# Date 2008-01-16 Time 06:03:42 PST -0800 (1200492222.36 s)
#phil __OFF__

Command line arguments: "../988.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7178
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 988

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.9914, 88.1178, 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: (71.3037, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 1.96405
Completeness in resolution range: 0.920276
Completeness with d_max=infinity: 0.917647

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2391
                             d_min =   1.9641

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2391 1.96405
Completeness in resolution range: 0.920276
Completeness with d_max=infinity: 0.917647

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2395 -  4.2046 [2228/2254]  2005   223  10.0%
  bin  2:  4.2046 -  3.3490 [2161/2181]  1948   213   9.9%
  bin  3:  3.3490 -  2.9290 [2105/2124]  1891   214  10.2%
  bin  4:  2.9290 -  2.6628 [2093/2123]  1878   215  10.3%
  bin  5:  2.6628 -  2.4728 [2105/2124]  1900   205   9.7%
  bin  6:  2.4728 -  2.3275 [2076/2101]  1867   209  10.1%
  bin  7:  2.3275 -  2.2113 [2065/2093]  1855   210  10.2%
  bin  8:  2.2113 -  2.1153 [2053/2089]  1848   205  10.0%
  bin  9:  2.1153 -  2.0341 [2044/2094]  1848   196   9.6%
  bin 10:  2.0341 -  1.9641 [ 659/2103]   590    69  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_988/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: 35
        2.42 -     3.04: 2199
        3.04 -     3.66: 4671
        3.66 -     4.28: 8972
        4.28 -     4.90: 12249
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.985 3.040 -x,y-1/2,-z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.016 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28121 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_988/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_988/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.9914 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4732   r_free= 0.4756   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.285071                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.6905 0.99   1450  161 0.3801 0.3551      6.5862      6.5258|
|  2:  4.6905 -  3.7411 0.99   1390  154 0.4085 0.4060      6.8278      6.7852|
|  3:  3.7411 -  3.2736 0.99   1373  153 0.4337 0.4037      6.6505      6.6523|
|  4:  3.2736 -  2.9767 0.99   1363  154 0.4706 0.5113      6.5258      6.5273|
|  5:  2.9767 -  2.7647 0.99   1350  147 0.5089 0.5016       6.361      6.3952|
|  6:  2.7647 -  2.6026 0.99   1347  152 0.5013 0.5251      6.2645      6.2153|
|  7:  2.6026 -  2.4728 0.99   1349  149 0.5113 0.5057      6.2293      6.1735|
|  8:  2.4728 -  2.3656 0.98   1326  148 0.5326 0.5509      6.1751      6.1581|
|  9:  2.3656 -  2.2748 0.98   1327  147 0.5199 0.5417      6.1273      6.1926|
| 10:  2.2748 -  2.1965 1.00   1333  155 0.5339 0.5322      6.0588      6.0626|
| 11:  2.1965 -  2.1280 0.98   1325  142 0.5147 0.5296      6.0311      6.0522|
| 12:  2.1280 -  2.0674 0.98   1318  141 0.5277 0.5166      5.9307      5.9366|
| 13:  2.0674 -  2.0131 0.84   1123  126 0.5230 0.5189       5.883      5.7988|
| 14:  2.0131 -  1.9641 0.19    256   30 0.5249 0.5559      5.8617      5.9116|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.6905  1450   161  0.74  31.02   0.81     0.78      62321.44|
|  2:  4.6905 -  3.7411  1390   154  0.72  33.95   0.89     0.82     104421.02|
|  3:  3.7411 -  3.2736  1373   153  0.57  46.34   0.91     0.76     118347.79|
|  4:  3.2736 -  2.9767  1363   154  0.45  55.76   0.88     0.63     114404.27|
|  5:  2.9767 -  2.7647  1350   147  0.37  62.09   0.87     0.54      89308.84|
|  6:  2.7647 -  2.6026  1347   152  0.34  64.63   0.88     0.48      76474.68|
|  7:  2.6026 -  2.4728  1349   149  0.33  65.34   0.90     0.46      68188.13|
|  8:  2.4728 -  2.3656  1326   148  0.30  67.59   0.88     0.44      62216.44|
|  9:  2.3656 -  2.2748  1327   147  0.30  67.70   0.91     0.44      59059.50|
| 10:  2.2748 -  2.1965  1333   155  0.28  69.25   0.90     0.43      52510.16|
| 11:  2.1965 -  2.1280  1325   142  0.26  70.79   0.94     0.40      52335.83|
| 12:  2.1280 -  2.0674  1318   141  0.25  71.43   0.89     0.40      46325.18|
| 13:  2.0674 -  2.0131  1123   126  0.26  70.43   0.92     0.44      40223.70|
| 14:  2.0131 -  1.9641   256    30  0.38  61.96   0.96     0.53      29663.46|
|alpha:            min =        0.40 max =            0.82 mean =         0.55|
|beta:             min =    29663.46 max =       118347.79 mean =     72803.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.30|
|phase err.(test): min =        0.00 max =           89.81 mean =        59.67|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.359909             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.824   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.369078              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.728   (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:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       26 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2000 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1856 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2815 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4618 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4354 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5580 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6669 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.304 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4732   r_free= 0.4756   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.285071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4657   r_free= 0.4720   ksol= 0.33   Bsol= 57.42   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,1.02,2.39,0.00,0.00,0.00); trace/3= 0.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.281807                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.431293              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.697   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.472859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.325   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4657      final r-factor (work) = 0.3757          |
| start r-factor (free) = 0.4720      final r-factor (free) = 0.4113          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6250 = 8.43 * 0.50 * 6.2750 + 1.00 * 0.1719                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2009 = 8.43 * 0.50 * 6.1870 + 1.00 * 0.1186                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3757      final r-factor (work) = 0.3412          |
| start r-factor (free) = 0.4113      final r-factor (free) = 0.4273          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1187 = 1.47 * 1.00 * 6.1870 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9963 = 1.47 * 1.00 * 6.0931 + 1.00 * 0.0221                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.61   19.96    None  None   None       |
|    all(noH): 2823   0      0.00    99.61   19.96    None  None   None       |
|    Sol.    : 438    0      0.00    99.61   39.24    None  None   None       |
|    Mac.    : 2385   0      0.00    69.50   16.41    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 -   9.961:  852   |   5:    49.803 -  59.763:  106        |
|      1:     9.961 -  19.921:  831   |   6:    59.763 -  69.724:   50        |
|      2:    19.921 -  29.882:  548   |   7:    69.724 -  79.685:   21        |
|      3:    29.882 -  39.842:  278   |   8:    79.685 -  89.645:    4        |
|      4:    39.842 -  49.803:  132   |   9:    89.645 -  99.606:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3412 r_free = 0.4273             target_work(ml) = 6.102         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3408 r_free = 0.4284             target_work(ml) = 6.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3408   r_free= 0.4284   ksol= 0.33   Bsol= 57.42   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,1.02,2.39,0.00,0.00,0.00); trace/3= 0.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.102194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3414   r_free= 0.4266   ksol= 0.36   Bsol= 85.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.21,1.54,-0.00,0.00,0.00); trace/3= 0.18                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.104499                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.306917              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.499   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.572885              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.474  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3414      final r-factor (work) = 0.2834          |
