# Date 2008-01-16 Time 04:50:18 PST -0800 (1200487818.61 s)
#phil __OFF__

Command line arguments: "../484.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14316
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 484

-------------------------------------------------------------------------------
  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, 45.7567, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95037
Completeness in resolution range: 0.966976
Completeness with d_max=infinity: 0.964026

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8359
                             d_min =   1.9504

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, 45.7567, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95037
Completeness in resolution range: 0.966976
Completeness with d_max=infinity: 0.964026

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8363 -  4.1737 [2122/2147]  1912   210   9.9%
  bin  2:  4.1737 -  3.3250 [2048/2068]  1843   205  10.0%
  bin  3:  3.3250 -  2.9083 [2019/2038]  1814   205  10.2%
  bin  4:  2.9083 -  2.6441 [1994/2024]  1798   196   9.8%
  bin  5:  2.6441 -  2.4555 [1987/2006]  1793   194   9.8%
  bin  6:  2.4555 -  2.3113 [1992/2017]  1788   204  10.2%
  bin  7:  2.3113 -  2.1959 [1937/1965]  1741   196  10.1%
  bin  8:  2.1959 -  2.1006 [1980/2016]  1780   200  10.1%
  bin  9:  2.1006 -  2.0199 [1951/1993]  1755   196  10.0%
  bin 10:  2.0199 -  1.9504 [1559/1984]  1406   153   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_484/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.38 -     2.09: 27
        2.09 -     2.79: 750
        2.79 -     3.49: 4659
        3.49 -     4.20: 9551
        4.20 -     4.90: 14144
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.384 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.414 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.543 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.658 3.040 -x+1,y+1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  ... (remaining 29126 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_484/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_484/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 45.75675 84.23025 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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4922   r_free= 0.4972   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.300547                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6553 0.99   1386  155 0.4105 0.4194      6.6208      6.6463|
|  2:  4.6553 -  3.7141 0.99   1331  146 0.4460 0.4463      6.8618       6.828|
|  3:  3.7141 -  3.2503 0.99   1299  142 0.4758 0.4721      6.7357      6.8128|
|  4:  3.2503 -  2.9556 0.99   1294  153 0.4815 0.4635      6.5705      6.5171|
|  5:  2.9556 -  2.7452 0.99   1290  138 0.5226 0.4881      6.3981      6.3862|
|  6:  2.7452 -  2.5843 0.99   1283  141 0.5212 0.5838      6.3014      6.2807|
|  7:  2.5843 -  2.4555 0.99   1277  135 0.5129 0.5098      6.2573      6.2363|
|  8:  2.4555 -  2.3490 0.98   1269  151 0.5232 0.5188      6.1929      6.1745|
|  9:  2.3490 -  2.2589 0.98   1243  138 0.5381 0.5658      6.1402      6.1669|
| 10:  2.2589 -  2.1812 1.00   1294  140 0.5118 0.5243      6.1126       6.143|
| 11:  2.1812 -  2.1132 0.97   1254  141 0.5301 0.5534      6.0523      6.0699|
| 12:  2.1132 -  2.0529 0.98   1251  139 0.5192 0.5146      5.9796       6.029|
| 13:  2.0529 -  1.9990 1.00   1263  137 0.5130 0.5086      5.8916      5.8393|
| 14:  1.9990 -  1.9504 0.70    896  103 0.5472 0.4495      5.8889      5.7451|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8363 -  4.6553  1386   155  0.63  39.86   0.81     0.70      92110.47|
|  2:  4.6553 -  3.7141  1331   146  0.63  40.84   0.88     0.76     136909.77|
|  3:  3.7141 -  3.2503  1299   142  0.52  50.00   0.91     0.72     143073.55|
|  4:  3.2503 -  2.9556  1294   153  0.41  58.91   0.92     0.59     127420.53|
|  5:  2.9556 -  2.7452  1290   138  0.32  66.20   0.87     0.47      97787.31|
|  6:  2.7452 -  2.5843  1283   141  0.23  72.74   0.88     0.33      88163.53|
|  7:  2.5843 -  2.4555  1277   135  0.20  74.73   0.91     0.28      77448.05|
|  8:  2.4555 -  2.3490  1269   151  0.18  76.64   0.92     0.27      72090.56|
|  9:  2.3490 -  2.2589  1243   138  0.23  73.18   0.90     0.33      62569.73|
| 10:  2.2589 -  2.1812  1294   140  0.25  71.02   0.96     0.37      55591.30|
| 11:  2.1812 -  2.1132  1254   141  0.25  71.20   0.96     0.39      51575.85|
| 12:  2.1132 -  2.0529  1251   139  0.29  68.27   1.00     0.47      45696.05|
| 13:  2.0529 -  1.9990  1263   137  0.36  63.26   0.96     0.58      36404.17|
| 14:  1.9990 -  1.9504   896   103  0.50  52.03   0.97     0.73      22897.42|
|alpha:            min =        0.27 max =            0.76 mean =         0.50|
|beta:             min =    22897.42 max =       143073.55 mean =     81016.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.98 mean =        62.75|
|phase err.(test): min =        0.00 max =           89.99 mean =        62.99|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.264013             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.927647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.785   (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 |  1.384 -  1.736:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.736 -  2.087:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.087 -  2.439:       57 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.439 -  2.790:      693 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.790 -  3.142:     2208 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.142 -  3.494:     2451 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.494 -  3.845:     4646 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.845 -  4.197:     4905 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.197 -  4.548:     6399 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.548 -  4.900:     7745 |
|-----------------------------------------------------------------------------|
|-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 |        0.208 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.105    4.900  1.384 |       0.912 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4922   r_free= 0.4972   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.300547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4823   r_free= 0.4838   ksol= 0.36   Bsol= 20.00   scale= 0.907   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.56,1.25,1.28,0.00,0.00,0.00); trace/3= -0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.296714                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.410802             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.245   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.960143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.690   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4823      final r-factor (work) = 0.4319          |
| start r-factor (free) = 0.4838      final r-factor (free) = 0.4577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9706 = 10.41 * 0.50 * 6.2940 + 1.00 * 0.2077                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.5825 = 10.41 * 0.50 * 6.2394 + 1.00 * 0.1041                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4319      final r-factor (work) = 0.3966          |
| start r-factor (free) = 0.4577      final r-factor (free) = 0.4618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2362 = 1.96 * 1.00 * 6.2394 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1554 = 1.96 * 1.00 * 6.1880 + 1.00 * 0.0260                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.73  20.24    None  None   None       |
|    all(noH): 2823   0      0.00    112.73  20.24    None  None   None       |
|    Sol.    : 438    0      0.00    112.73  32.41    None  None   None       |
|    Mac.    : 2385   0      0.00    100.54  18.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.273:  907   |   5:    56.366 -  67.639:   57        |
|      1:    11.273 -  22.546:  904   |   6:    67.639 -  78.912:   25        |
|      2:    22.546 -  33.819:  542   |   7:    78.912 -  90.185:    7        |
|      3:    33.819 -  45.093:  257   |   8:    90.185 - 101.458:    2        |
