# Date 2008-01-16 Time 06:41:43 PST -0800 (1200494503.26 s)
#phil __OFF__

Command line arguments: "../1244.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27531
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1244

-------------------------------------------------------------------------------
  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: (72.0062, 46.4607, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96113
Completeness in resolution range: 0.935393
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1768
                             d_min =   1.9611

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: (72.0062, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96113
Completeness in resolution range: 0.935393
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1772 -  4.1981 [2195/2225]  1979   216   9.8%
  bin  2:  4.1981 -  3.3439 [2114/2130]  1900   214  10.1%
  bin  3:  3.3439 -  2.9246 [2085/2104]  1873   212  10.2%
  bin  4:  2.9246 -  2.6588 [2068/2098]  1865   203   9.8%
  bin  5:  2.6588 -  2.4691 [2057/2076]  1856   201   9.8%
  bin  6:  2.4691 -  2.3241 [2044/2069]  1829   215  10.5%
  bin  7:  2.3241 -  2.2080 [2032/2066]  1829   203  10.0%
  bin  8:  2.2080 -  2.1122 [2022/2052]  1826   196   9.7%
  bin  9:  2.1122 -  2.0311 [1979/2065]  1783   196   9.9%
  bin 10:  2.0311 -  1.9611 [ 993/2057]   890   103  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1244/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 19
        2.29 -     2.94: 1635
        2.94 -     3.59: 4532
        3.59 -     4.25: 9263
        4.25 -     4.90: 13023
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.633 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.687 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 204 " - " O   HOH Z 296 "  1.847 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.912 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28467 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_1244/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1244/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 72.00625 46.4607 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4549   r_free= 0.4550   ksol= 0.00   Bsol= 0.00   scale= 0.905    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.257445                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6832 0.99   1424  161 0.3574 0.3674      6.5085       6.524|
|  2:  4.6832 -  3.7354 0.99   1374  148 0.3890 0.3619      6.7691      6.7838|
|  3:  3.7354 -  3.2686 0.99   1346  148 0.4282 0.4161       6.626       6.658|
|  4:  3.2686 -  2.9722 0.99   1343  159 0.4330 0.4478      6.4865      6.4664|
|  5:  2.9722 -  2.7606 0.99   1330  140 0.4720 0.4698      6.3325      6.3114|
|  6:  2.7606 -  2.5987 0.99   1331  151 0.4915 0.5002      6.2604      6.2864|
|  7:  2.5987 -  2.4691 0.99   1325  139 0.5076 0.4597      6.2322      6.1437|
|  8:  2.4691 -  2.3620 0.98   1298  156 0.5005 0.4946      6.1395      6.1596|
|  9:  2.3620 -  2.2714 0.98   1305  147 0.4958 0.4765      6.1272      6.0737|
| 10:  2.2714 -  2.1933 0.99   1293  142 0.5085 0.5596      6.0637      6.0996|
| 11:  2.1933 -  2.1249 0.99   1339  136 0.5130 0.5095       6.034      6.0576|
| 12:  2.1249 -  2.0643 0.97   1262  150 0.5047 0.5570      5.9402      5.9689|
| 13:  2.0643 -  2.0101 0.88   1159  133 0.5210 0.5379      5.8769      5.8238|
| 14:  2.0101 -  1.9611 0.37    501   49 0.5278 0.4717      5.8177      5.8205|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6832  1424   161  0.73  31.81   0.83     0.77      61838.06|
|  2:  4.6832 -  3.7354  1374   148  0.73  32.63   0.92     0.84      92249.79|
|  3:  3.7354 -  3.2686  1346   148  0.62  42.00   0.92     0.81     102398.94|
|  4:  3.2686 -  2.9722  1343   159  0.54  48.95   0.93     0.74      95803.46|
|  5:  2.9722 -  2.7606  1330   140  0.43  57.13   0.90     0.61      78918.21|
|  6:  2.7606 -  2.5987  1331   151  0.42  57.94   0.90     0.59      67331.25|
|  7:  2.5987 -  2.4691  1325   139  0.43  57.72   0.91     0.59      58635.78|
|  8:  2.4691 -  2.3620  1298   156  0.45  56.17   0.90     0.65      51686.42|
|  9:  2.3620 -  2.2714  1305   147  0.42  58.19   0.96     0.62      50027.03|
| 10:  2.2714 -  2.1933  1293   142  0.36  62.63   0.93     0.55      48975.22|
| 11:  2.1933 -  2.1249  1339   136  0.30  67.90   0.96     0.45      49323.92|
| 12:  2.1249 -  2.0643  1262   150  0.28  69.12   0.93     0.43      44027.53|
| 13:  2.0643 -  2.0101  1159   133  0.28  69.19   0.94     0.45      38720.56|
| 14:  2.0101 -  1.9611   501    49  0.31  66.54   0.91     0.49      32224.70|
|alpha:            min =        0.43 max =            0.84 mean =         0.62|
|beta:             min =    32224.70 max =       102398.94 mean =     64203.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.65|
|phase err.(test): min =        0.00 max =           89.89 mean =        54.84|
|-----------------------------------------------------------------------------|

============================== 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 = 10.086915             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.136   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.341020              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.595   (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 |  1.633 -  1.960:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.960 -  2.287:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.287 -  2.613:       58 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.613 -  2.940:     1577 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.940 -  3.267:     1915 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.267 -  3.593:     2617 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.593 -  3.920:     4761 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.920 -  4.247:     4502 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.573:     5937 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.573 -  4.900:     7086 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.633 |       0.340 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4549   r_free= 0.4550   ksol= 0.00   Bsol= 0.00   scale= 0.905    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.257445                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4467   r_free= 0.4464   ksol= 0.30   Bsol= 20.00   scale= 0.943   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,-1.46,1.07,-0.00,0.00,0.00); trace/3= 0.49                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.253017                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.131378              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.354   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.065515              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.412   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4467      final r-factor (work) = 0.3105          |
| start r-factor (free) = 0.4464      final r-factor (free) = 0.3532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5779 = 8.13 * 0.50 * 6.2487 + 1.00 * 0.1727                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.9449 = 8.13 * 0.50 * 6.1057 + 1.00 * 0.1208                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3105      final r-factor (work) = 0.2826          |
| start r-factor (free) = 0.3532      final r-factor (free) = 0.3577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5122 = 1.07 * 1.00 * 6.1057 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3869 = 1.07 * 1.00 * 5.9443 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.30   18.66    None  None   None       |
|    all(noH): 2823   0      0.00    95.30   18.66    None  None   None       |
|    Sol.    : 438    0      0.00    95.30   41.65    None  None   None       |
|    Mac.    : 2385   0      0.00    91.91   14.44    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 -   9.530:  912   |   5:    47.648 -  57.178:   99        |
|      1:     9.530 -  19.059:  963   |   6:    57.178 -  66.707:   64        |
|      2:    19.059 -  28.589:  415   |   7:    66.707 -  76.237:   26        |
|      3:    28.589 -  38.119:  205   |   8:    76.237 -  85.767:   14        |