| start r-factor (free) = 0.4266      final r-factor (free) = 0.3637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3369 = 6.31 * 0.50 * 6.0944 + 1.00 * 0.1184                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1338 = 6.31 * 0.50 * 6.0424 + 1.00 * 0.0793                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2834      final r-factor (work) = 0.2716          |
| start r-factor (free) = 0.3637      final r-factor (free) = 0.3489          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4835 = 0.57 * 1.00 * 6.0424 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4193 = 0.57 * 1.00 * 5.9453 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.97   19.38    None  None   None       |
|    all(noH): 2823   0      0.00    98.97   19.38    None  None   None       |
|    Sol.    : 438    0      0.00    98.97   39.85    None  None   None       |
|    Mac.    : 2385   0      0.00    72.44   15.62    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 -   9.897:  836   |   5:    49.483 -  59.380:   92        |
|      1:     9.897 -  19.793:  967   |   6:    59.380 -  69.277:   48        |
|      2:    19.793 -  29.690:  476   |   7:    69.277 -  79.173:   20        |
|      3:    29.690 -  39.587:  251   |   8:    79.173 -  89.070:    2        |
|      4:    39.587 -  49.483:  130   |   9:    89.070 -  98.967:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2716 r_free = 0.3489             target_work(ml) = 5.930         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2715 r_free = 0.3488             target_work(ml) = 5.929         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2715   r_free= 0.3488   ksol= 0.36   Bsol= 85.78   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.21,1.54,-0.00,0.00,0.00); trace/3= 0.18                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.929366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2719   r_free= 0.3488   ksol= 0.35   Bsol= 78.44   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.97,0.59,-0.00,0.00,0.00); trace/3= -0.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.929685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.875650              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.412   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.965104              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.022  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2719      final r-factor (work) = 0.2193          |
| start r-factor (free) = 0.3488      final r-factor (free) = 0.2877          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6010 = 3.88 * 0.50 * 5.9457 + 1.00 * 0.0793                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3912 = 3.88 * 0.50 * 5.8468 + 1.00 * 0.0610                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2193      final r-factor (work) = 0.2008          |
| start r-factor (free) = 0.2877      final r-factor (free) = 0.2787          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.0434 = 4.97 * 1.00 * 5.8468 + 1.00 * 0.0133                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.3474 = 4.97 * 1.00 * 5.7049 + 1.00 * 0.0218                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.31  20.96    None  None   None       |
|    all(noH): 2823   0      0.00    124.31  20.96    None  None   None       |
|    Sol.    : 438    0      3.53    124.31  51.77    None  None   None       |
|    Mac.    : 2385   0      0.00    104.32  15.30    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 -  12.431: 1257   |   5:    62.154 -  74.585:   88        |
|      1:    12.431 -  24.862:  853   |   6:    74.585 -  87.016:   49        |
|      2:    24.862 -  37.293:  264   |   7:    87.016 -  99.447:   25        |
|      3:    37.293 -  49.723:  155   |   8:    99.447 - 111.878:   15        |
|      4:    49.723 -  62.154:  115   |   9:   111.878 - 124.308:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2008 r_free = 0.2787             target_work(ml) = 5.692         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2007 r_free = 0.2787             target_work(ml) = 5.691         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2007   r_free= 0.2787   ksol= 0.35   Bsol= 78.44   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.97,0.59,-0.00,0.00,0.00); trace/3= -0.53                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.691275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2009   r_free= 0.2788   ksol= 0.35   Bsol= 96.57   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-1.84,-0.01,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.691091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.293946              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.901   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.332  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2009      final r-factor (work) = 0.1647          |
| start r-factor (free) = 0.2788      final r-factor (free) = 0.2316          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3137 = 4.29 * 0.50 * 5.7069 + 1.00 * 0.0610                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1133 = 4.29 * 0.50 * 5.6125 + 1.00 * 0.0635                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1647      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2316      final r-factor (free) = 0.2080          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4531 = 0.43 * 1.00 * 5.6125 + 1.00 * 0.0216                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3871 = 0.43 * 1.00 * 5.4799 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.38    115.11  19.14    None  None   None       |
|    all(noH): 2823   0      0.38    115.11  19.14    None  None   None       |
|    Sol.    : 438    0      5.50    115.11  48.79    None  None   None       |
|    Mac.    : 2385   0      0.38    100.78  13.69    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:     0.379 -  11.852: 1357   |   5:    57.746 -  69.220:   83        |
|      1:    11.852 -  23.326:  845   |   6:    69.220 -  80.693:   48        |
|      2:    23.326 -  34.799:  211   |   7:    80.693 -  92.167:   29        |
|      3:    34.799 -  46.273:  129   |   8:    92.167 - 103.640:   13        |
|      4:    46.273 -  57.746:  106   |   9:   103.640 - 115.114:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1518 r_free = 0.2080             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1516 r_free = 0.2078             target_work(ml) = 5.419         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1516   r_free= 0.2078   ksol= 0.35   Bsol= 96.57   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-1.84,-0.01,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.418656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1519   r_free= 0.2077   ksol= 0.33   Bsol= 80.29   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-2.36,-0.37,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.417353                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.888945              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.823  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.335067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.945  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1519      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2077      final r-factor (free) = 0.1906          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2392 = 1.89 * 0.50 * 5.4800 + 1.00 * 0.0635                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1324 = 1.89 * 0.50 * 5.3825 + 1.00 * 0.0488                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.1906      final r-factor (free) = 0.1861          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8165 = 0.34 * 1.00 * 5.3825 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7955 = 0.34 * 1.00 * 5.3244 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.82    109.72  18.54    None  None   None       |
|    all(noH): 2823   0      0.82    109.72  18.54    None  None   None       |
|    Sol.    : 438    0      5.94    109.72  47.18    None  None   None       |
|    Mac.    : 2385   0      0.82    101.15  13.29    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:     0.823 -  11.713: 1362   |   5:    55.272 -  66.162:   83        |
|      1:    11.713 -  22.603:  865   |   6:    66.162 -  77.052:   52        |
|      2:    22.603 -  33.493:  206   |   7:    77.052 -  87.942:   32        |
|      3:    33.493 -  44.383:  106   |   8:    87.942 -  98.832:   12        |
