# Date 2008-01-16 Time 04:45:22 PST -0800 (1200487522.26 s)
#phil __OFF__

Command line arguments: "../451.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11930
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 451

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.6339, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, 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: (69.5475, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95148
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932765

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8572
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95148
Completeness in resolution range: 0.935572
Completeness with d_max=infinity: 0.932765

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1761 [2201/2230]  1979   222  10.1%
  bin  2:  4.1761 -  3.3270 [2102/2125]  1893   209   9.9%
  bin  3:  3.3270 -  2.9100 [2074/2099]  1867   207  10.0%
  bin  4:  2.9100 -  2.6456 [2067/2084]  1867   200   9.7%
  bin  5:  2.6456 -  2.4569 [2047/2090]  1834   213  10.4%
  bin  6:  2.4569 -  2.3126 [2055/2083]  1858   197   9.6%
  bin  7:  2.3126 -  2.1971 [2014/2050]  1810   204  10.1%
  bin  8:  2.1971 -  2.1018 [2015/2057]  1812   203  10.1%
  bin  9:  2.1018 -  2.0211 [2007/2065]  1805   202  10.1%
  bin 10:  2.0211 -  1.9515 [1007/2055]   905   102  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_451/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 28
        2.12 -     2.81: 858
        2.81 -     3.51: 4504
        3.51 -     4.20: 9400
        4.20 -     4.90: 13874
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.422 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.453 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.550 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.674 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.680 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28659 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_451/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_451/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4512   r_free= 0.4458   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.258896                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1429  160 0.3576 0.3678      6.5269      6.5411|
|  2:  4.6581 -  3.7163 0.99   1371  149 0.3826 0.3727      6.7602      6.7319|
|  3:  3.7163 -  3.2521 0.99   1341  152 0.4099 0.4016      6.6227      6.7098|
|  4:  3.2521 -  2.9573 0.99   1336  147 0.4276 0.4096      6.4698      6.4508|
|  5:  2.9573 -  2.7468 0.99   1336  147 0.4663 0.4342      6.3333      6.2819|
|  6:  2.7468 -  2.5858 0.99   1319  148 0.4775 0.4511      6.2478      6.1627|
|  7:  2.5858 -  2.4569 0.98   1308  148 0.4887 0.4365      6.2322       6.162|
|  8:  2.4569 -  2.3503 0.98   1312  142 0.4986 0.5426      6.1565      6.2018|
|  9:  2.3503 -  2.2602 0.99   1319  147 0.5177 0.5171      6.1262      6.1246|
| 10:  2.2602 -  2.1824 0.98   1309  141 0.5074 0.5377      6.0913      6.1402|
| 11:  2.1824 -  2.1144 0.97   1284  146 0.5216 0.5300      6.0356        6.01|
| 12:  2.1144 -  2.0541 0.98   1286  145 0.5097 0.5524      5.9466      6.0068|
| 13:  2.0541 -  2.0002 0.92   1208  138 0.5174 0.5090      5.8691      5.8456|
| 14:  2.0002 -  1.9515 0.35    472   49 0.5522 0.4760      5.8312      5.6872|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1429   160  0.70  34.56   0.84     0.72      69892.38|
|  2:  4.6581 -  3.7163  1371   149  0.72  33.31   0.93     0.82      94402.74|
|  3:  3.7163 -  3.2521  1341   152  0.64  40.42   0.93     0.83      97887.22|
|  4:  3.2521 -  2.9573  1336   147  0.57  45.95   0.94     0.79      85655.91|
|  5:  2.9573 -  2.7468  1336   147  0.53  49.91   0.90     0.74      67344.58|
|  6:  2.7468 -  2.5858  1319   148  0.50  52.23   0.92     0.70      58143.44|
|  7:  2.5858 -  2.4569  1308   148  0.48  53.62   0.92     0.65      54516.45|
|  8:  2.4569 -  2.3503  1312   142  0.40  59.97   0.91     0.58      55967.80|
|  9:  2.3503 -  2.2602  1319   147  0.33  65.12   0.94     0.49      55037.37|
| 10:  2.2602 -  2.1824  1309   141  0.28  69.24   0.96     0.41      54607.55|
| 11:  2.1824 -  2.1144  1284   146  0.22  73.66   0.96     0.34      51673.10|
| 12:  2.1144 -  2.0541  1286   145  0.21  74.08   0.95     0.35      48518.13|
| 13:  2.0541 -  2.0002  1208   138  0.24  72.14   0.95     0.39      39807.73|
| 14:  2.0002 -  1.9515   472    49  0.33  65.57   0.91     0.50      30227.52|
