# Date 2008-01-16 Time 05:23:41 PST -0800 (1200489821.29 s)
#phil __OFF__

Command line arguments: "../714.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2148
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 714

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.8686, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00077
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   2.0008

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00077
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2808 [2183/2211]  1962   221  10.1%
  bin  2:  4.2808 -  3.4107 [2078/2097]  1870   208  10.0%
  bin  3:  3.4107 -  2.9834 [2075/2095]  1871   204   9.8%
  bin  4:  2.9834 -  2.7123 [2040/2065]  1833   207  10.1%
  bin  5:  2.7123 -  2.5189 [2022/2041]  1822   200   9.9%
  bin  6:  2.5189 -  2.3709 [2016/2062]  1813   203  10.1%
  bin  7:  2.3709 -  2.2526 [2017/2051]  1819   198   9.8%
  bin  8:  2.2526 -  2.1548 [2005/2040]  1796   209  10.4%
  bin  9:  2.1548 -  2.0721 [2007/2037]  1813   194   9.7%
  bin 10:  2.0721 -  2.0008 [1146/2035]  1031   115  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_714/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: 0.13 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:
        1.43 -     2.12: 7
        2.12 -     2.82: 829
        2.82 -     3.51: 4333
        3.51 -     4.21: 9095
        4.21 -     4.90: 13464
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.429 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.691 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.691 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.811 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27723 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_714/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_714/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.8686 88.54975 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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4658   r_free= 0.4606   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.278160                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1412  157 0.3684 0.3599      6.5536      6.5036|
|  2:  4.7744 -  3.8097 0.99   1364  153 0.4049 0.4545      6.8254      6.9311|
|  3:  3.8097 -  3.3340 0.99   1335  149 0.4476 0.3953       6.689      6.5949|
|  4:  3.3340 -  3.0319 0.99   1325  139 0.4501 0.4545      6.5128      6.4733|
|  5:  3.0319 -  2.8161 0.99   1312  150 0.4945 0.4322      6.3709      6.3816|
|  6:  2.8161 -  2.6510 0.98   1304  147 0.4956 0.5187      6.2633      6.1736|
|  7:  2.6510 -  2.5189 0.99   1306  145 0.4911 0.4719      6.2293      6.1416|
|  8:  2.5189 -  2.4097 0.98   1303  145 0.5037 0.4866      6.1812      6.1775|
|  9:  2.4097 -  2.3172 0.98   1305  144 0.5141 0.5120      6.1068      6.1733|
| 10:  2.3172 -  2.2375 0.98   1275  141 0.5259 0.4945         6.1      6.0801|
| 11:  2.2375 -  2.1678 0.99   1311  146 0.5176 0.4992      6.0275       6.039|
| 12:  2.1678 -  2.1060 0.98   1279  144 0.5125 0.5653       5.957      6.0218|
| 13:  2.1060 -  2.0507 0.97   1280  131 0.5306 0.5226       5.888      5.8139|
| 14:  2.0507 -  2.0008 0.40    519   68 0.4768 0.5090      5.8597      5.7747|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1412   157  0.72  32.44   0.82     0.74      64393.41|
|  2:  4.7744 -  3.8097  1364   153  0.71  34.31   0.89     0.79     101364.29|
|  3:  3.8097 -  3.3340  1335   149  0.62  42.42   0.87     0.77     106821.48|
|  4:  3.3340 -  3.0319  1325   139  0.53  49.14   0.89     0.69      94704.78|
|  5:  3.0319 -  2.8161  1312   150  0.47  54.54   0.87     0.62      72590.37|
|  6:  2.8161 -  2.6510  1304   147  0.41  58.72   0.87     0.56      65687.16|
|  7:  2.6510 -  2.5189  1306   145  0.42  58.48   0.90     0.55      59425.01|
|  8:  2.5189 -  2.4097  1303   145  0.40  60.08   0.89     0.54      55530.43|
|  9:  2.4097 -  2.3172  1305   144  0.38  61.34   0.88     0.56      52156.52|
| 10:  2.3172 -  2.2375  1275   141  0.37  61.91   0.90     0.54      48203.26|
| 11:  2.2375 -  2.1678  1311   146  0.32  65.74   0.90     0.49      47496.58|
| 12:  2.1678 -  2.1060  1279   144  0.27  69.58   0.91     0.41      45638.78|
| 13:  2.1060 -  2.0507  1280   131  0.23  72.86   0.88     0.35      40795.40|
| 14:  2.0507 -  2.0008   519    68  0.28  69.00   0.97     0.36      31046.28|
|alpha:            min =        0.35 max =            0.79 mean =         0.58|
|beta:             min =    31046.28 max =       106821.48 mean =     65038.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.61|
|phase err.(test): min =        0.00 max =           89.93 mean =        55.99|
|-----------------------------------------------------------------------------|

============================== 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 = 20.243545             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.198   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.433279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.602   (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 |  1.429 -  1.776:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.776 -  2.123:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.123 -  2.471:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.471 -  2.818:      807 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.818 -  3.165:     1999 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.165 -  3.512:     2334 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.512 -  3.859:     4515 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.859 -  4.206:     4580 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.206 -  4.553:     6081 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7383 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.429 |       0.267 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4658   r_free= 0.4606   ksol= 0.00   Bsol= 0.00   scale= 0.873    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.278160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4547   r_free= 0.4500   ksol= 0.30   Bsol= 50.00   scale= 0.924   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.74,3.25,4.24,0.00,0.00,0.00); trace/3= 1.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.269485                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.897692             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.751   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.195531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.213   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4547      final r-factor (work) = 0.3170          |
| start r-factor (free) = 0.4500      final r-factor (free) = 0.3439          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.1224 = 16.90 * 0.50 * 6.2673 + 1.00 * 0.1712                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.8041 = 16.90 * 0.50 * 6.1102 + 1.00 * 0.1800                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3170      final r-factor (work) = 0.2873          |
| start r-factor (free) = 0.3439      final r-factor (free) = 0.3558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3111 = 1.20 * 1.00 * 6.1102 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1223 = 1.20 * 1.00 * 5.9408 + 1.00 * 0.0199                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.77  18.63    None  None   None       |
|    all(noH): 2823   0      0.00    111.77  18.63    None  None   None       |
|    Sol.    : 438    0      0.00    111.77  42.73    None  None   None       |
|    Mac.    : 2385   0      0.00    92.11   14.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.178: 1159   |   5:    55.887 -  67.065:   72        |
|      1:    11.178 -  22.355:  890   |   6:    67.065 -  78.242:   41        |
|      2:    22.355 -  33.532:  357   |   7:    78.242 -  89.419:   13        |
|      3:    33.532 -  44.710:  161   |   8:    89.419 - 100.597:    6        |