|      4:    45.093 -  56.366:  121   |   9:   101.458 - 112.731:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3966 r_free = 0.4618             target_work(ml) = 6.194         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3964 r_free = 0.4622             target_work(ml) = 6.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3964   r_free= 0.4622   ksol= 0.36   Bsol= 20.00   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.56,1.25,1.28,0.00,0.00,0.00); trace/3= -0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.193199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3960   r_free= 0.4612   ksol= 0.36   Bsol= 38.78   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,1.36,1.31,0.00,0.00,0.00); trace/3= 0.56                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.195065                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.776241             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.064  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.000700              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.798  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3960      final r-factor (work) = 0.3549          |
| start r-factor (free) = 0.4612      final r-factor (free) = 0.4300          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.6597 = 12.78 * 0.50 * 6.1920 + 1.00 * 0.1041                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.4181 = 12.78 * 0.50 * 6.1549 + 1.00 * 0.0996                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3549      final r-factor (work) = 0.3427          |
| start r-factor (free) = 0.4300      final r-factor (free) = 0.4235          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1851 = 1.00 * 1.00 * 6.1549 + 1.00 * 0.0258                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1307 = 1.00 * 1.00 * 6.1087 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    124.06  19.53    None  None   None       |
|    all(noH): 2823   0      0.00    124.06  19.53    None  None   None       |
|    Sol.    : 438    0      0.00    124.06  31.37    None  None   None       |
|    Mac.    : 2385   0      0.00    102.78  17.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.406: 1035   |   5:    62.028 -  74.433:   32        |
|      1:    12.406 -  24.811:  989   |   6:    74.433 -  86.839:    5        |
|      2:    24.811 -  37.217:  500   |   7:    86.839 -  99.245:    4        |
|      3:    37.217 -  49.622:  180   |   8:    99.245 - 111.650:    1        |
|      4:    49.622 -  62.028:   76   |   9:   111.650 - 124.056:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3427 r_free = 0.4235             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3424 r_free = 0.4238             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3424   r_free= 0.4238   ksol= 0.36   Bsol= 38.78   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,1.36,1.31,0.00,0.00,0.00); trace/3= 0.56                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.100021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3426   r_free= 0.4235   ksol= 0.35   Bsol= 50.17   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,0.75,1.02,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.100409                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.089883             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.226  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.597771              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.995  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3426      final r-factor (work) = 0.2867          |
| start r-factor (free) = 0.4235      final r-factor (free) = 0.3724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.1424 = 14.09 * 0.50 * 6.1098 + 1.00 * 0.0996                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.6590 = 14.09 * 0.50 * 6.0406 + 1.00 * 0.1032                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2867      final r-factor (work) = 0.2698          |
| start r-factor (free) = 0.3724      final r-factor (free) = 0.3585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6765 = 0.60 * 1.00 * 6.0406 + 1.00 * 0.0656                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7495 = 0.60 * 1.00 * 5.9440 + 1.00 * 0.1963                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.36  18.00    None  None   None       |
|    all(noH): 2823   0      0.00    123.36  18.00    None  None   None       |
|    Sol.    : 438    0      0.00    123.36  33.55    None  None   None       |
|    Mac.    : 2385   0      0.00    101.20  15.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.336: 1199   |   5:    61.679 -  74.014:   20        |
|      1:    12.336 -  24.672:  972   |   6:    74.014 -  86.350:    3        |
|      2:    24.672 -  37.007:  377   |   7:    86.350 -  98.686:    4        |
|      3:    37.007 -  49.343:  178   |   8:    98.686 - 111.022:    1        |
|      4:    49.343 -  61.679:   68   |   9:   111.022 - 123.357:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2698 r_free = 0.3585             target_work(ml) = 5.923         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2696 r_free = 0.3585             target_work(ml) = 5.923         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2696   r_free= 0.3585   ksol= 0.35   Bsol= 50.17   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,0.75,1.02,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.922988                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2694   r_free= 0.3571   ksol= 0.34   Bsol= 50.70   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,-0.62,-0.09,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.921785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.791539              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.474  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 19.801451             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.249   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2694      final r-factor (work) = 0.2245          |
| start r-factor (free) = 0.3571      final r-factor (free) = 0.2965          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3154 = 5.79 * 0.50 * 5.9440 + 1.00 * 0.1029                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0200 = 5.79 * 0.50 * 5.8537 + 1.00 * 0.0690                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2245      final r-factor (work) = 0.2015          |
| start r-factor (free) = 0.2965      final r-factor (free) = 0.2808          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 115.9250 = 19.80 * 1.00 * 5.8537 + 1.00 * 0.0129                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 113.0724 = 19.80 * 1.00 * 5.7093 + 1.00 * 0.0201                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    128.06  19.39    None  None   None       |
|    all(noH): 2823   0      0.00    128.06  19.39    None  None   None       |
|    Sol.    : 438    0      0.00    128.06  46.57    None  None   None       |
|    Mac.    : 2385   0      0.00    116.25  14.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.806: 1439   |   5:    64.028 -  76.833:   76        |
|      1:    12.806 -  25.611:  729   |   6:    76.833 -  89.639:   37        |
|      2:    25.611 -  38.417:  251   |   7:    89.639 - 102.444:    6        |
|      3:    38.417 -  51.222:  153   |   8:   102.444 - 115.250:    3        |
|      4:    51.222 -  64.028:  127   |   9:   115.250 - 128.055:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2015 r_free = 0.2808             target_work(ml) = 5.683         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2013 r_free = 0.2802             target_work(ml) = 5.682         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2013   r_free= 0.2802   ksol= 0.34   Bsol= 50.70   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,-0.62,-0.09,-0.00,-0.00,-0.00); trace/3= -0.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.682422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2016   r_free= 0.2797   ksol= 0.32   Bsol= 46.61   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.99,-0.21,-0.00,-0.00,-0.00); trace/3= -0.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.680330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.397898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.582  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.757  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2016      final r-factor (work) = 0.1678          |
| start r-factor (free) = 0.2797      final r-factor (free) = 0.2344          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6233 = 4.40 * 0.50 * 5.7092 + 1.00 * 0.0690                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3946 = 4.40 * 0.50 * 5.6080 + 1.00 * 0.0628                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1678      final r-factor (work) = 0.1569          |
| start r-factor (free) = 0.2344      final r-factor (free) = 0.2081          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0790 = 0.19 * 1.00 * 5.6080 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0464 = 0.19 * 1.00 * 5.4867 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.98  16.96    None  None   None       |
|    all(noH): 2823   0      0.00    115.98  16.96    None  None   None       |
