# Date 2008-01-16 Time 05:06:36 PST -0800 (1200488796.50 s)
#phil __OFF__

Command line arguments: "../593.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11440
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 593

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 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: (69.8988, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99083
Completeness in resolution range: 0.935795
Completeness with d_max=infinity: 0.932943

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0370
                             d_min =   1.9908

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99083
Completeness in resolution range: 0.935795
Completeness with d_max=infinity: 0.932943

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0375 -  4.2597 [2205/2233]  1982   223  10.1%
  bin  2:  4.2597 -  3.3938 [2101/2124]  1890   211  10.0%
  bin  3:  3.3938 -  2.9686 [2066/2088]  1865   201   9.7%
  bin  4:  2.9686 -  2.6988 [2088/2107]  1876   212  10.2%
  bin  5:  2.6988 -  2.5063 [2026/2055]  1820   206  10.2%
  bin  6:  2.5063 -  2.3592 [2062/2104]  1856   206  10.0%
  bin  7:  2.3592 -  2.2414 [2021/2057]  1823   198   9.8%
  bin  8:  2.2414 -  2.1441 [2026/2064]  1818   208  10.3%
  bin  9:  2.1441 -  2.0618 [2027/2057]  1832   195   9.6%
  bin 10:  2.0618 -  1.9908 [ 967/2044]   868    99  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_593/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:
        1.38 -     2.09: 7
        2.09 -     2.79: 640
        2.79 -     3.49: 4391
        3.49 -     4.20: 9144
        4.20 -     4.90: 13588
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.385 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.717 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.717 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.740 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.765 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27765 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_593/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_593/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4693   r_free= 0.4642   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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.280417                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7509 0.99   1429  158 0.3715 0.3638       6.562      6.5227|
|  2:  4.7509 -  3.7908 0.99   1385  154 0.4099 0.4543      6.8242       6.919|
|  3:  3.7908 -  3.3175 0.99   1336  149 0.4507 0.4047      6.6852      6.6109|
|  4:  3.3175 -  3.0168 0.99   1344  145 0.4564 0.4440      6.5118      6.4752|
|  5:  3.0168 -  2.8021 0.99   1313  152 0.4991 0.4657       6.362      6.3796|
|  6:  2.8021 -  2.6378 0.98   1334  143 0.5022 0.5047      6.2748       6.171|
|  7:  2.6378 -  2.5063 0.99   1292  152 0.4915 0.4680      6.2259      6.1399|
|  8:  2.5063 -  2.3977 0.99   1337  140 0.5126 0.4975      6.1769      6.1617|
|  9:  2.3977 -  2.3057 0.98   1313  147 0.5095 0.5047      6.1078      6.1638|
| 10:  2.3057 -  2.2264 0.98   1305  144 0.5254 0.5069      6.0854      6.1029|
| 11:  2.2264 -  2.1570 0.98   1286  151 0.5202 0.5092      6.0266       6.027|
| 12:  2.1570 -  2.0955 0.99   1307  141 0.5203 0.5628      5.9483      5.9992|
| 13:  2.0955 -  2.0405 0.95   1271  128 0.5335 0.5488      5.8888      5.8359|
| 14:  2.0405 -  1.9908 0.30    378   55 0.4756 0.4803      5.8605      5.7437|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7509  1429   158  0.72  32.77   0.82     0.74      65588.42|
|  2:  4.7509 -  3.7908  1385   154  0.70  34.93   0.89     0.79     103655.74|
|  3:  3.7908 -  3.3175  1336   149  0.61  43.14   0.87     0.77     108840.93|
|  4:  3.3175 -  3.0168  1344   145  0.52  50.12   0.89     0.68      95130.34|
|  5:  3.0168 -  2.8021  1313   152  0.46  54.78   0.86     0.62      73073.93|
|  6:  2.8021 -  2.6378  1334   143  0.42  58.44   0.88     0.57      65915.49|
|  7:  2.6378 -  2.5063  1292   152  0.42  58.26   0.90     0.56      59316.74|
|  8:  2.5063 -  2.3977  1337   140  0.40  60.10   0.89     0.55      54837.70|
|  9:  2.3977 -  2.3057  1313   147  0.39  60.88   0.89     0.56      51682.89|
| 10:  2.3057 -  2.2264  1305   144  0.38  61.88   0.91     0.54      47533.02|
| 11:  2.2264 -  2.1570  1286   151  0.32  65.89   0.91     0.50      47685.49|
| 12:  2.1570 -  2.0955  1307   141  0.28  69.29   0.89     0.42      45459.12|
| 13:  2.0955 -  2.0405  1271   128  0.23  72.59   0.88     0.37      41287.68|
| 14:  2.0405 -  1.9908   378    55  0.28  69.37   0.98     0.35      31216.22|
|alpha:            min =        0.35 max =            0.79 mean =         0.59|
|beta:             min =    31216.22 max =       108840.93 mean =     65756.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.60|
|phase err.(test): min =        0.00 max =           89.76 mean =        55.92|
|-----------------------------------------------------------------------------|

============================== 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 = 17.590770             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.335   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.366471              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.345   (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 |  1.385 -  1.736:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.736 -  2.088:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.088 -  2.439:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.439 -  2.791:      614 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.791 -  3.142:     2088 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.142 -  3.494:     2303 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.494 -  3.845:     4465 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.845 -  4.197:     4679 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.197 -  4.548:     6132 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.548 -  4.900:     7456 |
|-----------------------------------------------------------------------------|
|-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 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.385 |       0.319 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4693   r_free= 0.4642   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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.280417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4590   r_free= 0.4541   ksol= 0.28   Bsol= 35.63   scale= 0.921   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.74,3.05,4.01,0.00,0.00,0.00); trace/3= 1.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.272652                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.555312             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.849   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.195901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.974   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4590      final r-factor (work) = 0.3293          |
| start r-factor (free) = 0.4541      final r-factor (free) = 0.3565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.8024 = 14.56 * 0.50 * 6.2696 + 1.00 * 0.1746                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.7070 = 14.56 * 0.50 * 6.1202 + 1.00 * 0.1666                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3293      final r-factor (work) = 0.2985          |
| start r-factor (free) = 0.3565      final r-factor (free) = 0.3666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3252 = 1.20 * 1.00 * 6.1202 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1653 = 1.20 * 1.00 * 5.9752 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.11  18.55    None  None   None       |
|    all(noH): 2823   0      0.00    109.11  18.55    None  None   None       |
|    Sol.    : 438    0      0.46    109.11  40.95    None  None   None       |
|    Mac.    : 2385   0      0.00    89.99   14.44    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 -  10.911: 1100   |   5:    54.553 -  65.464:   76        |
|      1:    10.911 -  21.821:  912   |   6:    65.464 -  76.375:   40        |
|      2:    21.821 -  32.732:  385   |   7:    76.375 -  87.285:    8        |
|      3:    32.732 -  43.643:  180   |   8:    87.285 -  98.196:    5        |
