 " =    2.052
peak=    4.080 closest distance to " CA  ALA A  51 " =    0.970
peak=    4.076 closest distance to " O   HOH Z 412 " =    3.696
peak=    4.058 closest distance to " O   HOH Z  40 " =    1.871
peak=    4.050 closest distance to " O   HOH Z  43 " =    2.035
peak=    4.046 closest distance to " O   HOH Z  80 " =    1.848
peak=    4.034 closest distance to " O   HOH Z 265 " =    2.101
peak=    4.033 closest distance to " O   HOH Z 433 " =    1.483
peak=    4.028 closest distance to " CA  ASP A 191 " =    0.835
peak=    4.019 closest distance to " CD  LYS A 166 " =    1.341
peak=    4.012 closest distance to " O   THR A 251 " =    1.252
peak=    4.002 closest distance to " CA  ALA A  21 " =    1.332
peak=    3.998 closest distance to " CB  ASN A 148 " =    1.304
peak=    3.995 closest distance to " O   HOH Z  67 " =    2.043
peak=    3.989 closest distance to " O   HOH Z 423 " =    1.850
peak=    3.985 closest distance to " CG2BVAL A  41 " =    0.917
peak=    3.980 closest distance to " CB  ASN A  39 " =    0.892
peak=    3.967 closest distance to " O   HOH Z 402 " =    1.561
peak=    3.966 closest distance to " CB  GLU A 152 " =    1.157
peak=    3.966 closest distance to " CZ  PHE A 192 " =    0.940
peak=    3.964 closest distance to " CB  TYR A 169 " =    0.842
peak=    3.946 closest distance to " O   HOH Z 383 " =    2.166
peak=    3.943 closest distance to " CA  ARG A 195 " =    1.149
peak=    3.928 closest distance to " C   ILE A 106 " =    1.882
peak=    3.914 closest distance to " CB  ARG A  79 " =    1.332
peak=    3.913 closest distance to " CB  GLU A 277 " =    3.801
peak=    3.902 closest distance to " CG1 ILE A  33 " =    1.285
peak=    3.869 closest distance to " O   HOH Z  21 " =    1.796
peak=    3.868 closest distance to " CG2 THR A 221 " =    1.023
peak=    3.857 closest distance to " O   HOH Z 236 " =    2.031
peak=    3.856 closest distance to " CD1 LEU A 300 " =    1.198
peak=    3.855 closest distance to " CA  ALA A 160 " =    0.957
peak=    3.853 closest distance to " CB  ASP A 124 " =    0.783
peak=    3.851 closest distance to " O   HOH Z  20 " =    1.762
peak=    3.832 closest distance to " O   HOH Z 418 " =    1.554
peak=    3.825 closest distance to " O   HOH Z  97 " =    2.097
peak=    3.814 closest distance to " NH2BARG A 145 " =    2.084
peak=    3.801 closest distance to " CG  ARG A  66 " =    2.648
peak=    3.799 closest distance to " CB  TRP A 179 " =    1.502
peak=    3.790 closest distance to " CB  SER A   3 " =    1.362
peak=    3.785 closest distance to " CB  ASP A 140 " =    0.826
peak=    3.782 closest distance to " O   HOH Z 389 " =    2.049
peak=    3.779 closest distance to " N   ASN A  39 " =    1.279
peak=    3.778 closest distance to " CA  ARG A  36 " =    1.176
peak=    3.771 closest distance to " O   HOH Z 128 " =    2.187
peak=    3.763 closest distance to " O   HOH Z 368 " =    2.083
peak=    3.760 closest distance to " OD1 ASN A  69 " =    2.492
peak=    3.754 closest distance to " O   SER A  87 " =    2.326
peak=    3.741 closest distance to " CA  ASP A 162 " =    1.189
peak=    3.732 closest distance to " O   HOH Z 193 " =    2.012
peak=    3.731 closest distance to " CA  GLU A 152 " =    0.886
peak=    3.731 closest distance to " CD2 LEU A 297 " =    0.947
peak=    3.724 closest distance to " O   HOH Z 374 " =    2.827
peak=    3.723 closest distance to " NE2 HIS A 115 " =    1.020
peak=    3.718 closest distance to " NZ  LYS A 117 " =    3.165
peak=    3.713 closest distance to " O   HOH Z  47 " =    1.349
peak=    3.711 closest distance to " O   HOH Z 403 " =    1.718
peak=    3.710 closest distance to " N   ILE A  33 " =    1.075
peak=    3.707 closest distance to " O   HOH Z 426 " =    1.521
peak=    3.705 closest distance to " CB  LEU A  83 " =    0.852
peak=    3.703 closest distance to " O   HOH Z 126 " =    2.072
peak=    3.699 closest distance to " CB  ASN A 187 " =    1.131
peak=    3.694 closest distance to " O   HOH Z 357 " =    2.080
peak=    3.690 closest distance to " CG1 VAL A 153 " =    1.003
peak=    3.687 closest distance to " CG2 VAL A  78 " =    1.085
peak=    3.679 closest distance to " CB  SER A 141 " =    1.058
peak=    3.675 closest distance to " O   HOH Z  30 " =    1.497
peak=    3.672 closest distance to " O   HOH Z 197 " =    2.005
peak=    3.665 closest distance to " O   HOH Z 126 " =    1.608
peak=    3.665 closest distance to " O   HOH Z 362 " =    3.456
peak=    3.661 closest distance to " O   HOH Z 344 " =    3.183
peak=    3.655 closest distance to " CB  MET A  40 " =    0.828
peak=    3.654 closest distance to " CD  ARG A 159 " =    0.828
peak=    3.650 closest distance to " OE1 GLN A  11 " =    1.997
peak=    3.646 closest distance to " O   HOH Z  59 " =    2.501
peak=    3.643 closest distance to " CA  ASP A 124 " =    0.801
peak=    3.637 closest distance to " O   ALA A 165 " =    1.371
peak=    3.627 closest distance to " CD2 TRP A 179 " =    1.284
peak=    3.619 closest distance to " CB  ARG A  79 " =    0.922
peak=    3.618 closest distance to " CA  ALA A 295 " =    1.123
peak=    3.613 closest distance to " NZ  LYS A 166 " =    3.130
peak=    3.608 closest distance to " CG  GLU A  37 " =    0.936
peak=    3.607 closest distance to " O   HOH Z 132 " =    2.751
peak=    3.600 closest distance to " CB  SER A  62 " =    0.865
peak=    3.600 closest distance to " O   HOH Z 196 " =    1.284