|      4:    38.119 -  47.648:  119   |   9:    85.767 -  95.296:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2826 r_free = 0.3577             target_work(ml) = 5.953         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2824 r_free = 0.3573             target_work(ml) = 5.952         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2824   r_free= 0.3573   ksol= 0.30   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,-1.46,1.07,-0.00,0.00,0.00); trace/3= 0.49                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.951995                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2810   r_free= 0.3571   ksol= 0.34   Bsol= 53.66   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.27,-1.71,-0.13,-0.00,-0.00,-0.00); trace/3= -0.53                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.949717                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.093775              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.502   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.860969              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.979   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2810      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.3571      final r-factor (free) = 0.2809          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2881 = 4.09 * 0.50 * 5.9443 + 1.00 * 0.1208                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0565 = 4.09 * 0.50 * 5.8576 + 1.00 * 0.0666                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2149      final r-factor (work) = 0.2012          |
| start r-factor (free) = 0.2809      final r-factor (free) = 0.2685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0646 = 0.86 * 1.00 * 5.8576 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9276 = 0.86 * 1.00 * 5.6997 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.10   18.35    None  None   None       |
|    all(noH): 2823   0      0.00    95.10   18.35    None  None   None       |
|    Sol.    : 438    0      2.15    95.10   42.92    None  None   None       |
|    Mac.    : 2385   0      0.00    93.25   13.83    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 -   9.510:  968   |   5:    47.548 -  57.058:   99        |
|      1:     9.510 -  19.019: 1004   |   6:    57.058 -  66.568:   65        |
|      2:    19.019 -  28.529:  320   |   7:    66.568 -  76.077:   34        |
|      3:    28.529 -  38.039:  174   |   8:    76.077 -  85.587:   13        |
|      4:    38.039 -  47.548:  140   |   9:    85.587 -  95.097:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2012 r_free = 0.2685             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2010 r_free = 0.2681             target_work(ml) = 5.678         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2010   r_free= 0.2681   ksol= 0.34   Bsol= 53.66   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.27,-1.71,-0.13,-0.00,-0.00,-0.00); trace/3= -0.53                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.677628                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2013   r_free= 0.2676   ksol= 0.33   Bsol= 53.66   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-1.74,-0.49,-0.00,-0.00,-0.00); trace/3= -0.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.676320                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.355777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.654   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.473288              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.563   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2013      final r-factor (work) = 0.1599          |
| start r-factor (free) = 0.2676      final r-factor (free) = 0.2166          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6306 = 3.36 * 0.50 * 5.7000 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4293 = 3.36 * 0.50 * 5.5866 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1599      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.2166      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6630 = 0.47 * 1.00 * 5.5866 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5805 = 0.47 * 1.00 * 5.4301 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.15   17.64    None  None   None       |
|    all(noH): 2823   0      0.00    94.15   17.64    None  None   None       |
|    Sol.    : 438    0      4.94    87.51   43.14    None  None   None       |
|    Mac.    : 2385   0      0.00    94.15   12.96    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 -   9.416:  979   |   5:    47.077 -  56.493:  102        |
|      1:     9.416 -  18.831: 1105   |   6:    56.493 -  65.908:   67        |
|      2:    18.831 -  28.246:  267   |   7:    65.908 -  75.324:   31        |
|      3:    28.246 -  37.662:  119   |   8:    75.324 -  84.739:   14        |
|      4:    37.662 -  47.077:  133   |   9:    84.739 -  94.154:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1465 r_free = 0.1982             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1464 r_free = 0.1981             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1981   ksol= 0.33   Bsol= 53.66   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-1.74,-0.49,-0.00,-0.00,-0.00); trace/3= -0.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.380547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1975   ksol= 0.33   Bsol= 56.02   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-2.16,-1.21,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.381312                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.905978              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.612  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190428              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.016  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1467      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1975      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9512 = 2.91 * 0.50 * 5.4341 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7915 = 2.91 * 0.50 * 5.3215 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0238 = 0.19 * 1.00 * 5.3215 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0062 = 0.19 * 1.00 * 5.2413 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    91.30   16.89    None  None   None       |
|    all(noH): 2823   0      0.99    91.30   16.89    None  None   None       |
|    Sol.    : 438    0      6.08    86.27   40.08    None  None   None       |
|    Mac.    : 2385   0      0.99    91.30   12.63    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:     0.994 -  10.024: 1087   |   5:    46.145 -  55.175:  103        |
|      1:    10.024 -  19.054: 1061   |   6:    55.175 -  64.205:   46        |
|      2:    19.054 -  28.084:  240   |   7:    64.205 -  73.235:   25        |
|      3:    28.084 -  37.114:  127   |   8:    73.235 -  82.265:    7        |
|      4:    37.114 -  46.145:  122   |   9:    82.265 -  91.295:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1234 r_free = 0.1675             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1672             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1672   ksol= 0.33   Bsol= 56.02   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-2.16,-1.21,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.215428                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1671   ksol= 0.32   Bsol= 48.14   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-2.34,-1.51,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.215361                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.095901              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.839  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.138852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.404  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5521 = 2.10 * 0.50 * 5.2414 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5022 = 2.10 * 0.50 * 5.1953 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7294 = 0.14 * 1.00 * 5.1953 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7265 = 0.14 * 1.00 * 5.1813 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.57    88.57   16.48    None  None   None       |