|alpha:            min =        0.34 max =            0.83 mean =         0.60|
|beta:             min =    30227.52 max =        97887.22 mean =     63617.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.56|
|phase err.(test): min =        0.00 max =           89.65 mean =        55.57|
|-----------------------------------------------------------------------------|

============================== 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 = 18.067736             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.038   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.552359              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.875   (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 |  1.422 -  1.769:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.769 -  2.117:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.117 -  2.465:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.465 -  2.813:      826 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.813 -  3.161:     2079 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.161 -  3.509:     2425 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.509 -  3.856:     4644 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.856 -  4.204:     4756 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.204 -  4.552:     6287 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.552 -  4.900:     7587 |
|-----------------------------------------------------------------------------|
|-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 |        0.198 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.422 |       0.725 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4512   r_free= 0.4458   ksol= 0.00   Bsol= 0.00   scale= 0.913    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.258896                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4416   r_free= 0.4358   ksol= 0.31   Bsol= 20.79   scale= 0.946   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,1.88,2.25,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.250961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.146390             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.828   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.131667              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.657   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4416      final r-factor (work) = 0.2899          |
| start r-factor (free) = 0.4358      final r-factor (free) = 0.3187          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.5325 = 15.15 * 0.50 * 6.2503 + 1.00 * 0.1978                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.2135 = 15.15 * 0.50 * 6.0833 + 1.00 * 0.1432                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2899      final r-factor (work) = 0.2643          |
| start r-factor (free) = 0.3187      final r-factor (free) = 0.3316          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8908 = 1.13 * 1.00 * 6.0833 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6633 = 1.13 * 1.00 * 5.8662 + 1.00 * 0.0247                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.91   18.12    None  None   None       |
|    all(noH): 2823   0      0.00    68.91   18.12    None  None   None       |
|    Sol.    : 438    0      2.26    68.91   39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    60.03   14.19    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:     0.000 -   6.891:  533   |   5:    34.457 -  41.348:  149        |
|      1:     6.891 -  13.783:  867   |   6:    41.348 -  48.240:  109        |
|      2:    13.783 -  20.674:  552   |   7:    48.240 -  55.131:   90        |
|      3:    20.674 -  27.565:  295   |   8:    55.131 -  62.022:   52        |
|      4:    27.565 -  34.457:  169   |   9:    62.022 -  68.914:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2643 r_free = 0.3316             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2636 r_free = 0.3311             target_work(ml) = 5.876         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2636   r_free= 0.3311   ksol= 0.31   Bsol= 20.79   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,1.88,2.25,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.876035                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2598   r_free= 0.3272   ksol= 0.33   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-0.21,-0.32,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.870258                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.581392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.694   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.462015              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.982   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2598      final r-factor (work) = 0.1992          |
