# Date 2008-01-16 Time 06:21:01 PST -0800 (1200493261.89 s)
#phil __OFF__

Command line arguments: "../1106.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6063
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1106

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 45.9914, 86.822, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 1.96408
Completeness in resolution range: 0.929666
Completeness with d_max=infinity: 0.927027

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2319
                             d_min =   1.9641

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 1.96408
Completeness in resolution range: 0.929666
Completeness with d_max=infinity: 0.927027

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2323 -  4.2046 [2215/2242]  1994   221  10.0%
  bin  2:  4.2046 -  3.3490 [2131/2151]  1918   213  10.0%
  bin  3:  3.3490 -  2.9291 [2096/2115]  1885   211  10.1%
  bin  4:  2.9291 -  2.6628 [2066/2096]  1856   210  10.2%
  bin  5:  2.6628 -  2.4728 [2071/2090]  1877   194   9.4%
  bin  6:  2.4728 -  2.3276 [2076/2101]  1857   219  10.5%
  bin  7:  2.3276 -  2.2114 [2022/2050]  1812   210  10.4%
  bin  8:  2.2114 -  2.1154 [2047/2083]  1847   200   9.8%
  bin  9:  2.1154 -  2.0341 [2026/2077]  1832   194   9.6%
  bin 10:  2.0341 -  1.9641 [ 839/2066]   752    87  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1106/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: 0.12 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:
        1.76 -     2.39: 30
        2.39 -     3.02: 2027
        3.02 -     3.64: 4642
        3.64 -     4.27: 9116
        4.27 -     4.90: 12426
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.761 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28236 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_1106/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1106/model_refine_001.geo

CPU time processing inputs: 7.76


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 45.9914 86.82195 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 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4450   r_free= 0.4440   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.258746                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.6905 0.99   1431  161 0.3630 0.3542      6.5345      6.5112|
|  2:  4.6905 -  3.7412 0.99   1386  153 0.3801 0.3602      6.7804      6.7193|
|  3:  3.7412 -  3.2736 0.99   1346  147 0.4036 0.3877      6.6137      6.6431|
|  4:  3.2736 -  2.9767 0.99   1356  154 0.4402 0.4661      6.4929      6.5145|
|  5:  2.9767 -  2.7647 0.99   1341  145 0.4646 0.4743      6.3414      6.3594|
|  6:  2.7647 -  2.6026 0.99   1344  152 0.4709 0.4639      6.2419      6.1992|
|  7:  2.6026 -  2.4728 0.99   1326  137 0.4889 0.4576      6.2224      6.1663|
|  8:  2.4728 -  2.3656 0.98   1310  158 0.4876 0.5184      6.1486      6.1872|
|  9:  2.3656 -  2.2748 0.98   1316  144 0.4841 0.5061        6.11       6.121|
| 10:  2.2748 -  2.1966 1.00   1315  158 0.5048 0.4870      6.0621      6.0424|
| 11:  2.1966 -  2.1281 0.98   1313  129 0.5023 0.5151      6.0216       6.052|
| 12:  2.1281 -  2.0674 0.98   1301  156 0.4974 0.5170      5.9297       5.957|
| 13:  2.0674 -  2.0131 0.91   1199  125 0.5016 0.4714       5.864      5.7925|
| 14:  2.0131 -  1.9641 0.26    346   40 0.5073 0.5742      5.8505      5.8786|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.6905  1431   161  0.74  30.69   0.82     0.79      60015.55|
|  2:  4.6905 -  3.7412  1386   153  0.74  31.95   0.91     0.84      91174.49|
|  3:  3.7412 -  3.2736  1346   147  0.62  42.20   0.94     0.80     103571.20|
|  4:  3.2736 -  2.9767  1356   154  0.52  50.10   0.91     0.72      98518.73|
|  5:  2.9767 -  2.7647  1341   145  0.44  56.24   0.90     0.63      79975.40|
|  6:  2.7647 -  2.6026  1344   152  0.42  57.97   0.91     0.60      68118.88|
|  7:  2.6026 -  2.4728  1326   137  0.41  59.34   0.92     0.56      61215.79|
|  8:  2.4728 -  2.3656  1310   158  0.39  60.68   0.90     0.55      55960.96|
|  9:  2.3656 -  2.2748  1316   144  0.39  60.87   0.95     0.55      50910.96|
| 10:  2.2748 -  2.1966  1315   158  0.38  61.27   0.93     0.56      46225.94|
| 11:  2.1966 -  2.1281  1313   129  0.37  62.65   0.95     0.56      45893.93|
| 12:  2.1281 -  2.0674  1301   156  0.34  64.91   0.94     0.53      42157.65|
| 13:  2.0674 -  2.0131  1199   125  0.32  66.37   0.94     0.52      37519.20|
| 14:  2.0131 -  1.9641   346    40  0.38  61.86   0.96     0.53      29430.20|
|alpha:            min =        0.52 max =            0.84 mean =         0.63|
|beta:             min =    29430.20 max =       103571.20 mean =     64468.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.04|
|phase err.(test): min =        0.00 max =           89.99 mean =        54.24|
|-----------------------------------------------------------------------------|

