# Date 2008-01-16 Time 05:56:28 PST -0800 (1200491788.35 s)
#phil __OFF__

Command line arguments: "../943.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30815
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 943

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.6339, 87.6859, 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: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02054
Completeness in resolution range: 0.9773
Completeness with d_max=infinity: 0.974189

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0205

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02054
Completeness in resolution range: 0.9773
Completeness with d_max=infinity: 0.974189

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1645 -  4.3227 [2105/2129]  1894   211  10.0%
  bin  2:  4.3227 -  3.4442 [2028/2047]  1826   202  10.0%
  bin  3:  3.4442 -  3.0127 [1993/2012]  1794   199  10.0%
  bin  4:  3.0127 -  2.7391 [1972/2002]  1774   198  10.0%
  bin  5:  2.7391 -  2.5437 [1976/1995]  1780   196   9.9%
  bin  6:  2.5437 -  2.3944 [1947/1972]  1748   199  10.2%
  bin  7:  2.3944 -  2.2749 [1948/1976]  1756   192   9.9%
  bin  8:  2.2749 -  2.1761 [1952/1988]  1757   195  10.0%
  bin  9:  2.1761 -  2.0926 [1905/1947]  1712   193  10.1%
  bin 10:  2.0926 -  2.0205 [1763/1976]  1589   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_943/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: 0.11 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:
        1.77 -     2.40: 9
        2.40 -     3.02: 2018
        3.02 -     3.65: 4544
        3.65 -     4.27: 8855
        4.27 -     4.90: 12318
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.773 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.087 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.216 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.216 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27739 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_943/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_943/model_refine_001.geo

CPU time processing inputs: 7.87


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.63395 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4086   r_free= 0.3980   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.200925                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1374  153 0.3165 0.3151      6.4239      6.3657|
|  2:  4.8209 -  3.8470 0.99   1307  146 0.3291 0.3386      6.6613      6.7033|
|  3:  3.8470 -  3.3668 0.99   1293  143 0.3656 0.3404      6.5649      6.5127|
|  4:  3.3668 -  3.0617 0.99   1284  139 0.3907 0.3994      6.4431      6.3897|
|  5:  3.0617 -  2.8438 0.99   1267  144 0.4223 0.3693      6.2846      6.2373|
|  6:  2.8438 -  2.6771 0.99   1277  141 0.4339 0.4402      6.2056        6.17|
|  7:  2.6771 -  2.5437 0.99   1266  140 0.4397 0.4286      6.1703      6.1065|
|  8:  2.5437 -  2.4334 0.98   1249  139 0.4530 0.4076      6.1323      6.1095|
|  9:  2.4334 -  2.3401 0.98   1253  143 0.4585 0.4495      6.0724       6.097|
| 10:  2.3401 -  2.2596 0.99   1246  136 0.4790 0.4252      6.0858      6.0351|
| 11:  2.2596 -  2.1892 0.98   1255  137 0.4743 0.4495      6.0091      6.0096|
| 12:  2.1892 -  2.1268 0.97   1237  142 0.4779 0.4863      5.9571      6.0386|
| 13:  2.1268 -  2.0709 1.00   1247  136 0.4772 0.4517      5.8688      5.8264|
| 14:  2.0709 -  2.0205 0.85   1075  120 0.4733 0.5255      5.8138       5.773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8209  1374   153  0.76  28.46   0.84     0.79      50957.73|
|  2:  4.8209 -  3.8470  1307   146  0.79  27.50   0.93     0.85      69201.03|
|  3:  3.8470 -  3.3668  1293   143  0.72  33.25   0.93     0.85      71733.03|
|  4:  3.3668 -  3.0617  1284   139  0.67  38.06   0.93     0.80      64674.82|
|  5:  3.0617 -  2.8438  1267   144  0.59  44.28   0.93     0.75      53060.74|
|  6:  2.8438 -  2.6771  1277   141  0.57  46.34   0.91     0.72      48328.92|
|  7:  2.6771 -  2.5437  1266   140  0.55  47.84   0.94     0.71      44189.95|
|  8:  2.5437 -  2.4334  1249   139  0.55  47.98   0.93     0.73      41282.41|
|  9:  2.4334 -  2.3401  1253   143  0.55  47.98   0.93     0.75      37770.84|
| 10:  2.3401 -  2.2596  1246   136  0.54  49.38   0.95     0.73      35796.48|
| 11:  2.2596 -  2.1892  1255   137  0.51  51.70   0.94     0.71      35592.35|
| 12:  2.1892 -  2.1268  1237   142  0.46  55.24   0.94     0.66      35644.64|
| 13:  2.1268 -  2.0709  1247   136  0.41  58.86   0.93     0.59      32887.02|
| 14:  2.0709 -  2.0205  1075   120  0.39  61.10   0.94     0.51      27844.22|
|alpha:            min =        0.51 max =            0.85 mean =         0.73|
|beta:             min =    27844.22 max =        71733.03 mean =     46757.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.98 mean =        45.19|
|phase err.(test): min =        0.00 max =           89.84 mean =        45.28|
|-----------------------------------------------------------------------------|

