# Date 2008-01-16 Time 05:33:33 PST -0800 (1200490413.31 s)
#phil __OFF__

Command line arguments: "../784.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24322
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 784

-------------------------------------------------------------------------------
  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: (70.6012, 46.93, 85.5261, 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: 3.26, 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: (70.6012, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98109
Completeness in resolution range: 0.962983
Completeness with d_max=infinity: 0.96001

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9811

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: (70.6012, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98109
Completeness in resolution range: 0.962983
Completeness with d_max=infinity: 0.96001

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2391 [2129/2157]  1918   211   9.9%
  bin  2:  4.2391 -  3.3773 [2051/2067]  1844   207  10.1%
  bin  3:  3.3773 -  2.9541 [2022/2041]  1818   204  10.1%
  bin  4:  2.9541 -  2.6857 [2017/2047]  1819   198   9.8%
  bin  5:  2.6857 -  2.4941 [1991/2010]  1792   199  10.0%
  bin  6:  2.4941 -  2.3476 [1981/2006]  1781   200  10.1%
  bin  7:  2.3476 -  2.2305 [1957/1990]  1764   193   9.9%
  bin  8:  2.2305 -  2.1337 [1974/2005]  1778   196   9.9%
  bin  9:  2.1337 -  2.0517 [1987/2029]  1785   202  10.2%
  bin 10:  2.0517 -  1.9811 [1480/1990]  1331   149  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_784/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: 10
        2.42 -     3.04: 2209
        3.04 -     3.66: 4683
        3.66 -     4.28: 9050
        4.28 -     4.90: 12389
  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 100 " - " O   HOH Z 352 "  2.170 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.182 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.259 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28336 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_784/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_784/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 85.5261 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: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2395   r_free= 0.2423   ksol= 0.00   Bsol= 0.00   scale= 1.004    |
|                                                                             |
| 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:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.769862                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7280 0.99   1385  154 0.2538 0.2539      6.2678      6.2049|
|  2:  4.7280 -  3.7724 0.99   1340  146 0.1856 0.1822      6.1358      6.1394|
|  3:  3.7724 -  3.3013 0.99   1303  147 0.1981 0.1898      6.0139      6.1176|
|  4:  3.3013 -  3.0021 0.99   1306  147 0.2007 0.2291      5.8901      5.9449|
|  5:  3.0021 -  2.7884 0.99   1291  141 0.2289 0.2176      5.7927       5.805|
|  6:  2.7884 -  2.6249 0.99   1281  147 0.2411 0.2410      5.7463      5.7406|
|  7:  2.6249 -  2.4941 0.99   1285  137 0.2420 0.2346      5.7438      5.6791|
|  8:  2.4941 -  2.3860 0.98   1267  147 0.2611 0.2539       5.702       5.708|
|  9:  2.3860 -  2.2945 0.98   1274  142 0.2537 0.2594       5.646      5.6476|
| 10:  2.2945 -  2.2155 0.99   1262  135 0.2583 0.3144      5.6199      5.7999|
| 11:  2.2155 -  2.1465 0.99   1273  143 0.2653 0.2628      5.5825      5.6349|
| 12:  2.1465 -  2.0853 0.97   1244  138 0.2627 0.2789      5.5482      5.6057|
| 13:  2.0853 -  2.0305 0.99   1266  139 0.2709 0.2672      5.4558      5.3988|
| 14:  2.0305 -  1.9811 0.66    853   96 0.2807 0.3128      5.4463      5.4359|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7280  1385   154  0.82  23.38   0.88     0.82      34886.98|
|  2:  4.7280 -  3.7724  1340   146  0.88  17.45   1.00     0.94      28871.06|
|  3:  3.7724 -  3.3013  1303   147  0.88  18.63   1.02     1.00      23891.77|
|  4:  3.3013 -  3.0021  1306   147  0.87  19.51   1.03     1.01      20051.75|
|  5:  3.0021 -  2.7884  1291   141  0.84  22.70   1.03     0.99      16344.05|
|  6:  2.7884 -  2.6249  1281   147  0.84  22.61   1.04     1.00      13916.59|
|  7:  2.6249 -  2.4941  1285   137  0.85  21.87   1.04     1.02      12452.82|
|  8:  2.4941 -  2.3860  1267   147  0.82  24.63   1.05     1.02      12467.94|
|  9:  2.3860 -  2.2945  1274   142  0.82  24.89   1.08     1.02      12103.10|
| 10:  2.2945 -  2.2155  1262   135  0.80  26.62   1.09     1.02      12185.69|
| 11:  2.2155 -  2.1465  1273   143  0.80  26.57   1.11     1.05      11115.94|
| 12:  2.1465 -  2.0853  1244   138  0.82  25.38   1.10     1.08      10390.29|
| 13:  2.0853 -  2.0305  1266   139  0.80  27.30   1.10     1.05       9081.94|
| 14:  2.0305 -  1.9811   853    96  0.80  27.28   1.09     0.99       8011.13|
|alpha:            min =        0.82 max =            1.08 mean =         1.00|
|beta:             min =     8011.13 max =        34886.98 mean =     16520.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.97 mean =        23.35|
|phase err.(test): min =        0.00 max =           89.49 mean =        23.12|
|-----------------------------------------------------------------------------|

============================== 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 = 2.614763              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.851   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.403501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.813   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      197 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2012 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1845 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2838 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4659 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4391 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5623 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6766 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.149 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    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: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2395   r_free= 0.2423   ksol= 0.00   Bsol= 0.00   scale= 1.004    |
|                                                                             |
| 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:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.769862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2205   r_free= 0.2236   ksol= 0.32   Bsol= 41.26   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.82,-0.29,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.734297                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.354717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.197480              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.713   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2205      final r-factor (work) = 0.1389          |
| start r-factor (free) = 0.2236      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9627 = 2.35 * 0.50 * 5.7777 + 1.00 * 0.1603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4762 = 2.35 * 0.50 * 5.4534 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1389      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0833 = 0.20 * 1.00 * 5.4534 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0726 = 0.20 * 1.00 * 5.2237 + 1.00 * 0.0410                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.29   16.43    None  None   None       |
|    all(noH): 2823   0      0.00    72.29   16.43    None  None   None       |
|    Sol.    : 438    0      7.26    62.57   37.05    None  None   None       |
|    Mac.    : 2385   0      0.00    72.29   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.230:  281   |   5:    36.147 -  43.377:  119        |
|      1:     7.230 -  14.459: 1515   |   6:    43.377 -  50.606:   80        |
|      2:    14.459 -  21.688:  485   |   7:    50.606 -  57.836:   63        |
|      3:    21.688 -  28.918:  144   |   8:    57.836 -  65.065:   12        |