|      4:    43.643 -  54.553:  114   |   9:    98.196 - 109.106:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2985 r_free = 0.3666             target_work(ml) = 5.984         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2982 r_free = 0.3665             target_work(ml) = 5.984         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2982   r_free= 0.3665   ksol= 0.28   Bsol= 35.63   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.74,3.05,4.01,0.00,0.00,0.00); trace/3= 1.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.983894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2949   r_free= 0.3631   ksol= 0.32   Bsol= 66.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,1.20,1.86,0.00,0.00,0.00); trace/3= 0.40                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.980084                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.404267             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.241   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.427758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.430  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2949      final r-factor (work) = 0.2127          |
| start r-factor (free) = 0.3631      final r-factor (free) = 0.2701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.2453 = 10.40 * 0.50 * 5.9742 + 1.00 * 0.1666                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.6540 = 10.40 * 0.50 * 5.8740 + 1.00 * 0.0967                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2127      final r-factor (work) = 0.1930          |
| start r-factor (free) = 0.2701      final r-factor (free) = 0.2467          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5322 = 0.43 * 1.00 * 5.8740 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4294 = 0.43 * 1.00 * 5.6509 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.32  17.88    None  None   None       |
|    all(noH): 2823   0      0.00    108.32  17.88    None  None   None       |
|    Sol.    : 438    0      3.44    108.32  41.93    None  None   None       |
|    Mac.    : 2385   0      0.00    90.45   13.46    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 -  10.832: 1213   |   5:    54.160 -  64.992:   79        |
|      1:    10.832 -  21.664:  919   |   6:    64.992 -  75.824:   36        |
|      2:    21.664 -  32.496:  259   |   7:    75.824 -  86.656:    9        |
|      3:    32.496 -  43.328:  181   |   8:    86.656 -  97.488:    3        |
|      4:    43.328 -  54.160:  121   |   9:    97.488 - 108.320:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1930 r_free = 0.2467             target_work(ml) = 5.611         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1928 r_free = 0.2469             target_work(ml) = 5.610         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1928   r_free= 0.2469   ksol= 0.32   Bsol= 66.72   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,1.20,1.86,0.00,0.00,0.00); trace/3= 0.40                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.610408                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1924   r_free= 0.2454   ksol= 0.34   Bsol= 77.64   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.28,0.65,-0.00,0.00,0.00); trace/3= -0.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.608777                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.287257              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.885  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.276257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.224  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1924      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2454      final r-factor (free) = 0.1952          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0434 = 5.29 * 0.50 * 5.6539 + 1.00 * 0.0967                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6537 = 5.29 * 0.50 * 5.5115 + 1.00 * 0.0833                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.1952      final r-factor (free) = 0.1874          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0461 = 1.28 * 1.00 * 5.5115 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8324 = 1.28 * 1.00 * 5.3427 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.57    107.87  17.95    None  None   None       |
|    all(noH): 2823   0      0.57    107.87  17.95    None  None   None       |
|    Sol.    : 438    0      5.11    107.87  45.65    None  None   None       |
|    Mac.    : 2385   0      0.57    97.55   12.87    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:     0.567 -  11.297: 1362   |   5:    54.219 -  64.950:   82        |
|      1:    11.297 -  22.028:  868   |   6:    64.950 -  75.680:   68        |
|      2:    22.028 -  32.758:  183   |   7:    75.680 -  86.411:   23        |
|      3:    32.758 -  43.489:  108   |   8:    86.411 -  97.141:    7        |
|      4:    43.489 -  54.219:  118   |   9:    97.141 - 107.872:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1358 r_free = 0.1874             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1358 r_free = 0.1874             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1358   r_free= 0.1874   ksol= 0.34   Bsol= 77.64   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.28,0.65,-0.00,0.00,0.00); trace/3= -0.60                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.320429                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1875   ksol= 0.34   Bsol= 82.69   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-0.74,0.40,-0.00,0.00,0.00); trace/3= -0.82                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.321788                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.915356              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.638  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.102  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1875      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5450 = 3.92 * 0.50 * 5.3439 + 1.00 * 0.0833                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4288 = 3.92 * 0.50 * 5.2853 + 1.00 * 0.0819                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9719 = 0.18 * 1.00 * 5.2853 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9626 = 0.18 * 1.00 * 5.2512 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    104.94  17.16    None  None   None       |
|    all(noH): 2823   0      0.78    104.94  17.16    None  None   None       |
|    Sol.    : 438    0      1.00    104.94  42.91    None  None   None       |
|    Mac.    : 2385   0      0.78    91.48   12.43    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:     0.775 -  11.192: 1415   |   5:    52.858 -  63.275:   79        |
|      1:    11.192 -  21.608:  851   |   6:    63.275 -  73.692:   59        |
|      2:    21.608 -  32.025:  171   |   7:    73.692 -  84.108:   16        |
|      3:    32.025 -  42.442:  116   |   8:    84.108 -  94.525:    8        |
|      4:    42.442 -  52.858:  105   |   9:    94.525 - 104.942:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1701             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1701             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1701   ksol= 0.34   Bsol= 82.69   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-0.74,0.40,-0.00,0.00,0.00); trace/3= -0.82                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.235597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1701   ksol= 0.33   Bsol= 72.40   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.01,0.21,-0.00,0.00,0.00); trace/3= -0.97                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.235322                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.944085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.091  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.722396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.392  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8110 = 2.94 * 0.50 * 5.2506 + 1.00 * 0.0819                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7681 = 2.94 * 0.50 * 5.2245 + 1.00 * 0.0774                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7843 = 0.72 * 1.00 * 5.2245 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7698 = 0.72 * 1.00 * 5.2028 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.71  16.94    None  None   None       |
|    all(noH): 2823   0      0.00    102.71  16.94    None  None   None       |
