# Date 2008-01-16 Time 05:56:58 PST -0800 (1200491818.51 s)
#phil __OFF__

Command line arguments: "../945.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 897
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 945

-------------------------------------------------------------------------------
  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, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


================================== 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, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02063
Completeness in resolution range: 0.968267
Completeness with d_max=infinity: 0.965213

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0206

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, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02063
Completeness in resolution range: 0.968267
Completeness with d_max=infinity: 0.965213

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3231 [2134/2158]  1918   216  10.1%
  bin  2:  4.3231 -  3.4445 [2037/2056]  1838   199   9.8%
  bin  3:  3.4445 -  3.0129 [2016/2035]  1814   202  10.0%
  bin  4:  3.0129 -  2.7392 [1990/2020]  1784   206  10.4%
  bin  5:  2.7392 -  2.5438 [1992/2011]  1797   195   9.8%
  bin  6:  2.5438 -  2.3945 [1973/1998]  1777   196   9.9%
  bin  7:  2.3945 -  2.2750 [1960/1988]  1764   196  10.0%
  bin  8:  2.2750 -  2.1762 [1973/2009]  1774   199  10.1%
  bin  9:  2.1762 -  2.0927 [1921/1963]  1727   194  10.1%
  bin 10:  2.0927 -  2.0206 [1593/1993]  1437   156   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_945/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: 0.15 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:
        1.73 -     2.36: 12
        2.36 -     3.00: 1858
        3.00 -     3.63: 4472
        3.63 -     4.27: 8880
        4.27 -     4.90: 12402
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.730 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.835 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.835 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.958 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27619 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_945/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_945/model_refine_001.geo

CPU time processing inputs: 9.33


============================ 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 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4512   r_free= 0.4465   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.258467                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1385  153 0.3507 0.3458      6.5072      6.4336|
|  2:  4.8215 -  3.8473 0.99   1319  150 0.3774 0.4104      6.7808      6.8774|
|  3:  3.8473 -  3.3670 0.99   1310  144 0.4200 0.3720      6.6559      6.5913|
|  4:  3.3670 -  3.0619 0.99   1297  138 0.4365 0.4373      6.5125      6.4386|
|  5:  3.0619 -  2.8440 0.99   1275  144 0.4718 0.4311      6.3535      6.3424|
|  6:  2.8440 -  2.6773 0.99   1292  147 0.4703 0.5131      6.2543      6.2145|
|  7:  2.6773 -  2.5438 0.99   1273  142 0.4893 0.4691      6.2267      6.1535|
|  8:  2.5438 -  2.4336 0.98   1276  137 0.4967 0.4562      6.1726      6.1639|
|  9:  2.4336 -  2.3402 0.98   1249  143 0.4953 0.5162      6.1011      6.1595|
| 10:  2.3402 -  2.2597 0.99   1277  139 0.5200 0.4741      6.1189      6.1122|
| 11:  2.2597 -  2.1893 0.98   1259  140 0.5154 0.5237      6.0339      6.0567|
| 12:  2.1893 -  2.1269 0.97   1246  139 0.5158 0.5200      5.9743      6.0461|
| 13:  2.1269 -  2.0710 1.00   1256  140 0.5164 0.5340      5.8964      5.8351|
| 14:  2.0710 -  2.0206 0.72    916  103 0.5058 0.5216      5.8403        5.78|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1385   153  0.74  30.25   0.82     0.77      57541.13|
|  2:  4.8215 -  3.8473  1319   150  0.75  30.94   0.90     0.82      87982.77|
|  3:  3.8473 -  3.3670  1310   144  0.66  38.98   0.89     0.80      92979.39|
|  4:  3.3670 -  3.0619  1297   138  0.58  45.71   0.89     0.71      85171.85|
|  5:  3.0619 -  2.8440  1275   144  0.49  52.68   0.90     0.63      68500.50|
|  6:  2.8440 -  2.6773  1292   147  0.45  56.02   0.88     0.58      64110.27|
|  7:  2.6773 -  2.5438  1273   142  0.42  58.00   0.89     0.57      58865.72|
|  8:  2.5438 -  2.4336  1276   137  0.42  58.34   0.88     0.57      54313.57|
|  9:  2.4336 -  2.3402  1249   143  0.41  59.19   0.90     0.58      50667.32|
| 10:  2.3402 -  2.2597  1277   139  0.40  60.20   0.91     0.56      46829.81|
| 11:  2.2597 -  2.1893  1259   140  0.36  63.34   0.90     0.52      46287.36|
| 12:  2.1893 -  2.1269  1246   139  0.34  64.81   0.90     0.49      42580.16|
| 13:  2.1269 -  2.0710  1256   140  0.32  65.84   0.88     0.47      37342.84|
| 14:  2.0710 -  2.0206   916   103  0.35  64.09   0.91     0.46      29750.98|
|alpha:            min =        0.46 max =            0.82 mean =         0.61|
|beta:             min =    29750.98 max =        92979.39 mean =     59613.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.95|
|phase err.(test): min =        0.00 max =           89.66 mean =        53.19|
|-----------------------------------------------------------------------------|

