# Date 2008-01-16 Time 04:37:45 PST -0800 (1200487065.28 s)
#phil __OFF__

Command line arguments: "../390.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28614
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 390

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.2261, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.97201
Completeness in resolution range: 0.969081
Completeness with d_max=infinity: 0.96607

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8842
                             d_min =   1.9720

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8842 1.97201
Completeness in resolution range: 0.969081
Completeness with d_max=infinity: 0.96607

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8847 -  4.2193 [2128/2152]  1914   214  10.1%
  bin  2:  4.2193 -  3.3617 [2031/2051]  1829   202   9.9%
  bin  3:  3.3617 -  2.9405 [2017/2036]  1814   203  10.1%
  bin  4:  2.9405 -  2.6733 [1982/2012]  1784   198  10.0%
  bin  5:  2.6733 -  2.4827 [1992/2011]  1790   202  10.1%
  bin  6:  2.4827 -  2.3369 [1973/1998]  1778   195   9.9%
  bin  7:  2.3369 -  2.2202 [1951/1979]  1756   195  10.0%
  bin  8:  2.2202 -  2.1239 [1971/2007]  1778   193   9.8%
  bin  9:  2.1239 -  2.0423 [1926/1968]  1729   197  10.2%
  bin 10:  2.0423 -  1.9720 [1618/2000]  1458   160   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_390/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 37
        2.42 -     3.04: 2228
        3.04 -     3.66: 4765
        3.66 -     4.28: 9185
        4.28 -     4.90: 12459
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.905 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.953 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.047 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  2.062 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28669 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_390/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_390/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.22605 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3570   r_free= 0.3480   ksol= 0.00   Bsol= 0.00   scale= 0.965    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.130616                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7059 0.99   1383  152 0.3030 0.2942       6.402       6.357|
|  2:  4.7059 -  3.7549 0.99   1318  152 0.2828 0.2527      6.5383      6.4608|
|  3:  3.7549 -  3.2861 0.99   1299  141 0.3105 0.2945      6.4674      6.5289|
|  4:  3.2861 -  2.9883 0.99   1300  143 0.3280 0.3530      6.3313      6.4026|
|  5:  2.9883 -  2.7756 0.99   1272  144 0.3725 0.3033      6.2125       6.086|
|  6:  2.7756 -  2.6129 0.99   1292  141 0.3718 0.4095      6.1291       6.093|
|  7:  2.6129 -  2.4827 0.99   1267  146 0.3802 0.3629      6.0851      6.0019|
|  8:  2.4827 -  2.3750 0.98   1276  135 0.3965 0.4276      6.0549      6.1448|
|  9:  2.3750 -  2.2839 0.98   1258  141 0.3936 0.4021      6.0202      6.0088|
| 10:  2.2839 -  2.2054 1.00   1278  144 0.3989 0.3631      5.9908      5.9134|
| 11:  2.2054 -  2.1366 0.97   1241  138 0.3970 0.4255      5.9234      5.9932|
| 12:  2.1366 -  2.0757 0.98   1253  136 0.4208 0.3803      5.9224       5.896|
| 13:  2.0757 -  2.0212 0.99   1259  138 0.4152 0.3952      5.7898      5.7666|
| 14:  2.0212 -  1.9720 0.73    934  108 0.4462 0.4095      5.8157      5.6969|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8847 -  4.7059  1383   152  0.78  27.01   0.86     0.81      46493.85|
|  2:  4.7059 -  3.7549  1318   152  0.82  24.25   0.97     0.92      55809.18|
|  3:  3.7549 -  3.2861  1299   141  0.77  28.96   0.99     0.94      57352.55|
|  4:  3.2861 -  2.9883  1300   143  0.73  32.55   0.99     0.92      51728.57|
|  5:  2.9883 -  2.7756  1272   144  0.68  37.45   0.98     0.88      41149.97|
|  6:  2.7756 -  2.6129  1292   141  0.68  37.32   0.96     0.87      35337.38|
|  7:  2.6129 -  2.4827  1267   146  0.66  39.25   1.00     0.87      33393.76|
|  8:  2.4827 -  2.3750  1276   135  0.63  41.24   1.00     0.85      32740.72|
|  9:  2.3750 -  2.2839  1258   141  0.64  41.33   1.00     0.85      31017.20|
| 10:  2.2839 -  2.2054  1278   144  0.62  42.66   1.02     0.85      28534.31|
| 11:  2.2054 -  2.1366  1241   138  0.62  42.94   1.03     0.88      27274.39|
| 12:  2.1366 -  2.0757  1253   136  0.61  43.71   1.03     0.87      24874.88|
| 13:  2.0757 -  2.0212  1259   138  0.59  45.28   1.02     0.84      21913.02|
| 14:  2.0212 -  1.9720   934   108  0.60  44.79   1.03     0.81      18443.34|
|alpha:            min =        0.81 max =            0.94 mean =         0.87|
|beta:             min =    18443.34 max =        57352.55 mean =     36699.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.99 mean =        37.49|
|phase err.(test): min =        0.00 max =           89.92 mean =        37.23|
|-----------------------------------------------------------------------------|

============================== 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 = 6.440714              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.505   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903598              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.121   (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 |  1.806 -  2.115:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       30 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      208 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2020 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1889 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2876 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4721 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4464 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5665 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6794 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.265 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3570   r_free= 0.3480   ksol= 0.00   Bsol= 0.00   scale= 0.965    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.130616                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3424   r_free= 0.3345   ksol= 0.33   Bsol= 30.76   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,2.40,-1.69,0.00,-0.00,-0.00); trace/3= -0.50                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.111947                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.597398              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.375   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.489091              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.046   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3424      final r-factor (work) = 0.2055          |
| start r-factor (free) = 0.3345      final r-factor (free) = 0.2331          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2763 = 5.60 * 0.50 * 6.1134 + 1.00 * 0.1666                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4114 = 5.60 * 0.50 * 5.8340 + 1.00 * 0.0837                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2055      final r-factor (work) = 0.1880          |
| start r-factor (free) = 0.2331      final r-factor (free) = 0.2440          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8592 = 0.49 * 1.00 * 5.8340 + 1.00 * 0.0058                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7404 = 0.49 * 1.00 * 5.5820 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.92   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    80.92   17.44    None  None   None       |
|    Sol.    : 438    0      7.78    80.92   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    79.61   13.28    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 -   8.092:  601   |   5:    40.458 -  48.550:  107        |
|      1:     8.092 -  16.183: 1263   |   6:    48.550 -  56.641:   87        |
|      2:    16.183 -  24.275:  407   |   7:    56.641 -  64.733:   45        |
|      3:    24.275 -  32.367:  156   |   8:    64.733 -  72.825:   19        |