|    Sol.    : 438    0      0.00    102.71  42.46    None  None   None       |
|    Mac.    : 2385   0      0.00    94.19   12.25    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 -  10.271: 1275   |   5:    51.353 -  61.623:   80        |
|      1:    10.271 -  20.541:  952   |   6:    61.623 -  71.894:   52        |
|      2:    20.541 -  30.812:  197   |   7:    71.894 -  82.165:   25        |
|      3:    30.812 -  41.082:  125   |   8:    82.165 -  92.435:    9        |
|      4:    41.082 -  51.353:  102   |   9:    92.435 - 102.706:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1657             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1658             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1658   ksol= 0.33   Bsol= 72.40   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.01,0.21,-0.00,0.00,0.00); trace/3= -0.97                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206102                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7509 0.99   1429  158 0.1008 0.1307      5.4206      5.5959|
|  2:  4.7509 -  3.7908 0.99   1385  154 0.0848 0.1061      5.4354      5.6253|
|  3:  3.7908 -  3.3175 0.99   1336  149 0.1097 0.1530      5.4924      5.8656|
|  4:  3.3175 -  3.0168 0.99   1344  145 0.1318 0.1696      5.5044      5.6476|
|  5:  3.0168 -  2.8021 0.99   1313  152 0.1451 0.1814      5.4028      5.5958|
|  6:  2.8021 -  2.6378 0.98   1334  143 0.1344 0.2221      5.2917      5.5706|
|  7:  2.6378 -  2.5063 0.99   1292  152 0.1380 0.1769      5.2448      5.4409|
|  8:  2.5063 -  2.3977 0.99   1337  140 0.1258 0.1747      5.1603      5.3496|
|  9:  2.3977 -  2.3057 0.98   1313  147 0.1259 0.2002      5.0868      5.3951|
| 10:  2.3057 -  2.2264 0.98   1305  144 0.1213 0.1766      5.0258      5.1983|
| 11:  2.2264 -  2.1570 0.98   1286  151 0.1231 0.1993      4.9747      5.3516|
| 12:  2.1570 -  2.0955 0.99   1307  141 0.1172 0.1663      4.9057      5.1429|
| 13:  2.0955 -  2.0405 0.95   1271  128 0.1129 0.1704      4.8099      5.0192|
| 14:  2.0405 -  1.9908 0.30    378   55 0.1020 0.1857      4.7218      5.0206|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7509  1429   158  0.94   9.58   0.96     0.93       7965.26|
|  2:  4.7509 -  3.7908  1385   154  0.95   8.28   1.00     0.98       9338.13|
|  3:  3.7908 -  3.3175  1336   149  0.93  11.73   1.02     1.01      10678.52|
|  4:  3.3175 -  3.0168  1344   145  0.91  14.95   1.00     0.98      11415.12|
|  5:  3.0168 -  2.8021  1313   152  0.89  17.44   0.99     0.97       9654.52|
|  6:  2.8021 -  2.6378  1334   143  0.88  18.22   0.97     0.95       8509.85|
|  7:  2.6378 -  2.5063  1292   152  0.89  17.23   0.99     0.95       7370.32|
|  8:  2.5063 -  2.3977  1337   140  0.89  17.08   0.98     0.94       6566.88|
|  9:  2.3977 -  2.3057  1313   147  0.89  17.26   0.99     0.94       5615.23|
| 10:  2.3057 -  2.2264  1305   144  0.89  16.96   0.98     0.93       5075.51|
| 11:  2.2264 -  2.1570  1286   151  0.89  17.14   0.97     0.93       4653.01|
| 12:  2.1570 -  2.0955  1307   141  0.90  16.84   0.99     0.98       4287.43|
| 13:  2.0955 -  2.0405  1271   128  0.90  16.92   0.97     0.95       3609.55|
| 14:  2.0405 -  1.9908   378    55  0.91  15.45   0.95     0.90       2933.64|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2933.64 max =        11415.12 mean =      7234.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.28|
|phase err.(test): min =        0.00 max =           88.71 mean =        14.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1657   ksol= 0.32   Bsol= 71.37   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-0.97,0.29,-0.00,0.00,0.00); trace/3= -0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206129                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1657   ksol= 0.32   Bsol= 71.37   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-0.97,0.29,-0.00,0.00,0.00); trace/3= -0.89                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7509 0.99   1429  158 0.1007 0.1306      5.4193      5.5965|
|  2:  4.7509 -  3.7908 0.99   1385  154 0.0849 0.1062      5.4357      5.6255|
|  3:  3.7908 -  3.3175 0.99   1336  149 0.1097 0.1531      5.4928      5.8659|
|  4:  3.3175 -  3.0168 0.99   1344  145 0.1318 0.1696      5.5046      5.6478|
|  5:  3.0168 -  2.8021 0.99   1313  152 0.1451 0.1814      5.4029      5.5957|
|  6:  2.8021 -  2.6378 0.98   1334  143 0.1343 0.2221      5.2916      5.5704|
|  7:  2.6378 -  2.5063 0.99   1292  152 0.1380 0.1771       5.245      5.4412|
|  8:  2.5063 -  2.3977 0.99   1337  140 0.1258 0.1747      5.1605      5.3498|
|  9:  2.3977 -  2.3057 0.98   1313  147 0.1259 0.2003      5.0869      5.3952|
| 10:  2.3057 -  2.2264 0.98   1305  144 0.1213 0.1767      5.0261      5.1988|
| 11:  2.2264 -  2.1570 0.98   1286  151 0.1230 0.1992      4.9747      5.3516|
| 12:  2.1570 -  2.0955 0.99   1307  141 0.1173 0.1663      4.9058      5.1429|
| 13:  2.0955 -  2.0405 0.95   1271  128 0.1129 0.1703      4.8099      5.0188|
| 14:  2.0405 -  1.9908 0.30    378   55 0.1019 0.1857      4.7222      5.0208|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7509  1429   158  0.94   9.58   0.96     0.93       7953.05|
|  2:  4.7509 -  3.7908  1385   154  0.95   8.28   1.00     0.98       9341.57|
|  3:  3.7908 -  3.3175  1336   149  0.93  11.73   1.02     1.01      10690.52|
|  4:  3.3175 -  3.0168  1344   145  0.91  14.96   1.00     0.99      11420.12|
|  5:  3.0168 -  2.8021  1313   152  0.89  17.44   0.99     0.97       9656.35|
|  6:  2.8021 -  2.6378  1334   143  0.88  18.22   0.98     0.95       8510.20|
|  7:  2.6378 -  2.5063  1292   152  0.89  17.23   0.99     0.96       7371.94|
|  8:  2.5063 -  2.3977  1337   140  0.89  17.09   0.99     0.95       6569.36|
|  9:  2.3977 -  2.3057  1313   147  0.89  17.27   0.99     0.94       5618.95|
| 10:  2.3057 -  2.2264  1305   144  0.89  16.97   0.98     0.93       5077.85|
| 11:  2.2264 -  2.1570  1286   151  0.89  17.14   0.98     0.93       4653.00|
| 12:  2.1570 -  2.0955  1307   141  0.90  16.84   0.99     0.98       4288.31|
| 13:  2.0955 -  2.0405  1271   128  0.90  16.91   0.98     0.96       3607.54|
| 14:  2.0405 -  1.9908   378    55  0.91  15.45   0.95     0.91       2930.94|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2930.94 max =        11420.12 mean =      7235.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.28|
|phase err.(test): min =        0.00 max =           88.74 mean =        14.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.71  16.94    None  None   None       |
|    all(noH): 2823   0      0.00    102.71  16.94    None  None   None       |
|    Sol.    : 438    0      0.00    102.71  42.46    None  None   None       |
|    Mac.    : 2385   0      0.00    94.19   12.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.274: 1275   |   5:    51.356 -  61.626:   80        |
|      1:    10.274 -  20.544:  952   |   6:    61.626 -  71.897:   52        |
|      2:    20.544 -  30.815:  197   |   7:    71.897 -  82.168:   25        |
|      3:    30.815 -  41.085:  125   |   8:    82.168 -  92.438:    9        |
|      4:    41.085 -  51.356:  102   |   9:    92.438 - 102.709:    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)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.648 - 5.416
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 316
   mapped sites are within: 0.723 - 5.416

peak=    6.193 closest distance to " O   HOH Z 210 " =    1.305
peak=    5.151 closest distance to " CB  GLN A 223 " =    1.417
peak=    4.985 closest distance to " O   HOH Z 113 " =    1.816
peak=    4.959 closest distance to " O   HOH Z  49 " =    1.534
peak=    4.886 closest distance to " CG  PRO A  54 " =    1.357
peak=    4.856 closest distance to " O   HOH Z 369 " =    2.100
peak=    4.686 closest distance to " CB  ARG A 190 " =    1.704
peak=    4.652 closest distance to " CZ  PHE A 218 " =    1.144
peak=    4.636 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.628 closest distance to " CB  GLU A 152 " =    1.169
peak=    4.616 closest distance to " CB  GLN A 183 " =    1.280
peak=    4.609 closest distance to " O   HOH Z 117 " =    1.196
peak=    4.532 closest distance to " CG  PRO A 280 " =    0.875
peak=    4.524 closest distance to " O   HOH Z 298 " =    1.920
peak=    4.497 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.426 closest distance to " CB  SER A  63 " =    1.119
peak=    4.407 closest distance to " CD2 TRP A 179 " =    1.307