|      4:    44.710 -  55.887:  120   |   9:   100.597 - 111.774:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2873 r_free = 0.3558             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2872 r_free = 0.3562             target_work(ml) = 5.950         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2872   r_free= 0.3562   ksol= 0.30   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.74,3.25,4.24,0.00,0.00,0.00); trace/3= 1.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.950383                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2831   r_free= 0.3523   ksol= 0.33   Bsol= 76.27   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.70,1.25,1.91,0.00,0.00,0.00); trace/3= 0.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.945467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.572526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.994   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.461117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.815  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2831      final r-factor (work) = 0.2035          |
| start r-factor (free) = 0.3523      final r-factor (free) = 0.2576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6049 = 9.57 * 0.50 * 5.9389 + 1.00 * 0.1799                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0381 = 9.57 * 0.50 * 5.8377 + 1.00 * 0.0972                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2035      final r-factor (work) = 0.1866          |
| start r-factor (free) = 0.2576      final r-factor (free) = 0.2362          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7120 = 0.46 * 1.00 * 5.8377 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6333 = 0.46 * 1.00 * 5.6121 + 1.00 * 0.0454                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.45  18.28    None  None   None       |
|    all(noH): 2823   0      0.00    111.45  18.28    None  None   None       |
|    Sol.    : 438    0      2.37    111.45  43.28    None  None   None       |
|    Mac.    : 2385   0      0.00    92.20   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:     0.000 -  11.145: 1248   |   5:    55.727 -  66.872:   75        |
|      1:    11.145 -  22.291:  893   |   6:    66.872 -  78.017:   41        |
|      2:    22.291 -  33.436:  264   |   7:    78.017 -  89.163:   12        |
|      3:    33.436 -  44.581:  166   |   8:    89.163 - 100.308:    5        |
|      4:    44.581 -  55.727:  115   |   9:   100.308 - 111.453:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1866 r_free = 0.2362             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1863 r_free = 0.2364             target_work(ml) = 5.576         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1863   r_free= 0.2364   ksol= 0.33   Bsol= 76.27   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.70,1.25,1.91,0.00,0.00,0.00); trace/3= 0.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.576447                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1861   r_free= 0.2355   ksol= 0.34   Bsol= 80.10   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-0.10,0.81,-0.00,0.00,0.00); trace/3= -0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.574751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.661558              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.725  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.528009              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.957   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1861      final r-factor (work) = 0.1556          |
| start r-factor (free) = 0.2355      final r-factor (free) = 0.2020          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3750 = 3.66 * 0.50 * 5.6135 + 1.00 * 0.0979                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1450 = 3.66 * 0.50 * 5.5027 + 1.00 * 0.0708                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1556      final r-factor (work) = 0.1428          |
| start r-factor (free) = 0.2020      final r-factor (free) = 0.1925          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9253 = 0.53 * 1.00 * 5.5027 + 1.00 * 0.0198                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8544 = 0.53 * 1.00 * 5.3821 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.61  17.66    None  None   None       |
|    all(noH): 2823   0      0.00    108.61  17.66    None  None   None       |
|    Sol.    : 438    0      4.26    108.61  44.37    None  None   None       |
|    Mac.    : 2385   0      0.00    92.04   12.75    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 -  10.861: 1313   |   5:    54.305 -  65.166:   88        |
|      1:    10.861 -  21.722:  900   |   6:    65.166 -  76.027:   48        |
|      2:    21.722 -  32.583:  203   |   7:    76.027 -  86.887:   18        |
|      3:    32.583 -  43.444:  119   |   8:    86.887 -  97.748:    5        |
|      4:    43.444 -  54.305:  125   |   9:    97.748 - 108.609:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1428 r_free = 0.1925             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1427 r_free = 0.1925             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1427   r_free= 0.1925   ksol= 0.34   Bsol= 80.10   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-0.10,0.81,-0.00,0.00,0.00); trace/3= -0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.356900                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1430   r_free= 0.1927   ksol= 0.34   Bsol= 82.43   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.69,0.44,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.358246                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.629726              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.360  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.308  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1430      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.1927      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1500 = 2.63 * 0.50 * 5.3840 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0599 = 2.63 * 0.50 * 5.3172 + 1.00 * 0.0684                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1735          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9233 = 0.17 * 1.00 * 5.3172 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9135 = 0.17 * 1.00 * 5.2791 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    101.21  16.56    None  None   None       |
|    all(noH): 2823   0      0.87    101.21  16.56    None  None   None       |
|    Sol.    : 438    0      4.98    101.21  40.32    None  None   None       |
|    Mac.    : 2385   0      0.87    80.84   12.20    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:     0.865 -  10.900: 1364   |   5:    51.037 -  61.072:   80        |
|      1:    10.900 -  20.934:  889   |   6:    61.072 -  71.106:   39        |
|      2:    20.934 -  30.968:  185   |   7:    71.106 -  81.140:   13        |
|      3:    30.968 -  41.003:  142   |   8:    81.140 -  91.175:    6        |
|      4:    41.003 -  51.037:  103   |   9:    91.175 - 101.209:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1297 r_free = 0.1735             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1296 r_free = 0.1736             target_work(ml) = 5.268         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1736   ksol= 0.34   Bsol= 82.43   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.69,0.44,-0.00,0.00,0.00); trace/3= -0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.268275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1736   ksol= 0.32   Bsol= 69.48   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-0.97,0.26,-0.00,0.00,0.00); trace/3= -0.91                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.267922                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.515127              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.928  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.114  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1722          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7066 = 2.52 * 0.50 * 5.2786 + 1.00 * 0.0684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6877 = 2.52 * 0.50 * 5.2605 + 1.00 * 0.0723                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1722      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7377 = 0.33 * 1.00 * 5.2605 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7357 = 0.33 * 1.00 * 5.2500 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.28   16.59    None  None   None       |
|    all(noH): 2823   0      0.00    98.28   16.59    None  None   None       |
|    Sol.    : 438    0      4.97    98.28   41.24    None  None   None       |
|    Mac.    : 2385   0      0.00    82.48   12.06    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 -   9.828: 1195   |   5:    49.142 -  58.971:   94        |