|      4:    32.367 -  40.458:  132   |   9:    72.825 -  80.916:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1880 r_free = 0.2440             target_work(ml) = 5.596         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1877 r_free = 0.2436             target_work(ml) = 5.595         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1877   r_free= 0.2436   ksol= 0.33   Bsol= 30.76   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,2.40,-1.69,0.00,-0.00,-0.00); trace/3= -0.50                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.595173                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1849   r_free= 0.2387   ksol= 0.31   Bsol= 37.41   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.19,-1.56,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.580397                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.881049              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.365   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.111197              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.566  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1849      final r-factor (work) = 0.1445          |
| start r-factor (free) = 0.2387      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3384 = 1.88 * 0.50 * 5.5869 + 1.00 * 0.0837                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1952 = 1.88 * 0.50 * 5.4709 + 1.00 * 0.0497                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1445      final r-factor (work) = 0.1396          |
| start r-factor (free) = 0.1911      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6187 = 0.11 * 1.00 * 5.4709 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6002 = 0.11 * 1.00 * 5.3405 + 1.00 * 0.0063                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.82    75.78   16.80    None  None   None       |
|    all(noH): 2823   0      1.82    75.78   16.80    None  None   None       |
|    Sol.    : 438    0      7.01    73.73   37.19    None  None   None       |
|    Mac.    : 2385   0      1.82    75.78   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.824 -   9.220:  726   |   5:    38.801 -  46.196:  107        |
|      1:     9.220 -  16.615: 1254   |   6:    46.196 -  53.591:   82        |
|      2:    16.615 -  24.010:  332   |   7:    53.591 -  60.986:   33        |
|      3:    24.010 -  31.405:  132   |   8:    60.986 -  68.382:   16        |
|      4:    31.405 -  38.801:  135   |   9:    68.382 -  75.777:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1396 r_free = 0.1813             target_work(ml) = 5.317         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1814             target_work(ml) = 5.316         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1814   ksol= 0.31   Bsol= 37.41   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.19,-1.56,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.315851                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1388   r_free= 0.1807   ksol= 0.32   Bsol= 41.07   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.28,-1.35,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.311559                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.916276              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.525  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.357565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.871  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1388      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1647 = 1.92 * 0.50 * 5.3385 + 1.00 * 0.0497                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0712 = 1.92 * 0.50 * 5.2382 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3556 = 2.36 * 1.00 * 5.2382 + 1.00 * 0.0063                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1662 = 2.36 * 1.00 * 5.1566 + 1.00 * 0.0093                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.64   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    89.64   17.52    None  None   None       |
|    Sol.    : 438    0      6.37    84.47   41.46    None  None   None       |
|    Mac.    : 2385   0      0.00    89.64   13.13    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 -   8.965:  733   |   5:    44.822 -  53.787:  103        |
|      1:     8.965 -  17.929: 1339   |   6:    53.787 -  62.751:   74        |
|      2:    17.929 -  26.894:  272   |   7:    62.751 -  71.716:   40        |
|      3:    26.894 -  35.858:  127   |   8:    71.716 -  80.680:   15        |
|      4:    35.858 -  44.822:  115   |   9:    80.680 -  89.645:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1583             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1145 r_free = 0.1584             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1584   ksol= 0.32   Bsol= 41.07   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.28,-1.35,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1582   ksol= 0.32   Bsol= 45.30   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.51,-1.31,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.148864                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.861755              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.907  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.795271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.958  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8520 = 1.86 * 0.50 * 5.1562 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8285 = 1.86 * 0.50 * 5.1304 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0893 = 0.80 * 1.00 * 5.1304 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0790 = 0.80 * 1.00 * 5.1172 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.23    91.24   17.33    None  None   None       |
|    all(noH): 2823   0      0.23    91.24   17.33    None  None   None       |
|    Sol.    : 438    0      5.99    85.08   41.09    None  None   None       |
|    Mac.    : 2385   0      0.23    91.24   12.97    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:     0.231 -   9.332:  872   |   5:    45.734 -  54.835:   95        |
|      1:     9.332 -  18.432: 1233   |   6:    54.835 -  63.935:   72        |
|      2:    18.432 -  27.533:  257   |   7:    63.935 -  73.036:   30        |
|      3:    27.533 -  36.633:  124   |   8:    73.036 -  82.136:   13        |
|      4:    36.633 -  45.734:  122   |   9:    82.136 -  91.237:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1542             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1542             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1542   ksol= 0.32   Bsol= 45.30   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.51,-1.31,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1546   ksol= 0.32   Bsol= 46.54   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.41,-1.09,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117761                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.073940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.945  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.042463              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.077  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3607 = 2.07 * 0.50 * 5.1187 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3524 = 2.07 * 0.50 * 5.1079 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 41.0895 = 8.04 * 1.00 * 5.1079 + 1.00 * 0.0094                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 41.0682 = 8.04 * 1.00 * 5.1052 + 1.00 * 0.0099                              |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.45   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    93.45   17.18    None  None   None       |
|    Sol.    : 438    0      5.89    86.35   40.85    None  None   None       |
|    Mac.    : 2385   0      0.00    93.45   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.345:  919   |   5:    46.723 -  56.067:   89        |
|      1:     9.345 -  18.689: 1203   |   6:    56.067 -  65.412:   64        |
|      2:    18.689 -  28.034:  248   |   7:    65.412 -  74.756:   28        |
|      3:    28.034 -  37.378:  127   |   8:    74.756 -  84.101:   14        |