peak=    4.391 closest distance to " CA  ARG A  36 " =    1.099
peak=    4.337 closest distance to " O   PRO A 198 " =    1.519
peak=    4.309 closest distance to " CG  PRO A  90 " =    1.288
peak=    4.287 closest distance to " CB  ARG A  79 " =    1.400
peak=    4.252 closest distance to " CG  PRO A 198 " =    1.217
peak=    4.227 closest distance to " O   HOH Z 232 " =    2.428
peak=    4.192 closest distance to " O   HOH Z 214 " =    1.351
peak=    4.167 closest distance to " O   HOH Z 234 " =    3.785
peak=    4.142 closest distance to " CB  PRO A  54 " =    0.912
peak=    4.136 closest distance to " O   HOH Z 412 " =    3.685
peak=    4.126 closest distance to " CB  GLU A 277 " =    3.830
peak=    4.092 closest distance to " O   HOH Z  43 " =    2.066
peak=    4.079 closest distance to " CZ  PHE A  38 " =    1.235
peak=    4.067 closest distance to " CZ3 TRP A 266 " =    1.123
peak=    4.039 closest distance to " NE2 GLN A  11 " =    1.131
peak=    4.036 closest distance to " CA  ALA A  51 " =    0.979
peak=    4.036 closest distance to " O   HOH Z 188 " =    2.854
peak=    4.016 closest distance to " O   HOH Z 403 " =    1.743
peak=    3.987 closest distance to " CA  ARG A 195 " =    1.233
peak=    3.986 closest distance to " O   HOH Z 368 " =    2.298
peak=    3.985 closest distance to " CD  LYS A 166 " =    1.406
peak=    3.962 closest distance to " O   HOH Z 346 " =    1.578
peak=    3.952 closest distance to " OG BSER A 134 " =    2.829
peak=    3.947 closest distance to " CG  PRO A 213 " =    1.203
peak=    3.947 closest distance to " O   SER A  87 " =    2.275
peak=    3.926 closest distance to " CG  PRO A 243 " =    1.078
peak=    3.925 closest distance to " CB  ASN A 148 " =    1.437
peak=    3.923 closest distance to " CB  GLU A 128 " =    1.084
peak=    3.914 closest distance to " CB  VAL A 202 " =    1.493
peak=    3.897 closest distance to " CD  ARG A 269 " =    0.980
peak=    3.897 closest distance to " O   HOH Z 362 " =    3.513
peak=    3.895 closest distance to " O   HOH Z 423 " =    1.869
peak=    3.885 closest distance to " CA  ALA A 160 " =    0.917
peak=    3.885 closest distance to " O   HOH Z 402 " =    1.497
peak=    3.884 closest distance to " O   HOH Z 261 " =    2.376
peak=    3.879 closest distance to " CG  ARG A  66 " =    2.565
peak=    3.876 closest distance to " O   ALA A 165 " =    1.360
peak=    3.866 closest distance to " O   HOH Z  65 " =    0.986
peak=    3.859 closest distance to " O   HOH Z 287 " =    1.822
peak=    3.854 closest distance to " ND2 ASN A 187 " =    1.500
peak=    3.845 closest distance to " CD1 LEU A  96 " =    0.775
peak=    3.841 closest distance to " CB  TYR A 169 " =    0.825
peak=    3.819 closest distance to " O   HOH Z  19 " =    1.569
peak=    3.794 closest distance to " CB  TRP A 266 " =    1.042
peak=    3.793 closest distance to " O   HOH Z 134 " =    1.592
peak=    3.791 closest distance to " O   HOH Z 383 " =    1.997
peak=    3.786 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.786 closest distance to " O   HOH Z  63 " =    1.918
peak=    3.757 closest distance to " O   HOH Z 248 " =    1.459
peak=    3.755 closest distance to " ND2 ASN A 249 " =    1.971
peak=    3.743 closest distance to " OG BSER A 164 " =    2.231
peak=    3.743 closest distance to " O   HOH Z 406 " =    1.622
peak=    3.740 closest distance to " NH2AARG A 275 " =    3.478
peak=    3.731 closest distance to " O  BHOH Z 338 " =    2.103
peak=    3.719 closest distance to " O   HOH Z 417 " =    3.229
peak=    3.718 closest distance to " O   HOH Z 132 " =    2.688
peak=    3.710 closest distance to " O   HOH Z  80 " =    1.896
peak=    3.695 closest distance to " CB  PHE A 204 " =    0.838
peak=    3.693 closest distance to " CA  ALA A 100 " =    0.995
peak=    3.691 closest distance to " O   HOH Z  35 " =    2.324
peak=    3.688 closest distance to " OH  TYR A 116 " =    1.189
peak=    3.687 closest distance to " N   ASN A  39 " =    1.267
peak=    3.686 closest distance to " O   HOH Z 286 " =    2.141
peak=    3.686 closest distance to " O   HOH Z 425 " =    1.424
peak=    3.684 closest distance to " O   HOH Z 316 " =    3.039
peak=    3.680 closest distance to " CB  TRP A 179 " =    1.461
peak=    3.680 closest distance to " CB  THR A  52 " =    0.823
peak=    3.676 closest distance to " CB  ASN A 142 " =    1.151
peak=    3.669 closest distance to " CG  ARG A 138 " =    1.364
peak=    3.668 closest distance to " O   HOH Z 142 " =    1.606
peak=    3.665 closest distance to " CB  PRO A  90 " =    1.178
peak=    3.663 closest distance to " O   HOH Z 193 " =    2.029
peak=    3.662 closest distance to " O   HOH Z  48 " =    1.802
peak=    3.662 closest distance to " O   HOH Z 183 " =    1.672
peak=    3.659 closest distance to " O   THR A 220 " =    1.136
peak=    3.657 closest distance to " O   HOH Z 353 " =    2.743
peak=    3.654 closest distance to " O   HOH Z 203 " =    1.741
peak=    3.650 closest distance to " CA  TYR A 116 " =    1.336
peak=    3.643 closest distance to " CB  VAL A 265 " =    1.222
peak=    3.641 closest distance to " O   HOH Z 345 " =    1.665
peak=    3.634 closest distance to " CE  LYS A  76 " =    0.853
peak=    3.634 closest distance to " O   HOH Z  40 " =    1.915
peak=    3.629 closest distance to " CD  LYS A  76 " =    2.057
peak=    3.627 closest distance to " O   HOH Z 298 " =    2.362
peak=    3.626 closest distance to " CG  MET A 185 " =    1.086
peak=    3.623 closest distance to " O   HOH Z  21 " =    1.791
peak=    3.617 closest distance to " CA  GLU A 152 " =    0.849
peak=    3.616 closest distance to " OD1 ASN A  69 " =    2.563
peak=    3.615 closest distance to " O   HOH Z 427 " =    2.960
peak=    3.610 closest distance to " NZ  LYS A 117 " =    2.930
peak=    3.610 closest distance to " CA  MET A 105 " =    1.100
peak=    3.605 closest distance to " O   HOH Z 209 " =    2.298
peak=    3.605 closest distance to " CG  GLU A  37 " =    0.994
peak=    3.605 closest distance to " O   HOH Z 258 " =    2.048
peak=    3.599 closest distance to " O   TYR A 116 " =    1.418
peak=    3.597 closest distance to " O   HOH Z 251 " =    1.568
peak=    3.594 closest distance to " O   HOH Z 294 " =    1.595
peak=    3.593 closest distance to " O   HOH Z 365 " =    2.646
peak=    3.580 closest distance to " CA  ALA A 295 " =    1.048
peak=    3.577 closest distance to " CB  SER A 141 " =    1.089
peak=    3.575 closest distance to " CA  VAL A 125 " =    1.237
peak=    3.568 closest distance to " N   CYS A 260 " =    0.870
peak=    3.566 closest distance to " O   HOH Z  76 " =    1.178
peak=    3.563 closest distance to " CA  ILE A 106 " =    0.812
peak=    3.561 closest distance to " O   HOH Z 280 " =    2.998
peak=    3.560 closest distance to " CB  LEU A 228 " =    1.146
peak=    3.559 closest distance to " CB  THR A  31 " =    1.676
peak=    3.553 closest distance to " CA  ASN A 176 " =    1.628
peak=    3.551 closest distance to " O   HOH Z 285 " =    2.374
peak=    3.551 closest distance to " OG  SER A 135 " =    1.290
peak=    3.549 closest distance to " CG  LEU A 167 " =    1.145
peak=    3.549 closest distance to " CB  PRO A  54 " =    1.372
peak=    3.548 closest distance to " O   HOH Z 336 " =    1.998
peak=    3.536 closest distance to " CB  LEU A  83 " =    0.810
peak=    3.535 closest distance to " CG2AVAL A  72 " =    1.916
peak=    3.533 closest distance to " CB  ASP A 140 " =    1.000
peak=    3.528 closest distance to " N   TYR A 116 " =    1.610
peak=    3.526 closest distance to " NH1AARG A 145 " =    1.406
peak=    3.525 closest distance to " O   HOH Z 325 " =    2.072
peak=    3.523 closest distance to " O   HOH Z 299 " =    4.412
peak=    3.507 closest distance to " O   HOH Z 126 " =    1.585
peak=    3.504 closest distance to " CB  GLU A  46 " =    1.014
peak=    3.502 closest distance to " O   HOH Z 357 " =    2.157
peak=    3.497 closest distance to " O   HOH Z 213 " =    2.183
peak=    3.496 closest distance to " N   HIS A 108 " =    1.846
peak=    3.494 closest distance to " CA  ASP A 162 " =    1.088
peak=    3.491 closest distance to " O   HOH Z 285 " =    2.162
peak=    3.489 closest distance to " O   HOH Z 265 " =    2.071
peak=    3.489 closest distance to " CD2 LEU A 297 " =    0.982
peak=    3.484 closest distance to " CA  GLN A  11 " =    1.608
peak=    3.480 closest distance to " CA  MET A 188 " =    1.032
peak=    3.479 closest distance to " O   HOH Z 433 " =    1.441
peak=    3.478 closest distance to " O   HOH Z 359 " =    1.744