|      1:     9.828 -  19.657:  996   |   6:    58.971 -  68.799:   50        |
|      2:    19.657 -  29.485:  208   |   7:    68.799 -  78.627:   16        |
|      3:    29.485 -  39.314:  133   |   8:    78.627 -  88.456:   10        |
|      4:    39.314 -  49.142:  115   |   9:    88.456 -  98.284:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1739             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1260 r_free = 0.1740             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1740   ksol= 0.32   Bsol= 69.48   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-0.97,0.26,-0.00,0.00,0.00); trace/3= -0.91                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252882                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1412  157 0.1024 0.1377      5.4236       5.598|
|  2:  4.7744 -  3.8097 0.99   1364  153 0.0889 0.1076      5.4731      5.6612|
|  3:  3.8097 -  3.3340 0.99   1335  149 0.1179 0.1610       5.564      5.9061|
|  4:  3.3340 -  3.0319 0.99   1325  139 0.1383 0.1842      5.5608      5.7208|
|  5:  3.0319 -  2.8161 0.99   1312  150 0.1561 0.1839      5.4656      5.6333|
|  6:  2.8161 -  2.6510 0.98   1304  147 0.1458 0.2267       5.343         5.6|
|  7:  2.6510 -  2.5189 0.99   1306  145 0.1473 0.1908      5.3036      5.4691|
|  8:  2.5189 -  2.4097 0.98   1303  145 0.1378 0.1913      5.2314      5.4559|
|  9:  2.4097 -  2.3172 0.98   1305  144 0.1397 0.2214      5.1738      5.4856|
| 10:  2.3172 -  2.2375 0.98   1275  141 0.1322 0.1708      5.0873      5.2013|
| 11:  2.2375 -  2.1678 0.99   1311  146 0.1275 0.1966      5.0155      5.3229|
| 12:  2.1678 -  2.1060 0.98   1279  144 0.1234 0.1896      4.9423      5.2656|
| 13:  2.1060 -  2.0507 0.97   1280  131 0.1213 0.1688      4.8503      5.0298|
| 14:  2.0507 -  2.0008 0.40    519   68 0.1089 0.2013      4.7489      5.0795|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1412   157  0.94   9.43   0.96     0.93       7751.20|
|  2:  4.7744 -  3.8097  1364   153  0.95   8.62   1.00     0.98       9799.45|
|  3:  3.8097 -  3.3340  1335   149  0.92  12.59   1.01     1.01      11981.82|
|  4:  3.3340 -  3.0319  1325   139  0.91  15.42   0.99     0.98      12670.77|
|  5:  3.0319 -  2.8161  1312   150  0.88  18.47   0.99     0.96      10795.62|
|  6:  2.8161 -  2.6510  1304   147  0.88  18.88   0.96     0.94       9145.64|
|  7:  2.6510 -  2.5189  1306   145  0.88  18.10   0.98     0.94       8060.45|
|  8:  2.5189 -  2.4097  1303   145  0.88  18.41   0.98     0.93       7516.99|
|  9:  2.4097 -  2.3172  1305   144  0.88  18.84   0.98     0.92       6598.40|
| 10:  2.3172 -  2.2375  1275   141  0.88  18.37   0.97     0.92       5673.99|
| 11:  2.2375 -  2.1678  1311   146  0.89  17.95   0.97     0.92       5063.58|
| 12:  2.1678 -  2.1060  1279   144  0.90  16.85   0.98     0.97       4498.10|
| 13:  2.1060 -  2.0507  1280   131  0.89  17.43   0.97     0.95       3795.37|
| 14:  2.0507 -  2.0008   519    68  0.91  15.81   0.94     0.89       2996.66|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     2996.66 max =        12670.77 mean =      7836.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.02|
|phase err.(test): min =        0.00 max =           89.67 mean =        15.36|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1738   ksol= 0.32   Bsol= 69.48   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.83,0.44,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252998                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1738   ksol= 0.32   Bsol= 69.48   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.83,0.44,-0.00,0.00,0.00); trace/3= -0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252998                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7744 0.99   1412  157 0.1025 0.1377      5.4242       5.599|
|  2:  4.7744 -  3.8097 0.99   1364  153 0.0889 0.1076      5.4736      5.6612|
|  3:  3.8097 -  3.3340 0.99   1335  149 0.1179 0.1611       5.564      5.9062|
|  4:  3.3340 -  3.0319 0.99   1325  139 0.1383 0.1842      5.5609      5.7209|
|  5:  3.0319 -  2.8161 0.99   1312  150 0.1561 0.1839      5.4655      5.6331|
|  6:  2.8161 -  2.6510 0.98   1304  147 0.1458 0.2267      5.3429      5.5998|
|  7:  2.6510 -  2.5189 0.99   1306  145 0.1473 0.1909      5.3036      5.4693|
|  8:  2.5189 -  2.4097 0.98   1303  145 0.1378 0.1912      5.2316      5.4557|
|  9:  2.4097 -  2.3172 0.98   1305  144 0.1397 0.2214      5.1739      5.4857|
| 10:  2.3172 -  2.2375 0.98   1275  141 0.1322 0.1709      5.0876      5.2017|
| 11:  2.2375 -  2.1678 0.99   1311  146 0.1275 0.1965      5.0156      5.3228|
| 12:  2.1678 -  2.1060 0.98   1279  144 0.1234 0.1897      4.9422      5.2656|
| 13:  2.1060 -  2.0507 0.97   1280  131 0.1213 0.1687      4.8503      5.0294|
| 14:  2.0507 -  2.0008 0.40    519   68 0.1089 0.2012      4.7491      5.0792|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7744  1412   157  0.94   9.43   0.96     0.93       7760.82|
|  2:  4.7744 -  3.8097  1364   153  0.95   8.63   1.00     0.98       9808.81|
|  3:  3.8097 -  3.3340  1335   149  0.92  12.60   1.01     1.02      11988.93|
|  4:  3.3340 -  3.0319  1325   139  0.91  15.43   1.00     0.98      12674.12|
|  5:  3.0319 -  2.8161  1312   150  0.88  18.47   0.99     0.97      10793.62|
|  6:  2.8161 -  2.6510  1304   147  0.88  18.88   0.97     0.95       9143.51|
|  7:  2.6510 -  2.5189  1306   145  0.88  18.10   0.99     0.95       8059.11|
|  8:  2.5189 -  2.4097  1303   145  0.88  18.42   0.98     0.94       7517.87|
|  9:  2.4097 -  2.3172  1305   144  0.88  18.84   0.99     0.93       6600.05|
| 10:  2.3172 -  2.2375  1275   141  0.88  18.37   0.98     0.93       5674.74|
| 11:  2.2375 -  2.1678  1311   146  0.89  17.95   0.98     0.93       5064.16|
| 12:  2.1678 -  2.1060  1279   144  0.90  16.85   0.99     0.98       4498.28|
| 13:  2.1060 -  2.0507  1280   131  0.89  17.43   0.98     0.96       3793.84|
| 14:  2.0507 -  2.0008   519    68  0.91  15.80   0.95     0.90       2994.36|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     2994.36 max =        12674.12 mean =      7838.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        16.02|
|phase err.(test): min =        0.00 max =           89.67 mean =        15.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.350)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.29   16.59    None  None   None       |
|    all(noH): 2823   0      0.00    98.29   16.59    None  None   None       |
|    Sol.    : 438    0      4.97    98.29   41.24    None  None   None       |
|    Mac.    : 2385   0      0.00    82.49   12.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.831: 1195   |   5:    49.145 -  58.973:   94        |
|      1:     9.831 -  19.660:  996   |   6:    58.973 -  68.802:   50        |
|      2:    19.660 -  29.488:  208   |   7:    68.802 -  78.630:   16        |
|      3:    29.488 -  39.317:  133   |   8:    78.630 -  88.459:   10        |
|      4:    39.317 -  49.145:  115   |   9:    88.459 -  98.287:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.681 - 5.488
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 306
   mapped sites are within: 0.732 - 5.488

peak=    6.082 closest distance to " O   HOH Z 210 " =    1.499
peak=    5.050 closest distance to " O   HOH Z  49 " =    1.550
peak=    5.035 closest distance to " O   HOH Z  54 " =    1.385
peak=    4.995 closest distance to " CG  PRO A  54 " =    1.445
peak=    4.923 closest distance to " CB  GLN A 223 " =    1.438
peak=    4.829 closest distance to " O   HOH Z 248 " =    1.521
peak=    4.807 closest distance to " CG  PRO A 280 " =    0.888
peak=    4.763 closest distance to " CB  SER A  63 " =    1.159
peak=    4.758 closest distance to " O   HOH Z 117 " =    1.325
peak=    4.718 closest distance to " CB  GLN A 183 " =    1.248
peak=    4.696 closest distance to " CD2 TRP A 179 " =    1.244
peak=    4.685 closest distance to " O   HOH Z  76 " =    1.277
peak=    4.659 closest distance to " O  BHOH Z  74 " =    1.236
peak=    4.645 closest distance to " CZ3 TRP A 266 " =    1.140
peak=    4.629 closest distance to " CG  PRO A  90 " =    1.333
peak=    4.510 closest distance to " O   HOH Z 113 " =    1.870
peak=    4.422 closest distance to " O   HOH Z 369 " =    2.052
peak=    4.394 closest distance to " CZ  PHE A 218 " =    1.175
peak=    4.387 closest distance to " CA  TYR A  30 " =    0.976