peak=    3.598 closest distance to " O   HOH Z 163 " =    1.674
peak=    3.596 closest distance to " O   HOH Z 214 " =    2.501
peak=    3.592 closest distance to " O   HOH Z 352 " =    1.942
peak=    3.590 closest distance to " O   ASN A  74 " =    1.606
peak=    3.588 closest distance to " ND2 ASN A 187 " =    1.478
peak=    3.581 closest distance to " O   HOH Z 247 " =    1.439
peak=    3.579 closest distance to " O   HOH Z 102 " =    1.306
peak=    3.578 closest distance to " CA  GLN A  88 " =    1.288
peak=    3.572 closest distance to " OD1 ASP A 238 " =    0.856
peak=    3.567 closest distance to " O   HOH Z 281 " =    4.740
peak=    3.565 closest distance to " O   HOH Z 303 " =    2.263
peak=    3.560 closest distance to " CB  ALA A 291 " =    1.188
peak=    3.557 closest distance to " O   HOH Z 316 " =    3.082
peak=    3.555 closest distance to " O   HOH Z 425 " =    1.349
peak=    3.551 closest distance to " CA  SER A  87 " =    0.977
peak=    3.540 closest distance to " CA  THR A 221 " =    0.907
peak=    3.538 closest distance to " OD1 ASN A 217 " =    1.696
peak=    3.525 closest distance to " CA  VAL A  41 " =    0.846
peak=    3.524 closest distance to " CB  GLN A 103 " =    0.901
peak=    3.524 closest distance to " CA  GLY A  98 " =    1.132
peak=    3.521 closest distance to " CD BLYS A 290 " =    1.009
peak=    3.520 closest distance to " CG1 VAL A 174 " =    1.211
peak=    3.518 closest distance to " CA  ILE A 106 " =    0.819
peak=    3.516 closest distance to " CD1 LEU A  96 " =    0.766
peak=    3.512 closest distance to " CZ  PHE A  38 " =    1.322
peak=    3.508 closest distance to " O   HOH Z 135 " =    1.961
peak=    3.505 closest distance to " O   HOH Z 406 " =    1.602
peak=    3.502 closest distance to " O   HOH Z 245 " =    1.364
peak=    3.499 closest distance to " CB  GLU A  46 " =    1.028
peak=    3.497 closest distance to " CB  MET A  47 " =    0.945
peak=    3.497 closest distance to " O   HOH Z 391 " =    3.031
peak=    3.493 closest distance to " O   HOH Z  88 " =    3.523
peak=    3.492 closest distance to " O   HOH Z 291 " =    1.506
peak=    3.487 closest distance to " CD2 LEU A 255 " =    1.635
peak=    3.484 closest distance to " CG AARG A 275 " =    1.184
peak=    3.481 closest distance to " O   HOH Z 109 " =    2.531
peak=    3.477 closest distance to " O   HOH Z 176 " =    1.672
peak=    3.476 closest distance to " CG2 ILE A 120 " =    0.906
peak=    3.474 closest distance to " CB  VAL A 265 " =    1.247
peak=    3.469 closest distance to " O   HOH Z 272 " =    1.904
peak=    3.464 closest distance to " CG2 VAL A 257 " =    0.916
peak=    3.464 closest distance to " OG BSER A 164 " =    2.397
peak=    3.463 closest distance to " O   HOH Z 403 " =    1.366
peak=    3.455 closest distance to " O   HOH Z  78 " =    1.677
peak=    3.443 closest distance to " CA  GLY A 241 " =    0.768
peak=    3.438 closest distance to " CZ3 TRP A 266 " =    1.061
peak=    3.438 closest distance to " O   HOH Z 371 " =    3.128
peak=    3.437 closest distance to " CE1 TYR A 186 " =    1.219
peak=    3.436 closest distance to " O   HOH Z 145 " =    2.317
peak=    3.435 closest distance to " CE  LYS A  76 " =    0.845
peak=    3.432 closest distance to " O   HOH Z 280 " =    3.065
peak=    3.432 closest distance to " O   HOH Z  19 " =    1.926
peak=    3.429 closest distance to " CB  PRO A 198 " =    0.995
peak=    3.424 closest distance to " CG  LEU A 167 " =    1.073
peak=    3.422 closest distance to " CD1 ILE A 106 " =    0.918
peak=    3.415 closest distance to " O   HOH Z 387 " =    2.751
peak=    3.414 closest distance to " CB  ALA A  71 " =    1.327
peak=    3.412 closest distance to " CB  PRO A 243 " =    1.234
peak=    3.410 closest distance to " CA  LYS A 117 " =    1.214
peak=    3.410 closest distance to " O   HOH Z  88 " =    1.648
peak=    3.404 closest distance to " CB  ASN A 142 " =    1.067
peak=    3.403 closest distance to " CA  ASN A 217 " =    1.344
peak=    3.400 closest distance to " OE1 GLU A   2 " =    1.986
peak=    3.393 closest distance to " CB  ALA A 248 " =    1.246
peak=    3.391 closest distance to " O   HOH Z 279 " =    2.240
peak=    3.389 closest distance to " C   GLY A  80 " =    1.138
peak=    3.389 closest distance to " N   TYR A  15 " =    0.746
peak=    3.387 closest distance to " O   HOH Z   1 " =    2.804
peak=    3.386 closest distance to " O   ALA A 158 " =    1.236
peak=    3.382 closest distance to " O   HOH Z 327 " =    2.317
peak=    3.381 closest distance to " O   HOH Z 427 " =    3.125
peak=    3.377 closest distance to " O   HOH Z 421 " =    1.727
peak=    3.377 closest distance to " NE2 GLN A  11 " =    0.989
peak=    3.375 closest distance to " CA  GLN A 223 " =    0.905
peak=    3.374 closest distance to " O   HOH Z  78 " =    2.091
peak=    3.374 closest distance to " O   HOH Z 147 " =    1.734
peak=    3.374 closest distance to " N   ASN A 252 " =    1.223
peak=    3.372 closest distance to " O   HOH Z 437 " =    1.403
peak=    3.369 closest distance to " CD  ARG A  66 " =    2.482
peak=    3.368 closest distance to " O   HOH Z  44 " =    1.754
peak=    3.367 closest distance to " NZ  LYS A 117 " =    1.366
peak=    3.365 closest distance to " CA  THR A 264 " =    0.826
peak=    3.364 closest distance to " O   THR A 220 " =    1.085
peak=    3.364 closest distance to " O   HOH Z  63 " =    1.906
peak=    3.364 closest distance to " O   HOH Z 261 " =    1.738