|      4:    44.383 -  55.272:  101   |   9:    98.832 - 109.722:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1357 r_free = 0.1861             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1356 r_free = 0.1860             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1860   ksol= 0.33   Bsol= 80.29   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-2.36,-0.37,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.311520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.6905 0.99   1450  161 0.0991 0.1404      5.4072      5.6322|
|  2:  4.6905 -  3.7411 0.99   1390  154 0.0920 0.1300      5.5164      5.7608|
|  3:  3.7411 -  3.2736 0.99   1373  153 0.1256 0.1754      5.6049      5.8943|
|  4:  3.2736 -  2.9767 0.99   1363  154 0.1568 0.2037      5.6344      5.7795|
|  5:  2.9767 -  2.7647 0.99   1350  147 0.1651 0.2135      5.5128      5.7385|
|  6:  2.7647 -  2.6026 0.99   1347  152 0.1584 0.2330      5.3909      5.6147|
|  7:  2.6026 -  2.4728 0.99   1349  149 0.1547 0.1898      5.3397      5.4677|
|  8:  2.4728 -  2.3656 0.98   1326  148 0.1521 0.2105      5.2624      5.5159|
|  9:  2.3656 -  2.2748 0.98   1327  147 0.1534 0.2117      5.2273      5.4566|
| 10:  2.2748 -  2.1965 1.00   1333  155 0.1403 0.1939      5.0992      5.3087|
| 11:  2.1965 -  2.1280 0.98   1325  142 0.1382 0.2031       5.092      5.4121|
| 12:  2.1280 -  2.0674 0.98   1318  141 0.1456 0.2192      5.0387      5.2752|
| 13:  2.0674 -  2.0131 0.84   1123  126 0.1353 0.1831      4.9208      5.0728|
| 14:  2.0131 -  1.9641 0.19    256   30 0.1192 0.1764      4.7881      5.0748|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.6905  1450   161  0.94   9.64   0.96     0.93       7850.93|
|  2:  4.6905 -  3.7411  1390   154  0.95   8.98   1.02     1.01      10615.22|
|  3:  3.7411 -  3.2736  1373   153  0.91  13.87   1.04     1.04      13421.84|
|  4:  3.2736 -  2.9767  1363   154  0.88  17.94   1.02     1.00      14686.22|
|  5:  2.9767 -  2.7647  1350   147  0.87  19.41   1.01     0.98      12057.43|
|  6:  2.7647 -  2.6026  1347   152  0.86  20.17   0.99     0.96       9893.53|
|  7:  2.6026 -  2.4728  1349   149  0.87  19.09   1.01     0.97       8846.10|
|  8:  2.4728 -  2.3656  1326   148  0.87  19.55   1.01     0.99       7653.55|
|  9:  2.3656 -  2.2748  1327   147  0.87  19.51   1.01     0.95       6999.23|
| 10:  2.2748 -  2.1965  1333   155  0.88  18.64   1.01     0.98       5762.69|
| 11:  2.1965 -  2.1280  1325   142  0.88  19.08   1.01     0.95       5778.84|
| 12:  2.1280 -  2.0674  1318   141  0.87  19.44   1.00     1.00       5407.63|
| 13:  2.0674 -  2.0131  1123   126  0.87  20.03   1.00     0.98       4508.21|
| 14:  2.0131 -  1.9641   256    30  0.92  14.86   1.00     0.98       3162.62|
|alpha:            min =        0.93 max =            1.04 mean =         0.98|
|beta:             min =     3162.62 max =        14686.22 mean =      8729.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        17.18|
|phase err.(test): min =        0.00 max =           89.93 mean =        16.68|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1859   ksol= 0.32   Bsol= 70.57   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.65,-0.54,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.311087                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1859   ksol= 0.32   Bsol= 70.57   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.65,-0.54,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.311087                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2395 -  4.6905 0.99   1450  161 0.0988 0.1394      5.4044      5.6267|
|  2:  4.6905 -  3.7411 0.99   1390  154 0.0916 0.1297      5.5131      5.7574|
|  3:  3.7411 -  3.2736 0.99   1373  153 0.1254 0.1753      5.6034       5.893|
|  4:  3.2736 -  2.9767 0.99   1363  154 0.1570 0.2039       5.635        5.78|
|  5:  2.9767 -  2.7647 0.99   1350  147 0.1654 0.2136      5.5136      5.7395|
|  6:  2.7647 -  2.6026 0.99   1347  152 0.1585 0.2331      5.3912      5.6145|
|  7:  2.6026 -  2.4728 0.99   1349  149 0.1548 0.1898      5.3401       5.468|
|  8:  2.4728 -  2.3656 0.98   1326  148 0.1522 0.2110       5.263      5.5177|
|  9:  2.3656 -  2.2748 0.98   1327  147 0.1533 0.2114      5.2273      5.4554|
| 10:  2.2748 -  2.1965 1.00   1333  155 0.1404 0.1940      5.0994      5.3098|
| 11:  2.1965 -  2.1280 0.98   1325  142 0.1381 0.2035      5.0916      5.4128|
| 12:  2.1280 -  2.0674 0.98   1318  141 0.1456 0.2192       5.039       5.275|
| 13:  2.0674 -  2.0131 0.84   1123  126 0.1353 0.1825      4.9204      5.0719|
| 14:  2.0131 -  1.9641 0.19    256   30 0.1193 0.1761      4.7874      5.0731|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2395 -  4.6905  1450   161  0.94   9.61   0.96     0.93       7802.61|
|  2:  4.6905 -  3.7411  1390   154  0.95   8.94   1.02     1.00      10551.99|
|  3:  3.7411 -  3.2736  1373   153  0.92  13.83   1.04     1.04      13353.67|
|  4:  3.2736 -  2.9767  1363   154  0.88  17.92   1.02     0.99      14660.81|
|  5:  2.9767 -  2.7647  1350   147  0.87  19.41   1.00     0.98      12056.47|
|  6:  2.7647 -  2.6026  1347   152  0.86  20.17   0.99     0.95       9897.33|
|  7:  2.6026 -  2.4728  1349   149  0.88  19.09   1.00     0.96       8853.15|
|  8:  2.4728 -  2.3656  1326   148  0.87  19.56   1.00     0.98       7662.98|
|  9:  2.3656 -  2.2748  1327   147  0.87  19.52   1.00     0.94       7004.51|
| 10:  2.2748 -  2.1965  1333   155  0.88  18.64   1.00     0.97       5767.06|
| 11:  2.1965 -  2.1280  1325   142  0.88  19.09   0.99     0.94       5785.63|
| 12:  2.1280 -  2.0674  1318   141  0.87  19.44   0.99     0.98       5410.26|
| 13:  2.0674 -  2.0131  1123   126  0.87  20.01   0.99     0.97       4504.32|
| 14:  2.0131 -  1.9641   256    30  0.92  14.81   0.99     0.96       3151.67|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3151.67 max =        14660.81 mean =      8715.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        17.17|
|phase err.(test): min =        0.00 max =           89.94 mean =        16.67|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.001)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.80    109.69  18.52    None  None   None       |
|    all(noH): 2823   0      0.80    109.69  18.52    None  None   None       |
|    Sol.    : 438    0      5.91    109.69  47.15    None  None   None       |
|    Mac.    : 2385   0      0.80    101.12  13.26    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:     0.795 -  11.685: 1362   |   5:    55.245 -  66.134:   83        |
|      1:    11.685 -  22.575:  865   |   6:    66.134 -  77.024:   52        |
|      2:    22.575 -  33.465:  206   |   7:    77.024 -  87.914:   32        |
|      3:    33.465 -  44.355:  106   |   8:    87.914 -  98.804:   12        |
|      4:    44.355 -  55.245:  101   |   9:    98.804 - 109.694:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.656 - 4.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 348
   mapped sites are within: 0.740 - 4.819

peak=    7.005 closest distance to " O   HOH Z 103 " =    1.058
peak=    6.435 closest distance to " O   HOH Z 245 " =    1.252
peak=    5.267 closest distance to " CG  PRO A  90 " =    1.409
peak=    5.240 closest distance to " O   HOH Z 222 " =    1.378
peak=    5.087 closest distance to " O   HOH Z 417 " =    2.215
peak=    5.039 closest distance to " CG  PRO A  54 " =    1.528
peak=    4.970 closest distance to " OE1 GLN A  73 " =    2.119
peak=    4.882 closest distance to " O   HOH Z  63 " =    1.698
peak=    4.784 closest distance to " CB  SER A  63 " =    1.404
peak=    4.723 closest distance to " O   HOH Z 287 " =    2.183
peak=    4.707 closest distance to " CB  SER A 216 " =    1.120
peak=    4.707 closest distance to " O   HOH Z 126 " =    2.088
peak=    4.679 closest distance to " CB  GLN A 223 " =    1.550
peak=    4.661 closest distance to " NE2 GLN A  11 " =    1.251
peak=    4.653 closest distance to " CB  PRO A  54 " =    1.220
peak=    4.638 closest distance to " O   HOH Z   7 " =    1.833
peak=    4.589 closest distance to " O   HOH Z 130 " =    0.993
peak=    4.564 closest distance to " O   HOH Z 403 " =    1.508
peak=    4.559 closest distance to " CB  ASN A 148 " =    1.392
peak=    4.547 closest distance to " CG  PRO A 198 " =    1.293
peak=    4.538 closest distance to " O   HOH Z  49 " =    1.500
peak=    4.478 closest distance to " O   HOH Z 105 " =    1.205
peak=    4.477 closest distance to " O   HOH Z  46 " =    1.162
peak=    4.464 closest distance to " O   PRO A 198 " =    1.339
peak=    4.445 closest distance to " O   HOH Z 232 " =    2.099
peak=    4.387 closest distance to " O   HOH Z  65 " =    1.194
peak=    4.381 closest distance to " O   HOH Z  66 " =    1.123
peak=    4.352 closest distance to " O   HOH Z  11 " =    1.180
peak=    4.328 closest distance to " O   HOH Z  39 " =    1.137