peak=    4.351 closest distance to " O   PRO A 198 " =    1.536
peak=    4.336 closest distance to " O   HOH Z 412 " =    3.626
peak=    4.318 closest distance to " CB  ASN A  39 " =    0.815
peak=    4.263 closest distance to " CB  ARG A 190 " =    1.652
peak=    4.243 closest distance to " O   HOH Z  65 " =    1.113
peak=    4.237 closest distance to " O   HOH Z  48 " =    1.974
peak=    4.202 closest distance to " O   HOH Z 298 " =    1.947
peak=    4.194 closest distance to " O   HOH Z 261 " =    2.267
peak=    4.164 closest distance to " CB  TYR A 169 " =    0.831
peak=    4.146 closest distance to " CA  GLU A 152 " =    0.898
peak=    4.117 closest distance to " CB  ARG A 275 " =    0.850
peak=    4.102 closest distance to " CG2AVAL A 121 " =    2.048
peak=    4.087 closest distance to " O   HOH Z 368 " =    2.292
peak=    4.074 closest distance to " O   HOH Z 176 " =    1.677
peak=    4.071 closest distance to " O   HOH Z 394 " =    1.556
peak=    4.070 closest distance to " CD  LYS A 166 " =    1.476
peak=    4.054 closest distance to " O   ALA A 165 " =    1.403
peak=    4.051 closest distance to " CG  ARG A  66 " =    2.690
peak=    4.050 closest distance to " CG AARG A 275 " =    1.253
peak=    4.045 closest distance to " O   HOH Z 402 " =    1.581
peak=    4.034 closest distance to " CB  ASN A 148 " =    1.458
peak=    4.021 closest distance to " CB  TRP A 179 " =    1.416
peak=    4.018 closest distance to " O   HOH Z 189 " =    2.866
peak=    4.005 closest distance to " O   HOH Z  35 " =    2.323
peak=    3.999 closest distance to " CB  GLU A 128 " =    1.050
peak=    3.994 closest distance to " CB  GLU A 152 " =    1.177
peak=    3.976 closest distance to " CB  GLU A 277 " =    3.853
peak=    3.965 closest distance to " CA  ARG A 195 " =    1.286
peak=    3.958 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.952 closest distance to " O   HOH Z  43 " =    2.087
peak=    3.950 closest distance to " O   HOH Z 425 " =    1.502
peak=    3.936 closest distance to " O   HOH Z 232 " =    2.520
peak=    3.935 closest distance to " NE2 GLN A  11 " =    1.307
peak=    3.931 closest distance to " CD  ARG A 269 " =    1.022
peak=    3.923 closest distance to " CG2 VAL A 197 " =    1.138
peak=    3.910 closest distance to " CB  PRO A  90 " =    1.221
peak=    3.901 closest distance to " O   HOH Z 433 " =    1.596
peak=    3.896 closest distance to " O   HOH Z 193 " =    2.017
peak=    3.888 closest distance to " O   HOH Z 287 " =    1.725
peak=    3.879 closest distance to " O   HOH Z 362 " =    3.377
peak=    3.879 closest distance to " CG  GLN A  11 " =    1.322
peak=    3.868 closest distance to " O   HOH Z 251 " =    1.604
peak=    3.842 closest distance to " CB  LEU A  83 " =    0.800
peak=    3.837 closest distance to " CA  ALA A 100 " =    1.097
peak=    3.837 closest distance to " CA  ARG A  36 " =    1.105
peak=    3.836 closest distance to " N   SER A 164 " =    1.039
peak=    3.814 closest distance to " CB  ASN A 142 " =    1.067
peak=    3.801 closest distance to " CZ  PHE A  38 " =    1.138
peak=    3.788 closest distance to " O   HOH Z 234 " =    3.932
peak=    3.781 closest distance to " O   HOH Z 280 " =    3.030
peak=    3.781 closest distance to " CB  VAL A 202 " =    1.477
peak=    3.780 closest distance to " O   HOH Z 214 " =    1.590
peak=    3.772 closest distance to " NH2 ARG A 156 " =    1.100
peak=    3.771 closest distance to " CB  ASP A 124 " =    0.810
peak=    3.764 closest distance to " CB  ALA A 291 " =    1.082
peak=    3.763 closest distance to " CD1 LEU A  96 " =    0.779
peak=    3.755 closest distance to " O   HOH Z 403 " =    1.657
peak=    3.748 closest distance to " CG2BVAL A  41 " =    0.867
peak=    3.739 closest distance to " O   HOH Z 346 " =    1.574
peak=    3.737 closest distance to " O   SER A  87 " =    2.375
peak=    3.736 closest distance to " CG  PRO A 198 " =    1.360
peak=    3.730 closest distance to " O   HOH Z 287 " =    2.112
peak=    3.720 closest distance to " O   HOH Z 126 " =    1.565
peak=    3.719 closest distance to " CB  PRO A  54 " =    0.885
peak=    3.716 closest distance to " CB  ASN A 187 " =    1.205
peak=    3.713 closest distance to " O   HOH Z 406 " =    1.677
peak=    3.712 closest distance to " CG  ARG A 138 " =    1.371
peak=    3.703 closest distance to " CB  ARG A  79 " =    1.200
peak=    3.700 closest distance to " CB  SER A  62 " =    0.918
peak=    3.700 closest distance to " CA  TYR A 116 " =    1.325
peak=    3.693 closest distance to " CD  ARG A 195 " =    0.989
peak=    3.686 closest distance to " O   HOH Z 394 " =    4.004
peak=    3.685 closest distance to " CA  ASP A 162 " =    1.033
peak=    3.676 closest distance to " O   HOH Z 417 " =    3.199
peak=    3.676 closest distance to " CG  PRO A 213 " =    1.252
peak=    3.671 closest distance to " CB  GLU A  37 " =    0.960
peak=    3.670 closest distance to " CA  ALA A 160 " =    0.929
peak=    3.659 closest distance to " O   HOH Z  80 " =    2.050
peak=    3.647 closest distance to " CG  PRO A 243 " =    1.078
peak=    3.641 closest distance to " ND2 ASN A 187 " =    1.454
peak=    3.637 closest distance to " NE2 GLN A  77 " =    3.244
peak=    3.636 closest distance to " O   HOH Z  69 " =    1.207
peak=    3.621 closest distance to " O   HOH Z  20 " =    1.537
peak=    3.619 closest distance to " CB  SER A 141 " =    1.119
peak=    3.619 closest distance to " CG  GLU A  37 " =    0.959
peak=    3.610 closest distance to " O   HOH Z 199 " =    1.634
peak=    3.609 closest distance to " CG  GLN A  58 " =    1.164
peak=    3.605 closest distance to " CG  GLN A  77 " =    0.932
peak=    3.604 closest distance to " CB  ASP A 191 " =    1.165
peak=    3.600 closest distance to " O   ASN A  74 " =    1.751
peak=    3.598 closest distance to " N   CYS A 260 " =    0.777
peak=    3.594 closest distance to " NH2AARG A 145 " =    1.145
peak=    3.593 closest distance to " CB  ASN A 285 " =    0.884
peak=    3.588 closest distance to " O   HOH Z 132 " =    2.934
peak=    3.585 closest distance to " CE1 TYR A  30 " =    1.059
peak=    3.583 closest distance to " O   HOH Z 357 " =    2.245
peak=    3.574 closest distance to " OG BSER A 164 " =    2.246
peak=    3.572 closest distance to " O   HOH Z 142 " =    2.092
peak=    3.570 closest distance to " O   HOH Z 291 " =    1.434
peak=    3.567 closest distance to " CB  MET A  40 " =    1.046
peak=    3.563 closest distance to " O   HOH Z  54 " =    1.350
peak=    3.560 closest distance to " CB  TRP A 266 " =    1.056
peak=    3.559 closest distance to " O   HOH Z 299 " =    4.501
peak=    3.547 closest distance to " O   HOH Z  40 " =    1.867
peak=    3.545 closest distance to " O   HOH Z  48 " =    1.504
peak=    3.544 closest distance to " CA  ILE A 106 " =    0.796
peak=    3.540 closest distance to " CD  PRO A  54 " =    0.948
peak=    3.533 closest distance to " CB  GLU A  46 " =    1.026
peak=    3.531 closest distance to " NH1AARG A 145 " =    1.330
peak=    3.527 closest distance to " O   THR A 220 " =    1.116
peak=    3.517 closest distance to " O   HOH Z 134 " =    1.486
peak=    3.515 closest distance to " CA  VAL A 125 " =    1.195
peak=    3.514 closest distance to " CB  GLN A  88 " =    1.188
peak=    3.509 closest distance to " O   HOH Z 132 " =    2.934
peak=    3.508 closest distance to " O   HOH Z 336 " =    1.897
peak=    3.508 closest distance to " O   HOH Z  88 " =    1.816
peak=    3.506 closest distance to " O   HOH Z  21 " =    1.809
peak=    3.504 closest distance to " O   HOH Z 196 " =    1.314
peak=    3.496 closest distance to " O   HOH Z 423 " =    1.783
peak=    3.491 closest distance to " CD2 LEU A 297 " =    1.083
peak=    3.485 closest distance to " O   HOH Z  19 " =    1.652
peak=    3.476 closest distance to " CD1 ILE A 199 " =    1.309
peak=    3.475 closest distance to " CG1 ILE A  33 " =    1.210
peak=    3.471 closest distance to " OG  SER A 276 " =    1.590
peak=    3.469 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.469 closest distance to " NZ  LYS A 117 " =    2.886
peak=    3.467 closest distance to " ND2 ASN A 249 " =    0.891
peak=    3.462 closest distance to " CB  GLN A  89 " =    1.282
peak=    3.461 closest distance to " CB  VAL A 265 " =    1.296
peak=    3.461 closest distance to " O   HOH Z 298 " =    2.258
peak=    3.460 closest distance to " O   PRO A 213 " =    1.428
peak=    3.457 closest distance to " CB  PRO A 198 " =    1.056
peak=    3.456 closest distance to " O   HOH Z 265 " =    2.110