|    Sol.    : 438    0      4.24    115.98  41.10    None  None   None       |
|    Mac.    : 2385   0      0.00    102.48  12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.598: 1498   |   5:    57.988 -  69.585:   49        |
|      1:    11.598 -  23.195:  765   |   6:    69.585 -  81.183:   26        |
|      2:    23.195 -  34.793:  202   |   7:    81.183 -  92.781:    6        |
|      3:    34.793 -  46.390:  152   |   8:    92.781 - 104.378:    3        |
|      4:    46.390 -  57.988:  121   |   9:   104.378 - 115.976:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1569 r_free = 0.2081             target_work(ml) = 5.427         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1564 r_free = 0.2071             target_work(ml) = 5.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1564   r_free= 0.2071   ksol= 0.32   Bsol= 46.61   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.99,-0.21,-0.00,-0.00,-0.00); trace/3= -0.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.423395                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6553 0.99   1386  155 0.1096 0.1545      5.5163      5.7233|
|  2:  4.6553 -  3.7141 0.99   1331  146 0.1137 0.1496      5.7043       5.961|
|  3:  3.7141 -  3.2503 0.99   1299  142 0.1444 0.1840      5.7533      6.0523|
|  4:  3.2503 -  2.9556 0.99   1294  153 0.1709 0.2178      5.7459      5.9009|
|  5:  2.9556 -  2.7452 0.99   1290  138 0.1804 0.2317      5.5931       5.779|
|  6:  2.7452 -  2.5843 0.99   1283  141 0.1713 0.2167      5.4819      5.6246|
|  7:  2.5843 -  2.4555 0.99   1277  135 0.1738 0.2262       5.432      5.6599|
|  8:  2.4555 -  2.3490 0.98   1269  151 0.1750 0.2501      5.3876      5.6506|
|  9:  2.3490 -  2.2589 0.98   1243  138 0.1736 0.2410       5.354      5.5462|
| 10:  2.2589 -  2.1812 1.00   1294  140 0.1661 0.2353      5.2737      5.4802|
| 11:  2.1812 -  2.1132 0.97   1254  141 0.1717 0.2406      5.2361       5.506|
| 12:  2.1132 -  2.0529 0.98   1251  139 0.1620 0.2046      5.1481      5.3752|
| 13:  2.0529 -  1.9990 1.00   1263  137 0.1664 0.2531       5.085      5.3999|
| 14:  1.9990 -  1.9504 0.70    896  103 0.1819 0.2049      5.0648      5.1683|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8363 -  4.6553  1386   155  0.91  12.54   0.98     0.96      11036.58|
|  2:  4.6553 -  3.7141  1331   146  0.92  12.01   1.05     1.03      15258.30|
|  3:  3.7141 -  3.2503  1299   142  0.89  16.44   1.06     1.05      18473.58|
|  4:  3.2503 -  2.9556  1294   153  0.87  19.58   1.05     1.01      18360.58|
|  5:  2.9556 -  2.7452  1290   138  0.85  21.01   1.02     0.98      13600.24|
|  6:  2.7452 -  2.5843  1283   141  0.86  20.82   1.01     0.98      11624.28|
|  7:  2.5843 -  2.4555  1277   135  0.84  22.14   1.04     1.00      11138.59|
|  8:  2.4555 -  2.3490  1269   151  0.84  22.99   1.02     0.97      10218.31|
|  9:  2.3490 -  2.2589  1243   138  0.84  22.37   1.04     0.99       9527.12|
| 10:  2.2589 -  2.1812  1294   140  0.84  22.28   1.04     1.00       8308.44|
| 11:  2.1812 -  2.1132  1254   141  0.85  22.00   1.05     1.00       7460.46|
| 12:  2.1132 -  2.0529  1251   139  0.86  20.85   1.05     1.03       6541.49|
| 13:  2.0529 -  1.9990  1263   137  0.85  22.16   1.04     1.03       5834.84|
| 14:  1.9990 -  1.9504   896   103  0.84  22.60   1.03     0.97       5132.82|
|alpha:            min =        0.96 max =            1.05 mean =         1.00|
|beta:             min =     5132.82 max =        18473.58 mean =     11066.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.96 mean =        19.84|
|phase err.(test): min =        0.00 max =           89.91 mean =        18.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1565   r_free= 0.2063   ksol= 0.31   Bsol= 36.67   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,-1.60,-0.61,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.422246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1565   r_free= 0.2063   ksol= 0.31   Bsol= 36.67   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,-1.60,-0.61,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.422246                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6553 0.99   1386  155 0.1113 0.1501       5.501      5.6811|
|  2:  4.6553 -  3.7141 0.99   1331  146 0.1143 0.1489      5.6984      5.9572|
|  3:  3.7141 -  3.2503 0.99   1299  142 0.1445 0.1812      5.7505      6.0369|
|  4:  3.2503 -  2.9556 0.99   1294  153 0.1703 0.2191      5.7449      5.9063|
|  5:  2.9556 -  2.7452 0.99   1290  138 0.1804 0.2319      5.5925      5.7822|
|  6:  2.7452 -  2.5843 0.99   1283  141 0.1711 0.2163      5.4822      5.6249|
|  7:  2.5843 -  2.4555 0.99   1277  135 0.1744 0.2259      5.4342      5.6603|
|  8:  2.4555 -  2.3490 0.98   1269  151 0.1751 0.2516      5.3892      5.6547|
|  9:  2.3490 -  2.2589 0.98   1243  138 0.1740 0.2411      5.3559      5.5462|
| 10:  2.2589 -  2.1812 1.00   1294  140 0.1663 0.2351      5.2758      5.4832|
| 11:  2.1812 -  2.1132 0.97   1254  141 0.1717 0.2414      5.2372      5.5086|
| 12:  2.1132 -  2.0529 0.98   1251  139 0.1623 0.2050      5.1492      5.3771|
| 13:  2.0529 -  1.9990 1.00   1263  137 0.1666 0.2532      5.0863      5.3991|
| 14:  1.9990 -  1.9504 0.70    896  103 0.1817 0.2047      5.0646      5.1687|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8363 -  4.6553  1386   155  0.92  11.83   0.98     0.96      10084.02|
|  2:  4.6553 -  3.7141  1331   146  0.93  11.70   1.05     1.03      14517.76|
|  3:  3.7141 -  3.2503  1299   142  0.89  16.35   1.05     1.05      18317.82|
|  4:  3.2503 -  2.9556  1294   153  0.87  19.51   1.04     1.00      18285.72|
|  5:  2.9556 -  2.7452  1290   138  0.85  21.09   1.01     0.96      13699.70|
|  6:  2.7452 -  2.5843  1283   141  0.86  20.83   1.00     0.97      11669.41|
|  7:  2.5843 -  2.4555  1277   135  0.84  22.17   1.01     0.98      11175.75|
|  8:  2.4555 -  2.3490  1269   151  0.84  23.05   1.00     0.95      10275.93|
|  9:  2.3490 -  2.2589  1243   138  0.84  22.41   1.01     0.97       9578.16|
| 10:  2.2589 -  2.1812  1294   140  0.84  22.34   1.02     0.97       8349.11|
| 11:  2.1812 -  2.1132  1254   141  0.85  22.02   1.02     0.98       7488.30|
| 12:  2.1132 -  2.0529  1251   139  0.86  20.87   1.02     1.00       6558.26|
| 13:  2.0529 -  1.9990  1263   137  0.85  22.17   1.01     1.01       5838.28|
| 14:  1.9990 -  1.9504   896   103  0.84  22.58   1.00     0.95       5131.24|
|alpha:            min =        0.95 max =            1.05 mean =         0.98|
|beta:             min =     5131.24 max =        18317.82 mean =     10946.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.97 mean =        19.78|
|phase err.(test): min =        0.00 max =           89.81 mean =        18.73|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.239)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.98  16.97    None  None   None       |
|    all(noH): 2823   0      0.00    115.98  16.97    None  None   None       |
|    Sol.    : 438    0      4.25    115.98  41.10    None  None   None       |
|    Mac.    : 2385   0      0.00    102.48  12.54    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 -  11.601: 1498   |   5:    57.991 -  69.588:   49        |
|      1:    11.601 -  23.198:  765   |   6:    69.588 -  81.186:   26        |
|      2:    23.198 -  34.796:  202   |   7:    81.186 -  92.784:    6        |
|      3:    34.796 -  46.393:  152   |   8:    92.784 - 104.381:    3        |
|      4:    46.393 -  57.991:  121   |   9:   104.381 - 115.979:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.458 - 5.742
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 343 from: 346
   mapped sites are within: 0.715 - 5.742

peak=   10.567 closest distance to " O   HOH Z 399 " =    1.336
peak=    7.726 closest distance to " O   HOH Z 390 " =    1.520
peak=    7.355 closest distance to " O   HOH Z 138 " =    1.281
peak=    6.927 closest distance to " O   SER A  62 " =    1.102
peak=    6.846 closest distance to " C   ASN A 285 " =    1.003
peak=    6.564 closest distance to " O   HOH Z 289 " =    1.760
peak=    6.406 closest distance to " OD1 ASP A 298 " =    2.129
peak=    6.344 closest distance to " O   HOH Z  61 " =    1.585
peak=    5.958 closest distance to " O   HOH Z 130 " =    1.595
peak=    5.827 closest distance to " O   HOH Z  65 " =    2.201
peak=    5.794 closest distance to " O   HOH Z 400 " =    1.155
peak=    5.701 closest distance to " O   HOH Z 103 " =    1.224
peak=    5.644 closest distance to " O   HOH Z 385 " =    2.260
peak=    5.466 closest distance to " C   ASN A 284 " =    0.809
peak=    5.361 closest distance to " O   HOH Z 222 " =    1.938
peak=    5.339 closest distance to " O   HOH Z 205 " =    1.254
peak=    5.335 closest distance to " O   HOH Z 363 " =    1.378