peak=    4.327 closest distance to " O   TYR A 116 " =    1.285
peak=    4.318 closest distance to " O   HOH Z 139 " =    1.251
peak=    4.313 closest distance to " CB  PRO A  90 " =    1.158
peak=    4.311 closest distance to " CE3 TRP A 274 " =    1.460
peak=    4.286 closest distance to " NH1AARG A 145 " =    1.220
peak=    4.271 closest distance to " O   HOH Z 423 " =    2.170
peak=    4.261 closest distance to " CG2 ILE A 120 " =    1.261
peak=    4.260 closest distance to " O   HOH Z 427 " =    2.256
peak=    4.237 closest distance to " O   HOH Z 295 " =    1.314
peak=    4.235 closest distance to " O   HOH Z 425 " =    1.603
peak=    4.206 closest distance to " O   HOH Z 375 " =    1.116
peak=    4.172 closest distance to " O   HOH Z 316 " =    3.083
peak=    4.143 closest distance to " CB  ALA A 114 " =    0.939
peak=    4.142 closest distance to " CB  SER A   3 " =    1.547
peak=    4.124 closest distance to " CB  LYS A 290 " =    0.927
peak=    4.112 closest distance to " O   HOH Z 419 " =    2.066
peak=    4.111 closest distance to " CZ  PHE A 218 " =    1.166
peak=    4.084 closest distance to " CB  ASP A 124 " =    0.922
peak=    4.083 closest distance to " CZ3 TRP A 266 " =    1.143
peak=    4.075 closest distance to " O   HOH Z 293 " =    1.498
peak=    4.067 closest distance to " O   HOH Z  69 " =    1.461
peak=    4.059 closest distance to " NZ ALYS A 290 " =    1.013
peak=    4.057 closest distance to " CB  SER A 210 " =    1.030
peak=    4.048 closest distance to " O   HOH Z  61 " =    1.838
peak=    4.042 closest distance to " O   HOH Z 201 " =    1.984
peak=    4.035 closest distance to " O   HOH Z   9 " =    1.794
peak=    4.028 closest distance to " O   HOH Z 380 " =    1.863
peak=    4.022 closest distance to " O   HOH Z 437 " =    1.820
peak=    4.019 closest distance to " N   GLN A 278 " =    1.033
peak=    4.010 closest distance to " O   HOH Z 369 " =    2.054
peak=    4.006 closest distance to " O   HOH Z 298 " =    2.126
peak=    4.004 closest distance to " CG2 THR A 221 " =    1.343
peak=    4.003 closest distance to " CG  LEU A 167 " =    1.307
peak=    3.978 closest distance to " CA  TYR A  30 " =    1.165
peak=    3.968 closest distance to " O   HOH Z 296 " =    1.254
peak=    3.967 closest distance to " O   HOH Z 361 " =    1.447
peak=    3.961 closest distance to " O   HOH Z  97 " =    1.422
peak=    3.951 closest distance to " CA  ALA A  51 " =    1.012
peak=    3.949 closest distance to " NE2 HIS A 207 " =    0.991
peak=    3.926 closest distance to " ND2BASN A 224 " =    0.850
peak=    3.919 closest distance to " CA  ARG A 195 " =    1.462
peak=    3.911 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.884 closest distance to " CD  ARG A 159 " =    0.861
peak=    3.881 closest distance to " O   HOH Z 158 " =    1.162
peak=    3.870 closest distance to " O   HOH Z 414 " =    1.366
peak=    3.857 closest distance to " CB  TYR A  30 " =    1.302
peak=    3.856 closest distance to " CA  VAL A 125 " =    1.165
peak=    3.855 closest distance to " CB  GLU A 128 " =    1.002
peak=    3.830 closest distance to " O   HOH Z 145 " =    1.917
peak=    3.820 closest distance to " CB  MET A  40 " =    0.839
peak=    3.807 closest distance to " O   HOH Z 126 " =    1.509
peak=    3.804 closest distance to " CA  ALA A 160 " =    1.164
peak=    3.803 closest distance to " OE1 GLN A  77 " =    1.239
peak=    3.802 closest distance to " O   HOH Z 422 " =    0.987
peak=    3.802 closest distance to " CB  SER A  62 " =    1.049
peak=    3.797 closest distance to " O   HOH Z 147 " =    1.082
peak=    3.791 closest distance to " O   ASN A 209 " =    1.687
peak=    3.788 closest distance to " CB  VAL A 202 " =    1.551
peak=    3.768 closest distance to " NZ  LYS A 119 " =    2.299
peak=    3.766 closest distance to " CB  ASN A 187 " =    1.046
peak=    3.762 closest distance to " CG  LYS A  76 " =    1.752
peak=    3.756 closest distance to " OE1 GLN A 240 " =    1.622
peak=    3.756 closest distance to " O   HOH Z 211 " =    1.453
peak=    3.752 closest distance to " CG  PRO A 243 " =    1.212
peak=    3.751 closest distance to " NZ  LYS A 166 " =    0.993
peak=    3.747 closest distance to " CB  MET A  47 " =    1.030
peak=    3.742 closest distance to " ND2 ASN A  60 " =    2.873
peak=    3.742 closest distance to " NH2AARG A 190 " =    1.886
peak=    3.725 closest distance to " O   HOH Z 385 " =    0.955
peak=    3.721 closest distance to " O   HOH Z  78 " =    1.725
peak=    3.704 closest distance to " CZ  PHE A  38 " =    1.303
peak=    3.689 closest distance to " CB  ARG A 275 " =    1.115
peak=    3.689 closest distance to " N   TYR A  15 " =    1.108
peak=    3.686 closest distance to " O   THR A 294 " =    1.000
peak=    3.682 closest distance to " O   HOH Z 117 " =    0.844
peak=    3.675 closest distance to " O   HOH Z 427 " =    1.186
peak=    3.671 closest distance to " CB  ALA A  10 " =    0.985
peak=    3.665 closest distance to " O  BHOH Z  74 " =    1.143
peak=    3.664 closest distance to " O   HOH Z 218 " =    1.595
peak=    3.662 closest distance to " CA  ALA A   7 " =    1.009
peak=    3.658 closest distance to " O   HOH Z  91 " =    2.347
peak=    3.657 closest distance to " O   HOH Z 359 " =    1.368
peak=    3.652 closest distance to " O   HOH Z  88 " =    4.026
peak=    3.649 closest distance to " N   VAL A 296 " =    1.810
peak=    3.648 closest distance to " O   HOH Z 278 " =    1.124
peak=    3.647 closest distance to " O   HOH Z 225 " =    1.726
peak=    3.636 closest distance to " O   HOH Z 389 " =    1.871
peak=    3.635 closest distance to " O   HOH Z 193 " =    1.496
peak=    3.635 closest distance to " OE2 GLU A  53 " =    1.206
peak=    3.634 closest distance to " O   HOH Z 393 " =    1.407
peak=    3.633 closest distance to " NZ  LYS A 117 " =    3.169
peak=    3.631 closest distance to " O   HOH Z  58 " =    1.884
peak=    3.624 closest distance to " CG2 VAL A 257 " =    0.960
peak=    3.621 closest distance to " CE  MET A  93 " =    1.414
peak=    3.615 closest distance to " CG  PRO A 213 " =    1.349
peak=    3.612 closest distance to " O   HOH Z 327 " =    1.800
peak=    3.610 closest distance to " N   CYS A 260 " =    0.932
peak=    3.609 closest distance to " CB  SER A 276 " =    1.196
peak=    3.596 closest distance to " O   HOH Z 411 " =    3.313
peak=    3.584 closest distance to " OG  SER A  26 " =    1.612
peak=    3.576 closest distance to " O   HOH Z  40 " =    2.102
peak=    3.571 closest distance to " CG  GLU A 277 " =    1.897
peak=    3.566 closest distance to " O   HOH Z  59 " =    1.725
peak=    3.565 closest distance to " O   HOH Z 132 " =    1.048
peak=    3.562 closest distance to " CA  ILE A 234 " =    1.131
peak=    3.557 closest distance to " O   HOH Z 394 " =    1.793
peak=    3.555 closest distance to " O   HOH Z 127 " =    1.071
peak=    3.553 closest distance to " CB  TRP A 266 " =    1.026
peak=    3.552 closest distance to " CG2BVAL A  41 " =    1.113
peak=    3.550 closest distance to " CB  GLN A  89 " =    1.247
peak=    3.550 closest distance to " CE3 TRP A 150 " =    1.203
peak=    3.549 closest distance to " CD  ARG A 195 " =    3.496
peak=    3.548 closest distance to " O   HOH Z 287 " =    2.090
peak=    3.542 closest distance to " O   HOH Z 167 " =    1.761
peak=    3.541 closest distance to " CB  PHE A  61 " =    1.217
peak=    3.539 closest distance to " CB  ARG A  79 " =    1.092
peak=    3.538 closest distance to " O   HOH Z 390 " =    1.341
peak=    3.537 closest distance to " O   HOH Z 111 " =    1.903
peak=    3.537 closest distance to " CB  VAL A 265 " =    1.324
peak=    3.533 closest distance to " CB  TRP A 179 " =    1.462
peak=    3.530 closest distance to " O   HOH Z 431 " =    1.193
peak=    3.529 closest distance to " N   SER A 271 " =    0.991
peak=    3.528 closest distance to " CA  ASN A 127 " =    1.226
peak=    3.522 closest distance to " CD1AILE A 234 " =    1.011
peak=    3.520 closest distance to " O   HOH Z 272 " =    1.868
peak=    3.517 closest distance to " CB  ALA A  43 " =    0.871
peak=    3.514 closest distance to " O   HOH Z  88 " =    3.542
peak=    3.513 closest distance to " CD BLYS A 290 " =    1.117
peak=    3.511 closest distance to " O   HOH Z 434 " =    1.659
peak=    3.510 closest distance to " O   HOH Z  30 " =    1.857
peak=    3.510 closest distance to " CA  SER A  95 " =    0.974
peak=    3.506 closest distance to " CA  GLU A 152 " =    1.110
peak=    3.495 closest distance to " O   HOH Z 171 " =    2.566
peak=    3.495 closest distance to " CE3 TRP A  85 " =    1.070
peak=    3.494 closest distance to " CB  ALA A 233 " =    1.163
peak=    3.493 closest distance to " CA  THR A 264 " =    0.872
peak=    3.482 closest distance to " N   ARG A 156 " =    1.276
peak=    3.481 closest distance to " CD  ARG A 259 " =    1.667
peak=    3.477 closest distance to " O   GLY A 302 " =    2.263