peak=    3.363 closest distance to " O   HOH Z 180 " =    2.161
peak=    3.362 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.362 closest distance to " O   HOH Z 174 " =    2.238
peak=    3.359 closest distance to " CZ3 TRP A  85 " =    0.954
peak=    3.356 closest distance to " CB  TYR A 116 " =    1.166
peak=    3.352 closest distance to " CB  ILE A 120 " =    1.345
peak=    3.349 closest distance to " O   TRP A 274 " =    1.746
peak=    3.348 closest distance to " CG2 ILE A 106 " =    0.935
peak=    3.346 closest distance to " O   HOH Z 432 " =    1.745
peak=    3.339 closest distance to " CB  THR A 157 " =    1.127
peak=    3.337 closest distance to " N   ASN A 127 " =    1.222
peak=    3.337 closest distance to " O   HOH Z 139 " =    4.750
peak=    3.334 closest distance to " CA  ASP A 140 " =    1.287
peak=    3.333 closest distance to " O   HOH Z 227 " =    1.658
peak=    3.328 closest distance to " O   HOH Z 214 " =    1.251
peak=    3.325 closest distance to " O   HOH Z 104 " =    2.579
peak=    3.320 closest distance to " O   HOH Z  22 " =    2.721
peak=    3.318 closest distance to " CD  ARG A 219 " =    1.172
peak=    3.316 closest distance to " O   HOH Z 173 " =    2.221
peak=    3.316 closest distance to " O   TYR A 116 " =    1.284
peak=    3.315 closest distance to " CB  ASN A 285 " =    0.855
peak=    3.314 closest distance to " O   HOH Z 250 " =    1.431
peak=    3.313 closest distance to " NH1 ARG A  14 " =    1.147
peak=    3.313 closest distance to " O   HOH Z 394 " =    1.688
peak=    3.313 closest distance to " O   HOH Z 345 " =    1.699
peak=    3.312 closest distance to " O   HOH Z 250 " =    1.538
peak=    3.307 closest distance to " O   HOH Z 234 " =    1.936
peak=    3.299 closest distance to " O   HOH Z 171 " =    3.878
peak=    3.298 closest distance to " CG2 THR A 220 " =    0.721
peak=    3.298 closest distance to " N   CYS A 260 " =    0.799
peak=    3.297 closest distance to " CG2 VAL A 197 " =    1.109
peak=    3.297 closest distance to " NH1AARG A 145 " =    1.157
peak=    3.293 closest distance to " CA  GLU A  46 " =    0.865
peak=    3.284 closest distance to " O   HOH Z 155 " =    3.352
peak=    3.283 closest distance to " OD2 ASP A 298 " =    3.877
peak=    3.282 closest distance to " O   HOH Z 185 " =    1.777
peak=    3.281 closest distance to " OG BSER A 134 " =    2.837
peak=    3.280 closest distance to " O   HOH Z  48 " =    1.878
peak=    3.280 closest distance to " O   HOH Z 294 " =    1.608
peak=    3.279 closest distance to " CD1 TRP A 266 " =    1.158
peak=    3.276 closest distance to " O   HOH Z  48 " =    1.422
peak=    3.274 closest distance to " O   HOH Z 346 " =    1.592
peak=    3.271 closest distance to " CB  PHE A  16 " =    0.999
peak=    3.271 closest distance to " CB  GLN A  88 " =    1.216
peak=    3.266 closest distance to " O   HOH Z 128 " =    1.760
peak=    3.261 closest distance to " CA  GLY A 196 " =    0.920
peak=    3.258 closest distance to " O   HOH Z 141 " =    1.616
peak=    3.246 closest distance to " CA  ARG A 102 " =    1.209
peak=    3.243 closest distance to " O   HOH Z 128 " =    2.121
peak=    3.238 closest distance to " C   TYR A 214 " =    1.540
peak=    3.238 closest distance to " CB  PHE A 204 " =    0.897
peak=    3.237 closest distance to " O   ASP A 124 " =    1.188
peak=    3.236 closest distance to " O   HOH Z 419 " =    2.976
peak=    3.232 closest distance to " CA  GLN A  11 " =    0.858
peak=    3.230 closest distance to " CA  MET A 105 " =    1.047
peak=    3.229 closest distance to " O   HOH Z 336 " =    1.699
peak=    3.228 closest distance to " N   ARG A 190 " =    0.954
peak=    3.228 closest distance to " O   HOH Z 301 " =    1.409
peak=    3.225 closest distance to " OG  SER A 245 " =    1.651
peak=    3.224 closest distance to " N   GLN A 278 " =    1.049
peak=    3.222 closest distance to " O   GLN A 278 " =    1.263
peak=    3.221 closest distance to " CG  GLN A  11 " =    1.233
peak=    3.218 closest distance to " CB  SER A 216 " =    0.827
peak=    3.205 closest distance to " CB  HIS A 108 " =    0.812
peak=    3.203 closest distance to " CA  THR A 221 " =    1.365
peak=    3.202 closest distance to " O   HOH Z 295 " =    1.478
peak=    3.201 closest distance to " CG2 THR A  29 " =    1.404
peak=    3.200 closest distance to " ND1 HIS A  81 " =    1.646
peak=    3.192 closest distance to " CB  ASN A 148 " =    1.987
peak=    3.190 closest distance to " CD1AILE A 234 " =    0.866
peak=    3.190 closest distance to " O   HOH Z 125 " =    3.738
peak=    3.189 closest distance to " CB  SER A  28 " =    1.102
peak=    3.185 closest distance to " O   VAL A  72 " =    3.289
peak=    3.185 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.181 closest distance to " CD1 LEU A 222 " =    0.773
peak=    3.175 closest distance to " CA  ASN A 215 " =    1.154
peak=    3.174 closest distance to " O   HOH Z 150 " =    1.553
peak=    3.169 closest distance to " OG1 THR A 294 " =    3.722
peak=    3.169 closest distance to " CG  ARG A 219 " =    1.216
peak=    3.168 closest distance to " CB  ALA A 100 " =    1.451
peak=    3.166 closest distance to " CA  GLU A 152 " =    1.405
peak=    3.165 closest distance to " NZ  LYS A  48 " =    1.248
peak=    3.163 closest distance to " O   HOH Z 355 " =    1.677
peak=    3.163 closest distance to " CA  ALA A  84 " =    1.295
peak=    3.162 closest distance to " CA  ALA A 154 " =    1.007