|    all(noH): 2823   0      1.57    88.57   16.48    None  None   None       |
|    Sol.    : 438    0      6.15    86.24   37.91    None  None   None       |
|    Mac.    : 2385   0      1.57    88.57   12.55    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:     1.572 -  10.271: 1125   |   5:    45.069 -  53.768:   94        |
|      1:    10.271 -  18.970: 1048   |   6:    53.768 -  62.468:   40        |
|      2:    18.970 -  27.670:  225   |   7:    62.468 -  71.167:   19        |
|      3:    27.670 -  36.369:  128   |   8:    71.167 -  79.867:    7        |
|      4:    36.369 -  45.069:  133   |   9:    79.867 -  88.566:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1609             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1607             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1607   ksol= 0.32   Bsol= 48.14   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-2.34,-1.51,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.176909                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6832 0.99   1424  161 0.1016 0.1369      5.4121      5.6153|
|  2:  4.6832 -  3.7354 0.99   1374  148 0.0906 0.1137      5.4871      5.6592|
|  3:  3.7354 -  3.2686 0.99   1346  148 0.1136 0.1655      5.5066      5.8791|
|  4:  3.2686 -  2.9722 0.99   1343  159 0.1304 0.1589      5.4939      5.5969|
|  5:  2.9722 -  2.7606 0.99   1330  140 0.1408 0.1787      5.3565      5.5398|
|  6:  2.7606 -  2.5987 0.99   1331  151 0.1269 0.1684      5.2232      5.4267|
|  7:  2.5987 -  2.4691 0.99   1325  139 0.1312 0.1808      5.1844      5.3683|
|  8:  2.4691 -  2.3620 0.98   1298  156 0.1199 0.1715      5.0611      5.3315|
|  9:  2.3620 -  2.2714 0.98   1305  147 0.1227 0.1914      5.0566      5.3488|
| 10:  2.2714 -  2.1933 0.99   1293  142 0.1147 0.1752      4.9515      5.2185|
| 11:  2.1933 -  2.1249 0.99   1339  136 0.1173 0.1767      4.9579      5.3112|
| 12:  2.1249 -  2.0643 0.97   1262  150 0.1143 0.1712      4.8842      5.0982|
| 13:  2.0643 -  2.0101 0.88   1159  133 0.1233 0.1741      4.8157      5.0532|
| 14:  2.0101 -  1.9611 0.37    501   49 0.1100 0.1384      4.6558      4.8605|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6832  1424   161  0.94   9.35   0.98     0.95       7544.12|
|  2:  4.6832 -  3.7354  1374   148  0.95   8.43   1.01     1.01       9745.20|
|  3:  3.7354 -  3.2686  1346   148  0.93  12.01   1.02     1.02      10909.81|
|  4:  3.2686 -  2.9722  1343   159  0.91  14.78   1.00     0.98      10963.43|
|  5:  2.9722 -  2.7606  1330   140  0.90  16.01   0.99     0.98       8410.19|
|  6:  2.7606 -  2.5987  1331   151  0.90  15.76   0.99     0.97       6953.96|
|  7:  2.5987 -  2.4691  1325   139  0.91  15.54   0.99     0.97       6143.81|
|  8:  2.4691 -  2.3620  1298   156  0.91  15.06   0.99     0.97       5157.94|
|  9:  2.3620 -  2.2714  1305   147  0.90  16.05   1.01     0.97       5069.39|
| 10:  2.2714 -  2.1933  1293   142  0.91  15.07   1.01     0.98       4265.27|
| 11:  2.1933 -  2.1249  1339   136  0.89  16.75   1.00     0.96       4446.40|
| 12:  2.1249 -  2.0643  1262   150  0.91  15.90   1.01     1.02       4058.42|
| 13:  2.0643 -  2.0101  1159   133  0.90  16.23   1.01     0.99       3397.82|
| 14:  2.0101 -  1.9611   501    49  0.91  14.88   0.99     0.96       2445.68|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2445.68 max =        10963.43 mean =      6647.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.32|
|phase err.(test): min =        0.00 max =           87.88 mean =        13.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1605   ksol= 0.32   Bsol= 48.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-2.38,-1.59,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.177885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1605   ksol= 0.32   Bsol= 48.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-2.38,-1.59,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.177885                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6832 0.99   1424  161 0.1004 0.1356      5.4092       5.612|
|  2:  4.6832 -  3.7354 0.99   1374  148 0.0911 0.1132      5.4928      5.6632|
|  3:  3.7354 -  3.2686 0.99   1346  148 0.1146 0.1661       5.509      5.8854|
|  4:  3.2686 -  2.9722 0.99   1343  159 0.1312 0.1583       5.497       5.597|
|  5:  2.9722 -  2.7606 0.99   1330  140 0.1413 0.1785      5.3592      5.5395|
|  6:  2.7606 -  2.5987 0.99   1331  151 0.1269 0.1683      5.2233      5.4306|
|  7:  2.5987 -  2.4691 0.99   1325  139 0.1311 0.1803      5.1851      5.3673|
|  8:  2.4691 -  2.3620 0.98   1298  156 0.1195 0.1723      5.0616      5.3365|
|  9:  2.3620 -  2.2714 0.98   1305  147 0.1224 0.1913      5.0563      5.3483|
| 10:  2.2714 -  2.1933 0.99   1293  142 0.1146 0.1749      4.9516      5.2178|
| 11:  2.1933 -  2.1249 0.99   1339  136 0.1174 0.1770      4.9583      5.3119|
| 12:  2.1249 -  2.0643 0.97   1262  150 0.1142 0.1714      4.8851      5.0998|
| 13:  2.0643 -  2.0101 0.88   1159  133 0.1232 0.1742      4.8156      5.0533|
| 14:  2.0101 -  1.9611 0.37    501   49 0.1099 0.1387      4.6552      4.8608|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6832  1424   161  0.94   9.67   0.98     0.95       7758.17|
|  2:  4.6832 -  3.7354  1374   148  0.95   8.43   1.01     1.01       9769.02|
|  3:  3.7354 -  3.2686  1346   148  0.93  11.96   1.02     1.02      10835.17|
|  4:  3.2686 -  2.9722  1343   159  0.91  14.88   1.00     0.97      11026.99|
|  5:  2.9722 -  2.7606  1330   140  0.90  16.00   0.99     0.98       8420.55|
|  6:  2.7606 -  2.5987  1331   151  0.90  15.79   0.98     0.96       6953.67|
|  7:  2.5987 -  2.4691  1325   139  0.91  15.59   0.99     0.97       6179.28|
|  8:  2.4691 -  2.3620  1298   156  0.91  15.10   0.98     0.96       5188.99|
|  9:  2.3620 -  2.2714  1305   147  0.90  16.06   1.00     0.96       5074.13|
| 10:  2.2714 -  2.1933  1293   142  0.91  15.09   1.00     0.97       4271.89|
| 11:  2.1933 -  2.1249  1339   136  0.89  16.79   0.99     0.95       4455.31|
| 12:  2.1249 -  2.0643  1262   150  0.91  15.94   1.00     1.01       4076.92|
| 13:  2.0643 -  2.0101  1159   133  0.90  16.23   1.00     0.98       3400.66|
| 14:  2.0101 -  1.9611   501    49  0.91  14.86   0.98     0.95       2440.32|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2440.32 max =        11026.99 mean =      6673.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.37|
|phase err.(test): min =        0.00 max =           87.82 mean =        13.90|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.822)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    88.51   16.43    None  None   None       |
|    all(noH): 2823   0      1.52    88.51   16.43    None  None   None       |
|    Sol.    : 438    0      6.09    86.18   37.85    None  None   None       |
|    Mac.    : 2385   0      1.52    88.51   12.49    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:     1.516 -  10.215: 1125   |   5:    45.013 -  53.712:   94        |
|      1:    10.215 -  18.914: 1048   |   6:    53.712 -  62.412:   40        |
|      2:    18.914 -  27.614:  225   |   7:    62.412 -  71.111:   19        |
|      3:    27.614 -  36.313:  128   |   8:    71.111 -  79.811:    7        |
|      4:    36.313 -  45.013:  133   |   9:    79.811 -  88.510:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.647 - 4.369
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 311
   mapped sites are within: 0.716 - 4.369

peak=    6.041 closest distance to " O   HOH Z 111 " =    2.168
peak=    5.472 closest distance to " CG  PRO A  54 " =    1.277
peak=    5.388 closest distance to " NE2 GLN A  11 " =    1.197
peak=    5.376 closest distance to " CB  GLN A 223 " =    1.505
peak=    5.155 closest distance to " O   HOH Z 183 " =    1.638
peak=    5.146 closest distance to " CB  SER A  63 " =    1.334
peak=    4.952 closest distance to " NH2AARG A 102 " =    1.047
peak=    4.949 closest distance to " O   HOH Z 403 " =    1.519
peak=    4.757 closest distance to " O   HOH Z 214 " =    1.365
peak=    4.719 closest distance to " O   HOH Z 369 " =    2.043
peak=    4.612 closest distance to " O   HOH Z 186 " =    1.455