============================== 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 = 7.013350              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.501   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.298364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.346   (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 |  1.773 -  2.086:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.086 -  2.399:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.399 -  2.711:      125 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.711 -  3.024:     1893 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.024 -  3.337:     1832 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.337 -  3.649:     2712 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.649 -  3.962:     4595 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.962 -  4.275:     4260 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.275 -  4.587:     5602 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.587 -  4.900:     6716 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.773 |       0.156 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4086   r_free= 0.3980   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.200925                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3994   r_free= 0.3903   ksol= 0.30   Bsol= 61.09   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,2.33,1.65,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.188178                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.299032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.346   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.716143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.170   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3994      final r-factor (work) = 0.2518          |
| start r-factor (free) = 0.3903      final r-factor (free) = 0.2757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6577 = 6.30 * 0.50 * 6.1896 + 1.00 * 0.1635                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9104 = 6.30 * 0.50 * 5.9747 + 1.00 * 0.0931                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2518      final r-factor (work) = 0.2289          |
| start r-factor (free) = 0.2757      final r-factor (free) = 0.2840          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2848 = 0.72 * 1.00 * 5.9747 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1313 = 0.72 * 1.00 * 5.7497 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.61   17.75    None  None   None       |
|    all(noH): 2823   0      0.00    98.61   17.75    None  None   None       |
|    Sol.    : 438    0      3.74    98.61   41.71    None  None   None       |
|    Mac.    : 2385   0      0.00    82.62   13.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.861: 1012   |   5:    49.304 -  59.164:   84        |
|      1:     9.861 -  19.722: 1040   |   6:    59.164 -  69.025:   50        |
|      2:    19.722 -  29.582:  312   |   7:    69.025 -  78.886:   31        |
|      3:    29.582 -  39.443:  159   |   8:    78.886 -  88.747:    9        |
|      4:    39.443 -  49.304:  124   |   9:    88.747 -  98.607:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2289 r_free = 0.2840             target_work(ml) = 5.757         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2286 r_free = 0.2838             target_work(ml) = 5.756         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2286   r_free= 0.2838   ksol= 0.30   Bsol= 61.09   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,2.33,1.65,0.00,0.00,0.00); trace/3= 0.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.756147                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2272   r_free= 0.2813   ksol= 0.33   Bsol= 85.98   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,0.12,-0.02,0.00,-0.00,-0.00); trace/3= -0.67                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.753859                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.483163              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.939   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.256383              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.601  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2272      final r-factor (work) = 0.1660          |
| start r-factor (free) = 0.2813      final r-factor (free) = 0.2058          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1124 = 3.48 * 0.50 * 5.7530 + 1.00 * 0.0931                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8730 = 3.48 * 0.50 * 5.6300 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1660      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2058      final r-factor (free) = 0.1921          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4571 = 0.26 * 1.00 * 5.6300 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4027 = 0.26 * 1.00 * 5.4314 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    98.41   17.27    None  None   None       |
|    all(noH): 2823   0      1.35    98.41   17.27    None  None   None       |
|    Sol.    : 438    0      4.98    98.41   41.40    None  None   None       |
|    Mac.    : 2385   0      1.35    81.89   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.355 -  11.061: 1326   |   5:    49.884 -  59.589:   84        |
|      1:    11.061 -  20.766:  853   |   6:    59.589 -  69.295:   44        |
|      2:    20.766 -  30.472:  216   |   7:    69.295 -  79.001:   26        |
|      3:    30.472 -  40.178:  141   |   8:    79.001 -  88.707:    9        |
|      4:    40.178 -  49.884:  122   |   9:    88.707 -  98.412:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1543 r_free = 0.1921             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1541 r_free = 0.1920             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1541   r_free= 0.1920   ksol= 0.33   Bsol= 85.98   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,0.12,-0.02,0.00,-0.00,-0.00); trace/3= -0.67                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.400427                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1540   r_free= 0.1917   ksol= 0.33   Bsol= 77.19   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-0.88,-0.28,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.398515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.963842              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.310  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.573536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.294  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.1917      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4007 = 1.96 * 0.50 * 5.4311 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2888 = 1.96 * 0.50 * 5.3259 + 1.00 * 0.0591                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1266          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1737          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 35.0204 = 6.57 * 1.00 * 5.3259 + 1.00 * 0.0102                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 34.5184 = 6.57 * 1.00 * 5.2491 + 1.00 * 0.0132                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.24  17.49    None  None   None       |
|    all(noH): 2823   0      0.00    100.24  17.49    None  None   None       |
|    Sol.    : 438    0      4.53    100.24  43.96    None  None   None       |
|    Mac.    : 2385   0      0.00    97.19   12.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.025: 1163   |   5:    50.122 -  60.147:   83        |
|      1:    10.025 -  20.049: 1013   |   6:    60.147 -  70.171:   67        |
|      2:    20.049 -  30.073:  203   |   7:    70.171 -  80.196:   36        |
|      3:    30.073 -  40.098:  136   |   8:    80.196 -  90.220:   11        |
|      4:    40.098 -  50.122:  102   |   9:    90.220 - 100.245:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1266 r_free = 0.1737             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1265 r_free = 0.1737             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1737   ksol= 0.33   Bsol= 77.19   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-0.88,-0.28,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.246781                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1734   ksol= 0.33   Bsol= 77.10   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-0.89,-0.01,-0.00,-0.00,-0.00); trace/3= -0.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.248045                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.636481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.461  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.899838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.624  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1268      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3555 = 1.64 * 0.50 * 5.2507 + 1.00 * 0.0591                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3488 = 1.64 * 0.50 * 5.2406 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1726      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7289 = 0.90 * 1.00 * 5.2406 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7237 = 0.90 * 1.00 * 5.2350 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.45  17.17    None  None   None       |