============================== 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 = 8.614792              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.766   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.140460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.748   (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 |  1.730 -  2.047:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.047 -  2.364:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.364 -  2.681:       81 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.681 -  2.998:     1777 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.998 -  3.315:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.315 -  3.632:     2631 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.632 -  3.949:     4599 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.949 -  4.266:     4281 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.266 -  4.583:     5619 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.583 -  4.900:     6783 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.730 |       0.190 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    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 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4512   r_free= 0.4465   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.258467                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4420   r_free= 0.4384   ksol= 0.30   Bsol= 59.99   scale= 0.935   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,1.60,4.64,0.00,0.00,0.00); trace/3= 1.26                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.249201                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.394941              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.387   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.112328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4420      final r-factor (work) = 0.3280          |
| start r-factor (free) = 0.4384      final r-factor (free) = 0.3519          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2682 = 7.39 * 0.50 * 6.2480 + 1.00 * 0.1664                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6979 = 7.39 * 0.50 * 6.1061 + 1.00 * 0.1208                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3280      final r-factor (work) = 0.2961          |
| start r-factor (free) = 0.3519      final r-factor (free) = 0.3628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7980 = 1.11 * 1.00 * 6.1061 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6568 = 1.11 * 1.00 * 5.9672 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.08  18.60    None  None   None       |
|    all(noH): 2823   0      0.00    115.08  18.60    None  None   None       |
|    Sol.    : 438    0      0.00    115.08  41.34    None  None   None       |
|    Mac.    : 2385   0      0.00    85.19   14.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.508: 1188   |   5:    57.538 -  69.046:   66        |
|      1:    11.508 -  23.015:  873   |   6:    69.046 -  80.554:   33        |
|      2:    23.015 -  34.523:  364   |   7:    80.554 -  92.061:   10        |
|      3:    34.523 -  46.031:  184   |   8:    92.061 - 103.569:    4        |
|      4:    46.031 -  57.538:  100   |   9:   103.569 - 115.077:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2961 r_free = 0.3628             target_work(ml) = 5.974         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2958 r_free = 0.3628             target_work(ml) = 5.974         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2958   r_free= 0.3628   ksol= 0.30   Bsol= 59.99   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,1.60,4.64,0.00,0.00,0.00); trace/3= 1.26                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.973735                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2945   r_free= 0.3606   ksol= 0.33   Bsol= 77.40   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.77,2.39,0.00,0.00,0.00); trace/3= 0.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.973614                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.540573              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.380   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.385067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.650  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2945      final r-factor (work) = 0.2150          |
| start r-factor (free) = 0.3606      final r-factor (free) = 0.2688          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6349 = 6.54 * 0.50 * 5.9671 + 1.00 * 0.1208                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2501 = 6.54 * 0.50 * 5.8591 + 1.00 * 0.0892                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2150      final r-factor (work) = 0.1953          |
| start r-factor (free) = 0.2688      final r-factor (free) = 0.2458          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2755 = 0.39 * 1.00 * 5.8591 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2917 = 0.39 * 1.00 * 5.6530 + 1.00 * 0.1149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.33  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    114.33  17.56    None  None   None       |
|    Sol.    : 438    0      2.55    114.33  41.98    None  None   None       |
|    Mac.    : 2385   0      0.00    84.70   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.433: 1365   |   5:    57.167 -  68.600:   67        |
|      1:    11.433 -  22.867:  813   |   6:    68.600 -  80.034:   23        |
|      2:    22.867 -  34.300:  260   |   7:    80.034 -  91.467:   10        |
|      3:    34.300 -  45.734:  173   |   8:    91.467 - 102.900:    3        |
|      4:    45.734 -  57.167:  108   |   9:   102.900 - 114.334:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1953 r_free = 0.2458             target_work(ml) = 5.616         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1951 r_free = 0.2459             target_work(ml) = 5.616         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1951   r_free= 0.2459   ksol= 0.33   Bsol= 77.40   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,0.77,2.39,0.00,0.00,0.00); trace/3= 0.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.616082                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1950   r_free= 0.2445   ksol= 0.33   Bsol= 80.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.26,1.13,-0.00,0.00,0.00); trace/3= -0.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.613828                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.428261              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.163  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.691306              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.949   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1950      final r-factor (work) = 0.1640          |
| start r-factor (free) = 0.2445      final r-factor (free) = 0.2071          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9541 = 2.43 * 0.50 * 5.6542 + 1.00 * 0.0892                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7790 = 2.43 * 0.50 * 5.5367 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1640      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2071      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3852 = 1.69 * 1.00 * 5.5367 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1851 = 1.69 * 1.00 * 5.4214 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.89  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    115.89  17.95    None  None   None       |
|    Sol.    : 438    0      3.87    115.89  46.33    None  None   None       |
|    Mac.    : 2385   0      0.00    99.32   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.589: 1440   |   5:    57.944 -  69.532:   87        |
|      1:    11.589 -  23.177:  801   |   6:    69.532 -  81.121:   55        |
|      2:    23.177 -  34.766:  191   |   7:    81.121 -  92.710:   16        |
|      3:    34.766 -  46.355:  115   |   8:    92.710 - 104.298:    7        |
|      4:    46.355 -  57.944:  109   |   9:   104.298 - 115.887:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1528 r_free = 0.2026             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1528 r_free = 0.2025             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1528   r_free= 0.2025   ksol= 0.33   Bsol= 80.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-0.26,1.13,-0.00,0.00,0.00); trace/3= -0.18                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.410333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1532   r_free= 0.2027   ksol= 0.34   Bsol= 93.23   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-0.58,0.71,-0.00,0.00,0.00); trace/3= -0.46                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.411131                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.619434              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.084  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.525178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.710  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1532      final r-factor (work) = 0.1304          |
| start r-factor (free) = 0.2027      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8706 = 3.62 * 0.50 * 5.4228 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7448 = 3.62 * 0.50 * 5.3421 + 1.00 * 0.0770                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1304      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1797      final r-factor (free) = 0.1745          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8211 = 0.53 * 1.00 * 5.3421 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7797 = 0.53 * 1.00 * 5.2677 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.66  17.15    None  None   None       |