| start r-factor (free) = 0.3272      final r-factor (free) = 0.2533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6476 = 3.58 * 0.50 * 5.8661 + 1.00 * 0.1432                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3915 = 3.58 * 0.50 * 5.7678 + 1.00 * 0.0631                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1992      final r-factor (work) = 0.1832          |
| start r-factor (free) = 0.2533      final r-factor (free) = 0.2365          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6923 = 0.46 * 1.00 * 5.7678 + 1.00 * 0.0274                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5979 = 0.46 * 1.00 * 5.6008 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.27   17.85    None  None   None       |
|    all(noH): 2823   0      0.00    84.27   17.85    None  None   None       |
|    Sol.    : 438    0      6.41    79.87   40.92    None  None   None       |
|    Mac.    : 2385   0      0.00    84.27   13.62    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 -   8.427:  742   |   5:    42.135 -  50.562:  116        |
|      1:     8.427 -  16.854: 1141   |   6:    50.562 -  58.989:   86        |
|      2:    16.854 -  25.281:  377   |   7:    58.989 -  67.416:   46        |
|      3:    25.281 -  33.708:  160   |   8:    67.416 -  75.843:   15        |
|      4:    33.708 -  42.135:  131   |   9:    75.843 -  84.270:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1832 r_free = 0.2365             target_work(ml) = 5.567         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1830 r_free = 0.2367             target_work(ml) = 5.567         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1830   r_free= 0.2367   ksol= 0.33   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-0.21,-0.32,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.566713                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1834   r_free= 0.2360   ksol= 0.32   Bsol= 44.14   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-0.83,-1.13,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.565319                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.171449              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.048   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.469903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.974  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1834      final r-factor (work) = 0.1462          |
| start r-factor (free) = 0.2360      final r-factor (free) = 0.1941          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1446 = 2.17 * 0.50 * 5.6013 + 1.00 * 0.0631                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9905 = 2.17 * 0.50 * 5.4679 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1462      final r-factor (work) = 0.1386          |
| start r-factor (free) = 0.1941      final r-factor (free) = 0.1852          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5797 = 0.47 * 1.00 * 5.4679 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5218 = 0.47 * 1.00 * 5.3458 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.79   17.70    None  None   None       |
|    all(noH): 2823   0      0.00    87.79   17.70    None  None   None       |
|    Sol.    : 438    0      6.46    81.08   42.10    None  None   None       |
|    Mac.    : 2385   0      0.00    87.79   13.22    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 -   8.779:  776   |   5:    43.893 -  52.672:  117        |
|      1:     8.779 -  17.557: 1234   |   6:    52.672 -  61.450:   87        |
|      2:    17.557 -  26.336:  308   |   7:    61.450 -  70.229:   40        |
|      3:    26.336 -  35.115:  127   |   8:    70.229 -  79.008:   17        |