peak=    3.451 closest distance to " O   HOH Z 102 " =    1.265
peak=    3.449 closest distance to " OG  SER A  28 " =    1.706
peak=    3.446 closest distance to " CG1 ILE A  20 " =    1.244
peak=    3.441 closest distance to " CB  ASP A 140 " =    0.858
peak=    3.441 closest distance to " O   HOH Z 189 " =    2.950
peak=    3.436 closest distance to " O   HOH Z  63 " =    1.865
peak=    3.429 closest distance to " CG2 ILE A 120 " =    1.237
peak=    3.428 closest distance to " CE1 HIS A 115 " =    1.001
peak=    3.427 closest distance to " O   HOH Z 285 " =    2.518
peak=    3.414 closest distance to " O   ASP A 124 " =    1.182
peak=    3.411 closest distance to " O   HOH Z 128 " =    2.201
peak=    3.400 closest distance to " NH2 ARG A  56 " =    1.086
peak=    3.399 closest distance to " N   ARG A 156 " =    1.599
peak=    3.399 closest distance to " O   HOH Z 238 " =    3.885
peak=    3.397 closest distance to " CA  ALA A 295 " =    1.056
peak=    3.394 closest distance to " O   HOH Z  15 " =    2.498
peak=    3.387 closest distance to " O   HOH Z 213 " =    1.897
peak=    3.387 closest distance to " OG BSER A 134 " =    2.852
peak=    3.387 closest distance to " NH1 ARG A 269 " =    0.818
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.382 closest distance to " O   HOH Z 366 " =    2.606
peak=    3.367 closest distance to " O   HOH Z 383 " =    2.087
peak=    3.360 closest distance to " CB  ALA A 299 " =    0.737
peak=    3.359 closest distance to " O   HOH Z 214 " =    3.244
peak=    3.358 closest distance to " NE2 GLN A  58 " =    3.670
peak=    3.358 closest distance to " O   TYR A 116 " =    1.385
peak=    3.352 closest distance to " O   HOH Z 250 " =    1.342
peak=    3.352 closest distance to " CA  GLY A   6 " =    0.776
peak=    3.352 closest distance to " O   HOH Z 293 " =    2.079
peak=    3.347 closest distance to " CA  GLY A  35 " =    0.905
peak=    3.346 closest distance to " CG2BVAL A 121 " =    0.802
peak=    3.344 closest distance to " O   HOH Z 393 " =    3.303
peak=    3.342 closest distance to " CE3 TRP A  85 " =    1.090
peak=    3.341 closest distance to " O   HOH Z 435 " =    2.922
peak=    3.337 closest distance to " O   HOH Z 148 " =    3.516
peak=    3.336 closest distance to " CB  ASN A  45 " =    1.112
peak=    3.335 closest distance to " CZ  PHE A 192 " =    1.101
peak=    3.334 closest distance to " O   HOH Z 250 " =    1.302
peak=    3.332 closest distance to " O   HOH Z 420 " =    5.488
peak=    3.329 closest distance to " CA  GLN A  94 " =    0.783
peak=    3.329 closest distance to " CA  ALA A 154 " =    1.085
peak=    3.329 closest distance to " O   HOH Z 371 " =    2.545
peak=    3.327 closest distance to " CB  ILE A 199 " =    1.157
peak=    3.324 closest distance to " O   HOH Z 150 " =    1.608
peak=    3.322 closest distance to " O   HOH Z 418 " =    1.499
peak=    3.321 closest distance to " NE2 GLN A  58 " =    5.081
peak=    3.315 closest distance to " N   ALA A   1 " =    2.172
peak=    3.315 closest distance to " O   HOH Z 285 " =    2.142
peak=    3.314 closest distance to " O   HOH Z 325 " =    2.248
peak=    3.313 closest distance to " O   HOH Z 389 " =    2.022
peak=    3.313 closest distance to " O   HOH Z 246 " =    1.512
peak=    3.310 closest distance to " CA  SER A  87 " =    1.044
peak=    3.310 closest distance to " O   HOH Z  44 " =    2.158
peak=    3.307 closest distance to " CB  SER A  62 " =    1.087
peak=    3.307 closest distance to " O   HOH Z 359 " =    1.729
peak=    3.306 closest distance to " O   HOH Z 345 " =    3.701
peak=    3.298 closest distance to " O   HOH Z 316 " =    3.071
peak=    3.298 closest distance to " OD2 ASP A 298 " =    3.762
peak=    3.296 closest distance to " CA  ALA A  21 " =    1.336
peak=    3.295 closest distance to " O   HOH Z 141 " =    1.586
peak=    3.294 closest distance to " CA  SER A  12 " =    1.610
peak=    3.290 closest distance to " O   HOH Z 180 " =    2.137
peak=    3.289 closest distance to " O   HOH Z 214 " =    2.488
peak=    3.288 closest distance to " N   ASN A  39 " =    1.238
peak=    3.288 closest distance to " CA  GLU A  46 " =    1.106
peak=    3.286 closest distance to " N   GLY A 111 " =    1.314
peak=    3.286 closest distance to " O   HOH Z 358 " =    1.252
peak=    3.282 closest distance to " CE1 HIS A  81 " =    1.613
peak=    3.282 closest distance to " CB  ASP A 298 " =    1.168
peak=    3.278 closest distance to " O   HOH Z 126 " =    2.067
peak=    3.277 closest distance to " CA  PRO A  54 " =    1.387
peak=    3.277 closest distance to " OD1 ASN A 301 " =    1.197
peak=    3.276 closest distance to " NH2AARG A 275 " =    3.505
peak=    3.270 closest distance to " O   HOH Z 146 " =    2.127
peak=    3.269 closest distance to " O   THR A 182 " =    1.498
peak=    3.268 closest distance to " O   HOH Z 361 " =    2.657
peak=    3.268 closest distance to " CG2 THR A  29 " =    1.371
peak=    3.264 closest distance to " CG  ASN A  39 " =    1.328
peak=    3.263 closest distance to " N   ASP A 132 " =    1.148
peak=    3.261 closest distance to " CA  ARG A 156 " =    1.175
peak=    3.259 closest distance to " CA  GLY A 267 " =    1.101
peak=    3.250 closest distance to " O   HOH Z 303 " =    2.445
peak=    3.246 closest distance to " CG  MET A 185 " =    1.157
peak=    3.246 closest distance to " CG2 ILE A 234 " =    1.253
peak=    3.245 closest distance to " O   HOH Z 142 " =    1.617
peak=    3.243 closest distance to " O  BHOH Z 338 " =    2.100
peak=    3.240 closest distance to " O   HOH Z 365 " =    2.623
peak=    3.240 closest distance to " CE3 TRP A 150 " =    1.191
peak=    3.234 closest distance to " N   TYR A 116 " =    1.620
peak=    3.233 closest distance to " CA  THR A 246 " =    1.000
peak=    3.233 closest distance to " CA  GLN A 223 " =    0.799
peak=    3.231 closest distance to " CG1 ILE A 120 " =    1.040
peak=    3.231 closest distance to " O   HOH Z 147 " =    1.591
peak=    3.230 closest distance to " O   HOH Z  88 " =    3.293
peak=    3.227 closest distance to " O   HOH Z 278 " =    0.941
peak=    3.226 closest distance to " CB  MET A  47 " =    0.930
peak=    3.225 closest distance to " O   ALA A 158 " =    1.162
peak=    3.222 closest distance to " CG1 VAL A 153 " =    1.133
peak=    3.209 closest distance to " O   HOH Z 258 " =    1.903
peak=    3.207 closest distance to " ND2AASN A 224 " =    0.881
peak=    3.206 closest distance to " OG  SER A 135 " =    1.290
peak=    3.205 closest distance to " O   HOH Z   1 " =    2.629
peak=    3.199 closest distance to " CB  PHE A 155 " =    0.797
peak=    3.194 closest distance to " OG  SER A 245 " =    1.613
peak=    3.193 closest distance to " O   HOH Z 408 " =    3.042
peak=    3.192 closest distance to " N   VAL A 126 " =    1.610
peak=    3.192 closest distance to " O   HOH Z 271 " =    2.501
peak=    3.192 closest distance to " CG  LEU A 167 " =    1.116
peak=    3.191 closest distance to " CD  LYS A 119 " =    1.736
peak=    3.188 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.183 closest distance to " O   HOH Z 353 " =    2.601
peak=    3.182 closest distance to " CB  THR A  52 " =    0.813
peak=    3.180 closest distance to " O   ASP A 200 " =    1.609
peak=    3.179 closest distance to " CB  ALA A 248 " =    1.372
peak=    3.178 closest distance to " O   HOH Z 183 " =    1.628
peak=    3.175 closest distance to " CB  ALA A  71 " =    1.386
peak=    3.172 closest distance to " CB  SER A   3 " =    1.582
peak=    3.171 closest distance to " CG2 THR A 220 " =    0.779
peak=    3.166 closest distance to " O   HOH Z 130 " =    2.201
peak=    3.164 closest distance to " CB  MET A 105 " =    0.909
peak=    3.164 closest distance to " O   HOH Z  88 " =    2.443
peak=    3.160 closest distance to " CB  PRO A 243 " =    1.398
peak=    3.160 closest distance to " O   HOH Z 259 " =    2.170
peak=    3.155 closest distance to " CD  ARG A  66 " =    2.192
peak=    3.148 closest distance to " O   HOH Z   4 " =    1.687
peak=    3.138 closest distance to " CA  ASP A 140 " =    1.482
peak=    3.134 closest distance to " O   HOH Z 313 " =    1.883
peak=    3.133 closest distance to " CB  PHE A  16 " =    1.087
peak=    3.131 closest distance to " O   HOH Z  47 " =    2.099
peak=    3.131 closest distance to " O   HOH Z 420 " =    2.087
peak=    3.129 closest distance to " CB  GLU A 236 " =    1.177
peak=    3.127 closest distance to " O   HOH Z 301 " =    1.378
peak=    3.124 closest distance to " CB  PHE A 283 " =    0.820