|      4:    28.918 -  36.147:  123   |   9:    65.065 -  72.294:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1601             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1285 r_free = 0.1599             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1599   ksol= 0.32   Bsol= 41.26   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.82,-0.29,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.228928                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1582   ksol= 0.33   Bsol= 46.03   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.86,-1.54,-0.00,-0.00,-0.00); trace/3= -2.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225932                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.179566              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.324  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247595              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.364   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1490          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7522 = 2.18 * 0.50 * 5.2277 + 1.00 * 0.0552                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6893 = 2.18 * 0.50 * 5.1636 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1490      final r-factor (free) = 0.1491          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3351 = 0.25 * 1.00 * 5.1636 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2725 = 0.25 * 1.00 * 5.1101 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.96    72.56   16.75    None  None   None       |
|    all(noH): 2823   0      1.96    72.56   16.75    None  None   None       |
|    Sol.    : 438    0      5.11    68.69   37.65    None  None   None       |
|    Mac.    : 2385   0      1.96    72.56   12.91    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:     1.961 -   9.021:  696   |   5:    37.262 -  44.322:  115        |
|      1:     9.021 -  16.081: 1255   |   6:    44.322 -  51.383:   93        |
|      2:    16.081 -  23.142:  348   |   7:    51.383 -  58.443:   63        |
|      3:    23.142 -  30.202:  120   |   8:    58.443 -  65.503:   20        |
|      4:    30.202 -  37.262:  108   |   9:    65.503 -  72.563:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1491             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1491             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1491   ksol= 0.33   Bsol= 46.03   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.86,-1.54,-0.00,-0.00,-0.00); trace/3= -2.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109698                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1490   ksol= 0.33   Bsol= 46.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.50,-1.55,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109324                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.248978              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.576  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386422              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.044  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1490      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8092 = 2.25 * 0.50 * 5.1108 + 1.00 * 0.0622                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7970 = 2.25 * 0.50 * 5.1001 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1072      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1512      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9781 = 0.39 * 1.00 * 5.1001 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9792 = 0.39 * 1.00 * 5.1021 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    73.34   16.65    None  None   None       |
|    all(noH): 2823   0      1.22    73.34   16.65    None  None   None       |
|    Sol.    : 438    0      5.41    68.83   37.71    None  None   None       |
|    Mac.    : 2385   0      1.22    73.34   12.79    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:     1.223 -   8.435:  598   |   5:    37.284 -  44.496:  118        |
|      1:     8.435 -  15.647: 1323   |   6:    44.496 -  51.708:   92        |
|      2:    15.647 -  22.859:  369   |   7:    51.708 -  58.920:   62        |
|      3:    22.859 -  30.072:  127   |   8:    58.920 -  66.132:   20        |
|      4:    30.072 -  37.284:  109   |   9:    66.132 -  73.344:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1521             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1066 r_free = 0.1522             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1522   ksol= 0.33   Bsol= 46.03   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.50,-1.55,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105964                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1522   ksol= 0.32   Bsol= 46.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.30,-1.47,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105817                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.373930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.458  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.240270              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.042  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5672 = 1.37 * 0.50 * 5.1024 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5660 = 1.37 * 0.50 * 5.1162 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3532 = 1.24 * 1.00 * 5.1162 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3559 = 1.24 * 1.00 * 5.1174 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    80.22   16.83    None  None   None       |
|    all(noH): 2823   0      0.36    80.22   16.83    None  None   None       |
|    Sol.    : 438    0      6.08    71.17   38.89    None  None   None       |
|    Mac.    : 2385   0      0.36    80.22   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.360 -   8.346:  641   |   5:    40.291 -  48.277:  114        |
|      1:     8.346 -  16.332: 1335   |   6:    48.277 -  56.264:   88        |
|      2:    16.332 -  24.319:  339   |   7:    56.264 -  64.250:   47        |
|      3:    24.319 -  32.305:  132   |   8:    64.250 -  72.236:   16        |
|      4:    32.305 -  40.291:  105   |   9:    72.236 -  80.223:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1545             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1084 r_free = 0.1546             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1546   ksol= 0.32   Bsol= 46.03   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.30,-1.47,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1545   ksol= 0.32   Bsol= 47.35   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.10,-1.31,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.921102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 167.401  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.288314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.079  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9675 = 1.92 * 0.50 * 5.1181 + 1.00 * 0.0514                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9704 = 1.92 * 0.50 * 5.1155 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.8304 = 3.29 * 1.00 * 5.1155 + 1.00 * 0.0089                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.8248 = 3.29 * 1.00 * 5.1135 + 1.00 * 0.0100                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.23   16.93    None  None   None       |
|    all(noH): 2823   0      0.00    95.23   16.93    None  None   None       |
|    Sol.    : 438    0      5.97    84.04   39.77    None  None   None       |
|    Mac.    : 2385   0      0.00    95.23   12.74    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 -   9.523:  992   |   5:    47.614 -  57.136:   95        |
|      1:     9.523 -  19.045: 1164   |   6:    57.136 -  66.659:   57        |
|      2:    19.045 -  28.568:  220   |   7:    66.659 -  76.182:   21        |
|      3:    28.568 -  38.091:  142   |   8:    76.182 -  85.704:    5        |