============================== 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 = 10.891627             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.872   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.435227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.801   (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 |  1.761 -  2.075:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.075 -  2.389:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.389 -  2.703:      125 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.703 -  3.017:     1902 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.017 -  3.331:     1893 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.331 -  3.645:     2749 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.645 -  3.958:     4711 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.958 -  4.272:     4405 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.272 -  4.586:     5648 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.586 -  4.900:     6778 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| 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  1.761 |       0.316 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    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 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4450   r_free= 0.4440   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.258746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4360   r_free= 0.4372   ksol= 0.34   Bsol= 50.00   scale= 0.940   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,2.20,-1.35,0.00,-0.00,-0.00); trace/3= 0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.251589                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.200172              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.982   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.183989              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.503   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4360      final r-factor (work) = 0.3224          |
| start r-factor (free) = 0.4372      final r-factor (free) = 0.3629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.9115 = 9.20 * 0.50 * 6.2476 + 1.00 * 0.1721                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.2939 = 9.20 * 0.50 * 6.1234 + 1.00 * 0.1256                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3224      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.3629      final r-factor (free) = 0.3740          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2564 = 1.18 * 1.00 * 6.1234 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1199 = 1.18 * 1.00 * 5.9859 + 1.00 * 0.0327                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.38  18.91    None  None   None       |
|    all(noH): 2823   0      0.00    112.38  18.91    None  None   None       |
|    Sol.    : 438    0      1.16    112.38  40.07    None  None   None       |
|    Mac.    : 2385   0      0.00    71.20   15.03    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 -  11.238: 1037   |   5:    56.191 -  67.429:   60        |
|      1:    11.238 -  22.477:  964   |   6:    67.429 -  78.668:   29        |
|      2:    22.477 -  33.715:  411   |   7:    78.668 -  89.906:    9        |
|      3:    33.715 -  44.953:  197   |   8:    89.906 - 101.144:    0        |
|      4:    44.953 -  56.191:  115   |   9:   101.144 - 112.382:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2932 r_free = 0.3740             target_work(ml) = 5.998         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2926 r_free = 0.3740             target_work(ml) = 5.997         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2926   r_free= 0.3740   ksol= 0.34   Bsol= 50.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,2.20,-1.35,0.00,-0.00,-0.00); trace/3= 0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.996946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2924   r_free= 0.3713   ksol= 0.35   Bsol= 77.94   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.26,-0.67,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.995100                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.432296              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.885   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.892604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.379   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2924      final r-factor (work) = 0.2244          |
| start r-factor (free) = 0.3713      final r-factor (free) = 0.2911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3786 = 6.43 * 0.50 * 5.9864 + 1.00 * 0.1256                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0643 = 6.43 * 0.50 * 5.9011 + 1.00 * 0.0855                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2244      final r-factor (work) = 0.2047          |
| start r-factor (free) = 0.2911      final r-factor (free) = 0.2703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2865 = 0.89 * 1.00 * 5.9011 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1227 = 0.89 * 1.00 * 5.7220 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.75  18.99    None  None   None       |
|    all(noH): 2823   0      0.00    115.75  18.99    None  None   None       |
|    Sol.    : 438    0      3.99    115.75  44.82    None  None   None       |
|    Mac.    : 2385   0      0.00    95.62   14.24    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 -  11.575: 1217   |   5:    57.876 -  69.451:   73        |
|      1:    11.575 -  23.150:  919   |   6:    69.451 -  81.026:   34        |
|      2:    23.150 -  34.725:  253   |   7:    81.026 -  92.601:   16        |
|      3:    34.725 -  46.301:  176   |   8:    92.601 - 104.176:    2        |
|      4:    46.301 -  57.876:  132   |   9:   104.176 - 115.751:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2047 r_free = 0.2703             target_work(ml) = 5.691         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2047 r_free = 0.2698             target_work(ml) = 5.690         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2047   r_free= 0.2698   ksol= 0.35   Bsol= 77.94   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.26,-0.67,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.690140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2046   r_free= 0.2692   ksol= 0.35   Bsol= 80.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-1.15,-0.33,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.688046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.444728              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.506   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.175878              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.804  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2046      final r-factor (work) = 0.1640          |
| start r-factor (free) = 0.2692      final r-factor (free) = 0.2224          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9407 = 3.44 * 0.50 * 5.7219 + 1.00 * 0.0855                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6997 = 3.44 * 0.50 * 5.5987 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1640      final r-factor (work) = 0.1553          |
| start r-factor (free) = 0.2224      final r-factor (free) = 0.2045          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9999 = 0.18 * 1.00 * 5.5987 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9705 = 0.18 * 1.00 * 5.4705 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    101.35  17.47    None  None   None       |
|    all(noH): 2823   0      1.61    101.35  17.47    None  None   None       |
|    Sol.    : 438    0      5.15    101.35  41.41    None  None   None       |
|    Mac.    : 2385   0      1.61    90.95   13.08    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:     1.615 -  11.588: 1321   |   5:    51.481 -  61.454:   85        |
|      1:    11.588 -  21.561:  902   |   6:    61.454 -  71.427:   39        |
|      2:    21.561 -  31.534:  199   |   7:    71.427 -  81.400:   15        |
|      3:    31.534 -  41.508:  139   |   8:    81.400 -  91.373:    3        |
|      4:    41.508 -  51.481:  119   |   9:    91.373 - 101.347:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1553 r_free = 0.2045             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1552 r_free = 0.2040             target_work(ml) = 5.425         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2040   ksol= 0.35   Bsol= 80.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-1.15,-0.33,-0.00,-0.00,-0.00); trace/3= -0.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.424894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1549   r_free= 0.2034   ksol= 0.33   Bsol= 62.32   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-2.37,-0.92,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.423221                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.066831              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.505  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.203  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1549      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.2034      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7137 = 2.07 * 0.50 * 5.4741 + 1.00 * 0.0567                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5902 = 2.07 * 0.50 * 5.3578 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1328      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1785      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4053 = 0.45 * 1.00 * 5.3578 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3657 = 0.45 * 1.00 * 5.2659 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.14   17.62    None  None   None       |
|    all(noH): 2823   0      0.00    98.14   17.62    None  None   None       |
|    Sol.    : 438    0      5.03    98.14   43.16    None  None   None       |
|    Mac.    : 2385   0      0.00    96.21   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.814:  994   |   5:    49.068 -  58.882:   93        |
|      1:     9.814 -  19.627: 1155   |   6:    58.882 -  68.695:   65        |
|      2:    19.627 -  29.441:  244   |   7:    68.695 -  78.509:   30        |
|      3:    29.441 -  39.255:  118   |   8:    78.509 -  88.323:    8        |
|      4:    39.255 -  49.068:  112   |   9:    88.323 -  98.136:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1277 r_free = 0.1762             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1762             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1762   ksol= 0.33   Bsol= 62.32   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-2.37,-0.92,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.258151                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1762   ksol= 0.32   Bsol= 62.32   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.56,-1.05,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.257910                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.687514              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.009  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.320054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.841  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1276      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4964 = 1.69 * 0.50 * 5.2658 + 1.00 * 0.0534                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4699 = 1.69 * 0.50 * 5.2371 + 1.00 * 0.0511                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6858 = 0.32 * 1.00 * 5.2371 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6785 = 0.32 * 1.00 * 5.2151 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.05   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    97.05   17.44    None  None   None       |
|    Sol.    : 438    0      5.76    96.41   42.41    None  None   None       |
|    Mac.    : 2385   0      0.00    97.05   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.705:  992   |   5:    48.524 -  58.228:   96        |
|      1:     9.705 -  19.409: 1161   |   6:    58.228 -  67.933:   61        |
|      2:    19.409 -  29.114:  242   |   7:    67.933 -  77.638:   29        |
|      3:    29.114 -  38.819:  119   |   8:    77.638 -  87.342:   10        |
|      4:    38.819 -  48.524:  109   |   9:    87.342 -  97.047:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1680             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1680             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1680   ksol= 0.32   Bsol= 62.32   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.56,-1.05,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.211957                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.6905 0.99   1431  161 0.0988 0.1347      5.3867      5.6092|
|  2:  4.6905 -  3.7412 0.99   1386  153 0.0888 0.1129      5.4742       5.639|
|  3:  3.7412 -  3.2736 0.99   1346  147 0.1154 0.1641      5.5302      5.8672|
|  4:  3.2736 -  2.9767 0.99   1356  154 0.1371 0.1763      5.5206      5.6443|
|  5:  2.9767 -  2.7647 0.99   1341  145 0.1425 0.1950      5.3853      5.6443|
|  6:  2.7647 -  2.6026 0.99   1344  152 0.1359 0.2027      5.2661      5.5152|
|  7:  2.6026 -  2.4728 0.99   1326  137 0.1362 0.1714      5.2227      5.3761|
|  8:  2.4728 -  2.3656 0.98   1310  158 0.1291 0.1750       5.126      5.3526|
|  9:  2.3656 -  2.2748 0.98   1316  144 0.1291 0.1944       5.105       5.377|
| 10:  2.2748 -  2.1966 1.00   1315  158 0.1202 0.1754      5.0002      5.2308|
| 11:  2.1966 -  2.1281 0.98   1313  129 0.1217 0.2009      5.0042      5.4161|
| 12:  2.1281 -  2.0674 0.98   1301  156 0.1240 0.1896      4.9357      5.1658|
| 13:  2.0674 -  2.0131 0.91   1199  125 0.1230 0.1740      4.8474      5.0531|
| 14:  2.0131 -  1.9641 0.26    346   40 0.1028 0.1531      4.6955      4.9479|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.6905  1431   161  0.94   9.20   0.97     0.95       7255.11|
|  2:  4.6905 -  3.7412  1386   153  0.95   8.35   1.01     1.00       9609.37|
|  3:  3.7412 -  3.2736  1346   147  0.93  12.05   1.03     1.02      11299.13|
|  4:  3.2736 -  2.9767  1356   154  0.90  15.81   1.01     0.98      11653.81|
|  5:  2.9767 -  2.7647  1341   145  0.90  16.51   1.00     0.99       9093.79|
|  6:  2.7647 -  2.6026  1344   152  0.89  17.26   0.99     0.96       7692.91|
|  7:  2.6026 -  2.4728  1326   137  0.90  16.46   1.00     0.98       6919.90|
|  8:  2.4728 -  2.3656  1310   158  0.90  16.61   0.98     0.95       5884.85|
|  9:  2.3656 -  2.2748  1316   144  0.89  17.00   1.00     0.95       5683.25|
| 10:  2.2748 -  2.1966  1315   158  0.89  16.91   1.00     0.97       4917.43|
| 11:  2.1966 -  2.1281  1313   129  0.89  17.09   0.99     0.93       4834.37|
| 12:  2.1281 -  2.0674  1301   156  0.89  17.47   1.00     1.00       4560.14|
| 13:  2.0674 -  2.0131  1199   125  0.89  18.05   0.99     0.97       3851.48|
| 14:  2.0131 -  1.9641   346    40  0.91  15.46   0.97     0.95       2934.69|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2934.69 max =        11653.81 mean =      7146.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.21|
|phase err.(test): min =        0.00 max =           89.61 mean =        14.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1677   ksol= 0.32   Bsol= 59.18   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.56,-1.05,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.212020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1677   ksol= 0.32   Bsol= 59.18   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.56,-1.05,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.212020                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.6905 0.99   1431  161 0.0998 0.1321      5.3818      5.5851|
|  2:  4.6905 -  3.7412 0.99   1386  153 0.0892 0.1114      5.4732      5.6392|
|  3:  3.7412 -  3.2736 0.99   1346  147 0.1155 0.1628      5.5303      5.8649|
|  4:  3.2736 -  2.9767 0.99   1356  154 0.1376 0.1773      5.5224      5.6493|
|  5:  2.9767 -  2.7647 0.99   1341  145 0.1424 0.1951      5.3876      5.6449|
|  6:  2.7647 -  2.6026 0.99   1344  152 0.1358 0.2029      5.2669      5.5161|
|  7:  2.6026 -  2.4728 0.99   1326  137 0.1363 0.1716      5.2233      5.3745|
|  8:  2.4728 -  2.3656 0.98   1310  158 0.1289 0.1752      5.1251      5.3527|
|  9:  2.3656 -  2.2748 0.98   1316  144 0.1292 0.1946      5.1051      5.3782|
| 10:  2.2748 -  2.1966 1.00   1315  158 0.1201 0.1755      5.0006      5.2318|
| 11:  2.1966 -  2.1281 0.98   1313  129 0.1216 0.2011      5.0048      5.4168|
| 12:  2.1281 -  2.0674 0.98   1301  156 0.1240 0.1898       4.936      5.1663|
| 13:  2.0674 -  2.0131 0.91   1199  125 0.1230 0.1742      4.8479      5.0539|
| 14:  2.0131 -  1.9641 0.26    346   40 0.1029 0.1532      4.6963       4.949|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.6905  1431   161  0.94   9.15   0.97     0.94       7051.37|
|  2:  4.6905 -  3.7412  1386   153  0.95   8.20   1.01     1.01       9389.93|
|  3:  3.7412 -  3.2736  1346   147  0.93  11.98   1.03     1.03      11203.30|
|  4:  3.2736 -  2.9767  1356   154  0.90  15.86   1.01     0.98      11726.23|
|  5:  2.9767 -  2.7647  1341   145  0.90  16.58   1.00     0.99       9175.38|
|  6:  2.7647 -  2.6026  1344   152  0.89  17.27   0.98     0.96       7706.42|
|  7:  2.6026 -  2.4728  1326   137  0.90  16.46   1.00     0.98       6923.08|
|  8:  2.4728 -  2.3656  1310   158  0.90  16.60   0.98     0.95       5876.33|
|  9:  2.3656 -  2.2748  1316   144  0.89  17.00   1.00     0.95       5684.65|
| 10:  2.2748 -  2.1966  1315   158  0.89  16.92   1.00     0.97       4925.09|
| 11:  2.1966 -  2.1281  1313   129  0.89  17.11   0.99     0.93       4846.67|
| 12:  2.1281 -  2.0674  1301   156  0.89  17.50   1.00     1.00       4569.27|
| 13:  2.0674 -  2.0131  1199   125  0.89  18.08   0.99     0.97       3859.66|
| 14:  2.0131 -  1.9641   346    40  0.91  15.49   0.97     0.95       2942.10|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2942.10 max =        11726.23 mean =      7120.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.40 mean =        14.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.05   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    97.05   17.44    None  None   None       |
|    Sol.    : 438    0      5.76    96.41   42.42    None  None   None       |
|    Mac.    : 2385   0      0.00    97.05   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.708:  992   |   5:    48.527 -  58.231:   96        |
|      1:     9.708 -  19.412: 1161   |   6:    58.231 -  67.936:   61        |
|      2:    19.412 -  29.117:  242   |   7:    67.936 -  77.641:   29        |
|      3:    29.117 -  38.822:  119   |   8:    77.641 -  87.345:   10        |
|      4:    38.822 -  48.527:  109   |   9:    87.345 -  97.050:    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)= 347         
Filter by distance & map next to the model:
   mapped sites are within: 0.579 - 4.651
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 347
   mapped sites are within: 0.745 - 4.651