peak=    3.161 closest distance to " O   HOH Z 258 " =    2.196
peak=    3.160 closest distance to " CB  ASN A 127 " =    0.933
peak=    3.160 closest distance to " O   HOH Z 158 " =    2.959
peak=    3.157 closest distance to " CE1 HIS A 108 " =    1.139
peak=    3.156 closest distance to " N   VAL A 126 " =    1.582
peak=    3.154 closest distance to " O   HOH Z 130 " =    2.219
peak=    3.151 closest distance to " NZ ALYS A 290 " =    1.038
peak=    3.149 closest distance to " CA  LYS A  48 " =    1.308
peak=    3.148 closest distance to " O   HOH Z 325 " =    2.186
peak=    3.147 closest distance to " CA  SER A  12 " =    1.555
peak=    3.146 closest distance to " N   ARG A 156 " =    1.464
peak=    3.146 closest distance to " OG  SER A  97 " =    3.617
peak=    3.134 closest distance to " O   HOH Z 116 " =    1.753
peak=    3.133 closest distance to " OD2 ASP A 200 " =    1.301
peak=    3.128 closest distance to " O   HOH Z 134 " =    2.514
peak=    3.124 closest distance to " O   HOH Z 409 " =    2.899
peak=    3.117 closest distance to " O   HOH Z 261 " =    1.648
peak=    3.115 closest distance to " OG  SER A  22 " =    2.827
peak=    3.106 closest distance to " O   HOH Z 353 " =    2.765
peak=    3.098 closest distance to " CE2 TYR A 186 " =    0.908
peak=    3.095 closest distance to " ND2 ASN A 249 " =    0.899
peak=    3.086 closest distance to " CB  PHE A 283 " =    0.754
peak=    3.085 closest distance to " CB  ALA A 104 " =    0.760
peak=    3.085 closest distance to " O   HOH Z 359 " =    1.436
peak=    3.079 closest distance to " CB  VAL A 257 " =    0.839
peak=    3.079 closest distance to " O   HOH Z 417 " =    3.155
peak=    3.079 closest distance to " NH2AARG A 190 " =    1.361
peak=    3.074 closest distance to " CG  LYS A  76 " =    1.055
peak=    3.072 closest distance to " O   HOH Z 167 " =    1.745
peak=    3.068 closest distance to " O   HOH Z 365 " =    2.937
peak=    3.058 closest distance to " CA  ALA A 100 " =    1.183
peak=    3.052 closest distance to " CB  ALA A  43 " =    0.866
peak=    3.047 closest distance to " CB  ASP A 140 " =    0.708

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.827 - 5.947
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 221
   mapped sites are within: 0.827 - 5.947

peak=   -4.492 closest distance to " O   HOH Z 266 " =    5.049
peak=   -4.270 closest distance to " CD  ARG A 156 " =    2.104
peak=   -4.266 closest distance to " O   HOH Z 166 " =    1.674
peak=   -4.223 closest distance to " O   PRO A 198 " =    1.280
peak=   -4.185 closest distance to " O   HOH Z   5 " =    1.600
peak=   -4.138 closest distance to " CD  GLN A 223 " =    1.306
peak=   -4.130 closest distance to " CD2 LEU A 237 " =    2.693
peak=   -4.103 closest distance to " NH2 ARG A  66 " =    1.647
peak=   -4.097 closest distance to " N   ALA A  43 " =    2.621
peak=   -4.060 closest distance to " O   HOH Z 196 " =    2.555
peak=   -4.032 closest distance to " C   ASN A 285 " =    2.472
peak=   -3.948 closest distance to " O   HOH Z  52 " =    1.636
peak=   -3.941 closest distance to " OD1 ASN A 148 " =    1.489
peak=   -3.914 closest distance to " O   HOH Z  19 " =    2.167
peak=   -3.904 closest distance to " CG1 VAL A 112 " =    2.606
peak=   -3.904 closest distance to " O   HOH Z 290 " =    1.145
peak=   -3.886 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.884 closest distance to " O   VAL A  67 " =    2.649
peak=   -3.883 closest distance to " CB  PRO A 243 " =    2.705
peak=   -3.859 closest distance to " ND2 ASN A  45 " =    1.869
peak=   -3.842 closest distance to " CH2 TRP A 179 " =    1.191
peak=   -3.842 closest distance to " O   HOH Z  13 " =    1.694
peak=   -3.834 closest distance to " CG  MET A  93 " =    2.558
peak=   -3.832 closest distance to " O   HOH Z 185 " =    2.439
peak=   -3.814 closest distance to " O   HOH Z 377 " =    1.069
peak=   -3.812 closest distance to " OXT GLY A 302 " =    2.989
peak=   -3.800 closest distance to " O   PRO A 163 " =    2.208
peak=   -3.794 closest distance to " CB  ALA A  10 " =    2.085
peak=   -3.793 closest distance to " C   HIS A 108 " =    1.116
peak=   -3.787 closest distance to " O   HOH Z 231 " =    2.346
peak=   -3.777 closest distance to " CG  ARG A  66 " =    2.481
peak=   -3.773 closest distance to " O   HOH Z 394 " =    1.566
peak=   -3.771 closest distance to " CE2 TYR A  30 " =    2.740
peak=   -3.754 closest distance to " OG  SER A  97 " =    2.251
peak=   -3.750 closest distance to " O   HOH Z 283 " =    2.206
peak=   -3.748 closest distance to " O   HOH Z 292 " =    4.567
peak=   -3.743 closest distance to " O   HOH Z  71 " =    1.618
peak=   -3.741 closest distance to " O   HOH Z 348 " =    2.311
peak=   -3.741 closest distance to " O   HOH Z 351 " =    1.541
peak=   -3.738 closest distance to " C   SER A 206 " =    1.497
peak=   -3.730 closest distance to " OE1 GLN A  58 " =    1.123
peak=   -3.706 closest distance to " CD  ARG A  14 " =    3.410
peak=   -3.683 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.680 closest distance to " CD2 PHE A  59 " =    2.506
peak=   -3.670 closest distance to " O   HOH Z 407 " =    3.730
peak=   -3.664 closest distance to " O   HOH Z 308 " =    1.729
peak=   -3.649 closest distance to " CD  GLN A  88 " =    0.835
peak=   -3.644 closest distance to " CG  ASP A 231 " =    0.837
peak=   -3.633 closest distance to " OD1 ASP A 191 " =    1.666