|    all(noH): 2823   0      0.00    100.45  17.17    None  None   None       |
|    Sol.    : 438    0      4.63    100.45  43.70    None  None   None       |
|    Mac.    : 2385   0      0.00    97.85   12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.045: 1235   |   5:    50.226 -  60.271:   80        |
|      1:    10.045 -  20.090:  957   |   6:    60.271 -  70.316:   66        |
|      2:    20.090 -  30.136:  190   |   7:    70.316 -  80.361:   35        |
|      3:    30.136 -  40.181:  139   |   8:    80.361 -  90.406:   11        |
|      4:    40.181 -  50.226:  101   |   9:    90.406 - 100.452:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1249 r_free = 0.1718             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1248 r_free = 0.1719             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1719   ksol= 0.33   Bsol= 77.10   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-0.89,-0.01,-0.00,-0.00,-0.00); trace/3= -0.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.233511                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1717   ksol= 0.33   Bsol= 76.80   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-0.66,0.32,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.233633                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.537746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.754  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.837590              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.806  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0870 = 1.54 * 0.50 * 5.2366 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0716 = 1.54 * 0.50 * 5.2223 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1689      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 35.7207 = 6.84 * 1.00 * 5.2223 + 1.00 * 0.0129                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 35.6348 = 6.84 * 1.00 * 5.2096 + 1.00 * 0.0140                              |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.85  16.90    None  None   None       |
|    all(noH): 2823   0      0.00    102.85  16.90    None  None   None       |
|    Sol.    : 438    0      4.88    102.20  43.42    None  None   None       |
|    Mac.    : 2385   0      0.00    102.85  12.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.285: 1342   |   5:    51.423 -  61.708:   82        |
|      1:    10.285 -  20.569:  873   |   6:    61.708 -  71.992:   59        |
|      2:    20.569 -  30.854:  194   |   7:    71.992 -  82.277:   29        |
|      3:    30.854 -  41.138:  126   |   8:    82.277 -  92.561:   11        |
|      4:    41.138 -  51.423:   98   |   9:    92.561 - 102.846:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1695             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1695             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1695   ksol= 0.33   Bsol= 76.80   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,-0.66,0.32,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.212482                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1374  153 0.1020 0.1305      5.4136      5.5265|
|  2:  4.8209 -  3.8470 0.99   1307  146 0.0853 0.1046      5.4335      5.5957|
|  3:  3.8470 -  3.3668 0.99   1293  143 0.1094 0.1516      5.5019      5.8733|
|  4:  3.3668 -  3.0617 0.99   1284  139 0.1287 0.1706      5.5114      5.6789|
|  5:  3.0617 -  2.8438 0.99   1267  144 0.1481 0.1925      5.4413        5.62|
|  6:  2.8438 -  2.6771 0.99   1277  141 0.1376 0.2146      5.3155      5.6019|
|  7:  2.6771 -  2.5437 0.99   1266  140 0.1399 0.1755      5.2507      5.3924|
|  8:  2.5437 -  2.4334 0.98   1249  139 0.1312 0.1864      5.1779      5.4274|
|  9:  2.4334 -  2.3401 0.98   1253  143 0.1284 0.2023      5.1146      5.3923|
| 10:  2.3401 -  2.2596 0.99   1246  136 0.1253 0.1877      5.0734      5.2888|
| 11:  2.2596 -  2.1892 0.98   1255  137 0.1246 0.1844      5.0185      5.2802|
| 12:  2.1892 -  2.1268 0.97   1237  142 0.1249 0.1871       4.985      5.3215|
| 13:  2.1268 -  2.0709 1.00   1247  136 0.1238 0.1946      4.8762      5.1571|
| 14:  2.0709 -  2.0205 0.85   1075  120 0.1128 0.1868      4.7386      5.0207|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8209  1374   153  0.94   9.54   0.96     0.93       7613.94|
|  2:  4.8209 -  3.8470  1307   146  0.95   7.97   1.00     0.98       8885.67|
|  3:  3.8470 -  3.3668  1293   143  0.94  11.09   1.02     1.01      10543.78|
|  4:  3.3668 -  3.0617  1284   139  0.92  14.24   1.00     0.98      11223.92|
|  5:  3.0617 -  2.8438  1267   144  0.89  17.48   1.00     0.98      10326.40|
|  6:  2.8438 -  2.6771  1277   141  0.89  17.42   0.98     0.96       8481.28|
|  7:  2.6771 -  2.5437  1266   140  0.89  17.13   0.99     0.96       7255.64|
|  8:  2.5437 -  2.4334  1249   139  0.90  16.54   0.98     0.94       6338.06|
|  9:  2.4334 -  2.3401  1253   143  0.90  16.90   0.99     0.94       5851.04|
| 10:  2.3401 -  2.2596  1246   136  0.89  17.66   0.98     0.93       5449.94|
| 11:  2.2596 -  2.1892  1255   137  0.89  17.07   0.97     0.92       4945.49|
| 12:  2.1892 -  2.1268  1237   142  0.90  17.03   0.99     0.98       4836.36|
| 13:  2.1268 -  2.0709  1247   136  0.90  16.67   0.96     0.94       3898.53|
| 14:  2.0709 -  2.0205  1075   120  0.90  15.91   0.94     0.89       2912.84|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     2912.84 max =        11223.92 mean =      7115.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1693   ksol= 0.32   Bsol= 73.02   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,-0.44,0.61,-0.00,0.00,0.00); trace/3= -0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.212526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1693   ksol= 0.32   Bsol= 73.02   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,-0.44,0.61,-0.00,0.00,0.00); trace/3= -0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.212526                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1374  153 0.1019 0.1305      5.4125      5.5268|
|  2:  4.8209 -  3.8470 0.99   1307  146 0.0852 0.1043      5.4328      5.5936|
|  3:  3.8470 -  3.3668 0.99   1293  143 0.1094 0.1516      5.5017      5.8743|
|  4:  3.3668 -  3.0617 0.99   1284  139 0.1288 0.1707      5.5123      5.6798|
|  5:  3.0617 -  2.8438 0.99   1267  144 0.1482 0.1926      5.4422      5.6205|
|  6:  2.8438 -  2.6771 0.99   1277  141 0.1376 0.2145      5.3158      5.6017|
|  7:  2.6771 -  2.5437 0.99   1266  140 0.1399 0.1756      5.2511       5.393|
|  8:  2.5437 -  2.4334 0.98   1249  139 0.1313 0.1863      5.1783      5.4274|
|  9:  2.4334 -  2.3401 0.98   1253  143 0.1283 0.2021      5.1145      5.3923|
| 10:  2.3401 -  2.2596 0.99   1246  136 0.1254 0.1879      5.0735      5.2894|
| 11:  2.2596 -  2.1892 0.98   1255  137 0.1246 0.1842      5.0185      5.2801|
| 12:  2.1892 -  2.1268 0.97   1237  142 0.1249 0.1869      4.9848      5.3212|
| 13:  2.1268 -  2.0709 1.00   1247  136 0.1238 0.1945       4.876       5.157|
| 14:  2.0709 -  2.0205 0.85   1075  120 0.1129 0.1866      4.7386      5.0203|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8209  1374   153  0.94   9.53   0.96     0.93       7607.02|
|  2:  4.8209 -  3.8470  1307   146  0.95   7.97   1.00     0.98       8873.27|
|  3:  3.8470 -  3.3668  1293   143  0.94  11.08   1.02     1.02      10532.03|
|  4:  3.3668 -  3.0617  1284   139  0.92  14.26   1.01     0.98      11238.57|
|  5:  3.0617 -  2.8438  1267   144  0.89  17.49   1.01     0.99      10338.31|
|  6:  2.8438 -  2.6771  1277   141  0.89  17.43   0.99     0.96       8488.45|
|  7:  2.6771 -  2.5437  1266   140  0.89  17.13   1.00     0.97       7260.33|
|  8:  2.5437 -  2.4334  1249   139  0.90  16.55   0.99     0.95       6339.17|
|  9:  2.4334 -  2.3401  1253   143  0.90  16.91   1.00     0.95       5855.20|
| 10:  2.3401 -  2.2596  1246   136  0.89  17.65   0.99     0.94       5449.62|
| 11:  2.2596 -  2.1892  1255   137  0.89  17.07   0.99     0.93       4946.75|
| 12:  2.1892 -  2.1268  1237   142  0.90  17.03   1.00     0.99       4834.73|
| 13:  2.1268 -  2.0709  1247   136  0.90  16.66   0.98     0.96       3896.63|
| 14:  2.0709 -  2.0205  1075   120  0.90  15.90   0.95     0.91       2911.21|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2911.21 max =        11238.57 mean =      7115.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.26 mean =        14.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.362)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.85  16.91    None  None   None       |
|    all(noH): 2823   0      0.00    102.85  16.91    None  None   None       |
|    Sol.    : 438    0      4.88    102.21  43.42    None  None   None       |
|    Mac.    : 2385   0      0.00    102.85  12.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.288: 1342   |   5:    51.426 -  61.711:   82        |
|      1:    10.288 -  20.572:  873   |   6:    61.711 -  71.995:   59        |
|      2:    20.572 -  30.857:  194   |   7:    71.995 -  82.280:   29        |
|      3:    30.857 -  41.141:  126   |   8:    82.280 -  92.564:   11        |
|      4:    41.141 -  51.426:   98   |   9:    92.564 - 102.849:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.532 - 4.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 320
   mapped sites are within: 0.708 - 4.819