peak=    3.476 closest distance to " CB  ASN A  60 " =    0.971
peak=    3.475 closest distance to " O   HOH Z  26 " =    1.443
peak=    3.475 closest distance to " O   HOH Z 258 " =    2.135
peak=    3.475 closest distance to " O   HOH Z 207 " =    0.884
peak=    3.472 closest distance to " CD  ARG A 269 " =    0.966
peak=    3.471 closest distance to " O   HOH Z 213 " =    2.095
peak=    3.470 closest distance to " OG ASER A 212 " =    1.457
peak=    3.464 closest distance to " O   HOH Z 181 " =    2.353
peak=    3.463 closest distance to " N   SER A  97 " =    0.855
peak=    3.461 closest distance to " O   HOH Z 132 " =    2.501
peak=    3.453 closest distance to " O   HOH Z 362 " =    1.930
peak=    3.448 closest distance to " CA  ARG A  36 " =    1.185
peak=    3.445 closest distance to " CA  ASN A 284 " =    0.904
peak=    3.444 closest distance to " O   HOH Z 244 " =    1.684
peak=    3.441 closest distance to " C   GLN A  73 " =    1.073
peak=    3.439 closest distance to " CB  HIS A  86 " =    0.970
peak=    3.424 closest distance to " CG2 ILE A  20 " =    1.544
peak=    3.423 closest distance to " CE2 PHE A  16 " =    0.878
peak=    3.422 closest distance to " OH  TYR A 116 " =    1.872
peak=    3.417 closest distance to " CB  GLU A 152 " =    1.125
peak=    3.414 closest distance to " CA  ILE A 263 " =    1.115
peak=    3.412 closest distance to " CB  PHE A 225 " =    1.461
peak=    3.408 closest distance to " CA  ILE A 106 " =    0.811
peak=    3.407 closest distance to " N   GLU A   2 " =    1.520
peak=    3.406 closest distance to " CB  ASP A  50 " =    1.128
peak=    3.398 closest distance to " O   HOH Z 220 " =    1.532
peak=    3.396 closest distance to " CG  GLN A  58 " =    1.036
peak=    3.393 closest distance to " O   HOH Z 368 " =    3.804
peak=    3.390 closest distance to " O   HOH Z 422 " =    2.411
peak=    3.390 closest distance to " CZ3 TRP A 266 " =    0.954
peak=    3.390 closest distance to " N   GLU A 152 " =    1.462
peak=    3.389 closest distance to " O   HOH Z 240 " =    1.972
peak=    3.385 closest distance to " O   HOH Z 183 " =    1.457
peak=    3.385 closest distance to " O   HOH Z 298 " =    4.192
peak=    3.383 closest distance to " O   HOH Z 216 " =    4.140
peak=    3.382 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.380 closest distance to " O   HOH Z   1 " =    1.715
peak=    3.380 closest distance to " CB  LEU A 228 " =    1.225
peak=    3.380 closest distance to " CG  TRP A 179 " =    2.213
peak=    3.379 closest distance to " O   HOH Z 130 " =    3.302
peak=    3.375 closest distance to " CA  SER A  87 " =    1.024
peak=    3.369 closest distance to " O   HOH Z 154 " =    1.711
peak=    3.368 closest distance to " CB  ASN A 142 " =    0.860
peak=    3.366 closest distance to " O   HOH Z 182 " =    1.173
peak=    3.366 closest distance to " NZ  LYS A 117 " =    1.320
peak=    3.364 closest distance to " CG1 ILE A 151 " =    1.126
peak=    3.361 closest distance to " CZ  PHE A 192 " =    0.979
peak=    3.357 closest distance to " O   HOH Z 153 " =    3.704
peak=    3.351 closest distance to " CG2 ILE A 239 " =    1.026
peak=    3.351 closest distance to " CD  ARG A  66 " =    2.037
peak=    3.350 closest distance to " OE1 GLU A 236 " =    1.540
peak=    3.349 closest distance to " CA  TYR A 116 " =    1.347
peak=    3.349 closest distance to " CB  SER A  99 " =    0.866
peak=    3.346 closest distance to " O   HOH Z 378 " =    1.090
peak=    3.341 closest distance to " CA  TRP A  92 " =    1.160
peak=    3.333 closest distance to " O   THR A 251 " =    1.211
peak=    3.333 closest distance to " N   GLN A  73 " =    0.949
peak=    3.332 closest distance to " CA  ARG A 102 " =    1.143
peak=    3.331 closest distance to " N   PHE A 130 " =    1.224
peak=    3.329 closest distance to " OG BSER A 212 " =    2.640
peak=    3.329 closest distance to " O   HOH Z 133 " =    0.872
peak=    3.328 closest distance to " CB  LEU A  83 " =    0.756
peak=    3.326 closest distance to " CA  ALA A 161 " =    1.063
peak=    3.325 closest distance to " NH1 ARG A  14 " =    1.154
peak=    3.323 closest distance to " CB  TRP A 150 " =    0.970
peak=    3.318 closest distance to " O   GLN A  55 " =    1.583
peak=    3.318 closest distance to " N   ARG A  66 " =    1.085
peak=    3.317 closest distance to " CG2 ILE A 151 " =    0.923
peak=    3.317 closest distance to " CB  LEU A 300 " =    0.931
peak=    3.316 closest distance to " O   HOH Z 358 " =    1.256
peak=    3.315 closest distance to " CB  SER A 141 " =    1.103
peak=    3.315 closest distance to " CG  ARG A 159 " =    0.822
peak=    3.313 closest distance to " CB  GLN A 183 " =    1.160
peak=    3.312 closest distance to " O   HOH Z 234 " =    3.996
peak=    3.311 closest distance to " O   HOH Z 120 " =    3.678
peak=    3.310 closest distance to " CB  ARG A 156 " =    1.089
peak=    3.309 closest distance to " O   HOH Z 273 " =    1.232
peak=    3.303 closest distance to " CB  ARG A 102 " =    0.781
peak=    3.297 closest distance to " O   HOH Z 106 " =    4.122
peak=    3.282 closest distance to " CG  GLN A  11 " =    2.169
peak=    3.282 closest distance to " CD2 LEU A   5 " =    1.333
peak=    3.281 closest distance to " CD  PRO A 243 " =    1.812
peak=    3.279 closest distance to " NH2AARG A 190 " =    2.046
peak=    3.279 closest distance to " CB  ASP A 171 " =    0.802
peak=    3.279 closest distance to " CD1 LEU A 300 " =    1.095
peak=    3.279 closest distance to " CA  PHE A 283 " =    1.210
peak=    3.278 closest distance to " O   HOH Z  53 " =    2.328
peak=    3.274 closest distance to " O   HOH Z 276 " =    1.100
peak=    3.269 closest distance to " O   HOH Z 207 " =    2.621
peak=    3.269 closest distance to " O   HOH Z 214 " =    2.477
peak=    3.267 closest distance to " C   GLU A 277 " =    1.295
peak=    3.266 closest distance to " CA  ASP A 124 " =    0.790
peak=    3.265 closest distance to " OG ASER A 212 " =    1.915
peak=    3.264 closest distance to " O   HOH Z 285 " =    2.315
peak=    3.262 closest distance to " N   ASN A 127 " =    1.310
peak=    3.258 closest distance to " O   HOH Z 119 " =    1.539
peak=    3.254 closest distance to " O   HOH Z 325 " =    2.155
peak=    3.246 closest distance to " CD  LYS A 166 " =    1.462
peak=    3.239 closest distance to " ND2 ASN A 249 " =    0.740
peak=    3.239 closest distance to " O   HOH Z 255 " =    1.095
peak=    3.234 closest distance to " CB  ARG A 190 " =    1.403
peak=    3.234 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.232 closest distance to " CA  SER A  12 " =    1.587
peak=    3.229 closest distance to " O   HOH Z 368 " =    1.947
peak=    3.228 closest distance to " O   HOH Z  68 " =    1.810
peak=    3.226 closest distance to " O   HOH Z 236 " =    1.681
peak=    3.225 closest distance to " O   HOH Z 284 " =    1.463
peak=    3.225 closest distance to " CD1 ILE A  33 " =    1.821
peak=    3.224 closest distance to " CG  GLN A  89 " =    1.549
peak=    3.220 closest distance to " O   HOH Z 158 " =    2.860
peak=    3.218 closest distance to " O   HOH Z 282 " =    2.115
peak=    3.217 closest distance to " O   HOH Z 288 " =    1.869
peak=    3.214 closest distance to " CE  LYS A  76 " =    0.855
peak=    3.213 closest distance to " N   ALA A 292 " =    1.123
peak=    3.210 closest distance to " O   THR A 220 " =    1.704
peak=    3.209 closest distance to " N   TRP A  70 " =    1.016
peak=    3.207 closest distance to " CA  ARG A 156 " =    1.052
peak=    3.206 closest distance to " OD1 ASP A 238 " =    1.016
peak=    3.202 closest distance to " O   HOH Z 104 " =    1.921
peak=    3.201 closest distance to " CB  ILE A 120 " =    1.273
peak=    3.200 closest distance to " O   HOH Z 302 " =    1.540
peak=    3.199 closest distance to " O   HOH Z 357 " =    2.200
peak=    3.197 closest distance to " O   HOH Z 352 " =    1.748
peak=    3.192 closest distance to " CB  TYR A 169 " =    0.993
peak=    3.189 closest distance to " CB  ASP A 200 " =    0.962
peak=    3.188 closest distance to " CA  VAL A 121 " =    1.005
peak=    3.183 closest distance to " CG  LEU A 281 " =    1.045
peak=    3.180 closest distance to " CG1 VAL A 296 " =    1.239
peak=    3.179 closest distance to " O   HOH Z 148 " =    1.502
peak=    3.178 closest distance to " CB  ALA A 161 " =    1.029
peak=    3.172 closest distance to " O   HOH Z 409 " =    4.819
peak=    3.169 closest distance to " ND1 HIS A  81 " =    1.743
peak=    3.166 closest distance to " NE2 GLN A  73 " =    1.767
peak=    3.166 closest distance to " CD2 HIS A  86 " =    0.925
peak=    3.166 closest distance to " CD  LYS A 119 " =    1.732
peak=    3.165 closest distance to " O   TRP A  70 " =    1.372
peak=    3.165 closest distance to " NH2 ARG A 269 " =    1.075
peak=    3.165 closest distance to " O   HOH Z  27 " =    0.957