|    all(noH): 2823   0      0.00    116.66  17.15    None  None   None       |
|    Sol.    : 438    0      2.51    116.66  44.39    None  None   None       |
|    Mac.    : 2385   0      0.00    97.81   12.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.666: 1531   |   5:    58.331 -  69.997:   71        |
|      1:    11.666 -  23.332:  755   |   6:    69.997 -  81.663:   43        |
|      2:    23.332 -  34.998:  168   |   7:    81.663 -  93.329:   16        |
|      3:    34.998 -  46.665:  125   |   8:    93.329 - 104.995:    5        |
|      4:    46.665 -  58.331:  107   |   9:   104.995 - 116.661:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1268 r_free = 0.1745             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1267 r_free = 0.1744             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1744   ksol= 0.34   Bsol= 93.23   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-0.58,0.71,-0.00,0.00,0.00); trace/3= -0.46                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248941                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1740   ksol= 0.33   Bsol= 81.79   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.55,0.86,-0.00,0.00,0.00); trace/3= -0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248524                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.935693              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.554  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.644456              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.342  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1266      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1740      final r-factor (free) = 0.1698          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8097 = 2.94 * 0.50 * 5.2681 + 1.00 * 0.0770                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7519 = 2.94 * 0.50 * 5.2288 + 1.00 * 0.0768                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1698      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3827 = 0.64 * 1.00 * 5.2288 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3699 = 0.64 * 1.00 * 5.2093 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.93  16.77    None  None   None       |
|    all(noH): 2823   0      0.00    116.93  16.77    None  None   None       |
|    Sol.    : 438    0      1.10    116.93  43.57    None  None   None       |
|    Mac.    : 2385   0      0.00    97.43   11.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.693: 1606   |   5:    58.465 -  70.158:   66        |
|      1:    11.693 -  23.386:  697   |   6:    70.158 -  81.851:   42        |
|      2:    23.386 -  35.079:  155   |   7:    81.851 -  93.545:   15        |
|      3:    35.079 -  46.772:  134   |   8:    93.545 - 105.238:    5        |
|      4:    46.772 -  58.465:  101   |   9:   105.238 - 116.931:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1690             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1193 r_free = 0.1690             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1690   ksol= 0.33   Bsol= 81.79   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.55,0.86,-0.00,0.00,0.00); trace/3= -0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.205074                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1385  153 0.0990 0.1312      5.3988      5.5483|
|  2:  4.8215 -  3.8473 0.99   1319  150 0.0837 0.1099      5.4327      5.6461|
|  3:  3.8473 -  3.3670 0.99   1310  144 0.1085 0.1528      5.5007      5.8653|
|  4:  3.3670 -  3.0619 0.99   1297  138 0.1285 0.1716      5.5134      5.6595|
|  5:  3.0619 -  2.8440 0.99   1275  144 0.1506 0.1953      5.4365      5.6438|
|  6:  2.8440 -  2.6773 0.99   1292  147 0.1351 0.2165      5.3114      5.5903|
|  7:  2.6773 -  2.5438 0.99   1273  142 0.1403 0.1770      5.2513      5.4091|
|  8:  2.5438 -  2.4336 0.98   1276  137 0.1302 0.1826      5.1652       5.436|
|  9:  2.4336 -  2.3402 0.98   1249  143 0.1260 0.1912      5.0973      5.3449|
| 10:  2.3402 -  2.2597 0.99   1277  139 0.1220 0.1843      5.0367      5.2867|
| 11:  2.2597 -  2.1893 0.98   1259  140 0.1249 0.1919      5.0191      5.2518|
| 12:  2.1893 -  2.1269 0.97   1246  139 0.1232 0.1881      4.9524      5.3207|
| 13:  2.1269 -  2.0710 1.00   1256  140 0.1183 0.1917      4.8552      5.1137|
| 14:  2.0710 -  2.0206 0.72    916  103 0.1084 0.1765      4.7049      4.9776|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1385   153  0.94   9.52   0.96     0.93       7809.59|
|  2:  4.8215 -  3.8473  1319   150  0.95   8.13   1.00     0.98       9164.48|
|  3:  3.8473 -  3.3670  1310   144  0.93  11.42   1.02     1.01      10812.37|
|  4:  3.3670 -  3.0619  1297   138  0.91  14.73   1.00     0.98      11628.55|
|  5:  3.0619 -  2.8440  1275   144  0.89  17.61   1.00     0.97      10081.80|
|  6:  2.8440 -  2.6773  1292   147  0.88  17.90   0.98     0.96       8763.71|
|  7:  2.6773 -  2.5438  1273   142  0.89  17.56   0.99     0.95       7407.61|
|  8:  2.5438 -  2.4336  1276   137  0.90  16.32   0.98     0.95       6245.17|
|  9:  2.4336 -  2.3402  1249   143  0.90  16.59   0.99     0.95       5698.43|
| 10:  2.3402 -  2.2597  1277   139  0.89  16.78   0.98     0.93       4958.71|
| 11:  2.2597 -  2.1893  1259   140  0.89  17.56   0.98     0.93       5074.05|
| 12:  2.1893 -  2.1269  1246   139  0.89  17.11   0.99     0.98       4607.47|
| 13:  2.1269 -  2.0710  1256   140  0.90  16.61   0.97     0.95       3804.17|
| 14:  2.0710 -  2.0206   916   103  0.91  14.93   0.94     0.90       2692.35|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2692.35 max =        11628.55 mean =      7178.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        15.14|
|phase err.(test): min =        0.00 max =           89.11 mean =        14.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1690   ksol= 0.32   Bsol= 75.97   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.55,0.84,-0.00,0.00,0.00); trace/3= -0.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.204822                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1690   ksol= 0.32   Bsol= 75.97   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.55,0.84,-0.00,0.00,0.00); trace/3= -0.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.204822                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1385  153 0.0987 0.1309      5.3945      5.5459|
|  2:  4.8215 -  3.8473 0.99   1319  150 0.0835 0.1097      5.4312      5.6436|
|  3:  3.8473 -  3.3670 0.99   1310  144 0.1085 0.1528      5.5002      5.8663|
|  4:  3.3670 -  3.0619 0.99   1297  138 0.1287 0.1717      5.5146      5.6601|
|  5:  3.0619 -  2.8440 0.99   1275  144 0.1507 0.1952      5.4375      5.6445|
|  6:  2.8440 -  2.6773 0.99   1292  147 0.1351 0.2168       5.312      5.5912|
|  7:  2.6773 -  2.5438 0.99   1273  142 0.1404 0.1772       5.252      5.4099|
|  8:  2.5438 -  2.4336 0.98   1276  137 0.1303 0.1824      5.1658      5.4362|
|  9:  2.4336 -  2.3402 0.98   1249  143 0.1259 0.1912      5.0971      5.3451|
| 10:  2.3402 -  2.2597 0.99   1277  139 0.1220 0.1845      5.0363      5.2872|
| 11:  2.2597 -  2.1893 0.98   1259  140 0.1249 0.1916      5.0189      5.2509|
| 12:  2.1893 -  2.1269 0.97   1246  139 0.1231 0.1878      4.9523      5.3197|
| 13:  2.1269 -  2.0710 1.00   1256  140 0.1183 0.1922      4.8552      5.1147|
| 14:  2.0710 -  2.0206 0.72    916  103 0.1084 0.1764      4.7052       4.977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1385   153  0.94   9.49   0.96     0.93       7757.79|
|  2:  4.8215 -  3.8473  1319   150  0.95   8.11   1.00     0.98       9125.26|
|  3:  3.8473 -  3.3670  1310   144  0.93  11.40   1.02     1.01      10791.37|
|  4:  3.3670 -  3.0619  1297   138  0.91  14.74   1.00     0.98      11646.38|
|  5:  3.0619 -  2.8440  1275   144  0.89  17.62   1.00     0.97      10100.97|
|  6:  2.8440 -  2.6773  1292   147  0.88  17.91   0.98     0.96       8778.56|
|  7:  2.6773 -  2.5438  1273   142  0.89  17.57   0.99     0.95       7418.82|
|  8:  2.5438 -  2.4336  1276   137  0.90  16.32   0.98     0.95       6249.07|
|  9:  2.4336 -  2.3402  1249   143  0.90  16.59   0.99     0.95       5702.10|
| 10:  2.3402 -  2.2597  1277   139  0.89  16.77   0.98     0.93       4953.36|
| 11:  2.2597 -  2.1893  1259   140  0.89  17.54   0.98     0.93       5069.01|
| 12:  2.1893 -  2.1269  1246   139  0.89  17.09   0.99     0.98       4605.52|
| 13:  2.1269 -  2.0710  1256   140  0.90  16.61   0.97     0.95       3803.44|
| 14:  2.0710 -  2.0206   916   103  0.91  14.92   0.95     0.91       2690.96|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2690.96 max =        11646.38 mean =      7173.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        15.13|
|phase err.(test): min =        0.00 max =           89.01 mean =        14.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.452)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.93  16.77    None  None   None       |
|    all(noH): 2823   0      0.00    116.93  16.77    None  None   None       |
|    Sol.    : 438    0      1.10    116.93  43.58    None  None   None       |
|    Mac.    : 2385   0      0.00    97.43   11.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.696: 1606   |   5:    58.468 -  70.161:   66        |
|      1:    11.696 -  23.389:  697   |   6:    70.161 -  81.854:   42        |
|      2:    23.389 -  35.082:  155   |   7:    81.854 -  93.547:   15        |
|      3:    35.082 -  46.775:  134   |   8:    93.547 - 105.241:    5        |
|      4:    46.775 -  58.468:  101   |   9:   105.241 - 116.934:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.625
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 317
   mapped sites are within: 0.722 - 4.625