peak=   -3.615 closest distance to " O   HOH Z 234 " =    4.497
peak=   -3.612 closest distance to " CB  ALA A 161 " =    2.689
peak=   -3.607 closest distance to " OD2 ASP A 171 " =    1.886
peak=   -3.595 closest distance to " CG  MET A 105 " =    0.896
peak=   -3.595 closest distance to " O   HOH Z   6 " =    1.469
peak=   -3.593 closest distance to " O   HOH Z 150 " =    1.147
peak=   -3.593 closest distance to " O   HOH Z 128 " =    2.560
peak=   -3.580 closest distance to " CA  GLY A 203 " =    2.345
peak=   -3.560 closest distance to " O   HOH Z 426 " =    1.801
peak=   -3.555 closest distance to " ND2 ASN A  45 " =    1.037
peak=   -3.554 closest distance to " O   ALA A  10 " =    1.759
peak=   -3.549 closest distance to " O   HOH Z 150 " =    1.980
peak=   -3.541 closest distance to " CD2 TYR A 293 " =    2.010
peak=   -3.541 closest distance to " O   HOH Z 252 " =    3.985
peak=   -3.534 closest distance to " CG  LEU A 101 " =    2.527
peak=   -3.525 closest distance to " CA  SER A 276 " =    1.497
peak=   -3.520 closest distance to " CA  GLY A 241 " =    3.174
peak=   -3.520 closest distance to " CD1 LEU A 228 " =    2.415
peak=   -3.518 closest distance to " CB  ALA A   9 " =    2.697
peak=   -3.516 closest distance to " NE1 TRP A 266 " =    2.274
peak=   -3.515 closest distance to " CB  ALA A 291 " =    2.387
peak=   -3.515 closest distance to " O   HOH Z 165 " =    1.889
peak=   -3.513 closest distance to " O   HOH Z  37 " =    1.861
peak=   -3.495 closest distance to " CG2 ILE A 263 " =    2.315
peak=   -3.488 closest distance to " CG  GLU A  53 " =    1.406
peak=   -3.487 closest distance to " CA  GLY A 241 " =    2.309
peak=   -3.486 closest distance to " O   HOH Z 166 " =    1.942
peak=   -3.483 closest distance to " O   HOH Z 275 " =    1.546
peak=   -3.483 closest distance to " O   HOH Z 377 " =    2.166
peak=   -3.482 closest distance to " OE1 GLN A 223 " =    2.024
peak=   -3.482 closest distance to " O   HOH Z 353 " =    2.287
peak=   -3.477 closest distance to " O   HOH Z 197 " =    2.107
peak=   -3.475 closest distance to " OH  TYR A 169 " =    0.993
peak=   -3.474 closest distance to " C   THR A 279 " =    1.103
peak=   -3.473 closest distance to " CE2 PHE A  61 " =    2.602
peak=   -3.473 closest distance to " ND2 ASN A  60 " =    1.505
peak=   -3.471 closest distance to " NE2 GLN A 103 " =    1.862
peak=   -3.470 closest distance to " CB  ASP A 132 " =    2.414
peak=   -3.468 closest distance to " CD2 LEU A 300 " =    2.943
peak=   -3.466 closest distance to " O   HOH Z 150 " =    1.833
peak=   -3.465 closest distance to " CG  PRO A 243 " =    1.713
peak=   -3.454 closest distance to " O   ALA A   1 " =    2.011
peak=   -3.451 closest distance to " C   ALA A 158 " =    1.381
peak=   -3.443 closest distance to " O   HOH Z  11 " =    1.864
peak=   -3.439 closest distance to " O   VAL A 189 " =    2.636
peak=   -3.434 closest distance to " CE3 TRP A 150 " =    2.061
peak=   -3.426 closest distance to " N   SER A 212 " =    1.931
peak=   -3.420 closest distance to " O   HOH Z  38 " =    1.261
peak=   -3.406 closest distance to " CA  GLY A 133 " =    2.339
peak=   -3.404 closest distance to " CB  TRP A  85 " =    2.383
peak=   -3.398 closest distance to " CE  MET A  93 " =    1.410
peak=   -3.397 closest distance to " O   HOH Z  15 " =    1.612
peak=   -3.391 closest distance to " O   HOH Z 111 " =    1.952
peak=   -3.387 closest distance to " NE2 GLN A 194 " =    1.844
peak=   -3.365 closest distance to " CD  ARG A 139 " =    1.574
peak=   -3.362 closest distance to " O   HOH Z 136 " =    1.974
peak=   -3.361 closest distance to " OH  TYR A 247 " =    2.232
peak=   -3.357 closest distance to " O   HOH Z 177 " =    1.766
peak=   -3.355 closest distance to " CG  ARG A 269 " =    2.337
peak=   -3.353 closest distance to " O   HOH Z 106 " =    2.127
peak=   -3.352 closest distance to " O   HOH Z  70 " =    2.261
peak=   -3.350 closest distance to " O   HOH Z  43 " =    1.407
peak=   -3.349 closest distance to " O   HOH Z 407 " =    1.012
peak=   -3.349 closest distance to " NH2 ARG A  66 " =    1.395
peak=   -3.340 closest distance to " CA  GLY A  98 " =    2.240
peak=   -3.340 closest distance to " CB  CYS A 254 " =    2.571
peak=   -3.333 closest distance to " O   HOH Z 283 " =    5.947
peak=   -3.331 closest distance to " OG  SER A  62 " =    1.623
peak=   -3.326 closest distance to " CD2 PHE A  61 " =    1.973
peak=   -3.326 closest distance to " NH2 ARG A  79 " =    1.691
peak=   -3.324 closest distance to " NH2 ARG A 159 " =    2.315
peak=   -3.323 closest distance to " NE2 GLN A  88 " =    0.987
peak=   -3.322 closest distance to " O   HOH Z 417 " =    2.787
peak=   -3.322 closest distance to " O   HOH Z 313 " =    1.365
peak=   -3.321 closest distance to " C   LEU A 143 " =    1.225
peak=   -3.321 closest distance to " CH2 TRP A 177 " =    2.038
peak=   -3.318 closest distance to " CB  ALA A  43 " =    2.622
peak=   -3.317 closest distance to " O   HOH Z 111 " =    1.314
peak=   -3.317 closest distance to " CE BMET A  47 " =    2.181
peak=   -3.315 closest distance to " CG2 VAL A 189 " =    2.216
peak=   -3.311 closest distance to " ND2 ASN A  60 " =    1.833
peak=   -3.309 closest distance to " CA  VAL A 197 " =    1.034
peak=   -3.308 closest distance to " OE2 GLU A 152 " =    2.350
peak=   -3.304 closest distance to " O   HOH Z 393 " =    1.560
peak=   -3.302 closest distance to " O   HOH Z 264 " =    1.790