peak=    5.291 closest distance to " O   HOH Z 332 " =    1.230
peak=    5.256 closest distance to " CG  PRO A  90 " =    1.180
peak=    5.218 closest distance to " O   HOH Z 358 " =    1.440
peak=    5.184 closest distance to " N   ASN A 285 " =    0.858
peak=    5.152 closest distance to " O   HOH Z 120 " =    1.014
peak=    5.116 closest distance to " O   HOH Z 415 " =    1.369
peak=    5.005 closest distance to " NE2 GLN A  11 " =    1.512
peak=    4.956 closest distance to " NH2 ARG A  56 " =    2.073
peak=    4.950 closest distance to " O   HOH Z  54 " =    1.736
peak=    4.947 closest distance to " O   HOH Z 278 " =    1.974
peak=    4.930 closest distance to " O   HOH Z 214 " =    1.586
peak=    4.899 closest distance to " O   HOH Z   7 " =    2.010
peak=    4.864 closest distance to " O   HOH Z 179 " =    1.164
peak=    4.860 closest distance to " OD1 ASN A  60 " =    1.192
peak=    4.852 closest distance to " N   GLY A 287 " =    0.965
peak=    4.836 closest distance to " O   HOH Z  78 " =    1.809
peak=    4.775 closest distance to " OD1 ASP A 286 " =    1.117
peak=    4.737 closest distance to " O   HOH Z  29 " =    1.397
peak=    4.704 closest distance to " O   HOH Z 424 " =    1.499
peak=    4.694 closest distance to " O   HOH Z 138 " =    2.015
peak=    4.689 closest distance to " O   HOH Z 117 " =    1.430
peak=    4.664 closest distance to " O   HOH Z  97 " =    1.837
peak=    4.661 closest distance to " O   HOH Z 244 " =    1.448
peak=    4.651 closest distance to " O   HOH Z 124 " =    1.743
peak=    4.608 closest distance to " O   HOH Z  46 " =    1.346
peak=    4.583 closest distance to " O   HOH Z 302 " =    1.660
peak=    4.567 closest distance to " O   HOH Z 250 " =    2.041
peak=    4.551 closest distance to " O   HOH Z 133 " =    1.579
peak=    4.550 closest distance to " O   HOH Z  53 " =    2.234
peak=    4.531 closest distance to " O   PRO A 198 " =    1.420
peak=    4.499 closest distance to " O   HOH Z 192 " =    1.567
peak=    4.426 closest distance to " O   HOH Z 427 " =    2.028
peak=    4.405 closest distance to " CB  ARG A 275 " =    1.212
peak=    4.351 closest distance to " O   HOH Z 116 " =    1.404
peak=    4.350 closest distance to " O   HOH Z 403 " =    1.932
peak=    4.334 closest distance to " O   HOH Z 223 " =    1.111
peak=    4.316 closest distance to " O   HOH Z 352 " =    1.823
peak=    4.314 closest distance to " O   HOH Z 316 " =    2.852
peak=    4.313 closest distance to " N   LYS A 119 " =    0.815
peak=    4.307 closest distance to " O   HOH Z 350 " =    1.252
peak=    4.284 closest distance to " O   HOH Z 402 " =    1.600
peak=    4.282 closest distance to " O   HOH Z 211 " =    1.719
peak=    4.271 closest distance to " N   SER A  63 " =    0.942
peak=    4.258 closest distance to " O   HOH Z 109 " =    1.695
peak=    4.220 closest distance to " O   HOH Z 135 " =    1.769
peak=    4.173 closest distance to " O   HOH Z 276 " =    1.790
peak=    4.164 closest distance to " O   HOH Z  28 " =    1.988
peak=    4.160 closest distance to " O   HOH Z 416 " =    1.836
peak=    4.159 closest distance to " OG ASER A 134 " =    1.344
peak=    4.146 closest distance to " CB  GLN A  77 " =    0.914
peak=    4.114 closest distance to " O   HOH Z 139 " =    1.989
peak=    4.114 closest distance to " O   HOH Z 126 " =    2.029
peak=    4.094 closest distance to " NH2 ARG A 269 " =    0.886
peak=    4.081 closest distance to " N   ASP A 286 " =    0.873
peak=    4.080 closest distance to " O   HOH Z 282 " =    1.714
peak=    4.061 closest distance to " CG  PRO A 213 " =    1.203
peak=    4.055 closest distance to " CG2 THR A 246 " =    1.025
peak=    4.050 closest distance to " O   HOH Z  59 " =    1.572
peak=    4.038 closest distance to " O   HOH Z 269 " =    3.051
peak=    4.037 closest distance to " CB  ALA A 104 " =    1.257
peak=    4.035 closest distance to " O   ALA A 165 " =    1.141
peak=    4.018 closest distance to " O   HOH Z 311 " =    1.626
peak=    4.013 closest distance to " O   HOH Z 255 " =    1.075
peak=    4.012 closest distance to " O   HOH Z 245 " =    1.403
peak=    4.011 closest distance to " NH2 ARG A  36 " =    1.063
peak=    3.993 closest distance to " ND2 ASN A 285 " =    0.980
peak=    3.986 closest distance to " N   ASN A 285 " =    1.009
peak=    3.984 closest distance to " CB  SER A 216 " =    0.995
peak=    3.957 closest distance to " O   HOH Z 383 " =    1.102
peak=    3.951 closest distance to " O   HOH Z 381 " =    1.185
peak=    3.946 closest distance to " O   HOH Z 258 " =    1.354
peak=    3.936 closest distance to " ND2 ASN A 110 " =    1.149
peak=    3.909 closest distance to " CG  PRO A 243 " =    1.276
peak=    3.906 closest distance to " CA  ARG A  36 " =    1.202
peak=    3.904 closest distance to " OD1 ASN A  45 " =    1.145
peak=    3.896 closest distance to " CB  ARG A 102 " =    0.891
peak=    3.875 closest distance to " O   HOH Z 269 " =    1.300
peak=    3.872 closest distance to " CB  ALA A   1 " =    1.299
peak=    3.870 closest distance to " CA  ASN A 284 " =    0.995
peak=    3.860 closest distance to " ND2 ASN A  69 " =    1.072
peak=    3.859 closest distance to " CE AMET A  47 " =    0.886
peak=    3.858 closest distance to " O   HOH Z 347 " =    1.374
peak=    3.838 closest distance to " O   HOH Z   6 " =    1.777
peak=    3.837 closest distance to " CB  ASP A 132 " =    3.716
peak=    3.829 closest distance to " CB  LYS A 290 " =    1.491
peak=    3.828 closest distance to " OE1 GLN A  55 " =    1.891
peak=    3.827 closest distance to " OG BSER A  12 " =    1.114
peak=    3.809 closest distance to " O   GLY A 302 " =    1.463
peak=    3.808 closest distance to " CD2 TRP A 179 " =    2.236
peak=    3.801 closest distance to " NZ  LYS A 117 " =    1.256
peak=    3.792 closest distance to " O   HOH Z   5 " =    1.643
peak=    3.786 closest distance to " O   HOH Z 145 " =    1.881
peak=    3.783 closest distance to " O   ASP A 286 " =    2.122
peak=    3.778 closest distance to " O   HOH Z   2 " =    2.025
peak=    3.778 closest distance to " O   HOH Z 182 " =    1.456
peak=    3.776 closest distance to " CA  GLY A 136 " =    0.923
peak=    3.776 closest distance to " C   ASN A 215 " =    1.311
peak=    3.763 closest distance to " O   HOH Z 375 " =    1.107
peak=    3.750 closest distance to " O   HOH Z  89 " =    1.502
peak=    3.747 closest distance to " CB  PRO A  54 " =    1.032
peak=    3.747 closest distance to " CB  ASN A  60 " =    0.856
peak=    3.739 closest distance to " O   HOH Z 137 " =    1.245
peak=    3.733 closest distance to " CG  PRO A  54 " =    1.283
peak=    3.731 closest distance to " O   HOH Z  69 " =    2.261
peak=    3.730 closest distance to " O   HOH Z 105 " =    1.418
peak=    3.730 closest distance to " O   HOH Z  92 " =    1.420
peak=    3.720 closest distance to " CG  LEU A 167 " =    1.351
peak=    3.702 closest distance to " O   HOH Z 287 " =    1.761
peak=    3.702 closest distance to " CB  GLN A 183 " =    0.960
peak=    3.699 closest distance to " O   HOH Z 123 " =    1.442
peak=    3.695 closest distance to " CB  SER A 276 " =    1.329
peak=    3.686 closest distance to " O   HOH Z 427 " =    1.262
peak=    3.667 closest distance to " N   ASN A  60 " =    1.051
peak=    3.665 closest distance to " O   HOH Z 134 " =    1.496
peak=    3.664 closest distance to " O   HOH Z 212 " =    1.840
peak=    3.658 closest distance to " O   HOH Z 369 " =    1.622
peak=    3.651 closest distance to " NH2 ARG A 219 " =    1.703
peak=    3.649 closest distance to " CB  GLU A 152 " =    1.117
peak=    3.649 closest distance to " O   HOH Z 232 " =    1.160
peak=    3.648 closest distance to " O   HOH Z 329 " =    1.471
peak=    3.637 closest distance to " O   HOH Z 112 " =    1.477
peak=    3.632 closest distance to " CB  ALA A  10 " =    1.021
peak=    3.630 closest distance to " N   SER A 210 " =    1.167
peak=    3.623 closest distance to " CB  ASP A 200 " =    1.071
peak=    3.621 closest distance to " OD2 ASP A 140 " =    1.177
peak=    3.616 closest distance to " O   HOH Z 417 " =    1.929
peak=    3.612 closest distance to " CE  MET A  93 " =    1.388
peak=    3.610 closest distance to " O   HOH Z 414 " =    1.607
peak=    3.609 closest distance to " O   HOH Z 360 " =    1.174
peak=    3.607 closest distance to " CD2 LEU A   5 " =    1.146
peak=    3.598 closest distance to " O   HOH Z 371 " =    1.917
peak=    3.598 closest distance to " O   HOH Z  47 " =    1.744
peak=    3.590 closest distance to " O   HOH Z 363 " =    2.884
peak=    3.583 closest distance to " NZ  LYS A  76 " =    1.175
peak=    3.571 closest distance to " N   GLN A  73 " =    1.441
peak=    3.571 closest distance to " O   HOH Z 366 " =    2.350
peak=    3.559 closest distance to " O   HOH Z 247 " =    1.213
peak=    3.556 closest distance to " O   ALA A 242 " =    0.914
peak=    3.555 closest distance to " C   VAL A  72 " =    1.143