peak=    3.122 closest distance to " OE2 GLU A  53 " =    1.123
peak=    3.122 closest distance to " CG1 ILE A  49 " =    1.610
peak=    3.111 closest distance to " N   TYR A  15 " =    0.732
peak=    3.111 closest distance to " O   ALA A 242 " =    1.453
peak=    3.106 closest distance to " CB  ALA A 100 " =    1.329
peak=    3.095 closest distance to " CG  LYS A  76 " =    1.076
peak=    3.089 closest distance to " O   HOH Z 343 " =    2.395
peak=    3.083 closest distance to " O   PHE A 192 " =    1.379
peak=    3.079 closest distance to " O   GLY A  91 " =    1.175
peak=    3.076 closest distance to " CB  ALA A  43 " =    0.880
peak=    3.070 closest distance to " CE1 HIS A 108 " =    1.101
peak=    3.070 closest distance to " CD1 LEU A 300 " =    1.089
peak=    3.069 closest distance to " CD  PRO A 213 " =    1.607
peak=    3.067 closest distance to " OD1 ASN A  69 " =    2.449
peak=    3.064 closest distance to " CA  CYS A 260 " =    1.551
peak=    3.039 closest distance to " CA  ASN A 249 " =    1.375
peak=    3.038 closest distance to " O   HOH Z 128 " =    2.036
peak=    3.024 closest distance to " OG  SER A  22 " =    2.790
peak=    3.012 closest distance to " O   ASP A 124 " =    1.778

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.453 - 5.936
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 214
   mapped sites are within: 0.707 - 5.936

peak=   -4.844 closest distance to " CD  GLN A  58 " =    0.824
peak=   -4.660 closest distance to " CE2 PHE A  61 " =    2.716
peak=   -4.583 closest distance to " O   PRO A 198 " =    1.339
peak=   -4.471 closest distance to " CG1 VAL A 250 " =    2.769
peak=   -4.453 closest distance to " CD  GLN A  88 " =    1.024
peak=   -4.360 closest distance to " CB  PRO A 243 " =    2.862
peak=   -4.355 closest distance to " CD  ARG A  14 " =    3.335
peak=   -4.230 closest distance to " O   VAL A  67 " =    2.869
peak=   -4.227 closest distance to " CA  VAL A  67 " =    3.063
peak=   -4.214 closest distance to " CD2 TYR A 293 " =    1.936
peak=   -4.207 closest distance to " CD  GLN A 223 " =    1.308
peak=   -4.166 closest distance to " O   HOH Z 211 " =    0.968
peak=   -4.161 closest distance to " O   HOH Z   5 " =    1.609
peak=   -4.157 closest distance to " CG  GLN A  58 " =    1.109
peak=   -4.155 closest distance to " O   HOH Z 166 " =    1.488
peak=   -4.139 closest distance to " CG  ARG A 269 " =    2.320
peak=   -4.138 closest distance to " CG  GLN A  11 " =    1.284
peak=   -4.053 closest distance to " O   HOH Z 150 " =    0.848
peak=   -3.998 closest distance to " N   ALA A  43 " =    2.781
peak=   -3.986 closest distance to " O   HOH Z 411 " =    5.606
peak=   -3.983 closest distance to " CG  GLN A 103 " =    2.474
peak=   -3.975 closest distance to " CG2 ILE A  49 " =    2.791
peak=   -3.948 closest distance to " OE1 GLN A  88 " =    0.998
peak=   -3.947 closest distance to " O   HOH Z 407 " =    0.949
peak=   -3.945 closest distance to " O   HOH Z 278 " =    0.866
peak=   -3.941 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.940 closest distance to " CD1 LEU A 101 " =    2.377
peak=   -3.905 closest distance to " O   HOH Z 114 " =    1.076
peak=   -3.903 closest distance to " O   HOH Z 203 " =    0.928
peak=   -3.884 closest distance to " C   ILE A 239 " =    2.178
peak=   -3.855 closest distance to " O   HOH Z 193 " =    1.049
peak=   -3.846 closest distance to " O   HOH Z 377 " =    1.060
peak=   -3.809 closest distance to " O   SER A 210 " =    1.812
peak=   -3.795 closest distance to " CD1 PHE A  59 " =    2.099
peak=   -3.786 closest distance to " O   HOH Z 368 " =    1.988
peak=   -3.775 closest distance to " CD  ARG A 156 " =    2.210
peak=   -3.771 closest distance to " O   HOH Z 290 " =    1.005
peak=   -3.765 closest distance to " OXT GLY A 302 " =    2.966
peak=   -3.754 closest distance to " O   HOH Z 196 " =    2.449
peak=   -3.753 closest distance to " CB  ALA A 291 " =    2.484
peak=   -3.745 closest distance to " CH2 TRP A 179 " =    1.214
peak=   -3.736 closest distance to " OD1 ASN A 148 " =    1.277
peak=   -3.729 closest distance to " CD1 LEU A  25 " =    2.508
peak=   -3.679 closest distance to " CD2 PHE A  61 " =    2.177
peak=   -3.678 closest distance to " CG2 THR A 221 " =    2.325
peak=   -3.675 closest distance to " O   HOH Z  88 " =    2.751
peak=   -3.668 closest distance to " O   HOH Z 154 " =    1.280
peak=   -3.666 closest distance to " O   HOH Z 216 " =    0.808
peak=   -3.665 closest distance to " CB  GLU A 277 " =    1.315
peak=   -3.661 closest distance to " O   HOH Z 149 " =    1.884
peak=   -3.657 closest distance to " OD1 ASP A 171 " =    1.568
peak=   -3.657 closest distance to " O   HOH Z   6 " =    1.292
peak=   -3.651 closest distance to " O   HOH Z 215 " =    1.066
peak=   -3.643 closest distance to " O   HOH Z 128 " =    2.752
peak=   -3.641 closest distance to " CB  ALA A  10 " =    2.230
peak=   -3.638 closest distance to " CG  GLU A  53 " =    1.537
peak=   -3.631 closest distance to " O   SER A 276 " =    1.775
peak=   -3.623 closest distance to " O   HOH Z 366 " =    1.566
peak=   -3.609 closest distance to " CA  GLY A 241 " =    3.329
peak=   -3.607 closest distance to " NE2 GLN A 194 " =    2.157
peak=   -3.602 closest distance to " CG  PRO A 243 " =    1.679
peak=   -3.595 closest distance to " C   HIS A 108 " =    1.090
peak=   -3.594 closest distance to " O   HOH Z 283 " =    2.283
peak=   -3.591 closest distance to " OG  SER A  97 " =    2.255
peak=   -3.574 closest distance to " O   HOH Z 150 " =    1.875
peak=   -3.568 closest distance to " O   HOH Z 205 " =    0.872
peak=   -3.561 closest distance to " CZ  TYR A 169 " =    1.884
peak=   -3.556 closest distance to " O   HOH Z 171 " =    2.286
peak=   -3.554 closest distance to " CE3 TRP A 150 " =    2.238
peak=   -3.552 closest distance to " O   HOH Z 403 " =    1.102
peak=   -3.550 closest distance to " CB  HIS A  86 " =    1.181
peak=   -3.549 closest distance to " CD  GLN A  73 " =    0.713
peak=   -3.536 closest distance to " C   ASN A 285 " =    2.332
peak=   -3.532 closest distance to " O   HOH Z  68 " =    1.550
peak=   -3.523 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -3.521 closest distance to " OE1 GLN A  88 " =    0.892
peak=   -3.515 closest distance to " O   HOH Z 418 " =    1.082
peak=   -3.512 closest distance to " OH  TYR A 247 " =    2.146
peak=   -3.505 closest distance to " O   HOH Z 348 " =    2.252
peak=   -3.493 closest distance to " CG2 VAL A 189 " =    2.171
peak=   -3.491 closest distance to " O   HOH Z 155 " =    1.935
peak=   -3.488 closest distance to " O   HOH Z 252 " =    3.691
peak=   -3.485 closest distance to " CH2 TRP A 150 " =    1.217
peak=   -3.483 closest distance to " CD1 ILE A 109 " =    2.869
peak=   -3.482 closest distance to " O   HOH Z 106 " =    2.063
peak=   -3.474 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.471 closest distance to " O   ALA A  34 " =    2.628
peak=   -3.471 closest distance to " O   GLY A 136 " =    2.443
peak=   -3.469 closest distance to " O   HOH Z 191 " =    5.936
peak=   -3.466 closest distance to " O   HOH Z 210 " =    0.707
peak=   -3.463 closest distance to " CB  ALA A  43 " =    2.637
peak=   -3.462 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -3.460 closest distance to " CG1 VAL A 189 " =    2.575
peak=   -3.459 closest distance to " O   SER A 206 " =    1.398
peak=   -3.459 closest distance to " CG1AVAL A 121 " =    1.394
peak=   -3.454 closest distance to " CD  GLN A 223 " =    0.844
peak=   -3.440 closest distance to " O   HOH Z 156 " =    3.604
peak=   -3.437 closest distance to " NH2 ARG A  79 " =    1.640
peak=   -3.432 closest distance to " CA  GLY A 241 " =    2.300
peak=   -3.425 closest distance to " O   HOH Z 351 " =    1.733
peak=   -3.423 closest distance to " O   HOH Z  64 " =    1.233
peak=   -3.421 closest distance to " CB  ALA A 129 " =    2.510
peak=   -3.420 closest distance to " NE2 GLN A 103 " =    1.858
peak=   -3.418 closest distance to " O   HOH Z 174 " =    2.248
peak=   -3.413 closest distance to " O   HOH Z 185 " =    2.590
peak=   -3.406 closest distance to " CZ  PHE A  38 " =    2.376
peak=   -3.396 closest distance to " O   HOH Z 407 " =    3.616
peak=   -3.389 closest distance to " CG  ARG A 259 " =    1.464
peak=   -3.388 closest distance to " O   HOH Z  52 " =    1.781
peak=   -3.387 closest distance to " O   HOH Z  19 " =    2.469
peak=   -3.385 closest distance to " O   HOH Z 200 " =    1.232
peak=   -3.376 closest distance to " N   ARG A 275 " =    1.508