peak=    3.473 closest distance to " CD  PRO A  54 " =    1.015
peak=    3.472 closest distance to " O   HOH Z  59 " =    2.476
peak=    3.472 closest distance to " CG1 ILE A  49 " =    1.717
peak=    3.472 closest distance to " CB  MET A  40 " =    1.031
peak=    3.472 closest distance to " CB  ASN A 285 " =    0.914
peak=    3.472 closest distance to " CA  GLU A  46 " =    0.913
peak=    3.470 closest distance to " O   HOH Z 180 " =    2.267
peak=    3.470 closest distance to " O   HOH Z  54 " =    1.146
peak=    3.466 closest distance to " O   HOH Z 366 " =    2.409
peak=    3.460 closest distance to " O   HOH Z 126 " =    1.908
peak=    3.457 closest distance to " CB  ALA A 291 " =    1.109
peak=    3.455 closest distance to " CB  PRO A 243 " =    1.398
peak=    3.454 closest distance to " ND2 ASN A 249 " =    0.911
peak=    3.453 closest distance to " O   HOH Z 214 " =    3.040
peak=    3.446 closest distance to " CG2 ILE A 120 " =    1.276
peak=    3.437 closest distance to " CA  ASN A 215 " =    0.950
peak=    3.437 closest distance to " CG1 VAL A 153 " =    1.065
peak=    3.432 closest distance to " O   HOH Z 422 " =    2.535
peak=    3.431 closest distance to " O   HOH Z 250 " =    1.334
peak=    3.431 closest distance to " CG2 VAL A 257 " =    0.759
peak=    3.421 closest distance to " O   HOH Z 303 " =    2.422
peak=    3.420 closest distance to " O   HOH Z  78 " =    1.728
peak=    3.414 closest distance to " CD1 ILE A 199 " =    1.142
peak=    3.414 closest distance to " CD  ARG A 159 " =    0.809
peak=    3.409 closest distance to " CG2 VAL A 197 " =    1.149
peak=    3.407 closest distance to " O   HOH Z 392 " =    2.215
peak=    3.405 closest distance to " CA  SER A  87 " =    1.067
peak=    3.401 closest distance to " O   HOH Z 227 " =    1.579
peak=    3.400 closest distance to " O   HOH Z 411 " =    1.733
peak=    3.397 closest distance to " O   ASN A  74 " =    1.727
peak=    3.396 closest distance to " O   HOH Z 196 " =    1.225
peak=    3.395 closest distance to " CG2 ILE A 234 " =    1.100
peak=    3.389 closest distance to " CB  ALA A 248 " =    1.376
peak=    3.387 closest distance to " CG AARG A 275 " =    1.275
peak=    3.382 closest distance to " NE2 GLN A  77 " =    3.270
peak=    3.371 closest distance to " N   SER A 164 " =    0.970
peak=    3.368 closest distance to " O   HOH Z 435 " =    3.014
peak=    3.367 closest distance to " O   ASP A 124 " =    1.158
peak=    3.365 closest distance to " O   PRO A 213 " =    1.494
peak=    3.363 closest distance to " CG2BVAL A  41 " =    0.891
peak=    3.360 closest distance to " CA  SER A  32 " =    1.667
peak=    3.357 closest distance to " O   HOH Z  20 " =    1.469
peak=    3.346 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.342 closest distance to " O   ASP A 191 " =    1.507
peak=    3.342 closest distance to " O   HOH Z 259 " =    2.350
peak=    3.338 closest distance to " CG  GLN A  58 " =    0.978
peak=    3.334 closest distance to " N   ILE A  20 " =    2.310
peak=    3.333 closest distance to " O   HOH Z  63 " =    2.175
peak=    3.332 closest distance to " CG2 ILE A  20 " =    1.275
peak=    3.328 closest distance to " O   HOH Z 148 " =    3.474
peak=    3.327 closest distance to " CB  ASN A 110 " =    1.131
peak=    3.325 closest distance to " O   HOH Z 313 " =    1.906
peak=    3.324 closest distance to " OG  SER A 245 " =    1.611
peak=    3.323 closest distance to " O   HOH Z 158 " =    3.055
peak=    3.322 closest distance to " CD  ARG A  66 " =    2.293
peak=    3.320 closest distance to " OD2 ASP A 298 " =    3.848
peak=    3.319 closest distance to " O   HOH Z 146 " =    2.281
peak=    3.314 closest distance to " CG1 ILE A  20 " =    1.273
peak=    3.313 closest distance to " N   ARG A 156 " =    1.471
peak=    3.311 closest distance to " O   HOH Z 393 " =    3.215
peak=    3.307 closest distance to " O   HOH Z  97 " =    2.205
peak=    3.304 closest distance to " O   HOH Z 130 " =    2.208
peak=    3.303 closest distance to " O   HOH Z 420 " =    1.841
peak=    3.298 closest distance to " OG  SER A  28 " =    1.466
peak=    3.290 closest distance to " CG1BVAL A  72 " =    3.166
peak=    3.289 closest distance to " CB  SER A   3 " =    1.427
peak=    3.287 closest distance to " O   HOH Z 420 " =    5.416
peak=    3.287 closest distance to " CA  ALA A 158 " =    1.493
peak=    3.285 closest distance to " CG2 THR A 220 " =    0.848
peak=    3.285 closest distance to " CB  ALA A 299 " =    0.932
peak=    3.285 closest distance to " CB  PRO A 198 " =    1.221
peak=    3.285 closest distance to " O   HOH Z 361 " =    2.578
peak=    3.285 closest distance to " NE2 HIS A 207 " =    1.078
peak=    3.284 closest distance to " NE2 GLN A  58 " =    4.788
peak=    3.283 closest distance to " OG  SER A  22 " =    2.728
peak=    3.279 closest distance to " CB  ASP A 191 " =    1.185
peak=    3.275 closest distance to " O   HOH Z 380 " =    1.798
peak=    3.271 closest distance to " CB  LYS A 117 " =    1.161
peak=    3.270 closest distance to " CB  ASN A 148 " =    2.049
peak=    3.268 closest distance to " O   HOH Z 116 " =    2.950
peak=    3.267 closest distance to " CA  GLN A  94 " =    0.772
peak=    3.265 closest distance to " O   HOH Z  30 " =    1.085
peak=    3.263 closest distance to " O   HOH Z 117 " =    1.880
peak=    3.262 closest distance to " NZ  LYS A  48 " =    1.228
peak=    3.261 closest distance to " CB  PHE A 283 " =    0.823
peak=    3.259 closest distance to " NH2 ARG A 156 " =    1.138
peak=    3.254 closest distance to " O   HOH Z 244 " =    1.734
peak=    3.252 closest distance to " O   HOH Z 327 " =    1.608
peak=    3.247 closest distance to " O   HOH Z  19 " =    1.624
peak=    3.247 closest distance to " OD2 ASP A 286 " =    3.247
peak=    3.244 closest distance to " CB  ALA A  43 " =    0.801
peak=    3.244 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.244 closest distance to " CE1 TYR A 186 " =    1.311
peak=    3.241 closest distance to " OE1 GLN A  55 " =    1.442
peak=    3.238 closest distance to " CB  ASN A 187 " =    1.232
peak=    3.238 closest distance to " O   HOH Z 271 " =    2.609
peak=    3.234 closest distance to " CB  ASP A 298 " =    1.181
peak=    3.233 closest distance to " O   HOH Z 409 " =    2.944
peak=    3.233 closest distance to " O   HOH Z 125 " =    3.847
peak=    3.231 closest distance to " CG  GLN A 205 " =    1.115
peak=    3.229 closest distance to " CA  ASP A 140 " =    1.348
peak=    3.226 closest distance to " NH2BARG A 145 " =    2.152
peak=    3.225 closest distance to " O   HOH Z 176 " =    1.491
peak=    3.215 closest distance to " CA  GLY A 267 " =    1.102
peak=    3.215 closest distance to " CD2 TYR A 186 " =    1.018
peak=    3.214 closest distance to " ND1 HIS A  81 " =    1.640
peak=    3.210 closest distance to " O   HOH Z 434 " =    3.014
peak=    3.209 closest distance to " O   HOH Z 394 " =    1.734
peak=    3.208 closest distance to " OG1 THR A 264 " =    0.747
peak=    3.204 closest distance to " O   HOH Z 418 " =    1.278
peak=    3.202 closest distance to " CB  GLU A  37 " =    0.874
peak=    3.202 closest distance to " CA  LYS A 166 " =    1.431
peak=    3.200 closest distance to " O   HOH Z 216 " =    4.981
peak=    3.199 closest distance to " O   ALA A 158 " =    1.150
peak=    3.198 closest distance to " O   HOH Z 128 " =    2.130
peak=    3.190 closest distance to " CA  ALA A 154 " =    1.025
peak=    3.184 closest distance to " CG2 THR A  29 " =    1.350
peak=    3.182 closest distance to " O   HOH Z 368 " =    4.206
peak=    3.179 closest distance to " CE3 TRP A 150 " =    1.116
peak=    3.177 closest distance to " O   HOH Z   1 " =    2.534
peak=    3.177 closest distance to " CD  GLN A 194 " =    1.588
peak=    3.176 closest distance to " O   HOH Z 345 " =    3.753
peak=    3.167 closest distance to " O   HOH Z  83 " =    1.565
peak=    3.163 closest distance to " CA  THR A 264 " =    0.905
peak=    3.163 closest distance to " CA  ALA A  84 " =    1.194
peak=    3.152 closest distance to " O   HOH Z 150 " =    1.453
peak=    3.150 closest distance to " O   HOH Z 240 " =    2.328
peak=    3.148 closest distance to " O   LEU A 228 " =    2.019
peak=    3.140 closest distance to " CB  ALA A   9 " =    1.631
peak=    3.136 closest distance to " N   ASP A 162 " =    1.181
peak=    3.134 closest distance to " O   HOH Z 416 " =    2.932
peak=    3.134 closest distance to " CE1 TYR A  30 " =    1.020
peak=    3.133 closest distance to " CB  GLN A 103 " =    0.952