peak=    5.688 closest distance to " O   HOH Z 210 " =    1.101
peak=    5.479 closest distance to " CB  GLN A 223 " =    1.482
peak=    5.086 closest distance to " CZ  PHE A 218 " =    1.143
peak=    5.063 closest distance to " O   HOH Z 113 " =    1.958
peak=    4.873 closest distance to " CB  ARG A 190 " =    1.585
peak=    4.837 closest distance to " CB  SER A  63 " =    1.193
peak=    4.734 closest distance to " CG  PRO A  54 " =    1.345
peak=    4.623 closest distance to " O   HOH Z 369 " =    2.157
peak=    4.548 closest distance to " CD  ARG A 269 " =    0.972
peak=    4.537 closest distance to " CB  GLN A 183 " =    1.287
peak=    4.469 closest distance to " O   HOH Z  49 " =    1.247
peak=    4.399 closest distance to " CZ3 TRP A 266 " =    1.144
peak=    4.372 closest distance to " CA  TYR A  30 " =    0.994
peak=    4.347 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.345 closest distance to " CA  ALA A  51 " =    0.987
peak=    4.331 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.319 closest distance to " CB  ARG A 275 " =    1.027
peak=    4.301 closest distance to " CB  GLU A 277 " =    3.862
peak=    4.274 closest distance to " CZ  PHE A  38 " =    1.202
peak=    4.237 closest distance to " O   HOH Z 298 " =    2.035
peak=    4.225 closest distance to " O   HOH Z 234 " =    3.897
peak=    4.199 closest distance to " CB  TRP A 266 " =    1.079
peak=    4.175 closest distance to " CB  VAL A 202 " =    1.537
peak=    4.171 closest distance to " CB  VAL A 265 " =    1.259
peak=    4.146 closest distance to " NE2 GLN A  11 " =    1.045
peak=    4.144 closest distance to " CB  ARG A  79 " =    1.243
peak=    4.142 closest distance to " CD1 LEU A  96 " =    0.853
peak=    4.135 closest distance to " CD  LYS A 166 " =    1.420
peak=    4.131 closest distance to " CD2 TRP A 179 " =    1.272
peak=    4.129 closest distance to " O   HOH Z 368 " =    2.233
peak=    4.127 closest distance to " O   HOH Z 189 " =    2.889
peak=    4.109 closest distance to " CG  PRO A 213 " =    1.161
peak=    4.108 closest distance to " O   PRO A 198 " =    1.569
peak=    4.093 closest distance to " NH1AARG A 145 " =    1.367
peak=    4.083 closest distance to " CA  ARG A 195 " =    1.201
peak=    4.075 closest distance to " CA  ALA A 160 " =    0.991
peak=    4.071 closest distance to " CB  PRO A  54 " =    0.935
peak=    4.016 closest distance to " O   HOH Z 412 " =    3.782
peak=    4.012 closest distance to " CA  ALA A 295 " =    1.085
peak=    4.000 closest distance to " CA  ARG A  36 " =    1.110
peak=    3.997 closest distance to " O   HOH Z  21 " =    1.845
peak=    3.994 closest distance to " O   HOH Z 142 " =    1.682
peak=    3.978 closest distance to " O   HOH Z 214 " =    1.362
peak=    3.972 closest distance to " CB  TYR A 169 " =    0.852
peak=    3.954 closest distance to " ND2 ASN A 187 " =    1.496
peak=    3.948 closest distance to " CG  PRO A 243 " =    1.073
peak=    3.933 closest distance to " CD  ARG A  66 " =    2.460
peak=    3.932 closest distance to " O   HOH Z  19 " =    1.989
peak=    3.928 closest distance to " O   HOH Z 248 " =    1.653
peak=    3.920 closest distance to " O   HOH Z 214 " =    2.487
peak=    3.915 closest distance to " CB  GLU A 128 " =    1.012
peak=    3.911 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.888 closest distance to " O   HOH Z 176 " =    1.595
peak=    3.883 closest distance to " O   HOH Z 427 " =    3.135
peak=    3.883 closest distance to " CB  ASN A  39 " =    0.892
peak=    3.880 closest distance to " CA  GLU A 152 " =    0.957
peak=    3.878 closest distance to " O   HOH Z 287 " =    1.859
peak=    3.869 closest distance to " O   HOH Z  54 " =    0.942
peak=    3.867 closest distance to " CA  VAL A 125 " =    1.315
peak=    3.852 closest distance to " O   ASN A  74 " =    1.561
peak=    3.826 closest distance to " CB  ASP A 140 " =    1.019
peak=    3.825 closest distance to " CA  TYR A  30 " =    1.060
peak=    3.808 closest distance to " O   HOH Z 346 " =    1.507
peak=    3.789 closest distance to " O   HOH Z  43 " =    1.976
peak=    3.786 closest distance to " CB  PRO A  90 " =    1.261
peak=    3.781 closest distance to " CB  GLU A 152 " =    1.207
peak=    3.767 closest distance to " CB  LEU A 228 " =    1.084
peak=    3.765 closest distance to " CG  MET A 185 " =    1.266
peak=    3.756 closest distance to " CB  ASP A 124 " =    0.722
peak=    3.751 closest distance to " O   HOH Z 406 " =    1.668
peak=    3.741 closest distance to " CA  ALA A 100 " =    0.971
peak=    3.739 closest distance to " O   SER A  87 " =    2.418
peak=    3.738 closest distance to " O   HOH Z 423 " =    1.839
peak=    3.736 closest distance to " O   TYR A 116 " =    1.332
peak=    3.733 closest distance to " CB  LEU A  83 " =    0.799
peak=    3.732 closest distance to " O   HOH Z 148 " =    3.433
peak=    3.730 closest distance to " O   HOH Z 193 " =    1.830
peak=    3.727 closest distance to " CG  ARG A 138 " =    1.264
peak=    3.724 closest distance to " O   HOH Z 261 " =    1.955
peak=    3.723 closest distance to " O   HOH Z 303 " =    2.345
peak=    3.718 closest distance to " O   HOH Z 361 " =    3.505
peak=    3.717 closest distance to " O   HOH Z 425 " =    1.375
peak=    3.709 closest distance to " OE1 GLN A  55 " =    1.476
peak=    3.707 closest distance to " CG2AVAL A 121 " =    2.292
peak=    3.705 closest distance to " O   THR A 220 " =    1.147
peak=    3.705 closest distance to " CG1 VAL A 153 " =    1.054
peak=    3.702 closest distance to " O   HOH Z 353 " =    2.738
peak=    3.695 closest distance to " O   ALA A 165 " =    1.392
peak=    3.694 closest distance to " O   HOH Z 271 " =    2.577
peak=    3.693 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.682 closest distance to " CG  GLU A  37 " =    0.966
peak=    3.676 closest distance to " N   HIS A 108 " =    1.927
peak=    3.676 closest distance to " CE  LYS A  76 " =    0.842
peak=    3.670 closest distance to " OG  SER A 245 " =    1.664
peak=    3.664 closest distance to " CG2 THR A 221 " =    0.985
peak=    3.659 closest distance to " CB  SER A 141 " =    1.135
peak=    3.654 closest distance to " O   HOH Z 265 " =    2.149
peak=    3.649 closest distance to " CD1 LEU A 300 " =    1.089
peak=    3.644 closest distance to " NE2 GLN A  77 " =    3.481
peak=    3.637 closest distance to " O   HOH Z 383 " =    2.055
peak=    3.630 closest distance to " O   HOH Z  80 " =    1.900
peak=    3.627 closest distance to " CB  ASN A 148 " =    1.514
peak=    3.619 closest distance to " CA  MET A 105 " =    1.061
peak=    3.618 closest distance to " O   HOH Z 402 " =    1.484
peak=    3.614 closest distance to " O   HOH Z 251 " =    1.598
peak=    3.603 closest distance to " O   HOH Z 359 " =    1.697
peak=    3.601 closest distance to " CB  GLN A  89 " =    1.288
peak=    3.600 closest distance to " O   HOH Z  76 " =    1.127
peak=    3.598 closest distance to " CB  ALA A 291 " =    1.090
peak=    3.595 closest distance to " CD  ARG A  66 " =    2.403
peak=    3.594 closest distance to " CB  TRP A 179 " =    1.396
peak=    3.593 closest distance to " CG  LEU A 167 " =    1.167
peak=    3.576 closest distance to " O   HOH Z 133 " =    2.892
peak=    3.575 closest distance to " CA  ALA A 154 " =    1.040
peak=    3.573 closest distance to " CD2 LEU A 297 " =    0.926
peak=    3.567 closest distance to " NZ  LYS A 117 " =    2.968
peak=    3.560 closest distance to " OE1 GLN A  88 " =    0.782
peak=    3.556 closest distance to " CB  ASN A 142 " =    1.002
peak=    3.551 closest distance to " O   HOH Z 280 " =    2.926
peak=    3.550 closest distance to " CA  PRO A  54 " =    1.392
peak=    3.548 closest distance to " CA  ARG A 139 " =    1.182
peak=    3.546 closest distance to " O   HOH Z 285 " =    2.341
peak=    3.536 closest distance to " O  BHOH Z 338 " =    2.297
peak=    3.534 closest distance to " CG2 VAL A 257 " =    0.777
peak=    3.531 closest distance to " N   ASN A  39 " =    1.313
peak=    3.525 closest distance to " CB  SER A  62 " =    0.800
peak=    3.520 closest distance to " O   HOH Z 134 " =    1.153
peak=    3.519 closest distance to " CD2 LEU A 255 " =    1.713
peak=    3.517 closest distance to " ND2 ASN A 249 " =    0.883
peak=    3.516 closest distance to " O   HOH Z 258 " =    1.984
peak=    3.515 closest distance to " CA  ILE A 106 " =    0.833
peak=    3.512 closest distance to " O   ASP A 124 " =    1.229
peak=    3.511 closest distance to " CB  SER A 210 " =    0.848
peak=    3.508 closest distance to " O   HOH Z 366 " =    2.639
peak=    3.505 closest distance to " O   HOH Z 126 " =    2.105
peak=    3.501 closest distance to " O   HOH Z 325 " =    2.258
peak=    3.500 closest distance to " O   HOH Z 180 " =    2.168
peak=    3.500 closest distance to " O   HOH Z 130 " =    2.246
peak=    3.497 closest distance to " NH2 ARG A 156 " =    1.138
peak=    3.495 closest distance to " O   THR A 182 " =    1.428
peak=    3.494 closest distance to " CA  ASP A 162 " =    1.072
peak=    3.488 closest distance to " CA  GLU A  46 " =    0.807
peak=    3.483 closest distance to " CB  ALA A  43 " =    0.888
peak=    3.483 closest distance to " O   HOH Z  48 " =    1.705
peak=    3.482 closest distance to " O   HOH Z 213 " =    1.968
peak=    3.479 closest distance to " O   HOH Z 294 " =    1.551
peak=    3.477 closest distance to " CG1 ILE A  33 " =    1.203
peak=    3.474 closest distance to " O   HOH Z  40 " =    2.080
peak=    3.471 closest distance to " O   HOH Z 316 " =    3.134
peak=    3.470 closest distance to " CA  SER A  87 " =    1.025
peak=    3.468 closest distance to " N   ASN A 127 " =    1.328
peak=    3.467 closest distance to " NH2AARG A 275 " =    3.422
peak=    3.465 closest distance to " OD1 ASN A  69 " =    2.542
peak=    3.459 closest distance to " CB  GLN A  88 " =    1.237
peak=    3.455 closest distance to " O   HOH Z 130 " =    1.085
peak=    3.454 closest distance to " O   HOH Z  63 " =    1.832
peak=    3.452 closest distance to " CZ  PHE A 192 " =    1.067