peak=    3.551 closest distance to " O   HOH Z 261 " =    2.153
peak=    3.539 closest distance to " O   HOH Z 389 " =    1.589
peak=    3.536 closest distance to " CG  GLN A  88 " =    1.056
peak=    3.535 closest distance to " CD2 LEU A  25 " =    1.245
peak=    3.535 closest distance to " O   HOH Z 393 " =    1.618
peak=    3.532 closest distance to " NE AARG A 275 " =    1.455
peak=    3.531 closest distance to " OE1 GLN A  58 " =    5.516
peak=    3.529 closest distance to " O   GLU A   2 " =    0.778
peak=    3.529 closest distance to " O   HOH Z 279 " =    1.070
peak=    3.528 closest distance to " O   HOH Z 291 " =    1.470
peak=    3.527 closest distance to " N   ALA A 100 " =    0.743
peak=    3.527 closest distance to " O   HOH Z  88 " =    2.651
peak=    3.525 closest distance to " CB  VAL A 202 " =    1.518
peak=    3.525 closest distance to " CG  PRO A 198 " =    1.602
peak=    3.515 closest distance to " O   HOH Z  68 " =    1.827
peak=    3.513 closest distance to " NE1 TRP A 274 " =    1.109
peak=    3.504 closest distance to " CB  SER A   3 " =    1.383
peak=    3.504 closest distance to " O   HOH Z 272 " =    1.744
peak=    3.503 closest distance to " O   HOH Z 133 " =    2.271
peak=    3.500 closest distance to " CB  TRP A 179 " =    1.332
peak=    3.499 closest distance to " CB  ARG A  79 " =    1.099
peak=    3.496 closest distance to " CB  ALA A 244 " =    1.031
peak=    3.495 closest distance to " N   GLU A   2 " =    1.282
peak=    3.489 closest distance to " O   HOH Z 326 " =    1.349
peak=    3.483 closest distance to " CD1 PHE A 283 " =    0.886
peak=    3.481 closest distance to " O   HOH Z  63 " =    1.690
peak=    3.477 closest distance to " CG2 THR A  29 " =    0.980
peak=    3.469 closest distance to " N   ARG A 156 " =    1.333
peak=    3.468 closest distance to " CB  THR A 235 " =    1.335
peak=    3.461 closest distance to " CD2 HIS A 115 " =    1.007
peak=    3.458 closest distance to " CA  THR A 221 " =    0.853
peak=    3.453 closest distance to " O   HOH Z 361 " =    2.611
peak=    3.452 closest distance to " O   HOH Z 158 " =    2.186
peak=    3.451 closest distance to " CA  SER A 273 " =    0.901
peak=    3.451 closest distance to " CB  GLN A 122 " =    1.193
peak=    3.446 closest distance to " NZ  LYS A 289 " =    1.328
peak=    3.446 closest distance to " O   HOH Z 137 " =    1.556
peak=    3.444 closest distance to " O   HOH Z 392 " =    1.449
peak=    3.443 closest distance to " N   VAL A 121 " =    1.005
peak=    3.442 closest distance to " O   HOH Z 137 " =    1.072
peak=    3.441 closest distance to " CB  ALA A   8 " =    0.933
peak=    3.441 closest distance to " O   HOH Z 353 " =    1.751
peak=    3.435 closest distance to " OG BSER A 258 " =    1.052
peak=    3.432 closest distance to " CE  LYS A  48 " =    1.086
peak=    3.428 closest distance to " O   HOH Z 161 " =    1.033
peak=    3.423 closest distance to " CB  ASN A 285 " =    0.984
peak=    3.422 closest distance to " CG2 THR A 251 " =    1.699
peak=    3.421 closest distance to " CA  SER A  62 " =    1.136
peak=    3.417 closest distance to " CB  MET A  47 " =    1.397
peak=    3.416 closest distance to " O   HOH Z 143 " =    1.118
peak=    3.414 closest distance to " O   HOH Z 217 " =    3.127
peak=    3.414 closest distance to " O   HOH Z  15 " =    1.364
peak=    3.413 closest distance to " O   HOH Z 286 " =    2.408
peak=    3.410 closest distance to " CG2 THR A 294 " =    1.162
peak=    3.408 closest distance to " O   SER A 164 " =    1.179
peak=    3.405 closest distance to " O   HOH Z  24 " =    1.604
peak=    3.401 closest distance to " O   HOH Z 124 " =    1.651
peak=    3.399 closest distance to " O   HOH Z 225 " =    1.517
peak=    3.388 closest distance to " CB  ASP A 124 " =    1.144
peak=    3.382 closest distance to " CB  MET A 105 " =    1.113
peak=    3.378 closest distance to " O   HOH Z 207 " =    1.512
peak=    3.378 closest distance to " NH1 ARG A  36 " =    1.153
peak=    3.374 closest distance to " CA  ASN A 285 " =    1.065
peak=    3.371 closest distance to " O   HOH Z 114 " =    2.453
peak=    3.366 closest distance to " CB  ASP A 140 " =    0.764
peak=    3.361 closest distance to " O   HOH Z 334 " =    2.040
peak=    3.358 closest distance to " N   ALA A   1 " =    1.565
peak=    3.353 closest distance to " CG1BVAL A 121 " =    1.732
peak=    3.353 closest distance to " O   HOH Z 196 " =    1.739
peak=    3.352 closest distance to " O   HOH Z 273 " =    1.308
peak=    3.351 closest distance to " CB  ALA A 137 " =    0.923
peak=    3.347 closest distance to " NZ BLYS A 290 " =    1.220
peak=    3.341 closest distance to " O   SER A  87 " =    2.287
peak=    3.338 closest distance to " O   HOH Z 178 " =    1.245
peak=    3.338 closest distance to " O   HOH Z 340 " =    1.310
peak=    3.338 closest distance to " CB  SER A 210 " =    0.906
peak=    3.332 closest distance to " O   LYS A 119 " =    0.915
peak=    3.329 closest distance to " CB  ASN A 148 " =    1.782
peak=    3.326 closest distance to " C   GLY A 147 " =    1.066
peak=    3.323 closest distance to " O   HOH Z 183 " =    1.194
peak=    3.321 closest distance to " CG  ASP A 238 " =    0.855
peak=    3.320 closest distance to " CB  SER A  12 " =    1.645
peak=    3.318 closest distance to " O   HOH Z 423 " =    1.899
peak=    3.317 closest distance to " O   HOH Z  88 " =    2.592
peak=    3.315 closest distance to " O   HOH Z 379 " =    3.459
peak=    3.307 closest distance to " O   HOH Z 132 " =    1.259
peak=    3.305 closest distance to " N   TYR A  15 " =    1.121
peak=    3.304 closest distance to " O   HOH Z 167 " =    1.567
peak=    3.298 closest distance to " OD2 ASP A 286 " =    2.336
peak=    3.294 closest distance to " CB  GLU A 277 " =    1.079
peak=    3.292 closest distance to " O   HOH Z 126 " =    1.483
peak=    3.288 closest distance to " O   HOH Z 128 " =    1.833
peak=    3.286 closest distance to " N   PHE A  59 " =    0.724
peak=    3.286 closest distance to " CB  GLN A  88 " =    1.451
peak=    3.285 closest distance to " O   HOH Z 186 " =    1.328
peak=    3.284 closest distance to " O   SER A  26 " =    1.894
peak=    3.284 closest distance to " O   HOH Z 239 " =    1.598
peak=    3.283 closest distance to " ND2 ASN A 285 " =    0.933
peak=    3.282 closest distance to " O   HOH Z 422 " =    2.563
peak=    3.277 closest distance to " N   GLN A 278 " =    1.113
peak=    3.276 closest distance to " O   HOH Z 412 " =    2.080
peak=    3.276 closest distance to " CB  GLN A 223 " =    1.728
peak=    3.274 closest distance to " O   HOH Z 139 " =    2.347
peak=    3.274 closest distance to " CA  ILE A 120 " =    0.872
peak=    3.271 closest distance to " CD  ARG A 138 " =    0.918
peak=    3.268 closest distance to " NH2BARG A 190 " =    1.466
peak=    3.266 closest distance to " CD2 LEU A 255 " =    1.099
peak=    3.263 closest distance to " O   HOH Z 384 " =    1.772
peak=    3.262 closest distance to " O   HOH Z 124 " =    4.161
peak=    3.262 closest distance to " CG1 VAL A 153 " =    0.894
peak=    3.261 closest distance to " O   HOH Z 112 " =    2.146
peak=    3.261 closest distance to " O   SER A 271 " =    1.340
peak=    3.254 closest distance to " O   ALA A 244 " =    0.972
peak=    3.246 closest distance to " CE AMET A  47 " =    1.056
peak=    3.245 closest distance to " NE2 GLN A 278 " =    3.527
peak=    3.244 closest distance to " NH1 ARG A 139 " =    1.235
peak=    3.243 closest distance to " CB  GLN A  11 " =    1.484
peak=    3.243 closest distance to " O   HOH Z 128 " =    1.201
peak=    3.243 closest distance to " O   HOH Z 128 " =    2.122
peak=    3.242 closest distance to " O   HOH Z 248 " =    2.270
peak=    3.242 closest distance to " N   ASN A 142 " =    1.315
peak=    3.241 closest distance to " CA  LEU A 282 " =    1.040
peak=    3.238 closest distance to " CE1 TYR A  68 " =    1.085
peak=    3.236 closest distance to " CE  LYS A 289 " =    1.187
peak=    3.234 closest distance to " O   HOH Z 230 " =    1.944
peak=    3.234 closest distance to " O   HOH Z 192 " =    2.178
peak=    3.232 closest distance to " O   HOH Z 206 " =    1.213
peak=    3.230 closest distance to " O   HOH Z 368 " =    3.828
peak=    3.228 closest distance to " O   HOH Z 209 " =    1.196
peak=    3.224 closest distance to " NE BARG A 275 " =    1.209
peak=    3.221 closest distance to " O   HOH Z 158 " =    1.646
peak=    3.212 closest distance to " CA  TYR A 247 " =    1.319
peak=    3.208 closest distance to " O   HOH Z 423 " =    1.755
peak=    3.206 closest distance to " N   ARG A 275 " =    0.839
peak=    3.191 closest distance to " CA  ILE A  20 " =    0.928
peak=    3.191 closest distance to " CA  ASN A 217 " =    1.145
peak=    3.189 closest distance to " CG2 VAL A 232 " =    1.294
peak=    3.187 closest distance to " CA  GLY A 203 " =    1.615
peak=    3.180 closest distance to " O   HOH Z  45 " =    1.885