peak=    4.589 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.576 closest distance to " O   HOH Z 144 " =    1.646
peak=    4.567 closest distance to " O   HOH Z 425 " =    1.471
peak=    4.559 closest distance to " O   HOH Z 282 " =    1.691
peak=    4.554 closest distance to " CB  PRO A  54 " =    0.880
peak=    4.540 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.528 closest distance to " O   HOH Z 134 " =    1.572
peak=    4.527 closest distance to " CG  PRO A 243 " =    1.106
peak=    4.518 closest distance to " CB  GLU A 152 " =    1.242
peak=    4.486 closest distance to " O   HOH Z 126 " =    2.008
peak=    4.479 closest distance to " O   HOH Z 232 " =    2.190
peak=    4.478 closest distance to " O   HOH Z  78 " =    2.254
peak=    4.465 closest distance to " CG  PRO A 198 " =    1.336
peak=    4.415 closest distance to " O   HOH Z 236 " =    1.946
peak=    4.415 closest distance to " CB  GLN A 183 " =    1.175
peak=    4.390 closest distance to " O   HOH Z 260 " =    1.308
peak=    4.387 closest distance to " CG  PRO A  90 " =    1.081
peak=    4.387 closest distance to " O   HOH Z 135 " =    1.794
peak=    4.380 closest distance to " CB  LEU A 228 " =    1.043
peak=    4.372 closest distance to " O   HOH Z  48 " =    1.654
peak=    4.370 closest distance to " C   PRO A 198 " =    1.538
peak=    4.344 closest distance to " O   HOH Z 193 " =    1.880
peak=    4.314 closest distance to " CB  SER A   3 " =    1.488
peak=    4.302 closest distance to " O   HOH Z 368 " =    1.972
peak=    4.260 closest distance to " O   HOH Z 423 " =    1.768
peak=    4.246 closest distance to " O   HOH Z  21 " =    1.757
peak=    4.237 closest distance to " O   HOH Z 437 " =    1.954
peak=    4.236 closest distance to " CB  GLU A 128 " =    0.977
peak=    4.179 closest distance to " O   HOH Z 272 " =    1.941
peak=    4.165 closest distance to " CB  SER A 216 " =    0.852
peak=    4.163 closest distance to " O   HOH Z 108 " =    1.658
peak=    4.157 closest distance to " NH1AARG A 145 " =    1.124
peak=    4.139 closest distance to " O   HOH Z  15 " =    2.173
peak=    4.116 closest distance to " ND2 ASN A 187 " =    1.547
peak=    4.106 closest distance to " O   HOH Z 298 " =    1.862
peak=    4.101 closest distance to " NE AARG A 275 " =    1.567
peak=    4.098 closest distance to " OD2 ASP A 286 " =    2.912
peak=    4.064 closest distance to " CD  ARG A 159 " =    0.808
peak=    4.037 closest distance to " O   HOH Z  10 " =    1.827
peak=    4.027 closest distance to " CD BLYS A 290 " =    1.085
peak=    4.020 closest distance to " O   HOH Z 344 " =    3.301
peak=    4.007 closest distance to " O   HOH Z 126 " =    1.595
peak=    4.002 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.996 closest distance to " O   HOH Z 132 " =    2.295
peak=    3.978 closest distance to " CA  THR A 264 " =    0.829
peak=    3.971 closest distance to " O   HOH Z 112 " =    1.371
peak=    3.965 closest distance to " O   HOH Z   7 " =    1.267
peak=    3.963 closest distance to " CB  ASN A 187 " =    0.973
peak=    3.959 closest distance to " CG  LEU A 167 " =    1.187
peak=    3.927 closest distance to " O   HOH Z 427 " =    2.838
peak=    3.923 closest distance to " CG1 ILE A  33 " =    1.251
peak=    3.911 closest distance to " OD1 ASN A  69 " =    2.527
peak=    3.910 closest distance to " O   HOH Z 193 " =    1.927
peak=    3.909 closest distance to " O   HOH Z   2 " =    1.652
peak=    3.894 closest distance to " O   HOH Z 189 " =    2.361
peak=    3.887 closest distance to " O   HOH Z 316 " =    3.070
peak=    3.882 closest distance to " CB  GLU A 236 " =    1.164
peak=    3.874 closest distance to " O   HOH Z  68 " =    1.670
peak=    3.871 closest distance to " CB  TRP A 266 " =    0.922
peak=    3.870 closest distance to " O   HOH Z  58 " =    1.994
peak=    3.869 closest distance to " N   TYR A  15 " =    0.861
peak=    3.863 closest distance to " O   HOH Z 263 " =    2.206
peak=    3.856 closest distance to " O   ASP A 132 " =    3.830
peak=    3.844 closest distance to " OD1 ASN A 217 " =    1.571
peak=    3.842 closest distance to " CA  SER A  87 " =    0.917
peak=    3.836 closest distance to " CB  VAL A 265 " =    1.271
peak=    3.827 closest distance to " O   HOH Z 182 " =    1.389
peak=    3.824 closest distance to " O   HOH Z 281 " =    4.369
peak=    3.818 closest distance to " O   HOH Z 128 " =    1.530
peak=    3.813 closest distance to " O   HOH Z  85 " =    2.214
peak=    3.803 closest distance to " O   HOH Z  88 " =    3.544
peak=    3.799 closest distance to " CB  GLU A 152 " =    1.475
peak=    3.795 closest distance to " CA  ASN A 215 " =    1.314
peak=    3.789 closest distance to " ND1 HIS A  86 " =    1.777
peak=    3.789 closest distance to " N   ASN A  39 " =    1.368
peak=    3.787 closest distance to " O   HOH Z  61 " =    1.624
peak=    3.784 closest distance to " O   HOH Z  40 " =    2.193
peak=    3.768 closest distance to " CA  ALA A  21 " =    1.155
peak=    3.765 closest distance to " CA  TYR A 186 " =    1.506
peak=    3.765 closest distance to " CZ3 TRP A 123 " =    1.260
peak=    3.762 closest distance to " O   HOH Z 128 " =    2.054
peak=    3.753 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.731 closest distance to " CB  ARG A 139 " =    0.965
peak=    3.731 closest distance to " O   HOH Z 303 " =    2.326
peak=    3.731 closest distance to " CG2 THR A 221 " =    1.053
peak=    3.727 closest distance to " O   HOH Z 409 " =    2.494
peak=    3.720 closest distance to " O   HOH Z 261 " =    1.733
peak=    3.719 closest distance to " CG2 VAL A 257 " =    0.991
peak=    3.693 closest distance to " CB  TYR A 169 " =    0.759
peak=    3.674 closest distance to " CA  MET A  40 " =    1.102
peak=    3.674 closest distance to " NH1 ARG A  56 " =    1.141
peak=    3.669 closest distance to " O   SER A  87 " =    2.295
peak=    3.669 closest distance to " O   HOH Z 419 " =    1.888
peak=    3.661 closest distance to " CZ  PHE A 192 " =    0.903
peak=    3.654 closest distance to " CD  ARG A  14 " =    1.344
peak=    3.651 closest distance to " CA  LYS A  48 " =    1.308
peak=    3.646 closest distance to " CD1 LEU A 300 " =    1.316
peak=    3.645 closest distance to " CB  MET A  47 " =    1.032
peak=    3.645 closest distance to " CG  ARG A 159 " =    0.862
peak=    3.641 closest distance to " O   HOH Z 133 " =    2.299
peak=    3.640 closest distance to " NE  ARG A  66 " =    3.595
peak=    3.631 closest distance to " O   HOH Z  66 " =    2.122
peak=    3.628 closest distance to " O   HOH Z 411 " =    3.563
peak=    3.625 closest distance to " O   HOH Z 247 " =    1.348
peak=    3.618 closest distance to " O   HOH Z 313 " =    1.773
peak=    3.618 closest distance to " O   HOH Z  44 " =    1.773
peak=    3.608 closest distance to " CB  ILE A 120 " =    1.033
peak=    3.597 closest distance to " N   ARG A 156 " =    1.289
peak=    3.589 closest distance to " O   HOH Z 289 " =    1.653
peak=    3.589 closest distance to " O   HOH Z 207 " =    1.738
peak=    3.587 closest distance to " O   HOH Z 139 " =    2.976
peak=    3.587 closest distance to " N   PHE A 130 " =    1.242
peak=    3.586 closest distance to " CB  TRP A 179 " =    1.577
peak=    3.578 closest distance to " O   HOH Z 153 " =    1.803
peak=    3.574 closest distance to " CD BARG A 102 " =    1.262
peak=    3.571 closest distance to " CA  ILE A 234 " =    0.984
peak=    3.571 closest distance to " NH2AARG A 190 " =    1.491
peak=    3.565 closest distance to " O   HOH Z 410 " =    1.732
peak=    3.564 closest distance to " CA  THR A 221 " =    0.910
peak=    3.563 closest distance to " O   HOH Z 334 " =    1.518
peak=    3.554 closest distance to " CD1 ILE A  33 " =    1.593
peak=    3.546 closest distance to " CA  PRO A  54 " =    1.332
peak=    3.546 closest distance to " CE  LYS A  76 " =    0.887
peak=    3.545 closest distance to " O   HOH Z 217 " =    3.067
peak=    3.543 closest distance to " O   HOH Z  98 " =    1.816
peak=    3.535 closest distance to " O   HOH Z   1 " =    1.987
peak=    3.531 closest distance to " CA  ALA A 299 " =    0.977
peak=    3.530 closest distance to " O   HOH Z 295 " =    1.515
peak=    3.529 closest distance to " OE1 GLN A  58 " =    1.040