peak=    3.443 closest distance to " O   HOH Z 174 " =    2.467
peak=    3.439 closest distance to " O   HOH Z 273 " =    1.078
peak=    3.437 closest distance to " O   HOH Z 192 " =    1.912
peak=    3.430 closest distance to " CA  ALA A 291 " =    0.832
peak=    3.428 closest distance to " OD1 ASN A 217 " =    1.547
peak=    3.424 closest distance to " O   HOH Z  78 " =    1.608
peak=    3.424 closest distance to " O   HOH Z  88 " =    3.469
peak=    3.422 closest distance to " O   HOH Z  97 " =    2.063
peak=    3.418 closest distance to " CB  GLU A  37 " =    0.868
peak=    3.416 closest distance to " CA  ARG A 156 " =    1.139
peak=    3.404 closest distance to " CG2BVAL A  41 " =    0.851
peak=    3.403 closest distance to " CG1 ILE A  20 " =    1.357
peak=    3.399 closest distance to " O   HOH Z  59 " =    2.321
peak=    3.398 closest distance to " CB  ARG A 138 " =    0.990
peak=    3.395 closest distance to " CG AARG A 275 " =    1.247
peak=    3.393 closest distance to " OG BSER A 164 " =    2.390
peak=    3.392 closest distance to " OG BSER A 134 " =    2.868
peak=    3.390 closest distance to " O   THR A 251 " =    1.157
peak=    3.387 closest distance to " O   HOH Z 299 " =    4.429
peak=    3.387 closest distance to " CB  GLU A  46 " =    0.939
peak=    3.384 closest distance to " O   HOH Z 158 " =    2.985
peak=    3.383 closest distance to " OG  SER A  22 " =    2.799
peak=    3.379 closest distance to " ND1 HIS A  81 " =    1.708
peak=    3.369 closest distance to " CG2 THR A 220 " =    0.844
peak=    3.367 closest distance to " ND2 ASN A 249 " =    1.975
peak=    3.365 closest distance to " CB  LEU A  96 " =    1.380
peak=    3.360 closest distance to " CA  ASN A 215 " =    1.051
peak=    3.357 closest distance to " CH2 TRP A  70 " =    0.922
peak=    3.357 closest distance to " CG  PHE A 204 " =    0.848
peak=    3.357 closest distance to " CG  GLN A  11 " =    1.571
peak=    3.351 closest distance to " CA  TYR A 116 " =    1.360
peak=    3.348 closest distance to " O   HOH Z 357 " =    2.733
peak=    3.343 closest distance to " O   HOH Z 422 " =    2.601
peak=    3.342 closest distance to " O   HOH Z 125 " =    3.787
peak=    3.341 closest distance to " O   HOH Z 116 " =    3.234
peak=    3.338 closest distance to " CG2 ILE A 234 " =    0.993
peak=    3.338 closest distance to " CA  ALA A 158 " =    1.325
peak=    3.338 closest distance to " O   HOH Z 207 " =    1.205
peak=    3.338 closest distance to " OH  TYR A 116 " =    1.114
peak=    3.337 closest distance to " O   HOH Z 357 " =    2.077
peak=    3.337 closest distance to " OD2 ASP A  50 " =    3.020
peak=    3.336 closest distance to " CB  PRO A 243 " =    1.492
peak=    3.335 closest distance to " OG  SER A 135 " =    1.296
peak=    3.334 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.334 closest distance to " O   HOH Z 305 " =    3.663
peak=    3.333 closest distance to " O   HOH Z   9 " =    2.220
peak=    3.332 closest distance to " O   HOH Z 393 " =    3.104
peak=    3.329 closest distance to " O   HOH Z 290 " =    1.058
peak=    3.329 closest distance to " CB  LYS A 117 " =    1.168
peak=    3.328 closest distance to " NZ  LYS A  48 " =    1.346
peak=    3.327 closest distance to " OE1 GLN A  11 " =    2.087
peak=    3.326 closest distance to " NH2BARG A 145 " =    2.243
peak=    3.325 closest distance to " O   HOH Z  63 " =    2.400
peak=    3.321 closest distance to " O   PRO A 213 " =    1.465
peak=    3.321 closest distance to " O   HOH Z 285 " =    2.116
peak=    3.316 closest distance to " CE1 HIS A 115 " =    0.965
peak=    3.315 closest distance to " O   HOH Z 380 " =    1.965
peak=    3.315 closest distance to " CB  ALA A 248 " =    1.316
peak=    3.315 closest distance to " N   ARG A 156 " =    1.489
peak=    3.314 closest distance to " CB  ALA A 104 " =    0.785
peak=    3.312 closest distance to " O   HOH Z 193 " =    2.214
peak=    3.311 closest distance to " O   HOH Z  44 " =    2.052
peak=    3.307 closest distance to " O   ASP A 191 " =    1.451
peak=    3.307 closest distance to " O   HOH Z 361 " =    2.659
peak=    3.303 closest distance to " O   HOH Z 391 " =    3.046
peak=    3.301 closest distance to " O   HOH Z 171 " =    3.993
peak=    3.298 closest distance to " CB  ALA A 299 " =    0.874
peak=    3.297 closest distance to " CA  ASN A 127 " =    1.138
peak=    3.294 closest distance to " OG  SER A  28 " =    1.538
peak=    3.293 closest distance to " CB  ASP A 298 " =    1.173
peak=    3.287 closest distance to " O   HOH Z 211 " =    1.147
peak=    3.286 closest distance to " O   HOH Z 313 " =    1.545
peak=    3.285 closest distance to " O   HOH Z 365 " =    2.897
peak=    3.282 closest distance to " CA  ALA A  21 " =    1.284
peak=    3.279 closest distance to " CG2 ILE A 120 " =    1.113
peak=    3.275 closest distance to " CA  THR A 221 " =    0.925
peak=    3.273 closest distance to " NE2 HIS A 207 " =    1.074
peak=    3.273 closest distance to " O   HOH Z 371 " =    2.906
peak=    3.273 closest distance to " O   HOH Z 146 " =    2.148
peak=    3.272 closest distance to " OD2 ASP A 298 " =    3.960
peak=    3.266 closest distance to " O   HOH Z 298 " =    2.439
peak=    3.265 closest distance to " CD1 ILE A 199 " =    1.170
peak=    3.263 closest distance to " CG1AVAL A 121 " =    0.809
peak=    3.261 closest distance to " O   HOH Z  90 " =    2.398
peak=    3.253 closest distance to " NE  ARG A  79 " =    1.020
peak=    3.251 closest distance to " N   TYR A 247 " =    1.064
peak=    3.250 closest distance to " O   HOH Z 279 " =    2.352
peak=    3.243 closest distance to " O   HOH Z 199 " =    1.620
peak=    3.238 closest distance to " O   HOH Z 183 " =    1.458
peak=    3.236 closest distance to " CA  ALA A 233 " =    1.665
peak=    3.236 closest distance to " CD  LYS A 193 " =    2.073
peak=    3.236 closest distance to " O   HOH Z 124 " =    2.019
peak=    3.234 closest distance to " CB  ASN A 285 " =    0.968
peak=    3.234 closest distance to " CA  ASP A 124 " =    0.795
peak=    3.229 closest distance to " O   HOH Z 417 " =    3.222
peak=    3.225 closest distance to " NE2 GLN A  58 " =    4.625
peak=    3.223 closest distance to " CG2 ILE A 239 " =    0.737
peak=    3.217 closest distance to " O   HOH Z 132 " =    2.972
peak=    3.217 closest distance to " CD  PRO A  54 " =    0.964
peak=    3.217 closest distance to " OE1 GLN A 223 " =    3.578
peak=    3.216 closest distance to " CB  ASP A 107 " =    1.227
peak=    3.215 closest distance to " O   HOH Z 150 " =    1.294
peak=    3.211 closest distance to " CG2 ILE A  20 " =    1.332
peak=    3.210 closest distance to " CG  GLN A  55 " =    2.538
peak=    3.208 closest distance to " CA  GLY A  35 " =    0.897
peak=    3.208 closest distance to " CG  MET A 185 " =    1.086
peak=    3.207 closest distance to " O   HOH Z  78 " =    2.050
peak=    3.202 closest distance to " N   TYR A  15 " =    0.818
peak=    3.199 closest distance to " N   VAL A 265 " =    1.309
peak=    3.197 closest distance to " OG  SER A   3 " =    1.713
peak=    3.196 closest distance to " O   HOH Z 343 " =    2.300
peak=    3.187 closest distance to " CD ALYS A 290 " =    0.980
peak=    3.187 closest distance to " O   HOH Z 116 " =    1.798
peak=    3.186 closest distance to " CE3 TRP A 150 " =    1.140
peak=    3.185 closest distance to " CB  TYR A 116 " =    0.914
peak=    3.183 closest distance to " CA  MET A 188 " =    1.058
peak=    3.181 closest distance to " O   HOH Z  88 " =    1.824
peak=    3.175 closest distance to " O   HOH Z 336 " =    4.378
peak=    3.172 closest distance to " CE1 HIS A 108 " =    1.064
peak=    3.170 closest distance to " CB  GLN A 103 " =    0.865
peak=    3.170 closest distance to " O   HOH Z 394 " =    1.802
peak=    3.169 closest distance to " O   HOH Z 291 " =    1.469
peak=    3.166 closest distance to " CG  ARG A 219 " =    1.114
peak=    3.157 closest distance to " O   ASN A 209 " =    1.316
peak=    3.152 closest distance to " O   HOH Z 368 " =    4.255
peak=    3.152 closest distance to " CA  ASP A 140 " =    1.473
peak=    3.151 closest distance to " N   ILE A  33 " =    0.969
peak=    3.149 closest distance to " O   ALA A 158 " =    1.246
peak=    3.145 closest distance to " O   HOH Z 392 " =    2.662
peak=    3.145 closest distance to " O   HOH Z 203 " =    1.680
peak=    3.142 closest distance to " NE1 TRP A  92 " =    1.810
peak=    3.139 closest distance to " O   HOH Z 403 " =    1.534
peak=    3.134 closest distance to " CB  LEU A 300 " =    0.936
peak=    3.133 closest distance to " O   HOH Z 287 " =    2.197
peak=    3.133 closest distance to " CB  PHE A 204 " =    0.860
peak=    3.132 closest distance to " CA  ASP A 191 " =    0.984
peak=    3.130 closest distance to " CB  MET A  47 " =    0.911
peak=    3.129 closest distance to " O   HOH Z 327 " =    1.837
peak=    3.124 closest distance to " O   ASP A 200 " =    1.693
peak=    3.119 closest distance to " CA  THR A 264 " =    0.824
peak=    3.119 closest distance to " CD  LYS A  76 " =    1.922
peak=    3.113 closest distance to " O   HOH Z 350 " =    1.944
peak=    3.112 closest distance to " CB  ARG A 156 " =    0.992
peak=    3.110 closest distance to " C   ALA A 299 " =    1.120
peak=    3.103 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.101 closest distance to " CD1 ILE A  33 " =    1.822
peak=    3.100 closest distance to " O   PHE A  61 " =    1.412
peak=    3.098 closest distance to " O   HOH Z  88 " =    2.725
peak=    3.097 closest distance to " CG1 ILE A  49 " =    1.556
peak=    3.097 closest distance to " CB  SER A 216 " =    1.010
peak=    3.084 closest distance to " CD  PRO A 213 " =    1.513
peak=    3.068 closest distance to " O   HOH Z 353 " =    2.698
peak=    3.059 closest distance to " CA  THR A 221 " =    1.452
peak=    3.057 closest distance to " OG1 THR A 279 " =    1.855
peak=    3.031 closest distance to " O   HOH Z 272 " =    1.871
peak=    3.003 closest distance to " O   ASP A 124 " =    1.780