peak=    3.131 closest distance to " O   HOH Z 358 " =    2.155
peak=    3.131 closest distance to " CD1 LEU A 300 " =    1.122
peak=    3.131 closest distance to " O   HOH Z 371 " =    2.567
peak=    3.130 closest distance to " CB  PHE A  16 " =    1.239
peak=    3.128 closest distance to " O   HOH Z 109 " =    2.500
peak=    3.126 closest distance to " CA  GLY A  35 " =    0.893
peak=    3.119 closest distance to " CB  ARG A 138 " =    1.018
peak=    3.114 closest distance to " O   HOH Z 162 " =    1.576
peak=    3.113 closest distance to " CB  ALA A 100 " =    1.302
peak=    3.113 closest distance to " CB  ALA A 114 " =    0.723
peak=    3.107 closest distance to " CA  ALA A 233 " =    1.596
peak=    3.106 closest distance to " O   HOH Z 132 " =    2.763
peak=    3.105 closest distance to " O   HOH Z 258 " =    1.802
peak=    3.102 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.098 closest distance to " OG BSER A 212 " =    2.719
peak=    3.096 closest distance to " CB  PHE A 204 " =    0.733
peak=    3.092 closest distance to " CA  ALA A 248 " =    1.167
peak=    3.092 closest distance to " O   GLY A  91 " =    1.274
peak=    3.084 closest distance to " CA  ASN A 249 " =    1.412
peak=    3.083 closest distance to " O   THR A 182 " =    1.461
peak=    3.077 closest distance to " O   HOH Z 126 " =    1.698
peak=    3.075 closest distance to " CB  ASP A 200 " =    1.138
peak=    3.075 closest distance to " O   HOH Z 196 " =    2.653
peak=    3.068 closest distance to " O   HOH Z 343 " =    2.365
peak=    3.061 closest distance to " CA  ALA A 299 " =    0.945
peak=    3.052 closest distance to " O   HOH Z 171 " =    4.057
peak=    3.028 closest distance to " CB  ASN A 215 " =    1.202
peak=    3.021 closest distance to " OE1 GLN A 223 " =    2.379
peak=    2.938 closest distance to " O   HOH Z 130 " =    2.544

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.802 - 5.910
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.802 - 5.910

peak=   -4.669 closest distance to " CD  GLN A  58 " =    0.881
peak=   -4.631 closest distance to " CD  ARG A  14 " =    3.469
peak=   -4.490 closest distance to " CD2 LEU A 237 " =    2.753
peak=   -4.471 closest distance to " CB  PRO A 243 " =    2.781
peak=   -4.398 closest distance to " O   PRO A 198 " =    1.346
peak=   -4.391 closest distance to " CE2 PHE A  61 " =    2.639
peak=   -4.224 closest distance to " O   HOH Z  10 " =    1.647
peak=   -4.221 closest distance to " CG2 ILE A  49 " =    2.739
peak=   -4.207 closest distance to " CG1 VAL A 112 " =    2.626
peak=   -4.203 closest distance to " CD  ARG A 156 " =    2.107
peak=   -4.143 closest distance to " O   HOH Z 193 " =    1.251
peak=   -4.136 closest distance to " O   HOH Z 266 " =    5.494
peak=   -4.125 closest distance to " CD1 LEU A 101 " =    2.438
peak=   -4.085 closest distance to " O   HOH Z 196 " =    2.344
peak=   -4.064 closest distance to " O   VAL A  67 " =    2.867
peak=   -4.060 closest distance to " CD2 TYR A 293 " =    1.938
peak=   -4.030 closest distance to " OXT GLY A 302 " =    2.978
peak=   -4.018 closest distance to " O   HOH Z 377 " =    2.036
peak=   -4.010 closest distance to " O   HOH Z 166 " =    1.617
peak=   -4.000 closest distance to " CA  VAL A  67 " =    3.076
peak=   -3.974 closest distance to " CA  ASP A 298 " =    1.099
peak=   -3.918 closest distance to " O   ALA A  34 " =    2.450
peak=   -3.885 closest distance to " CH2 TRP A 179 " =    1.237
peak=   -3.884 closest distance to " O   HOH Z 283 " =    2.151
peak=   -3.875 closest distance to " O   HOH Z 348 " =    2.266
peak=   -3.852 closest distance to " CE3 TRP A 150 " =    2.227
peak=   -3.843 closest distance to " NE2 GLN A 223 " =    1.117
peak=   -3.801 closest distance to " N   ALA A  43 " =    2.739
peak=   -3.795 closest distance to " O   HOH Z 374 " =    1.947
peak=   -3.766 closest distance to " O   HOH Z 264 " =    1.688
peak=   -3.762 closest distance to " CA  GLY A 241 " =    3.271
peak=   -3.757 closest distance to " O   HOH Z 368 " =    1.900
peak=   -3.757 closest distance to " O   GLY A 136 " =    2.401
peak=   -3.756 closest distance to " CD  GLN A 223 " =    1.407
peak=   -3.748 closest distance to " CG  ARG A  66 " =    2.489
peak=   -3.744 closest distance to " O   HOH Z 278 " =    1.114
peak=   -3.743 closest distance to " ND2 ASN A 249 " =    2.260
peak=   -3.739 closest distance to " CE2 TYR A  30 " =    2.725
peak=   -3.732 closest distance to " O   HOH Z 366 " =    1.544
peak=   -3.728 closest distance to " OG  SER A  97 " =    2.188
peak=   -3.717 closest distance to " O   HOH Z 394 " =    1.531
peak=   -3.713 closest distance to " O   HOH Z 150 " =    2.216
peak=   -3.707 closest distance to " CD1 PHE A  59 " =    2.082
peak=   -3.705 closest distance to " CG  ARG A 269 " =    2.301
peak=   -3.705 closest distance to " CG  GLU A  53 " =    1.595
peak=   -3.697 closest distance to " CD  GLN A  88 " =    0.895
peak=   -3.686 closest distance to " O   HOH Z 185 " =    2.564
peak=   -3.680 closest distance to " CZ  TYR A 169 " =    1.818
peak=   -3.678 closest distance to " CG  GLN A  58 " =    1.127
peak=   -3.670 closest distance to " O   HOH Z 128 " =    2.732
peak=   -3.665 closest distance to " O   SER A 210 " =    1.791
peak=   -3.662 closest distance to " O   HOH Z 154 " =    1.498
peak=   -3.645 closest distance to " CG  GLN A  11 " =    1.587
peak=   -3.644 closest distance to " O   HOH Z 174 " =    3.603
peak=   -3.644 closest distance to " O   HOH Z 150 " =    1.016
peak=   -3.641 closest distance to " O   HOH Z 290 " =    1.149
peak=   -3.614 closest distance to " CB  ALA A  43 " =    2.587
peak=   -3.611 closest distance to " O   HOH Z 198 " =    1.553
peak=   -3.598 closest distance to " CB  ASP A 132 " =    2.368
peak=   -3.594 closest distance to " C   ASN A 285 " =    2.268
peak=   -3.589 closest distance to " NH2 ARG A  79 " =    2.236
peak=   -3.588 closest distance to " CG  LEU A  83 " =    2.105
peak=   -3.583 closest distance to " O   VAL A 189 " =    2.651
peak=   -3.581 closest distance to " O   HOH Z 165 " =    1.941
peak=   -3.578 closest distance to " C   SER A 206 " =    1.484
peak=   -3.575 closest distance to " O   HOH Z 252 " =    3.666
peak=   -3.573 closest distance to " C   HIS A 108 " =    1.088
peak=   -3.571 closest distance to " CD2 HIS A 207 " =    2.329
peak=   -3.568 closest distance to " CG  GLN A 103 " =    2.552
peak=   -3.566 closest distance to " O   HOH Z 210 " =    0.802
peak=   -3.557 closest distance to " N   SER A 276 " =    1.503
peak=   -3.554 closest distance to " O   HOH Z 211 " =    1.260
peak=   -3.552 closest distance to " CB  ALA A  10 " =    2.239
peak=   -3.545 closest distance to " OE1 GLN A  88 " =    0.914
peak=   -3.543 closest distance to " O   HOH Z  19 " =    2.437
peak=   -3.543 closest distance to " ND2 ASN A  45 " =    1.944
peak=   -3.540 closest distance to " O   HOH Z 106 " =    2.012
peak=   -3.537 closest distance to " O   PRO A 163 " =    2.092
peak=   -3.534 closest distance to " O   HOH Z 197 " =    1.981
peak=   -3.533 closest distance to " O   ALA A  10 " =    1.742
peak=   -3.513 closest distance to " O   HOH Z  13 " =    1.984
peak=   -3.510 closest distance to " CA  GLY A 241 " =    2.357
peak=   -3.506 closest distance to " C   LEU A 143 " =    1.098
peak=   -3.494 closest distance to " OD1 ASN A 148 " =    1.432
peak=   -3.494 closest distance to " CG1 VAL A 112 " =    2.675
peak=   -3.492 closest distance to " O   ILE A 109 " =    2.624
peak=   -3.489 closest distance to " CD2 PHE A  61 " =    2.103
peak=   -3.484 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.482 closest distance to " O   SER A 276 " =    1.728
peak=   -3.479 closest distance to " O   HOH Z 177 " =    1.911
peak=   -3.461 closest distance to " O   HOH Z 102 " =    1.556
peak=   -3.461 closest distance to " O   HOH Z  71 " =    2.694
peak=   -3.457 closest distance to " CG2 ILE A 263 " =    2.293
peak=   -3.453 closest distance to " O   HOH Z 135 " =    1.665
peak=   -3.448 closest distance to " CG  PRO A 243 " =    1.745
peak=   -3.441 closest distance to " CD  GLN A  88 " =    1.094
peak=   -3.434 closest distance to " O   HOH Z  90 " =    3.867
peak=   -3.432 closest distance to " O   HOH Z  37 " =    1.944
peak=   -3.430 closest distance to " O   HOH Z 234 " =    4.304
peak=   -3.416 closest distance to " O   HOH Z  60 " =    1.876
peak=   -3.416 closest distance to " CB  TRP A  85 " =    2.561
peak=   -3.411 closest distance to " CB  ALA A 129 " =    2.453