peak=    5.893 closest distance to " CB  GLN A 223 " =    1.422
peak=    5.799 closest distance to " O   HOH Z 210 " =    1.168
peak=    5.293 closest distance to " CG  PRO A  54 " =    1.368
peak=    5.252 closest distance to " NH2 ARG A  56 " =    2.290
peak=    5.131 closest distance to " CG  PRO A 198 " =    1.194
peak=    4.986 closest distance to " CB  ARG A 190 " =    1.668
peak=    4.971 closest distance to " O   HOH Z 232 " =    2.306
peak=    4.963 closest distance to " CB  SER A  63 " =    1.250
peak=    4.922 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.787 closest distance to " CB  GLN A 183 " =    1.276
peak=    4.683 closest distance to " CZ  PHE A 218 " =    1.114
peak=    4.666 closest distance to " CD  ARG A 269 " =    0.983
peak=    4.496 closest distance to " CA  ALA A  51 " =    0.975
peak=    4.451 closest distance to " CB  ARG A 275 " =    0.933
peak=    4.450 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.428 closest distance to " O   HOH Z 369 " =    2.281
peak=    4.362 closest distance to " CA  ARG A 195 " =    1.200
peak=    4.332 closest distance to " C   PRO A 198 " =    1.513
peak=    4.321 closest distance to " O   HOH Z 298 " =    2.024
peak=    4.301 closest distance to " O   HOH Z 189 " =    2.805
peak=    4.276 closest distance to " CD2 TRP A 179 " =    1.332
peak=    4.272 closest distance to " O   HOH Z 234 " =    3.890
peak=    4.259 closest distance to " CA  TYR A  30 " =    0.948
peak=    4.247 closest distance to " CB  TYR A 169 " =    0.779
peak=    4.228 closest distance to " CB  TRP A 266 " =    1.055
peak=    4.227 closest distance to " CZ3 TRP A 266 " =    1.122
peak=    4.197 closest distance to " O   HOH Z  49 " =    1.030
peak=    4.138 closest distance to " CB  VAL A 202 " =    1.569
peak=    4.129 closest distance to " CA  ALA A 160 " =    0.969
peak=    4.123 closest distance to " O   HOH Z 368 " =    2.151
peak=    4.123 closest distance to " O   HOH Z 412 " =    3.802
peak=    4.100 closest distance to " CA  ARG A  36 " =    1.112
peak=    4.063 closest distance to " CB  ARG A  79 " =    1.366
peak=    4.060 closest distance to " O   HOH Z 265 " =    2.225
peak=    4.060 closest distance to " CB  ASP A 124 " =    0.818
peak=    4.047 closest distance to " O   HOH Z  43 " =    1.971
peak=    4.041 closest distance to " CB  ASP A 140 " =    0.968
peak=    4.040 closest distance to " O   HOH Z 402 " =    1.532
peak=    4.037 closest distance to " CB  GLU A 128 " =    1.078
peak=    4.018 closest distance to " O   HOH Z 134 " =    1.393
peak=    3.995 closest distance to " CA  GLU A 152 " =    0.912
peak=    3.992 closest distance to " O   HOH Z 133 " =    2.703
peak=    3.983 closest distance to " CB  ASN A 148 " =    1.352
peak=    3.966 closest distance to " CZ  PHE A  38 " =    1.307
peak=    3.966 closest distance to " O   HOH Z 271 " =    2.604
peak=    3.957 closest distance to " CG2BVAL A  41 " =    0.897
peak=    3.955 closest distance to " O   HOH Z  15 " =    2.301
peak=    3.941 closest distance to " CG  ARG A 138 " =    1.224
peak=    3.940 closest distance to " CB  ASN A  39 " =    0.925
peak=    3.934 closest distance to " CD  LYS A 166 " =    1.326
peak=    3.918 closest distance to " CG  PRO A 243 " =    1.115
peak=    3.909 closest distance to " CB  GLU A 277 " =    3.839
peak=    3.891 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.880 closest distance to " NH2 ARG A 156 " =    1.227
peak=    3.878 closest distance to " O   THR A 251 " =    1.129
peak=    3.860 closest distance to " O   HOH Z 346 " =    1.621
peak=    3.859 closest distance to " O   HOH Z  40 " =    1.723
peak=    3.858 closest distance to " CA  VAL A 125 " =    1.368
peak=    3.855 closest distance to " N   HIS A 108 " =    1.881
peak=    3.853 closest distance to " O   SER A  87 " =    2.339
peak=    3.852 closest distance to " CB  SER A  62 " =    0.879
peak=    3.850 closest distance to " CB  LEU A 228 " =    1.092
peak=    3.842 closest distance to " CG  ARG A  66 " =    2.534
peak=    3.835 closest distance to " O   HOH Z 203 " =    1.759
peak=    3.827 closest distance to " O   ALA A 165 " =    1.414
peak=    3.825 closest distance to " CD1 LEU A 300 " =    1.235
peak=    3.820 closest distance to " O   HOH Z 425 " =    1.391
peak=    3.819 closest distance to " O   TYR A 116 " =    1.342
peak=    3.815 closest distance to " O   HOH Z  97 " =    2.071
peak=    3.806 closest distance to " ND2 ASN A 187 " =    1.447
peak=    3.803 closest distance to " CD1 LEU A  96 " =    0.784
peak=    3.797 closest distance to " O   HOH Z  78 " =    1.647
peak=    3.796 closest distance to " O   HOH Z 285 " =    2.626
peak=    3.789 closest distance to " O   HOH Z 427 " =    3.269
peak=    3.781 closest distance to " CA  MET A 105 " =    1.097
peak=    3.773 closest distance to " O   HOH Z 433 " =    1.516
peak=    3.772 closest distance to " O   HOH Z  80 " =    1.860
peak=    3.772 closest distance to " CD2 LEU A 297 " =    1.006
peak=    3.764 closest distance to " O   ASN A  74 " =    1.600
peak=    3.753 closest distance to " O   HOH Z  44 " =    2.084
peak=    3.747 closest distance to " O   HOH Z 102 " =    1.332
peak=    3.745 closest distance to " O   HOH Z 361 " =    3.344
peak=    3.744 closest distance to " CG1 VAL A 153 " =    1.079
peak=    3.734 closest distance to " CB  TRP A 179 " =    1.368
peak=    3.730 closest distance to " O   HOH Z 214 " =    2.178
peak=    3.725 closest distance to " NH1AARG A 145 " =    1.323
peak=    3.721 closest distance to " O   HOH Z  19 " =    2.078
peak=    3.713 closest distance to " CB  VAL A 265 " =    1.283
peak=    3.712 closest distance to " O   HOH Z 287 " =    1.784
peak=    3.708 closest distance to " O   HOH Z 403 " =    1.463
peak=    3.704 closest distance to " CG1 ILE A  33 " =    1.211
peak=    3.703 closest distance to " CE1 HIS A 115 " =    1.065
peak=    3.703 closest distance to " NZ  LYS A 117 " =    3.094
peak=    3.697 closest distance to " CA  PRO A  54 " =    1.402
peak=    3.679 closest distance to " CA  SER A  87 " =    1.125
peak=    3.678 closest distance to " OD1 ASN A  69 " =    2.489
peak=    3.675 closest distance to " O   THR A 220 " =    1.133
peak=    3.673 closest distance to " CA  ALA A 295 " =    1.127
peak=    3.671 closest distance to " O   HOH Z 131 " =    2.424
peak=    3.670 closest distance to " CG2 VAL A 257 " =    0.858
peak=    3.667 closest distance to " N   ILE A  33 " =    0.920
peak=    3.659 closest distance to " O   HOH Z 316 " =    3.147
peak=    3.652 closest distance to " NE2 GLN A  77 " =    3.417
peak=    3.638 closest distance to " CA  ASP A 124 " =    0.834
peak=    3.635 closest distance to " O   HOH Z 180 " =    2.130
peak=    3.634 closest distance to " CB  LEU A  83 " =    0.860
peak=    3.631 closest distance to " O   HOH Z 124 " =    2.003
peak=    3.631 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.618 closest distance to " CB  GLU A  46 " =    1.035
peak=    3.617 closest distance to " O   HOH Z 294 " =    1.560
peak=    3.608 closest distance to " NE2 GLN A  11 " =    0.983
peak=    3.606 closest distance to " CB  GLN A  89 " =    1.204
peak=    3.599 closest distance to " CE  LYS A  76 " =    0.825
peak=    3.590 closest distance to " CB  ASN A 142 " =    1.100
peak=    3.589 closest distance to " O   HOH Z 383 " =    2.250
peak=    3.584 closest distance to " O   HOH Z  88 " =    1.866
peak=    3.578 closest distance to " ND2 ASN A 249 " =    0.862
peak=    3.577 closest distance to " CG AARG A 275 " =    1.194
peak=    3.563 closest distance to " O   HOH Z 126 " =    1.647
peak=    3.560 closest distance to " CA  ALA A  21 " =    1.312
peak=    3.552 closest distance to " O   HOH Z 403 " =    1.526
peak=    3.552 closest distance to " CA  GLU A  46 " =    0.918
peak=    3.546 closest distance to " N   ASN A 127 " =    1.278
peak=    3.542 closest distance to " N   CYS A 260 " =    0.821
peak=    3.542 closest distance to " N   ASN A  39 " =    1.333
peak=    3.541 closest distance to " CD1 LEU A 255 " =    1.749
peak=    3.533 closest distance to " N   ARG A 156 " =    1.577
peak=    3.532 closest distance to " O   HOH Z 389 " =    1.962
peak=    3.530 closest distance to " CD BLYS A 290 " =    0.945
peak=    3.529 closest distance to " CA  ASP A 191 " =    0.894
peak=    3.526 closest distance to " O   HOH Z 353 " =    2.724
peak=    3.521 closest distance to " N   SER A 164 " =    1.022
peak=    3.520 closest distance to " O   HOH Z 214 " =    1.319
peak=    3.516 closest distance to " CZ3 TRP A  85 " =    0.869
peak=    3.515 closest distance to " O   HOH Z 199 " =    1.657
peak=    3.514 closest distance to " CB  ALA A 291 " =    1.236
peak=    3.513 closest distance to " CA  ALA A 154 " =    1.036
peak=    3.508 closest distance to " O   HOH Z 325 " =    2.299
peak=    3.506 closest distance to " O   HOH Z 391 " =    2.963
peak=    3.506 closest distance to " CE1 TYR A 186 " =    1.256
peak=    3.504 closest distance to " CG  GLN A  11 " =    1.277
peak=    3.503 closest distance to " O   HOH Z 193 " =    1.779
peak=    3.487 closest distance to " O   HOH Z 279 " =    2.249
peak=    3.487 closest distance to " CB  ALA A 248 " =    1.388
peak=    3.485 closest distance to " O   HOH Z 247 " =    1.487
peak=    3.482 closest distance to " OE1 GLN A  11 " =    2.058
peak=    3.479 closest distance to " CB  MET A  47 " =    0.902
peak=    3.477 closest distance to " O   HOH Z 423 " =    1.808
peak=    3.476 closest distance to " O   HOH Z 261 " =    1.792
peak=    3.472 closest distance to " CB  GLU A 152 " =    1.203
peak=    3.471 closest distance to " CG  LEU A 167 " =    1.110
peak=    3.466 closest distance to " OG BSER A 164 " =    2.380
peak=    3.465 closest distance to " OG  SER A 245 " =    1.657
peak=    3.464 closest distance to " O   HOH Z  20 " =    1.518
peak=    3.461 closest distance to " CB  ASN A 285 " =    0.959
peak=    3.459 closest distance to " N   GLY A  98 " =    1.108
peak=    3.458 closest distance to " O   HOH Z 406 " =    1.593
peak=    3.456 closest distance to " O   HOH Z 141 " =    1.712