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.834 - 5.980
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 220
   mapped sites are within: 0.834 - 5.980

peak=   -4.647 closest distance to " CB  PRO A 243 " =    2.747
peak=   -4.635 closest distance to " CG1 VAL A 250 " =    2.730
peak=   -4.610 closest distance to " CG1 VAL A 112 " =    2.592
peak=   -4.405 closest distance to " O   HOH Z  10 " =    1.582
peak=   -4.283 closest distance to " O   PRO A 198 " =    1.367
peak=   -4.230 closest distance to " CD  ARG A 156 " =    2.125
peak=   -4.198 closest distance to " O   HOH Z 266 " =    5.677
peak=   -4.188 closest distance to " CD  ARG A  14 " =    3.413
peak=   -4.179 closest distance to " O   HOH Z 196 " =    2.341
peak=   -4.125 closest distance to " CD  GLN A 223 " =    1.350
peak=   -4.088 closest distance to " CE2 PHE A  61 " =    2.639
peak=   -4.058 closest distance to " CA  ASP A 298 " =    1.096
peak=   -4.024 closest distance to " CD2 TYR A 293 " =    1.986
peak=   -3.999 closest distance to " CH2 TRP A 179 " =    1.197
peak=   -3.990 closest distance to " O   HOH Z 283 " =    2.444
peak=   -3.969 closest distance to " CG  ARG A 269 " =    2.393
peak=   -3.941 closest distance to " CA  VAL A  67 " =    3.068
peak=   -3.940 closest distance to " CG2 ILE A  49 " =    2.787
peak=   -3.938 closest distance to " O   HOH Z 211 " =    1.066
peak=   -3.934 closest distance to " O   HOH Z 394 " =    1.596
peak=   -3.893 closest distance to " O   HOH Z 166 " =    1.705
peak=   -3.891 closest distance to " O   HOH Z 368 " =    1.795
peak=   -3.882 closest distance to " N   ALA A  43 " =    2.761
peak=   -3.879 closest distance to " O   HOH Z 128 " =    2.710
peak=   -3.875 closest distance to " O   GLY A 136 " =    2.387
peak=   -3.854 closest distance to " CD  GLN A  58 " =    0.905
peak=   -3.854 closest distance to " CE2 TYR A  30 " =    2.715
peak=   -3.840 closest distance to " OD1 ASN A 148 " =    1.441
peak=   -3.834 closest distance to " OG  SER A  97 " =    2.326
peak=   -3.829 closest distance to " O   HOH Z 193 " =    1.393
peak=   -3.823 closest distance to " O   VAL A  67 " =    2.719
peak=   -3.820 closest distance to " CD1 LEU A 101 " =    2.453
peak=   -3.810 closest distance to " O   HOH Z 150 " =    1.397
peak=   -3.800 closest distance to " NE2 GLN A 194 " =    2.029
peak=   -3.799 closest distance to " O   HOH Z 185 " =    2.384
peak=   -3.798 closest distance to " O   HOH Z 348 " =    2.292
peak=   -3.795 closest distance to " CD  GLN A  88 " =    0.919
peak=   -3.774 closest distance to " O   HOH Z 114 " =    1.008
peak=   -3.759 closest distance to " CB  ALA A  10 " =    2.255
peak=   -3.758 closest distance to " CB  ALA A 291 " =    2.491
peak=   -3.754 closest distance to " C   HIS A 108 " =    1.054
peak=   -3.741 closest distance to " O   HOH Z 377 " =    2.007
peak=   -3.726 closest distance to " CG  MET A 105 " =    0.995
peak=   -3.724 closest distance to " O   HOH Z 438 " =    3.127
peak=   -3.716 closest distance to " CA  GLY A 241 " =    3.310
peak=   -3.710 closest distance to " CB  HIS A  86 " =    1.175
peak=   -3.698 closest distance to " CG  GLN A  11 " =    1.542
peak=   -3.697 closest distance to " O   HOH Z 149 " =    2.183
peak=   -3.685 closest distance to " O   HOH Z  37 " =    1.948
peak=   -3.681 closest distance to " O   ALA A  34 " =    2.536
peak=   -3.662 closest distance to " O   SER A 210 " =    1.905
peak=   -3.654 closest distance to " CD1 PHE A  59 " =    2.129
peak=   -3.652 closest distance to " O   HOH Z  64 " =    1.466
peak=   -3.631 closest distance to " O   HOH Z 216 " =    0.834
peak=   -3.630 closest distance to " CD  ARG A  79 " =    1.254
peak=   -3.624 closest distance to " O   HOH Z 234 " =    4.531
peak=   -3.619 closest distance to " CB  ALA A 161 " =    2.609
peak=   -3.617 closest distance to " C   ASN A 285 " =    2.443
peak=   -3.614 closest distance to " OE1 GLN A 223 " =    2.352
peak=   -3.606 closest distance to " O   HOH Z 407 " =    3.564
peak=   -3.600 closest distance to " O   HOH Z 421 " =    3.669
peak=   -3.591 closest distance to " O   HOH Z 106 " =    2.035
peak=   -3.585 closest distance to " CG  LYS A 193 " =    2.689
peak=   -3.582 closest distance to " ND2 ASN A  45 " =    2.153
peak=   -3.573 closest distance to " O   HOH Z 150 " =    2.226
peak=   -3.569 closest distance to " O   TYR A 186 " =    1.835
peak=   -3.560 closest distance to " CE3 TRP A 150 " =    2.227
peak=   -3.558 closest distance to " O   HOH Z 357 " =    1.956
peak=   -3.557 closest distance to " CG  ARG A  66 " =    2.360
peak=   -3.548 closest distance to " CG  GLU A  53 " =    1.658
peak=   -3.544 closest distance to " C   GLY A  17 " =    1.261
peak=   -3.543 closest distance to " CA  GLY A 241 " =    2.372
peak=   -3.539 closest distance to " CB  ALA A 129 " =    2.495
peak=   -3.534 closest distance to " OD1 ASP A 171 " =    1.557
peak=   -3.525 closest distance to " CG  GLU A 277 " =    1.268
peak=   -3.520 closest distance to " CG2 VAL A 189 " =    2.217
peak=   -3.512 closest distance to " O   HOH Z  52 " =    1.560
peak=   -3.506 closest distance to " CB  TRP A  85 " =    2.578
peak=   -3.498 closest distance to " O   HOH Z 154 " =    1.473
peak=   -3.495 closest distance to " O   HOH Z 264 " =    1.747
peak=   -3.490 closest distance to " CG1 VAL A 265 " =    2.369
peak=   -3.487 closest distance to " ND2 ASN A 249 " =    2.402
peak=   -3.479 closest distance to " O   HOH Z 426 " =    1.742
peak=   -3.476 closest distance to " O   HOH Z   6 " =    2.288
peak=   -3.476 closest distance to " O   HOH Z  38 " =    1.497
peak=   -3.465 closest distance to " O   SER A 276 " =    1.806
peak=   -3.464 closest distance to " CE3 TRP A  70 " =    1.863
peak=   -3.452 closest distance to " O   HOH Z   6 " =    1.400
peak=   -3.450 closest distance to " O   HOH Z  60 " =    2.348
peak=   -3.441 closest distance to " O   HOH Z 111 " =    1.647
peak=   -3.441 closest distance to " CB  PHE A  16 " =    2.544
peak=   -3.439 closest distance to " CD1 TRP A  70 " =    1.100
peak=   -3.439 closest distance to " CG2 THR A 221 " =    2.345
peak=   -3.435 closest distance to " O   HOH Z 371 " =    1.439
peak=   -3.423 closest distance to " CD2 PHE A  61 " =    2.112
peak=   -3.421 closest distance to " OH  TYR A 247 " =    2.293
peak=   -3.420 closest distance to " CG  GLN A  58 " =    1.185
peak=   -3.413 closest distance to " CA  GLY A 203 " =    2.465
peak=   -3.411 closest distance to " OG BSER A 134 " =    1.404
peak=   -3.406 closest distance to " O   ALA A  10 " =    1.653
peak=   -3.405 closest distance to " O   HOH Z 232 " =    1.654
peak=   -3.401 closest distance to " CB  ALA A  43 " =    2.681
peak=   -3.400 closest distance to " O   HOH Z  78 " =    1.996
peak=   -3.389 closest distance to " OD2 ASP A 171 " =    1.863
peak=   -3.380 closest distance to " CD2 LEU A 237 " =    2.943
peak=   -3.369 closest distance to " SG ACYS A 201 " =    1.172
peak=   -3.369 closest distance to " CG  PRO A 243 " =    1.774
peak=   -3.358 closest distance to " O   HOH Z 298 " =    2.602
peak=   -3.357 closest distance to " CE BMET A  47 " =    2.048