peak=    6.365 closest distance to " NE2 GLN A  11 " =    1.317
peak=    5.431 closest distance to " O   HOH Z   7 " =    1.696
peak=    5.277 closest distance to " CB  GLN A 223 " =    1.464
peak=    5.222 closest distance to " O   HOH Z 417 " =    1.867
peak=    5.113 closest distance to " CG  PRO A  54 " =    1.441
peak=    5.094 closest distance to " O   HOH Z 144 " =    1.857
peak=    5.093 closest distance to " O   HOH Z  63 " =    1.603
peak=    5.038 closest distance to " O   HOH Z 126 " =    2.091
peak=    4.966 closest distance to " O   HOH Z 222 " =    1.228
peak=    4.915 closest distance to " O   HOH Z 232 " =    2.203
peak=    4.900 closest distance to " CG  PRO A 198 " =    1.294
peak=    4.738 closest distance to " O   HOH Z 427 " =    2.325
peak=    4.703 closest distance to " O   HOH Z 111 " =    1.820
peak=    4.682 closest distance to " O   HOH Z 425 " =    1.546
peak=    4.666 closest distance to " CB  ASN A 148 " =    1.357
peak=    4.632 closest distance to " CG  PRO A  90 " =    1.208
peak=    4.628 closest distance to " O   HOH Z 287 " =    2.196
peak=    4.603 closest distance to " O   HOH Z 369 " =    2.108
peak=    4.597 closest distance to " O   HOH Z 423 " =    2.012
peak=    4.587 closest distance to " O   HOH Z 183 " =    1.585
peak=    4.579 closest distance to " CB  SER A  63 " =    1.386
peak=    4.563 closest distance to " CB  PRO A  54 " =    1.059
peak=    4.508 closest distance to " O   HOH Z 403 " =    1.356
peak=    4.469 closest distance to " O   HOH Z 133 " =    2.410
peak=    4.453 closest distance to " O   HOH Z 298 " =    2.126
peak=    4.426 closest distance to " O   HOH Z 316 " =    3.071
peak=    4.359 closest distance to " CB  SER A   3 " =    1.506
peak=    4.306 closest distance to " CG  PRO A 213 " =    1.338
peak=    4.277 closest distance to " CD  ARG A 159 " =    0.834
peak=    4.274 closest distance to " O   HOH Z 380 " =    1.718
peak=    4.260 closest distance to " O   HOH Z  78 " =    1.633
peak=    4.244 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.232 closest distance to " O   HOH Z 427 " =    1.158
peak=    4.226 closest distance to " O   HOH Z   9 " =    1.462
peak=    4.226 closest distance to " CB  SER A 216 " =    0.946
peak=    4.222 closest distance to " CG  LEU A 167 " =    1.249
peak=    4.217 closest distance to " CB  ARG A 275 " =    0.973
peak=    4.194 closest distance to " CB  ASP A 124 " =    0.867
peak=    4.191 closest distance to " O   HOH Z 419 " =    2.167
peak=    4.187 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.170 closest distance to " O   HOH Z 437 " =    1.905
peak=    4.146 closest distance to " O   HOH Z 139 " =    1.180
peak=    4.135 closest distance to " CB  TRP A 266 " =    1.032
peak=    4.107 closest distance to " CB  ASN A 187 " =    1.034
peak=    4.101 closest distance to " CB  ARG A 190 " =    1.766
peak=    4.098 closest distance to " O   PRO A 198 " =    1.298
peak=    4.097 closest distance to " O   HOH Z   1 " =    1.918
peak=    4.083 closest distance to " CB  GLU A 128 " =    1.020
peak=    4.069 closest distance to " O   HOH Z  49 " =    1.340
peak=    4.044 closest distance to " O   HOH Z  61 " =    1.641
peak=    4.029 closest distance to " O   HOH Z 209 " =    2.177
peak=    4.022 closest distance to " CA  TYR A  30 " =    1.136
peak=    4.019 closest distance to " O   HOH Z 167 " =    1.825
peak=    4.017 closest distance to " O   ASN A 209 " =    1.498
peak=    4.014 closest distance to " CZ  PHE A 218 " =    1.075
peak=    3.986 closest distance to " CG2 THR A 221 " =    1.042
peak=    3.942 closest distance to " ND2 ASN A 187 " =    1.538
peak=    3.931 closest distance to " O   HOH Z 394 " =    1.744
peak=    3.927 closest distance to " CA  ILE A 234 " =    1.058
peak=    3.920 closest distance to " O   HOH Z 193 " =    1.709
peak=    3.876 closest distance to " NH1AARG A 145 " =    1.177
peak=    3.872 closest distance to " O   HOH Z  30 " =    1.738
peak=    3.863 closest distance to " O   HOH Z  78 " =    2.002
peak=    3.853 closest distance to " CG2 VAL A 257 " =    1.015
peak=    3.832 closest distance to " NE AARG A 275 " =    1.545
peak=    3.831 closest distance to " O   HOH Z  88 " =    3.965
peak=    3.825 closest distance to " CD1 LEU A 300 " =    1.242
peak=    3.819 closest distance to " CG  PRO A 243 " =    1.101
peak=    3.817 closest distance to " O   HOH Z 225 " =    1.506
peak=    3.813 closest distance to " CG1 ILE A 151 " =    1.130
peak=    3.801 closest distance to " O   HOH Z 195 " =    1.420
peak=    3.800 closest distance to " CD BLYS A 290 " =    1.036
peak=    3.798 closest distance to " O   HOH Z 258 " =    2.178
peak=    3.797 closest distance to " O   HOH Z 214 " =    2.043
peak=    3.788 closest distance to " N   ALA A   1 " =    2.162
peak=    3.774 closest distance to " CZ  PHE A 192 " =    0.952
peak=    3.768 closest distance to " CB  VAL A 265 " =    1.338
peak=    3.754 closest distance to " O   HOH Z   2 " =    1.912
peak=    3.754 closest distance to " CB  VAL A 202 " =    1.693
peak=    3.747 closest distance to " O   HOH Z  65 " =    0.941
peak=    3.737 closest distance to " CB  ASN A  39 " =    0.970
peak=    3.737 closest distance to " O   HOH Z  58 " =    2.004
peak=    3.736 closest distance to " O   HOH Z 365 " =    2.657
peak=    3.736 closest distance to " O   HOH Z 389 " =    1.946
peak=    3.733 closest distance to " CB  ASN A 142 " =    0.938
peak=    3.732 closest distance to " O   TYR A 116 " =    1.295
peak=    3.726 closest distance to " O   HOH Z 132 " =    2.448
peak=    3.723 closest distance to " O   HOH Z 126 " =    1.462
peak=    3.722 closest distance to " CD  ARG A  66 " =    2.110
peak=    3.714 closest distance to " O   HOH Z 392 " =    1.247
peak=    3.709 closest distance to " O   HOH Z 234 " =    3.901
peak=    3.706 closest distance to " CB  LEU A 228 " =    1.075
peak=    3.690 closest distance to " O   HOH Z 245 " =    1.029
peak=    3.686 closest distance to " CG  TRP A 179 " =    2.236
peak=    3.686 closest distance to " O   HOH Z  10 " =    1.855
peak=    3.685 closest distance to " O   HOH Z   9 " =    2.041
peak=    3.680 closest distance to " O   HOH Z 128 " =    2.254
peak=    3.669 closest distance to " CE3 TRP A 274 " =    1.306
peak=    3.665 closest distance to " O   HOH Z  59 " =    1.574
peak=    3.664 closest distance to " O   HOH Z 302 " =    1.667
peak=    3.663 closest distance to " O   HOH Z  20 " =    1.945
peak=    3.659 closest distance to " CB  ARG A  79 " =    1.283
peak=    3.656 closest distance to " CB  SER A 210 " =    0.829
peak=    3.651 closest distance to " O   HOH Z 422 " =    2.772
peak=    3.648 closest distance to " O   HOH Z   1 " =    1.701
peak=    3.647 closest distance to " O   HOH Z 217 " =    2.767
peak=    3.644 closest distance to " O   HOH Z  40 " =    2.164
peak=    3.642 closest distance to " CA  ARG A 102 " =    1.211
peak=    3.640 closest distance to " CA  THR A 264 " =    0.835
peak=    3.639 closest distance to " O   HOH Z 180 " =    2.179
peak=    3.630 closest distance to " CB  SER A 212 " =    1.298
peak=    3.629 closest distance to " NE  ARG A  66 " =    3.508
peak=    3.628 closest distance to " CA  ARG A 195 " =    1.376