peak=    3.453 closest distance to " CB  SER A   3 " =    1.433
peak=    3.445 closest distance to " O   HOH Z  21 " =    1.846
peak=    3.442 closest distance to " O   HOH Z 158 " =    3.010
peak=    3.440 closest distance to " O   HOH Z 261 " =    1.506
peak=    3.440 closest distance to " CA  MET A  40 " =    1.202
peak=    3.431 closest distance to " NH2BARG A 145 " =    2.186
peak=    3.428 closest distance to " CB  SER A 141 " =    1.081
peak=    3.424 closest distance to " O   HOH Z 126 " =    2.203
peak=    3.420 closest distance to " O   HOH Z 291 " =    1.487
peak=    3.418 closest distance to " CB  ALA A  43 " =    0.902
peak=    3.414 closest distance to " CZ  PHE A 192 " =    0.979
peak=    3.408 closest distance to " OD2 ASP A 298 " =    3.909
peak=    3.406 closest distance to " CA  ASN A 217 " =    1.240
peak=    3.405 closest distance to " CG1 ILE A 120 " =    0.999
peak=    3.405 closest distance to " O   HOH Z  63 " =    1.865
peak=    3.403 closest distance to " CB  MET A  40 " =    0.797
peak=    3.403 closest distance to " O   ASP A 124 " =    1.183
peak=    3.386 closest distance to " O   HOH Z 361 " =    2.601
peak=    3.384 closest distance to " O   HOH Z 176 " =    1.566
peak=    3.379 closest distance to " O   HOH Z 258 " =    1.970
peak=    3.376 closest distance to " O   ALA A 158 " =    1.226
peak=    3.373 closest distance to " O   HOH Z   1 " =    2.595
peak=    3.372 closest distance to " CA  ASN A 176 " =    1.248
peak=    3.369 closest distance to " CA  ALA A 100 " =    1.059
peak=    3.369 closest distance to " O   HOH Z 142 " =    1.484
peak=    3.363 closest distance to " N   VAL A 265 " =    1.083
peak=    3.361 closest distance to " O   HOH Z 248 " =    1.666
peak=    3.357 closest distance to " O   HOH Z 371 " =    3.025
peak=    3.357 closest distance to " CB  ALA A  34 " =    0.758
peak=    3.356 closest distance to " CB  PRO A 243 " =    1.454
peak=    3.354 closest distance to " O   HOH Z 132 " =    2.832
peak=    3.353 closest distance to " CG  GLU A  37 " =    0.872
peak=    3.348 closest distance to " N   ASN A 252 " =    1.287
peak=    3.346 closest distance to " CA  ASP A 162 " =    1.116
peak=    3.344 closest distance to " CA  THR A 221 " =    0.895
peak=    3.340 closest distance to " C   TYR A 214 " =    1.603
peak=    3.340 closest distance to " OD1 ASP A 238 " =    0.770
peak=    3.337 closest distance to " CA  ARG A 156 " =    1.072
peak=    3.335 closest distance to " O   HOH Z 305 " =    3.775
peak=    3.333 closest distance to " O   HOH Z 128 " =    2.253
peak=    3.323 closest distance to " CG2 ILE A 151 " =    0.960
peak=    3.320 closest distance to " O   HOH Z 357 " =    2.102
peak=    3.320 closest distance to " O   HOH Z 250 " =    1.418
peak=    3.312 closest distance to " O   HOH Z 422 " =    2.622
peak=    3.312 closest distance to " OG  SER A  22 " =    2.814
peak=    3.310 closest distance to " O   HOH Z  48 " =    1.776
peak=    3.309 closest distance to " OH  TYR A 116 " =    1.067
peak=    3.306 closest distance to " O   HOH Z 359 " =    1.563
peak=    3.306 closest distance to " CA  GLY A 211 " =    1.296
peak=    3.304 closest distance to " O   HOH Z 377 " =    1.171
peak=    3.303 closest distance to " CB  ALA A 114 " =    0.717
peak=    3.302 closest distance to " CB  PRO A 198 " =    1.027
peak=    3.300 closest distance to " CA  ALA A 291 " =    0.784
peak=    3.297 closest distance to " C   GLY A  80 " =    1.069
peak=    3.295 closest distance to " O   HOH Z 298 " =    2.539
peak=    3.293 closest distance to " OG1 THR A  82 " =    0.948
peak=    3.292 closest distance to " CB  MET A 105 " =    0.906
peak=    3.292 closest distance to " CB  ASN A 187 " =    1.231
peak=    3.291 closest distance to " O   PHE A  61 " =    1.316
peak=    3.290 closest distance to " O   HOH Z  32 " =    1.733
peak=    3.289 closest distance to " O   HOH Z 303 " =    2.235
peak=    3.287 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.286 closest distance to " CB  GLU A  37 " =    0.785
peak=    3.286 closest distance to " CA  MET A 188 " =    1.017
peak=    3.283 closest distance to " CA  ALA A 233 " =    1.676
peak=    3.282 closest distance to " O   HOH Z 139 " =    4.819
peak=    3.277 closest distance to " O   HOH Z 238 " =    2.410
peak=    3.271 closest distance to " OG  SER A  28 " =    1.486
peak=    3.268 closest distance to " CG2AVAL A 121 " =    2.262
peak=    3.265 closest distance to " CB  ALA A 242 " =    0.844
peak=    3.260 closest distance to " CE1 HIS A 108 " =    1.133
peak=    3.257 closest distance to " CG2 ILE A 234 " =    0.905
peak=    3.252 closest distance to " CD1 TRP A 266 " =    1.246
peak=    3.251 closest distance to " N   VAL A 126 " =    1.512
peak=    3.251 closest distance to " O   HOH Z 280 " =    2.971
peak=    3.248 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.248 closest distance to " CG  MET A 185 " =    1.281
peak=    3.243 closest distance to " CB  TYR A 116 " =    0.913
peak=    3.241 closest distance to " O   HOH Z 156 " =    2.716
peak=    3.238 closest distance to " O   HOH Z 166 " =    3.847
peak=    3.238 closest distance to " O  BHOH Z 338 " =    2.223
peak=    3.236 closest distance to " CA  THR A 221 " =    1.530
peak=    3.232 closest distance to " CA  ARG A 102 " =    1.165
peak=    3.230 closest distance to " CB  TYR A 247 " =    0.962
peak=    3.229 closest distance to " CB  SER A 210 " =    0.913
peak=    3.226 closest distance to " O   HOH Z 368 " =    4.107
peak=    3.226 closest distance to " CA  ASN A 215 " =    1.112
peak=    3.221 closest distance to " O   HOH Z 344 " =    3.154
peak=    3.221 closest distance to " CD1 ILE A 199 " =    0.944
peak=    3.218 closest distance to " NE2 GLN A  58 " =    4.441
peak=    3.215 closest distance to " N   TYR A 247 " =    1.126
peak=    3.215 closest distance to " CG1BVAL A  72 " =    1.969
peak=    3.213 closest distance to " O   HOH Z 272 " =    1.910
peak=    3.212 closest distance to " O   HOH Z 109 " =    2.756
peak=    3.211 closest distance to " OG BSER A 134 " =    2.787
peak=    3.208 closest distance to " CG2 THR A  29 " =    1.394
peak=    3.202 closest distance to " CB  ASN A 110 " =    1.171
peak=    3.199 closest distance to " O   HOH Z 313 " =    1.777
peak=    3.197 closest distance to " NH1 ARG A 269 " =    0.737
peak=    3.196 closest distance to " CD  ARG A 139 " =    1.355
peak=    3.195 closest distance to " O   HOH Z 193 " =    1.960
peak=    3.195 closest distance to " CB  ALA A   9 " =    1.587
peak=    3.194 closest distance to " O   HOH Z 393 " =    3.133
peak=    3.193 closest distance to " CB  SER A 216 " =    0.926
peak=    3.192 closest distance to " O   THR A 182 " =    1.438
peak=    3.190 closest distance to " O   HOH Z 147 " =    1.701
peak=    3.189 closest distance to " CG2 ILE A  20 " =    1.313
peak=    3.188 closest distance to " O   HOH Z 293 " =    2.099
peak=    3.188 closest distance to " O   HOH Z  68 " =    1.925
peak=    3.186 closest distance to " CD1 LEU A 222 " =    0.708
peak=    3.185 closest distance to " O   HOH Z  63 " =    2.288
peak=    3.185 closest distance to " O   THR A 294 " =    1.382
peak=    3.184 closest distance to " CA  LEU A  83 " =    1.320
peak=    3.179 closest distance to " CH2 TRP A  70 " =    0.908
peak=    3.179 closest distance to " O   HOH Z 135 " =    1.811
peak=    3.178 closest distance to " CG1 ILE A 151 " =    0.995
peak=    3.178 closest distance to " O   ASP A 200 " =    1.692
peak=    3.177 closest distance to " CB  SER A 212 " =    1.084
peak=    3.174 closest distance to " CB  LEU A  96 " =    1.250
peak=    3.171 closest distance to " CG  MET A 185 " =    0.984
peak=    3.170 closest distance to " CB  LYS A 117 " =    1.183
peak=    3.170 closest distance to " O   HOH Z 285 " =    1.722
peak=    3.167 closest distance to " O   HOH Z 301 " =    1.885
peak=    3.164 closest distance to " CA  THR A  42 " =    0.960
peak=    3.163 closest distance to " CA  ILE A 106 " =    0.834
peak=    3.163 closest distance to " O   ASP A 191 " =    1.509
peak=    3.159 closest distance to " CG2 THR A 220 " =    0.822
peak=    3.158 closest distance to " O   HOH Z 251 " =    1.538
peak=    3.158 closest distance to " O   HOH Z 327 " =    1.736
peak=    3.156 closest distance to " O   HOH Z 163 " =    1.617
peak=    3.154 closest distance to " ND1 HIS A  81 " =    1.653
peak=    3.143 closest distance to " N   GLU A  44 " =    1.085
peak=    3.141 closest distance to " O   HOH Z  44 " =    1.662
peak=    3.140 closest distance to " CA  GLN A  88 " =    1.350
peak=    3.140 closest distance to " O   HOH Z 339 " =    2.271
peak=    3.139 closest distance to " O   HOH Z 128 " =    2.009
peak=    3.138 closest distance to " O   HOH Z  66 " =    2.072
peak=    3.136 closest distance to " O   HOH Z 437 " =    1.143
peak=    3.132 closest distance to " O   HOH Z 171 " =    3.917
peak=    3.129 closest distance to " O   HOH Z 357 " =    2.527
peak=    3.126 closest distance to " O   HOH Z 201 " =    2.850
peak=    3.125 closest distance to " CA  ALA A 129 " =    0.993
peak=    3.124 closest distance to " O   HOH Z 421 " =    1.829
peak=    3.123 closest distance to " O   HOH Z 106 " =    4.042
peak=    3.121 closest distance to " CD  GLU A 236 " =    0.996
peak=    3.108 closest distance to " O   HOH Z 167 " =    1.638
peak=    3.105 closest distance to " CG2 VAL A 268 " =    1.065
peak=    3.104 closest distance to " CA  THR A 264 " =    0.888
peak=    3.104 closest distance to " CE3 TRP A 150 " =    1.139
peak=    3.100 closest distance to " CB  THR A  52 " =    0.806
peak=    3.092 closest distance to " CD  ARG A  66 " =    2.010
peak=    3.086 closest distance to " CB  ASN A 215 " =    1.132
peak=    3.078 closest distance to " CB  GLN A 103 " =    0.875
peak=    3.075 closest distance to " CG2 ILE A  49 " =    1.328
peak=    3.075 closest distance to " CG2 ILE A 120 " =    1.093
peak=    3.074 closest distance to " O   TRP A 274 " =    1.753
peak=    3.067 closest distance to " O   HOH Z 213 " =    1.893
peak=    3.006 closest distance to " O   ASP A 124 " =    1.794