peak=   -3.298 closest distance to " O   HOH Z 372 " =    2.582
peak=   -3.287 closest distance to " O   HOH Z  90 " =    1.886
peak=   -3.283 closest distance to " CD2 PHE A 225 " =    1.312
peak=   -3.280 closest distance to " CG  GLU A 277 " =    1.300
peak=   -3.278 closest distance to " CD2 LEU A 167 " =    1.880
peak=   -3.277 closest distance to " O   HOH Z 368 " =    1.881
peak=   -3.274 closest distance to " CB  PHE A 192 " =    1.994
peak=   -3.272 closest distance to " CD  LYS A 289 " =    2.431
peak=   -3.272 closest distance to " O   HOH Z 422 " =    1.400
peak=   -3.269 closest distance to " O   HOH Z 423 " =    2.331
peak=   -3.263 closest distance to " O   HOH Z 301 " =    2.310
peak=   -3.263 closest distance to " CD1 ILE A 151 " =    2.386
peak=   -3.262 closest distance to " N   ALA A 226 " =    2.127
peak=   -3.250 closest distance to " O   HOH Z 191 " =    5.708
peak=   -3.248 closest distance to " OE1 GLN A  88 " =    1.058
peak=   -3.246 closest distance to " O   HOH Z 102 " =    1.596
peak=   -3.245 closest distance to " CD1 LEU A 167 " =    2.124
peak=   -3.240 closest distance to " CB  ASP A 286 " =    2.194
peak=   -3.238 closest distance to " CD1 LEU A   5 " =    2.516
peak=   -3.238 closest distance to " O   HOH Z 118 " =    3.571
peak=   -3.237 closest distance to " O   GLY A 203 " =    2.387
peak=   -3.231 closest distance to " NH2AARG A 275 " =    5.386
peak=   -3.228 closest distance to " CG1 VAL A  78 " =    2.704
peak=   -3.226 closest distance to " OD1 ASN A 187 " =    1.614
peak=   -3.224 closest distance to " OG BSER A 210 " =    2.105
peak=   -3.221 closest distance to " O   HOH Z  58 " =    1.113
peak=   -3.218 closest distance to " CG  ARG A 219 " =    2.711
peak=   -3.216 closest distance to " O   HOH Z 251 " =    1.913
peak=   -3.212 closest distance to " CD1 ILE A 263 " =    2.051
peak=   -3.208 closest distance to " CD  ARG A 195 " =    5.079
peak=   -3.207 closest distance to " OG BSER A 134 " =    1.315
peak=   -3.205 closest distance to " O   ALA A 160 " =    1.593
peak=   -3.203 closest distance to " CB  ARG A  79 " =    2.566
peak=   -3.201 closest distance to " CD  GLU A 236 " =    1.038
peak=   -3.201 closest distance to " O   HOH Z 174 " =    1.977
peak=   -3.197 closest distance to " O   HOH Z 236 " =    1.516
peak=   -3.196 closest distance to " O   HOH Z  17 " =    1.461
peak=   -3.195 closest distance to " CG1 VAL A 125 " =    2.042
peak=   -3.194 closest distance to " C   ASN A 187 " =    1.961
peak=   -3.193 closest distance to " O   HOH Z 418 " =    1.383
peak=   -3.190 closest distance to " CZ  PHE A  38 " =    1.991
peak=   -3.189 closest distance to " O   HOH Z 134 " =    2.228
peak=   -3.189 closest distance to " O   HOH Z 311 " =    3.729
peak=   -3.188 closest distance to " O   HOH Z 151 " =    1.787
peak=   -3.188 closest distance to " O   THR A  18 " =    1.729
peak=   -3.184 closest distance to " O   HOH Z 232 " =    1.573
peak=   -3.178 closest distance to " O   HOH Z 430 " =    5.719
peak=   -3.178 closest distance to " ND2 ASN A 249 " =    2.260
peak=   -3.177 closest distance to " O   HOH Z 414 " =    1.556
peak=   -3.171 closest distance to " O   HOH Z 350 " =    1.927
peak=   -3.170 closest distance to " O   HOH Z 200 " =    1.338
peak=   -3.165 closest distance to " O   HOH Z 259 " =    2.058
peak=   -3.165 closest distance to " O   HOH Z 117 " =    4.527
peak=   -3.164 closest distance to " CZ  TYR A 169 " =    1.823
peak=   -3.163 closest distance to " CD1 PHE A  16 " =    2.606
peak=   -3.163 closest distance to " CA  SER A  62 " =    2.491
peak=   -3.161 closest distance to " O   VAL A  67 " =    2.847
peak=   -3.159 closest distance to " O   PHE A 218 " =    1.474
peak=   -3.158 closest distance to " O   HOH Z 241 " =    1.160
peak=   -3.157 closest distance to " O   HOH Z  78 " =    1.831
peak=   -3.156 closest distance to " CG  TRP A 266 " =    1.867
peak=   -3.147 closest distance to " O   HOH Z 210 " =    1.144
peak=   -3.146 closest distance to " NE  ARG A 138 " =    2.143
peak=   -3.145 closest distance to " CD1 TRP A 179 " =    1.032
peak=   -3.143 closest distance to " CH2 TRP A 150 " =    1.093
peak=   -3.137 closest distance to " CE3 TRP A 274 " =    2.510
peak=   -3.137 closest distance to " CG1 VAL A 112 " =    2.690
peak=   -3.135 closest distance to " O   ALA A  34 " =    2.540
peak=   -3.135 closest distance to " ND2 ASN A  69 " =    1.541
peak=   -3.133 closest distance to " O   ASP A  27 " =    2.090
peak=   -3.130 closest distance to " CG  LEU A 281 " =    1.857
peak=   -3.127 closest distance to " CA  PRO A 198 " =    1.183
peak=   -3.126 closest distance to " O   HOH Z 193 " =    2.320
peak=   -3.125 closest distance to " O   HOH Z 371 " =    1.686
peak=   -3.122 closest distance to " CB  TYR A  15 " =    2.337
peak=   -3.121 closest distance to " OG BSER A 134 " =    1.987
peak=   -3.116 closest distance to " O   HOH Z 392 " =    1.424
peak=   -3.116 closest distance to " OD2 ASP A 171 " =    2.393
peak=   -3.110 closest distance to " OG  SER A  87 " =    1.659
peak=   -3.103 closest distance to " OG1 THR A  82 " =    1.374
peak=   -3.099 closest distance to " O   TRP A  92 " =    1.878
peak=   -3.099 closest distance to " O   HOH Z 380 " =    4.636
peak=   -3.079 closest distance to " CG  LYS A 119 " =    2.948
peak=   -3.064 closest distance to " O   HOH Z 210 " =    0.827