peak=    3.626 closest distance to " OD1BASN A 224 " =    2.295
peak=    3.623 closest distance to " CB  GLU A 152 " =    1.361
peak=    3.618 closest distance to " O   HOH Z 261 " =    1.906
peak=    3.616 closest distance to " O   HOH Z  57 " =    1.147
peak=    3.606 closest distance to " N   VAL A 296 " =    1.784
peak=    3.605 closest distance to " N   TYR A  15 " =    0.973
peak=    3.605 closest distance to " CB  GLU A 236 " =    1.266
peak=    3.603 closest distance to " O   HOH Z 411 " =    3.371
peak=    3.590 closest distance to " O   HOH Z 135 " =    1.687
peak=    3.587 closest distance to " O   HOH Z 170 " =    1.184
peak=    3.586 closest distance to " O   HOH Z 362 " =    1.965
peak=    3.575 closest distance to " N   ASN A 127 " =    1.408
peak=    3.571 closest distance to " N   PHE A 130 " =    1.213
peak=    3.569 closest distance to " CB  ALA A  43 " =    0.883
peak=    3.559 closest distance to " O   HOH Z 352 " =    1.704
peak=    3.556 closest distance to " CA  SER A  87 " =    1.045
peak=    3.555 closest distance to " CA  GLY A 267 " =    1.287
peak=    3.551 closest distance to " CE  LYS A  76 " =    0.839
peak=    3.549 closest distance to " O   HOH Z 393 " =    1.333
peak=    3.546 closest distance to " O   HOH Z 329 " =    3.878
peak=    3.541 closest distance to " CA  TYR A 116 " =    1.307
peak=    3.540 closest distance to " CA  ASN A 215 " =    1.279
peak=    3.539 closest distance to " OD1 ASN A  69 " =    2.474
peak=    3.535 closest distance to " O   HOH Z 284 " =    1.365
peak=    3.532 closest distance to " CB  SER A 276 " =    1.187
peak=    3.532 closest distance to " O   HOH Z  44 " =    2.639
peak=    3.531 closest distance to " O   ASN A  74 " =    1.465
peak=    3.531 closest distance to " O   HOH Z 145 " =    1.832
peak=    3.529 closest distance to " CB  THR A 157 " =    1.177
peak=    3.527 closest distance to " CA  LEU A 101 " =    1.524
peak=    3.518 closest distance to " N   SER A  97 " =    0.928
peak=    3.512 closest distance to " OH  TYR A 186 " =    1.063
peak=    3.509 closest distance to " CA  ALA A 160 " =    0.907
peak=    3.506 closest distance to " CA  ARG A  36 " =    1.302
peak=    3.504 closest distance to " OE1 GLN A 240 " =    1.674
peak=    3.498 closest distance to " CB  TRP A 150 " =    1.108
peak=    3.494 closest distance to " O   HOH Z 116 " =    2.995
peak=    3.493 closest distance to " CA  ALA A  51 " =    1.026
peak=    3.492 closest distance to " O   SER A  87 " =    2.329
peak=    3.490 closest distance to " CG  GLU A   2 " =    1.190
peak=    3.477 closest distance to " O   HOH Z  85 " =    2.041
peak=    3.476 closest distance to " O   HOH Z 368 " =    3.746
peak=    3.470 closest distance to " CB  ALA A 114 " =    0.926
peak=    3.470 closest distance to " O   HOH Z  68 " =    1.912
peak=    3.469 closest distance to " O   HOH Z 184 " =    1.701
peak=    3.464 closest distance to " CB  TYR A 116 " =    0.916
peak=    3.463 closest distance to " O   HOH Z 175 " =    2.164
peak=    3.461 closest distance to " N   GLN A 278 " =    1.117
peak=    3.461 closest distance to " O   HOH Z  59 " =    2.110
peak=    3.457 closest distance to " CB  LEU A 143 " =    1.205
peak=    3.455 closest distance to " CA  MET A 105 " =    0.914
peak=    3.455 closest distance to " CZ  PHE A  38 " =    1.308
peak=    3.454 closest distance to " O   HOH Z 285 " =    2.573
peak=    3.453 closest distance to " CD1 ILE A  33 " =    1.690
peak=    3.451 closest distance to " O   HOH Z 371 " =    2.644
peak=    3.448 closest distance to " CA  ASN A 127 " =    1.115
peak=    3.447 closest distance to " O   HOH Z 158 " =    2.602
peak=    3.442 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.440 closest distance to " O   HOH Z 250 " =    1.374
peak=    3.440 closest distance to " O   HOH Z  21 " =    1.739
peak=    3.439 closest distance to " O   HOH Z 122 " =    1.761
peak=    3.438 closest distance to " OD2 ASP A 286 " =    2.850
peak=    3.430 closest distance to " O   HOH Z 145 " =    3.847
peak=    3.430 closest distance to " O   HOH Z   7 " =    3.613
peak=    3.430 closest distance to " O   HOH Z  51 " =    1.874
peak=    3.425 closest distance to " CB  GLU A 277 " =    3.646
peak=    3.422 closest distance to " CG1 VAL A 153 " =    0.921
peak=    3.422 closest distance to " O   HOH Z 368 " =    1.919
peak=    3.420 closest distance to " NH1 ARG A  14 " =    0.930
peak=    3.417 closest distance to " O   GLN A  55 " =    1.826
peak=    3.415 closest distance to " CB  PRO A 243 " =    1.182
peak=    3.413 closest distance to " NE2 GLN A  58 " =    3.883
peak=    3.409 closest distance to " O   HOH Z 410 " =    1.622
peak=    3.409 closest distance to " OE2 GLU A  53 " =    1.991
peak=    3.409 closest distance to " N   GLU A   2 " =    1.418
peak=    3.408 closest distance to " O   HOH Z 115 " =    1.825
peak=    3.406 closest distance to " CG  ARG A 159 " =    0.836
peak=    3.403 closest distance to " ND1 HIS A  81 " =    1.582
peak=    3.402 closest distance to " N   SER A 271 " =    0.965
peak=    3.401 closest distance to " O   HOH Z  61 " =    1.577
peak=    3.398 closest distance to " OG BSER A 134 " =    2.997
peak=    3.397 closest distance to " O   HOH Z 414 " =    1.330
peak=    3.397 closest distance to " NZ ALYS A 290 " =    0.952
peak=    3.397 closest distance to " O   HOH Z 288 " =    1.942
peak=    3.397 closest distance to " CA  SER A  95 " =    0.977
peak=    3.396 closest distance to " OG BSER A  99 " =    2.333
peak=    3.394 closest distance to " O   HOH Z 124 " =    1.889
peak=    3.390 closest distance to " CB  ALA A   1 " =    4.651
peak=    3.387 closest distance to " CA  ALA A 154 " =    0.986
peak=    3.383 closest distance to " OG  SER A  26 " =    1.657
peak=    3.374 closest distance to " CB  ALA A  10 " =    0.888
peak=    3.368 closest distance to " O   HOH Z 409 " =    2.138
peak=    3.367 closest distance to " ND2 ASN A  60 " =    3.023
peak=    3.366 closest distance to " CD  PRO A 243 " =    1.770
peak=    3.360 closest distance to " O   HOH Z 144 " =    2.189
peak=    3.358 closest distance to " O   HOH Z 313 " =    1.707
peak=    3.357 closest distance to " CB  ARG A  79 " =    1.101
peak=    3.355 closest distance to " O   HOH Z 175 " =    3.733
peak=    3.355 closest distance to " O   HOH Z 171 " =    2.863
peak=    3.350 closest distance to " O   HOH Z 425 " =    2.054
peak=    3.339 closest distance to " CD  LYS A 166 " =    1.385
peak=    3.335 closest distance to " N   ARG A 156 " =    1.334
peak=    3.330 closest distance to " O   HOH Z 188 " =    2.397
peak=    3.328 closest distance to " CG  LYS A  76 " =    1.660
peak=    3.321 closest distance to " O   ALA A 233 " =    1.790
peak=    3.320 closest distance to " O   HOH Z 434 " =    1.453
peak=    3.320 closest distance to " O   HOH Z 310 " =    2.437
peak=    3.318 closest distance to " O   HOH Z 405 " =    1.577
peak=    3.317 closest distance to " OG BSER A 212 " =    2.719
peak=    3.308 closest distance to " ND2BASN A 224 " =    0.745
peak=    3.306 closest distance to " OG  SER A  62 " =    2.872
peak=    3.305 closest distance to " O   HOH Z 327 " =    2.021
peak=    3.304 closest distance to " O   HOH Z 181 " =    2.276
peak=    3.303 closest distance to " CA  TYR A 186 " =    1.547