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.892 - 5.848
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.892 - 5.848

peak=   -4.500 closest distance to " CD  GLN A  58 " =    0.931
peak=   -4.459 closest distance to " O   HOH Z 411 " =    5.522
peak=   -4.425 closest distance to " CG1 VAL A 250 " =    2.677
peak=   -4.326 closest distance to " CG1 VAL A 112 " =    2.631
peak=   -4.318 closest distance to " O   HOH Z  10 " =    1.634
peak=   -4.268 closest distance to " CE2 PHE A  61 " =    2.620
peak=   -4.225 closest distance to " CD  ARG A 156 " =    2.109
peak=   -4.167 closest distance to " CG  ARG A 269 " =    2.409
peak=   -4.162 closest distance to " CA  ASP A 298 " =    1.065
peak=   -4.143 closest distance to " CD  GLN A 223 " =    1.380
peak=   -4.072 closest distance to " O   HOH Z 231 " =    2.404
peak=   -4.060 closest distance to " O   HOH Z  73 " =    2.348
peak=   -4.045 closest distance to " C   HIS A 108 " =    1.071
peak=   -4.028 closest distance to " CB  PRO A 243 " =    2.735
peak=   -4.001 closest distance to " CD2 TYR A 293 " =    1.900
peak=   -3.988 closest distance to " O   HOH Z 196 " =    2.344
peak=   -3.957 closest distance to " O   HOH Z 166 " =    1.692
peak=   -3.950 closest distance to " CB  ALA A 291 " =    2.495
peak=   -3.948 closest distance to " OD1 ASN A 148 " =    1.393
peak=   -3.941 closest distance to " C   ASN A 285 " =    2.454
peak=   -3.936 closest distance to " CD1 PHE A  59 " =    2.023
peak=   -3.926 closest distance to " CD  ARG A  14 " =    3.479
peak=   -3.915 closest distance to " CG2 ILE A  49 " =    2.865
peak=   -3.899 closest distance to " CB  ALA A 161 " =    2.695
peak=   -3.896 closest distance to " ND2BASN A 224 " =    1.885
peak=   -3.894 closest distance to " N   ALA A  43 " =    2.722
peak=   -3.878 closest distance to " O   HOH Z 128 " =    2.684
peak=   -3.840 closest distance to " O   PRO A 198 " =    1.342
peak=   -3.838 closest distance to " O   HOH Z  37 " =    1.871
peak=   -3.828 closest distance to " O   VAL A  67 " =    2.578
peak=   -3.810 closest distance to " O   ALA A  34 " =    2.556
peak=   -3.792 closest distance to " CE3 TRP A 150 " =    2.182
peak=   -3.766 closest distance to " O   HOH Z 377 " =    2.058
peak=   -3.763 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.759 closest distance to " CH2 TRP A 179 " =    1.191
peak=   -3.759 closest distance to " CG  GLN A  11 " =    1.581
peak=   -3.758 closest distance to " CA  VAL A  67 " =    3.020
peak=   -3.753 closest distance to " OXT GLY A 302 " =    3.163
peak=   -3.735 closest distance to " CA  GLY A 241 " =    3.258
peak=   -3.728 closest distance to " CD1 ILE A 151 " =    2.452
peak=   -3.717 closest distance to " OG  SER A  97 " =    2.257
peak=   -3.716 closest distance to " O   HOH Z  38 " =    1.249
peak=   -3.712 closest distance to " CB  ASP A 132 " =    2.416
peak=   -3.702 closest distance to " CG  MET A 105 " =    0.992
peak=   -3.701 closest distance to " O   HOH Z 418 " =    1.228
peak=   -3.699 closest distance to " O   HOH Z 211 " =    1.406
peak=   -3.682 closest distance to " O   HOH Z 394 " =    1.686
peak=   -3.678 closest distance to " CA  GLY A 241 " =    2.292
peak=   -3.676 closest distance to " CG  PRO A 198 " =    1.990
peak=   -3.659 closest distance to " O   SER A 276 " =    1.813
peak=   -3.655 closest distance to " OD2 ASP A 171 " =    1.918
peak=   -3.650 closest distance to " O   HOH Z   6 " =    2.017
peak=   -3.650 closest distance to " O   HOH Z  19 " =    2.008
peak=   -3.640 closest distance to " O   HOH Z 185 " =    2.412
peak=   -3.636 closest distance to " O   HOH Z 150 " =    2.189
peak=   -3.635 closest distance to " O   HOH Z 292 " =    4.641
peak=   -3.631 closest distance to " CG  GLU A 277 " =    1.322
peak=   -3.625 closest distance to " O   GLY A  17 " =    1.203
peak=   -3.621 closest distance to " CB  ALA A  10 " =    2.133
peak=   -3.618 closest distance to " CD1 LEU A 101 " =    2.451
peak=   -3.612 closest distance to " O   HOH Z 275 " =    1.635
peak=   -3.598 closest distance to " NH2 ARG A  79 " =    1.498
peak=   -3.577 closest distance to " OD1 ASP A 191 " =    1.522
peak=   -3.575 closest distance to " O   SER A 210 " =    1.878
peak=   -3.574 closest distance to " NE2 GLN A 103 " =    1.905
peak=   -3.568 closest distance to " NE2 GLN A 194 " =    1.982
peak=   -3.567 closest distance to " CD2 PHE A  61 " =    2.114
peak=   -3.549 closest distance to " CB  PHE A 208 " =    2.293
peak=   -3.548 closest distance to " CG  PRO A 243 " =    1.686
peak=   -3.534 closest distance to " O   HOH Z  52 " =    1.613
peak=   -3.531 closest distance to " CG  ARG A  66 " =    2.471
peak=   -3.517 closest distance to " O   HOH Z   6 " =    1.372
peak=   -3.513 closest distance to " CA  GLY A 133 " =    2.426
peak=   -3.508 closest distance to " CE3 TRP A  70 " =    1.950
peak=   -3.506 closest distance to " CE  MET A  93 " =    1.734
peak=   -3.502 closest distance to " CD1 PHE A  16 " =    2.512
peak=   -3.496 closest distance to " CD  GLN A  88 " =    0.955
peak=   -3.488 closest distance to " NE  ARG A  79 " =    1.248
peak=   -3.487 closest distance to " CB  TRP A  85 " =    2.390
peak=   -3.485 closest distance to " ND2 ASN A  45 " =    1.123
peak=   -3.483 closest distance to " CG  GLU A  53 " =    1.494
peak=   -3.469 closest distance to " CB  ALA A  43 " =    2.799
peak=   -3.466 closest distance to " O   HOH Z 114 " =    3.608
peak=   -3.463 closest distance to " O   HOH Z 216 " =    1.490
peak=   -3.458 closest distance to " ND2 ASN A  45 " =    2.070
peak=   -3.454 closest distance to " OG BSER A 134 " =    1.331
peak=   -3.453 closest distance to " CA  GLY A 203 " =    2.426
peak=   -3.453 closest distance to " O   TYR A 186 " =    1.839
peak=   -3.445 closest distance to " O   HOH Z 149 " =    2.008
peak=   -3.445 closest distance to " OE1 GLN A  88 " =    1.037
peak=   -3.442 closest distance to " O   HOH Z 393 " =    1.354
peak=   -3.423 closest distance to " O   HOH Z 114 " =    1.180
peak=   -3.420 closest distance to " CB  ALA A   9 " =    2.623
peak=   -3.419 closest distance to " C   SER A 206 " =    1.416
peak=   -3.411 closest distance to " O   HOH Z 287 " =    2.007
peak=   -3.410 closest distance to " O   HOH Z 240 " =    3.742
peak=   -3.409 closest distance to " O   HOH Z 102 " =    1.570
peak=   -3.407 closest distance to " O   HOH Z 285 " =    1.490
peak=   -3.403 closest distance to " CD  GLU A 236 " =    1.132
peak=   -3.402 closest distance to " CG1 VAL A 125 " =    1.967
peak=   -3.398 closest distance to " O   HOH Z 171 " =    2.208
peak=   -3.389 closest distance to " NE2 GLN A  88 " =    1.988
peak=   -3.378 closest distance to " O   HOH Z 197 " =    1.964
peak=   -3.373 closest distance to " O   ALA A  10 " =    1.680