|      4:    38.091 -  47.614:  122   |   9:    85.704 -  95.227:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1561             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1561             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1561   ksol= 0.32   Bsol= 47.35   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.10,-1.31,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116816                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7280 0.99   1385  154 0.0955 0.1276      5.3531      5.5018|
|  2:  4.7280 -  3.7724 0.99   1340  146 0.0819 0.1061      5.4045      5.5924|
|  3:  3.7724 -  3.3013 0.99   1303  147 0.1007 0.1498      5.4441      5.8558|
|  4:  3.3013 -  3.0021 0.99   1306  147 0.1158 0.1538      5.4346      5.5761|
|  5:  3.0021 -  2.7884 0.99   1291  141 0.1259 0.1780      5.2983      5.5478|
|  6:  2.7884 -  2.6249 0.99   1281  147 0.1141 0.1745      5.1828      5.4234|
|  7:  2.6249 -  2.4941 0.99   1285  137 0.1183 0.1620      5.1303      5.3588|
|  8:  2.4941 -  2.3860 0.98   1267  147 0.1097 0.1715      5.0272      5.3018|
|  9:  2.3860 -  2.2945 0.98   1274  142 0.1112 0.1752      5.0047      5.3225|
| 10:  2.2945 -  2.2155 0.99   1262  135 0.1045 0.1777      4.9304      5.1862|
| 11:  2.2155 -  2.1465 0.99   1273  143 0.1089 0.1777       4.925      5.2882|
| 12:  2.1465 -  2.0853 0.97   1244  138 0.1061 0.1555       4.866      5.1154|
| 13:  2.0853 -  2.0305 0.99   1266  139 0.1083 0.1791      4.7762      5.0911|
| 14:  2.0305 -  1.9811 0.66    853   96 0.1010 0.1715      4.6343      4.9089|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7280  1385   154  0.94   8.80   0.98     0.95       6683.75|
|  2:  4.7280 -  3.7724  1340   146  0.96   7.54   1.02     1.00       8550.32|
|  3:  3.7724 -  3.3013  1303   147  0.94  11.02   1.03     1.02       9937.17|
|  4:  3.3013 -  3.0021  1306   147  0.92  13.54   1.01     0.99      10282.85|
|  5:  3.0021 -  2.7884  1291   141  0.90  15.85   0.99     0.97       8106.65|
|  6:  2.7884 -  2.6249  1281   147  0.91  15.44   0.98     0.96       6920.35|
|  7:  2.6249 -  2.4941  1285   137  0.91  14.84   0.99     0.96       5852.18|
|  8:  2.4941 -  2.3860  1267   147  0.91  14.71   0.99     0.97       5027.77|
|  9:  2.3860 -  2.2945  1274   142  0.91  14.75   1.00     0.97       4775.64|
| 10:  2.2945 -  2.2155  1262   135  0.91  15.04   0.99     0.95       4207.64|
| 11:  2.2155 -  2.1465  1273   143  0.90  16.59   0.99     0.95       4351.14|
| 12:  2.1465 -  2.0853  1244   138  0.92  14.54   1.00     0.98       3920.09|
| 13:  2.0853 -  2.0305  1266   139  0.90  15.88   1.00     0.99       3350.28|
| 14:  2.0305 -  1.9811   853    96  0.92  14.30   0.97     0.93       2419.04|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2419.04 max =        10282.85 mean =      6150.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.70|
|phase err.(test): min =        0.00 max =           89.07 mean =        13.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1560   ksol= 0.32   Bsol= 49.31   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.86,-1.10,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116753                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1560   ksol= 0.32   Bsol= 49.31   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.86,-1.10,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116753                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7280 0.99   1385  154 0.0956 0.1279      5.3541      5.5035|
|  2:  4.7280 -  3.7724 0.99   1340  146 0.0821 0.1062      5.4062      5.5931|
|  3:  3.7724 -  3.3013 0.99   1303  147 0.1007 0.1498      5.4444      5.8556|
|  4:  3.3013 -  3.0021 0.99   1306  147 0.1157 0.1537      5.4339      5.5756|
|  5:  3.0021 -  2.7884 0.99   1291  141 0.1258 0.1777      5.2974      5.5464|
|  6:  2.7884 -  2.6249 0.99   1281  147 0.1139 0.1744       5.182      5.4229|
|  7:  2.6249 -  2.4941 0.99   1285  137 0.1183 0.1619      5.1299      5.3585|
|  8:  2.4941 -  2.3860 0.98   1267  147 0.1097 0.1713       5.027       5.301|
|  9:  2.3860 -  2.2945 0.98   1274  142 0.1112 0.1754      5.0047      5.3232|
| 10:  2.2945 -  2.2155 0.99   1262  135 0.1045 0.1776      4.9305      5.1855|
| 11:  2.2155 -  2.1465 0.99   1273  143 0.1089 0.1777      4.9248       5.288|
| 12:  2.1465 -  2.0853 0.97   1244  138 0.1061 0.1555      4.8657      5.1151|
| 13:  2.0853 -  2.0305 0.99   1266  139 0.1083 0.1790      4.7759      5.0903|
| 14:  2.0305 -  1.9811 0.66    853   96 0.1010 0.1715      4.6341      4.9092|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7280  1385   154  0.94   8.82   0.98     0.95       6701.60|
|  2:  4.7280 -  3.7724  1340   146  0.96   7.56   1.02     1.00       8567.75|
|  3:  3.7724 -  3.3013  1303   147  0.94  11.03   1.03     1.02       9941.54|
|  4:  3.3013 -  3.0021  1306   147  0.92  13.53   1.02     1.00      10267.02|
|  5:  3.0021 -  2.7884  1291   141  0.90  15.84   1.00     0.97       8095.33|
|  6:  2.7884 -  2.6249  1281   147  0.91  15.43   0.99     0.96       6907.83|
|  7:  2.6249 -  2.4941  1285   137  0.91  14.83   1.00     0.97       5845.20|
|  8:  2.4941 -  2.3860  1267   147  0.91  14.70   1.00     0.98       5023.59|
|  9:  2.3860 -  2.2945  1274   142  0.91  14.75   1.01     0.98       4775.49|
| 10:  2.2945 -  2.2155  1262   135  0.91  15.05   1.00     0.96       4207.75|
| 11:  2.2155 -  2.1465  1273   143  0.90  16.58   1.00     0.96       4347.91|
| 12:  2.1465 -  2.0853  1244   138  0.92  14.53   1.01     1.00       3916.53|
| 13:  2.0853 -  2.0305  1266   139  0.90  15.88   1.01     1.00       3347.53|
| 14:  2.0305 -  1.9811   853    96  0.92  14.30   0.98     0.95       2418.75|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2418.75 max =        10267.02 mean =      6148.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.70|
|phase err.(test): min =        0.00 max =           89.17 mean =        13.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.869)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.23   16.94    None  None   None       |
|    all(noH): 2823   0      0.00    95.23   16.94    None  None   None       |
|    Sol.    : 438    0      5.98    84.05   39.78    None  None   None       |
|    Mac.    : 2385   0      0.00    95.23   12.74    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 -   9.526:  992   |   5:    47.617 -  57.139:   95        |
|      1:     9.526 -  19.048: 1164   |   6:    57.139 -  66.662:   57        |
|      2:    19.048 -  28.571:  220   |   7:    66.662 -  76.185:   21        |
|      3:    28.571 -  38.094:  142   |   8:    76.185 -  85.707:    5        |
|      4:    38.094 -  47.617:  122   |   9:    85.707 -  95.230:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 289         
Filter by distance & map next to the model:
   mapped sites are within: 0.590 - 5.464
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 289
   mapped sites are within: 0.747 - 5.464

peak=    5.558 closest distance to " CG  PRO A  54 " =    1.241
peak=    5.340 closest distance to " NH2 ARG A  56 " =    2.214
peak=    5.243 closest distance to " CB  SER A  63 " =    1.203
peak=    5.240 closest distance to " O   HOH Z 126 " =    1.878
peak=    5.198 closest distance to " CB  GLN A 223 " =    1.460
peak=    5.075 closest distance to " CB  ARG A 275 " =    0.899
peak=    4.978 closest distance to " NE2 GLN A  11 " =    1.060
peak=    4.814 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.790 closest distance to " O   HOH Z 142 " =    1.681
peak=    4.727 closest distance to " CB  PRO A  54 " =    0.928
peak=    4.727 closest distance to " O   HOH Z  78 " =    1.700
peak=    4.719 closest distance to " C   PRO A 198 " =    1.512
peak=    4.702 closest distance to " CG  PRO A  90 " =    1.059
peak=    4.687 closest distance to " CA  TYR A  30 " =    0.936
peak=    4.606 closest distance to " O   HOH Z 298 " =    1.918
peak=    4.589 closest distance to " OD1 ASN A  69 " =    2.547
peak=    4.538 closest distance to " O   HOH Z  15 " =    2.221
peak=    4.484 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.466 closest distance to " O   HOH Z 232 " =    2.352
peak=    4.446 closest distance to " O   HOH Z 236 " =    2.046