|      4:    37.378 -  46.723:  127   |   9:    84.101 -  93.445:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1549             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1549             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1549   ksol= 0.32   Bsol= 46.54   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.41,-1.09,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109072                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7059 0.99   1383  152 0.0949 0.1256      5.3545      5.5073|
|  2:  4.7059 -  3.7549 0.99   1318  152 0.0813 0.1108      5.4091      5.6119|
|  3:  3.7549 -  3.2861 0.99   1299  141 0.1030 0.1517      5.4586      5.8584|
|  4:  3.2861 -  2.9883 0.99   1300  143 0.1139 0.1588      5.4138      5.5678|
|  5:  2.9883 -  2.7756 0.99   1272  144 0.1231 0.1649      5.2912      5.5166|
|  6:  2.7756 -  2.6129 0.99   1292  141 0.1127 0.1942      5.1647      5.4734|
|  7:  2.6129 -  2.4827 0.99   1267  146 0.1201 0.1515      5.1261      5.3091|
|  8:  2.4827 -  2.3750 0.98   1276  135 0.1106 0.1658      5.0321      5.3253|
|  9:  2.3750 -  2.2839 0.98   1258  141 0.1104 0.1708      4.9972      5.2557|
| 10:  2.2839 -  2.2054 1.00   1278  144 0.1060 0.1659      4.9217      5.2024|
| 11:  2.2054 -  2.1366 0.97   1241  138 0.1069 0.1686      4.9119       5.202|
| 12:  2.1366 -  2.0757 0.98   1253  136 0.1092 0.1692      4.8575      5.2422|
| 13:  2.0757 -  2.0212 0.99   1259  138 0.1052 0.1731      4.7608      5.0291|
| 14:  2.0212 -  1.9720 0.73    934  108 0.0975 0.1663      4.6452      4.9095|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8847 -  4.7059  1383   152  0.94   8.99   0.98     0.95       6865.24|
|  2:  4.7059 -  3.7549  1318   152  0.95   7.70   1.02     1.01       8795.33|
|  3:  3.7549 -  3.2861  1299   141  0.94  10.90   1.04     1.03      10100.33|
|  4:  3.2861 -  2.9883  1300   143  0.92  13.06   1.01     1.00       9788.67|
|  5:  2.9883 -  2.7756  1272   144  0.91  15.15   1.01     0.98       7943.51|
|  6:  2.7756 -  2.6129  1292   141  0.91  15.35   0.99     0.97       6602.13|
|  7:  2.6129 -  2.4827  1267   146  0.91  15.33   0.99     0.95       5855.22|
|  8:  2.4827 -  2.3750  1276   135  0.92  14.28   0.99     0.97       4913.40|
|  9:  2.3750 -  2.2839  1258   141  0.91  14.74   1.01     0.98       4781.57|
| 10:  2.2839 -  2.2054  1278   144  0.91  14.86   1.00     0.96       4112.76|
| 11:  2.2054 -  2.1366  1241   138  0.90  15.89   0.99     0.96       4272.02|
| 12:  2.1366 -  2.0757  1253   136  0.91  14.98   1.01     1.00       3789.74|
| 13:  2.0757 -  2.0212  1259   138  0.91  15.55   1.00     0.98       3233.07|
| 14:  2.0212 -  1.9720   934   108  0.92  13.78   0.98     0.95       2524.66|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2524.66 max =        10100.33 mean =      6069.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.55|
|phase err.(test): min =        0.00 max =           88.84 mean =        13.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1549   ksol= 0.32   Bsol= 46.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.26,-0.89,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1549   ksol= 0.32   Bsol= 46.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.26,-0.89,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109172                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8847 -  4.7059 0.99   1383  152 0.0950 0.1258      5.3562      5.5094|
|  2:  4.7059 -  3.7549 0.99   1318  152 0.0813 0.1107      5.4094      5.6116|
|  3:  3.7549 -  3.2861 0.99   1299  141 0.1030 0.1517      5.4586      5.8586|
|  4:  3.2861 -  2.9883 0.99   1300  143 0.1139 0.1589      5.4138      5.5681|
|  5:  2.9883 -  2.7756 0.99   1272  144 0.1231 0.1649      5.2911      5.5164|
|  6:  2.7756 -  2.6129 0.99   1292  141 0.1127 0.1941      5.1646      5.4732|
|  7:  2.6129 -  2.4827 0.99   1267  146 0.1201 0.1516      5.1262      5.3093|
|  8:  2.4827 -  2.3750 0.98   1276  135 0.1107 0.1659      5.0322      5.3253|
|  9:  2.3750 -  2.2839 0.98   1258  141 0.1104 0.1706      4.9973      5.2552|
| 10:  2.2839 -  2.2054 1.00   1278  144 0.1060 0.1661      4.9217      5.2034|
| 11:  2.2054 -  2.1366 0.97   1241  138 0.1069 0.1685       4.912       5.202|
| 12:  2.1366 -  2.0757 0.98   1253  136 0.1092 0.1691      4.8573      5.2421|
| 13:  2.0757 -  2.0212 0.99   1259  138 0.1052 0.1730      4.7605      5.0284|
| 14:  2.0212 -  1.9720 0.73    934  108 0.0975 0.1661      4.6446      4.9087|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8847 -  4.7059  1383   152  0.94   9.00   0.98     0.95       6893.88|
|  2:  4.7059 -  3.7549  1318   152  0.95   7.71   1.03     1.02       8811.13|
|  3:  3.7549 -  3.2861  1299   141  0.94  10.90   1.04     1.03      10099.93|
|  4:  3.2861 -  2.9883  1300   143  0.92  13.06   1.02     1.00       9787.87|
|  5:  2.9883 -  2.7756  1272   144  0.91  15.15   1.01     0.99       7939.85|
|  6:  2.7756 -  2.6129  1292   141  0.91  15.35   1.00     0.97       6600.89|
|  7:  2.6129 -  2.4827  1267   146  0.91  15.33   0.99     0.96       5855.68|
|  8:  2.4827 -  2.3750  1276   135  0.92  14.29   1.00     0.98       4912.83|
|  9:  2.3750 -  2.2839  1258   141  0.91  14.75   1.02     0.99       4782.84|
| 10:  2.2839 -  2.2054  1278   144  0.91  14.86   1.00     0.97       4112.98|
| 11:  2.2054 -  2.1366  1241   138  0.90  15.89   1.00     0.97       4273.68|
| 12:  2.1366 -  2.0757  1253   136  0.91  14.98   1.02     1.01       3788.99|
| 13:  2.0757 -  2.0212  1259   138  0.91  15.54   1.01     0.99       3229.96|
| 14:  2.0212 -  1.9720   934   108  0.92  13.76   0.99     0.96       2519.76|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2519.76 max =        10099.93 mean =      6072.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.82 mean =        13.55|
|phase err.(test): min =        0.00 max =           88.83 mean =        13.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.45   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    93.45   17.18    None  None   None       |
|    Sol.    : 438    0      5.89    86.36   40.85    None  None   None       |
|    Mac.    : 2385   0      0.00    93.45   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.348:  919   |   5:    46.726 -  56.070:   89        |
|      1:     9.348 -  18.692: 1203   |   6:    56.070 -  65.415:   64        |
|      2:    18.692 -  28.037:  248   |   7:    65.415 -  74.759:   28        |
|      3:    28.037 -  37.381:  127   |   8:    74.759 -  84.104:   14        |
|      4:    37.381 -  46.726:  127   |   9:    84.104 -  93.448:    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)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 4.659
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 294
   mapped sites are within: 0.735 - 4.659

peak=    6.232 closest distance to " NE2 GLN A  11 " =    1.228
peak=    5.818 closest distance to " O   HOH Z 144 " =    1.805
peak=    5.661 closest distance to " O   HOH Z 126 " =    1.940
peak=    5.410 closest distance to " NH2 ARG A  56 " =    2.100
peak=    5.362 closest distance to " CG  PRO A  54 " =    1.235
peak=    5.229 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.914 closest distance to " CB  GLN A 223 " =    1.499
peak=    4.865 closest distance to " CG  PRO A 213 " =    1.272
peak=    4.791 closest distance to " O   HOH Z 427 " =    2.783
peak=    4.754 closest distance to " O   HOH Z  78 " =    1.759
peak=    4.635 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.608 closest distance to " CB  SER A  63 " =    1.177
peak=    4.605 closest distance to " O   HOH Z 287 " =    1.975
peak=    4.575 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.554 closest distance to " O   HOH Z 369 " =    2.259
peak=    4.527 closest distance to " CB  PRO A  54 " =    0.986
peak=    4.420 closest distance to " O   HOH Z 298 " =    1.881
peak=    4.417 closest distance to " C   PRO A 198 " =    1.424
peak=    4.387 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.378 closest distance to " CB  ARG A  79 " =    1.451
peak=    4.369 closest distance to " CG  PRO A  90 " =    1.112
peak=    4.359 closest distance to " O   HOH Z 303 " =    2.206
peak=    4.346 closest distance to " ND2 ASN A 187 " =    1.507