peak=   -3.403 closest distance to " O   HOH Z 191 " =    5.910
peak=   -3.403 closest distance to " OE1 GLN A  88 " =    1.008
peak=   -3.401 closest distance to " O   HOH Z 156 " =    3.543
peak=   -3.398 closest distance to " CG  GLU A 277 " =    1.197
peak=   -3.397 closest distance to " O   TRP A  92 " =    2.038
peak=   -3.389 closest distance to " O   HOH Z 216 " =    0.985
peak=   -3.387 closest distance to " O   GLY A  17 " =    1.115
peak=   -3.386 closest distance to " CG2BVAL A  41 " =    1.743
peak=   -3.383 closest distance to " N   THR A  52 " =    1.775
peak=   -3.383 closest distance to " CG1 VAL A  78 " =    2.574
peak=   -3.380 closest distance to " OD1 ASP A 171 " =    1.566
peak=   -3.379 closest distance to " CB  ALA A 291 " =    2.453
peak=   -3.376 closest distance to " CD2 PHE A 192 " =    2.078
peak=   -3.368 closest distance to " O   HOH Z 196 " =    1.509
peak=   -3.367 closest distance to " CG  MET A 105 " =    0.987
peak=   -3.366 closest distance to " O   HOH Z 285 " =    1.674
peak=   -3.363 closest distance to " NE2 GLN A 103 " =    1.806
peak=   -3.363 closest distance to " CD2 LEU A 300 " =    2.829
peak=   -3.361 closest distance to " CZ  PHE A  38 " =    2.305
peak=   -3.361 closest distance to " C   THR A 279 " =    1.114
peak=   -3.347 closest distance to " CD1 TRP A  70 " =    1.086
peak=   -3.340 closest distance to " O   HOH Z 166 " =    1.733
peak=   -3.340 closest distance to " CD  ARG A  79 " =    1.255
peak=   -3.333 closest distance to " CG2 VAL A 189 " =    2.218
peak=   -3.332 closest distance to " O   HOH Z 149 " =    2.049
peak=   -3.330 closest distance to " O   HOH Z  64 " =    1.473
peak=   -3.327 closest distance to " CA  GLY A 203 " =    2.436
peak=   -3.326 closest distance to " O   HOH Z 171 " =    2.279
peak=   -3.312 closest distance to " O   HOH Z 407 " =    3.298
peak=   -3.310 closest distance to " O   HOH Z  52 " =    1.783
peak=   -3.309 closest distance to " CE1 TYR A 247 " =    2.748
peak=   -3.308 closest distance to " CD  PRO A 243 " =    2.108
peak=   -3.304 closest distance to " O   HOH Z 174 " =    2.396
peak=   -3.296 closest distance to " CG  HIS A  86 " =    1.160
peak=   -3.293 closest distance to " N   ALA A 226 " =    1.965
peak=   -3.292 closest distance to " CB  PRO A 163 " =    2.531
peak=   -3.286 closest distance to " CB  ALA A 248 " =    2.282
peak=   -3.279 closest distance to " CE BMET A  47 " =    2.053
peak=   -3.269 closest distance to " NE2 GLN A  88 " =    1.894
peak=   -3.266 closest distance to " O   HOH Z 210 " =    1.289
peak=   -3.266 closest distance to " OG BSER A 134 " =    1.414
peak=   -3.262 closest distance to " CG1AVAL A  41 " =    2.626
peak=   -3.260 closest distance to " O   HOH Z 389 " =    1.551
peak=   -3.255 closest distance to " CB  PHE A  59 " =    2.376
peak=   -3.245 closest distance to " O   HOH Z 110 " =    1.365
peak=   -3.245 closest distance to " CD1 ILE A 109 " =    2.889
peak=   -3.241 closest distance to " O   HOH Z 150 " =    1.638
peak=   -3.239 closest distance to " O   HOH Z 407 " =    1.121
peak=   -3.238 closest distance to " O   HOH Z 372 " =    2.397
peak=   -3.234 closest distance to " OE1 GLN A 223 " =    2.373
peak=   -3.230 closest distance to " O   HOH Z   6 " =    1.587
peak=   -3.230 closest distance to " CG  ASP A 286 " =    1.576
peak=   -3.229 closest distance to " CB  PHE A  16 " =    2.487
peak=   -3.218 closest distance to " O   HOH Z 256 " =    2.414
peak=   -3.204 closest distance to " CD1 ILE A 263 " =    1.931
peak=   -3.201 closest distance to " OD1 ASN A 249 " =    2.220
peak=   -3.198 closest distance to " O   TYR A 186 " =    1.799
peak=   -3.196 closest distance to " CG2 THR A  18 " =    2.887
peak=   -3.195 closest distance to " CH2 TRP A 150 " =    1.123
peak=   -3.194 closest distance to " CD2 TYR A 247 " =    2.442
peak=   -3.193 closest distance to " SD  MET A 105 " =    2.356
peak=   -3.192 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.175 closest distance to " OD2 ASP A  50 " =    2.126
peak=   -3.174 closest distance to " O   HOH Z 308 " =    1.668
peak=   -3.173 closest distance to " O   GLN A  94 " =    2.143
peak=   -3.173 closest distance to " O   HOH Z 396 " =    2.029
peak=   -3.172 closest distance to " O   HOH Z   9 " =    2.555
peak=   -3.171 closest distance to " CD2 LEU A 237 " =    2.861
peak=   -3.163 closest distance to " O   HOH Z   6 " =    1.910
peak=   -3.163 closest distance to " O   HOH Z  40 " =    3.050
peak=   -3.161 closest distance to " SG BCYS A 201 " =    2.331
peak=   -3.156 closest distance to " CD1 ILE A 106 " =    2.275
peak=   -3.153 closest distance to " O   HOH Z 357 " =    2.189
peak=   -3.153 closest distance to " OD2 ASP A 171 " =    1.867
peak=   -3.149 closest distance to " CA  GLY A 241 " =    2.914
peak=   -3.146 closest distance to " O   HOH Z 418 " =    1.370
peak=   -3.142 closest distance to " NH2 ARG A  79 " =    1.599
peak=   -3.142 closest distance to " O   GLN A 240 " =    2.573
peak=   -3.136 closest distance to " CZ  PHE A  38 " =    2.042
peak=   -3.134 closest distance to " O   PHE A 218 " =    1.531
peak=   -3.129 closest distance to " O   HOH Z 111 " =    3.753
peak=   -3.124 closest distance to " O   HOH Z 340 " =    1.770
peak=   -3.124 closest distance to " CZ3 TRP A 274 " =    2.460
peak=   -3.120 closest distance to " CA  GLY A  75 " =    2.583
peak=   -3.120 closest distance to " O   HOH Z 422 " =    1.460
peak=   -3.116 closest distance to " O   ARG A  24 " =    2.139
peak=   -3.112 closest distance to " OD1 ASN A 173 " =    1.316
peak=   -3.111 closest distance to " CE  MET A  93 " =    1.842
peak=   -3.098 closest distance to " CB  ALA A 114 " =    2.525
peak=   -3.098 closest distance to " CD2 LEU A 300 " =    2.915
peak=   -3.088 closest distance to " NE1 TRP A 266 " =    2.597
peak=   -3.076 closest distance to " CA  LYS A 166 " =    2.164
peak=   -3.073 closest distance to " OD2 ASP A 171 " =    2.401
peak=   -3.070 closest distance to " O   HOH Z  78 " =    1.955
peak=   -3.065 closest distance to " O   HOH Z 134 " =    2.830
peak=   -3.061 closest distance to " C   MET A 188 " =    1.603
peak=   -3.061 closest distance to " O   HOH Z 236 " =    1.619
peak=   -3.060 closest distance to " N   ARG A 275 " =    1.716
peak=   -3.058 closest distance to " O   HOH Z 150 " =    2.049
peak=   -3.041 closest distance to " O   HOH Z 166 " =    1.499

================= 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    :  0.4693 0.4642   6.280417e+00   6.264351e+00
   1_bss:  0.4590 0.4541   6.272652e+00   6.253554e+00
   1_xyz:  0.3293 0.3565   6.030604e+00   6.099947e+00
   1_adp:  0.2985 0.3666   5.983825e+00   6.114831e+00
   1_occ:  0.2982 0.3665   5.983894e+00   6.115642e+00
   2_bss:  0.2949 0.3631   5.980084e+00   6.113449e+00
   2_xyz:  0.2127 0.2701   5.694658e+00   5.878786e+00
   2_adp:  0.1930 0.2467   5.610678e+00   5.804766e+00
   2_occ:  0.1928 0.2469   5.610408e+00   5.804847e+00
   3_bss:  0.1924 0.2454   5.608777e+00   5.802343e+00
   3_xyz:  0.1493 0.1952   5.385870e+00   5.598466e+00
   3_adp:  0.1358 0.1874   5.320823e+00   5.550703e+00
   3_occ:  0.1358 0.1874   5.320429e+00   5.550366e+00
   4_bss:  0.1362 0.1875   5.321788e+00   5.550136e+00
   4_xyz:  0.1242 0.1763   5.250219e+00   5.490814e+00
   4_adp:  0.1237 0.1701   5.235761e+00   5.462016e+00
   4_occ:  0.1236 0.1701   5.235597e+00   5.462074e+00
   5_bss:  0.1235 0.1701   5.235322e+00   5.461920e+00
   5_xyz:  0.1199 0.1652   5.210173e+00   5.437439e+00
   5_adp:  0.1184 0.1657   5.206293e+00   5.441517e+00
   5_occ:  0.1183 0.1658   5.206102e+00   5.441498e+00
   5_bss:  0.1183 0.1657   5.206129e+00   5.441649e+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:  0.284  35.629  -3.740   3.047   4.011   0.000   0.000   0.000
   1_xyz:  0.284  35.629  -3.740   3.047   4.011   0.000   0.000   0.000
   1_adp:  0.284  35.629  -3.740   3.047   4.011   0.000   0.000   0.000
   1_occ:  0.284  35.629  -3.740   3.047   4.011   0.000   0.000   0.000
   2_bss:  0.323  66.725  -1.873   1.198   1.863   0.000   0.000   0.000
   2_xyz:  0.323  66.725  -1.873   1.198   1.863   0.000   0.000   0.000
   2_adp:  0.323  66.725  -1.873   1.198   1.863   0.000   0.000   0.000
   2_occ:  0.323  66.725  -1.873   1.198   1.863   0.000   0.000   0.000
   3_bss:  0.335  77.640  -2.179  -0.280   0.650  -0.000   0.000   0.000
   3_xyz:  0.335  77.640  -2.179  -0.280   0.650  -0.000   0.000   0.000