peak=    4.428 closest distance to " CB  GLU A 128 " =    1.077
peak=    4.384 closest distance to " CB  TYR A 169 " =    0.773
peak=    4.357 closest distance to " CB  GLU A 152 " =    1.197
peak=    4.320 closest distance to " O   HOH Z 193 " =    1.830
peak=    4.290 closest distance to " ND2 ASN A 187 " =    1.388
peak=    4.281 closest distance to " O   HOH Z 369 " =    2.154
peak=    4.231 closest distance to " O   HOH Z 234 " =    3.694
peak=    4.218 closest distance to " O   HOH Z 427 " =    2.933
peak=    4.192 closest distance to " CG  PRO A 198 " =    1.211
peak=    4.188 closest distance to " CB  ASN A 148 " =    1.388
peak=    4.157 closest distance to " O   HOH Z 261 " =    2.180
peak=    4.097 closest distance to " CB  VAL A 265 " =    1.256
peak=    4.071 closest distance to " CB  ARG A  79 " =    1.375
peak=    4.070 closest distance to " O   HOH Z 403 " =    1.710
peak=    4.039 closest distance to " O   HOH Z 203 " =    1.834
peak=    4.016 closest distance to " O   HOH Z 316 " =    3.084
peak=    4.001 closest distance to " NZ  LYS A 117 " =    3.214
peak=    3.995 closest distance to " CG2 VAL A 257 " =    0.906
peak=    3.990 closest distance to " O   HOH Z  40 " =    1.782
peak=    3.987 closest distance to " O   HOH Z 158 " =    3.002
peak=    3.970 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.968 closest distance to " O   HOH Z 344 " =    3.181
peak=    3.964 closest distance to " CB  ARG A 190 " =    1.665
peak=    3.959 closest distance to " CB  TRP A 179 " =    1.345
peak=    3.953 closest distance to " CD2 LEU A 297 " =    0.893
peak=    3.951 closest distance to " O   HOH Z  43 " =    1.841
peak=    3.951 closest distance to " OD2 ASP A 286 " =    2.865
peak=    3.945 closest distance to " O   HOH Z 250 " =    1.491
peak=    3.932 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.929 closest distance to " CA  ASN A 215 " =    1.224
peak=    3.926 closest distance to " O   HOH Z 303 " =    2.062
peak=    3.923 closest distance to " CA  ALA A  21 " =    1.191
peak=    3.922 closest distance to " O   HOH Z 214 " =    2.061
peak=    3.912 closest distance to " CG1 ILE A  33 " =    1.241
peak=    3.911 closest distance to " O   HOH Z 346 " =    1.622
peak=    3.908 closest distance to " CB  SER A   3 " =    1.322
peak=    3.896 closest distance to " CB  VAL A 202 " =    1.570
peak=    3.891 closest distance to " CB  ASP A 140 " =    0.963
peak=    3.869 closest distance to " CG  ARG A  66 " =    2.464
peak=    3.864 closest distance to " CB  GLU A 277 " =    3.604
peak=    3.848 closest distance to " O   HOH Z 368 " =    2.011
peak=    3.848 closest distance to " O   HOH Z 392 " =    3.123
peak=    3.842 closest distance to " O   MET A 105 " =    1.831
peak=    3.830 closest distance to " CE  LYS A  76 " =    0.876
peak=    3.826 closest distance to " CG2 ILE A 120 " =    1.042
peak=    3.810 closest distance to " O   HOH Z 425 " =    1.998
peak=    3.803 closest distance to " CB  SER A 212 " =    1.082
peak=    3.788 closest distance to " CG2 THR A 221 " =    1.103
peak=    3.787 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.778 closest distance to " O   HOH Z  61 " =    1.570
peak=    3.773 closest distance to " O   HOH Z 189 " =    2.207
peak=    3.771 closest distance to " CA  THR A 221 " =    0.996
peak=    3.760 closest distance to " CD1 LEU A 300 " =    1.258
peak=    3.752 closest distance to " O   HOH Z 280 " =    2.964
peak=    3.750 closest distance to " O   HOH Z 402 " =    1.407
peak=    3.750 closest distance to " O   HOH Z 389 " =    1.893
peak=    3.743 closest distance to " O   HOH Z 193 " =    1.704
peak=    3.732 closest distance to " O   HOH Z  10 " =    1.845
peak=    3.730 closest distance to " O   HOH Z 108 " =    2.476
peak=    3.727 closest distance to " O   HOH Z 172 " =    3.578
peak=    3.725 closest distance to " O   HOH Z 132 " =    2.490
peak=    3.712 closest distance to " CZ  PHE A 218 " =    1.037
peak=    3.708 closest distance to " CA  THR A 264 " =    0.841
peak=    3.706 closest distance to " NH1AARG A 145 " =    1.150
peak=    3.696 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.693 closest distance to " OG BSER A 164 " =    2.334
peak=    3.677 closest distance to " O   SER A  87 " =    2.348
peak=    3.664 closest distance to " O   HOH Z  44 " =    1.798
peak=    3.657 closest distance to " O   HOH Z  54 " =    1.713
peak=    3.654 closest distance to " O   HOH Z  59 " =    2.030
peak=    3.649 closest distance to " CD BLYS A 290 " =    1.119
peak=    3.642 closest distance to " ND1 HIS A  81 " =    1.584
peak=    3.633 closest distance to " O   HOH Z  66 " =    2.037
peak=    3.631 closest distance to " O   HOH Z 426 " =    1.572
peak=    3.624 closest distance to " CB  TYR A 169 " =    0.791
peak=    3.622 closest distance to " CD  ARG A 269 " =    0.931
peak=    3.616 closest distance to " O   HOH Z 156 " =    3.369
peak=    3.612 closest distance to " NH2BARG A 145 " =    2.068
peak=    3.604 closest distance to " CA  ALA A 291 " =    0.858
peak=    3.600 closest distance to " CA  MET A  40 " =    1.082
peak=    3.595 closest distance to " CA  ALA A  51 " =    0.931
peak=    3.590 closest distance to " O   HOH Z 209 " =    2.362
peak=    3.576 closest distance to " O   HOH Z   9 " =    2.090
peak=    3.568 closest distance to " CB  SER A 216 " =    0.865
peak=    3.567 closest distance to " O   HOH Z 213 " =    1.716
peak=    3.560 closest distance to " CD2 LEU A 255 " =    1.414
peak=    3.557 closest distance to " O   HOH Z 133 " =    1.542
peak=    3.554 closest distance to " O   HOH Z 193 " =    2.093
peak=    3.554 closest distance to " O   HOH Z   1 " =    1.879
peak=    3.552 closest distance to " O   HOH Z 135 " =    1.657
peak=    3.552 closest distance to " O   HOH Z 180 " =    2.204
peak=    3.544 closest distance to " CB  MET A  47 " =    1.059
peak=    3.542 closest distance to " O   HOH Z 128 " =    2.299
peak=    3.542 closest distance to " O   HOH Z   6 " =    2.230
peak=    3.541 closest distance to " O   HOH Z 368 " =    3.668
peak=    3.538 closest distance to " CA  ARG A  36 " =    1.051
peak=    3.538 closest distance to " O   HOH Z  21 " =    1.734
peak=    3.538 closest distance to " ND2 ASN A 110 " =    1.784
peak=    3.533 closest distance to " CD2 TRP A 179 " =    1.372
peak=    3.532 closest distance to " O   HOH Z 423 " =    1.851
peak=    3.527 closest distance to " O   HOH Z  97 " =    1.937
peak=    3.524 closest distance to " O   HOH Z  61 " =    1.504
peak=    3.517 closest distance to " O   HOH Z 291 " =    1.546
peak=    3.511 closest distance to " O   HOH Z 407 " =    2.589
peak=    3.499 closest distance to " O   HOH Z 133 " =    2.467
peak=    3.495 closest distance to " O   HOH Z 298 " =    2.596
peak=    3.489 closest distance to " O   HOH Z 147 " =    1.762
peak=    3.487 closest distance to " O   HOH Z 185 " =    1.739
peak=    3.486 closest distance to " O   HOH Z 199 " =    1.511
peak=    3.484 closest distance to " CD  ARG A  66 " =    2.435
peak=    3.481 closest distance to " CA  ASP A 140 " =    1.130
peak=    3.478 closest distance to " O   HOH Z  93 " =    2.652
peak=    3.477 closest distance to " CD1 ILE A 106 " =    0.771
peak=    3.475 closest distance to " CG1BVAL A  72 " =    1.542
peak=    3.473 closest distance to " CB  ALA A 291 " =    1.449
peak=    3.469 closest distance to " CB  SER A 141 " =    1.028
peak=    3.467 closest distance to " CA  ARG A 195 " =    1.243
peak=    3.466 closest distance to " O   HOH Z 411 " =    3.832
peak=    3.464 closest distance to " O   HOH Z 329 " =    3.719
peak=    3.464 closest distance to " O   HOH Z 290 " =    0.932
peak=    3.457 closest distance to " NH2 ARG A 156 " =    1.143
peak=    3.454 closest distance to " CG  LEU A 167 " =    1.206
peak=    3.451 closest distance to " O   HOH Z 345 " =    3.414
peak=    3.448 closest distance to " O   HOH Z 209 " =    2.478
peak=    3.443 closest distance to " O   HOH Z 295 " =    1.489
peak=    3.441 closest distance to " O   HOH Z 337 " =    3.761
peak=    3.437 closest distance to " O   HOH Z  64 " =    2.141
peak=    3.437 closest distance to " O   HOH Z  63 " =    2.079