peak=    4.304 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.296 closest distance to " O   HOH Z 371 " =    1.897
peak=    4.295 closest distance to " CG2 VAL A 257 " =    0.822
peak=    4.289 closest distance to " O   HOH Z 193 " =    1.728
peak=    4.275 closest distance to " O   HOH Z 209 " =    2.237
peak=    4.246 closest distance to " O   HOH Z   9 " =    2.168
peak=    4.216 closest distance to " NZ  LYS A 117 " =    3.119
peak=    4.214 closest distance to " O   HOH Z 203 " =    1.801
peak=    4.201 closest distance to " CB  ASN A 148 " =    1.414
peak=    4.199 closest distance to " O   HOH Z 419 " =    2.303
peak=    4.183 closest distance to " O   HOH Z 272 " =    1.804
peak=    4.167 closest distance to " CB  GLU A 152 " =    1.322
peak=    4.150 closest distance to " CB  ARG A 190 " =    1.633
peak=    4.148 closest distance to " CD  ARG A  66 " =    2.357
peak=    4.141 closest distance to " OG BSER A 164 " =    2.175
peak=    4.140 closest distance to " O   HOH Z 158 " =    2.996
peak=    4.125 closest distance to " OG ASER A 258 " =    3.068
peak=    4.109 closest distance to " O   HOH Z  44 " =    1.734
peak=    4.084 closest distance to " O   HOH Z  61 " =    1.635
peak=    4.073 closest distance to " O   HOH Z 417 " =    1.146
peak=    4.073 closest distance to " O   HOH Z 234 " =    3.574
peak=    4.022 closest distance to " O   HOH Z 144 " =    2.166
peak=    4.020 closest distance to " CG  PRO A 198 " =    1.200
peak=    4.014 closest distance to " O   HOH Z   1 " =    1.928
peak=    4.013 closest distance to " O   SER A  87 " =    2.144
peak=    4.010 closest distance to " O   HOH Z 133 " =    2.652
peak=    4.004 closest distance to " O   HOH Z 425 " =    2.083
peak=    3.991 closest distance to " O   HOH Z 236 " =    1.360
peak=    3.989 closest distance to " CB  GLU A 128 " =    1.019
peak=    3.983 closest distance to " O   HOH Z 423 " =    1.326
peak=    3.960 closest distance to " O   HOH Z 346 " =    1.654
peak=    3.936 closest distance to " CE  LYS A  76 " =    0.872
peak=    3.933 closest distance to " CG1 ILE A  33 " =    1.215
peak=    3.926 closest distance to " O   HOH Z 132 " =    2.278
peak=    3.912 closest distance to " CG  PRO A 243 " =    1.090
peak=    3.896 closest distance to " O   HOH Z 405 " =    1.216
peak=    3.883 closest distance to " O   HOH Z 402 " =    1.418
peak=    3.874 closest distance to " CB  SER A   3 " =    1.253
peak=    3.872 closest distance to " O   HOH Z  61 " =    1.462
peak=    3.871 closest distance to " O   HOH Z   1 " =    1.637
peak=    3.869 closest distance to " CB  TRP A 266 " =    1.100
peak=    3.862 closest distance to " O   HOH Z 368 " =    3.602
peak=    3.848 closest distance to " OD1 ASN A  69 " =    2.634
peak=    3.840 closest distance to " O   HOH Z 250 " =    1.501
peak=    3.829 closest distance to " O   HOH Z 362 " =    2.586
peak=    3.823 closest distance to " CA  ASN A 215 " =    1.105
peak=    3.819 closest distance to " O   HOH Z 327 " =    1.592
peak=    3.818 closest distance to " O   HOH Z  63 " =    1.415
peak=    3.816 closest distance to " O   HOH Z 189 " =    2.249
peak=    3.813 closest distance to " CB  LEU A 228 " =    1.096
peak=    3.811 closest distance to " O   HOH Z 128 " =    2.131
peak=    3.800 closest distance to " O   HOH Z 112 " =    1.061
peak=    3.793 closest distance to " CB  GLU A 277 " =    3.516
peak=    3.788 closest distance to " O   HOH Z 380 " =    1.599
peak=    3.784 closest distance to " CD2 TRP A 179 " =    1.342
peak=    3.778 closest distance to " O   HOH Z  66 " =    2.140
peak=    3.762 closest distance to " O   HOH Z 357 " =    1.877
peak=    3.718 closest distance to " CD  ARG A 159 " =    0.735
peak=    3.713 closest distance to " CZ  PHE A 218 " =    1.044
peak=    3.706 closest distance to " CB  LYS A 117 " =    1.218
peak=    3.702 closest distance to " O   HOH Z 368 " =    2.042
peak=    3.696 closest distance to " O   HOH Z 407 " =    2.249
peak=    3.694 closest distance to " O   HOH Z  93 " =    2.263
peak=    3.687 closest distance to " O   HOH Z 392 " =    3.026
peak=    3.667 closest distance to " O   HOH Z 128 " =    2.037
peak=    3.666 closest distance to " O   HOH Z 344 " =    3.221
peak=    3.666 closest distance to " ND1 HIS A  86 " =    1.803
peak=    3.660 closest distance to " O   HOH Z 403 " =    1.649
peak=    3.660 closest distance to " O   HOH Z  10 " =    1.810
peak=    3.652 closest distance to " CB  ARG A 139 " =    1.018
peak=    3.650 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.645 closest distance to " O   HOH Z   3 " =    1.963
peak=    3.633 closest distance to " CG1BVAL A  72 " =    1.392
peak=    3.629 closest distance to " O   HOH Z 180 " =    2.204
peak=    3.625 closest distance to " O   HOH Z 286 " =    2.368
peak=    3.620 closest distance to " CB  THR A  31 " =    1.700
peak=    3.613 closest distance to " O   HOH Z 371 " =    3.054
peak=    3.611 closest distance to " O   HOH Z 365 " =    2.774
peak=    3.601 closest distance to " O   HOH Z  40 " =    2.149
peak=    3.601 closest distance to " O   HOH Z 214 " =    2.215
peak=    3.600 closest distance to " O   HOH Z 389 " =    1.752
peak=    3.594 closest distance to " N   PHE A 130 " =    1.206
peak=    3.580 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.570 closest distance to " CB  SER A  62 " =    1.332
peak=    3.568 closest distance to " O   HOH Z 437 " =    1.607
peak=    3.564 closest distance to " O   HOH Z  59 " =    1.517
peak=    3.564 closest distance to " O   HOH Z 305 " =    3.525
peak=    3.563 closest distance to " CG2 ILE A 120 " =    1.048
peak=    3.561 closest distance to " CB  THR A 157 " =    1.108
peak=    3.556 closest distance to " NH1AARG A 145 " =    1.197
peak=    3.553 closest distance to " O   HOH Z 124 " =    2.281
peak=    3.544 closest distance to " NH2BARG A 145 " =    2.049
peak=    3.543 closest distance to " CB  SER A  26 " =    1.650
peak=    3.542 closest distance to " CB  TRP A 179 " =    1.334
peak=    3.542 closest distance to " CA  ALA A 233 " =    0.949
peak=    3.541 closest distance to " NH2AARG A 190 " =    1.892
peak=    3.528 closest distance to " CB  ILE A 120 " =    1.400
peak=    3.527 closest distance to " O   HOH Z 219 " =    2.262
peak=    3.524 closest distance to " CD BLYS A 290 " =    1.201
peak=    3.522 closest distance to " O   HOH Z 325 " =    3.790
peak=    3.520 closest distance to " N   TYR A 116 " =    1.542
peak=    3.517 closest distance to " O  BHOH Z 338 " =    2.355
peak=    3.516 closest distance to " O   HOH Z 359 " =    1.387
peak=    3.509 closest distance to " CD2 LEU A 297 " =    0.974
peak=    3.509 closest distance to " O   HOH Z 337 " =    3.607
peak=    3.504 closest distance to " O   HOH Z 345 " =    3.334
peak=    3.503 closest distance to " O   HOH Z 193 " =    1.819
peak=    3.497 closest distance to " O   HOH Z 425 " =    1.251
peak=    3.490 closest distance to " O   HOH Z 290 " =    0.925
peak=    3.488 closest distance to " O   HOH Z 213 " =    1.991
peak=    3.484 closest distance to " O   HOH Z 193 " =    1.987
peak=    3.482 closest distance to " CB  GLN A  89 " =    1.468
peak=    3.479 closest distance to " O   HOH Z 291 " =    1.478
peak=    3.476 closest distance to " O   ASN A  74 " =    1.503
peak=    3.475 closest distance to " O   HOH Z 172 " =    3.063
peak=    3.474 closest distance to " O   HOH Z  88 " =    2.514
peak=    3.473 closest distance to " O   HOH Z 245 " =    1.306
peak=    3.465 closest distance to " O   HOH Z 175 " =    2.160
peak=    3.463 closest distance to " CB  TYR A 116 " =    0.790
peak=    3.459 closest distance to " NE2 GLN A  73 " =    3.694
peak=    3.450 closest distance to " OG  SER A  62 " =    2.862
peak=    3.447 closest distance to " CA  ALA A  84 " =    1.339
peak=    3.446 closest distance to " NH1BARG A 145 " =    1.276
peak=    3.445 closest distance to " O   HOH Z  43 " =    1.882
peak=    3.437 closest distance to " O   HOH Z  64 " =    2.376
peak=    3.437 closest distance to " CB  SER A 212 " =    1.063
peak=    3.436 closest distance to " OD1BASN A 224 " =    2.249
peak=    3.436 closest distance to " N   ASN A  39 " =    1.260
peak=    3.429 closest distance to " O   HOH Z   6 " =    1.987