peak=    3.162 closest distance to " CA  GLY A  80 " =    0.867
peak=    3.158 closest distance to " NH2BARG A 190 " =    1.246
peak=    3.158 closest distance to " O   HOH Z  51 " =    1.843
peak=    3.157 closest distance to " O   HOH Z 146 " =    1.519
peak=    3.153 closest distance to " CG2 VAL A 232 " =    1.017
peak=    3.153 closest distance to " CG  GLN A  88 " =    0.990
peak=    3.152 closest distance to " O   HOH Z 131 " =    1.331
peak=    3.148 closest distance to " CA  GLU A  46 " =    0.802
peak=    3.146 closest distance to " O   MET A 105 " =    1.676
peak=    3.132 closest distance to " CG  ARG A 138 " =    1.441
peak=    3.131 closest distance to " O   HOH Z 215 " =    1.660
peak=    3.126 closest distance to " O   ASP A 124 " =    1.084
peak=    3.124 closest distance to " OD2 ASP A 286 " =    2.706
peak=    3.123 closest distance to " CB  GLU A 175 " =    1.067
peak=    3.121 closest distance to " O   HOH Z 124 " =    1.785
peak=    3.117 closest distance to " O   HOH Z 425 " =    2.069
peak=    3.114 closest distance to " CA  ALA A 295 " =    1.039
peak=    3.109 closest distance to " O   HOH Z 186 " =    3.293
peak=    3.109 closest distance to " N   PHE A 218 " =    0.912
peak=    3.107 closest distance to " CA  ALA A 292 " =    1.001
peak=    3.107 closest distance to " O   HOH Z 148 " =    2.283
peak=    3.098 closest distance to " O   HOH Z 392 " =    3.045
peak=    3.094 closest distance to " CA  MET A 105 " =    0.865
peak=    3.094 closest distance to " CB  PHE A 130 " =    0.972
peak=    3.093 closest distance to " O   HOH Z 213 " =    2.277
peak=    3.091 closest distance to " NH2AARG A 145 " =    1.162
peak=    3.089 closest distance to " O   HOH Z  43 " =    1.079
peak=    3.083 closest distance to " O   HOH Z 140 " =    2.100
peak=    3.080 closest distance to " ND2 ASN A 187 " =    1.657
peak=    3.076 closest distance to " OD2 ASP A 286 " =    3.059
peak=    3.075 closest distance to " O   HOH Z 172 " =    2.335
peak=    3.068 closest distance to " N   SER A 210 " =    1.089
peak=    3.054 closest distance to " CB  TRP A 274 " =    1.018
peak=    3.054 closest distance to " OD1 ASP A 200 " =    1.636
peak=    3.050 closest distance to " CA  ASP A 149 " =    1.455
peak=    3.046 closest distance to " O   ASN A 142 " =    1.051
peak=    3.046 closest distance to " O   HOH Z 128 " =    2.860
peak=    3.021 closest distance to " O   HOH Z  78 " =    1.882
peak=    3.019 closest distance to " CA  ALA A 129 " =    1.223

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.601 - 5.585
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 210
   mapped sites are within: 0.706 - 5.585

peak=   -5.084 closest distance to " O   PRO A 198 " =    1.151
peak=   -4.468 closest distance to " OE1 GLN A  88 " =    0.940
peak=   -4.287 closest distance to " CG  GLN A  88 " =    0.854
peak=   -4.247 closest distance to " O   HOH Z  28 " =    1.085
peak=   -4.216 closest distance to " SD  MET A 105 " =    1.033
peak=   -4.200 closest distance to " CD  ARG A  14 " =    3.168
peak=   -4.196 closest distance to " O   PRO A 163 " =    1.926
peak=   -4.185 closest distance to " CB  PRO A 243 " =    2.509
peak=   -4.182 closest distance to " O   ALA A  10 " =    1.609
peak=   -4.163 closest distance to " O   HOH Z 216 " =    1.310
peak=   -4.162 closest distance to " O   HOH Z 231 " =    0.716
peak=   -4.157 closest distance to " OG  SER A  97 " =    2.095
peak=   -4.145 closest distance to " CD  ARG A 156 " =    1.993
peak=   -4.133 closest distance to " O   HOH Z  60 " =    1.322
peak=   -4.073 closest distance to " CB  GLN A  55 " =    1.273
peak=   -4.036 closest distance to " C   VAL A  72 " =    0.919
peak=   -3.983 closest distance to " O   HOH Z 111 " =    1.695
peak=   -3.967 closest distance to " O   HOH Z  39 " =    0.816
peak=   -3.959 closest distance to " CD2 TYR A 293 " =    1.947
peak=   -3.929 closest distance to " O   HOH Z  24 " =    0.992
peak=   -3.919 closest distance to " OE1 GLU A  44 " =    1.787
peak=   -3.913 closest distance to " O   HOH Z  32 " =    1.750
peak=   -3.905 closest distance to " CB  ALA A   9 " =    2.500
peak=   -3.902 closest distance to " O   HOH Z 275 " =    1.779
peak=   -3.897 closest distance to " O   HOH Z 231 " =    2.104
peak=   -3.896 closest distance to " O   GLN A 240 " =    3.172
peak=   -3.888 closest distance to " CB  ALA A  43 " =    2.581
peak=   -3.883 closest distance to " CD1 LEU A 101 " =    2.310
peak=   -3.865 closest distance to " CB  ALA A 291 " =    2.236
peak=   -3.828 closest distance to " O   SER A  22 " =    2.907
peak=   -3.824 closest distance to " CB  ASP A  27 " =    2.506
peak=   -3.822 closest distance to " CD1 TRP A 179 " =    1.113
peak=   -3.799 closest distance to " CG2 ILE A 120 " =    0.849
peak=   -3.795 closest distance to " CD2 TYR A 116 " =    2.162
peak=   -3.793 closest distance to " O   HOH Z 100 " =    1.016
peak=   -3.767 closest distance to " O   HOH Z 298 " =    2.520
peak=   -3.762 closest distance to " CD1 TYR A 247 " =    2.771
peak=   -3.759 closest distance to " CD  LYS A 166 " =    2.570
peak=   -3.753 closest distance to " CG2 ILE A  49 " =    2.816
peak=   -3.749 closest distance to " N   ALA A  43 " =    2.446
peak=   -3.738 closest distance to " O   HOH Z 313 " =    1.388
peak=   -3.728 closest distance to " NE2 GLN A 194 " =    1.968
peak=   -3.722 closest distance to " CA  HIS A 207 " =    1.115
peak=   -3.710 closest distance to " O   HOH Z 276 " =    1.041
peak=   -3.685 closest distance to " CG1 VAL A 265 " =    2.519
peak=   -3.671 closest distance to " CE2 TYR A  30 " =    2.493
peak=   -3.653 closest distance to " CD2 PHE A  61 " =    2.049
peak=   -3.653 closest distance to " O   HOH Z  52 " =    2.163
peak=   -3.651 closest distance to " O   HOH Z  69 " =    1.408
peak=   -3.642 closest distance to " O   VAL A 125 " =    2.364
peak=   -3.631 closest distance to " CG  LEU A  83 " =    2.237
peak=   -3.629 closest distance to " CZ3 TRP A 179 " =    1.309
peak=   -3.624 closest distance to " O   HOH Z 389 " =    2.346
peak=   -3.623 closest distance to " CB  ALA A 131 " =    1.928
peak=   -3.616 closest distance to " O   SER A 135 " =    1.446
peak=   -3.614 closest distance to " CB  ALA A 160 " =    2.114
peak=   -3.612 closest distance to " CA  GLY A  98 " =    1.777
peak=   -3.608 closest distance to " CZ  PHE A 130 " =    1.047
peak=   -3.603 closest distance to " C   ILE A 239 " =    1.923
peak=   -3.602 closest distance to " O   GLY A  80 " =    2.501
peak=   -3.593 closest distance to " O   HOH Z 316 " =    1.897
peak=   -3.591 closest distance to " N   THR A 157 " =    1.665
peak=   -3.579 closest distance to " O   ASP A 253 " =    1.737
peak=   -3.577 closest distance to " ND2 ASN A 209 " =    1.947
peak=   -3.576 closest distance to " O   HOH Z 290 " =    1.097
peak=   -3.568 closest distance to " NE2 GLN A 223 " =    1.583
peak=   -3.550 closest distance to " O   HOH Z 185 " =    2.236
peak=   -3.537 closest distance to " N   ASP A 270 " =    1.304
peak=   -3.534 closest distance to " OD1 ASN A  60 " =    0.798
peak=   -3.534 closest distance to " O   HOH Z 163 " =    1.638
peak=   -3.513 closest distance to " CA  GLY A 133 " =    1.990
peak=   -3.510 closest distance to " CB  ASP A 132 " =    2.587
peak=   -3.507 closest distance to " CG1BVAL A  41 " =    2.745
peak=   -3.506 closest distance to " CA  ASN A 110 " =    0.975
peak=   -3.482 closest distance to " O   HOH Z 368 " =    1.603
peak=   -3.481 closest distance to " NE2 GLN A  55 " =    0.930
peak=   -3.474 closest distance to " C   PHE A  59 " =    1.088
peak=   -3.472 closest distance to " O   ILE A  49 " =    1.676
peak=   -3.467 closest distance to " CG  GLN A  88 " =    1.258
peak=   -3.467 closest distance to " O   HOH Z  70 " =    2.215
peak=   -3.466 closest distance to " O   HOH Z 286 " =    1.373
peak=   -3.463 closest distance to " CG  GLN A 223 " =    2.402
peak=   -3.454 closest distance to " OG  SER A  32 " =    0.870
peak=   -3.453 closest distance to " O   HOH Z 166 " =    1.758
peak=   -3.452 closest distance to " OE1 GLU A  44 " =    1.089
peak=   -3.451 closest distance to " O   HOH Z 198 " =    1.834
peak=   -3.450 closest distance to " CZ2 TRP A 274 " =    0.943
peak=   -3.444 closest distance to " NH1AARG A 275 " =    2.007
peak=   -3.443 closest distance to " O   HOH Z 385 " =    1.240
peak=   -3.439 closest distance to " CA  GLY A 241 " =    2.269
peak=   -3.437 closest distance to " CA  GLY A 203 " =    2.404
peak=   -3.434 closest distance to " CG2 THR A 178 " =    2.152
peak=   -3.434 closest distance to " OG BSER A 134 " =    1.647
peak=   -3.425 closest distance to " CD2 PHE A  16 " =    2.372
peak=   -3.424 closest distance to " ND2 ASN A  45 " =    2.719
peak=   -3.418 closest distance to " O   HOH Z 404 " =    1.153