peak=   -3.368 closest distance to " CD1 TRP A  70 " =    1.051
peak=   -3.367 closest distance to " CE BMET A  47 " =    1.841
peak=   -3.360 closest distance to " O   HOH Z 174 " =    3.464
peak=   -3.356 closest distance to " ND2 ASN A  45 " =    2.031
peak=   -3.356 closest distance to " CA  GLY A 241 " =    2.977
peak=   -3.354 closest distance to " O   HOH Z   9 " =    0.843
peak=   -3.350 closest distance to " C   THR A 279 " =    1.258
peak=   -3.348 closest distance to " NH2 ARG A  79 " =    2.260
peak=   -3.347 closest distance to " O   HOH Z 411 " =    1.181
peak=   -3.345 closest distance to " O   HOH Z 422 " =    1.273
peak=   -3.342 closest distance to " CD  PRO A 243 " =    1.962
peak=   -3.339 closest distance to " CB  ALA A 291 " =    2.433
peak=   -3.334 closest distance to " O   HOH Z  78 " =    1.976
peak=   -3.330 closest distance to " O   HOH Z 371 " =    1.089
peak=   -3.327 closest distance to " C   LEU A 143 " =    1.181
peak=   -3.321 closest distance to " O   HOH Z 345 " =    3.061
peak=   -3.320 closest distance to " O   HOH Z 103 " =    2.058
peak=   -3.320 closest distance to " CG1 VAL A 112 " =    2.577
peak=   -3.320 closest distance to " O   HOH Z  40 " =    3.022
peak=   -3.320 closest distance to " CA  GLY A 241 " =    3.345
peak=   -3.319 closest distance to " CB  ALA A   9 " =    2.417
peak=   -3.317 closest distance to " O   HOH Z 331 " =    1.160
peak=   -3.312 closest distance to " CD2 HIS A 207 " =    2.172
peak=   -3.311 closest distance to " O   HOH Z  54 " =    1.791
peak=   -3.304 closest distance to " O   HOH Z  90 " =    3.773
peak=   -3.302 closest distance to " CZ  ARG A 259 " =    0.896
peak=   -3.301 closest distance to " O   ALA A  10 " =    1.762
peak=   -3.292 closest distance to " CA  PRO A 280 " =    1.044
peak=   -3.289 closest distance to " O   HOH Z 234 " =    4.460
peak=   -3.288 closest distance to " CG2AVAL A  41 " =    2.893
peak=   -3.285 closest distance to " CB  TRP A  85 " =    2.552
peak=   -3.284 closest distance to " O   HOH Z 394 " =    1.728
peak=   -3.281 closest distance to " O   PRO A 163 " =    2.087
peak=   -3.278 closest distance to " CE1 HIS A  81 " =    1.629
peak=   -3.278 closest distance to " OE1 GLN A 223 " =    2.244
peak=   -3.277 closest distance to " CD  ARG A  79 " =    1.229
peak=   -3.275 closest distance to " O   HOH Z 221 " =    1.040
peak=   -3.272 closest distance to " O   HOH Z 222 " =    1.078
peak=   -3.261 closest distance to " O   HOH Z  37 " =    1.600
peak=   -3.260 closest distance to " O   HOH Z  65 " =    0.717
peak=   -3.255 closest distance to " O   HOH Z 197 " =    1.839
peak=   -3.250 closest distance to " O   HOH Z 285 " =    1.691
peak=   -3.249 closest distance to " CG1 VAL A  78 " =    2.738
peak=   -3.249 closest distance to " O   HOH Z 189 " =    1.885
peak=   -3.241 closest distance to " CG  ASP A 286 " =    1.557
peak=   -3.241 closest distance to " CD2 PHE A 192 " =    2.185
peak=   -3.241 closest distance to " NE2 GLN A 278 " =    1.258
peak=   -3.240 closest distance to " CE2 PHE A 192 " =    2.193
peak=   -3.240 closest distance to " O   HOH Z  56 " =    1.525
peak=   -3.236 closest distance to " O   HOH Z  49 " =    0.708
peak=   -3.236 closest distance to " O   HOH Z 165 " =    1.860
peak=   -3.235 closest distance to " O   TYR A 186 " =    1.852
peak=   -3.232 closest distance to " O   HOH Z  60 " =    1.938
peak=   -3.231 closest distance to " OG  SER A 273 " =    2.267
peak=   -3.230 closest distance to " NH2 ARG A 159 " =    2.366
peak=   -3.229 closest distance to " O   HOH Z 424 " =    2.779
peak=   -3.224 closest distance to " O   HOH Z 340 " =    1.597
peak=   -3.211 closest distance to " CD  GLN A  88 " =    0.858
peak=   -3.211 closest distance to " O   HOH Z  55 " =    1.532
peak=   -3.209 closest distance to " OG BSER A 210 " =    1.412
peak=   -3.205 closest distance to " O   HOH Z 287 " =    1.720
peak=   -3.203 closest distance to " O   TYR A 247 " =    2.897
peak=   -3.202 closest distance to " O   HOH Z 392 " =    1.376
peak=   -3.202 closest distance to " CA  SER A  62 " =    2.582
peak=   -3.199 closest distance to " O   HOH Z 140 " =    2.096
peak=   -3.198 closest distance to " O   HOH Z 196 " =    1.773
peak=   -3.195 closest distance to " C   VAL A 265 " =    0.871
peak=   -3.193 closest distance to " O   SER A 271 " =    2.094
peak=   -3.187 closest distance to " CE3 TRP A 150 " =    1.427
peak=   -3.185 closest distance to " OD2 ASP A 298 " =    0.964
peak=   -3.183 closest distance to " N   GLN A 223 " =    1.039
peak=   -3.180 closest distance to " N   ALA A 226 " =    1.948
peak=   -3.179 closest distance to " OE2 GLU A 152 " =    1.542
peak=   -3.177 closest distance to " CB  PHE A  16 " =    2.447
peak=   -3.166 closest distance to " O   ALA A   7 " =    1.547
peak=   -3.165 closest distance to " O   TRP A  92 " =    2.037
peak=   -3.164 closest distance to " O   GLN A  11 " =    1.238
peak=   -3.160 closest distance to " OD2 ASP A 270 " =    1.156
peak=   -3.153 closest distance to " O   HOH Z 211 " =    1.054
peak=   -3.152 closest distance to " O   ALA A  21 " =    2.015
peak=   -3.152 closest distance to " CZ  TYR A  68 " =    1.147
peak=   -3.150 closest distance to " CG  ASN A  45 " =    0.849
peak=   -3.132 closest distance to " CG2BVAL A  41 " =    1.766
peak=   -3.132 closest distance to " CG2 VAL A 189 " =    1.959
peak=   -3.126 closest distance to " CD1 ILE A 263 " =    2.029
peak=   -3.121 closest distance to " CB  ALA A 131 " =    2.346
peak=   -3.119 closest distance to " CG  LEU A  83 " =    2.057
peak=   -3.119 closest distance to " O   HOH Z 135 " =    2.010
peak=   -3.119 closest distance to " O   HOH Z 278 " =    0.846
peak=   -3.115 closest distance to " CG  ASP A 132 " =    2.362
peak=   -3.108 closest distance to " C   ARG A  79 " =    2.702
peak=   -3.094 closest distance to " CG  TRP A 266 " =    1.819
peak=   -3.086 closest distance to " CA  VAL A 197 " =    0.933
peak=   -3.081 closest distance to " CD  ARG A 195 " =    5.080
peak=   -3.064 closest distance to " CB  ASN A  45 " =    2.064
peak=   -3.059 closest distance to " ND2 ASN A 249 " =    2.337
peak=   -3.037 closest distance to " O   TRP A  70 " =    1.985
peak=   -3.036 closest distance to " OE1 GLN A  88 " =    0.971
peak=   -3.020 closest distance to " CG  ARG A 259 " =    2.463

================= 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    :  0.4658 0.4606   6.278160e+00   6.260502e+00
   1_bss:  0.4547 0.4500   6.269485e+00   6.250477e+00
   1_xyz:  0.3170 0.3439   5.999387e+00   6.072074e+00
   1_adp:  0.2873 0.3558   5.950347e+00   6.089601e+00
   1_occ:  0.2872 0.3562   5.950383e+00   6.090110e+00
   2_bss:  0.2831 0.3523   5.945467e+00   6.086707e+00
   2_xyz:  0.2035 0.2576   5.652698e+00   5.838432e+00
   2_adp:  0.1866 0.2362   5.576615e+00   5.771299e+00
   2_occ:  0.1863 0.2364   5.576447e+00   5.771889e+00
   3_bss:  0.1861 0.2355   5.574751e+00   5.769987e+00
   3_xyz:  0.1556 0.2020   5.422488e+00   5.630396e+00
   3_adp:  0.1428 0.1925   5.357399e+00   5.576302e+00
   3_occ:  0.1427 0.1925   5.356900e+00   5.575813e+00
   4_bss:  0.1430 0.1927   5.358246e+00   5.576190e+00
   4_xyz:  0.1300 0.1780   5.277113e+00   5.503860e+00
   4_adp:  0.1297 0.1735   5.268470e+00   5.484025e+00
   4_occ:  0.1296 0.1736   5.268275e+00   5.484049e+00
   5_bss:  0.1294 0.1736   5.267922e+00   5.483750e+00
   5_xyz:  0.1273 0.1722   5.256792e+00   5.477534e+00
   5_adp:  0.1260 0.1739   5.253016e+00   5.480227e+00
   5_occ:  0.1260 0.1740   5.252882e+00   5.480126e+00
   5_bss:  0.1259 0.1738   5.252998e+00   5.480192e+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:  0.297  50.001  -3.742   3.253   4.236   0.000   0.000   0.000
   1_xyz:  0.297  50.001  -3.742   3.253   4.236   0.000   0.000   0.000
   1_adp:  0.297  50.001  -3.742   3.253   4.236   0.000   0.000   0.000
   1_occ:  0.297  50.001  -3.742   3.253   4.236   0.000   0.000   0.000
   2_bss:  0.332  76.267  -1.698   1.245   1.906   0.000   0.000   0.000
   2_xyz:  0.332  76.267  -1.698   1.245   1.906   0.000   0.000   0.000
   2_adp:  0.332  76.267  -1.698   1.245   1.906   0.000   0.000   0.000
   2_occ:  0.332  76.267  -1.698   1.245   1.906   0.000   0.000   0.000
   3_bss:  0.336  80.104  -1.855  -0.098   0.807  -0.000   0.000   0.000
   3_xyz:  0.336  80.104  -1.855  -0.098   0.807  -0.000   0.000   0.000
   3_adp:  0.336  80.104  -1.855  -0.098   0.807  -0.000   0.000   0.000