peak=    3.436 closest distance to " O   HOH Z  19 " =    2.482
peak=    3.428 closest distance to " ND1 HIS A  86 " =    1.733
peak=    3.427 closest distance to " O   HOH Z 391 " =    2.910
peak=    3.423 closest distance to " CB  ARG A 139 " =    0.925
peak=    3.418 closest distance to " N   ASN A 127 " =    1.245
peak=    3.413 closest distance to " N   ARG A 156 " =    1.305
peak=    3.412 closest distance to " O   HOH Z 305 " =    3.623
peak=    3.410 closest distance to " O   THR A 251 " =    1.234
peak=    3.409 closest distance to " CA  ALA A 158 " =    1.180
peak=    3.402 closest distance to " O   HOH Z 327 " =    1.731
peak=    3.401 closest distance to " O   GLY A  57 " =    2.664
peak=    3.397 closest distance to " OD1 ASN A 217 " =    1.758
peak=    3.385 closest distance to " O   HOH Z 272 " =    1.806
peak=    3.370 closest distance to " CB  ALA A 248 " =    1.343
peak=    3.363 closest distance to " O   HOH Z  88 " =    3.397
peak=    3.360 closest distance to " CE1 TYR A 186 " =    1.278
peak=    3.355 closest distance to " CD  LYS A 166 " =    1.266
peak=    3.353 closest distance to " O   HOH Z 421 " =    1.773
peak=    3.352 closest distance to " CD  GLU A 152 " =    0.764
peak=    3.351 closest distance to " CB  MET A  40 " =    0.839
peak=    3.350 closest distance to " CB  THR A 157 " =    1.100
peak=    3.350 closest distance to " CB  LEU A 143 " =    1.091
peak=    3.350 closest distance to " OG  SER A  22 " =    2.677
peak=    3.346 closest distance to " O   HOH Z  54 " =    2.421
peak=    3.343 closest distance to " CB  TRP A 179 " =    1.433
peak=    3.342 closest distance to " O   HOH Z 423 " =    2.962
peak=    3.341 closest distance to " CB  LEU A 255 " =    0.783
peak=    3.336 closest distance to " O   HOH Z 406 " =    1.562
peak=    3.336 closest distance to " CB  ASN A 142 " =    1.036
peak=    3.333 closest distance to " O   HOH Z 173 " =    1.812
peak=    3.325 closest distance to " O   HOH Z 175 " =    2.142
peak=    3.323 closest distance to " CB  HIS A 108 " =    0.829
peak=    3.322 closest distance to " CA  ALA A  84 " =    1.332
peak=    3.308 closest distance to " CD  LYS A 119 " =    1.153
peak=    3.308 closest distance to " O   HOH Z 134 " =    1.301
peak=    3.304 closest distance to " O   HOH Z 171 " =    2.070
peak=    3.302 closest distance to " CB  SER A  62 " =    1.241
peak=    3.302 closest distance to " CB  TYR A 116 " =    0.827
peak=    3.298 closest distance to " CG1 ILE A 151 " =    0.941
peak=    3.298 closest distance to " CB  GLN A  88 " =    1.247
peak=    3.297 closest distance to " O   THR A 220 " =    1.325
peak=    3.295 closest distance to " CA  MET A 105 " =    1.015
peak=    3.293 closest distance to " CB  ASN A  39 " =    0.911
peak=    3.292 closest distance to " CG2 VAL A 197 " =    1.108
peak=    3.291 closest distance to " O   HOH Z 234 " =    1.780
peak=    3.289 closest distance to " O   HOH Z 279 " =    2.181
peak=    3.288 closest distance to " CA  LYS A 117 " =    1.201
peak=    3.288 closest distance to " O   HOH Z 148 " =    3.318
peak=    3.286 closest distance to " O   HOH Z 273 " =    2.690
peak=    3.283 closest distance to " CD1 LEU A  96 " =    0.747
peak=    3.277 closest distance to " CB  ALA A   1 " =    4.658
peak=    3.274 closest distance to " CB  PHE A  16 " =    0.998
peak=    3.274 closest distance to " OG  SER A  62 " =    2.932
peak=    3.272 closest distance to " O   HOH Z 211 " =    2.805
peak=    3.272 closest distance to " O   HOH Z  44 " =    3.293
peak=    3.267 closest distance to " CG  MET A 185 " =    1.040
peak=    3.263 closest distance to " O   HOH Z 219 " =    1.995
peak=    3.260 closest distance to " O   HOH Z 281 " =    4.049
peak=    3.251 closest distance to " CA  ALA A  43 " =    1.246
peak=    3.251 closest distance to " O   HOH Z 359 " =    1.378
peak=    3.232 closest distance to " O   HOH Z 435 " =    1.948
peak=    3.232 closest distance to " N   ASN A  39 " =    1.346
peak=    3.230 closest distance to " CB  GLN A  89 " =    1.286
peak=    3.227 closest distance to " CB  ASN A 110 " =    1.172
peak=    3.227 closest distance to " O   HOH Z 437 " =    1.312
peak=    3.223 closest distance to " O   ALA A 165 " =    1.440
peak=    3.221 closest distance to " N   VAL A 126 " =    1.331
peak=    3.218 closest distance to " O   HOH Z 163 " =    1.701
peak=    3.216 closest distance to " CZ2 TRP A 179 " =    1.588
peak=    3.215 closest distance to " O   HOH Z 116 " =    1.741
peak=    3.212 closest distance to " CG2BVAL A  41 " =    0.864
peak=    3.212 closest distance to " O   HOH Z 261 " =    1.449
peak=    3.205 closest distance to " O   HOH Z 366 " =    3.223
peak=    3.202 closest distance to " O   HOH Z 411 " =    1.795
peak=    3.202 closest distance to " O   HOH Z 327 " =    2.164
peak=    3.201 closest distance to " OD1BASN A 224 " =    2.348
peak=    3.200 closest distance to " OG1 THR A 294 " =    2.415
peak=    3.199 closest distance to " CB  ALA A  34 " =    1.068
peak=    3.199 closest distance to " CA  LEU A 101 " =    1.587
peak=    3.195 closest distance to " CB  THR A  31 " =    1.787
peak=    3.187 closest distance to " CG  GLN A  77 " =    2.179
peak=    3.186 closest distance to " O  BHOH Z 338 " =    2.288
peak=    3.185 closest distance to " O   HOH Z 313 " =    1.890
peak=    3.182 closest distance to " O   TRP A 274 " =    1.866
peak=    3.175 closest distance to " O   HOH Z 261 " =    2.119
peak=    3.173 closest distance to " O   HOH Z  49 " =    2.152
peak=    3.170 closest distance to " O   ALA A 158 " =    1.256
peak=    3.167 closest distance to " O   HOH Z 156 " =    2.930
peak=    3.166 closest distance to " CA  GLY A  80 " =    1.077
peak=    3.164 closest distance to " O   HOH Z 144 " =    1.804
peak=    3.161 closest distance to " CD  ARG A 219 " =    1.021
peak=    3.160 closest distance to " CE  LYS A  48 " =    1.044
peak=    3.159 closest distance to " CB  SER A  26 " =    1.623
peak=    3.155 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.153 closest distance to " CG  MET A 113 " =    1.265
peak=    3.153 closest distance to " CD2 HIS A  81 " =    1.087
peak=    3.152 closest distance to " CA  ALA A 233 " =    1.361
peak=    3.152 closest distance to " C   TYR A 214 " =    1.429
peak=    3.151 closest distance to " CA  SER A 146 " =    1.705
peak=    3.151 closest distance to " OD1 ASP A 171 " =    1.236
peak=    3.149 closest distance to " CG  PRO A 213 " =    0.996
peak=    3.149 closest distance to " CB  ASN A 215 " =    1.115
peak=    3.145 closest distance to " O   HOH Z 383 " =    1.794
peak=    3.145 closest distance to " O   HOH Z 419 " =    1.924
peak=    3.145 closest distance to " CB  ILE A 120 " =    1.271
peak=    3.144 closest distance to " O   ALA A   1 " =    1.663
peak=    3.142 closest distance to " N   SER A 135 " =    1.285
peak=    3.138 closest distance to " O   HOH Z 425 " =    1.210
peak=    3.137 closest distance to " CG  LYS A  76 " =    1.011
peak=    3.133 closest distance to " O   HOH Z 430 " =    5.464
peak=    3.125 closest distance to " O   HOH Z 128 " =    2.044
peak=    3.119 closest distance to " O   HOH Z 166 " =    3.826
peak=    3.118 closest distance to " O   HOH Z 409 " =    3.039
peak=    3.118 closest distance to " O   HOH Z 374 " =    2.593
peak=    3.117 closest distance to " CA  ASN A 217 " =    1.251
peak=    3.117 closest distance to " CB  ALA A   9 " =    1.533
peak=    3.116 closest distance to " O   HOH Z 353 " =    2.729
peak=    3.110 closest distance to " O   HOH Z 403 " =    1.305
peak=    3.108 closest distance to " O   HOH Z 112 " =    1.583
peak=    3.103 closest distance to " O   HOH Z 336 " =    1.744
peak=    3.102 closest distance to " OG  SER A 206 " =    1.286
peak=    3.101 closest distance to " CA  ARG A 102 " =    1.091
peak=    3.100 closest distance to " O   HOH Z 227 " =    1.634
peak=    3.099 closest distance to " CB  ASN A 224 " =    1.030
peak=    3.099 closest distance to " O   HOH Z 371 " =    3.455
peak=    3.093 closest distance to " N   GLN A 278 " =    1.114
peak=    3.075 closest distance to " NH1AARG A 145 " =    0.886
peak=    3.072 closest distance to " N   ALA A 154 " =    1.002