   3_adp:  0.335  77.640  -2.179  -0.280   0.650  -0.000   0.000   0.000
   3_occ:  0.335  77.640  -2.179  -0.280   0.650  -0.000   0.000   0.000
   4_bss:  0.338  82.687  -2.111  -0.738   0.398  -0.000   0.000   0.000
   4_xyz:  0.338  82.687  -2.111  -0.738   0.398  -0.000   0.000   0.000
   4_adp:  0.338  82.687  -2.111  -0.738   0.398  -0.000   0.000   0.000
   4_occ:  0.338  82.687  -2.111  -0.738   0.398  -0.000   0.000   0.000
   5_bss:  0.327  72.400  -2.108  -1.011   0.212  -0.000   0.000   0.000
   5_xyz:  0.327  72.400  -2.108  -1.011   0.212  -0.000   0.000   0.000
   5_adp:  0.327  72.400  -2.108  -1.011   0.212  -0.000   0.000   0.000
   5_occ:  0.327  72.400  -2.108  -1.011   0.212  -0.000   0.000   0.000
   5_bss:  0.322  71.370  -1.990  -0.972   0.288  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.628 0.4496  0.5878    65746.661
   1_bss:  54.349 0.4647  0.6332    62862.670
   1_xyz:  39.765 0.6451  0.8484    36462.259
   1_adp:  40.999 0.6296  0.8267    38344.534
   1_occ:  41.059 0.6289  0.8254    38473.297
   2_bss:  40.425 0.6367  0.8201    37813.765
   2_xyz:  27.877 0.7796  0.9600    19185.586
   2_adp:  24.838 0.8131  0.9720    16115.902
   2_occ:  24.850 0.8129  0.9715    16132.279
   3_bss:  24.683 0.8146  0.9408    15974.860
   3_xyz:  18.820 0.8727  0.9771     9908.535
   3_adp:  17.733 0.8828  0.9705     9132.387
   3_occ:  17.724 0.8829  0.9706     9129.472
   4_bss:  17.710 0.8830  0.9635     9117.878
   4_xyz:  16.349 0.8952  0.9701     7965.420
   4_adp:  15.724 0.9009  0.9663     7610.309
   4_occ:  15.727 0.9009  0.9662     7608.449
   5_bss:  15.721 0.9009  0.9614     7601.512
   5_xyz:  15.170 0.9056  0.9644     7182.914
   5_adp:  15.226 0.9053  0.9565     7233.965
   5_occ:  15.224 0.9053  0.9565     7233.099
   5_bss:  15.226 0.9053  0.9592     7234.450
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7464e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7464e-01
   1_xyz:   1.774  0.015  0.112 16.502  0.007  4.116   1.6657e-01
   1_adp:   1.774  0.015  0.112 16.502  0.007  4.116   1.6657e-01
   1_occ:   1.774  0.015  0.112 16.502  0.007  4.116   1.6657e-01
   2_bss:   1.774  0.015  0.112 16.502  0.007  4.116   1.6657e-01
   2_xyz:   1.322  0.010  0.089 15.268  0.006  4.116   9.6674e-02
   2_adp:   1.322  0.010  0.089 15.268  0.006  4.116   9.6674e-02
   2_occ:   1.322  0.010  0.089 15.268  0.006  4.116   9.6674e-02
   3_bss:   1.322  0.010  0.089 15.268  0.006  4.116   9.6674e-02
   3_xyz:   1.185  0.011  0.084 14.699  0.005  4.114   8.3284e-02
   3_adp:   1.185  0.011  0.084 14.699  0.005  4.114   8.3284e-02
   3_occ:   1.185  0.011  0.084 14.699  0.005  4.114   8.3284e-02
   4_bss:   1.185  0.011  0.084 14.699  0.005  4.114   8.3284e-02
   4_xyz:   1.189  0.011  0.085 14.732  0.004  4.123   8.1862e-02
   4_adp:   1.189  0.011  0.085 14.732  0.004  4.123   8.1862e-02
   4_occ:   1.189  0.011  0.085 14.732  0.004  4.123   8.1862e-02
   5_bss:   1.189  0.011  0.085 14.732  0.004  4.123   8.1862e-02
   5_xyz:   1.138  0.011  0.085 14.549  0.004  4.117   7.7439e-02
   5_adp:   1.138  0.011  0.085 14.549  0.004  4.117   7.7439e-02
   5_occ:   1.138  0.011  0.085 14.549  0.004  4.117   7.7439e-02
   5_bss:   1.138  0.011  0.085 14.549  0.004  4.117   7.7439e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.385   2.4510e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.385   2.4510e-01
   1_xyz:  12.279  0.104  0.379 83.302  0.045  1.875   1.3729e-01
   1_adp:  12.279  0.104  0.379 83.302  0.045  1.875   1.3729e-01
   1_occ:  12.279  0.104  0.379 83.302  0.045  1.875   1.3729e-01
   2_bss:  12.279  0.104  0.379 83.302  0.045  1.875   1.3729e-01
   2_xyz:   8.013  0.055  0.274 85.436  0.059  2.171   8.7215e-02
   2_adp:   8.013  0.055  0.274 85.436  0.059  2.171   8.7215e-02
   2_occ:   8.013  0.055  0.274 85.436  0.059  2.171   8.7215e-02
   3_bss:   8.013  0.055  0.274 85.436  0.059  2.171   8.7215e-02
   3_xyz:   8.367  0.068  0.234 82.580  0.038  2.263   6.7519e-02
   3_adp:   8.367  0.068  0.234 82.580  0.038  2.263   6.7519e-02
   3_occ:   8.367  0.068  0.234 82.580  0.038  2.263   6.7519e-02
   4_bss:   8.367  0.068  0.234 82.580  0.038  2.263   6.7519e-02
   4_xyz:   8.612  0.055  0.312 83.283  0.038  2.203   5.8492e-02
   4_adp:   8.612  0.055  0.312 83.283  0.038  2.203   5.8492e-02
   4_occ:   8.612  0.055  0.312 83.283  0.038  2.203   5.8492e-02
   5_bss:   8.612  0.055  0.312 83.283  0.038  2.203   5.8492e-02
   5_xyz:   8.467  0.052  0.292 81.818  0.033  2.325   5.2715e-02
   5_adp:   8.467  0.052  0.292 81.818  0.033  2.325   5.2715e-02
   5_occ:   8.467  0.052  0.292 81.818  0.033  2.325   5.2715e-02
   5_bss:   8.467  0.052  0.292 81.818  0.033  2.325   5.2715e-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: 109.11   0.00  18.55  89.99   0.00  14.44 109.11   0.46  40.95
   1_occ: 109.11   0.00  18.55  89.99   0.00  14.44 109.11   0.46  40.95
   2_bss: 109.11   0.00  18.55  89.99   0.00  14.44 109.11   0.46  40.95
   2_xyz: 109.11   0.00  18.55  89.99   0.00  14.44 109.11   0.46  40.95
   2_adp: 108.32   0.00  17.88  90.45   0.00  13.46 108.32   3.44  41.93
   2_occ: 108.32   0.00  17.88  90.45   0.00  13.46 108.32   3.44  41.93
   3_bss: 108.32   0.00  17.88  90.45   0.00  13.46 108.32   3.44  41.93
   3_xyz: 108.32   0.00  17.88  90.45   0.00  13.46 108.32   3.44  41.93
   3_adp: 107.87   0.57  17.95  97.55   0.57  12.87 107.87   5.11  45.65
   3_occ: 107.87   0.57  17.95  97.55   0.57  12.87 107.87   5.11  45.65
   4_bss: 107.87   0.57  17.95  97.55   0.57  12.87 107.87   5.11  45.65
   4_xyz: 107.87   0.57  17.95  97.55   0.57  12.87 107.87   5.11  45.65
   4_adp: 104.94   0.78  17.16  91.48   0.78  12.43 104.94   1.00  42.91
   4_occ: 104.94   0.78  17.16  91.48   0.78  12.43 104.94   1.00  42.91
   5_bss: 104.94   0.78  17.16  91.48   0.78  12.43 104.94   1.00  42.91
   5_xyz: 104.94   0.78  17.16  91.48   0.78  12.43 104.94   1.00  42.91
   5_adp: 102.71   0.00  16.94  94.19   0.00  12.25 102.71   0.00  42.46
   5_occ: 102.71   0.00  16.94  94.19   0.00  12.25 102.71   0.00  42.46
   5_bss: 102.71   0.00  16.94  94.19   0.00  12.26 102.71   0.00  42.46
------------------------------------------------------------------------
 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:    1.876    0.027    0.501
   1_adp:    1.876    0.027    0.501
   1_occ:    1.876    0.027    0.501
   2_bss:    1.876    0.027    0.501
   2_xyz:    1.744    0.025    0.662
   2_adp:    1.744    0.025    0.662
   2_occ:    1.744    0.025    0.662
   3_bss:    1.744    0.025    0.662
   3_xyz:    1.824    0.089    0.772
   3_adp:    1.824    0.089    0.772
   3_occ:    1.824    0.089    0.772
   4_bss:    1.824    0.089    0.772
   4_xyz:    1.885    0.030    0.798
   4_adp:    1.885    0.030    0.798
   4_occ:    1.885    0.030    0.798
   5_bss:    1.885    0.030    0.798
   5_xyz:    1.918    0.074    0.815
   5_adp:    1.918    0.074    0.815
   5_occ:    1.918    0.074    0.815
   5_bss:    1.918    0.074    0.815
------------------------------------------------------------------------

CPU time actual refinement: 337.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_593/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_593/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_593/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_593/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_593/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.68 
  Macro-tasks:
    bulk solvent and scale       = 49.34  
    individual site refinement   = 133.39 
    weights calculation          = 28.57  
    collect and process          = 6.35   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 217.76 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 104.77 
    alpha_beta                      = 8.09   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.34 
    fmodel                         = 7.76   
    r_factors                      = 0.26   
    phase_errors                   = 10.60  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 248.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.788 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    644 calls, 104.45 s
gradients_fft:          589 calls, 100.11 s

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

# Date 2008-01-16 Time 05:12:26 PST -0800 (1200489146.08 s)
Start R-work = 0.4693, R-free = 0.4642 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4590, R-free = 0.4541
Final R-work = 0.1183, R-free = 0.1657