peak=    3.177 closest distance to " O   HOH Z  42 " =    1.611
peak=    3.176 closest distance to " O   HOH Z  30 " =    1.411
peak=    3.175 closest distance to " CG2 ILE A 151 " =    1.164
peak=    3.174 closest distance to " O   HOH Z 259 " =    1.484
peak=    3.173 closest distance to " O   HOH Z 380 " =    2.071
peak=    3.170 closest distance to " O   HOH Z 411 " =    3.447
peak=    3.169 closest distance to " O   HOH Z  44 " =    1.523
peak=    3.165 closest distance to " O   HOH Z 250 " =    1.273
peak=    3.165 closest distance to " O   HOH Z 225 " =    2.014
peak=    3.164 closest distance to " N   GLY A 111 " =    1.311
peak=    3.163 closest distance to " O   ILE A  20 " =    1.536
peak=    3.161 closest distance to " O   HOH Z 410 " =    1.605
peak=    3.158 closest distance to " CA  GLU A 152 " =    1.045
peak=    3.156 closest distance to " CG  ARG A  66 " =    2.471
peak=    3.156 closest distance to " O   ASP A 286 " =    2.085
peak=    3.155 closest distance to " O   HOH Z 334 " =    1.451
peak=    3.154 closest distance to " CB  ASP A 298 " =    1.071
peak=    3.149 closest distance to " CD  PRO A 243 " =    1.436
peak=    3.143 closest distance to " CD1 LEU A 228 " =    1.717
peak=    3.136 closest distance to " O   HOH Z 412 " =    1.412
peak=    3.129 closest distance to " CB  ASP A 286 " =    0.955
peak=    3.129 closest distance to " O   HOH Z 116 " =    5.555
peak=    3.125 closest distance to " CA  ARG A 219 " =    2.090
peak=    3.123 closest distance to " OD1 ASN A  45 " =    1.386
peak=    3.120 closest distance to " OE1 GLN A  88 " =    1.029
peak=    3.119 closest distance to " CG  ASN A 301 " =    0.730
peak=    3.114 closest distance to " CA  PRO A 213 " =    0.715
peak=    3.112 closest distance to " OE1 GLN A  77 " =    0.974
peak=    3.111 closest distance to " O   HOH Z 293 " =    1.447
peak=    3.111 closest distance to " O   HOH Z 104 " =    1.864
peak=    3.108 closest distance to " O   HOH Z 353 " =    1.742
peak=    3.105 closest distance to " O   HOH Z 359 " =    1.630
peak=    3.102 closest distance to " CB  ARG A  66 " =    0.913
peak=    3.098 closest distance to " O   HOH Z 423 " =    1.802
peak=    3.098 closest distance to " O   HOH Z 344 " =    1.265
peak=    3.094 closest distance to " OG BSER A 134 " =    2.903
peak=    3.094 closest distance to " OD2 ASP A 253 " =    1.325
peak=    3.092 closest distance to " C   GLY A 302 " =    1.803
peak=    3.081 closest distance to " O   HOH Z 145 " =    2.436
peak=    3.080 closest distance to " CE1 PHE A 225 " =    1.068
peak=    3.077 closest distance to " CA  PHE A 130 " =    1.127
peak=    3.075 closest distance to " C   ASP A 298 " =    1.110
peak=    3.074 closest distance to " CB  GLU A 128 " =    1.020
peak=    3.072 closest distance to " CB  VAL A 126 " =    1.062
peak=    3.060 closest distance to " O   HOH Z 365 " =    2.328
peak=    3.047 closest distance to " CB  THR A 221 " =    1.158
peak=    3.042 closest distance to " O   HOH Z  10 " =    1.747
peak=    3.028 closest distance to " O   HOH Z 434 " =    5.742

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.167 - 5.315
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 218
   mapped sites are within: 0.710 - 5.315

peak=   -5.520 closest distance to " O   SER A  62 " =    0.903
peak=   -5.383 closest distance to " O   ASN A 285 " =    0.957
peak=   -4.848 closest distance to " O   LYS A 119 " =    0.790
peak=   -4.458 closest distance to " N   ASN A  60 " =    1.041
peak=   -4.426 closest distance to " O   PRO A 198 " =    1.138
peak=   -4.401 closest distance to " C   ASN A 284 " =    1.107
peak=   -4.354 closest distance to " CD1 TRP A 179 " =    0.849
peak=   -4.314 closest distance to " N   GLN A  58 " =    1.088
peak=   -4.296 closest distance to " O   HOH Z 290 " =    0.870
peak=   -4.260 closest distance to " O   HOH Z  60 " =    1.705
peak=   -4.252 closest distance to " O   HOH Z 264 " =    0.921
peak=   -4.196 closest distance to " O   HOH Z 350 " =    0.795
peak=   -4.195 closest distance to " CD  ARG A  14 " =    3.034
peak=   -4.185 closest distance to " O   HOH Z 242 " =    1.481
peak=   -4.170 closest distance to " O   HOH Z 163 " =    1.501
peak=   -4.167 closest distance to " CZ  ARG A  36 " =    1.501
peak=   -4.139 closest distance to " O   ASP A 286 " =    0.937
peak=   -4.136 closest distance to " O   HOH Z  13 " =    1.476
peak=   -4.130 closest distance to " O   HOH Z 322 " =    0.710
peak=   -4.074 closest distance to " N   LYS A 119 " =    0.862
peak=   -4.047 closest distance to " OG  SER A  97 " =    2.356
peak=   -4.025 closest distance to " O   HOH Z 381 " =    0.812
peak=   -3.986 closest distance to " O   HOH Z  88 " =    1.313
peak=   -3.959 closest distance to " O   HOH Z  24 " =    0.990
peak=   -3.941 closest distance to " O   HOH Z 234 " =    4.714
peak=   -3.930 closest distance to " O   HOH Z 317 " =    3.095
peak=   -3.927 closest distance to " O   HOH Z 388 " =    1.775
peak=   -3.913 closest distance to " O   LYS A 119 " =    0.894
peak=   -3.911 closest distance to " ND2 ASN A 209 " =    1.691
peak=   -3.903 closest distance to " NH2 ARG A  79 " =    1.827
peak=   -3.872 closest distance to " CB  CYS A 201 " =    2.468
peak=   -3.871 closest distance to " CB  ASN A 285 " =    1.652
peak=   -3.867 closest distance to " O   HOH Z 244 " =    1.204
peak=   -3.848 closest distance to " O   HOH Z 208 " =    1.054
peak=   -3.843 closest distance to " CA  GLY A  23 " =    2.551
peak=   -3.831 closest distance to " O   HOH Z  39 " =    1.185
peak=   -3.829 closest distance to " CD2 TYR A 293 " =    1.997
peak=   -3.808 closest distance to " O   ALA A  51 " =    1.320
peak=   -3.789 closest distance to " CA  GLY A 133 " =    1.873
peak=   -3.788 closest distance to " O   HOH Z 205 " =    0.737
peak=   -3.765 closest distance to " O   ASP A 191 " =    2.049
peak=   -3.743 closest distance to " O   LYS A  76 " =    0.989
peak=   -3.735 closest distance to " O   HOH Z 246 " =    1.538
peak=   -3.715 closest distance to " O   GLY A 136 " =    1.513
peak=   -3.703 closest distance to " O   GLU A  44 " =    1.809
peak=   -3.700 closest distance to " CG  GLN A  88 " =    0.810
peak=   -3.694 closest distance to " CG  PRO A 243 " =    0.935
peak=   -3.685 closest distance to " O   HOH Z  73 " =    1.410
peak=   -3.679 closest distance to " OG1 THR A 294 " =    2.427
peak=   -3.667 closest distance to " O   HOH Z 377 " =    1.917
peak=   -3.653 closest distance to " CD2 LEU A 297 " =    1.223
peak=   -3.642 closest distance to " CD  PRO A  90 " =    1.695
peak=   -3.641 closest distance to " C   VAL A  72 " =    1.014
peak=   -3.637 closest distance to " O   HOH Z  98 " =    1.712
peak=   -3.617 closest distance to " O   ASN A 301 " =    1.397
peak=   -3.612 closest distance to " CG  PRO A 213 " =    0.747
peak=   -3.609 closest distance to " O   HOH Z 413 " =    4.406
peak=   -3.608 closest distance to " O   HOH Z 220 " =    0.760
peak=   -3.589 closest distance to " CA  ASN A 127 " =    1.309
peak=   -3.588 closest distance to " OG ASER A 134 " =    1.253
peak=   -3.585 closest distance to " CD1 LEU A  25 " =    2.004
peak=   -3.584 closest distance to " O   HOH Z 323 " =    1.576
peak=   -3.584 closest distance to " C   SER A  63 " =    1.111
peak=   -3.581 closest distance to " OD2 ASP A 140 " =    1.066
peak=   -3.580 closest distance to " CG  ASN A  60 " =    1.118
peak=   -3.566 closest distance to " SD  MET A 105 " =    1.970
peak=   -3.562 closest distance to " O   HOH Z 397 " =    1.494
peak=   -3.560 closest distance to " O   HOH Z 198 " =    2.531
peak=   -3.559 closest distance to " CB  ALA A 248 " =    1.951
peak=   -3.548 closest distance to " O   HOH Z 185 " =    1.918
peak=   -3.545 closest distance to " CG  ASP A  50 " =    0.849
peak=   -3.544 closest distance to " N   GLN A  88 " =    1.743
peak=   -3.539 closest distance to " NH2AARG A 275 " =    5.315
peak=   -3.539 closest distance to " O   HOH Z   2 " =    1.747
peak=   -3.538 closest distance to " O   HOH Z 409 " =    3.105
peak=   -3.535 closest distance to " O   HOH Z 247 " =    0.935
peak=   -3.522 closest distance to " O   HOH Z 392 " =    0.899
peak=   -3.516 closest distance to " C   ASP A 124 " =    1.999
peak=   -3.516 closest distance to " CA  ALA A 161 " =    1.238
peak=   -3.513 closest distance to " O   HOH Z 140 " =    4.679
peak=   -3.509 closest distance to " CG BLYS A 290 " =    0.837
peak=   -3.504 closest distance to " CG  GLN A  73 " =    1.241
peak=   -3.502 closest distance to " O   HOH Z 256 " =    0.958
peak=   -3.498 closest distance to " NH1 ARG A  56 " =    2.468
peak=   -3.492 closest distance to " O   ASP A 162 " =    2.203
peak=   -3.491 closest distance to " O   HOH Z 255 " =    0.842
peak=   -3.481 closest distance to " CD2 LEU A 237 " =    2.701
peak=   -3.463 closest distance to " N   GLN A 122 " =    1.538