peak=   -3.413 closest distance to " CG2 VAL A 112 " =    2.684
peak=   -3.406 closest distance to " CD  GLU A 277 " =    0.865
peak=   -3.404 closest distance to " O   GLY A 203 " =    2.576
peak=   -3.398 closest distance to " O   HOH Z  28 " =    2.052
peak=   -3.391 closest distance to " O   HOH Z 300 " =    2.265
peak=   -3.386 closest distance to " CA  ILE A 120 " =    1.148
peak=   -3.382 closest distance to " O   HOH Z 407 " =    3.206
peak=   -3.378 closest distance to " O   GLU A 152 " =    1.471
peak=   -3.375 closest distance to " O   HOH Z 134 " =    1.542
peak=   -3.369 closest distance to " O   ASP A  27 " =    1.860
peak=   -3.366 closest distance to " NH2AARG A 275 " =    5.585
peak=   -3.365 closest distance to " NZ  LYS A 166 " =    1.246
peak=   -3.355 closest distance to " O   HOH Z 411 " =    5.310
peak=   -3.353 closest distance to " O   HOH Z  11 " =    1.710
peak=   -3.348 closest distance to " O   HOH Z 200 " =    3.541
peak=   -3.345 closest distance to " O   HOH Z 103 " =    1.284
peak=   -3.345 closest distance to " OG  SER A 245 " =    1.536
peak=   -3.342 closest distance to " OE1 GLN A 183 " =    1.762
peak=   -3.340 closest distance to " O   HOH Z 131 " =    3.765
peak=   -3.338 closest distance to " O   HOH Z 165 " =    2.288
peak=   -3.337 closest distance to " O   HOH Z  69 " =    2.150
peak=   -3.337 closest distance to " O   HOH Z 351 " =    1.580
peak=   -3.336 closest distance to " CD2 LEU A 143 " =    2.532
peak=   -3.331 closest distance to " CB  ASP A 171 " =    2.388
peak=   -3.328 closest distance to " O   HOH Z 414 " =    1.801
peak=   -3.321 closest distance to " O   HOH Z  26 " =    0.840
peak=   -3.317 closest distance to " O   HOH Z  58 " =    0.711
peak=   -3.317 closest distance to " O   HOH Z 147 " =    2.163
peak=   -3.306 closest distance to " O   HOH Z 410 " =    2.296
peak=   -3.303 closest distance to " O   HOH Z 318 " =    1.754
peak=   -3.301 closest distance to " CG2 THR A 221 " =    2.152
peak=   -3.295 closest distance to " CA  GLY A 241 " =    3.203
peak=   -3.293 closest distance to " O   HOH Z 193 " =    1.471
peak=   -3.287 closest distance to " O   HOH Z 348 " =    2.015
peak=   -3.287 closest distance to " OG  SER A  63 " =    1.274
peak=   -3.287 closest distance to " CB  PRO A  54 " =    2.382
peak=   -3.287 closest distance to " O   HOH Z 278 " =    1.174
peak=   -3.285 closest distance to " O   PHE A 218 " =    1.466
peak=   -3.284 closest distance to " CB  TRP A  85 " =    2.018
peak=   -3.278 closest distance to " O   HOH Z  37 " =    2.111
peak=   -3.278 closest distance to " NE2 GLN A 122 " =    0.952
peak=   -3.269 closest distance to " O   HOH Z 188 " =    0.913
peak=   -3.268 closest distance to " O   HOH Z 282 " =    4.525
peak=   -3.262 closest distance to " O   HOH Z 425 " =    0.920
peak=   -3.258 closest distance to " CD  LYS A 289 " =    2.340
peak=   -3.251 closest distance to " CD1 TYR A 214 " =    1.598
peak=   -3.250 closest distance to " C   ALA A 158 " =    1.554
peak=   -3.244 closest distance to " O   HOH Z  51 " =    1.089
peak=   -3.240 closest distance to " C   ASN A 285 " =    2.342
peak=   -3.239 closest distance to " CA  HIS A  86 " =    2.078
peak=   -3.237 closest distance to " CB  TYR A  68 " =    1.081
peak=   -3.236 closest distance to " O   HOH Z 364 " =    2.941
peak=   -3.230 closest distance to " CG1 VAL A 197 " =    2.540
peak=   -3.226 closest distance to " O   HOH Z  52 " =    0.902
peak=   -3.226 closest distance to " CG2 ILE A 151 " =    2.550
peak=   -3.224 closest distance to " CB  ALA A 100 " =    2.320
peak=   -3.220 closest distance to " O   HOH Z 108 " =    1.213
peak=   -3.208 closest distance to " O   HOH Z 128 " =    2.531
peak=   -3.206 closest distance to " O   HOH Z  10 " =    1.538
peak=   -3.204 closest distance to " CB  PHE A 130 " =    1.164
peak=   -3.201 closest distance to " N   PRO A  54 " =    1.050
peak=   -3.200 closest distance to " O   HOH Z 132 " =    4.967
peak=   -3.200 closest distance to " O   HOH Z  68 " =    1.399
peak=   -3.198 closest distance to " O   HOH Z 201 " =    1.792
peak=   -3.194 closest distance to " O   HOH Z  37 " =    1.272
peak=   -3.194 closest distance to " CG2 VAL A 232 " =    2.107
peak=   -3.192 closest distance to " CD2 TYR A 172 " =    2.317
peak=   -3.186 closest distance to " O   HOH Z 389 " =    1.153
peak=   -3.182 closest distance to " CZ  ARG A  36 " =    1.451
peak=   -3.181 closest distance to " O   HOH Z 371 " =    2.239
peak=   -3.178 closest distance to " CG2BVAL A  41 " =    1.240
peak=   -3.176 closest distance to " CG  ASN A  39 " =    1.801
peak=   -3.176 closest distance to " N   GLN A  58 " =    1.437
peak=   -3.175 closest distance to " O   SER A 141 " =    1.694
peak=   -3.174 closest distance to " CG2 THR A  52 " =    3.205
peak=   -3.167 closest distance to " O   HOH Z 166 " =    1.245
peak=   -3.167 closest distance to " O   HOH Z 384 " =    3.381
peak=   -3.154 closest distance to " OE1 GLU A 236 " =    1.066
peak=   -3.153 closest distance to " CG1 VAL A 112 " =    2.758
peak=   -3.151 closest distance to " CZ  TYR A 169 " =    1.862
peak=   -3.147 closest distance to " O   HOH Z 270 " =    2.958
peak=   -3.144 closest distance to " O   HOH Z 413 " =    3.431
peak=   -3.142 closest distance to " CB  GLN A  11 " =    1.443
peak=   -3.129 closest distance to " O   VAL A  67 " =    2.825
peak=   -3.128 closest distance to " O   HOH Z 165 " =    1.815
peak=   -3.126 closest distance to " O   HOH Z 251 " =    0.950
peak=   -3.120 closest distance to " O   HOH Z 281 " =    2.844
peak=   -3.115 closest distance to " O   HOH Z 103 " =    0.759
peak=   -3.114 closest distance to " O   ALA A   1 " =    1.892
peak=   -3.112 closest distance to " CB  PRO A 163 " =    2.409
peak=   -3.112 closest distance to " CB  HIS A  86 " =    1.162
peak=   -3.111 closest distance to " C   HIS A 108 " =    1.231
peak=   -3.110 closest distance to " O   HOH Z 105 " =    0.840
peak=   -3.108 closest distance to " O   ARG A  56 " =    4.374
peak=   -3.107 closest distance to " O   HOH Z 368 " =    2.000
peak=   -3.098 closest distance to " O   HOH Z 337 " =    1.447
peak=   -3.097 closest distance to " O   HOH Z 390 " =    2.374
peak=   -3.095 closest distance to " O   HOH Z 364 " =    1.900
peak=   -3.091 closest distance to " O   HOH Z  46 " =    0.706
peak=   -3.082 closest distance to " O   HOH Z  49 " =    1.440
peak=   -3.081 closest distance to " CG1 VAL A  78 " =    2.460
peak=   -3.076 closest distance to " CG  TRP A 266 " =    1.667
peak=   -3.073 closest distance to " CB  ASP A 132 " =    2.394
peak=   -3.068 closest distance to " O   HOH Z 147 " =    0.950
peak=   -3.066 closest distance to " CG2 ILE A 120 " =    0.967
peak=   -3.058 closest distance to " CE3 TRP A  70 " =    1.702
peak=   -3.056 closest distance to " CB  TYR A  15 " =    1.966
peak=   -3.053 closest distance to " O   HOH Z 394 " =    1.643
peak=   -3.042 closest distance to " CB  CYS A 254 " =    2.010
peak=   -3.036 closest distance to " CA  GLY A 133 " =    2.192
peak=   -3.033 closest distance to " O   HOH Z 438 " =    1.817

================= 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    :  0.4732 0.4756   6.285071e+00   6.273160e+00
   1_bss:  0.4657 0.4720   6.281807e+00   6.268740e+00
   1_xyz:  0.3757 0.4113   6.141891e+00   6.190168e+00
   1_adp:  0.3412 0.4273   6.102158e+00   6.209407e+00
   1_occ:  0.3408 0.4284   6.102194e+00   6.210039e+00
   2_bss:  0.3414 0.4266   6.104499e+00   6.210237e+00
   2_xyz:  0.2834 0.3637   5.955412e+00   6.105626e+00
   2_adp:  0.2716 0.3489   5.929755e+00   6.079119e+00
   2_occ:  0.2715 0.3488   5.929366e+00   6.078942e+00
   3_bss:  0.2719 0.3488   5.929685e+00   6.078540e+00
   3_xyz:  0.2193 0.2877   5.745030e+00   5.930880e+00
   3_adp:  0.2008 0.2787   5.691695e+00   5.905630e+00
   3_occ:  0.2007 0.2787   5.691275e+00   5.905417e+00
   4_bss:  0.2009 0.2788   5.691091e+00   5.904585e+00
   4_xyz:  0.1647 0.2316   5.502759e+00   5.749224e+00
   4_adp:  0.1518 0.2080   5.419694e+00   5.648084e+00
   4_occ:  0.1516 0.2078   5.418656e+00   5.646959e+00
   5_bss:  0.1519 0.2077   5.417353e+00   5.645110e+00
   5_xyz:  0.1390 0.1906   5.332848e+00   5.558399e+00
   5_adp:  0.1357 0.1861   5.311919e+00   5.535324e+00
   5_occ:  0.1356 0.1860   5.311520e+00   5.534741e+00
   5_bss:  0.1355 0.1859   5.311087e+00   5.534127e+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:  0.326  57.417  -1.359   1.023   2.389   0.000   0.000   0.000
   1_xyz:  0.326  57.417  -1.359   1.023   2.389   0.000   0.000   0.000
   1_adp:  0.326  57.417  -1.359   1.023   2.389   0.000   0.000   0.000
   1_occ:  0.326  57.417  -1.359   1.023   2.389   0.000   0.000   0.000
   2_bss:  0.358  85.777  -0.783  -0.208   1.539  -0.000   0.000   0.000
   2_xyz:  0.358  85.777  -0.783  -0.208   1.539  -0.000   0.000   0.000