peak=    3.302 closest distance to " O   HOH Z 172 " =    2.543
peak=    3.299 closest distance to " O   HOH Z 344 " =    3.427
peak=    3.299 closest distance to " O   HOH Z 153 " =    3.697
peak=    3.297 closest distance to " CD  ARG A  66 " =    2.359
peak=    3.297 closest distance to " O   THR A 220 " =    1.509
peak=    3.293 closest distance to " O   HOH Z 222 " =    2.265
peak=    3.290 closest distance to " CB  GLU A  46 " =    1.016
peak=    3.290 closest distance to " O   HOH Z 265 " =    1.978
peak=    3.286 closest distance to " O   HOH Z 108 " =    2.214
peak=    3.284 closest distance to " CE3 TRP A  85 " =    0.889
peak=    3.283 closest distance to " O   HOH Z 217 " =    1.684
peak=    3.282 closest distance to " CB  LYS A 117 " =    1.241
peak=    3.282 closest distance to " CB  TRP A 179 " =    1.576
peak=    3.282 closest distance to " CA  GLU A 152 " =    1.140
peak=    3.279 closest distance to " O   HOH Z 130 " =    1.042
peak=    3.278 closest distance to " O   HOH Z  39 " =    0.974
peak=    3.278 closest distance to " O   HOH Z 378 " =    0.994
peak=    3.277 closest distance to " O   HOH Z  44 " =    1.970
peak=    3.276 closest distance to " CA  ALA A 158 " =    1.129
peak=    3.276 closest distance to " CG  GLN A 278 " =    1.217
peak=    3.274 closest distance to " CB  MET A  47 " =    1.019
peak=    3.274 closest distance to " O   HOH Z 148 " =    3.439
peak=    3.273 closest distance to " OG  SER A  22 " =    2.927
peak=    3.272 closest distance to " O   HOH Z 359 " =    1.326
peak=    3.271 closest distance to " CD  ARG A 269 " =    0.985
peak=    3.270 closest distance to " CG BARG A 275 " =    1.504
peak=    3.270 closest distance to " O   HOH Z 207 " =    2.265
peak=    3.270 closest distance to " CG  GLN A 278 " =    3.720
peak=    3.269 closest distance to " NH1BARG A 145 " =    1.256
peak=    3.265 closest distance to " CB  TYR A  30 " =    1.403
peak=    3.265 closest distance to " O   HOH Z 298 " =    4.321
peak=    3.258 closest distance to " NZ  LYS A 117 " =    1.315
peak=    3.257 closest distance to " O   HOH Z 245 " =    0.921
peak=    3.253 closest distance to " CB  GLN A  88 " =    1.340
peak=    3.251 closest distance to " CB  PRO A  90 " =    1.016
peak=    3.245 closest distance to " CA  ASP A 124 " =    0.791
peak=    3.244 closest distance to " O   THR A 251 " =    1.275
peak=    3.241 closest distance to " ND2 ASN A 249 " =    0.768
peak=    3.241 closest distance to " CA  ALA A 180 " =    1.258
peak=    3.234 closest distance to " O   HOH Z 282 " =    2.184
peak=    3.226 closest distance to " NE1 TRP A 274 " =    0.962
peak=    3.226 closest distance to " CD2 TRP A 179 " =    1.236
peak=    3.224 closest distance to " O   THR A 294 " =    0.999
peak=    3.221 closest distance to " CH2 TRP A 150 " =    1.029
peak=    3.219 closest distance to " CB  PHE A 204 " =    0.761
peak=    3.219 closest distance to " O   HOH Z  80 " =    1.572
peak=    3.218 closest distance to " O   HOH Z 213 " =    1.959
peak=    3.217 closest distance to " O   HOH Z 153 " =    1.545
peak=    3.216 closest distance to " O   HOH Z   3 " =    2.422
peak=    3.204 closest distance to " CA  ALA A 299 " =    0.872
peak=    3.201 closest distance to " CB  ALA A 184 " =    1.019
peak=    3.201 closest distance to " NZ  LYS A 119 " =    1.348
peak=    3.200 closest distance to " O   HOH Z 158 " =    1.546
peak=    3.198 closest distance to " CB  ALA A 114 " =    1.410
peak=    3.198 closest distance to " CB  ARG A 139 " =    1.063
peak=    3.195 closest distance to " CD2 PHE A  59 " =    1.829
peak=    3.187 closest distance to " O   MET A 105 " =    1.854
peak=    3.185 closest distance to " O   HOH Z 438 " =    2.072
peak=    3.184 closest distance to " CA  ASP A  50 " =    1.239
peak=    3.183 closest distance to " O   HOH Z 193 " =    2.070
peak=    3.183 closest distance to " CA  GLU A  46 " =    0.904
peak=    3.182 closest distance to " CD2 LEU A 255 " =    1.787
peak=    3.181 closest distance to " O   HOH Z  88 " =    2.991
peak=    3.181 closest distance to " OD1 ASN A 217 " =    1.401
peak=    3.179 closest distance to " CA  ALA A 291 " =    0.897
peak=    3.177 closest distance to " C   PRO A 198 " =    1.519
peak=    3.175 closest distance to " CA  ARG A 156 " =    1.013
peak=    3.174 closest distance to " CG  GLU A 277 " =    1.963
peak=    3.174 closest distance to " CG1BVAL A  72 " =    1.225
peak=    3.171 closest distance to " CG  MET A 113 " =    1.228
peak=    3.169 closest distance to " CA  ALA A 100 " =    1.103
peak=    3.167 closest distance to " O   HOH Z 392 " =    2.026
peak=    3.166 closest distance to " O   HOH Z 128 " =    1.911
peak=    3.165 closest distance to " O   HOH Z   3 " =    2.152
peak=    3.161 closest distance to " O   HOH Z 189 " =    2.519
peak=    3.161 closest distance to " O   HOH Z 417 " =    1.707
peak=    3.158 closest distance to " CA  GLY A 241 " =    0.773
peak=    3.158 closest distance to " CB  MET A  40 " =    0.806
peak=    3.155 closest distance to " O   HOH Z 154 " =    2.059
peak=    3.143 closest distance to " CB  LEU A  83 " =    0.868
peak=    3.135 closest distance to " CB  TRP A 274 " =    1.319
peak=    3.125 closest distance to " O   HOH Z 373 " =    1.573
peak=    3.125 closest distance to " CA  ASN A 217 " =    1.193
peak=    3.124 closest distance to " CB  LEU A 300 " =    0.919
peak=    3.124 closest distance to " O   HOH Z 345 " =    3.448
peak=    3.123 closest distance to " O   HOH Z  50 " =    1.552
peak=    3.123 closest distance to " O   HOH Z 219 " =    2.082
peak=    3.122 closest distance to " O   HOH Z 273 " =    2.836
peak=    3.122 closest distance to " CB  ARG A 138 " =    0.941
peak=    3.112 closest distance to " O   HOH Z 272 " =    2.241
peak=    3.112 closest distance to " CB  ASP A 171 " =    0.808
peak=    3.109 closest distance to " SD  MET A  93 " =    1.161
peak=    3.103 closest distance to " CG BARG A 102 " =    1.836
peak=    3.103 closest distance to " CB  GLU A 152 " =    0.930
peak=    3.101 closest distance to " CB  ALA A  34 " =    1.222
peak=    3.097 closest distance to " CB  HIS A 108 " =    0.749
peak=    3.096 closest distance to " CB  ASN A 215 " =    1.179
peak=    3.092 closest distance to " C   GLU A 277 " =    1.380
peak=    3.089 closest distance to " NH1 ARG A  56 " =    1.151
peak=    3.088 closest distance to " O   HOH Z 286 " =    2.261
peak=    3.084 closest distance to " O   HOH Z 421 " =    2.753
peak=    3.078 closest distance to " O   HOH Z 113 " =    1.868
peak=    3.078 closest distance to " OG BSER A 258 " =    0.923
peak=    3.076 closest distance to " O   HOH Z  17 " =    1.767
peak=    3.068 closest distance to " CB  ILE A 120 " =    1.382
peak=    3.056 closest distance to " O   HOH Z 386 " =    2.650
peak=    3.054 closest distance to " O   HOH Z 280 " =    3.055
peak=    3.048 closest distance to " O   HOH Z 110 " =    1.646
peak=    3.046 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.031 closest distance to " CA  TYR A  30 " =    1.083
peak=    3.031 closest distance to " CA  ILE A 106 " =    0.788
peak=    3.021 closest distance to " CB  ASN A 285 " =    0.837
peak=    3.008 closest distance to " O   HOH Z  88 " =    3.649