peak=    3.528 closest distance to " O   HOH Z 156 " =    2.829
peak=    3.526 closest distance to " CG  GLN A  88 " =    1.046
peak=    3.525 closest distance to " OD1BASN A 224 " =    2.214
peak=    3.522 closest distance to " CB  ALA A 291 " =    1.380
peak=    3.519 closest distance to " O   HOH Z 352 " =    1.879
peak=    3.518 closest distance to " O   HOH Z 108 " =    1.860
peak=    3.512 closest distance to " CA  ALA A 158 " =    1.130
peak=    3.511 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.507 closest distance to " O   HOH Z 345 " =    3.492
peak=    3.505 closest distance to " O   HOH Z 133 " =    1.811
peak=    3.498 closest distance to " O   HOH Z  44 " =    3.230
peak=    3.491 closest distance to " CB  ARG A  79 " =    1.333
peak=    3.488 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.488 closest distance to " CA  ALA A 154 " =    0.970
peak=    3.486 closest distance to " O   HOH Z  59 " =    1.945
peak=    3.486 closest distance to " CG BARG A 275 " =    1.530
peak=    3.481 closest distance to " O   HOH Z   1 " =    1.810
peak=    3.479 closest distance to " OE1 GLN A  11 " =    2.161
peak=    3.475 closest distance to " O   HOH Z 374 " =    2.827
peak=    3.463 closest distance to " CA  ASP A 191 " =    0.737
peak=    3.459 closest distance to " O   MET A 105 " =    1.810
peak=    3.458 closest distance to " O   HOH Z 193 " =    2.245
peak=    3.457 closest distance to " CG  PRO A 280 " =    0.772
peak=    3.455 closest distance to " O   HOH Z 175 " =    3.600
peak=    3.454 closest distance to " CG  GLN A 144 " =    0.966
peak=    3.453 closest distance to " O   HOH Z   9 " =    2.019
peak=    3.452 closest distance to " O   HOH Z 394 " =    1.717
peak=    3.451 closest distance to " O   HOH Z 371 " =    2.687
peak=    3.447 closest distance to " NH2 ARG A 156 " =    1.308
peak=    3.446 closest distance to " O   HOH Z 273 " =    2.761
peak=    3.435 closest distance to " CB  ARG A 190 " =    1.681
peak=    3.431 closest distance to " CB  TYR A 116 " =    0.904
peak=    3.428 closest distance to " O   HOH Z 263 " =    1.709
peak=    3.420 closest distance to " CB  ASN A  39 " =    0.885
peak=    3.419 closest distance to " ND2 ASN A 249 " =    1.954
peak=    3.414 closest distance to " O   HOH Z 148 " =    3.276
peak=    3.403 closest distance to " CB  ALA A 104 " =    0.716
peak=    3.399 closest distance to " CB  SER A 276 " =    1.229
peak=    3.396 closest distance to " O   HOH Z  97 " =    1.844
peak=    3.396 closest distance to " O   HOH Z 163 " =    2.019
peak=    3.396 closest distance to " CD2 HIS A  81 " =    1.336
peak=    3.395 closest distance to " O   HOH Z 294 " =    1.601
peak=    3.394 closest distance to " CB  ILE A 234 " =    1.013
peak=    3.390 closest distance to " O   HOH Z   6 " =    2.059
peak=    3.388 closest distance to " O   TYR A 116 " =    1.355
peak=    3.387 closest distance to " CB  THR A 157 " =    1.111
peak=    3.385 closest distance to " CB  SER A 212 " =    1.125
peak=    3.385 closest distance to " CD  LYS A 119 " =    1.296
peak=    3.383 closest distance to " O   HOH Z  80 " =    1.633
peak=    3.380 closest distance to " CZ  PHE A 218 " =    0.996
peak=    3.378 closest distance to " O   HOH Z 115 " =    2.099
peak=    3.378 closest distance to " O   HOH Z  61 " =    1.611
peak=    3.377 closest distance to " O   THR A 220 " =    1.426
peak=    3.373 closest distance to " CA  LEU A 282 " =    1.164
peak=    3.370 closest distance to " SD  MET A  93 " =    1.506
peak=    3.370 closest distance to " O   HOH Z 180 " =    2.021
peak=    3.369 closest distance to " OG1 THR A 294 " =    1.670
peak=    3.365 closest distance to " CB  ALA A  71 " =    1.374
peak=    3.364 closest distance to " O   HOH Z  89 " =    1.601
peak=    3.364 closest distance to " O   HOH Z 116 " =    1.651
peak=    3.356 closest distance to " O   ALA A 233 " =    1.852
peak=    3.351 closest distance to " NZ ALYS A 290 " =    1.035
peak=    3.350 closest distance to " CA  CYS A 201 " =    1.595
peak=    3.349 closest distance to " CB  MET A  40 " =    0.775
peak=    3.348 closest distance to " CD2 LEU A 255 " =    1.323
peak=    3.345 closest distance to " O   HOH Z 213 " =    1.975
peak=    3.339 closest distance to " CG1 VAL A 153 " =    0.948
peak=    3.336 closest distance to " CA  GLY A 267 " =    1.226
peak=    3.328 closest distance to " O   HOH Z 214 " =    2.569
peak=    3.328 closest distance to " N   ASN A 127 " =    1.304
peak=    3.325 closest distance to " O   HOH Z 277 " =    2.597
peak=    3.323 closest distance to " O   HOH Z 387 " =    3.117
peak=    3.323 closest distance to " O   HOH Z 184 " =    1.448
peak=    3.321 closest distance to " O   HOH Z  17 " =    2.159
peak=    3.321 closest distance to " O   HOH Z 392 " =    2.074
peak=    3.321 closest distance to " O   HOH Z 379 " =    1.911
peak=    3.319 closest distance to " O   HOH Z 359 " =    4.014
peak=    3.318 closest distance to " CE2 TYR A 247 " =    1.329
peak=    3.316 closest distance to " O   HOH Z 291 " =    1.934
peak=    3.314 closest distance to " O   HOH Z 271 " =    2.322
peak=    3.310 closest distance to " CB  LEU A 143 " =    1.057
peak=    3.310 closest distance to " CB  LEU A 300 " =    1.013
peak=    3.309 closest distance to " CB  ALA A 184 " =    1.082
peak=    3.307 closest distance to " O   HOH Z 302 " =    1.970
peak=    3.305 closest distance to " O   HOH Z 171 " =    2.057
peak=    3.304 closest distance to " O   HOH Z 391 " =    2.941
peak=    3.302 closest distance to " CB  ASP A 171 " =    0.798
peak=    3.298 closest distance to " O   HOH Z 236 " =    1.581
peak=    3.295 closest distance to " O   HOH Z 152 " =    2.710
peak=    3.293 closest distance to " O   HOH Z  64 " =    2.113
peak=    3.293 closest distance to " O   HOH Z 154 " =    1.987
peak=    3.292 closest distance to " C   GLU A 277 " =    1.434
peak=    3.290 closest distance to " O   ALA A   1 " =    1.578
peak=    3.286 closest distance to " CB  LEU A 255 " =    0.763
peak=    3.284 closest distance to " O   HOH Z 334 " =    3.068
peak=    3.282 closest distance to " CA  ASP A 124 " =    0.743
peak=    3.281 closest distance to " CD1 ILE A 263 " =    1.345
peak=    3.277 closest distance to " O   HOH Z 281 " =    2.020
peak=    3.275 closest distance to " CD  PRO A 243 " =    1.789
peak=    3.274 closest distance to " O   HOH Z 147 " =    1.699
peak=    3.272 closest distance to " O   HOH Z 255 " =    1.493
peak=    3.269 closest distance to " CB  ARG A 138 " =    1.028
peak=    3.268 closest distance to " CG  PRO A 213 " =    1.035
peak=    3.257 closest distance to " CB  ALA A  34 " =    1.170
peak=    3.256 closest distance to " O   HOH Z 175 " =    2.196
peak=    3.254 closest distance to " O   HOH Z 345 " =    1.773
peak=    3.253 closest distance to " CG1BVAL A  72 " =    1.572
peak=    3.249 closest distance to " NE1 TRP A 266 " =    1.342
peak=    3.247 closest distance to " CG BARG A 102 " =    1.892
peak=    3.244 closest distance to " CA  ALA A  43 " =    1.307
peak=    3.243 closest distance to " CZ  PHE A 208 " =    1.147
peak=    3.238 closest distance to " NH2 ARG A 219 " =    1.749
peak=    3.229 closest distance to " NE2 GLN A  73 " =    3.636
peak=    3.221 closest distance to " CB  ALA A 291 " =    3.444
peak=    3.220 closest distance to " O   ARG A  56 " =    1.773
peak=    3.214 closest distance to " O   HOH Z 329 " =    3.532
peak=    3.213 closest distance to " CB  ASN A 142 " =    0.884
peak=    3.213 closest distance to " CA  ARG A 102 " =    1.212
peak=    3.204 closest distance to " CD1 TRP A 266 " =    1.302
peak=    3.204 closest distance to " O   HOH Z 216 " =    2.415
peak=    3.202 closest distance to " O   HOH Z 368 " =    3.597
peak=    3.202 closest distance to " O   HOH Z 124 " =    1.334
peak=    3.199 closest distance to " CB  PRO A 198 " =    0.826
peak=    3.198 closest distance to " O   ASN A 209 " =    1.399
peak=    3.197 closest distance to " CB  ALA A  43 " =    0.972
peak=    3.190 closest distance to " O   HOH Z 407 " =    2.003
peak=    3.190 closest distance to " CA  PHE A 208 " =    1.014
peak=    3.185 closest distance to " O   HOH Z 373 " =    1.947
peak=    3.182 closest distance to " NH2BARG A 145 " =    1.997
peak=    3.176 closest distance to " CG  GLN A  55 " =    1.806