   2_adp:  0.358  85.777  -0.783  -0.208   1.539  -0.000   0.000   0.000
   2_occ:  0.358  85.777  -0.783  -0.208   1.539  -0.000   0.000   0.000
   3_bss:  0.347  78.438  -1.218  -0.967   0.588  -0.000   0.000   0.000
   3_xyz:  0.347  78.438  -1.218  -0.967   0.588  -0.000   0.000   0.000
   3_adp:  0.347  78.438  -1.218  -0.967   0.588  -0.000   0.000   0.000
   3_occ:  0.347  78.438  -1.218  -0.967   0.588  -0.000   0.000   0.000
   4_bss:  0.348  96.566  -1.656  -1.835  -0.008  -0.000  -0.000  -0.000
   4_xyz:  0.348  96.566  -1.656  -1.835  -0.008  -0.000  -0.000  -0.000
   4_adp:  0.348  96.566  -1.656  -1.835  -0.008  -0.000  -0.000  -0.000
   4_occ:  0.348  96.566  -1.656  -1.835  -0.008  -0.000  -0.000  -0.000
   5_bss:  0.332  80.291  -1.878  -2.363  -0.374  -0.000  -0.000  -0.000
   5_xyz:  0.332  80.291  -1.878  -2.363  -0.374  -0.000  -0.000  -0.000
   5_adp:  0.332  80.291  -1.878  -2.363  -0.374  -0.000  -0.000  -0.000
   5_occ:  0.332  80.291  -1.878  -2.363  -0.374  -0.000  -0.000  -0.000
   5_bss:  0.324  70.570  -2.085  -2.653  -0.544  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.339 0.4012  0.5452    72808.041
   1_bss:  58.837 0.4066  0.5724    71568.668
   1_xyz:  46.929 0.5579  0.7630    50189.691
   1_adp:  48.701 0.5351  0.7500    53613.706
   1_occ:  48.845 0.5332  0.7470    53840.216
   2_bss:  48.696 0.5351  0.7375    53727.536
   2_xyz:  39.354 0.6487  0.8751    36746.802
   2_adp:  37.349 0.6730  0.8935    34022.300
   2_occ:  37.332 0.6732  0.8933    33983.016
   3_bss:  37.255 0.6740  0.8722    33879.611
   3_xyz:  29.613 0.7607  0.9597    22176.607
   3_adp:  28.440 0.7736  0.9516    20478.407
   3_occ:  28.429 0.7737  0.9515    20443.253
   4_bss:  28.383 0.7742  0.9314    20418.024
   4_xyz:  23.171 0.8283  0.9706    13728.765
   4_adp:  20.105 0.8601  0.9808    11126.874
   4_occ:  20.067 0.8605  0.9808    11083.821
   5_bss:  20.008 0.8610  0.9683    11013.542
   5_xyz:  17.786 0.8821  0.9807     9094.036
   5_adp:  17.149 0.8884  0.9791     8738.208
   5_occ:  17.135 0.8885  0.9791     8729.691
   5_bss:  17.123 0.8886  0.9706     8715.949
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7191e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7191e-01
   1_xyz:   1.452  0.011  0.098 15.704  0.006  4.108   1.1862e-01
   1_adp:   1.452  0.011  0.098 15.704  0.006  4.108   1.1862e-01
   1_occ:   1.452  0.011  0.098 15.704  0.006  4.108   1.1862e-01
   2_bss:   1.452  0.011  0.098 15.704  0.006  4.108   1.1862e-01
   2_xyz:   1.194  0.009  0.086 14.615  0.005  4.110   7.9268e-02
   2_adp:   1.194  0.009  0.086 14.615  0.005  4.110   7.9268e-02
   2_occ:   1.194  0.009  0.086 14.615  0.005  4.110   7.9268e-02
   3_bss:   1.194  0.009  0.086 14.615  0.005  4.110   7.9268e-02
   3_xyz:   0.996  0.007  0.070 14.487  0.004  4.119   6.1044e-02
   3_adp:   0.996  0.007  0.070 14.487  0.004  4.119   6.1044e-02
   3_occ:   0.996  0.007  0.070 14.487  0.004  4.119   6.1044e-02
   4_bss:   0.996  0.007  0.070 14.487  0.004  4.119   6.1044e-02
   4_xyz:   1.052  0.008  0.077 14.441  0.004  4.113   6.3511e-02
   4_adp:   1.052  0.008  0.077 14.441  0.004  4.113   6.3511e-02
   4_occ:   1.052  0.008  0.077 14.441  0.004  4.113   6.3511e-02
   5_bss:   1.052  0.008  0.077 14.441  0.004  4.113   6.3511e-02
   5_xyz:   0.880  0.006  0.066 14.244  0.003  4.119   4.8756e-02
   5_adp:   0.880  0.006  0.066 14.244  0.003  4.119   4.8756e-02
   5_occ:   0.880  0.006  0.066 14.244  0.003  4.119   4.8756e-02
   5_bss:   0.880  0.006  0.066 14.244  0.003  4.119   4.8756e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4230e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4230e-01
   1_xyz:   8.230  0.066  0.292 83.239  0.046  2.050   1.3279e-01
   1_adp:   8.230  0.066  0.292 83.239  0.046  2.050   1.3279e-01
   1_occ:   8.230  0.066  0.292 83.239  0.046  2.050   1.3279e-01
   2_bss:   8.230  0.066  0.292 83.239  0.046  2.050   1.3279e-01
   2_xyz:   7.080  0.098  0.301 77.536  0.044  2.270   7.6785e-02
   2_adp:   7.080  0.098  0.301 77.536  0.044  2.270   7.6785e-02
   2_occ:   7.080  0.098  0.301 77.536  0.044  2.270   7.6785e-02
   3_bss:   7.080  0.098  0.301 77.536  0.044  2.270   7.6785e-02
   3_xyz:   7.651  0.065  0.260 77.436  0.026  2.332   7.7852e-02
   3_adp:   7.651  0.065  0.260 77.436  0.026  2.332   7.7852e-02
   3_occ:   7.651  0.065  0.260 77.436  0.026  2.332   7.7852e-02
   4_bss:   7.651  0.065  0.260 77.436  0.026  2.332   7.7852e-02
   4_xyz:   6.924  0.041  0.227 81.011  0.046  2.404   4.6899e-02
   4_adp:   6.924  0.041  0.227 81.011  0.046  2.404   4.6899e-02
   4_occ:   6.924  0.041  0.227 81.011  0.046  2.404   4.6899e-02
   5_bss:   6.924  0.041  0.227 81.011  0.046  2.404   4.6899e-02
   5_xyz:   8.089  0.039  0.230 79.426  0.030  2.379   4.7023e-02
   5_adp:   8.089  0.039  0.230 79.426  0.030  2.379   4.7023e-02
   5_occ:   8.089  0.039  0.230 79.426  0.030  2.379   4.7023e-02
   5_bss:   8.089  0.039  0.230 79.426  0.030  2.379   4.7023e-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:  99.61   0.00  19.96  69.50   0.00  16.41  99.61   0.00  39.24
   1_occ:  99.61   0.00  19.96  69.50   0.00  16.41  99.61   0.00  39.24
   2_bss:  99.61   0.00  19.96  69.50   0.00  16.41  99.61   0.00  39.24
   2_xyz:  99.61   0.00  19.96  69.50   0.00  16.41  99.61   0.00  39.24
   2_adp:  98.97   0.00  19.38  72.44   0.00  15.62  98.97   0.00  39.85
   2_occ:  98.97   0.00  19.38  72.44   0.00  15.62  98.97   0.00  39.85
   3_bss:  98.97   0.00  19.38  72.44   0.00  15.62  98.97   0.00  39.85
   3_xyz:  98.97   0.00  19.38  72.44   0.00  15.62  98.97   0.00  39.85
   3_adp: 124.31   0.00  20.96 104.32   0.00  15.30 124.31   3.53  51.77
   3_occ: 124.31   0.00  20.96 104.32   0.00  15.30 124.31   3.53  51.77
   4_bss: 124.31   0.00  20.96 104.32   0.00  15.30 124.31   3.53  51.77
   4_xyz: 124.31   0.00  20.96 104.32   0.00  15.30 124.31   3.53  51.77
   4_adp: 115.11   0.38  19.14 100.78   0.38  13.69 115.11   5.50  48.79
   4_occ: 115.11   0.38  19.14 100.78   0.38  13.69 115.11   5.50  48.79
   5_bss: 115.11   0.38  19.14 100.78   0.38  13.69 115.11   5.50  48.79
   5_xyz: 115.11   0.38  19.14 100.78   0.38  13.69 115.11   5.50  48.79
   5_adp: 109.72   0.82  18.54 101.15   0.82  13.29 109.72   5.94  47.18
   5_occ: 109.72   0.82  18.54 101.15   0.82  13.29 109.72   5.94  47.18
   5_bss: 109.69   0.80  18.52 101.12   0.80  13.26 109.69   5.91  47.15
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.764    0.015    0.324
   1_adp:    1.764    0.015    0.324
   1_occ:    1.764    0.015    0.324
   2_bss:    1.764    0.015    0.324
   2_xyz:    1.288    0.037    0.469
   2_adp:    1.288    0.037    0.469
   2_occ:    1.288    0.037    0.469
   3_bss:    1.288    0.037    0.469
   3_xyz:    1.394    0.010    0.629
   3_adp:    1.394    0.010    0.629
   3_occ:    1.394    0.010    0.629
   4_bss:    1.394    0.010    0.629
   4_xyz:    1.305    0.029    0.722
   4_adp:    1.305    0.029    0.722
   4_occ:    1.305    0.029    0.722
   5_bss:    1.305    0.029    0.722
   5_xyz:    1.417    0.039    0.756
   5_adp:    1.417    0.039    0.756
   5_occ:    1.417    0.039    0.756
   5_bss:    1.417    0.039    0.756
------------------------------------------------------------------------

CPU time actual refinement: 368.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_988/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_988/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_988/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_988/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_988/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.46 
  Macro-tasks:
    bulk solvent and scale       = 59.65  
    individual site refinement   = 144.13 
    weights calculation          = 30.13  
    collect and process          = 6.43   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 240.47 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 114.90 
    alpha_beta                      = 8.35   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 121.78 
    fmodel                         = 9.53   
    r_factors                      = 0.46   
    phase_errors                   = 10.30  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 269.21 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.225 micro seconds
Total CPU time: 6.37 minutes
from_scatterers_fft:    630 calls, 114.48 s
gradients_fft:          575 calls, 109.06 s

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

# Date 2008-01-16 Time 06:10:05 PST -0800 (1200492605.38 s)
Start R-work = 0.4732, R-free = 0.4756 (no bulk solvent and anisotropic scale)
Final R-work = 0.1562, R-free = 0.2031 (no bulk solvent and anisotropic scale)

Start R-work = 0.4657, R-free = 0.4720
Final R-work = 0.1355, R-free = 0.1859