peak=   -3.450 closest distance to " O   HOH Z 425 " =    0.746
peak=   -3.436 closest distance to " N   ASN A 284 " =    0.946
peak=   -3.432 closest distance to " O   HOH Z   1 " =    3.580
peak=   -3.431 closest distance to " O   ASP A  65 " =    1.017
peak=   -3.420 closest distance to " O   TRP A  70 " =    1.419
peak=   -3.419 closest distance to " CB  SER A 146 " =    2.281
peak=   -3.394 closest distance to " O   SER A  97 " =    1.311
peak=   -3.392 closest distance to " CE3 TRP A 274 " =    2.660
peak=   -3.388 closest distance to " O   HOH Z 143 " =    1.049
peak=   -3.383 closest distance to " O   ARG A  66 " =    1.077
peak=   -3.382 closest distance to " O   HOH Z 129 " =    0.916
peak=   -3.380 closest distance to " O   SER A  22 " =    1.140
peak=   -3.379 closest distance to " O   ASN A 215 " =    1.826
peak=   -3.379 closest distance to " CB  ASP A  27 " =    2.403
peak=   -3.376 closest distance to " O   HOH Z 332 " =    0.857
peak=   -3.375 closest distance to " N   SER A 206 " =    1.726
peak=   -3.356 closest distance to " CB  ASN A  74 " =    1.008
peak=   -3.346 closest distance to " OG BSER A  99 " =    2.102
peak=   -3.344 closest distance to " C   ALA A 114 " =    2.023
peak=   -3.344 closest distance to " NH1 ARG A  36 " =    0.710
peak=   -3.343 closest distance to " O   HOH Z 250 " =    1.303
peak=   -3.340 closest distance to " CD  LYS A  76 " =    0.784
peak=   -3.337 closest distance to " N   ALA A   1 " =    1.095
peak=   -3.332 closest distance to " CG  LYS A 193 " =    2.220
peak=   -3.327 closest distance to " CB  VAL A 125 " =    1.560
peak=   -3.326 closest distance to " O   SER A  62 " =    1.630
peak=   -3.326 closest distance to " CG  PRO A 213 " =    1.423
peak=   -3.322 closest distance to " CB  ASN A 252 " =    2.037
peak=   -3.321 closest distance to " CB  PHE A  59 " =    1.581
peak=   -3.318 closest distance to " CB  ALA A 291 " =    2.014
peak=   -3.317 closest distance to " CG  MET A 105 " =    0.837
peak=   -3.310 closest distance to " C   ASP A 124 " =    1.192
peak=   -3.303 closest distance to " OG  SER A   3 " =    0.744
peak=   -3.282 closest distance to " CD  PRO A 198 " =    1.283
peak=   -3.272 closest distance to " O   HOH Z 124 " =    2.545
peak=   -3.271 closest distance to " CZ3 TRP A 274 " =    1.073
peak=   -3.268 closest distance to " O   HOH Z 128 " =    1.020
peak=   -3.267 closest distance to " CA  TYR A  68 " =    2.684
peak=   -3.262 closest distance to " CG1BVAL A  72 " =    4.687
peak=   -3.261 closest distance to " CB  ASN A 285 " =    1.507
peak=   -3.260 closest distance to " O   SER A 146 " =    1.195
peak=   -3.254 closest distance to " O   HOH Z 197 " =    3.371
peak=   -3.254 closest distance to " O   HOH Z 207 " =    1.633
peak=   -3.249 closest distance to " C   HIS A 108 " =    1.262
peak=   -3.248 closest distance to " O   HOH Z 126 " =    1.786
peak=   -3.240 closest distance to " CE1 PHE A  16 " =    1.624
peak=   -3.238 closest distance to " CD  GLU A 277 " =    0.960
peak=   -3.235 closest distance to " O   GLN A 194 " =    1.218
peak=   -3.221 closest distance to " O   PRO A  54 " =    1.343
peak=   -3.220 closest distance to " CB  THR A 157 " =    1.210
peak=   -3.216 closest distance to " O   HOH Z 406 " =    0.986
peak=   -3.214 closest distance to " O   HOH Z  56 " =    0.857
peak=   -3.210 closest distance to " CB  GLN A  77 " =    1.166
peak=   -3.207 closest distance to " OD2 ASP A 270 " =    1.015
peak=   -3.207 closest distance to " N   SER A 276 " =    1.016
peak=   -3.207 closest distance to " CG  PRO A 163 " =    2.530
peak=   -3.204 closest distance to " CB  ASP A 162 " =    2.383
peak=   -3.198 closest distance to " N   ILE A  33 " =    1.906
peak=   -3.195 closest distance to " ND2 ASN A 285 " =    1.106
peak=   -3.193 closest distance to " CB  ALA A 227 " =    2.298
peak=   -3.182 closest distance to " O   HOH Z 100 " =    1.048
peak=   -3.181 closest distance to " C   ALA A 158 " =    1.345
peak=   -3.174 closest distance to " CG1 VAL A 153 " =    2.167
peak=   -3.174 closest distance to " OG1 THR A 178 " =    1.021
peak=   -3.172 closest distance to " O   THR A 235 " =    1.059
peak=   -3.172 closest distance to " ND2 ASN A  60 " =    4.335
peak=   -3.169 closest distance to " O   HOH Z  77 " =    1.679
peak=   -3.164 closest distance to " OD1 ASN A 301 " =    1.944
peak=   -3.162 closest distance to " O   HOH Z 390 " =    0.713
peak=   -3.161 closest distance to " O   ASN A 284 " =    0.942
peak=   -3.155 closest distance to " CG2AVAL A  41 " =    2.870
peak=   -3.155 closest distance to " O   HOH Z  76 " =    0.970
peak=   -3.154 closest distance to " CD1 LEU A  96 " =    2.106
peak=   -3.154 closest distance to " O   SER A 245 " =    1.339
peak=   -3.153 closest distance to " O   PRO A 243 " =    2.458
peak=   -3.152 closest distance to " CG2 THR A  31 " =    2.157
peak=   -3.152 closest distance to " O   PHE A  61 " =    0.949
peak=   -3.148 closest distance to " O   HOH Z   6 " =    1.902
peak=   -3.142 closest distance to " O   HOH Z   4 " =    0.891
peak=   -3.140 closest distance to " CD1 PHE A  59 " =    1.373
peak=   -3.138 closest distance to " O   HOH Z  37 " =    1.600
peak=   -3.136 closest distance to " O   HOH Z 135 " =    0.956
peak=   -3.135 closest distance to " OG  SER A 206 " =    1.273
peak=   -3.133 closest distance to " O   PRO A 163 " =    1.220
peak=   -3.133 closest distance to " CD1 TYR A 247 " =    2.543
peak=   -3.128 closest distance to " O   HOH Z 105 " =    1.139
peak=   -3.127 closest distance to " O   HOH Z 179 " =    1.151
peak=   -3.126 closest distance to " CB  SER A 273 " =    1.389
peak=   -3.126 closest distance to " O   HOH Z 266 " =    4.318
peak=   -3.126 closest distance to " O   ILE A  49 " =    1.595
peak=   -3.125 closest distance to " O   HOH Z 117 " =    0.770
peak=   -3.122 closest distance to " O   HOH Z 278 " =    1.397
peak=   -3.121 closest distance to " O   HOH Z 387 " =    2.205
peak=   -3.117 closest distance to " OG ASER A 216 " =    1.515
peak=   -3.108 closest distance to " O   HOH Z 426 " =    1.465
peak=   -3.104 closest distance to " O   HOH Z 231 " =    0.960
peak=   -3.103 closest distance to " OD1 ASP A 200 " =    1.503
peak=   -3.100 closest distance to " N   ARG A  14 " =    1.051
peak=   -3.098 closest distance to " O   HOH Z 313 " =    1.069
peak=   -3.096 closest distance to " O   HOH Z 390 " =    2.020
peak=   -3.078 closest distance to " O   HOH Z 187 " =    1.846
peak=   -3.075 closest distance to " O   PHE A 225 " =    0.834
peak=   -3.074 closest distance to " O   SER A  62 " =    1.794
peak=   -3.074 closest distance to " O   HOH Z 125 " =    3.234
peak=   -3.071 closest distance to " CD1 TRP A  85 " =    1.030
peak=   -3.069 closest distance to " CB  GLN A 240 " =    2.330
peak=   -3.066 closest distance to " CZ3 TRP A 123 " =    1.755
peak=   -3.065 closest distance to " OE1 GLU A 277 " =    2.209
peak=   -3.043 closest distance to " O   HOH Z 429 " =    2.197
peak=   -3.031 closest distance to " C   ASP A 286 " =    1.252

================= 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    :  0.4922 0.4972   6.300547e+00   6.293721e+00
   1_bss:  0.4823 0.4838   6.296714e+00   6.282165e+00
   1_xyz:  0.4319 0.4577   6.228131e+00   6.258542e+00
   1_adp:  0.3966 0.4618   6.193603e+00   6.262478e+00
   1_occ:  0.3964 0.4622   6.193199e+00   6.262406e+00
   2_bss:  0.3960 0.4612   6.195065e+00   6.263516e+00
   2_xyz:  0.3549 0.4300   6.116779e+00   6.225276e+00
   2_adp:  0.3427 0.4235   6.100035e+00   6.214831e+00
   2_occ:  0.3424 0.4238   6.100021e+00   6.215228e+00
   3_bss:  0.3426 0.4235   6.100409e+00   6.215061e+00
   3_xyz:  0.2867 0.3724   5.965678e+00   6.124553e+00
   3_adp:  0.2698 0.3585   5.923136e+00   6.095384e+00
   3_occ:  0.2696 0.3585   5.922988e+00   6.095317e+00
   4_bss:  0.2694 0.3571   5.921785e+00   6.093073e+00
   4_xyz:  0.2245 0.2965   5.757577e+00   5.947546e+00
   4_adp:  0.2015 0.2808   5.683474e+00   5.905139e+00
   4_occ:  0.2013 0.2802   5.682422e+00   5.903966e+00
   5_bss:  0.2016 0.2797   5.680330e+00   5.901879e+00
   5_xyz:  0.1678 0.2344   5.507166e+00   5.750714e+00
   5_adp:  0.1569 0.2081   5.426666e+00   5.647302e+00
   5_occ:  0.1564 0.2071   5.423395e+00   5.643591e+00
   5_bss:  0.1565 0.2063   5.422246e+00   5.640378e+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:  0.359  20.000  -3.556   1.249   1.285   0.000   0.000   0.000
   1_xyz:  0.359  20.000  -3.556   1.249   1.285   0.000   0.000   0.000
   1_adp:  0.359  20.000  -3.556   1.249   1.285   0.000   0.000   0.000
   1_occ:  0.359  20.000  -3.556   1.249   1.285   0.000   0.000   0.000
   2_bss:  0.356  38.775  -0.989   1.362   1.312   0.000   0.000   0.000
   2_xyz:  0.356  38.775  -0.989   1.362   1.312   0.000   0.000   0.000
   2_adp:  0.356  38.775  -0.989   1.362   1.312   0.000   0.000   0.000