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.580 - 5.681
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 203
   mapped sites are within: 0.774 - 5.681

peak=   -4.909 closest distance to " O   PRO A 198 " =    1.194
peak=   -4.608 closest distance to " CD  ARG A  14 " =    3.403
peak=   -4.359 closest distance to " CB  PRO A 243 " =    2.503
peak=   -4.313 closest distance to " O   HOH Z 290 " =    1.139
peak=   -4.271 closest distance to " O   HOH Z  65 " =    1.177
peak=   -4.230 closest distance to " CZ3 TRP A 179 " =    1.168
peak=   -4.055 closest distance to " OE1 GLN A  88 " =    1.065
peak=   -4.044 closest distance to " CB  ALA A 291 " =    2.218
peak=   -4.031 closest distance to " CA  GLY A  98 " =    1.807
peak=   -4.012 closest distance to " CG  MET A 105 " =    0.914
peak=   -3.994 closest distance to " C   ALA A 158 " =    1.632
peak=   -3.987 closest distance to " O   HOH Z 313 " =    1.561
peak=   -3.987 closest distance to " O   HOH Z 377 " =    1.747
peak=   -3.984 closest distance to " O   HOH Z 389 " =    2.083
peak=   -3.976 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.964 closest distance to " N   THR A 157 " =    1.534
peak=   -3.950 closest distance to " CA  GLY A 203 " =    2.267
peak=   -3.920 closest distance to " O   HOH Z 185 " =    2.115
peak=   -3.920 closest distance to " CB  ASP A  27 " =    2.453
peak=   -3.910 closest distance to " OG BSER A 134 " =    1.394
peak=   -3.905 closest distance to " O   HOH Z 407 " =    3.327
peak=   -3.896 closest distance to " CG  GLN A  88 " =    0.862
peak=   -3.892 closest distance to " O   HOH Z  60 " =    1.802
peak=   -3.891 closest distance to " CD  ARG A 156 " =    2.090
peak=   -3.889 closest distance to " O   HOH Z  39 " =    1.056
peak=   -3.861 closest distance to " O   HOH Z 102 " =    1.568
peak=   -3.858 closest distance to " O   SER A  22 " =    2.807
peak=   -3.817 closest distance to " OD1 ASP A 191 " =    1.933
peak=   -3.802 closest distance to " CA  GLY A 241 " =    2.236
peak=   -3.795 closest distance to " O   ILE A  49 " =    1.618
peak=   -3.790 closest distance to " N   ALA A  43 " =    2.427
peak=   -3.788 closest distance to " O   HOH Z 282 " =    4.471
peak=   -3.784 closest distance to " O   HOH Z 166 " =    1.261
peak=   -3.763 closest distance to " CG1 VAL A  78 " =    2.427
peak=   -3.752 closest distance to " O   HOH Z 298 " =    1.015
peak=   -3.747 closest distance to " O   HOH Z  22 " =    2.394
peak=   -3.744 closest distance to " CB  ALA A  43 " =    2.449
peak=   -3.744 closest distance to " O   HOH Z 231 " =    1.848
peak=   -3.733 closest distance to " O   HOH Z 211 " =    1.341
peak=   -3.732 closest distance to " CD2 TYR A 293 " =    1.843
peak=   -3.714 closest distance to " O   HOH Z 111 " =    1.851
peak=   -3.712 closest distance to " O   SER A 135 " =    1.432
peak=   -3.706 closest distance to " O   ALA A  10 " =    1.678
peak=   -3.694 closest distance to " O   HOH Z  28 " =    1.467
peak=   -3.664 closest distance to " C   LEU A 143 " =    1.281
peak=   -3.660 closest distance to " O   TYR A 247 " =    2.886
peak=   -3.653 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.652 closest distance to " O   HOH Z  49 " =    1.354
peak=   -3.651 closest distance to " O   HOH Z 372 " =    2.476
peak=   -3.644 closest distance to " O   HOH Z  52 " =    1.218
peak=   -3.639 closest distance to " CG2 THR A 178 " =    2.228
peak=   -3.638 closest distance to " O   PRO A 243 " =    2.265
peak=   -3.616 closest distance to " CB  ALA A   9 " =    2.410
peak=   -3.603 closest distance to " CB  TRP A  85 " =    2.452
peak=   -3.584 closest distance to " O   HOH Z 384 " =    3.074
peak=   -3.583 closest distance to " O   HOH Z 118 " =    1.273
peak=   -3.575 closest distance to " O   PRO A 163 " =    1.869
peak=   -3.567 closest distance to " O   HOH Z 193 " =    2.024
peak=   -3.547 closest distance to " O   HOH Z 281 " =    2.899
peak=   -3.538 closest distance to " O   HOH Z  38 " =    1.308
peak=   -3.532 closest distance to " O   ALA A 180 " =    1.235
peak=   -3.526 closest distance to " CE2 TYR A  30 " =    2.604
peak=   -3.514 closest distance to " N   ASP A 171 " =    2.436
peak=   -3.513 closest distance to " O   ASP A 162 " =    2.287
peak=   -3.509 closest distance to " O   HOH Z 266 " =    4.960
peak=   -3.505 closest distance to " O   HOH Z  11 " =    1.791
peak=   -3.503 closest distance to " CB  ALA A 248 " =    2.010
peak=   -3.502 closest distance to " O   HOH Z  24 " =    1.185
peak=   -3.496 closest distance to " O   HOH Z 166 " =    1.651
peak=   -3.478 closest distance to " CB  ALA A 114 " =    2.540
peak=   -3.476 closest distance to " OG  SER A 245 " =    1.291
peak=   -3.475 closest distance to " O   HOH Z  51 " =    0.975
peak=   -3.470 closest distance to " CD1 LEU A 255 " =    3.059
peak=   -3.469 closest distance to " O   HOH Z  76 " =    1.224
peak=   -3.466 closest distance to " CZ2 TRP A 274 " =    0.938
peak=   -3.461 closest distance to " ND2 ASN A 209 " =    1.960
peak=   -3.447 closest distance to " O   HOH Z 385 " =    1.912
peak=   -3.440 closest distance to " NH2AARG A 275 " =    5.681
peak=   -3.440 closest distance to " CG1BVAL A  41 " =    2.903
peak=   -3.437 closest distance to " O   ALA A   1 " =    1.143
peak=   -3.422 closest distance to " O   PHE A 218 " =    1.328
peak=   -3.421 closest distance to " CB  PHE A 283 " =    2.793
peak=   -3.419 closest distance to " O   HOH Z 298 " =    2.560
peak=   -3.416 closest distance to " O   HOH Z  90 " =    2.919
peak=   -3.411 closest distance to " CG2 VAL A 232 " =    2.086
peak=   -3.409 closest distance to " OG  SER A  87 " =    1.333
peak=   -3.409 closest distance to " CZ BARG A 275 " =    1.582
peak=   -3.405 closest distance to " O   HOH Z 134 " =    1.445
peak=   -3.404 closest distance to " C   GLU A 236 " =    0.851
peak=   -3.404 closest distance to " CD2 LEU A 143 " =    2.581
peak=   -3.402 closest distance to " O   GLY A  80 " =    2.334
peak=   -3.395 closest distance to " CG  GLN A 223 " =    2.183
peak=   -3.394 closest distance to " O   HOH Z 147 " =    1.398
peak=   -3.391 closest distance to " OE1 GLN A  58 " =    3.096
peak=   -3.372 closest distance to " N   ASP A 270 " =    1.309
peak=   -3.372 closest distance to " CB  PRO A  90 " =    1.398
peak=   -3.369 closest distance to " CE1 TYR A 169 " =    2.598
peak=   -3.359 closest distance to " CE BMET A  47 " =    1.336