peak=    3.426 closest distance to " CB  ALA A  34 " =    1.108
peak=    3.423 closest distance to " CD  PRO A 243 " =    1.568
peak=    3.422 closest distance to " CB  ASP A 140 " =    0.957
peak=    3.419 closest distance to " O   HOH Z 146 " =    1.617
peak=    3.408 closest distance to " OD2 ASP A 286 " =    2.753
peak=    3.402 closest distance to " O   HOH Z 298 " =    2.468
peak=    3.395 closest distance to " CG  LEU A 167 " =    1.240
peak=    3.394 closest distance to " O   HOH Z  88 " =    2.424
peak=    3.394 closest distance to " O   HOH Z 336 " =    1.854
peak=    3.391 closest distance to " O   HOH Z 248 " =    1.583
peak=    3.391 closest distance to " O   HOH Z 391 " =    2.864
peak=    3.391 closest distance to " O   HOH Z 153 " =    1.634
peak=    3.389 closest distance to " CG2 VAL A 197 " =    1.076
peak=    3.384 closest distance to " CG AARG A 275 " =    1.037
peak=    3.380 closest distance to " O   HOH Z 422 " =    2.618
peak=    3.379 closest distance to " CA  ASP A 162 " =    1.088
peak=    3.379 closest distance to " O   HOH Z  44 " =    2.940
peak=    3.367 closest distance to " O   HOH Z 126 " =    1.491
peak=    3.364 closest distance to " CA  SER A 146 " =    1.803
peak=    3.362 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.361 closest distance to " CB  ALA A 114 " =    1.471
peak=    3.359 closest distance to " O   HOH Z  89 " =    2.075
peak=    3.347 closest distance to " CA  PHE A 283 " =    1.282
peak=    3.346 closest distance to " CG2 THR A 221 " =    1.129
peak=    3.343 closest distance to " O   HOH Z 421 " =    1.904
peak=    3.342 closest distance to " O   HOH Z 265 " =    2.263
peak=    3.341 closest distance to " CB  SER A 216 " =    0.816
peak=    3.339 closest distance to " O   HOH Z 257 " =    2.191
peak=    3.337 closest distance to " CD1 ILE A 106 " =    0.880
peak=    3.336 closest distance to " O   HOH Z  21 " =    1.763
peak=    3.335 closest distance to " CB  ALA A 291 " =    1.383
peak=    3.330 closest distance to " O   HOH Z 284 " =    2.959
peak=    3.329 closest distance to " O   HOH Z 411 " =    3.749
peak=    3.328 closest distance to " O   HOH Z 207 " =    1.673
peak=    3.324 closest distance to " O   HOH Z 272 " =    2.158
peak=    3.322 closest distance to " CB  GLN A  88 " =    1.223
peak=    3.322 closest distance to " O   HOH Z 415 " =    3.637
peak=    3.319 closest distance to " CB  ASN A 110 " =    1.087
peak=    3.316 closest distance to " CG  MET A 185 " =    1.319
peak=    3.315 closest distance to " OG BSER A  99 " =    2.270
peak=    3.310 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.310 closest distance to " ND2 ASN A 249 " =    0.830
peak=    3.308 closest distance to " CD  LYS A 166 " =    1.293
peak=    3.302 closest distance to " CB  HIS A 108 " =    0.804
peak=    3.302 closest distance to " O   HOH Z 116 " =    2.847
peak=    3.302 closest distance to " CB  LEU A 300 " =    0.889
peak=    3.302 closest distance to " O   HOH Z 227 " =    1.828
peak=    3.299 closest distance to " N   SER A 134 " =    1.396
peak=    3.293 closest distance to " CB  ALA A   1 " =    4.659
peak=    3.286 closest distance to " O   HOH Z 426 " =    1.912
peak=    3.286 closest distance to " CA  ILE A 234 " =    1.035
peak=    3.285 closest distance to " CA  MET A  40 " =    1.084
peak=    3.283 closest distance to " CB  ALA A  21 " =    1.984
peak=    3.282 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.281 closest distance to " O   HOH Z 423 " =    2.478
peak=    3.279 closest distance to " CA  ALA A 291 " =    0.815
peak=    3.278 closest distance to " O   HOH Z 261 " =    2.343
peak=    3.267 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.267 closest distance to " OE2 GLU A  53 " =    1.998
peak=    3.263 closest distance to " O   HOH Z  66 " =    2.067
peak=    3.261 closest distance to " O   HOH Z 203 " =    1.176
peak=    3.257 closest distance to " O   HOH Z 135 " =    1.662
peak=    3.257 closest distance to " O   HOH Z 433 " =    1.813
peak=    3.256 closest distance to " CB  ASN A 142 " =    0.983
peak=    3.255 closest distance to " O   HOH Z   2 " =    1.262
peak=    3.252 closest distance to " CA  ALA A 299 " =    0.924
peak=    3.251 closest distance to " CA  MET A 105 " =    0.923
peak=    3.248 closest distance to " CG  LYS A  76 " =    0.975
peak=    3.247 closest distance to " CA  ARG A  36 " =    0.983
peak=    3.243 closest distance to " CD1 ILE A 263 " =    1.344
peak=    3.242 closest distance to " O   HOH Z  40 " =    1.968
peak=    3.241 closest distance to " CA  THR A 264 " =    0.845
peak=    3.238 closest distance to " O  BHOH Z  74 " =    1.360
peak=    3.235 closest distance to " O   HOH Z 406 " =    1.521
peak=    3.218 closest distance to " CG  GLN A  77 " =    2.382
peak=    3.217 closest distance to " CA  ARG A 102 " =    1.090
peak=    3.209 closest distance to " CD2 LEU A 255 " =    1.461
peak=    3.205 closest distance to " CB  LYS A 290 " =    1.431
peak=    3.203 closest distance to " CA  ALA A  51 " =    0.944
peak=    3.203 closest distance to " CG2 THR A 294 " =    1.633
peak=    3.201 closest distance to " CB  SER A 273 " =    0.806
peak=    3.201 closest distance to " CB  MET A  47 " =    1.189
peak=    3.201 closest distance to " O   HOH Z 373 " =    1.423
peak=    3.200 closest distance to " CZ3 TRP A 266 " =    1.119
peak=    3.200 closest distance to " CA  ASN A 127 " =    1.057
peak=    3.199 closest distance to " O   HOH Z 303 " =    3.153
peak=    3.198 closest distance to " CB  ASN A 215 " =    1.060
peak=    3.197 closest distance to " O   HOH Z 279 " =    2.216
peak=    3.196 closest distance to " CG  MET A  40 " =    2.368
peak=    3.195 closest distance to " CA  ALA A 158 " =    1.183
peak=    3.193 closest distance to " O   HOH Z 153 " =    3.756
peak=    3.191 closest distance to " CA  ALA A  21 " =    1.124
peak=    3.190 closest distance to " O   HOH Z  59 " =    1.995
peak=    3.190 closest distance to " CB  ALA A 248 " =    1.377
peak=    3.185 closest distance to " O   HOH Z 423 " =    1.719
peak=    3.183 closest distance to " O   HOH Z 109 " =    2.499
peak=    3.183 closest distance to " O   HOH Z 128 " =    1.938
peak=    3.181 closest distance to " CG  MET A 113 " =    1.159
peak=    3.181 closest distance to " O   HOH Z 173 " =    1.927
peak=    3.174 closest distance to " O   HOH Z  85 " =    2.324
peak=    3.173 closest distance to " O   HOH Z 325 " =    2.502
peak=    3.172 closest distance to " O   HOH Z  71 " =    2.388
peak=    3.171 closest distance to " N   GLN A 278 " =    1.218
peak=    3.169 closest distance to " CA  ALA A 233 " =    1.007
peak=    3.163 closest distance to " OG BSER A 134 " =    2.863
peak=    3.160 closest distance to " O   HOH Z  30 " =    1.589
peak=    3.159 closest distance to " O   HOH Z 432 " =    1.744
peak=    3.159 closest distance to " SD BMET A  47 " =    1.410
peak=    3.157 closest distance to " O   HOH Z  47 " =    1.783
peak=    3.155 closest distance to " O   HOH Z 329 " =    3.847
peak=    3.152 closest distance to " O   MET A 105 " =    1.835
peak=    3.152 closest distance to " N   ARG A 156 " =    1.286
peak=    3.149 closest distance to " O   HOH Z 266 " =    3.324
peak=    3.146 closest distance to " CG1 VAL A 189 " =    1.948
peak=    3.140 closest distance to " O   HOH Z 303 " =    1.694
peak=    3.137 closest distance to " CG2 ILE A  20 " =    1.528
peak=    3.134 closest distance to " O   HOH Z 271 " =    2.464
peak=    3.131 closest distance to " CG BARG A 102 " =    1.766
peak=    3.130 closest distance to " O   HOH Z  43 " =    2.699
peak=    3.119 closest distance to " CB  ALA A 114 " =    0.986
peak=    3.113 closest distance to " O   HOH Z 302 " =    1.641
peak=    3.112 closest distance to " NH1 ARG A  14 " =    1.229
peak=    3.107 closest distance to " O   HOH Z 286 " =    2.387
peak=    3.101 closest distance to " NE2 GLN A  58 " =    3.822
peak=    3.088 closest distance to " O   HOH Z 409 " =    2.511
peak=    3.081 closest distance to " O   HOH Z 342 " =    0.813
peak=    3.077 closest distance to " O   THR A 220 " =    1.311
peak=    3.077 closest distance to " NZ  LYS A 117 " =    1.644
peak=    3.076 closest distance to " CA  ALA A 233 " =    1.650