   2_occ:  0.356  38.775  -0.989   1.362   1.312   0.000   0.000   0.000
   3_bss:  0.354  50.171  -0.214   0.747   1.024   0.000   0.000   0.000
   3_xyz:  0.354  50.171  -0.214   0.747   1.024   0.000   0.000   0.000
   3_adp:  0.354  50.171  -0.214   0.747   1.024   0.000   0.000   0.000
   3_occ:  0.354  50.171  -0.214   0.747   1.024   0.000   0.000   0.000
   4_bss:  0.344  50.699  -0.760  -0.615  -0.086  -0.000  -0.000  -0.000
   4_xyz:  0.344  50.699  -0.760  -0.615  -0.086  -0.000  -0.000  -0.000
   4_adp:  0.344  50.699  -0.760  -0.615  -0.086  -0.000  -0.000  -0.000
   4_occ:  0.344  50.699  -0.760  -0.615  -0.086  -0.000  -0.000  -0.000
   5_bss:  0.322  46.615  -0.972  -0.993  -0.205  -0.000  -0.000  -0.000
   5_xyz:  0.322  46.615  -0.972  -0.993  -0.205  -0.000  -0.000  -0.000
   5_adp:  0.322  46.615  -0.972  -0.993  -0.205  -0.000  -0.000  -0.000
   5_occ:  0.322  46.615  -0.972  -0.993  -0.205  -0.000  -0.000  -0.000
   5_bss:  0.312  36.666  -1.372  -1.599  -0.607  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.774 0.3579  0.4985    81017.294
   1_bss:  61.118 0.3781  0.5246    76487.047
   1_xyz:  55.704 0.4475  0.6120    66312.743
   1_adp:  56.877 0.4321  0.5933    68409.179
   1_occ:  56.907 0.4317  0.5922    68458.632
   2_bss:  56.777 0.4334  0.6167    68633.066
   2_xyz:  49.880 0.5209  0.7451    55707.650
   2_adp:  48.072 0.5441  0.7774    53852.131
   2_occ:  48.118 0.5435  0.7762    53861.081
   3_bss:  48.063 0.5441  0.7758    53739.200
   3_xyz:  40.146 0.6403  0.8988    38722.775
   3_adp:  37.424 0.6732  0.9176    35242.077
   3_occ:  37.457 0.6728  0.9165    35237.245
   4_bss:  37.313 0.6742  0.8851    34897.569
   4_xyz:  30.117 0.7560  0.9622    23106.300
   4_adp:  28.081 0.7785  0.9575    20604.224
   4_occ:  28.037 0.7790  0.9577    20524.903
   5_bss:  27.949 0.7797  0.9499    20332.004
   5_xyz:  23.034 0.8310  0.9892    14008.841
   5_adp:  19.839 0.8637  1.0015    11192.034
   5_occ:  19.738 0.8646  1.0017    11068.027
   5_bss:  19.671 0.8650  0.9841    10947.569
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.105   2.0773e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.105   2.0773e-01
   1_xyz:   1.384  0.010  0.094 15.605  0.005  4.100   1.0413e-01
   1_adp:   1.384  0.010  0.094 15.605  0.005  4.100   1.0413e-01
   1_occ:   1.384  0.010  0.094 15.605  0.005  4.100   1.0413e-01
   2_bss:   1.384  0.010  0.094 15.605  0.005  4.100   1.0413e-01
   2_xyz:   1.340  0.009  0.085 15.445  0.005  4.103   9.9574e-02
   2_adp:   1.340  0.009  0.085 15.445  0.005  4.103   9.9574e-02
   2_occ:   1.340  0.009  0.085 15.445  0.005  4.103   9.9574e-02
   3_bss:   1.340  0.009  0.085 15.445  0.005  4.103   9.9574e-02
   3_xyz:   1.359  0.011  0.088 15.563  0.005  4.110   1.0325e-01
   3_adp:   1.359  0.011  0.088 15.563  0.005  4.110   1.0325e-01
   3_occ:   1.359  0.011  0.088 15.563  0.005  4.110   1.0325e-01
   4_bss:   1.359  0.011  0.088 15.563  0.005  4.110   1.0325e-01
   4_xyz:   1.080  0.007  0.072 14.853  0.004  4.109   6.8988e-02
   4_adp:   1.080  0.007  0.072 14.853  0.004  4.109   6.8988e-02
   4_occ:   1.080  0.007  0.072 14.853  0.004  4.109   6.8988e-02
   5_bss:   1.080  0.007  0.072 14.853  0.004  4.109   6.8988e-02
   5_xyz:   1.011  0.007  0.067 14.835  0.003  4.104   6.2827e-02
   5_adp:   1.011  0.007  0.067 14.835  0.003  4.104   6.2827e-02
   5_occ:   1.011  0.007  0.067 14.835  0.003  4.104   6.2827e-02
   5_bss:   1.011  0.007  0.067 14.835  0.003  4.104   6.2827e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.384   2.3754e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.384   2.3754e-01
   1_xyz:   9.401  0.085  0.471 83.173  0.029  1.985   8.3353e-02
   1_adp:   9.401  0.085  0.471 83.173  0.029  1.985   8.3353e-02
   1_occ:   9.401  0.085  0.471 83.173  0.029  1.985   8.3353e-02
   2_bss:   9.401  0.085  0.471 83.173  0.029  1.985   8.3353e-02
   2_xyz:   8.390  0.059  0.293 78.519  0.034  2.053   7.5787e-02
   2_adp:   8.390  0.059  0.293 78.519  0.034  2.053   7.5787e-02
   2_occ:   8.390  0.059  0.293 78.519  0.034  2.053   7.5787e-02
   3_bss:   8.390  0.059  0.293 78.519  0.034  2.053   7.5787e-02
   3_xyz:  10.463  0.087  0.363 71.957  0.020  2.125   9.5281e-02
   3_adp:  10.463  0.087  0.363 71.957  0.020  2.125   9.5281e-02
   3_occ:  10.463  0.087  0.363 71.957  0.020  2.125   9.5281e-02
   4_bss:  10.463  0.087  0.363 71.957  0.020  2.125   9.5281e-02
   4_xyz:   6.139  0.045  0.243 71.627  0.027  2.165   5.2997e-02
   4_adp:   6.139  0.045  0.243 71.627  0.027  2.165   5.2997e-02
   4_occ:   6.139  0.045  0.243 71.627  0.027  2.165   5.2997e-02
   5_bss:   6.139  0.045  0.243 71.627  0.027  2.165   5.2997e-02
   5_xyz:   9.212  0.039  0.214 76.746  0.023  2.253   8.2308e-02
   5_adp:   9.212  0.039  0.214 76.746  0.023  2.253   8.2308e-02
   5_occ:   9.212  0.039  0.214 76.746  0.023  2.253   8.2308e-02
   5_bss:   9.212  0.039  0.214 76.746  0.023  2.253   8.2308e-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: 112.73   0.00  20.24 100.54   0.00  18.00 112.73   0.00  32.41
   1_occ: 112.73   0.00  20.24 100.54   0.00  18.00 112.73   0.00  32.41
   2_bss: 112.73   0.00  20.24 100.54   0.00  18.00 112.73   0.00  32.41
   2_xyz: 112.73   0.00  20.24 100.54   0.00  18.00 112.73   0.00  32.41
   2_adp: 124.06   0.00  19.53 102.78   0.00  17.36 124.06   0.00  31.37
   2_occ: 124.06   0.00  19.53 102.78   0.00  17.36 124.06   0.00  31.37
   3_bss: 124.06   0.00  19.53 102.78   0.00  17.36 124.06   0.00  31.37
   3_xyz: 124.06   0.00  19.53 102.78   0.00  17.36 124.06   0.00  31.37
   3_adp: 123.36   0.00  18.00 101.20   0.00  15.15 123.36   0.00  33.55
   3_occ: 123.36   0.00  18.00 101.20   0.00  15.15 123.36   0.00  33.55
   4_bss: 123.36   0.00  18.00 101.20   0.00  15.15 123.36   0.00  33.55
   4_xyz: 123.36   0.00  18.00 101.20   0.00  15.15 123.36   0.00  33.55
   4_adp: 128.06   0.00  19.39 116.25   0.00  14.41 128.06   0.00  46.57
   4_occ: 128.06   0.00  19.39 116.25   0.00  14.41 128.06   0.00  46.57
   5_bss: 128.06   0.00  19.39 116.25   0.00  14.41 128.06   0.00  46.57
   5_xyz: 128.06   0.00  19.39 116.25   0.00  14.41 128.06   0.00  46.57
   5_adp: 115.98   0.00  16.96 102.48   0.00  12.53 115.98   4.24  41.10
   5_occ: 115.98   0.00  16.96 102.48   0.00  12.53 115.98   4.24  41.10
   5_bss: 115.98   0.00  16.97 102.48   0.00  12.54 115.98   4.25  41.10
------------------------------------------------------------------------
 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:    1.585    0.010    0.249
   1_adp:    1.585    0.010    0.249
   1_occ:    1.585    0.010    0.249
   2_bss:    1.585    0.010    0.249
   2_xyz:    1.768    0.020    0.439
   2_adp:    1.768    0.020    0.439
   2_occ:    1.768    0.020    0.439
   3_bss:    1.768    0.020    0.439
   3_xyz:    1.814    0.046    0.650
   3_adp:    1.814    0.046    0.650
   3_occ:    1.814    0.046    0.650
   4_bss:    1.814    0.046    0.650
   4_xyz:    1.842    0.063    0.783
   4_adp:    1.842    0.063    0.783
   4_occ:    1.842    0.063    0.783
   5_bss:    1.842    0.063    0.783
   5_xyz:    1.892    0.122    0.876
   5_adp:    1.892    0.122    0.876
   5_occ:    1.892    0.122    0.876
   5_bss:    1.892    0.122    0.876
------------------------------------------------------------------------

CPU time actual refinement: 343.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_484/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_484/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_484/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_484/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_484/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.22 
  Macro-tasks:
    bulk solvent and scale       = 44.52  
    individual site refinement   = 141.79 
    weights calculation          = 29.61  
    collect and process          = 6.24   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 222.27 
  Micro-tasks:
    mask                            = 2.99   
    f_calc                          = 109.15 
    alpha_beta                      = 8.29   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 118.11 
    fmodel                         = 7.17   
    r_factors                      = 0.21   
    phase_errors                   = 9.68   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 257.03 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.902 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    634 calls, 108.92 s
gradients_fft:          579 calls, 105.36 s

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

# Date 2008-01-16 Time 04:56:14 PST -0800 (1200488174.34 s)
Start R-work = 0.4922, R-free = 0.4972 (no bulk solvent and anisotropic scale)
Final R-work = 0.1735, R-free = 0.2225 (no bulk solvent and anisotropic scale)

Start R-work = 0.4823, R-free = 0.4838
Final R-work = 0.1565, R-free = 0.2063