peak=   -3.359 closest distance to " NH2 ARG A  79 " =    1.869
peak=   -3.358 closest distance to " O   VAL A  67 " =    2.435
peak=   -3.354 closest distance to " O   HOH Z  73 " =    2.088
peak=   -3.347 closest distance to " O   HOH Z 286 " =    1.686
peak=   -3.336 closest distance to " O   HOH Z 201 " =    1.837
peak=   -3.331 closest distance to " O   GLN A 240 " =    1.996
peak=   -3.329 closest distance to " CD  LYS A 289 " =    2.364
peak=   -3.327 closest distance to " O   HOH Z   1 " =    1.314
peak=   -3.322 closest distance to " CB  PHE A 192 " =    1.737
peak=   -3.321 closest distance to " OXT GLY A 302 " =    3.279
peak=   -3.309 closest distance to " C   ASN A 285 " =    2.431
peak=   -3.309 closest distance to " OG BSER A 134 " =    1.853
peak=   -3.308 closest distance to " ND2 ASN A 285 " =    2.112
peak=   -3.305 closest distance to " O   HOH Z 168 " =    1.895
peak=   -3.301 closest distance to " CB  PRO A  54 " =    2.469
peak=   -3.300 closest distance to " CB  ASN A  39 " =    2.257
peak=   -3.300 closest distance to " ND2 ASN A  60 " =    4.018
peak=   -3.296 closest distance to " CG  LEU A 282 " =    2.492
peak=   -3.294 closest distance to " OD2 ASP A  27 " =    1.794
peak=   -3.290 closest distance to " O   HOH Z 253 " =    4.236
peak=   -3.288 closest distance to " CE1 PHE A 225 " =    2.192
peak=   -3.285 closest distance to " CA  GLY A 133 " =    1.959
peak=   -3.283 closest distance to " O   HOH Z 318 " =    1.820
peak=   -3.282 closest distance to " ND2 ASN A 187 " =    1.429
peak=   -3.281 closest distance to " CD2 TYR A 293 " =    2.131
peak=   -3.271 closest distance to " O   GLY A 211 " =    1.228
peak=   -3.270 closest distance to " O   HOH Z 198 " =    1.980
peak=   -3.268 closest distance to " CG1 VAL A 197 " =    2.316
peak=   -3.267 closest distance to " O   HOH Z  43 " =    1.576
peak=   -3.264 closest distance to " CB  TYR A  15 " =    2.162
peak=   -3.263 closest distance to " CB  PHE A 130 " =    1.229
peak=   -3.262 closest distance to " ND2 ASN A 215 " =    2.302
peak=   -3.262 closest distance to " CG2BVAL A  41 " =    1.132
peak=   -3.257 closest distance to " CB  CYS A 254 " =    2.013
peak=   -3.251 closest distance to " CG  ASN A  39 " =    1.741
peak=   -3.244 closest distance to " CG  LEU A  83 " =    2.056
peak=   -3.241 closest distance to " CD  GLN A  58 " =    0.875
peak=   -3.240 closest distance to " O   HOH Z 131 " =    4.044
peak=   -3.237 closest distance to " O   HOH Z 414 " =    1.704
peak=   -3.236 closest distance to " O   HOH Z 317 " =    1.481
peak=   -3.228 closest distance to " O   SER A  62 " =    2.334
peak=   -3.227 closest distance to " O   HOH Z   6 " =    1.437
peak=   -3.226 closest distance to " N   HIS A  81 " =    1.274
peak=   -3.220 closest distance to " N   VAL A 232 " =    2.378
peak=   -3.217 closest distance to " O   HOH Z  32 " =    2.061
peak=   -3.217 closest distance to " CG  ARG A  66 " =    1.739
peak=   -3.215 closest distance to " NH2 ARG A 219 " =    1.820
peak=   -3.214 closest distance to " O   VAL A 189 " =    2.366
peak=   -3.210 closest distance to " O   HOH Z 432 " =    3.679
peak=   -3.208 closest distance to " O   MET A  47 " =    2.720
peak=   -3.205 closest distance to " CG  PRO A 163 " =    2.398
peak=   -3.203 closest distance to " CG  TRP A 266 " =    1.618
peak=   -3.196 closest distance to " O   VAL A 125 " =    2.178
peak=   -3.194 closest distance to " CG  LEU A 167 " =    0.872
peak=   -3.192 closest distance to " CB  ASP A 132 " =    2.340
peak=   -3.187 closest distance to " CG  ARG A 269 " =    2.461
peak=   -3.186 closest distance to " O   HOH Z 275 " =    1.629
peak=   -3.185 closest distance to " O   HOH Z 191 " =    5.503
peak=   -3.182 closest distance to " O   GLY A  17 " =    1.222
peak=   -3.179 closest distance to " O   HOH Z 126 " =    1.924
peak=   -3.179 closest distance to " CE2 PHE A 218 " =    2.456
peak=   -3.178 closest distance to " O   HOH Z 218 " =    3.635
peak=   -3.171 closest distance to " O   HOH Z 198 " =    1.741
peak=   -3.169 closest distance to " ND2 ASN A  45 " =    1.112
peak=   -3.168 closest distance to " CE3 TRP A 123 " =    1.449
peak=   -3.163 closest distance to " OG  SER A 206 " =    1.901
peak=   -3.162 closest distance to " C   LEU A 222 " =    0.774
peak=   -3.158 closest distance to " CE  LYS A  76 " =    2.863
peak=   -3.157 closest distance to " O   GLU A 152 " =    1.373
peak=   -3.145 closest distance to " CG1 VAL A 125 " =    1.819
peak=   -3.142 closest distance to " O   HOH Z 427 " =    1.858
peak=   -3.141 closest distance to " O   HOH Z 377 " =    0.793
peak=   -3.137 closest distance to " CB  ALA A 131 " =    1.969
peak=   -3.134 closest distance to " CA  GLY A  57 " =    2.137
peak=   -3.133 closest distance to " O   HOH Z 251 " =    1.173
peak=   -3.131 closest distance to " OD2 ASP A 171 " =    1.667
peak=   -3.130 closest distance to " ND2BASN A 224 " =    1.547
peak=   -3.125 closest distance to " CB  ALA A 100 " =    2.349
peak=   -3.123 closest distance to " O   ASN A 127 " =    1.463
peak=   -3.119 closest distance to " CB  SER A 245 " =    2.252
peak=   -3.118 closest distance to " O   HOH Z 186 " =    1.135
peak=   -3.111 closest distance to " CG1 VAL A 250 " =    2.637
peak=   -3.111 closest distance to " CE  MET A  93 " =    1.178
peak=   -3.111 closest distance to " CG1 VAL A 112 " =    2.497
peak=   -3.110 closest distance to " O   ASP A  27 " =    1.811
peak=   -3.108 closest distance to " CG2 THR A  52 " =    3.151
peak=   -3.107 closest distance to " NE2 GLN A  58 " =    3.058
peak=   -3.104 closest distance to " NZ  LYS A 166 " =    1.170
peak=   -3.102 closest distance to " O   HOH Z 109 " =    1.840
peak=   -3.102 closest distance to " NE2 GLN A  55 " =    0.844
peak=   -3.087 closest distance to " CE3 TRP A 274 " =    2.541
peak=   -3.076 closest distance to " O   HOH Z 353 " =    2.006
peak=   -3.073 closest distance to " O   HOH Z 348 " =    2.157
peak=   -3.070 closest distance to " O   HOH Z 359 " =    1.547
peak=   -3.063 closest distance to " O   HOH Z 410 " =    2.312
peak=   -3.060 closest distance to " CA  ILE A 263 " =    0.958
peak=   -3.043 closest distance to " N   SER A 141 " =    1.892
peak=   -3.043 closest distance to " ND2 ASN A  45 " =    2.212
peak=   -3.023 closest distance to " O   PRO A 163 " =    1.535
peak=   -3.007 closest distance to " O   HOH Z   2 " =    1.594