peak=    3.071 closest distance to " O   HOH Z  88 " =    2.876
peak=    3.068 closest distance to " CA  ALA A 154 " =    0.948
peak=    3.068 closest distance to " CD1AILE A 234 " =    0.962
peak=    3.066 closest distance to " NZ  LYS A  76 " =    1.321
peak=    3.050 closest distance to " O   HOH Z 201 " =    3.198
peak=    3.043 closest distance to " CB  LYS A 117 " =    1.131
peak=    3.040 closest distance to " O   HOH Z 285 " =    3.002
peak=    3.034 closest distance to " O   HOH Z 357 " =    1.874
peak=    3.013 closest distance to " O   HOH Z 302 " =    1.875

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.820 - 5.573
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.820 - 5.573

peak=   -4.887 closest distance to " O   HOH Z 266 " =    4.795
peak=   -4.519 closest distance to " CD  ARG A 156 " =    2.009
peak=   -4.463 closest distance to " CG  GLN A 223 " =    2.076
peak=   -4.359 closest distance to " O   HOH Z 198 " =    2.091
peak=   -4.342 closest distance to " CB  PRO A 243 " =    2.642
peak=   -4.332 closest distance to " O   VAL A  67 " =    2.710
peak=   -4.288 closest distance to " C   HIS A 108 " =    1.064
peak=   -4.252 closest distance to " O   HOH Z 377 " =    2.045
peak=   -4.215 closest distance to " CB  ALA A 161 " =    2.580
peak=   -4.188 closest distance to " OG BSER A 134 " =    1.187
peak=   -4.130 closest distance to " O   HOH Z 372 " =    2.447
peak=   -4.095 closest distance to " SG  CYS A 254 " =    3.428
peak=   -4.093 closest distance to " CG1 VAL A 112 " =    2.803
peak=   -4.075 closest distance to " O   HOH Z 231 " =    2.255
peak=   -4.059 closest distance to " O   HOH Z 126 " =    1.872
peak=   -3.994 closest distance to " O   HOH Z 389 " =    1.834
peak=   -3.993 closest distance to " N   ALA A  43 " =    2.618
peak=   -3.917 closest distance to " CZ  PHE A  59 " =    1.600
peak=   -3.913 closest distance to " CD  ARG A 139 " =    1.535
peak=   -3.893 closest distance to " O   HOH Z  43 " =    1.600
peak=   -3.892 closest distance to " O   HOH Z 114 " =    3.152
peak=   -3.878 closest distance to " O   HOH Z 435 " =    2.790
peak=   -3.866 closest distance to " N   SER A 212 " =    2.053
peak=   -3.864 closest distance to " CG  ASP A 231 " =    0.820
peak=   -3.863 closest distance to " O   HOH Z 290 " =    1.222
peak=   -3.848 closest distance to " OXT GLY A 302 " =    2.822
peak=   -3.844 closest distance to " CE  MET A 105 " =    2.270
peak=   -3.835 closest distance to " ND2 ASN A  45 " =    1.797
peak=   -3.822 closest distance to " CE2 PHE A 218 " =    2.480
peak=   -3.820 closest distance to " CD1 PHE A  59 " =    1.865
peak=   -3.817 closest distance to " CE2 TYR A  30 " =    2.747
peak=   -3.816 closest distance to " O   HOH Z 353 " =    2.180
peak=   -3.797 closest distance to " CG  PHE A 283 " =    2.763
peak=   -3.796 closest distance to " O   PRO A 163 " =    2.081
peak=   -3.780 closest distance to " O   HOH Z 185 " =    2.265
peak=   -3.767 closest distance to " O   HOH Z  10 " =    1.520
peak=   -3.764 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.753 closest distance to " CD  GLN A  58 " =    1.129
peak=   -3.752 closest distance to " NH2AARG A 275 " =    5.333
peak=   -3.745 closest distance to " ND2 ASN A  45 " =    1.019
peak=   -3.736 closest distance to " CG  ARG A 269 " =    2.367
peak=   -3.724 closest distance to " CG2 ILE A 263 " =    2.283
peak=   -3.704 closest distance to " O   HOH Z  52 " =    1.384
peak=   -3.691 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.691 closest distance to " CB  TYR A  15 " =    2.209
peak=   -3.690 closest distance to " O   HOH Z  13 " =    1.685
peak=   -3.685 closest distance to " NH1 ARG A 195 " =    2.637
peak=   -3.683 closest distance to " CZ3 TRP A 179 " =    1.152
peak=   -3.673 closest distance to " CD1 LEU A 228 " =    2.261
peak=   -3.666 closest distance to " O   HOH Z 196 " =    2.086
peak=   -3.648 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.645 closest distance to " CA  VAL A  67 " =    2.724
peak=   -3.644 closest distance to " OG  SER A  97 " =    2.147
peak=   -3.643 closest distance to " O   HOH Z 292 " =    4.521
peak=   -3.633 closest distance to " OD1 ASN A 187 " =    1.519
peak=   -3.623 closest distance to " O   HOH Z 311 " =    3.656
peak=   -3.580 closest distance to " CD1 LEU A 101 " =    2.385
peak=   -3.570 closest distance to " CD2 PHE A 192 " =    2.073
peak=   -3.561 closest distance to " N   GLN A  58 " =    1.651
peak=   -3.560 closest distance to " OG  SER A  62 " =    1.686
peak=   -3.559 closest distance to " CB  ASN A  39 " =    2.335
peak=   -3.528 closest distance to " C   ASN A 285 " =    2.472
peak=   -3.519 closest distance to " CD2 LEU A 300 " =    2.894
peak=   -3.517 closest distance to " O   SER A 135 " =    1.490
peak=   -3.516 closest distance to " CG1 VAL A 250 " =    2.594
peak=   -3.514 closest distance to " O   HOH Z 407 " =    3.053
peak=   -3.510 closest distance to " CB  ALA A 131 " =    2.086
peak=   -3.506 closest distance to " OE1 GLN A  88 " =    1.204
peak=   -3.499 closest distance to " CZ  TYR A 169 " =    1.740
peak=   -3.489 closest distance to " O   HOH Z 313 " =    1.940
peak=   -3.488 closest distance to " CB  ALA A 291 " =    2.377
peak=   -3.484 closest distance to " CA  GLY A  98 " =    1.963
peak=   -3.483 closest distance to " CA  GLY A 203 " =    2.254
peak=   -3.474 closest distance to " NE2 GLN A  88 " =    1.898
peak=   -3.468 closest distance to " C   ALA A 158 " =    1.312
peak=   -3.460 closest distance to " O   HOH Z 198 " =    1.498
peak=   -3.459 closest distance to " SG ACYS A 201 " =    1.926
peak=   -3.456 closest distance to " O   ARG A 145 " =    1.568
peak=   -3.453 closest distance to " O   HOH Z  93 " =    2.053
peak=   -3.446 closest distance to " N   ALA A 248 " =    1.554
peak=   -3.443 closest distance to " O   HOH Z 351 " =    1.531
peak=   -3.443 closest distance to " OD1 ASN A 148 " =    1.608
peak=   -3.441 closest distance to " CA  GLY A 241 " =    3.080
peak=   -3.438 closest distance to " O   HOH Z 211 " =    1.668
peak=   -3.432 closest distance to " O   HOH Z   6 " =    1.576
peak=   -3.424 closest distance to " O   HOH Z  11 " =    2.174
peak=   -3.422 closest distance to " O   LYS A 117 " =    1.657
peak=   -3.418 closest distance to " CB  PHE A 208 " =    2.252
peak=   -3.414 closest distance to " CB  ALA A  43 " =    2.514
peak=   -3.411 closest distance to " O   PHE A 218 " =    1.590
peak=   -3.409 closest distance to " O   GLY A 211 " =    1.452
peak=   -3.409 closest distance to " O   HOH Z 253 " =    3.915
peak=   -3.403 closest distance to " CG  ARG A  66 " =    2.398
peak=   -3.398 closest distance to " N   THR A 235 " =    1.344
peak=   -3.389 closest distance to " OG BSER A 134 " =    1.757
peak=   -3.387 closest distance to " O   HOH Z 394 " =    1.478
peak=   -3.387 closest distance to " OD2 ASP A 191 " =    1.529
peak=   -3.386 closest distance to " OD1 ASP A 171 " =    1.590
peak=   -3.375 closest distance to " CD  LYS A 289 " =    2.438
peak=   -3.375 closest distance to " O   ALA A 161 " =    1.631
peak=   -3.374 closest distance to " CD  ARG A 195 " =    5.205
peak=   -3.373 closest distance to " CA  GLY A 133 " =    1.997
peak=   -3.361 closest distance to " CD2 PHE A 225 " =    1.176
peak=   -3.352 closest distance to " ND2 ASN A 249 " =    2.123
peak=   -3.352 closest distance to " O   MET A  40 " =    2.675
peak=   -3.351 closest distance to " CG  TRP A 266 " =    1.799
peak=   -3.350 closest distance to " CB  ALA A 248 " =    2.006
peak=   -3.349 closest distance to " O   HOH Z 298 " =    1.256
peak=   -3.349 closest distance to " O   HOH Z  98 " =    2.243
peak=   -3.347 closest distance to " CB  ASP A 286 " =    2.215
peak=   -3.334 closest distance to " C   LEU A 143 " =    1.146
peak=   -3.331 closest distance to " O   HOH Z 111 " =    2.328
peak=   -3.327 closest distance to " O   HOH Z  38 " =    1.543
peak=   -3.325 closest distance to " OG  SER A  26 " =    1.261
peak=   -3.324 closest distance to " CG1 VAL A 125 " =    2.374
peak=   -3.320 closest distance to " NH2 ARG A  79 " =    1.973