|      4:    35.115 -  43.893:  109   |   9:    79.008 -  87.786:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1386 r_free = 0.1852             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1385 r_free = 0.1852             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1852   ksol= 0.32   Bsol= 44.14   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-0.83,-1.13,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322921                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1390   r_free= 0.1856   ksol= 0.32   Bsol= 44.14   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.36,-1.67,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.325649                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.650519              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.746  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.891513              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.798  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1856      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4681 = 1.65 * 0.50 * 5.3489 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4098 = 1.65 * 0.50 * 5.2804 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7173 = 0.89 * 1.00 * 5.2804 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6640 = 0.89 * 1.00 * 5.2199 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.95    101.73  17.71    None  None   None       |
|    all(noH): 2823   0      0.95    101.73  17.71    None  None   None       |
|    Sol.    : 438    0      5.87    86.91   43.01    None  None   None       |
|    Mac.    : 2385   0      0.95    101.73  13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.953 -  11.031: 1275   |   5:    51.343 -  61.422:  106        |
|      1:    11.031 -  21.109:  932   |   6:    61.422 -  71.500:   46        |
|      2:    21.109 -  31.187:  207   |   7:    71.500 -  81.578:   24        |
|      3:    31.187 -  41.265:  104   |   8:    81.578 -  91.656:    7        |
|      4:    41.265 -  51.343:  118   |   9:    91.656 - 101.734:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1689             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1688             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1688   ksol= 0.32   Bsol= 44.14   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.36,-1.67,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214556                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1688   ksol= 0.32   Bsol= 46.80   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.43,-1.69,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214417                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.101314              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.687  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.169214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.076  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5363 = 2.10 * 0.50 * 5.2197 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5099 = 2.10 * 0.50 * 5.1878 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1638      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8882 = 0.17 * 1.00 * 5.1878 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8831 = 0.17 * 1.00 * 5.1732 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.90    94.55   16.79    None  None   None       |
|    all(noH): 2823   0      1.90    94.55   16.79    None  None   None       |
|    Sol.    : 438    0      5.57    87.85   39.20    None  None   None       |
|    Mac.    : 2385   0      1.90    94.55   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.904 -  11.168: 1332   |   5:    48.225 -  57.489:   86        |
|      1:    11.168 -  20.433:  893   |   6:    57.489 -  66.753:   34        |
|      2:    20.433 -  29.697:  189   |   7:    66.753 -  76.017:   19        |
|      3:    29.697 -  38.961:  134   |   8:    76.017 -  85.281:    7        |
|      4:    38.961 -  48.225:  124   |   9:    85.281 -  94.545:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1605             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1605   ksol= 0.32   Bsol= 46.80   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.43,-1.69,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163458                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1429  160 0.0974 0.1253      5.3644      5.5226|
|  2:  4.6581 -  3.7163 0.99   1371  149 0.0841 0.1076      5.4176      5.6228|
|  3:  3.7163 -  3.2521 0.99   1341  152 0.1062 0.1592      5.4673      5.8541|
|  4:  3.2521 -  2.9573 0.99   1336  147 0.1287 0.1557      5.4803      5.6479|
|  5:  2.9573 -  2.7468 0.99   1336  147 0.1344 0.1748      5.3319      5.4787|
|  6:  2.7468 -  2.5858 0.99   1319  148 0.1298 0.1995      5.2464      5.4759|
|  7:  2.5858 -  2.4569 0.98   1308  148 0.1269 0.1758      5.1737        5.39|