   3_occ:  0.336  80.104  -1.855  -0.098   0.807  -0.000   0.000   0.000
   4_bss:  0.336  82.426  -1.975  -0.695   0.441  -0.000   0.000   0.000
   4_xyz:  0.336  82.426  -1.975  -0.695   0.441  -0.000   0.000   0.000
   4_adp:  0.336  82.426  -1.975  -0.695   0.441  -0.000   0.000   0.000
   4_occ:  0.336  82.426  -1.975  -0.695   0.441  -0.000   0.000   0.000
   5_bss:  0.324  69.480  -2.009  -0.970   0.264  -0.000   0.000   0.000
   5_xyz:  0.324  69.480  -2.009  -0.970   0.264  -0.000   0.000   0.000
   5_adp:  0.324  69.480  -2.009  -0.970   0.264  -0.000   0.000   0.000
   5_occ:  0.324  69.480  -2.009  -0.970   0.264  -0.000   0.000   0.000
   5_bss:  0.324  69.483  -1.804  -0.826   0.439  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.646 0.4492  0.5809    65026.815
   1_bss:  54.361 0.4644  0.6294    62221.284
   1_xyz:  37.856 0.6678  0.8701    33298.323
   1_adp:  39.140 0.6519  0.8448    35250.636
   1_occ:  39.203 0.6511  0.8436    35349.394
   2_bss:  38.527 0.6594  0.8368    34716.777
   2_xyz:  26.315 0.7964  0.9661    17278.823
   2_adp:  23.693 0.8248  0.9786    14752.479
   2_occ:  23.711 0.8247  0.9783    14799.059
   3_bss:  23.566 0.8261  0.9510    14664.712
   3_xyz:  19.411 0.8675  0.9754    10572.340
   3_adp:  18.216 0.8786  0.9696     9587.606
   3_occ:  18.203 0.8787  0.9698     9578.444
   4_bss:  18.201 0.8787  0.9578     9588.560
   4_xyz:  16.579 0.8932  0.9656     8162.794
   4_adp:  16.066 0.8981  0.9609     7920.649
   4_occ:  16.063 0.8982  0.9609     7919.722
   5_bss:  16.058 0.8982  0.9558     7910.580
   5_xyz:  15.903 0.8996  0.9563     7806.030
   5_adp:  15.960 0.8991  0.9492     7836.601
   5_occ:  15.952 0.8992  0.9492     7835.032
   5_bss:  15.955 0.8992  0.9550     7837.030
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7124e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7124e-01
   1_xyz:   1.848  0.016  0.113 16.740  0.008  4.119   1.7999e-01
   1_adp:   1.848  0.016  0.113 16.740  0.008  4.119   1.7999e-01
   1_occ:   1.848  0.016  0.113 16.740  0.008  4.119   1.7999e-01
   2_bss:   1.848  0.016  0.113 16.740  0.008  4.119   1.7999e-01
   2_xyz:   1.323  0.011  0.090 15.217  0.006  4.143   9.7167e-02
   2_adp:   1.323  0.011  0.090 15.217  0.006  4.143   9.7167e-02
   2_occ:   1.323  0.011  0.090 15.217  0.006  4.143   9.7167e-02
   3_bss:   1.323  0.011  0.090 15.217  0.006  4.143   9.7167e-02
   3_xyz:   1.104  0.009  0.077 14.569  0.004  4.133   7.0810e-02
   3_adp:   1.104  0.009  0.077 14.569  0.004  4.133   7.0810e-02
   3_occ:   1.104  0.009  0.077 14.569  0.004  4.133   7.0810e-02
   4_bss:   1.104  0.009  0.077 14.569  0.004  4.133   7.0810e-02
   4_xyz:   1.096  0.009  0.080 14.466  0.004  4.142   6.8422e-02
   4_adp:   1.096  0.009  0.080 14.466  0.004  4.142   6.8422e-02
   4_occ:   1.096  0.009  0.080 14.466  0.004  4.142   6.8422e-02
   5_bss:   1.096  0.009  0.080 14.466  0.004  4.142   6.8422e-02
   5_xyz:   1.095  0.010  0.082 14.493  0.004  4.115   7.2344e-02
   5_adp:   1.095  0.010  0.082 14.493  0.004  4.115   7.2344e-02
   5_occ:   1.095  0.010  0.082 14.493  0.004  4.115   7.2344e-02
   5_bss:   1.095  0.010  0.082 14.493  0.004  4.115   7.2344e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.429   2.4521e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.429   2.4521e-01
   1_xyz:  12.713  0.118  0.354 83.355  0.050  1.851   1.3171e-01
   1_adp:  12.713  0.118  0.354 83.355  0.050  1.851   1.3171e-01
   1_occ:  12.713  0.118  0.354 83.355  0.050  1.851   1.3171e-01
   2_bss:  12.713  0.118  0.354 83.355  0.050  1.851   1.3171e-01
   2_xyz:   7.561  0.059  0.291 84.111  0.069  2.137   9.8326e-02
   2_adp:   7.561  0.059  0.291 84.111  0.069  2.137   9.8326e-02
   2_occ:   7.561  0.059  0.291 84.111  0.069  2.137   9.8326e-02
   3_bss:   7.561  0.059  0.291 84.111  0.069  2.137   9.8326e-02
   3_xyz:   7.887  0.067  0.243 83.351  0.032  2.291   4.7632e-02
   3_adp:   7.887  0.067  0.243 83.351  0.032  2.291   4.7632e-02
   3_occ:   7.887  0.067  0.243 83.351  0.032  2.291   4.7632e-02
   4_bss:   7.887  0.067  0.243 83.351  0.032  2.291   4.7632e-02
   4_xyz:   8.001  0.046  0.266 82.932  0.037  2.262   5.0175e-02
   4_adp:   8.001  0.046  0.266 82.932  0.037  2.262   5.0175e-02
   4_occ:   8.001  0.046  0.266 82.932  0.037  2.262   5.0175e-02
   5_bss:   8.001  0.046  0.266 82.932  0.037  2.262   5.0175e-02
   5_xyz:   8.134  0.055  0.283 83.022  0.034  2.245   5.0372e-02
   5_adp:   8.134  0.055  0.283 83.022  0.034  2.245   5.0372e-02
   5_occ:   8.134  0.055  0.283 83.022  0.034  2.245   5.0372e-02
   5_bss:   8.134  0.055  0.283 83.022  0.034  2.245   5.0372e-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: 111.77   0.00  18.63  92.11   0.00  14.20 111.77   0.00  42.73
   1_occ: 111.77   0.00  18.63  92.11   0.00  14.20 111.77   0.00  42.73
   2_bss: 111.77   0.00  18.63  92.11   0.00  14.20 111.77   0.00  42.73
   2_xyz: 111.77   0.00  18.63  92.11   0.00  14.20 111.77   0.00  42.73
   2_adp: 111.45   0.00  18.28  92.20   0.00  13.69 111.45   2.37  43.28
   2_occ: 111.45   0.00  18.28  92.20   0.00  13.69 111.45   2.37  43.28
   3_bss: 111.45   0.00  18.28  92.20   0.00  13.69 111.45   2.37  43.28
   3_xyz: 111.45   0.00  18.28  92.20   0.00  13.69 111.45   2.37  43.28
   3_adp: 108.61   0.00  17.66  92.04   0.00  12.75 108.61   4.26  44.37
   3_occ: 108.61   0.00  17.66  92.04   0.00  12.75 108.61   4.26  44.37
   4_bss: 108.61   0.00  17.66  92.04   0.00  12.75 108.61   4.26  44.37
   4_xyz: 108.61   0.00  17.66  92.04   0.00  12.75 108.61   4.26  44.37
   4_adp: 101.21   0.87  16.56  80.84   0.87  12.20 101.21   4.98  40.32
   4_occ: 101.21   0.87  16.56  80.84   0.87  12.20 101.21   4.98  40.32
   5_bss: 101.21   0.87  16.56  80.84   0.87  12.20 101.21   4.98  40.32
   5_xyz: 101.21   0.87  16.56  80.84   0.87  12.20 101.21   4.98  40.32
   5_adp:  98.28   0.00  16.59  82.48   0.00  12.06  98.28   4.97  41.24
   5_occ:  98.28   0.00  16.59  82.48   0.00  12.06  98.28   4.97  41.24
   5_bss:  98.29   0.00  16.59  82.49   0.00  12.06  98.29   4.97  41.24
------------------------------------------------------------------------
 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:    1.636    0.019    0.536
   1_adp:    1.636    0.019    0.536
   1_occ:    1.636    0.019    0.536
   2_bss:    1.636    0.019    0.536
   2_xyz:    1.520    0.051    0.676
   2_adp:    1.520    0.051    0.676
   2_occ:    1.520    0.051    0.676
   3_bss:    1.520    0.051    0.676
   3_xyz:    1.462    0.072    0.755
   3_adp:    1.462    0.072    0.755
   3_occ:    1.462    0.072    0.755
   4_bss:    1.462    0.072    0.755
   4_xyz:    1.449    0.048    0.786
   4_adp:    1.449    0.048    0.786
   4_occ:    1.449    0.048    0.786
   5_bss:    1.449    0.048    0.786
   5_xyz:    1.444    0.052    0.788
   5_adp:    1.444    0.052    0.788
   5_occ:    1.444    0.052    0.788
   5_bss:    1.444    0.052    0.788
------------------------------------------------------------------------

CPU time actual refinement: 342.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_714/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_714/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_714/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_714/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_714/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.07 
  Macro-tasks:
    bulk solvent and scale       = 53.04  
    individual site refinement   = 135.45 
    weights calculation          = 29.77  
    collect and process          = 6.56   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 224.94 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 103.60 
    alpha_beta                      = 8.18   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.71 
    fmodel                         = 8.83   
    r_factors                      = 0.31   
    phase_errors                   = 10.79  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 247.60 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.800 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    646 calls, 103.20 s
gradients_fft:          591 calls,  99.27 s

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

# Date 2008-01-16 Time 05:29:36 PST -0800 (1200490176.08 s)
Start R-work = 0.4658, R-free = 0.4606 (no bulk solvent and anisotropic scale)
Final R-work = 0.1447, R-free = 0.1896 (no bulk solvent and anisotropic scale)

Start R-work = 0.4547, R-free = 0.4500
Final R-work = 0.1259, R-free = 0.1738