peak=    3.175 closest distance to " CE BMET A  47 " =    1.403
peak=    3.172 closest distance to " O   HOH Z 380 " =    1.915
peak=    3.170 closest distance to " CG2 ILE A 109 " =    1.029
peak=    3.166 closest distance to " O   HOH Z 248 " =    1.897
peak=    3.157 closest distance to " OH  TYR A 186 " =    1.153
peak=    3.155 closest distance to " OG  SER A 206 " =    1.204
peak=    3.152 closest distance to " O   HOH Z 158 " =    2.754
peak=    3.152 closest distance to " CG1 ILE A 151 " =    0.906
peak=    3.152 closest distance to " CA  ASP A 162 " =    1.159
peak=    3.150 closest distance to " CB  SER A 210 " =    0.743
peak=    3.146 closest distance to " O   HOH Z 244 " =    1.741
peak=    3.141 closest distance to " O   HOH Z  73 " =    1.559
peak=    3.141 closest distance to " OG BSER A 164 " =    2.567
peak=    3.136 closest distance to " NH2BARG A 190 " =    1.611
peak=    3.135 closest distance to " OG  SER A  97 " =    3.560
peak=    3.135 closest distance to " O   HOH Z 173 " =    1.908
peak=    3.125 closest distance to " ND1 HIS A  81 " =    1.586
peak=    3.125 closest distance to " O   HOH Z 334 " =    1.789
peak=    3.124 closest distance to " O   HOH Z 299 " =    2.350
peak=    3.121 closest distance to " O   HOH Z 332 " =    1.588
peak=    3.120 closest distance to " O   HOH Z  88 " =    2.666
peak=    3.118 closest distance to " O   HOH Z  53 " =    2.589
peak=    3.117 closest distance to " O   ALA A 165 " =    1.382
peak=    3.114 closest distance to " CB  ALA A 256 " =    1.441
peak=    3.106 closest distance to " O   HOH Z 417 " =    3.663
peak=    3.104 closest distance to " NH2 ARG A 159 " =    1.319
peak=    3.102 closest distance to " O   GLY A 147 " =    1.438
peak=    3.094 closest distance to " CB  GLU A 277 " =    3.542
peak=    3.091 closest distance to " O   HOH Z 383 " =    2.091
peak=    3.071 closest distance to " CB  TRP A 150 " =    1.441
peak=    3.068 closest distance to " O   HOH Z 184 " =    1.976
peak=    3.067 closest distance to " NZ  LYS A 166 " =    2.945
peak=    3.061 closest distance to " O   HOH Z 128 " =    2.214
peak=    3.052 closest distance to " O   GLY A 302 " =    1.708
peak=    3.039 closest distance to " OD1 ASP A 238 " =    1.080
peak=    3.033 closest distance to " O   HOH Z 149 " =    1.920
peak=    3.025 closest distance to " NZ  LYS A  76 " =    1.251
peak=    3.012 closest distance to " O   HOH Z 334 " =    1.416
peak=    2.952 closest distance to " O   HOH Z 153 " =    1.585

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.347 - 5.618
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 190
   mapped sites are within: 0.729 - 5.618

peak=   -5.068 closest distance to " O   HOH Z 290 " =    1.001
peak=   -4.701 closest distance to " O   HOH Z 377 " =    1.482
peak=   -4.416 closest distance to " O   PRO A 198 " =    1.252
peak=   -4.341 closest distance to " C   ALA A 158 " =    1.392
peak=   -4.317 closest distance to " CD  GLN A  88 " =    0.778
peak=   -4.242 closest distance to " CD  ARG A  14 " =    3.278
peak=   -4.236 closest distance to " CB  PRO A 243 " =    2.524
peak=   -4.229 closest distance to " O   HOH Z 231 " =    1.137
peak=   -4.172 closest distance to " C   ASN A 285 " =    2.583
peak=   -4.143 closest distance to " O   HOH Z 377 " =    0.729
peak=   -4.098 closest distance to " CG  MET A 105 " =    0.953
peak=   -4.095 closest distance to " CG  LYS A 193 " =    2.465
peak=   -4.061 closest distance to " O   HOH Z  98 " =    1.902
peak=   -4.035 closest distance to " OE1 GLN A  88 " =    1.054
peak=   -4.001 closest distance to " O   HOH Z 166 " =    1.165
peak=   -3.918 closest distance to " ND2 ASN A  45 " =    0.936
peak=   -3.910 closest distance to " SG  CYS A 254 " =    3.197
peak=   -3.906 closest distance to " O   HOH Z 388 " =    1.916
peak=   -3.879 closest distance to " O   HOH Z 298 " =    1.299
peak=   -3.877 closest distance to " O   HOH Z  71 " =    0.939
peak=   -3.859 closest distance to " N   ALA A  43 " =    2.238
peak=   -3.803 closest distance to " CD2 LEU A 237 " =    2.785
peak=   -3.794 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.779 closest distance to " CD  ARG A 195 " =    5.162
peak=   -3.774 closest distance to " CA  ASP A  27 " =    2.421
peak=   -3.772 closest distance to " CD1 LEU A 228 " =    2.452
peak=   -3.755 closest distance to " O   HOH Z 266 " =    4.382
peak=   -3.740 closest distance to " CA  GLY A 241 " =    2.336
peak=   -3.700 closest distance to " O   HOH Z 407 " =    3.373
peak=   -3.699 closest distance to " CB  ALA A 291 " =    2.202
peak=   -3.675 closest distance to " O   HOH Z 185 " =    2.340
peak=   -3.674 closest distance to " O   HOH Z  43 " =    1.438
peak=   -3.645 closest distance to " O   VAL A  67 " =    2.730
peak=   -3.643 closest distance to " OXT GLY A 302 " =    2.837
peak=   -3.639 closest distance to " O   ALA A 161 " =    1.574
peak=   -3.637 closest distance to " CE  MET A  93 " =    1.163
peak=   -3.636 closest distance to " NH2AARG A 275 " =    5.618
peak=   -3.620 closest distance to " CB  TRP A  85 " =    2.521
peak=   -3.619 closest distance to " CD1 LEU A 101 " =    2.572
peak=   -3.618 closest distance to " CG  GLN A 223 " =    1.903
peak=   -3.611 closest distance to " CD  ARG A 156 " =    1.851
peak=   -3.608 closest distance to " OG ASER A 216 " =    1.108
peak=   -3.602 closest distance to " O   HOH Z 275 " =    1.648
peak=   -3.598 closest distance to " CB  CYS A 254 " =    2.289
peak=   -3.583 closest distance to " NE2 GLN A  88 " =    0.926
peak=   -3.578 closest distance to " CB  PHE A 283 " =    2.708
peak=   -3.578 closest distance to " O   HOH Z 389 " =    1.923
peak=   -3.574 closest distance to " CZ3 TRP A 179 " =    1.136
peak=   -3.572 closest distance to " O   HOH Z  13 " =    1.022
peak=   -3.569 closest distance to " O   HOH Z  51 " =    1.125
peak=   -3.566 closest distance to " O   HOH Z  52 " =    1.334
peak=   -3.545 closest distance to " O   HOH Z  97 " =    1.393
peak=   -3.536 closest distance to " O   HOH Z 435 " =    2.748
peak=   -3.533 closest distance to " CG  LEU A  83 " =    1.884
peak=   -3.512 closest distance to " OG  SER A  97 " =    2.196
peak=   -3.510 closest distance to " CB  ALA A  43 " =    2.378
peak=   -3.508 closest distance to " CD1 PHE A  59 " =    1.848
peak=   -3.504 closest distance to " CG  TRP A 266 " =    1.751
peak=   -3.499 closest distance to " CA  GLY A 203 " =    2.151
peak=   -3.489 closest distance to " O   PRO A 163 " =    1.876
peak=   -3.489 closest distance to " C   LEU A 143 " =    1.422
peak=   -3.488 closest distance to " CZ BARG A 275 " =    1.792
peak=   -3.486 closest distance to " CG  GLU A 152 " =    0.765
peak=   -3.485 closest distance to " O   HOH Z 198 " =    2.526
peak=   -3.475 closest distance to " O   HOH Z 438 " =    1.125
peak=   -3.470 closest distance to " O   GLY A 211 " =    1.454
peak=   -3.468 closest distance to " CE  MET A 105 " =    2.154
peak=   -3.454 closest distance to " O   GLY A 196 " =    1.188
peak=   -3.451 closest distance to " O   HOH Z  93 " =    1.372
peak=   -3.447 closest distance to " N   VAL A 232 " =    2.551
peak=   -3.432 closest distance to " O   HOH Z 340 " =    0.973
peak=   -3.427 closest distance to " CE2 TYR A  30 " =    2.875
peak=   -3.424 closest distance to " CA  VAL A 153 " =    2.261
peak=   -3.419 closest distance to " O   HOH Z 213 " =    1.588
peak=   -3.414 closest distance to " CB  PRO A  54 " =    2.425
peak=   -3.412 closest distance to " O   VAL A 189 " =    2.437
peak=   -3.406 closest distance to " O   HOH Z  90 " =    1.443
peak=   -3.395 closest distance to " O   HOH Z 184 " =    1.782
peak=   -3.392 closest distance to " OD1 ASN A  39 " =    2.221
peak=   -3.384 closest distance to " CG1 VAL A 250 " =    2.619
peak=   -3.373 closest distance to " CD2 TYR A 293 " =    2.036
peak=   -3.360 closest distance to " O   HOH Z  63 " =    1.406
peak=   -3.359 closest distance to " OG  SER A   3 " =    1.654
peak=   -3.359 closest distance to " OD2 ASP A 171 " =    2.142
peak=   -3.356 closest distance to " N   MET A 188 " =    1.764
peak=   -3.354 closest distance to " O   HOH Z 241 " =    1.196
peak=   -3.352 closest distance to " O   HOH Z  98 " =    2.239
peak=   -3.348 closest distance to " CB  ASN A  39 " =    2.071