|  8:  2.4569 -  2.3503 0.98   1312  142 0.1218 0.1645      5.0892      5.2715|
|  9:  2.3503 -  2.2602 0.99   1319  147 0.1228 0.1901      5.0435      5.3166|
| 10:  2.2602 -  2.1824 0.98   1309  141 0.1172 0.1805      4.9946      5.2657|
| 11:  2.1824 -  2.1144 0.97   1284  146 0.1147 0.1779      4.9389      5.2146|
| 12:  2.1144 -  2.0541 0.98   1286  145 0.1164 0.1709       4.871      5.0946|
| 13:  2.0541 -  2.0002 0.92   1208  138 0.1154 0.1900      4.7829      5.0554|
| 14:  2.0002 -  1.9515 0.35    472   49 0.1185 0.1716      4.7109      4.9222|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1429   160  0.94   8.92   0.98     0.96       6914.51|
|  2:  4.6581 -  3.7163  1371   149  0.96   7.62   1.02     1.01       8634.32|
|  3:  3.7163 -  3.2521  1341   152  0.93  11.27   1.03     1.02      10080.15|
|  4:  3.2521 -  2.9573  1336   147  0.91  14.28   1.01     0.99      10674.40|
|  5:  2.9573 -  2.7468  1336   147  0.90  16.29   1.00     0.97       8350.98|
|  6:  2.7468 -  2.5858  1319   148  0.90  16.30   0.99     0.96       7350.75|
|  7:  2.5858 -  2.4569  1308   148  0.90  15.74   0.99     0.97       6273.82|
|  8:  2.4569 -  2.3503  1312   142  0.90  15.78   1.00     0.98       5585.58|
|  9:  2.3503 -  2.2602  1319   147  0.90  16.03   1.00     0.97       5049.77|
| 10:  2.2602 -  2.1824  1309   141  0.90  15.86   1.00     0.96       4702.82|
| 11:  2.1824 -  2.1144  1284   146  0.90  16.51   1.00     0.97       4421.67|
| 12:  2.1144 -  2.0541  1286   145  0.91  15.17   1.00     0.99       3790.35|
| 13:  2.0541 -  2.0002  1208   138  0.90  16.11   1.00     1.00       3258.47|
| 14:  2.0002 -  1.9515   472    49  0.89  16.37   0.99     0.95       2736.46|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2736.46 max =        10674.40 mean =      6493.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.33 mean =        13.86|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1608   ksol= 0.32   Bsol= 46.73   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.40,-1.59,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.165399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1608   ksol= 0.32   Bsol= 46.73   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.40,-1.59,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.165399                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6581 0.99   1429  160 0.0974 0.1267      5.3711      5.5289|
|  2:  4.6581 -  3.7163 0.99   1371  149 0.0857 0.1087      5.4332      5.6444|
|  3:  3.7163 -  3.2521 0.99   1341  152 0.1062 0.1591      5.4748      5.8523|
|  4:  3.2521 -  2.9573 0.99   1336  147 0.1293 0.1562      5.4817      5.6471|
|  5:  2.9573 -  2.7468 0.99   1336  147 0.1349 0.1741      5.3326      5.4757|
|  6:  2.7468 -  2.5858 0.99   1319  148 0.1297 0.1993      5.2444      5.4728|
|  7:  2.5858 -  2.4569 0.98   1308  148 0.1268 0.1755       5.172      5.3908|
|  8:  2.4569 -  2.3503 0.98   1312  142 0.1216 0.1647      5.0885      5.2707|
|  9:  2.3503 -  2.2602 0.99   1319  147 0.1225 0.1899      5.0414      5.3153|
| 10:  2.2602 -  2.1824 0.98   1309  141 0.1170 0.1807      4.9937      5.2663|
| 11:  2.1824 -  2.1144 0.97   1284  146 0.1149 0.1776      4.9385      5.2134|
| 12:  2.1144 -  2.0541 0.98   1286  145 0.1163 0.1715       4.871      5.0975|
| 13:  2.0541 -  2.0002 0.92   1208  138 0.1153 0.1900      4.7833      5.0551|
| 14:  2.0002 -  1.9515 0.35    472   49 0.1188 0.1711      4.7116      4.9216|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8576 -  4.6581  1429   160  0.94   9.00   0.98     0.96       7086.58|
|  2:  4.6581 -  3.7163  1371   149  0.95   7.91   1.02     1.01       8949.64|
|  3:  3.7163 -  3.2521  1341   152  0.93  11.50   1.03     1.02      10426.38|
|  4:  3.2521 -  2.9573  1336   147  0.91  14.29   1.01     0.99      10680.71|
|  5:  2.9573 -  2.7468  1336   147  0.90  16.26   1.00     0.97       8312.22|
|  6:  2.7468 -  2.5858  1319   148  0.90  16.27   0.99     0.96       7321.41|
|  7:  2.5858 -  2.4569  1308   148  0.90  15.71   0.99     0.97       6244.13|
|  8:  2.4569 -  2.3503  1312   142  0.90  15.78   1.00     0.98       5581.67|
|  9:  2.3503 -  2.2602  1319   147  0.90  16.02   1.00     0.98       5039.63|
| 10:  2.2602 -  2.1824  1309   141  0.90  15.84   1.00     0.96       4694.95|
| 11:  2.1824 -  2.1144  1284   146  0.90  16.52   1.01     0.97       4421.14|
| 12:  2.1144 -  2.0541  1286   145  0.91  15.17   1.00     0.99       3794.24|
| 13:  2.0541 -  2.0002  1208   138  0.90  16.12   1.00     1.00       3262.18|