================= 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    :  0.4450 0.4440   6.258746e+00   6.252270e+00
   1_bss:  0.4360 0.4372   6.251589e+00   6.243792e+00
   1_xyz:  0.3224 0.3629   6.044993e+00   6.105538e+00
   1_adp:  0.2932 0.3740   5.997798e+00   6.128908e+00
   1_occ:  0.2926 0.3740   5.996946e+00   6.128847e+00
   2_bss:  0.2924 0.3713   5.995100e+00   6.125823e+00
   2_xyz:  0.2244 0.2911   5.763706e+00   5.938704e+00
   2_adp:  0.2047 0.2703   5.690826e+00   5.886647e+00
   2_occ:  0.2047 0.2698   5.690140e+00   5.886140e+00
   3_bss:  0.2046 0.2692   5.688046e+00   5.883672e+00
   3_xyz:  0.1640 0.2224   5.488003e+00   5.710592e+00
   3_adp:  0.1553 0.2045   5.425946e+00   5.630450e+00
   3_occ:  0.1552 0.2040   5.424894e+00   5.628934e+00
   4_bss:  0.1549 0.2034   5.423221e+00   5.626027e+00
   4_xyz:  0.1328 0.1785   5.284578e+00   5.501784e+00
   4_adp:  0.1277 0.1762   5.258209e+00   5.485814e+00
   4_occ:  0.1276 0.1762   5.258151e+00   5.485917e+00
   5_bss:  0.1276 0.1762   5.257910e+00   5.485894e+00
   5_xyz:  0.1216 0.1690   5.218120e+00   5.452184e+00
   5_adp:  0.1206 0.1680   5.212129e+00   5.447365e+00
   5_occ:  0.1205 0.1680   5.211957e+00   5.447358e+00
   5_bss:  0.1207 0.1677   5.212020e+00   5.445945e+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:  0.337  50.001   0.697   2.204  -1.354   0.000  -0.000  -0.000
   1_xyz:  0.337  50.001   0.697   2.204  -1.354   0.000  -0.000  -0.000
   1_adp:  0.337  50.001   0.697   2.204  -1.354   0.000  -0.000  -0.000
   1_occ:  0.337  50.001   0.697   2.204  -1.354   0.000  -0.000  -0.000
   2_bss:  0.352  77.941  -0.530  -0.258  -0.671  -0.000  -0.000  -0.000
   2_xyz:  0.352  77.941  -0.530  -0.258  -0.671  -0.000  -0.000  -0.000
   2_adp:  0.352  77.941  -0.530  -0.258  -0.671  -0.000  -0.000  -0.000
   2_occ:  0.352  77.941  -0.530  -0.258  -0.671  -0.000  -0.000  -0.000
   3_bss:  0.351  80.000  -0.977  -1.149  -0.335  -0.000  -0.000  -0.000
   3_xyz:  0.351  80.000  -0.977  -1.149  -0.335  -0.000  -0.000  -0.000
   3_adp:  0.351  80.000  -0.977  -1.149  -0.335  -0.000  -0.000  -0.000
   3_occ:  0.351  80.000  -0.977  -1.149  -0.335  -0.000  -0.000  -0.000
   4_bss:  0.329  62.316  -1.744  -2.366  -0.918  -0.000  -0.000  -0.000
   4_xyz:  0.329  62.316  -1.744  -2.366  -0.918  -0.000  -0.000  -0.000
   4_adp:  0.329  62.316  -1.744  -2.366  -0.918  -0.000  -0.000  -0.000
   4_occ:  0.329  62.316  -1.744  -2.366  -0.918  -0.000  -0.000  -0.000
   5_bss:  0.324  62.316  -1.899  -2.560  -1.045  -0.000  -0.000  -0.000
   5_xyz:  0.324  62.316  -1.899  -2.560  -1.045  -0.000  -0.000  -0.000
   5_adp:  0.324  62.316  -1.899  -2.560  -1.045  -0.000  -0.000  -0.000
   5_occ:  0.324  62.316  -1.899  -2.560  -1.045  -0.000  -0.000  -0.000
   5_bss:  0.319  59.183  -1.902  -2.563  -1.048  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.063 0.4694  0.6349    64463.478
   1_bss:  53.543 0.4747  0.6586    62670.758
   1_xyz:  39.172 0.6531  0.8670    37544.812
   1_adp:  41.133 0.6284  0.8409    40144.480
   1_occ:  41.140 0.6283  0.8398    40117.240
   2_bss:  40.671 0.6338  0.8192    39359.457
   2_xyz:  30.214 0.7540  0.9432    22535.224
   2_adp:  27.716 0.7820  0.9531    19623.597
   2_occ:  27.688 0.7822  0.9530    19580.220
   3_bss:  27.570 0.7833  0.9423    19401.743
   3_xyz:  21.920 0.8416  0.9865    12648.862
   3_adp:  19.577 0.8658  0.9970    10797.520
   3_occ:  19.547 0.8660  0.9967    10754.673
   4_bss:  19.481 0.8665  0.9674    10669.216
   4_xyz:  16.471 0.8940  0.9798     8056.137
   4_adp:  16.058 0.8980  0.9779     7825.600
   4_occ:  16.060 0.8979  0.9777     7825.440
   5_bss:  16.055 0.8980  0.9723     7823.319
   5_xyz:  15.310 0.9043  0.9760     7235.132
   5_adp:  15.156 0.9058  0.9745     7152.007
   5_occ:  15.155 0.9058  0.9744     7145.792
   5_bss:  15.148 0.9057  0.9744     7120.055
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7212e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7212e-01
   1_xyz:   1.499  0.011  0.103 16.037  0.006  4.109   1.2561e-01
   1_adp:   1.499  0.011  0.103 16.037  0.006  4.109   1.2561e-01
   1_occ:   1.499  0.011  0.103 16.037  0.006  4.109   1.2561e-01
   2_bss:   1.499  0.011  0.103 16.037  0.006  4.109   1.2561e-01
   2_xyz:   1.219  0.010  0.084 14.664  0.004  4.111   8.5483e-02
   2_adp:   1.219  0.010  0.084 14.664  0.004  4.111   8.5483e-02
   2_occ:   1.219  0.010  0.084 14.664  0.004  4.111   8.5483e-02
   3_bss:   1.219  0.010  0.084 14.664  0.004  4.111   8.5483e-02
   3_xyz:   0.965  0.007  0.071 14.411  0.003  4.118   5.6717e-02
   3_adp:   0.965  0.007  0.071 14.411  0.003  4.118   5.6717e-02
   3_occ:   0.965  0.007  0.071 14.411  0.003  4.118   5.6717e-02
   4_bss:   0.965  0.007  0.071 14.411  0.003  4.118   5.6717e-02
   4_xyz:   0.943  0.006  0.071 14.293  0.003  4.113   5.3360e-02
   4_adp:   0.943  0.006  0.071 14.293  0.003  4.113   5.3360e-02
   4_occ:   0.943  0.006  0.071 14.293  0.003  4.113   5.3360e-02
   5_bss:   0.943  0.006  0.071 14.293  0.003  4.113   5.3360e-02
   5_xyz:   0.914  0.006  0.069 14.318  0.003  4.117   5.1087e-02
   5_adp:   0.914  0.006  0.069 14.318  0.003  4.117   5.1087e-02
   5_occ:   0.914  0.006  0.069 14.318  0.003  4.117   5.1087e-02
   5_bss:   0.914  0.006  0.069 14.318  0.003  4.117   5.1087e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.761   2.4156e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.761   2.4156e-01
   1_xyz:   9.790  0.064  0.393 86.540  0.035  2.107   1.0628e-01
   1_adp:   9.790  0.064  0.393 86.540  0.035  2.107   1.0628e-01
   1_occ:   9.790  0.064  0.393 86.540  0.035  2.107   1.0628e-01
   2_bss:   9.790  0.064  0.393 86.540  0.035  2.107   1.0628e-01
   2_xyz:   6.639  0.052  0.246 83.407  0.031  2.159   1.4404e-01
   2_adp:   6.639  0.052  0.246 83.407  0.031  2.159   1.4404e-01
   2_occ:   6.639  0.052  0.246 83.407  0.031  2.159   1.4404e-01
   3_bss:   6.639  0.052  0.246 83.407  0.031  2.159   1.4404e-01
   3_xyz:   8.726  0.042  0.248 83.779  0.025  2.264   5.6067e-02
   3_adp:   8.726  0.042  0.248 83.779  0.025  2.264   5.6067e-02
   3_occ:   8.726  0.042  0.248 83.779  0.025  2.264   5.6067e-02
   4_bss:   8.726  0.042  0.248 83.779  0.025  2.264   5.6067e-02
   4_xyz:   8.101  0.044  0.212 82.428  0.031  2.342   4.0933e-02
   4_adp:   8.101  0.044  0.212 82.428  0.031  2.342   4.0933e-02
   4_occ:   8.101  0.044  0.212 82.428  0.031  2.342   4.0933e-02
   5_bss:   8.101  0.044  0.212 82.428  0.031  2.342   4.0933e-02
   5_xyz:   8.227  0.037  0.216 83.521  0.035  2.327   3.2407e-02
   5_adp:   8.227  0.037  0.216 83.521  0.035  2.327   3.2407e-02
   5_occ:   8.227  0.037  0.216 83.521  0.035  2.327   3.2407e-02
   5_bss:   8.227  0.037  0.216 83.521  0.035  2.327   3.2407e-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: 112.38   0.00  18.91  71.20   0.00  15.03 112.38   1.16  40.07
   1_occ: 112.38   0.00  18.91  71.20   0.00  15.03 112.38   1.16  40.07
   2_bss: 112.38   0.00  18.91  71.20   0.00  15.03 112.38   1.16  40.07
   2_xyz: 112.38   0.00  18.91  71.20   0.00  15.03 112.38   1.16  40.07
   2_adp: 115.75   0.00  18.99  95.62   0.00  14.24 115.75   3.99  44.82
   2_occ: 115.75   0.00  18.99  95.62   0.00  14.24 115.75   3.99  44.82
   3_bss: 115.75   0.00  18.99  95.62   0.00  14.24 115.75   3.99  44.82
   3_xyz: 115.75   0.00  18.99  95.62   0.00  14.24 115.75   3.99  44.82
   3_adp: 101.35   1.61  17.47  90.95   1.61  13.08 101.35   5.15  41.41
   3_occ: 101.35   1.61  17.47  90.95   1.61  13.08 101.35   5.15  41.41
   4_bss: 101.35   1.61  17.47  90.95   1.61  13.08 101.35   5.15  41.41
   4_xyz: 101.35   1.61  17.47  90.95   1.61  13.08 101.35   5.15  41.41
   4_adp:  98.14   0.00  17.62  96.21   0.00  12.93  98.14   5.03  43.16
   4_occ:  98.14   0.00  17.62  96.21   0.00  12.93  98.14   5.03  43.16
   5_bss:  98.14   0.00  17.62  96.21   0.00  12.93  98.14   5.03  43.16
   5_xyz:  98.14   0.00  17.62  96.21   0.00  12.93  98.14   5.03  43.16
   5_adp:  97.05   0.00  17.44  97.05   0.00  12.85  96.41   5.76  42.41
   5_occ:  97.05   0.00  17.44  97.05   0.00  12.85  96.41   5.76  42.41
   5_bss:  97.05   0.00  17.44  97.05   0.00  12.85  96.41   5.76  42.42
------------------------------------------------------------------------
 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:    1.707    0.020    0.370
   1_adp:    1.707    0.020    0.370
   1_occ:    1.707    0.020    0.370
   2_bss:    1.707    0.020    0.370
   2_xyz:    1.311    0.036    0.536
   2_adp:    1.311    0.036    0.536
   2_occ:    1.311    0.036    0.536
   3_bss:    1.311    0.036    0.536
   3_xyz:    1.400    0.036    0.641
   3_adp:    1.400    0.036    0.641
   3_occ:    1.400    0.036    0.641
   4_bss:    1.400    0.036    0.641
   4_xyz:    1.386    0.062    0.689
   4_adp:    1.386    0.062    0.689
   4_occ:    1.386    0.062    0.689
   5_bss:    1.386    0.062    0.689
   5_xyz:    1.529    0.055    0.710
   5_adp:    1.529    0.055    0.710
   5_occ:    1.529    0.055    0.710
   5_bss:    1.529    0.055    0.710
------------------------------------------------------------------------

CPU time actual refinement: 302.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1106/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_1106/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1106/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1106/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1106/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 302.60 
  Macro-tasks:
    bulk solvent and scale       = 39.11  
    individual site refinement   = 122.85 
    weights calculation          = 24.73  
    collect and process          = 5.38   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 192.16 
  Micro-tasks:
    mask                            = 2.06   
    f_calc                          = 98.02  
    alpha_beta                      = 6.91   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 105.25 
    fmodel                         = 6.93   
    r_factors                      = 0.30   
    phase_errors                   = 8.82   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 229.50 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.255 micro seconds
Total CPU time: 5.23 minutes
from_scatterers_fft:    660 calls, 97.75 s
gradients_fft:          605 calls, 93.68 s

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

# Date 2008-01-16 Time 06:26:15 PST -0800 (1200493575.47 s)
Start R-work = 0.4450, R-free = 0.4440 (no bulk solvent and anisotropic scale)
Final R-work = 0.1427, R-free = 0.1869 (no bulk solvent and anisotropic scale)

Start R-work = 0.4360, R-free = 0.4372
Final R-work = 0.1207, R-free = 0.1677