peak=   -3.320 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.318 closest distance to " O   HOH Z 166 " =    1.883
peak=   -3.315 closest distance to " OH  TYR A 169 " =    1.000
peak=   -3.314 closest distance to " O   HOH Z 385 " =    2.085
peak=   -3.309 closest distance to " CG  PHE A 283 " =    2.662
peak=   -3.306 closest distance to " N   ALA A 226 " =    2.071
peak=   -3.304 closest distance to " O   HOH Z 361 " =    3.397
peak=   -3.304 closest distance to " O   HOH Z  90 " =    2.860
peak=   -3.303 closest distance to " O   HOH Z 166 " =    1.492
peak=   -3.303 closest distance to " O   HOH Z 102 " =    1.617
peak=   -3.301 closest distance to " O   HOH Z 417 " =    2.517
peak=   -3.298 closest distance to " CG1 VAL A 112 " =    2.585
peak=   -3.286 closest distance to " O   VAL A 189 " =    2.546
peak=   -3.284 closest distance to " OD1 ASP A 191 " =    1.660
peak=   -3.284 closest distance to " C   MET A 188 " =    1.475
peak=   -3.284 closest distance to " OD2 ASP A 171 " =    1.769
peak=   -3.284 closest distance to " CD  GLU A 236 " =    1.048
peak=   -3.281 closest distance to " OD1 ASP A 191 " =    1.545
peak=   -3.279 closest distance to " CG  GLU A   2 " =    1.911
peak=   -3.279 closest distance to " NH2BARG A 275 " =    1.947
peak=   -3.272 closest distance to " OH  TYR A 214 " =    1.259
peak=   -3.271 closest distance to " CB  PRO A 163 " =    2.492
peak=   -3.268 closest distance to " OG1 THR A 178 " =    1.279
peak=   -3.263 closest distance to " O   HOH Z 385 " =    1.995
peak=   -3.258 closest distance to " N   THR A 157 " =    1.522
peak=   -3.257 closest distance to " O   VAL A 174 " =    2.008
peak=   -3.250 closest distance to " O   SER A  95 " =    1.509
peak=   -3.250 closest distance to " O   TRP A  70 " =    1.488
peak=   -3.247 closest distance to " NZ  LYS A 119 " =    3.532
peak=   -3.247 closest distance to " CB  ASP A 286 " =    1.872
peak=   -3.247 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.245 closest distance to " O   HOH Z 317 " =    2.396
peak=   -3.240 closest distance to " O   HOH Z 322 " =    1.602
peak=   -3.240 closest distance to " CE3 TRP A 274 " =    2.370
peak=   -3.238 closest distance to " O   HOH Z  37 " =    1.863
peak=   -3.234 closest distance to " O   HOH Z  19 " =    2.459
peak=   -3.228 closest distance to " CD1 LEU A 297 " =    2.427
peak=   -3.226 closest distance to " C   GLN A 205 " =    1.922
peak=   -3.222 closest distance to " O   HOH Z  11 " =    1.754
peak=   -3.215 closest distance to " ND2 ASN A 187 " =    1.591
peak=   -3.214 closest distance to " CD1 ILE A 239 " =    2.109
peak=   -3.213 closest distance to " CB  TRP A  85 " =    2.361
peak=   -3.204 closest distance to " O   PRO A 198 " =    1.324
peak=   -3.203 closest distance to " CG2 VAL A 189 " =    2.102
peak=   -3.200 closest distance to " O   ALA A  51 " =    1.323
peak=   -3.200 closest distance to " OD2 ASP A 171 " =    2.213
peak=   -3.199 closest distance to " O   HOH Z  88 " =    2.146
peak=   -3.198 closest distance to " N   ALA A   9 " =    1.578
peak=   -3.192 closest distance to " O   HOH Z 148 " =    3.367
peak=   -3.183 closest distance to " NH2 ARG A  66 " =    2.134
peak=   -3.183 closest distance to " NH1 ARG A  36 " =    2.058
peak=   -3.182 closest distance to " OXT GLY A 302 " =    3.343
peak=   -3.172 closest distance to " O   HOH Z 184 " =    1.831
peak=   -3.171 closest distance to " CG  GLU A 277 " =    1.184
peak=   -3.171 closest distance to " O   HOH Z 266 " =    5.110
peak=   -3.170 closest distance to " O   HOH Z 252 " =    4.319
peak=   -3.165 closest distance to " O   HOH Z 191 " =    5.573
peak=   -3.163 closest distance to " O   HOH Z 350 " =    1.785
peak=   -3.162 closest distance to " CE3 TRP A 150 " =    2.063
peak=   -3.160 closest distance to " CD2 TYR A 247 " =    2.524
peak=   -3.151 closest distance to " CD2 PHE A  61 " =    2.586
peak=   -3.145 closest distance to " O   HOH Z  73 " =    2.243
peak=   -3.145 closest distance to " N   ASN A  60 " =    1.436
peak=   -3.138 closest distance to " O   HOH Z  44 " =    2.158
peak=   -3.137 closest distance to " O   HOH Z 396 " =    1.659
peak=   -3.127 closest distance to " O   HOH Z 234 " =    4.120
peak=   -3.125 closest distance to " O   ALA A 292 " =    1.961
peak=   -3.122 closest distance to " N   GLN A  58 " =    1.243
peak=   -3.117 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.117 closest distance to " CG  PHE A  59 " =    2.064
peak=   -3.115 closest distance to " O   HOH Z 281 " =    2.657
peak=   -3.113 closest distance to " O   HOH Z 414 " =    1.633
peak=   -3.112 closest distance to " CG1 VAL A 197 " =    2.248
peak=   -3.110 closest distance to " O   LEU A 167 " =    1.486
peak=   -3.097 closest distance to " CG  ASN A 301 " =    2.016
peak=   -3.093 closest distance to " CA  GLY A 241 " =    2.776
peak=   -3.089 closest distance to " O   GLN A 240 " =    2.428
peak=   -3.089 closest distance to " N   TYR A  68 " =    3.092
peak=   -3.082 closest distance to " CD2 TYR A 293 " =    1.986
peak=   -3.077 closest distance to " CG  ARG A 269 " =    2.044
peak=   -3.076 closest distance to " O   HOH Z 323 " =    1.389
peak=   -3.076 closest distance to " O   HOH Z 139 " =    2.892
peak=   -3.074 closest distance to " O   HOH Z  97 " =    1.711
peak=   -3.072 closest distance to " CD1 TYR A 247 " =    2.707
peak=   -3.067 closest distance to " CB  ASN A  69 " =    1.150
peak=   -3.066 closest distance to " CG2 THR A 221 " =    2.274
peak=   -3.064 closest distance to " O   HOH Z 137 " =    1.454
peak=   -3.044 closest distance to " CD2 LEU A 237 " =    2.542
peak=   -3.040 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.037 closest distance to " OD1 ASP A 200 " =    1.398
peak=   -3.035 closest distance to " O   PRO A 198 " =    1.640

================= 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    :  0.2395 0.2423   5.769862e+00   5.789265e+00
   1_bss:  0.2205 0.2236   5.734297e+00   5.740236e+00
   1_xyz:  0.1389 0.1584   5.280726e+00   5.396747e+00
   1_adp:  0.1290 0.1601   5.231982e+00   5.417600e+00
   1_occ:  0.1285 0.1599   5.228928e+00   5.415105e+00
   2_bss:  0.1284 0.1582   5.225932e+00   5.407490e+00
   2_xyz:  0.1137 0.1490   5.129038e+00   5.343738e+00
   2_adp:  0.1097 0.1491   5.109945e+00   5.340300e+00
   2_occ:  0.1096 0.1491   5.109698e+00   5.340347e+00
   3_bss:  0.1095 0.1490   5.109324e+00   5.339997e+00
   3_xyz:  0.1072 0.1512   5.105447e+00   5.350686e+00
   3_adp:  0.1067 0.1521   5.105654e+00   5.355680e+00
   3_occ:  0.1066 0.1522   5.105964e+00   5.356412e+00
   4_bss:  0.1066 0.1522   5.105817e+00   5.356274e+00
   4_xyz:  0.1090 0.1531   5.121169e+00   5.365077e+00
   4_adp:  0.1085 0.1545   5.123005e+00   5.371847e+00
   4_occ:  0.1084 0.1546   5.123282e+00   5.372354e+00
   5_bss:  0.1083 0.1545   5.123170e+00   5.372193e+00
   5_xyz:  0.1066 0.1552   5.115760e+00   5.373607e+00
   5_adp:  0.1064 0.1561   5.116851e+00   5.377307e+00
   5_occ:  0.1063 0.1561   5.116816e+00   5.377351e+00
   5_bss:  0.1062 0.1560   5.116753e+00   5.377190e+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:  0.316  41.256  -2.570  -2.825  -0.291  -0.000  -0.000  -0.000
   1_xyz:  0.316  41.256  -2.570  -2.825  -0.291  -0.000  -0.000  -0.000
   1_adp:  0.316  41.256  -2.570  -2.825  -0.291  -0.000  -0.000  -0.000
   1_occ:  0.316  41.256  -2.570  -2.825  -0.291  -0.000  -0.000  -0.000
   2_bss:  0.327  46.028  -2.877  -2.864  -1.545  -0.000  -0.000  -0.000
   2_xyz:  0.327  46.028  -2.877  -2.864  -1.545  -0.000  -0.000  -0.000
   2_adp:  0.327  46.028  -2.877  -2.864  -1.545  -0.000  -0.000  -0.000
   2_occ:  0.327  46.028  -2.877  -2.864  -1.545  -0.000  -0.000  -0.000
   3_bss:  0.327  46.028  -2.624  -2.498  -1.552  -0.000  -0.000  -0.000
   3_xyz:  0.327  46.028  -2.624  -2.498  -1.552  -0.000  -0.000  -0.000
   3_adp:  0.327  46.028  -2.624  -2.498  -1.552  -0.000  -0.000  -0.000
   3_occ:  0.327  46.028  -2.624  -2.498  -1.552  -0.000  -0.000  -0.000
   4_bss:  0.323  46.028  -2.444  -2.302  -1.467  -0.000  -0.000  -0.000
   4_xyz:  0.323  46.028  -2.444  -2.302  -1.467  -0.000  -0.000  -0.000
   4_adp:  0.323  46.028  -2.444  -2.302  -1.467  -0.000  -0.000  -0.000