peak=    3.076 closest distance to " O   HOH Z  88 " =    3.074
peak=    3.075 closest distance to " CD1AILE A 234 " =    0.862
peak=    3.075 closest distance to " CE AMET A  47 " =    1.395
peak=    3.071 closest distance to " O   HOH Z 128 " =    2.591
peak=    3.070 closest distance to " O   HOH Z 285 " =    2.661
peak=    3.066 closest distance to " NZ  LYS A 119 " =    1.247
peak=    3.056 closest distance to " ND1 HIS A  81 " =    1.504
peak=    3.056 closest distance to " O   HOH Z 291 " =    1.814
peak=    3.037 closest distance to " O   HOH Z 213 " =    1.615

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.774 - 5.976
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.774 - 5.976

peak=   -4.621 closest distance to " O   HOH Z 377 " =    2.079
peak=   -4.604 closest distance to " O   HOH Z 266 " =    4.932
peak=   -4.525 closest distance to " CD  ARG A 156 " =    2.071
peak=   -4.486 closest distance to " CB  PRO A 243 " =    2.634
peak=   -4.467 closest distance to " OG BSER A 134 " =    1.264
peak=   -4.384 closest distance to " SG  CYS A 254 " =    3.305
peak=   -4.302 closest distance to " C   HIS A 108 " =    1.119
peak=   -4.289 closest distance to " CG  GLN A 223 " =    1.913
peak=   -4.229 closest distance to " CG1 VAL A 112 " =    2.843
peak=   -4.199 closest distance to " O   HOH Z 231 " =    2.266
peak=   -4.086 closest distance to " O   VAL A  67 " =    2.651
peak=   -4.063 closest distance to " O   PRO A 198 " =    1.289
peak=   -4.030 closest distance to " CB  ASN A  39 " =    2.312
peak=   -4.021 closest distance to " CE  MET A 105 " =    2.322
peak=   -4.011 closest distance to " O   HOH Z 198 " =    1.850
peak=   -4.010 closest distance to " O   HOH Z 372 " =    2.409
peak=   -3.989 closest distance to " O   HOH Z 313 " =    1.810
peak=   -3.979 closest distance to " CE2 PHE A 218 " =    2.416
peak=   -3.964 closest distance to " CD1 LEU A 255 " =    2.861
peak=   -3.953 closest distance to " CG  GLN A  58 " =    1.111
peak=   -3.952 closest distance to " CB  PHE A 192 " =    1.956
peak=   -3.932 closest distance to " CA  VAL A  67 " =    2.891
peak=   -3.915 closest distance to " ND2 ASN A  45 " =    1.754
peak=   -3.901 closest distance to " O   HOH Z 389 " =    1.904
peak=   -3.860 closest distance to " CB  ALA A 291 " =    2.172
peak=   -3.845 closest distance to " OD2 ASP A 191 " =    1.383
peak=   -3.839 closest distance to " CE2 TYR A  30 " =    2.713
peak=   -3.830 closest distance to " O   HOH Z 351 " =    1.608
peak=   -3.828 closest distance to " O   HOH Z 407 " =    2.887
peak=   -3.822 closest distance to " O   ALA A 161 " =    1.645
peak=   -3.815 closest distance to " N   GLN A  58 " =    1.692
peak=   -3.813 closest distance to " CB  ALA A  43 " =    2.436
peak=   -3.788 closest distance to " O   HOH Z 185 " =    2.115
peak=   -3.766 closest distance to " CA  GLY A  98 " =    1.789
peak=   -3.755 closest distance to " O   HOH Z 385 " =    1.943
peak=   -3.747 closest distance to " ND2 ASN A  45 " =    1.067
peak=   -3.742 closest distance to " O   SER A 135 " =    1.440
peak=   -3.740 closest distance to " CZ  TYR A 169 " =    1.674
peak=   -3.727 closest distance to " O   HOH Z  13 " =    1.617
peak=   -3.723 closest distance to " O   PHE A 218 " =    1.513
peak=   -3.720 closest distance to " O   HOH Z 290 " =    1.186
peak=   -3.718 closest distance to " CB  ALA A 248 " =    2.299
peak=   -3.716 closest distance to " CG  PHE A 283 " =    2.582
peak=   -3.701 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.699 closest distance to " O   PRO A 243 " =    2.575
peak=   -3.693 closest distance to " OD1 ASN A 187 " =    1.614
peak=   -3.684 closest distance to " O   HOH Z 395 " =    5.140
peak=   -3.670 closest distance to " O   HOH Z 317 " =    1.512
peak=   -3.666 closest distance to " CB  ALA A 291 " =    2.187
peak=   -3.665 closest distance to " O   HOH Z 102 " =    1.511
peak=   -3.655 closest distance to " CB  TYR A  15 " =    2.183
peak=   -3.655 closest distance to " CZ3 TRP A 179 " =    1.244
peak=   -3.654 closest distance to " O   HOH Z 263 " =    2.946
peak=   -3.652 closest distance to " O   ARG A 145 " =    1.537
peak=   -3.641 closest distance to " CB  ALA A 248 " =    2.056
peak=   -3.639 closest distance to " CA  GLY A 203 " =    2.273
peak=   -3.630 closest distance to " CZ  PHE A  59 " =    1.466
peak=   -3.623 closest distance to " N   ALA A 248 " =    1.595
peak=   -3.612 closest distance to " N   THR A 157 " =    1.479
peak=   -3.606 closest distance to " O   HOH Z  60 " =    2.303
peak=   -3.605 closest distance to " OD1 ASP A 171 " =    1.571
peak=   -3.601 closest distance to " CB  PHE A 208 " =    2.217
peak=   -3.598 closest distance to " N   ALA A  43 " =    2.521
peak=   -3.592 closest distance to " OD1 ASP A 191 " =    1.855
peak=   -3.564 closest distance to " CD  ARG A 139 " =    1.531
peak=   -3.560 closest distance to " O   SER A  95 " =    1.464
peak=   -3.556 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.551 closest distance to " O   HOH Z  63 " =    1.858
peak=   -3.548 closest distance to " CB  ALA A 161 " =    2.520
peak=   -3.548 closest distance to " ND2 ASN A 249 " =    2.354
peak=   -3.539 closest distance to " OXT GLY A 302 " =    2.921
peak=   -3.537 closest distance to " O   HOH Z 362 " =    5.976
peak=   -3.532 closest distance to " O   HOH Z 140 " =    1.654
peak=   -3.521 closest distance to " O   HOH Z 298 " =    1.249
peak=   -3.511 closest distance to " CD2 LEU A 237 " =    2.759
peak=   -3.509 closest distance to " O   HOH Z 211 " =    1.620
peak=   -3.507 closest distance to " OD1 ASN A 148 " =    1.546
peak=   -3.507 closest distance to " O   HOH Z  38 " =    1.824
peak=   -3.505 closest distance to " ND2 ASN A 187 " =    1.477
peak=   -3.499 closest distance to " CG2 THR A 178 " =    2.187
peak=   -3.498 closest distance to " CG2 ILE A 263 " =    2.277
peak=   -3.482 closest distance to " O   VAL A 189 " =    2.557
peak=   -3.478 closest distance to " CB  TRP A  85 " =    2.408
peak=   -3.462 closest distance to " O   HOH Z  52 " =    1.337
peak=   -3.460 closest distance to " O   HOH Z 126 " =    1.925
peak=   -3.452 closest distance to " O   PRO A 163 " =    1.968
peak=   -3.449 closest distance to " N   ASP A 286 " =    2.357
peak=   -3.444 closest distance to " O   HOH Z  43 " =    1.781
peak=   -3.441 closest distance to " NH2BARG A 275 " =    1.780
peak=   -3.432 closest distance to " O   HOH Z 266 " =    4.694
peak=   -3.429 closest distance to " CD2 PHE A 225 " =    1.140
peak=   -3.429 closest distance to " NE  ARG A  36 " =    1.902
peak=   -3.425 closest distance to " O   SER A 146 " =    1.074
peak=   -3.423 closest distance to " CG  ASP A 231 " =    0.774
peak=   -3.420 closest distance to " O   ALA A  10 " =    1.651
peak=   -3.413 closest distance to " O   HOH Z 166 " =    2.148
peak=   -3.412 closest distance to " O   HOH Z 131 " =    4.056
peak=   -3.408 closest distance to " O   SER A  22 " =    2.479
peak=   -3.407 closest distance to " O   HOH Z  90 " =    2.361
peak=   -3.402 closest distance to " O   VAL A 174 " =    2.250
peak=   -3.394 closest distance to " OG  SER A  97 " =    2.109
peak=   -3.388 closest distance to " O   HOH Z 191 " =    5.662
peak=   -3.388 closest distance to " CA  GLY A  57 " =    2.137
peak=   -3.385 closest distance to " O   MET A  40 " =    2.732
peak=   -3.384 closest distance to " O   HOH Z 114 " =    2.948
peak=   -3.380 closest distance to " O   HOH Z 165 " =    2.171
peak=   -3.374 closest distance to " O   HOH Z 137 " =    1.377
peak=   -3.372 closest distance to " OG  SER A  87 " =    1.342
peak=   -3.368 closest distance to " O   HOH Z 353 " =    2.219
peak=   -3.366 closest distance to " CA  GLY A 133 " =    1.943
peak=   -3.361 closest distance to " CD  LYS A 289 " =    2.336
peak=   -3.359 closest distance to " O   HOH Z 198 " =    1.659
peak=   -3.357 closest distance to " C   ALA A 158 " =    1.397
peak=   -3.352 closest distance to " O   SER A 210 " =    1.991
peak=   -3.348 closest distance to " CA  ASP A 298 " =    1.061
peak=   -3.337 closest distance to " O   HOH Z 298 " =    2.384
peak=   -3.326 closest distance to " O   TRP A  70 " =    1.440
peak=   -3.324 closest distance to " O   HOH Z  24 " =    1.322