peak=   -3.064 closest distance to " OG  SER A  63 " =    1.204
peak=   -3.047 closest distance to " O   HOH Z 414 " =    1.456
peak=   -3.002 closest distance to " CA  GLY A 241 " =    2.825

================= 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    :  0.4096 0.3928   6.216499e+00   6.186591e+00
   1_bss:  0.3983 0.3826   6.203992e+00   6.170174e+00
   1_xyz:  0.3031 0.3273   5.992691e+00   6.054033e+00
   1_adp:  0.2775 0.3340   5.939385e+00   6.063919e+00
   1_occ:  0.2772 0.3339   5.938746e+00   6.063921e+00
   2_bss:  0.2761 0.3323   5.938115e+00   6.063185e+00
   2_xyz:  0.2097 0.2523   5.676183e+00   5.832731e+00
   2_adp:  0.1914 0.2392   5.611417e+00   5.783453e+00
   2_occ:  0.1912 0.2389   5.610757e+00   5.782762e+00
   3_bss:  0.1911 0.2383   5.609564e+00   5.779503e+00
   3_xyz:  0.1469 0.1898   5.369174e+00   5.576368e+00
   3_adp:  0.1361 0.1792   5.303006e+00   5.515642e+00
   3_occ:  0.1360 0.1791   5.302455e+00   5.514997e+00
   4_bss:  0.1362 0.1792   5.303916e+00   5.514819e+00
   4_xyz:  0.1225 0.1680   5.221532e+00   5.451948e+00
   4_adp:  0.1193 0.1674   5.206356e+00   5.445228e+00
   4_occ:  0.1193 0.1673   5.206320e+00   5.445366e+00
   5_bss:  0.1192 0.1673   5.206176e+00   5.445264e+00
   5_xyz:  0.1197 0.1673   5.209937e+00   5.444458e+00
   5_adp:  0.1198 0.1661   5.206452e+00   5.437473e+00
   5_occ:  0.1197 0.1662   5.206549e+00   5.437897e+00
   5_bss:  0.1197 0.1661   5.206619e+00   5.438048e+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  50.000  -0.933   4.735  -1.902   0.000  -0.000  -0.000
   1_xyz:  0.300  50.000  -0.933   4.735  -1.902   0.000  -0.000  -0.000
   1_adp:  0.300  50.000  -0.933   4.735  -1.902   0.000  -0.000  -0.000
   1_occ:  0.300  50.000  -0.933   4.735  -1.902   0.000  -0.000  -0.000
   2_bss:  0.322  66.366  -1.164   2.141  -0.871   0.000  -0.000  -0.000
   2_xyz:  0.322  66.366  -1.164   2.141  -0.871   0.000  -0.000  -0.000
   2_adp:  0.322  66.366  -1.164   2.141  -0.871   0.000  -0.000  -0.000
   2_occ:  0.322  66.366  -1.164   2.141  -0.871   0.000  -0.000  -0.000
   3_bss:  0.323  71.775  -1.239   0.496  -0.638   0.000  -0.000  -0.000
   3_xyz:  0.323  71.775  -1.239   0.496  -0.638   0.000  -0.000  -0.000
   3_adp:  0.323  71.775  -1.239   0.496  -0.638   0.000  -0.000  -0.000
   3_occ:  0.323  71.775  -1.239   0.496  -0.638   0.000  -0.000  -0.000
   4_bss:  0.328  71.004  -1.415  -0.429  -0.555  -0.000  -0.000  -0.000
   4_xyz:  0.328  71.004  -1.415  -0.429  -0.555  -0.000  -0.000  -0.000
   4_adp:  0.328  71.004  -1.415  -0.429  -0.555  -0.000  -0.000  -0.000
   4_occ:  0.328  71.004  -1.415  -0.429  -0.555  -0.000  -0.000  -0.000
   5_bss:  0.325  69.013  -1.246  -0.570  -0.342  -0.000  -0.000  -0.000
   5_xyz:  0.325  69.013  -1.246  -0.570  -0.342  -0.000  -0.000  -0.000
   5_adp:  0.325  69.013  -1.246  -0.570  -0.342  -0.000  -0.000  -0.000
   5_occ:  0.325  69.013  -1.246  -0.570  -0.342  -0.000  -0.000  -0.000
   5_bss:  0.322  69.014  -1.122  -0.574  -0.165  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.448 0.5913  0.7523    48026.863
   1_bss:  43.622 0.5997  0.7795    45048.018
   1_xyz:  36.071 0.6895  0.8740    31497.724
   1_adp:  36.474 0.6843  0.8551    32053.160
   1_occ:  36.512 0.6837  0.8540    32031.442
   2_bss:  36.232 0.6871  0.8445    31829.280
   2_xyz:  26.212 0.7975  0.9477    16881.511
   2_adp:  24.062 0.8210  0.9494    14996.638
   2_occ:  24.041 0.8212  0.9494    14970.658
   3_bss:  23.890 0.8227  0.9350    14813.095
   3_xyz:  18.362 0.8764  0.9717     9247.145
   3_adp:  16.771 0.8914  0.9698     8210.468
   3_occ:  16.757 0.8916  0.9697     8200.562
   4_bss:  16.764 0.8915  0.9588     8217.255
   4_xyz:  15.394 0.9033  0.9652     7202.249
   4_adp:  15.164 0.9056  0.9575     7128.535
   4_occ:  15.165 0.9056  0.9574     7130.586
   5_bss:  15.163 0.9056  0.9603     7129.263
   5_xyz:  15.121 0.9060  0.9600     7079.994
   5_adp:  14.975 0.9073  0.9529     7014.945
   5_occ:  14.983 0.9073  0.9528     7021.699
   5_bss:  14.987 0.9072  0.9563     7024.493
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6713e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6713e-01
   1_xyz:   1.397  0.011  0.086 15.352  0.006  4.116   9.9878e-02
   1_adp:   1.397  0.011  0.086 15.352  0.006  4.116   9.9878e-02
   1_occ:   1.397  0.011  0.086 15.352  0.006  4.116   9.9878e-02
   2_bss:   1.397  0.011  0.086 15.352  0.006  4.116   9.9878e-02
   2_xyz:   1.236  0.009  0.086 14.759  0.005  4.137   7.9426e-02
   2_adp:   1.236  0.009  0.086 14.759  0.005  4.137   7.9426e-02
   2_occ:   1.236  0.009  0.086 14.759  0.005  4.137   7.9426e-02
   3_bss:   1.236  0.009  0.086 14.759  0.005  4.137   7.9426e-02
   3_xyz:   1.094  0.009  0.077 14.739  0.004  4.131   7.1079e-02
   3_adp:   1.094  0.009  0.077 14.739  0.004  4.131   7.1079e-02
   3_occ:   1.094  0.009  0.077 14.739  0.004  4.131   7.1079e-02
   4_bss:   1.094  0.009  0.077 14.739  0.004  4.131   7.1079e-02
   4_xyz:   1.113  0.010  0.080 14.825  0.004  4.117   7.2313e-02
   4_adp:   1.113  0.010  0.080 14.825  0.004  4.117   7.2313e-02
   4_occ:   1.113  0.010  0.080 14.825  0.004  4.117   7.2313e-02
   5_bss:   1.113  0.010  0.080 14.825  0.004  4.117   7.2313e-02
   5_xyz:   0.973  0.008  0.072 14.508  0.003  4.118   5.7289e-02
   5_adp:   0.973  0.008  0.072 14.508  0.003  4.118   5.7289e-02
   5_occ:   0.973  0.008  0.072 14.508  0.003  4.118   5.7289e-02