   4_occ:  0.323  46.028  -2.444  -2.302  -1.467  -0.000  -0.000  -0.000
   5_bss:  0.322  47.348  -2.244  -2.097  -1.307  -0.000  -0.000  -0.000
   5_xyz:  0.322  47.348  -2.244  -2.097  -1.307  -0.000  -0.000  -0.000
   5_adp:  0.322  47.348  -2.244  -2.097  -1.307  -0.000  -0.000  -0.000
   5_occ:  0.322  47.348  -2.244  -2.097  -1.307  -0.000  -0.000  -0.000
   5_bss:  0.322  49.308  -1.998  -1.858  -1.095  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  23.326 0.8328  0.9995    16520.012
   1_bss:  21.742 0.8464  0.9511    13301.942
   1_xyz:  13.920 0.9166  0.9919     6568.931
   1_adp:  14.393 0.9125  0.9901     6769.001
   1_occ:  14.343 0.9129  0.9900     6708.825
   2_bss:  14.204 0.9139  0.9718     6586.104
   2_xyz:  13.036 0.9227  0.9756     5821.458
   2_adp:  12.998 0.9230  0.9730     5735.084
   2_occ:  13.000 0.9230  0.9730     5734.603
   3_bss:  12.994 0.9230  0.9801     5733.421
   3_xyz:  13.135 0.9220  0.9789     5857.591
   3_adp:  13.219 0.9214  0.9733     5905.245
   3_occ:  13.234 0.9213  0.9732     5913.798
   4_bss:  13.231 0.9213  0.9786     5911.335
   4_xyz:  13.382 0.9202  0.9779     6009.960
   4_adp:  13.545 0.9189  0.9716     6080.120
   4_occ:  13.556 0.9188  0.9715     6086.195
   5_bss:  13.554 0.9188  0.9781     6084.372
   5_xyz:  13.580 0.9186  0.9780     6111.747
   5_adp:  13.662 0.9179  0.9709     6149.560
   5_occ:  13.665 0.9179  0.9708     6150.695
   5_bss:  13.663 0.9179  0.9792     6149.321
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6030e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6030e-01
   1_xyz:   0.962  0.006  0.069 14.892  0.004  4.112   5.5578e-02
   1_adp:   0.962  0.006  0.069 14.892  0.004  4.112   5.5578e-02
   1_occ:   0.962  0.006  0.069 14.892  0.004  4.112   5.5578e-02
   2_bss:   0.962  0.006  0.069 14.892  0.004  4.112   5.5578e-02
   2_xyz:   1.012  0.008  0.077 14.992  0.004  4.122   6.2167e-02
   2_adp:   1.012  0.008  0.077 14.992  0.004  4.122   6.2167e-02
   2_occ:   1.012  0.008  0.077 14.992  0.004  4.122   6.2167e-02
   3_bss:   1.012  0.008  0.077 14.992  0.004  4.122   6.2167e-02
   3_xyz:   1.007  0.008  0.077 15.006  0.004  4.122   6.2032e-02
   3_adp:   1.007  0.008  0.077 15.006  0.004  4.122   6.2032e-02
   3_occ:   1.007  0.008  0.077 15.006  0.004  4.122   6.2032e-02
   4_bss:   1.007  0.008  0.077 15.006  0.004  4.122   6.2032e-02
   4_xyz:   0.901  0.006  0.070 14.749  0.004  4.121   5.1372e-02
   4_adp:   0.901  0.006  0.070 14.749  0.004  4.121   5.1372e-02
   4_occ:   0.901  0.006  0.070 14.749  0.004  4.121   5.1372e-02
   5_bss:   0.901  0.006  0.070 14.749  0.004  4.121   5.1372e-02
   5_xyz:   0.960  0.007  0.074 14.835  0.004  4.123   5.6686e-02
   5_adp:   0.960  0.007  0.074 14.835  0.004  4.123   5.6686e-02
   5_occ:   0.960  0.007  0.074 14.835  0.004  4.123   5.6686e-02
   5_bss:   0.960  0.007  0.074 14.835  0.004  4.123   5.6686e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4059e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4059e-01
   1_xyz:   7.446  0.031  0.275 85.426  0.033  2.385   8.5877e-02
   1_adp:   7.446  0.031  0.275 85.426  0.033  2.385   8.5877e-02
   1_occ:   7.446  0.031  0.275 85.426  0.033  2.385   8.5877e-02
   2_bss:   7.446  0.031  0.275 85.426  0.033  2.385   8.5877e-02
   2_xyz:   6.752  0.041  0.233 84.400  0.039  2.308   5.5412e-02
   2_adp:   6.752  0.041  0.233 84.400  0.039  2.308   5.5412e-02
   2_occ:   6.752  0.041  0.233 84.400  0.039  2.308   5.5412e-02
   3_bss:   6.752  0.041  0.233 84.400  0.039  2.308   5.5412e-02
   3_xyz:   6.761  0.041  0.246 82.953  0.036  2.305   4.6300e-02
   3_adp:   6.761  0.041  0.246 82.953  0.036  2.305   4.6300e-02
   3_occ:   6.761  0.041  0.246 82.953  0.036  2.305   4.6300e-02
   4_bss:   6.761  0.041  0.246 82.953  0.036  2.305   4.6300e-02
   4_xyz:   6.760  0.039  0.217 83.402  0.035  2.369   3.0790e-02
   4_adp:   6.760  0.039  0.217 83.402  0.035  2.369   3.0790e-02
   4_occ:   6.760  0.039  0.217 83.402  0.035  2.369   3.0790e-02
   5_bss:   6.760  0.039  0.217 83.402  0.035  2.369   3.0790e-02
   5_xyz:   6.719  0.040  0.227 83.100  0.034  2.312   3.7907e-02
   5_adp:   6.719  0.040  0.227 83.100  0.034  2.312   3.7907e-02
   5_occ:   6.719  0.040  0.227 83.100  0.034  2.312   3.7907e-02
   5_bss:   6.719  0.040  0.227 83.100  0.034  2.312   3.7907e-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:  72.29   0.00  16.43  72.29   0.00  12.65  62.57   7.26  37.05
   1_occ:  72.29   0.00  16.43  72.29   0.00  12.65  62.57   7.26  37.05
   2_bss:  72.29   0.00  16.43  72.29   0.00  12.65  62.57   7.26  37.05
   2_xyz:  72.29   0.00  16.43  72.29   0.00  12.65  62.57   7.26  37.05
   2_adp:  72.56   1.96  16.75  72.56   1.96  12.91  68.69   5.11  37.65
   2_occ:  72.56   1.96  16.75  72.56   1.96  12.91  68.69   5.11  37.65
   3_bss:  72.56   1.96  16.75  72.56   1.96  12.91  68.69   5.11  37.65
   3_xyz:  72.56   1.96  16.75  72.56   1.96  12.91  68.69   5.11  37.65
   3_adp:  73.34   1.22  16.65  73.34   1.22  12.79  68.83   5.41  37.71
   3_occ:  73.34   1.22  16.65  73.34   1.22  12.79  68.83   5.41  37.71
   4_bss:  73.34   1.22  16.65  73.34   1.22  12.79  68.83   5.41  37.71
   4_xyz:  73.34   1.22  16.65  73.34   1.22  12.79  68.83   5.41  37.71
   4_adp:  80.22   0.36  16.83  80.22   0.36  12.78  71.17   6.08  38.89
   4_occ:  80.22   0.36  16.83  80.22   0.36  12.78  71.17   6.08  38.89
   5_bss:  80.22   0.36  16.83  80.22   0.36  12.78  71.17   6.08  38.89
   5_xyz:  80.22   0.36  16.83  80.22   0.36  12.78  71.17   6.08  38.89
   5_adp:  95.23   0.00  16.93  95.23   0.00  12.74  84.04   5.97  39.77
   5_occ:  95.23   0.00  16.93  95.23   0.00  12.74  84.04   5.97  39.77
   5_bss:  95.23   0.00  16.94  95.23   0.00  12.74  84.05   5.98  39.78
------------------------------------------------------------------------
 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:    0.845    0.008    0.193
   1_adp:    0.845    0.008    0.193
   1_occ:    0.845    0.008    0.193
   2_bss:    0.845    0.008    0.193
   2_xyz:    0.625    0.006    0.220
   2_adp:    0.625    0.006    0.220
   2_occ:    0.625    0.006    0.220
   3_bss:    0.625    0.006    0.220
   3_xyz:    0.783    0.015    0.234
   3_adp:    0.783    0.015    0.234
   3_occ:    0.783    0.015    0.234
   4_bss:    0.783    0.015    0.234
   4_xyz:    0.838    0.011    0.237
   4_adp:    0.838    0.011    0.237
   4_occ:    0.838    0.011    0.237
   5_bss:    0.838    0.011    0.237
   5_xyz:    0.934    0.013    0.241
   5_adp:    0.934    0.013    0.241
   5_occ:    0.934    0.013    0.241
   5_bss:    0.934    0.013    0.241
------------------------------------------------------------------------

CPU time actual refinement: 320.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_784/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_784/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_784/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_784/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_784/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.18 
  Macro-tasks:
    bulk solvent and scale       = 38.12  
    individual site refinement   = 132.44 
    weights calculation          = 29.32  
    collect and process          = 6.55   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 206.52 
  Micro-tasks:
    mask                            = 0.59   
    f_calc                          = 101.46 
    alpha_beta                      = 7.99   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 110.83 
    fmodel                         = 6.54   
    r_factors                      = 0.21   
    phase_errors                   = 11.51  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 240.59 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.537 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    644 calls, 101.12 s
gradients_fft:          589 calls,  97.23 s

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

# Date 2008-01-16 Time 05:39:07 PST -0800 (1200490747.48 s)
Start R-work = 0.2395, R-free = 0.2423 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.2205, R-free = 0.2236
Final R-work = 0.1062, R-free = 0.1560