peak=   -3.356 closest distance to " O   HOH Z 290 " =    1.167
peak=   -3.341 closest distance to " CG1BVAL A  72 " =    2.448
peak=   -3.339 closest distance to " CG1 VAL A 125 " =    1.926
peak=   -3.339 closest distance to " O   HOH Z  60 " =    1.617
peak=   -3.337 closest distance to " CA  GLY A 133 " =    2.418
peak=   -3.336 closest distance to " CD1 LEU A   5 " =    2.552
peak=   -3.336 closest distance to " CE1 PHE A 225 " =    2.332
peak=   -3.336 closest distance to " CB  ASP A 132 " =    2.384
peak=   -3.335 closest distance to " O   PRO A 163 " =    2.063
peak=   -3.332 closest distance to " O   HOH Z 191 " =    5.980
peak=   -3.330 closest distance to " O   HOH Z 196 " =    2.037
peak=   -3.330 closest distance to " O   HOH Z 174 " =    2.363
peak=   -3.329 closest distance to " O   HOH Z 171 " =    2.313
peak=   -3.322 closest distance to " O   HOH Z 359 " =    2.988
peak=   -3.318 closest distance to " O   HOH Z  19 " =    2.191
peak=   -3.316 closest distance to " O   GLN A  94 " =    2.238
peak=   -3.312 closest distance to " NE2 GLN A 103 " =    1.831
peak=   -3.311 closest distance to " NE2 HIS A  86 " =    1.145
peak=   -3.306 closest distance to " O   HOH Z 396 " =    1.970
peak=   -3.303 closest distance to " NE2 GLN A 240 " =    1.846
peak=   -3.302 closest distance to " CD2 PHE A 225 " =    1.194
peak=   -3.301 closest distance to " OD1 ASN A 173 " =    1.342
peak=   -3.296 closest distance to " CG1 VAL A 112 " =    2.762
peak=   -3.295 closest distance to " CG  PRO A 163 " =    2.017
peak=   -3.292 closest distance to " CH2 TRP A 150 " =    1.199
peak=   -3.291 closest distance to " CD2 HIS A 207 " =    2.270
peak=   -3.288 closest distance to " CZ3 TRP A 274 " =    2.346
peak=   -3.287 closest distance to " CG2BVAL A  41 " =    1.938
peak=   -3.285 closest distance to " O   VAL A 189 " =    1.817
peak=   -3.284 closest distance to " O   HOH Z 174 " =    3.726
peak=   -3.284 closest distance to " CE  MET A  93 " =    1.830
peak=   -3.282 closest distance to " O   HOH Z 133 " =    1.374
peak=   -3.277 closest distance to " C   ARG A  79 " =    2.658
peak=   -3.273 closest distance to " O   HOH Z 198 " =    2.054
peak=   -3.268 closest distance to " O   HOH Z 278 " =    1.287
peak=   -3.265 closest distance to " O   SER A 271 " =    2.089
peak=   -3.264 closest distance to " O   HOH Z 102 " =    1.532
peak=   -3.263 closest distance to " O   HOH Z 210 " =    1.706
peak=   -3.259 closest distance to " O   HOH Z 210 " =    0.997
peak=   -3.255 closest distance to " CD  ARG A 139 " =    1.560
peak=   -3.254 closest distance to " N   THR A  52 " =    1.638
peak=   -3.250 closest distance to " CG2 THR A 178 " =    2.407
peak=   -3.249 closest distance to " OE1 GLN A 223 " =    2.225
peak=   -3.246 closest distance to " CG  GLN A 103 " =    2.554
peak=   -3.244 closest distance to " O   HOH Z 156 " =    3.499
peak=   -3.242 closest distance to " OG BSER A 210 " =    1.622
peak=   -3.242 closest distance to " ND2 ASN A 187 " =    1.672
peak=   -3.241 closest distance to " O   PHE A 218 " =    1.455
peak=   -3.241 closest distance to " CG1AVAL A  41 " =    2.659
peak=   -3.236 closest distance to " O   HOH Z 418 " =    1.354
peak=   -3.236 closest distance to " O   HOH Z 275 " =    1.640
peak=   -3.234 closest distance to " O   HOH Z 197 " =    2.031
peak=   -3.226 closest distance to " CG  LEU A  83 " =    2.168
peak=   -3.226 closest distance to " O   HOH Z 219 " =    4.469
peak=   -3.218 closest distance to " O   HOH Z 111 " =    1.834
peak=   -3.217 closest distance to " OD1 ASP A 191 " =    1.577
peak=   -3.207 closest distance to " CD  GLN A  88 " =    0.921
peak=   -3.203 closest distance to " NH2 ARG A 159 " =    2.433
peak=   -3.190 closest distance to " SD  MET A  40 " =    1.952
peak=   -3.186 closest distance to " O   HOH Z 200 " =    1.575
peak=   -3.185 closest distance to " C   ALA A 158 " =    1.500
peak=   -3.183 closest distance to " O   HOH Z 351 " =    1.732
peak=   -3.183 closest distance to " C   LEU A 143 " =    1.155
peak=   -3.182 closest distance to " O   HOH Z 145 " =    1.073
peak=   -3.182 closest distance to " O   HOH Z 357 " =    2.086
peak=   -3.179 closest distance to " O   HOH Z  71 " =    2.633
peak=   -3.179 closest distance to " CG  TRP A 266 " =    1.796
peak=   -3.179 closest distance to " O   HOH Z 189 " =    2.098
peak=   -3.178 closest distance to " O   GLY A 203 " =    2.376
peak=   -3.175 closest distance to " O   HOH Z   9 " =    2.247
peak=   -3.175 closest distance to " CB  SER A  62 " =    5.482
peak=   -3.174 closest distance to " O   HOH Z  44 " =    0.860
peak=   -3.173 closest distance to " N   SER A 276 " =    1.457
peak=   -3.172 closest distance to " CB  ALA A 248 " =    2.339
peak=   -3.171 closest distance to " CE  MET A 105 " =    2.478
peak=   -3.170 closest distance to " O   HOH Z 198 " =    1.424
peak=   -3.170 closest distance to " O   HOH Z 163 " =    5.258
peak=   -3.153 closest distance to " CZ  PHE A  38 " =    2.555
peak=   -3.152 closest distance to " OH  TYR A 247 " =    1.943
peak=   -3.150 closest distance to " O   HOH Z 275 " =    1.784
peak=   -3.148 closest distance to " NE2 GLN A 223 " =    1.367
peak=   -3.137 closest distance to " NH2 ARG A  79 " =    1.555
peak=   -3.136 closest distance to " OG1 THR A  82 " =    1.438
peak=   -3.135 closest distance to " CD1 ILE A 263 " =    1.984
peak=   -3.134 closest distance to " CD2 LEU A 222 " =    2.194
peak=   -3.134 closest distance to " CD  PRO A 243 " =    1.972
peak=   -3.134 closest distance to " O   HOH Z 285 " =    1.874
peak=   -3.126 closest distance to " O   HOH Z 251 " =    1.916
peak=   -3.126 closest distance to " O   HOH Z 236 " =    1.564
peak=   -3.125 closest distance to " O   ARG A  56 " =    4.131
peak=   -3.124 closest distance to " CB  ALA A 131 " =    2.328
peak=   -3.122 closest distance to " CG1 VAL A 112 " =    2.788
peak=   -3.122 closest distance to " OG BSER A 134 " =    2.008
peak=   -3.119 closest distance to " O   HOH Z 377 " =    1.224
peak=   -3.104 closest distance to " N   ILE A 120 " =    1.037
peak=   -3.103 closest distance to " NH2AARG A 275 " =    5.449
peak=   -3.097 closest distance to " CG  ASN A 252 " =    1.525
peak=   -3.094 closest distance to " CA  GLY A 241 " =    2.916
peak=   -3.093 closest distance to " CG1 VAL A 265 " =    2.710
peak=   -3.092 closest distance to " OG BSER A 210 " =    2.115
peak=   -3.090 closest distance to " C   GLY A 262 " =    2.165
peak=   -3.078 closest distance to " CB  PRO A 163 " =    2.544
peak=   -3.074 closest distance to " CG  ARG A 259 " =    1.430
peak=   -3.069 closest distance to " OG BSER A 212 " =    1.534
peak=   -3.069 closest distance to " N   ALA A 248 " =    1.844
peak=   -3.063 closest distance to " CZ  TYR A  68 " =    1.146
peak=   -3.050 closest distance to " CG1 VAL A  78 " =    2.577
peak=   -3.043 closest distance to " C   LEU A 222 " =    0.953
peak=   -3.035 closest distance to " CZ  TYR A 169 " =    1.870
peak=   -3.024 closest distance to " CG2 VAL A 189 " =    1.952
peak=   -3.016 closest distance to " CB  ALA A 291 " =    1.916