peak=   -3.370 closest distance to " NE  ARG A  66 " =    4.273
peak=   -3.368 closest distance to " CE BMET A  47 " =    1.852
peak=   -3.363 closest distance to " ND2 ASN A 249 " =    2.452
peak=   -3.359 closest distance to " CB  PHE A 192 " =    1.876
peak=   -3.358 closest distance to " CA  GLY A 241 " =    2.870
peak=   -3.355 closest distance to " CG  HIS A  86 " =    1.134
peak=   -3.354 closest distance to " O   HOH Z 351 " =    1.643
peak=   -3.353 closest distance to " CE  MET A 105 " =    2.662
peak=   -3.347 closest distance to " CG2 ILE A 263 " =    2.378
peak=   -3.346 closest distance to " O   HOH Z 198 " =    2.221
peak=   -3.338 closest distance to " OH  TYR A 247 " =    1.749
peak=   -3.335 closest distance to " O   VAL A 189 " =    2.513
peak=   -3.332 closest distance to " NH2 ARG A  66 " =    1.947
peak=   -3.328 closest distance to " O   HOH Z 377 " =    1.178
peak=   -3.326 closest distance to " O   HOH Z 426 " =    1.683
peak=   -3.323 closest distance to " O   PHE A 218 " =    1.457
peak=   -3.315 closest distance to " CD  LYS A 289 " =    2.404
peak=   -3.312 closest distance to " O   HOH Z 166 " =    1.897
peak=   -3.307 closest distance to " OG1 THR A  82 " =    1.440
peak=   -3.306 closest distance to " CZ  PHE A  38 " =    2.613
peak=   -3.305 closest distance to " O   PRO A 163 " =    2.074
peak=   -3.298 closest distance to " O   HOH Z  69 " =    1.914
peak=   -3.295 closest distance to " O   HOH Z  64 " =    1.661
peak=   -3.291 closest distance to " O   HOH Z 407 " =    3.599
peak=   -3.290 closest distance to " CZ  TYR A 169 " =    1.840
peak=   -3.288 closest distance to " NH2 ARG A 159 " =    2.324
peak=   -3.287 closest distance to " OD1 ASP A 171 " =    1.467
peak=   -3.284 closest distance to " O   GLY A  98 " =    2.105
peak=   -3.282 closest distance to " O   HOH Z 251 " =    1.747
peak=   -3.274 closest distance to " CG2 VAL A 189 " =    2.199
peak=   -3.273 closest distance to " C   LEU A 143 " =    1.185
peak=   -3.265 closest distance to " CZ  PHE A 155 " =    1.231
peak=   -3.265 closest distance to " CG1 VAL A  78 " =    2.697
peak=   -3.264 closest distance to " O   HOH Z  60 " =    1.887
peak=   -3.261 closest distance to " OD2 ASP A 191 " =    1.570
peak=   -3.260 closest distance to " O   HOH Z 191 " =    5.848
peak=   -3.257 closest distance to " CD2 PHE A 225 " =    1.258
peak=   -3.254 closest distance to " SG  CYS A 168 " =    1.287
peak=   -3.251 closest distance to " N   THR A  52 " =    1.543
peak=   -3.242 closest distance to " O   HOH Z 234 " =    4.477
peak=   -3.240 closest distance to " CD  ARG A 139 " =    1.549
peak=   -3.239 closest distance to " O   HOH Z 165 " =    1.887
peak=   -3.231 closest distance to " O   HOH Z 124 " =    4.380
peak=   -3.231 closest distance to " O   HOH Z 111 " =    1.772
peak=   -3.231 closest distance to " O   HOH Z 111 " =    1.588
peak=   -3.224 closest distance to " O   SER A 271 " =    2.130
peak=   -3.222 closest distance to " OG BSER A 210 " =    2.177
peak=   -3.221 closest distance to " O   HOH Z 396 " =    1.783
peak=   -3.212 closest distance to " OG  SER A  62 " =    1.808
peak=   -3.212 closest distance to " CG1 VAL A 112 " =    2.878
peak=   -3.209 closest distance to " O   HOH Z 150 " =    1.370
peak=   -3.208 closest distance to " O   GLU A 152 " =    1.384
peak=   -3.201 closest distance to " ND2 ASN A  69 " =    1.657
peak=   -3.200 closest distance to " N   ILE A 120 " =    0.998
peak=   -3.200 closest distance to " ND1 HIS A 115 " =    2.054
peak=   -3.199 closest distance to " O   GLN A 240 " =    2.726
peak=   -3.196 closest distance to " O   HOH Z 264 " =    1.845
peak=   -3.192 closest distance to " O   HOH Z  51 " =    1.644
peak=   -3.190 closest distance to " CG  LEU A 281 " =    1.863
peak=   -3.189 closest distance to " O   HOH Z 154 " =    1.540
peak=   -3.188 closest distance to " N   SER A 276 " =    1.411
peak=   -3.185 closest distance to " O   HOH Z 259 " =    2.170
peak=   -3.183 closest distance to " C   GLU A  46 " =    0.957
peak=   -3.181 closest distance to " CH2 TRP A 150 " =    1.129
peak=   -3.180 closest distance to " CG2BVAL A  41 " =    1.560
peak=   -3.177 closest distance to " NE2 GLN A 223 " =    1.516
peak=   -3.176 closest distance to " CE1 HIS A  86 " =    1.163
peak=   -3.175 closest distance to " O   VAL A 189 " =    1.734
peak=   -3.174 closest distance to " O   HOH Z 156 " =    3.591
peak=   -3.166 closest distance to " O   HOH Z 371 " =    1.514
peak=   -3.163 closest distance to " O   HOH Z 189 " =    2.024
peak=   -3.163 closest distance to " O   HOH Z 117 " =    4.506
peak=   -3.159 closest distance to " ND2 ASN A 187 " =    1.705
peak=   -3.153 closest distance to " C   ASN A 187 " =    1.942
peak=   -3.152 closest distance to " O   HOH Z  13 " =    1.879
peak=   -3.150 closest distance to " CA  VAL A 197 " =    1.012
peak=   -3.141 closest distance to " O   HOH Z 350 " =    2.019
peak=   -3.140 closest distance to " O   HOH Z  40 " =    3.177
peak=   -3.139 closest distance to " CD2 PHE A  59 " =    2.503
peak=   -3.137 closest distance to " ND2 ASN A  60 " =    1.382
peak=   -3.131 closest distance to " CG1 VAL A 112 " =    2.848
peak=   -3.129 closest distance to " CG  PRO A 163 " =    2.181
peak=   -3.128 closest distance to " N   ALA A 226 " =    2.115
peak=   -3.127 closest distance to " O   HOH Z 251 " =    5.029
peak=   -3.124 closest distance to " OE1 GLN A  88 " =    0.892
peak=   -3.117 closest distance to " O   TRP A  92 " =    1.946
peak=   -3.114 closest distance to " OD2 ASP A 270 " =    1.146
peak=   -3.111 closest distance to " O   PRO A 243 " =    1.790
peak=   -3.107 closest distance to " SD  MET A  40 " =    2.020
peak=   -3.105 closest distance to " CG1AVAL A  41 " =    2.587
peak=   -3.102 closest distance to " O   GLY A 262 " =    2.403
peak=   -3.098 closest distance to " O   HOH Z 290 " =    1.182
peak=   -3.091 closest distance to " CA  ASN A 127 " =    1.013
peak=   -3.086 closest distance to " C   GLY A 262 " =    2.104
peak=   -3.083 closest distance to " O   HOH Z  82 " =    2.063
peak=   -3.082 closest distance to " CD2 LEU A 300 " =    2.708
peak=   -3.070 closest distance to " CB  TYR A  15 " =    2.276
peak=   -3.066 closest distance to " C   ARG A  79 " =    2.612
peak=   -3.064 closest distance to " ND2 ASN A  45 " =    1.349
peak=   -3.062 closest distance to " OD1 ASN A 187 " =    1.602
peak=   -3.058 closest distance to " O   HOH Z  70 " =    2.120
peak=   -3.057 closest distance to " O   HOH Z 407 " =    1.172
peak=   -3.053 closest distance to " O   HOH Z 145 " =    2.589
peak=   -3.044 closest distance to " CG  TRP A 266 " =    1.825
peak=   -3.014 closest distance to " CE  LYS A  76 " =    2.430