peak=   -3.319 closest distance to " CG2 ILE A  49 " =    2.728
peak=   -3.319 closest distance to " CB  ASP A 132 " =    2.364
peak=   -3.315 closest distance to " OE2 GLU A 152 " =    1.127
peak=   -3.312 closest distance to " CD1 LEU A 228 " =    2.077
peak=   -3.311 closest distance to " O   HOH Z 339 " =    1.842
peak=   -3.310 closest distance to " OG  SER A 245 " =    1.333
peak=   -3.307 closest distance to " O   HOH Z  11 " =    1.802
peak=   -3.300 closest distance to " CG2 VAL A 296 " =    1.893
peak=   -3.299 closest distance to " OE1 GLN A 183 " =    1.468
peak=   -3.295 closest distance to " CB  ALA A   7 " =    2.039
peak=   -3.295 closest distance to " CE3 TRP A 274 " =    2.238
peak=   -3.290 closest distance to " N   PHE A  59 " =    1.849
peak=   -3.283 closest distance to " O   HOH Z 351 " =    1.702
peak=   -3.283 closest distance to " OG BSER A 134 " =    1.621
peak=   -3.274 closest distance to " CZ2 TRP A 274 " =    0.963
peak=   -3.273 closest distance to " O   HOH Z 103 " =    1.689
peak=   -3.272 closest distance to " NE2 GLN A 278 " =    1.646
peak=   -3.269 closest distance to " CB  ASP A 286 " =    2.259
peak=   -3.267 closest distance to " ND2 ASN A  39 " =    1.347
peak=   -3.266 closest distance to " SD BMET A  47 " =    1.065
peak=   -3.262 closest distance to " CG1 VAL A 230 " =    1.996
peak=   -3.259 closest distance to " O   HOH Z 166 " =    1.299
peak=   -3.257 closest distance to " O   HOH Z  15 " =    1.564
peak=   -3.257 closest distance to " O   HOH Z 359 " =    3.339
peak=   -3.251 closest distance to " O   HOH Z 111 " =    2.110
peak=   -3.249 closest distance to " CB  PRO A 163 " =    2.403
peak=   -3.247 closest distance to " O   ALA A 180 " =    1.194
peak=   -3.245 closest distance to " CG1 VAL A  78 " =    2.830
peak=   -3.240 closest distance to " CB  ILE A  33 " =    2.852
peak=   -3.237 closest distance to " C   LEU A 143 " =    1.064
peak=   -3.235 closest distance to " CE1 TYR A 169 " =    2.575
peak=   -3.225 closest distance to " O   HOH Z 393 " =    3.371
peak=   -3.225 closest distance to " O   ALA A  34 " =    2.442
peak=   -3.222 closest distance to " CB  ALA A 131 " =    1.989
peak=   -3.217 closest distance to " O   VAL A 197 " =    1.561
peak=   -3.213 closest distance to " CG2 VAL A 189 " =    1.942
peak=   -3.209 closest distance to " OG  SER A  97 " =    1.681
peak=   -3.209 closest distance to " CD2 PHE A  61 " =    2.225
peak=   -3.206 closest distance to " O   ASP A 162 " =    2.104
peak=   -3.204 closest distance to " O   HOH Z 253 " =    3.759
peak=   -3.204 closest distance to " NH2 ARG A  79 " =    2.060
peak=   -3.200 closest distance to " O   HOH Z 418 " =    1.619
peak=   -3.196 closest distance to " O   HOH Z 256 " =    1.515
peak=   -3.190 closest distance to " O   HOH Z 218 " =    3.374
peak=   -3.189 closest distance to " O   ILE A  49 " =    1.715
peak=   -3.187 closest distance to " OD2 ASP A  50 " =    1.561
peak=   -3.183 closest distance to " CE  LYS A  76 " =    2.790
peak=   -3.182 closest distance to " OD2 ASP A 171 " =    2.060
peak=   -3.181 closest distance to " N   SER A 276 " =    1.188
peak=   -3.180 closest distance to " O   ALA A  51 " =    1.211
peak=   -3.178 closest distance to " O   ILE A 106 " =    2.072
peak=   -3.178 closest distance to " NH1 ARG A 195 " =    2.667
peak=   -3.178 closest distance to " O   GLN A  89 " =    1.532
peak=   -3.173 closest distance to " CB  CYS A 201 " =    2.452
peak=   -3.171 closest distance to " O   GLN A 240 " =    1.805
peak=   -3.170 closest distance to " CG  ARG A 269 " =    2.527
peak=   -3.169 closest distance to " O   HOH Z  60 " =    1.977
peak=   -3.166 closest distance to " O   HOH Z 369 " =    2.173
peak=   -3.165 closest distance to " O   HOH Z 427 " =    1.530
peak=   -3.165 closest distance to " CD1 LEU A 101 " =    2.225
peak=   -3.164 closest distance to " O   GLY A  80 " =    2.439
peak=   -3.162 closest distance to " CA  GLY A  57 " =    2.120
peak=   -3.162 closest distance to " NH2AARG A 275 " =    5.146
peak=   -3.153 closest distance to " OE1 GLN A 223 " =    2.065
peak=   -3.141 closest distance to " O   HOH Z 281 " =    2.626
peak=   -3.141 closest distance to " ND2BASN A 224 " =    1.846
peak=   -3.140 closest distance to " CA  TRP A 274 " =    1.470
peak=   -3.134 closest distance to " OH  TYR A 214 " =    1.255
peak=   -3.126 closest distance to " O   HOH Z 357 " =    2.024
peak=   -3.125 closest distance to " CB  ASP A 132 " =    2.224
peak=   -3.123 closest distance to " O   GLU A 152 " =    1.408
peak=   -3.122 closest distance to " C   MET A 188 " =    1.480
peak=   -3.122 closest distance to " O   HOH Z   6 " =    1.496
peak=   -3.119 closest distance to " C   GLY A  17 " =    1.070
peak=   -3.119 closest distance to " CB  ALA A 244 " =    2.047
peak=   -3.112 closest distance to " O   HOH Z 123 " =    2.556
peak=   -3.110 closest distance to " O   HOH Z 388 " =    2.064
peak=   -3.110 closest distance to " O   HOH Z 421 " =    2.911
peak=   -3.104 closest distance to " SD  MET A 188 " =    2.214
peak=   -3.098 closest distance to " CA  ASP A  27 " =    2.422
peak=   -3.097 closest distance to " O   HOH Z 394 " =    1.368
peak=   -3.095 closest distance to " O   HOH Z  93 " =    2.155
peak=   -3.091 closest distance to " O   HOH Z 282 " =    1.444
peak=   -3.089 closest distance to " O   HOH Z 250 " =    1.386
peak=   -3.088 closest distance to " CG1 VAL A 197 " =    2.087
peak=   -3.088 closest distance to " O   HOH Z 288 " =    1.353
peak=   -3.087 closest distance to " C   ALA A 114 " =    2.231
peak=   -3.080 closest distance to " CG  GLU A   2 " =    2.070
peak=   -3.078 closest distance to " CD  GLN A  77 " =    1.490
peak=   -3.071 closest distance to " CB  GLN A  11 " =    1.898
peak=   -3.064 closest distance to " ND2 ASN A  60 " =    1.344
peak=   -3.063 closest distance to " O   HOH Z 414 " =    1.901

================= 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    :  0.3570 0.3480   6.130616e+00   6.107467e+00
   1_bss:  0.3424 0.3345   6.111947e+00   6.080497e+00
   1_xyz:  0.2055 0.2331   5.648215e+00   5.746017e+00
   1_adp:  0.1880 0.2440   5.596417e+00   5.782883e+00
   1_occ:  0.1877 0.2436   5.595173e+00   5.781493e+00
   2_bss:  0.1849 0.2387   5.580397e+00   5.764416e+00
   2_xyz:  0.1445 0.1911   5.353058e+00   5.566200e+00
   2_adp:  0.1396 0.1813   5.316584e+00   5.515159e+00
   2_occ:  0.1393 0.1814   5.315851e+00   5.515303e+00
   3_bss:  0.1388 0.1807   5.311559e+00   5.510188e+00
   3_xyz:  0.1196 0.1604   5.179429e+00   5.396284e+00
   3_adp:  0.1145 0.1583   5.150065e+00   5.382163e+00
   3_occ:  0.1145 0.1584   5.150121e+00   5.382410e+00
   4_bss:  0.1144 0.1582   5.148864e+00   5.381213e+00
   4_xyz:  0.1098 0.1547   5.120947e+00   5.365027e+00
   4_adp:  0.1090 0.1542   5.116379e+00   5.362646e+00
   4_occ:  0.1089 0.1542   5.116443e+00   5.362824e+00
   5_bss:  0.1090 0.1546   5.117761e+00   5.363262e+00
   5_xyz:  0.1066 0.1545   5.107331e+00   5.363592e+00
   5_adp:  0.1063 0.1549   5.108911e+00   5.368668e+00
   5_occ:  0.1063 0.1549   5.109072e+00   5.368958e+00
   5_bss:  0.1062 0.1549   5.109172e+00   5.369052e+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:  0.331  30.758  -2.204   2.396  -1.691   0.000  -0.000  -0.000
   1_xyz:  0.331  30.758  -2.204   2.396  -1.691   0.000  -0.000  -0.000
   1_adp:  0.331  30.758  -2.204   2.396  -1.691   0.000  -0.000  -0.000
   1_occ:  0.331  30.758  -2.204   2.396  -1.691   0.000  -0.000  -0.000
   2_bss:  0.309  37.415  -2.791  -1.188  -1.556  -0.000  -0.000  -0.000
   2_xyz:  0.309  37.415  -2.791  -1.188  -1.556  -0.000  -0.000  -0.000
   2_adp:  0.309  37.415  -2.791  -1.188  -1.556  -0.000  -0.000  -0.000
   2_occ:  0.309  37.415  -2.791  -1.188  -1.556  -0.000  -0.000  -0.000
   3_bss:  0.320  41.075  -2.925  -2.280  -1.354  -0.000  -0.000  -0.000
   3_xyz:  0.320  41.075  -2.925  -2.280  -1.354  -0.000  -0.000  -0.000
   3_adp:  0.320  41.075  -2.925  -2.280  -1.354  -0.000  -0.000  -0.000
   3_occ:  0.320  41.075  -2.925  -2.280  -1.354  -0.000  -0.000  -0.000
   4_bss:  0.319  45.297  -2.901  -2.514  -1.315  -0.000  -0.000  -0.000
   4_xyz:  0.319  45.297  -2.901  -2.514  -1.315  -0.000  -0.000  -0.000