================= 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    :  0.4512 0.4465   6.258467e+00   6.242850e+00
   1_bss:  0.4420 0.4384   6.249201e+00   6.232641e+00
   1_xyz:  0.3280 0.3519   6.027534e+00   6.084349e+00
   1_adp:  0.2961 0.3628   5.974002e+00   6.096768e+00
   1_occ:  0.2958 0.3628   5.973735e+00   6.097119e+00
   2_bss:  0.2945 0.3606   5.973614e+00   6.097309e+00
   2_xyz:  0.2150 0.2688   5.694955e+00   5.869110e+00
   2_adp:  0.1953 0.2458   5.616389e+00   5.798050e+00
   2_occ:  0.1951 0.2459   5.616082e+00   5.798493e+00
   3_bss:  0.1950 0.2445   5.613828e+00   5.795117e+00
   3_xyz:  0.1640 0.2071   5.457619e+00   5.648062e+00
   3_adp:  0.1528 0.2026   5.410792e+00   5.623041e+00
   3_occ:  0.1528 0.2025   5.410333e+00   5.622406e+00
   4_bss:  0.1532 0.2027   5.411131e+00   5.622480e+00
   4_xyz:  0.1304 0.1797   5.279527e+00   5.515451e+00
   4_adp:  0.1268 0.1745   5.249409e+00   5.482199e+00
   4_occ:  0.1267 0.1744   5.248941e+00   5.481836e+00
   5_bss:  0.1266 0.1740   5.248524e+00   5.481040e+00
   5_xyz:  0.1205 0.1698   5.213581e+00   5.454370e+00
   5_adp:  0.1194 0.1690   5.205426e+00   5.447448e+00
   5_occ:  0.1193 0.1690   5.205074e+00   5.447345e+00
   5_bss:  0.1193 0.1690   5.204822e+00   5.447228e+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:  0.296  59.986  -2.456   1.595   4.638   0.000   0.000   0.000
   1_xyz:  0.296  59.986  -2.456   1.595   4.638   0.000   0.000   0.000
   1_adp:  0.296  59.986  -2.456   1.595   4.638   0.000   0.000   0.000
   1_occ:  0.296  59.986  -2.456   1.595   4.638   0.000   0.000   0.000
   2_bss:  0.325  77.398  -1.353   0.773   2.386   0.000   0.000   0.000
   2_xyz:  0.325  77.398  -1.353   0.773   2.386   0.000   0.000   0.000
   2_adp:  0.325  77.398  -1.353   0.773   2.386   0.000   0.000   0.000
   2_occ:  0.325  77.398  -1.353   0.773   2.386   0.000   0.000   0.000
   3_bss:  0.334  80.000  -1.403  -0.265   1.127  -0.000   0.000   0.000
   3_xyz:  0.334  80.000  -1.403  -0.265   1.127  -0.000   0.000   0.000
   3_adp:  0.334  80.000  -1.403  -0.265   1.127  -0.000   0.000   0.000
   3_occ:  0.334  80.000  -1.403  -0.265   1.127  -0.000   0.000   0.000
   4_bss:  0.339  93.227  -1.503  -0.577   0.713  -0.000   0.000   0.000
   4_xyz:  0.339  93.227  -1.503  -0.577   0.713  -0.000   0.000   0.000
   4_adp:  0.339  93.227  -1.503  -0.577   0.713  -0.000   0.000   0.000
   4_occ:  0.339  93.227  -1.503  -0.577   0.713  -0.000   0.000   0.000
   5_bss:  0.332  81.788  -1.162  -0.554   0.864  -0.000   0.000   0.000
   5_xyz:  0.332  81.788  -1.162  -0.554   0.864  -0.000   0.000   0.000
   5_adp:  0.332  81.788  -1.162  -0.554   0.864  -0.000   0.000   0.000
   5_occ:  0.332  81.788  -1.162  -0.554   0.864  -0.000   0.000   0.000
   5_bss:  0.323  75.974  -1.048  -0.554   0.837  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.978 0.4831  0.6141    59608.548
   1_bss:  52.045 0.4938  0.6599    57434.410
   1_xyz:  38.465 0.6609  0.8576    34521.718
   1_adp:  39.352 0.6497  0.8332    35928.232
   1_occ:  39.375 0.6494  0.8327    35984.227
   2_bss:  39.056 0.6534  0.8217    35826.496
   2_xyz:  27.537 0.7836  0.9498    18709.994
   2_adp:  24.447 0.8174  0.9586    15707.574
   2_occ:  24.464 0.8172  0.9582    15724.866
   3_bss:  24.269 0.8191  0.9344    15509.943
   3_xyz:  19.920 0.8625  0.9667    11021.297
   3_adp:  19.146 0.8701  0.9601    10493.399
   3_occ:  19.127 0.8703  0.9602    10476.188
   4_bss:  19.113 0.8704  0.9511    10466.833
   4_xyz:  16.797 0.8911  0.9624     8300.397
   4_adp:  15.971 0.8986  0.9551     7781.507
   4_occ:  15.959 0.8987  0.9552     7771.257
   5_bss:  15.951 0.8987  0.9611     7754.985
   5_xyz:  15.293 0.9046  0.9646     7284.961
   5_adp:  15.079 0.9066  0.9565     7183.983
   5_occ:  15.071 0.9067  0.9565     7177.139
   5_bss:  15.067 0.9067  0.9576     7172.701
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6639e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6639e-01
   1_xyz:   1.553  0.011  0.094 15.584  0.006  4.117   1.2082e-01
   1_adp:   1.553  0.011  0.094 15.584  0.006  4.117   1.2082e-01
   1_occ:   1.553  0.011  0.094 15.584  0.006  4.117   1.2082e-01
   2_bss:   1.553  0.011  0.094 15.584  0.006  4.117   1.2082e-01
   2_xyz:   1.286  0.010  0.089 14.964  0.005  4.116   8.9168e-02
   2_adp:   1.286  0.010  0.089 14.964  0.005  4.116   8.9168e-02
   2_occ:   1.286  0.010  0.089 14.964  0.005  4.116   8.9168e-02
   3_bss:   1.286  0.010  0.089 14.964  0.005  4.116   8.9168e-02
   3_xyz:   0.970  0.007  0.066 14.743  0.003  4.129   5.6808e-02
   3_adp:   0.970  0.007  0.066 14.743  0.003  4.129   5.6808e-02
   3_occ:   0.970  0.007  0.066 14.743  0.003  4.129   5.6808e-02
   4_bss:   0.970  0.007  0.066 14.743  0.003  4.129   5.6808e-02
   4_xyz:   1.137  0.011  0.084 14.903  0.004  4.117   7.7047e-02
   4_adp:   1.137  0.011  0.084 14.903  0.004  4.117   7.7047e-02
   4_occ:   1.137  0.011  0.084 14.903  0.004  4.117   7.7047e-02
   5_bss:   1.137  0.011  0.084 14.903  0.004  4.117   7.7047e-02
   5_xyz:   1.122  0.011  0.082 14.856  0.004  4.124   7.6792e-02
   5_adp:   1.122  0.011  0.082 14.856  0.004  4.124   7.6792e-02
   5_occ:   1.122  0.011  0.082 14.856  0.004  4.124   7.6792e-02
   5_bss:   1.122  0.011  0.082 14.856  0.004  4.124   7.6792e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.730   2.4564e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.730   2.4564e-01
   1_xyz:   9.908  0.060  0.384 84.383  0.057  2.064   1.3446e-01
   1_adp:   9.908  0.060  0.384 84.383  0.057  2.064   1.3446e-01
   1_occ:   9.908  0.060  0.384 84.383  0.057  2.064   1.3446e-01
   2_bss:   9.908  0.060  0.384 84.383  0.057  2.064   1.3446e-01
   2_xyz:   8.577  0.074  0.286 82.097  0.043  2.221   7.6054e-02
   2_adp:   8.577  0.074  0.286 82.097  0.043  2.221   7.6054e-02
   2_occ:   8.577  0.074  0.286 82.097  0.043  2.221   7.6054e-02
   3_bss:   8.577  0.074  0.286 82.097  0.043  2.221   7.6054e-02
   3_xyz:   7.555  0.038  0.260 82.320  0.041  2.366   4.8060e-02
   3_adp:   7.555  0.038  0.260 82.320  0.041  2.366   4.8060e-02
   3_occ:   7.555  0.038  0.260 82.320  0.041  2.366   4.8060e-02
   4_bss:   7.555  0.038  0.260 82.320  0.041  2.366   4.8060e-02
   4_xyz:   7.817  0.069  0.286 85.110  0.048  2.287   5.3940e-02
   4_adp:   7.817  0.069  0.286 85.110  0.048  2.287   5.3940e-02
   4_occ:   7.817  0.069  0.286 85.110  0.048  2.287   5.3940e-02
   5_bss:   7.817  0.069  0.286 85.110  0.048  2.287   5.3940e-02
   5_xyz:   8.041  0.051  0.285 82.397  0.041  2.396   6.4767e-02
   5_adp:   8.041  0.051  0.285 82.397  0.041  2.396   6.4767e-02
   5_occ:   8.041  0.051  0.285 82.397  0.041  2.396   6.4767e-02
   5_bss:   8.041  0.051  0.285 82.397  0.041  2.396   6.4767e-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: 115.08   0.00  18.60  85.19   0.00  14.42 115.08   0.00  41.34
   1_occ: 115.08   0.00  18.60  85.19   0.00  14.42 115.08   0.00  41.34
   2_bss: 115.08   0.00  18.60  85.19   0.00  14.42 115.08   0.00  41.34
   2_xyz: 115.08   0.00  18.60  85.19   0.00  14.42 115.08   0.00  41.34
   2_adp: 114.33   0.00  17.56  84.70   0.00  13.08 114.33   2.55  41.98
   2_occ: 114.33   0.00  17.56  84.70   0.00  13.08 114.33   2.55  41.98
   3_bss: 114.33   0.00  17.56  84.70   0.00  13.08 114.33   2.55  41.98
   3_xyz: 114.33   0.00  17.56  84.70   0.00  13.08 114.33   2.55  41.98
   3_adp: 115.89   0.00  17.95  99.32   0.00  12.74 115.89   3.87  46.33
   3_occ: 115.89   0.00  17.95  99.32   0.00  12.74 115.89   3.87  46.33
   4_bss: 115.89   0.00  17.95  99.32   0.00  12.74 115.89   3.87  46.33
   4_xyz: 115.89   0.00  17.95  99.32   0.00  12.74 115.89   3.87  46.33
   4_adp: 116.66   0.00  17.15  97.81   0.00  12.15 116.66   2.51  44.39
   4_occ: 116.66   0.00  17.15  97.81   0.00  12.15 116.66   2.51  44.39
   5_bss: 116.66   0.00  17.15  97.81   0.00  12.15 116.66   2.51  44.39
   5_xyz: 116.66   0.00  17.15  97.81   0.00  12.15 116.66   2.51  44.39
   5_adp: 116.93   0.00  16.77  97.43   0.00  11.85 116.93   1.10  43.57
   5_occ: 116.93   0.00  16.77  97.43   0.00  11.85 116.93   1.10  43.57
   5_bss: 116.93   0.00  16.77  97.43   0.00  11.85 116.93   1.10  43.58
------------------------------------------------------------------------
 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:    1.822    0.027    0.373
   1_adp:    1.822    0.027    0.373
   1_occ:    1.822    0.027    0.373
   2_bss:    1.822    0.027    0.373
   2_xyz:    1.408    0.056    0.560
   2_adp:    1.408    0.056    0.560
   2_occ:    1.408    0.056    0.560
   3_bss:    1.408    0.056    0.560
   3_xyz:    1.348    0.051    0.638
   3_adp:    1.348    0.051    0.638
   3_occ:    1.348    0.051    0.638
   4_bss:    1.348    0.051    0.638
   4_xyz:    1.277    0.071    0.695
   4_adp:    1.277    0.071    0.695
   4_occ:    1.277    0.071    0.695
   5_bss:    1.277    0.071    0.695
   5_xyz:    1.379    0.040    0.716
   5_adp:    1.379    0.040    0.716
   5_occ:    1.379    0.040    0.716
   5_bss:    1.379    0.040    0.716
------------------------------------------------------------------------

CPU time actual refinement: 350.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_945/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_945/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_945/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_945/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_945/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.08 
  Macro-tasks:
    bulk solvent and scale       = 62.26  
    individual site refinement   = 136.72 
    weights calculation          = 29.64  
    collect and process          = 6.61   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 235.37 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 102.57 
    alpha_beta                      = 8.43   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 111.99 
    fmodel                         = 10.02  
    r_factors                      = 0.41   
    phase_errors                   = 10.49  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 247.66 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.904 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    634 calls, 102.20 s
gradients_fft:          579 calls,  98.38 s

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

# Date 2008-01-16 Time 06:03:01 PST -0800 (1200492181.37 s)
Start R-work = 0.4512, R-free = 0.4465 (no bulk solvent and anisotropic scale)
Final R-work = 0.1357, R-free = 0.1825 (no bulk solvent and anisotropic scale)

Start R-work = 0.4420, R-free = 0.4384
Final R-work = 0.1193, R-free = 0.1690