================= 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    :  0.4086 0.3980   6.200925e+00   6.178145e+00
   1_bss:  0.3994 0.3903   6.188178e+00   6.163446e+00
   1_xyz:  0.2518 0.2757   5.814533e+00   5.886370e+00
   1_adp:  0.2289 0.2840   5.756557e+00   5.909221e+00
   1_occ:  0.2286 0.2838   5.756147e+00   5.909557e+00
   2_bss:  0.2272 0.2813   5.753859e+00   5.906615e+00
   2_xyz:  0.1660 0.2058   5.465839e+00   5.648122e+00
   2_adp:  0.1543 0.1921   5.401462e+00   5.584978e+00
   2_occ:  0.1541 0.1920   5.400427e+00   5.584612e+00
   3_bss:  0.1540 0.1917   5.398515e+00   5.581906e+00
   3_xyz:  0.1322 0.1734   5.272257e+00   5.481284e+00
   3_adp:  0.1266 0.1737   5.246724e+00   5.471305e+00
   3_occ:  0.1265 0.1737   5.246781e+00   5.471464e+00
   4_bss:  0.1268 0.1734   5.248045e+00   5.471162e+00
   4_xyz:  0.1249 0.1726   5.237326e+00   5.464950e+00
   4_adp:  0.1249 0.1718   5.233564e+00   5.459887e+00
   4_occ:  0.1248 0.1719   5.233511e+00   5.459859e+00
   5_bss:  0.1247 0.1717   5.233633e+00   5.459967e+00
   5_xyz:  0.1217 0.1689   5.214226e+00   5.445760e+00
   5_adp:  0.1210 0.1695   5.212475e+00   5.448275e+00
   5_occ:  0.1209 0.1695   5.212482e+00   5.448455e+00
   5_bss:  0.1208 0.1693   5.212526e+00   5.448503e+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:  0.299  61.088  -2.421   2.330   1.649   0.000   0.000   0.000
   1_xyz:  0.299  61.088  -2.421   2.330   1.649   0.000   0.000   0.000
   1_adp:  0.299  61.088  -2.421   2.330   1.649   0.000   0.000   0.000
   1_occ:  0.299  61.088  -2.421   2.330   1.649   0.000   0.000   0.000
   2_bss:  0.332  85.979  -2.124   0.124  -0.019   0.000  -0.000  -0.000
   2_xyz:  0.332  85.979  -2.124   0.124  -0.019   0.000  -0.000  -0.000
   2_adp:  0.332  85.979  -2.124   0.124  -0.019   0.000  -0.000  -0.000
   2_occ:  0.332  85.979  -2.124   0.124  -0.019   0.000  -0.000  -0.000
   3_bss:  0.332  77.185  -2.114  -0.877  -0.277  -0.000  -0.000  -0.000
   3_xyz:  0.332  77.185  -2.114  -0.877  -0.277  -0.000  -0.000  -0.000
   3_adp:  0.332  77.185  -2.114  -0.877  -0.277  -0.000  -0.000  -0.000
   3_occ:  0.332  77.185  -2.114  -0.877  -0.277  -0.000  -0.000  -0.000
   4_bss:  0.329  77.102  -1.669  -0.887  -0.008  -0.000  -0.000  -0.000
   4_xyz:  0.329  77.102  -1.669  -0.887  -0.008  -0.000  -0.000  -0.000
   4_adp:  0.329  77.102  -1.669  -0.887  -0.008  -0.000  -0.000  -0.000
   4_occ:  0.329  77.102  -1.669  -0.887  -0.008  -0.000  -0.000  -0.000
   5_bss:  0.329  76.805  -1.290  -0.665   0.320  -0.000   0.000   0.000
   5_xyz:  0.329  76.805  -1.290  -0.665   0.320  -0.000   0.000   0.000
   5_adp:  0.329  76.805  -1.290  -0.665   0.320  -0.000   0.000   0.000
   5_occ:  0.329  76.805  -1.290  -0.665   0.320  -0.000   0.000   0.000
   5_bss:  0.324  73.018  -0.943  -0.445   0.609  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.195 0.5810  0.7273    46755.144
   1_bss:  44.440 0.5887  0.7544    44449.262
   1_xyz:  28.024 0.7803  0.9535    19918.117
   1_adp:  28.808 0.7712  0.9343    21038.306
   1_occ:  28.834 0.7709  0.9332    21036.685
   2_bss:  28.557 0.7740  0.9003    20825.587
   2_xyz:  20.177 0.8596  0.9661    10931.808
   2_adp:  18.289 0.8782  0.9659     9533.305
   2_occ:  18.272 0.8784  0.9660     9525.544
   3_bss:  18.188 0.8791  0.9527     9439.928
   3_xyz:  15.899 0.8993  0.9641     7625.086
   3_adp:  15.634 0.9018  0.9527     7496.342
   3_occ:  15.636 0.9017  0.9525     7496.716
   4_bss:  15.640 0.9017  0.9606     7507.224
   4_xyz:  15.502 0.9030  0.9611     7411.942
   4_adp:  15.366 0.9041  0.9505     7339.975
   4_occ:  15.364 0.9042  0.9504     7340.088
   5_bss:  15.367 0.9041  0.9610     7343.048
   5_xyz:  15.030 0.9070  0.9637     7076.226
   5_adp:  15.056 0.9069  0.9529     7114.614
   5_occ:  15.055 0.9069  0.9528     7114.776
   5_bss:  15.056 0.9069  0.9626     7115.329
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6350e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6350e-01
   1_xyz:   1.352  0.011  0.081 15.221  0.006  4.119   9.3127e-02
   1_adp:   1.352  0.011  0.081 15.221  0.006  4.119   9.3127e-02
   1_occ:   1.352  0.011  0.081 15.221  0.006  4.119   9.3127e-02
   2_bss:   1.352  0.011  0.081 15.221  0.006  4.119   9.3127e-02
   2_xyz:   1.127  0.008  0.080 14.728  0.004  4.138   6.7805e-02
   2_adp:   1.127  0.008  0.080 14.728  0.004  4.138   6.7805e-02
   2_occ:   1.127  0.008  0.080 14.728  0.004  4.138   6.7805e-02
   3_bss:   1.127  0.008  0.080 14.728  0.004  4.138   6.7805e-02
   3_xyz:   1.001  0.008  0.073 14.715  0.003  4.147   5.9125e-02
   3_adp:   1.001  0.008  0.073 14.715  0.003  4.147   5.9125e-02
   3_occ:   1.001  0.008  0.073 14.715  0.003  4.147   5.9125e-02
   4_bss:   1.001  0.008  0.073 14.715  0.003  4.147   5.9125e-02
   4_xyz:   0.995  0.008  0.075 14.689  0.004  4.115   6.0709e-02
   4_adp:   0.995  0.008  0.075 14.689  0.004  4.115   6.0709e-02
   4_occ:   0.995  0.008  0.075 14.689  0.004  4.115   6.0709e-02
   5_bss:   0.995  0.008  0.075 14.689  0.004  4.115   6.0709e-02
   5_xyz:   0.963  0.008  0.073 14.571  0.003  4.119   5.6322e-02
   5_adp:   0.963  0.008  0.073 14.571  0.003  4.119   5.6322e-02
   5_occ:   0.963  0.008  0.073 14.571  0.003  4.119   5.6322e-02
   5_bss:   0.963  0.008  0.073 14.571  0.003  4.119   5.6322e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.773   2.4472e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.773   2.4472e-01
   1_xyz:   8.884  0.073  0.310 84.876  0.042  2.178   7.6693e-02
   1_adp:   8.884  0.073  0.310 84.876  0.042  2.178   7.6693e-02
   1_occ:   8.884  0.073  0.310 84.876  0.042  2.178   7.6693e-02
   2_bss:   8.884  0.073  0.310 84.876  0.042  2.178   7.6693e-02
   2_xyz:   7.463  0.046  0.239 80.731  0.050  2.307   5.0738e-02
   2_adp:   7.463  0.046  0.239 80.731  0.050  2.307   5.0738e-02
   2_occ:   7.463  0.046  0.239 80.731  0.050  2.307   5.0738e-02
   3_bss:   7.463  0.046  0.239 80.731  0.050  2.307   5.0738e-02
   3_xyz:   7.321  0.040  0.219 82.746  0.038  2.345   4.4613e-02
   3_adp:   7.321  0.040  0.219 82.746  0.038  2.345   4.4613e-02
   3_occ:   7.321  0.040  0.219 82.746  0.038  2.345   4.4613e-02
   4_bss:   7.321  0.040  0.219 82.746  0.038  2.345   4.4613e-02
   4_xyz:   7.287  0.043  0.228 82.388  0.040  2.349   5.4431e-02
   4_adp:   7.287  0.043  0.228 82.388  0.040  2.349   5.4431e-02
   4_occ:   7.287  0.043  0.228 82.388  0.040  2.349   5.4431e-02
   5_bss:   7.287  0.043  0.228 82.388  0.040  2.349   5.4431e-02
   5_xyz:   7.236  0.043  0.240 80.810  0.041  2.433   3.3483e-02
   5_adp:   7.236  0.043  0.240 80.810  0.041  2.433   3.3483e-02
   5_occ:   7.236  0.043  0.240 80.810  0.041  2.433   3.3483e-02
   5_bss:   7.236  0.043  0.240 80.810  0.041  2.433   3.3483e-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:  98.61   0.00  17.75  82.62   0.00  13.35  98.61   3.74  41.71
   1_occ:  98.61   0.00  17.75  82.62   0.00  13.35  98.61   3.74  41.71
   2_bss:  98.61   0.00  17.75  82.62   0.00  13.35  98.61   3.74  41.71
   2_xyz:  98.61   0.00  17.75  82.62   0.00  13.35  98.61   3.74  41.71
   2_adp:  98.41   1.35  17.27  81.89   1.35  12.84  98.41   4.98  41.40
   2_occ:  98.41   1.35  17.27  81.89   1.35  12.84  98.41   4.98  41.40
   3_bss:  98.41   1.35  17.27  81.89   1.35  12.84  98.41   4.98  41.40
   3_xyz:  98.41   1.35  17.27  81.89   1.35  12.84  98.41   4.98  41.40
   3_adp: 100.24   0.00  17.49  97.19   0.00  12.63 100.24   4.53  43.96
   3_occ: 100.24   0.00  17.49  97.19   0.00  12.63 100.24   4.53  43.96
   4_bss: 100.24   0.00  17.49  97.19   0.00  12.63 100.24   4.53  43.96
   4_xyz: 100.24   0.00  17.49  97.19   0.00  12.63 100.24   4.53  43.96
   4_adp: 100.45   0.00  17.17  97.85   0.00  12.30 100.45   4.63  43.70
   4_occ: 100.45   0.00  17.17  97.85   0.00  12.30 100.45   4.63  43.70
   5_bss: 100.45   0.00  17.17  97.85   0.00  12.30 100.45   4.63  43.70
   5_xyz: 100.45   0.00  17.17  97.85   0.00  12.30 100.45   4.63  43.70
   5_adp: 102.85   0.00  16.90 102.85   0.00  12.03 102.20   4.88  43.42
   5_occ: 102.85   0.00  16.90 102.85   0.00  12.03 102.20   4.88  43.42
   5_bss: 102.85   0.00  16.91 102.85   0.00  12.04 102.21   4.88  43.42
------------------------------------------------------------------------
 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:    1.502    0.022    0.395
   1_adp:    1.502    0.022    0.395
   1_occ:    1.502    0.022    0.395
   2_bss:    1.502    0.022    0.395
   2_xyz:    1.209    0.027    0.490
   2_adp:    1.209    0.027    0.490
   2_occ:    1.209    0.027    0.490
   3_bss:    1.209    0.027    0.490
   3_xyz:    1.192    0.044    0.560
   3_adp:    1.192    0.044    0.560
   3_occ:    1.192    0.044    0.560
   4_bss:    1.192    0.044    0.560
   4_xyz:    1.180    0.047    0.562
   4_adp:    1.180    0.047    0.562
   4_occ:    1.180    0.047    0.562
   5_bss:    1.180    0.047    0.562
   5_xyz:    1.181    0.099    0.581
   5_adp:    1.181    0.099    0.581
   5_occ:    1.181    0.099    0.581
   5_bss:    1.181    0.099    0.581
------------------------------------------------------------------------

CPU time actual refinement: 299.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_943/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_943/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_943/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_943/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_943/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 299.49 
  Macro-tasks:
    bulk solvent and scale       = 52.70  
    individual site refinement   = 120.46 
    weights calculation          = 24.99  
    collect and process          = 5.63   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 203.88 
  Micro-tasks:
    mask                            = 1.47   
    f_calc                          = 87.72  
    alpha_beta                      = 6.96   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 97.27  
    fmodel                         = 8.01   
    r_factors                      = 0.40   
    phase_errors                   = 9.06   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 212.11 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.116 micro seconds
Total CPU time: 5.18 minutes
from_scatterers_fft:    655 calls, 87.49 s
gradients_fft:          600 calls, 84.86 s

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

# Date 2008-01-16 Time 06:01:38 PST -0800 (1200492098.36 s)
Start R-work = 0.4086, R-free = 0.3980 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1827 (no bulk solvent and anisotropic scale)

Start R-work = 0.3994, R-free = 0.3903
Final R-work = 0.1208, R-free = 0.1693