peak=   -3.347 closest distance to " O   GLY A 203 " =    2.455
peak=   -3.343 closest distance to " CE  LYS A  76 " =    2.761
peak=   -3.341 closest distance to " O   HOH Z  65 " =    1.245
peak=   -3.336 closest distance to " O   HOH Z 186 " =    0.819
peak=   -3.336 closest distance to " O   TRP A  70 " =    1.480
peak=   -3.335 closest distance to " CG1 VAL A 197 " =    2.259
peak=   -3.328 closest distance to " O   HOH Z 134 " =    2.143
peak=   -3.327 closest distance to " CB  PRO A 163 " =    2.638
peak=   -3.318 closest distance to " OG BSER A 134 " =    1.245
peak=   -3.317 closest distance to " CG  PRO A 163 " =    2.302
peak=   -3.315 closest distance to " O   SER A 135 " =    1.493
peak=   -3.310 closest distance to " O   HOH Z 283 " =    2.223
peak=   -3.309 closest distance to " O   ILE A 109 " =    2.599
peak=   -3.304 closest distance to " O   HOH Z 168 " =    1.624
peak=   -3.303 closest distance to " ND2 ASN A  60 " =    1.954
peak=   -3.302 closest distance to " O   PRO A 243 " =    2.212
peak=   -3.302 closest distance to " O   HOH Z  92 " =    1.124
peak=   -3.299 closest distance to " O   HOH Z 319 " =    2.628
peak=   -3.299 closest distance to " O   HOH Z 313 " =    2.044
peak=   -3.298 closest distance to " O   HOH Z 222 " =    1.231
peak=   -3.297 closest distance to " OD1 ASN A 148 " =    1.658
peak=   -3.295 closest distance to " C   HIS A 108 " =    1.152
peak=   -3.291 closest distance to " CZ  ARG A 259 " =    0.864
peak=   -3.290 closest distance to " O   HOH Z 281 " =    2.982
peak=   -3.290 closest distance to " OG ASER A 134 " =    1.194
peak=   -3.288 closest distance to " CD1 TRP A 179 " =    0.916
peak=   -3.287 closest distance to " O   HOH Z 111 " =    2.410
peak=   -3.280 closest distance to " O   HOH Z  88 " =    2.601
peak=   -3.278 closest distance to " O   HOH Z 176 " =    0.747
peak=   -3.277 closest distance to " O   VAL A  67 " =    2.616
peak=   -3.270 closest distance to " O   HOH Z  53 " =    1.503
peak=   -3.267 closest distance to " CG1 VAL A 112 " =    2.887
peak=   -3.264 closest distance to " O   HOH Z 353 " =    2.237
peak=   -3.259 closest distance to " CD1 ILE A 239 " =    1.972
peak=   -3.258 closest distance to " OG  SER A  87 " =    1.379
peak=   -3.258 closest distance to " O   GLY A  80 " =    2.369
peak=   -3.257 closest distance to " O   HOH Z  22 " =    2.640
peak=   -3.255 closest distance to " O   HOH Z 219 " =    1.112
peak=   -3.252 closest distance to " O   HOH Z 111 " =    0.900
peak=   -3.251 closest distance to " O   HOH Z 323 " =    1.353
peak=   -3.248 closest distance to " CD  GLN A  58 " =    1.207
peak=   -3.247 closest distance to " N   GLN A  58 " =    1.690
peak=   -3.244 closest distance to " O   HOH Z 148 " =    2.113
peak=   -3.240 closest distance to " O   SER A  62 " =    2.093
peak=   -3.236 closest distance to " O   HOH Z 368 " =    2.465
peak=   -3.235 closest distance to " CD1 LEU A 101 " =    2.714
peak=   -3.235 closest distance to " CB  PHE A 192 " =    1.723
peak=   -3.231 closest distance to " O   HOH Z 436 " =    1.071
peak=   -3.227 closest distance to " O   HOH Z 109 " =    1.300
peak=   -3.225 closest distance to " OD1 ASP A 191 " =    1.839
peak=   -3.221 closest distance to " CE3 TRP A 123 " =    1.334
peak=   -3.217 closest distance to " CB  LEU A 167 " =    2.083
peak=   -3.217 closest distance to " C   LEU A 222 " =    0.803
peak=   -3.213 closest distance to " O   HOH Z 351 " =    1.416
peak=   -3.211 closest distance to " CG2 VAL A 232 " =    2.045
peak=   -3.210 closest distance to " O   HOH Z  51 " =    1.192
peak=   -3.209 closest distance to " O   HOH Z 426 " =    1.682
peak=   -3.194 closest distance to " OXT GLY A 302 " =    3.314
peak=   -3.190 closest distance to " CG  TRP A 266 " =    1.404
peak=   -3.182 closest distance to " CD1 TYR A 169 " =    2.443
peak=   -3.180 closest distance to " OG  SER A 245 " =    0.932
peak=   -3.176 closest distance to " O   HOH Z 426 " =    2.314
peak=   -3.163 closest distance to " O   SER A  62 " =    1.565
peak=   -3.163 closest distance to " O   HOH Z  35 " =    1.047
peak=   -3.161 closest distance to " CE3 TRP A 150 " =    1.795
peak=   -3.155 closest distance to " O   ASN A 301 " =    1.416
peak=   -3.154 closest distance to " OG1 THR A 182 " =    1.869
peak=   -3.150 closest distance to " O   HOH Z 137 " =    1.559
peak=   -3.149 closest distance to " CD2 LEU A 300 " =    2.860
peak=   -3.147 closest distance to " O   PRO A 198 " =    1.210
peak=   -3.145 closest distance to " O   HOH Z  20 " =    2.313
peak=   -3.141 closest distance to " O   HOH Z 173 " =    0.780
peak=   -3.134 closest distance to " O   HOH Z  56 " =    0.872
peak=   -3.133 closest distance to " SG ACYS A 201 " =    2.200
peak=   -3.133 closest distance to " O   HOH Z 417 " =    2.547
peak=   -3.133 closest distance to " CD1 ILE A 199 " =    2.645
peak=   -3.133 closest distance to " O   HOH Z 198 " =    1.431
peak=   -3.133 closest distance to " O   HOH Z 210 " =    0.863
peak=   -3.132 closest distance to " CD  ARG A 159 " =    1.303
peak=   -3.129 closest distance to " CD  ARG A 139 " =    1.594
peak=   -3.121 closest distance to " OD1 ASN A 301 " =    1.772
peak=   -3.121 closest distance to " CZ  PHE A  59 " =    1.557
peak=   -3.115 closest distance to " O   HOH Z  10 " =    1.527
peak=   -3.115 closest distance to " OG1 THR A   4 " =    1.955
peak=   -3.115 closest distance to " CZ  TYR A 169 " =    1.806
peak=   -3.111 closest distance to " N   SER A 212 " =    1.880
peak=   -3.106 closest distance to " CG  MET A 185 " =    2.884
peak=   -3.089 closest distance to " O   HOH Z 282 " =    4.409
peak=   -3.086 closest distance to " O   HOH Z 140 " =    4.801
peak=   -3.079 closest distance to " CD1 LEU A 297 " =    2.615
peak=   -3.076 closest distance to " O   HOH Z 262 " =    2.149
peak=   -3.025 closest distance to " O   HOH Z 396 " =    1.758
peak=   -3.024 closest distance to " CB  CYS A 201 " =    2.587

================= 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    :  0.4549 0.4550   6.257445e+00   6.255000e+00
   1_bss:  0.4467 0.4464   6.253017e+00   6.245912e+00
   1_xyz:  0.3105 0.3532   5.999993e+00   6.087435e+00
   1_adp:  0.2826 0.3577   5.953180e+00   6.103859e+00
   1_occ:  0.2824 0.3573   5.951995e+00   6.102848e+00
   2_bss:  0.2810 0.3571   5.949717e+00   6.099887e+00
   2_xyz:  0.2149 0.2809   5.725218e+00   5.914304e+00
   2_adp:  0.2012 0.2685   5.678285e+00   5.877049e+00
   2_occ:  0.2010 0.2681   5.677628e+00   5.876157e+00
   3_bss:  0.2013 0.2676   5.676320e+00   5.874811e+00
   3_xyz:  0.1599 0.2166   5.463923e+00   5.690098e+00
   3_adp:  0.1465 0.1982   5.381470e+00   5.606605e+00
   3_occ:  0.1464 0.1981   5.380547e+00   5.605586e+00
   4_bss:  0.1467 0.1975   5.381312e+00   5.604647e+00
   4_xyz:  0.1264 0.1747   5.249162e+00   5.487745e+00
   4_adp:  0.1234 0.1675   5.216688e+00   5.446508e+00
   4_occ:  0.1232 0.1672   5.215428e+00   5.445447e+00
   5_bss:  0.1231 0.1671   5.215361e+00   5.445274e+00
   5_xyz:  0.1171 0.1620   5.180386e+00   5.415039e+00
   5_adp:  0.1171 0.1609   5.177717e+00   5.410925e+00
   5_occ:  0.1170 0.1607   5.176909e+00   5.410484e+00
   5_bss:  0.1171 0.1605   5.177885e+00   5.411705e+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  20.000   1.866  -1.462   1.065  -0.000   0.000   0.000
   1_xyz:  0.300  20.000   1.866  -1.462   1.065  -0.000   0.000   0.000
   1_adp:  0.300  20.000   1.866  -1.462   1.065  -0.000   0.000   0.000
   1_occ:  0.300  20.000   1.866  -1.462   1.065  -0.000   0.000   0.000
   2_bss:  0.343  53.656   0.270  -1.715  -0.132  -0.000  -0.000  -0.000
   2_xyz:  0.343  53.656   0.270  -1.715  -0.132  -0.000  -0.000  -0.000
   2_adp:  0.343  53.656   0.270  -1.715  -0.132  -0.000  -0.000  -0.000
   2_occ:  0.343  53.656   0.270  -1.715  -0.132  -0.000  -0.000  -0.000
   3_bss:  0.332  53.656  -0.324  -1.744  -0.487  -0.000  -0.000  -0.000
   3_xyz:  0.332  53.656  -0.324  -1.744  -0.487  -0.000  -0.000  -0.000
   3_adp:  0.332  53.656  -0.324  -1.744  -0.487  -0.000  -0.000  -0.000
   3_occ:  0.332  53.656  -0.324  -1.744  -0.487  -0.000  -0.000  -0.000
   4_bss:  0.330  56.023  -1.149  -2.160  -1.206  -0.000  -0.000  -0.000
   4_xyz:  0.330  56.023  -1.149  -2.160  -1.206  -0.000  -0.000  -0.000