   5_bss:   0.973  0.008  0.072 14.508  0.003  4.118   5.7289e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.425   2.4435e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.425   2.4435e-01
   1_xyz:  11.650  0.066  0.382 88.083  0.047  2.096   8.5731e-02
   1_adp:  11.650  0.066  0.382 88.083  0.047  2.096   8.5731e-02
   1_occ:  11.650  0.066  0.382 88.083  0.047  2.096   8.5731e-02
   2_bss:  11.650  0.066  0.382 88.083  0.047  2.096   8.5731e-02
   2_xyz:   7.493  0.048  0.257 88.664  0.047  2.280   7.8657e-02
   2_adp:   7.493  0.048  0.257 88.664  0.047  2.280   7.8657e-02
   2_occ:   7.493  0.048  0.257 88.664  0.047  2.280   7.8657e-02
   3_bss:   7.493  0.048  0.257 88.664  0.047  2.280   7.8657e-02
   3_xyz:   7.992  0.066  0.250 82.898  0.035  2.243   5.8301e-02
   3_adp:   7.992  0.066  0.250 82.898  0.035  2.243   5.8301e-02
   3_occ:   7.992  0.066  0.250 82.898  0.035  2.243   5.8301e-02
   4_bss:   7.992  0.066  0.250 82.898  0.035  2.243   5.8301e-02
   4_xyz:   7.817  0.051  0.279 83.531  0.038  2.306   5.0536e-02
   4_adp:   7.817  0.051  0.279 83.531  0.038  2.306   5.0536e-02
   4_occ:   7.817  0.051  0.279 83.531  0.038  2.306   5.0536e-02
   5_bss:   7.817  0.051  0.279 83.531  0.038  2.306   5.0536e-02
   5_xyz:   7.555  0.050  0.238 81.078  0.035  2.408   4.0965e-02
   5_adp:   7.555  0.050  0.238 81.078  0.035  2.408   4.0965e-02
   5_occ:   7.555  0.050  0.238 81.078  0.035  2.408   4.0965e-02
   5_bss:   7.555  0.050  0.238 81.078  0.035  2.408   4.0965e-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:  95.06   0.00  17.46  81.21   0.00  13.78  95.06   2.01  37.49
   1_occ:  95.06   0.00  17.46  81.21   0.00  13.78  95.06   2.01  37.49
   2_bss:  95.06   0.00  17.46  81.21   0.00  13.78  95.06   2.01  37.49
   2_xyz:  95.06   0.00  17.46  81.21   0.00  13.78  95.06   2.01  37.49
   2_adp:  95.12   0.00  17.47  91.26   0.00  13.18  95.12   2.40  40.84
   2_occ:  95.12   0.00  17.47  91.26   0.00  13.18  95.12   2.40  40.84
   3_bss:  95.12   0.00  17.47  91.26   0.00  13.18  95.12   2.40  40.84
   3_xyz:  95.12   0.00  17.47  91.26   0.00  13.18  95.12   2.40  40.84
   3_adp:  93.64   1.09  16.84  93.64   1.09  12.35  92.34   1.72  41.29
   3_occ:  93.64   1.09  16.84  93.64   1.09  12.35  92.34   1.72  41.29
   4_bss:  93.64   1.09  16.84  93.64   1.09  12.35  92.34   1.72  41.29
   4_xyz:  93.64   1.09  16.84  93.64   1.09  12.35  92.34   1.72  41.29
   4_adp:  99.29   0.00  16.66  99.29   0.00  12.07  98.89   1.94  41.65
   4_occ:  99.29   0.00  16.66  99.29   0.00  12.07  98.89   1.94  41.65
   5_bss:  99.29   0.00  16.66  99.29   0.00  12.07  98.89   1.94  41.65
   5_xyz:  99.29   0.00  16.66  99.29   0.00  12.07  98.89   1.94  41.65
   5_adp:  98.92   0.00  16.31  98.92   0.00  11.80  98.04   3.76  40.83
   5_occ:  98.92   0.00  16.31  98.92   0.00  11.80  98.04   3.76  40.83
   5_bss:  98.92   0.00  16.31  98.92   0.00  11.81  98.04   3.76  40.84
------------------------------------------------------------------------
 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:    1.789    0.022    0.320
   1_adp:    1.789    0.022    0.320
   1_occ:    1.789    0.022    0.320
   2_bss:    1.789    0.022    0.320
   2_xyz:    1.271    0.052    0.487
   2_adp:    1.271    0.052    0.487
   2_occ:    1.271    0.052    0.487
   3_bss:    1.271    0.052    0.487
   3_xyz:    1.308    0.028    0.616
   3_adp:    1.308    0.028    0.616
   3_occ:    1.308    0.028    0.616
   4_bss:    1.308    0.028    0.616
   4_xyz:    1.328    0.067    0.653
   4_adp:    1.328    0.067    0.653
   4_occ:    1.328    0.067    0.653
   5_bss:    1.328    0.067    0.653
   5_xyz:    1.317    0.093    0.667
   5_adp:    1.317    0.093    0.667
   5_occ:    1.317    0.093    0.667
   5_bss:    1.317    0.093    0.667
------------------------------------------------------------------------

CPU time actual refinement: 316.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1072/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_1072/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1072/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1072/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1072/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.06 
  Macro-tasks:
    bulk solvent and scale       = 37.10  
    individual site refinement   = 125.36 
    weights calculation          = 29.18  
    collect and process          = 6.58   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 198.33 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 99.96  
    alpha_beta                      = 8.72   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 108.10 
    fmodel                         = 6.61   
    r_factors                      = 0.20   
    phase_errors                   = 10.65  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 237.46 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.576 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    630 calls, 99.54 s
gradients_fft:          575 calls, 95.48 s

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

# Date 2008-01-16 Time 06:21:23 PST -0800 (1200493283.27 s)
Start R-work = 0.4096, R-free = 0.3928 (no bulk solvent and anisotropic scale)
Final R-work = 0.1366, R-free = 0.1808 (no bulk solvent and anisotropic scale)

Start R-work = 0.3983, R-free = 0.3826
Final R-work = 0.1197, R-free = 0.1661