   4_adp:  0.319  45.297  -2.901  -2.514  -1.315  -0.000  -0.000  -0.000
   4_occ:  0.319  45.297  -2.901  -2.514  -1.315  -0.000  -0.000  -0.000
   5_bss:  0.321  46.542  -2.703  -2.406  -1.086  -0.000  -0.000  -0.000
   5_xyz:  0.321  46.542  -2.703  -2.406  -1.086  -0.000  -0.000  -0.000
   5_adp:  0.321  46.542  -2.703  -2.406  -1.086  -0.000  -0.000  -0.000
   5_occ:  0.321  46.542  -2.703  -2.406  -1.086  -0.000  -0.000  -0.000
   5_bss:  0.322  46.317  -2.498  -2.263  -0.887  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.461 0.6759  0.8695    36698.699
   1_bss:  36.344 0.6868  0.8652    33269.461
   1_xyz:  22.356 0.8400  1.0052    13883.795
   1_adp:  23.531 0.8274  0.9962    14922.159
   1_occ:  23.502 0.8276  0.9961    14859.003
   2_bss:  22.823 0.8342  0.9572    14101.716
   2_xyz:  17.738 0.8827  0.9876     8969.420
   2_adp:  16.470 0.8948  0.9947     8230.975
   2_occ:  16.469 0.8948  0.9945     8225.714
   3_bss:  16.331 0.8959  0.9833     8119.219
   3_xyz:  14.225 0.9128  0.9900     6453.193
   3_adp:  13.893 0.9157  0.9861     6263.600
   3_occ:  13.896 0.9157  0.9860     6266.160
   4_bss:  13.865 0.9159  0.9844     6248.674
   4_xyz:  13.477 0.9192  0.9849     6002.015
   4_adp:  13.396 0.9199  0.9788     5964.616
   4_occ:  13.399 0.9199  0.9787     5966.066
   5_bss:  13.412 0.9198  0.9853     5975.831
   5_xyz:  13.417 0.9198  0.9857     6021.176
   5_adp:  13.502 0.9191  0.9789     6065.656
   5_occ:  13.507 0.9191  0.9788     6069.327
   5_bss:  13.509 0.9191  0.9855     6071.992
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6661e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6661e-01
   1_xyz:   1.214  0.009  0.079 15.141  0.006  4.107   8.3733e-02
   1_adp:   1.214  0.009  0.079 15.141  0.006  4.107   8.3733e-02
   1_occ:   1.214  0.009  0.079 15.141  0.006  4.107   8.3733e-02
   2_bss:   1.214  0.009  0.079 15.141  0.006  4.107   8.3733e-02
   2_xyz:   0.908  0.005  0.067 14.467  0.004  4.114   4.9664e-02
   2_adp:   0.908  0.005  0.067 14.467  0.004  4.114   4.9664e-02
   2_occ:   0.908  0.005  0.067 14.467  0.004  4.114   4.9664e-02
   3_bss:   0.908  0.005  0.067 14.467  0.004  4.114   4.9664e-02
   3_xyz:   0.931  0.005  0.070 14.602  0.004  4.109   5.2265e-02
   3_adp:   0.931  0.005  0.070 14.602  0.004  4.109   5.2265e-02
   3_occ:   0.931  0.005  0.070 14.602  0.004  4.109   5.2265e-02
   4_bss:   0.931  0.005  0.070 14.602  0.004  4.109   5.2265e-02
   4_xyz:   0.929  0.006  0.070 14.589  0.004  4.109   5.2767e-02
   4_adp:   0.929  0.006  0.070 14.589  0.004  4.109   5.2767e-02
   4_occ:   0.929  0.006  0.070 14.589  0.004  4.109   5.2767e-02
   5_bss:   0.929  0.006  0.070 14.589  0.004  4.109   5.2767e-02
   5_xyz:   0.960  0.006  0.073 14.586  0.004  4.109   5.5662e-02
   5_adp:   0.960  0.006  0.073 14.586  0.004  4.109   5.5662e-02
   5_occ:   0.960  0.006  0.073 14.586  0.004  4.109   5.5662e-02
   5_bss:   0.960  0.006  0.073 14.586  0.004  4.109   5.5662e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3849e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3849e-01
   1_xyz:   7.680  0.066  0.290 86.193  0.052  2.149   9.6280e-02
   1_adp:   7.680  0.066  0.290 86.193  0.052  2.149   9.6280e-02
   1_occ:   7.680  0.066  0.290 86.193  0.052  2.149   9.6280e-02
   2_bss:   7.680  0.066  0.290 86.193  0.052  2.149   9.6280e-02
   2_xyz:   6.304  0.038  0.190 82.461  0.039  2.393   4.2445e-02
   2_adp:   6.304  0.038  0.190 82.461  0.039  2.393   4.2445e-02
   2_occ:   6.304  0.038  0.190 82.461  0.039  2.393   4.2445e-02
   3_bss:   6.304  0.038  0.190 82.461  0.039  2.393   4.2445e-02
   3_xyz:   6.649  0.038  0.218 84.614  0.037  2.326   3.3609e-02
   3_adp:   6.649  0.038  0.218 84.614  0.037  2.326   3.3609e-02
   3_occ:   6.649  0.038  0.218 84.614  0.037  2.326   3.3609e-02
   4_bss:   6.649  0.038  0.218 84.614  0.037  2.326   3.3609e-02
   4_xyz:   6.450  0.043  0.220 83.677  0.037  2.319   3.8889e-02
   4_adp:   6.450  0.043  0.220 83.677  0.037  2.319   3.8889e-02
   4_occ:   6.450  0.043  0.220 83.677  0.037  2.319   3.8889e-02
   5_bss:   6.450  0.043  0.220 83.677  0.037  2.319   3.8889e-02
   5_xyz:   6.388  0.040  0.244 84.386  0.035  2.301   4.0621e-02
   5_adp:   6.388  0.040  0.244 84.386  0.035  2.301   4.0621e-02
   5_occ:   6.388  0.040  0.244 84.386  0.035  2.301   4.0621e-02
   5_bss:   6.388  0.040  0.244 84.386  0.035  2.301   4.0621e-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:  80.92   0.00  17.44  79.61   0.00  13.28  80.92   7.78  40.13
   1_occ:  80.92   0.00  17.44  79.61   0.00  13.28  80.92   7.78  40.13
   2_bss:  80.92   0.00  17.44  79.61   0.00  13.28  80.92   7.78  40.13
   2_xyz:  80.92   0.00  17.44  79.61   0.00  13.28  80.92   7.78  40.13
   2_adp:  75.78   1.82  16.80  75.78   1.82  13.05  73.73   7.01  37.19
   2_occ:  75.78   1.82  16.80  75.78   1.82  13.05  73.73   7.01  37.19
   3_bss:  75.78   1.82  16.80  75.78   1.82  13.05  73.73   7.01  37.19
   3_xyz:  75.78   1.82  16.80  75.78   1.82  13.05  73.73   7.01  37.19
   3_adp:  89.64   0.00  17.52  89.64   0.00  13.13  84.47   6.37  41.46
   3_occ:  89.64   0.00  17.52  89.64   0.00  13.13  84.47   6.37  41.46
   4_bss:  89.64   0.00  17.52  89.64   0.00  13.13  84.47   6.37  41.46
   4_xyz:  89.64   0.00  17.52  89.64   0.00  13.13  84.47   6.37  41.46
   4_adp:  91.24   0.23  17.33  91.24   0.23  12.97  85.08   5.99  41.09
   4_occ:  91.24   0.23  17.33  91.24   0.23  12.97  85.08   5.99  41.09
   5_bss:  91.24   0.23  17.33  91.24   0.23  12.97  85.08   5.99  41.09
   5_xyz:  91.24   0.23  17.33  91.24   0.23  12.97  85.08   5.99  41.09
   5_adp:  93.45   0.00  17.18  93.45   0.00  12.83  86.35   5.89  40.85
   5_occ:  93.45   0.00  17.18  93.45   0.00  12.83  86.35   5.89  40.85
   5_bss:  93.45   0.00  17.18  93.45   0.00  12.83  86.36   5.89  40.85
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.195    0.016    0.359
   1_adp:    1.195    0.016    0.359
   1_occ:    1.195    0.016    0.359
   2_bss:    1.195    0.016    0.359
   2_xyz:    0.973    0.039    0.413
   2_adp:    0.973    0.039    0.413
   2_occ:    0.973    0.039    0.413
   3_bss:    0.973    0.039    0.413
   3_xyz:    0.959    0.018    0.471
   3_adp:    0.959    0.018    0.471
   3_occ:    0.959    0.018    0.471
   4_bss:    0.959    0.018    0.471
   4_xyz:    1.020    0.027    0.490
   4_adp:    1.020    0.027    0.490
   4_occ:    1.020    0.027    0.490
   5_bss:    1.020    0.027    0.490
   5_xyz:    1.137    0.050    0.502
   5_adp:    1.137    0.050    0.502
   5_occ:    1.137    0.050    0.502
   5_bss:    1.137    0.050    0.502
------------------------------------------------------------------------

CPU time actual refinement: 324.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_390/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_390/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_390/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_390/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_390/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.56 
  Macro-tasks:
    bulk solvent and scale       = 39.14  
    individual site refinement   = 133.35 
    weights calculation          = 29.19  
    collect and process          = 6.57   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 208.36 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 102.33 
    alpha_beta                      = 8.15   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 111.34 
    fmodel                         = 6.54   
    r_factors                      = 0.17   
    phase_errors                   = 11.11  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 242.90 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.619 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    634 calls, 101.94 s
gradients_fft:          579 calls,  98.10 s

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

# Date 2008-01-16 Time 04:43:22 PST -0800 (1200487402.95 s)
Start R-work = 0.3570, R-free = 0.3480 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1741 (no bulk solvent and anisotropic scale)

Start R-work = 0.3424, R-free = 0.3345
Final R-work = 0.1062, R-free = 0.1549