   4_adp:  0.330  56.023  -1.149  -2.160  -1.206  -0.000  -0.000  -0.000
   4_occ:  0.330  56.023  -1.149  -2.160  -1.206  -0.000  -0.000  -0.000
   5_bss:  0.323  48.139  -1.525  -2.341  -1.507  -0.000  -0.000  -0.000
   5_xyz:  0.323  48.139  -1.525  -2.341  -1.507  -0.000  -0.000  -0.000
   5_adp:  0.323  48.139  -1.525  -2.341  -1.507  -0.000  -0.000  -0.000
   5_occ:  0.323  48.139  -1.525  -2.341  -1.507  -0.000  -0.000  -0.000
   5_bss:  0.323  48.083  -1.620  -2.378  -1.590  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.671 0.4615  0.6233    64203.212
   1_bss:  53.670 0.4727  0.6520    61166.944
   1_xyz:  37.475 0.6728  0.8891    34415.552
   1_adp:  38.958 0.6541  0.8662    35909.063
   1_occ:  38.959 0.6539  0.8646    35790.120
   2_bss:  38.710 0.6567  0.8402    35402.042
   2_xyz:  29.184 0.7658  0.9480    21173.530
   2_adp:  27.370 0.7860  0.9538    19273.305
   2_occ:  27.343 0.7863  0.9538    19235.288
   3_bss:  27.269 0.7870  0.9424    19102.762
   3_xyz:  21.375 0.8476  0.9886    12272.030
   3_adp:  18.972 0.8716  0.9961    10237.052
   3_occ:  18.938 0.8719  0.9960    10196.898
   4_bss:  18.908 0.8722  0.9735    10174.652
   4_xyz:  16.212 0.8959  0.9859     7773.957
   4_adp:  15.154 0.9054  0.9888     7188.914
   4_occ:  15.113 0.9058  0.9889     7158.614
   5_bss:  15.112 0.9058  0.9786     7142.830
   5_xyz:  14.482 0.9111  0.9806     6700.230
   5_adp:  14.294 0.9130  0.9805     6659.946
   5_occ:  14.274 0.9132  0.9805     6647.829
   5_bss:  14.321 0.9127  0.9759     6674.769
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7266e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7266e-01
   1_xyz:   1.460  0.011  0.097 15.963  0.006  4.111   1.2085e-01
   1_adp:   1.460  0.011  0.097 15.963  0.006  4.111   1.2085e-01
   1_occ:   1.460  0.011  0.097 15.963  0.006  4.111   1.2085e-01
   2_bss:   1.460  0.011  0.097 15.963  0.006  4.111   1.2085e-01
   2_xyz:   1.109  0.007  0.074 14.170  0.005  4.109   6.6620e-02
   2_adp:   1.109  0.007  0.074 14.170  0.005  4.109   6.6620e-02
   2_occ:   1.109  0.007  0.074 14.170  0.005  4.109   6.6620e-02
   3_bss:   1.109  0.007  0.074 14.170  0.005  4.109   6.6620e-02
   3_xyz:   0.948  0.006  0.067 14.379  0.003  4.115   5.5542e-02
   3_adp:   0.948  0.006  0.067 14.379  0.003  4.115   5.5542e-02
   3_occ:   0.948  0.006  0.067 14.379  0.003  4.115   5.5542e-02
   4_bss:   0.948  0.006  0.067 14.379  0.003  4.115   5.5542e-02
   4_xyz:   1.018  0.007  0.073 14.477  0.004  4.122   5.9438e-02
   4_adp:   1.018  0.007  0.073 14.477  0.004  4.122   5.9438e-02
   4_occ:   1.018  0.007  0.073 14.477  0.004  4.122   5.9438e-02
   5_bss:   1.018  0.007  0.073 14.477  0.004  4.122   5.9438e-02
   5_xyz:   0.991  0.007  0.071 14.593  0.004  4.111   5.7819e-02
   5_adp:   0.991  0.007  0.071 14.593  0.004  4.111   5.7819e-02
   5_occ:   0.991  0.007  0.071 14.593  0.004  4.111   5.7819e-02
   5_bss:   0.991  0.007  0.071 14.593  0.004  4.111   5.7819e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.633   2.4019e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.633   2.4019e-01
   1_xyz:  10.180  0.061  0.456 85.044  0.031  2.101   1.1090e-01
   1_adp:  10.180  0.061  0.456 85.044  0.031  2.101   1.1090e-01
   1_occ:  10.180  0.061  0.456 85.044  0.031  2.101   1.1090e-01
   2_bss:  10.180  0.061  0.456 85.044  0.031  2.101   1.1090e-01
   2_xyz:   6.687  0.039  0.224 82.240  0.050  2.356   6.6146e-02
   2_adp:   6.687  0.039  0.224 82.240  0.050  2.356   6.6146e-02
   2_occ:   6.687  0.039  0.224 82.240  0.050  2.356   6.6146e-02
   3_bss:   6.687  0.039  0.224 82.240  0.050  2.356   6.6146e-02
   3_xyz:   8.782  0.037  0.306 79.140  0.021  2.327   5.6160e-02
   3_adp:   8.782  0.037  0.306 79.140  0.021  2.327   5.6160e-02
   3_occ:   8.782  0.037  0.306 79.140  0.021  2.327   5.6160e-02
   4_bss:   8.782  0.037  0.306 79.140  0.021  2.327   5.6160e-02
   4_xyz:   8.457  0.047  0.236 82.326  0.031  2.302   4.5929e-02
   4_adp:   8.457  0.047  0.236 82.326  0.031  2.302   4.5929e-02
   4_occ:   8.457  0.047  0.236 82.326  0.031  2.302   4.5929e-02
   5_bss:   8.457  0.047  0.236 82.326  0.031  2.302   4.5929e-02
   5_xyz:   8.358  0.047  0.209 84.704  0.033  2.314   3.9628e-02
   5_adp:   8.358  0.047  0.209 84.704  0.033  2.314   3.9628e-02
   5_occ:   8.358  0.047  0.209 84.704  0.033  2.314   3.9628e-02
   5_bss:   8.358  0.047  0.209 84.704  0.033  2.314   3.9628e-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:  95.30   0.00  18.66  91.91   0.00  14.44  95.30   0.00  41.65
   1_occ:  95.30   0.00  18.66  91.91   0.00  14.44  95.30   0.00  41.65
   2_bss:  95.30   0.00  18.66  91.91   0.00  14.44  95.30   0.00  41.65
   2_xyz:  95.30   0.00  18.66  91.91   0.00  14.44  95.30   0.00  41.65
   2_adp:  95.10   0.00  18.35  93.25   0.00  13.83  95.10   2.15  42.92
   2_occ:  95.10   0.00  18.35  93.25   0.00  13.83  95.10   2.15  42.92
   3_bss:  95.10   0.00  18.35  93.25   0.00  13.83  95.10   2.15  42.92
   3_xyz:  95.10   0.00  18.35  93.25   0.00  13.83  95.10   2.15  42.92
   3_adp:  94.15   0.00  17.64  94.15   0.00  12.96  87.51   4.94  43.14
   3_occ:  94.15   0.00  17.64  94.15   0.00  12.96  87.51   4.94  43.14
   4_bss:  94.15   0.00  17.64  94.15   0.00  12.96  87.51   4.94  43.14
   4_xyz:  94.15   0.00  17.64  94.15   0.00  12.96  87.51   4.94  43.14
   4_adp:  91.30   0.99  16.89  91.30   0.99  12.63  86.27   6.08  40.08
   4_occ:  91.30   0.99  16.89  91.30   0.99  12.63  86.27   6.08  40.08
   5_bss:  91.30   0.99  16.89  91.30   0.99  12.63  86.27   6.08  40.08
   5_xyz:  91.30   0.99  16.89  91.30   0.99  12.63  86.27   6.08  40.08
   5_adp:  88.57   1.57  16.48  88.57   1.57  12.55  86.24   6.15  37.91
   5_occ:  88.57   1.57  16.48  88.57   1.57  12.55  86.24   6.15  37.91
   5_bss:  88.51   1.52  16.43  88.51   1.52  12.49  86.18   6.09  37.85
------------------------------------------------------------------------
 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:    1.935    0.019    0.378
   1_adp:    1.935    0.019    0.378
   1_occ:    1.935    0.019    0.378
   2_bss:    1.935    0.019    0.378
   2_xyz:    1.284    0.054    0.497
   2_adp:    1.284    0.054    0.497
   2_occ:    1.284    0.054    0.497
   3_bss:    1.284    0.054    0.497
   3_xyz:    1.244    0.066    0.617
   3_adp:    1.244    0.066    0.617
   3_occ:    1.244    0.066    0.617
   4_bss:    1.244    0.066    0.617
   4_xyz:    1.286    0.088    0.665
   4_adp:    1.286    0.088    0.665
   4_occ:    1.286    0.088    0.665
   5_bss:    1.286    0.088    0.665
   5_xyz:    1.223    0.062    0.684
   5_adp:    1.223    0.062    0.684
   5_occ:    1.223    0.062    0.684
   5_bss:    1.223    0.062    0.684
------------------------------------------------------------------------

CPU time actual refinement: 349.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1244/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_1244/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1244/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1244/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1244/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.58 
  Macro-tasks:
    bulk solvent and scale       = 41.13  
    individual site refinement   = 141.67 
    weights calculation          = 29.93  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 219.36 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 114.60 
    alpha_beta                      = 8.43   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 121.35 
    fmodel                         = 7.34   
    r_factors                      = 0.26   
    phase_errors                   = 10.62  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 266.45 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.991 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    638 calls, 114.23 s
gradients_fft:          583 calls, 108.33 s

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

# Date 2008-01-16 Time 06:47:47 PST -0800 (1200494867.34 s)
Start R-work = 0.4549, R-free = 0.4550 (no bulk solvent and anisotropic scale)
Final R-work = 0.1407, R-free = 0.1822 (no bulk solvent and anisotropic scale)

Start R-work = 0.4467, R-free = 0.4464
Final R-work = 0.1171, R-free = 0.1605