| 14:  2.0002 -  1.9515   472    49  0.89  16.37   0.99     0.95       2737.33|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2737.33 max =        10680.71 mean =      6550.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.32|
|phase err.(test): min =        0.00 max =           87.22 mean =        13.93|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.616)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    94.48   16.72    None  None   None       |
|    all(noH): 2823   0      1.84    94.48   16.72    None  None   None       |
|    Sol.    : 438    0      5.50    87.78   39.13    None  None   None       |
|    Mac.    : 2385   0      1.84    94.48   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.836 -  11.100: 1332   |   5:    48.156 -  57.421:   86        |
|      1:    11.100 -  20.364:  893   |   6:    57.421 -  66.685:   34        |
|      2:    20.364 -  29.628:  189   |   7:    66.685 -  75.949:   19        |
|      3:    29.628 -  38.892:  134   |   8:    75.949 -  85.213:    7        |
|      4:    38.892 -  48.156:  124   |   9:    85.213 -  94.477:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.420 - 5.930
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 319
   mapped sites are within: 0.702 - 5.930

peak=    7.361 closest distance to " O   HOH Z 138 " =    1.039
peak=    5.538 closest distance to " NH2 ARG A  56 " =    2.216
peak=    5.452 closest distance to " O   HOH Z 124 " =    1.589
peak=    5.244 closest distance to " CB  SER A  63 " =    1.146
peak=    5.232 closest distance to " O   HOH Z 142 " =    1.610
peak=    5.148 closest distance to " CG  PRO A  54 " =    1.255
peak=    4.981 closest distance to " O   HOH Z 132 " =    1.420
peak=    4.917 closest distance to " O   HOH Z 272 " =    1.896
peak=    4.909 closest distance to " O   HOH Z 234 " =    3.682
peak=    4.880 closest distance to " CB  GLN A 223 " =    1.429
peak=    4.813 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.775 closest distance to " CG  PRO A 213 " =    1.226
peak=    4.760 closest distance to " O   HOH Z  11 " =    1.369
peak=    4.759 closest distance to " O   HOH Z 403 " =    1.805
peak=    4.697 closest distance to " O   HOH Z 278 " =    1.137
peak=    4.696 closest distance to " O   HOH Z  97 " =    1.916
peak=    4.689 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.667 closest distance to " O   HOH Z 199 " =    1.102
peak=    4.651 closest distance to " O   HOH Z 108 " =    1.477
peak=    4.636 closest distance to " O   HOH Z  15 " =    2.091
peak=    4.596 closest distance to " O   HOH Z 368 " =    2.024
peak=    4.556 closest distance to " O   PRO A 198 " =    1.578
peak=    4.530 closest distance to " CB  SER A   3 " =    1.335
peak=    4.510 closest distance to " O   HOH Z 193 " =    1.766
peak=    4.503 closest distance to " O   HOH Z  80 " =    1.701
peak=    4.488 closest distance to " O   HOH Z 126 " =    1.853
peak=    4.443 closest distance to " O   HOH Z  40 " =    1.679
peak=    4.443 closest distance to " CB  GLN A 183 " =    1.291
peak=    4.427 closest distance to " O   HOH Z 316 " =    2.902
peak=    4.384 closest distance to " O   SER A  87 " =    2.112
peak=    4.357 closest distance to " O   HOH Z 402 " =    1.427
peak=    4.350 closest distance to " CB  GLU A 277 " =    3.538
peak=    4.346 closest distance to " O   HOH Z 189 " =    1.738
peak=    4.342 closest distance to " O   HOH Z 209 " =    2.397
peak=    4.337 closest distance to " CG1 ILE A  33 " =    1.369
peak=    4.311 closest distance to " O   HOH Z  59 " =    2.315
peak=    4.309 closest distance to " CA  TYR A  30 " =    1.034
peak=    4.291 closest distance to " CB  SER A 141 " =    1.063
peak=    4.277 closest distance to " CA  ALA A  21 " =    1.240
peak=    4.237 closest distance to " O   HOH Z 411 " =    3.439
peak=    4.235 closest distance to " O   HOH Z 334 " =    1.513
peak=    4.234 closest distance to " NH2BARG A 145 " =    2.032
peak=    4.221 closest distance to " NH2 ARG A 156 " =    1.170
peak=    4.213 closest distance to " O   HOH Z  43 " =    1.488
peak=    4.201 closest distance to " CB  GLU A 152 " =    1.129
peak=    4.198 closest distance to " O   HOH Z 247 " =    1.394
peak=    4.185 closest distance to " CG  ARG A  66 " =    2.716
peak=    4.180 closest distance to " CB  GLU A 128 " =    1.138
peak=    4.161 closest distance to " O   HOH Z 426 " =    1.446
peak=    4.147 closest distance to " O   HOH Z 227 " =    1.629
peak=    4.141 closest distance to " O   HOH Z 313 " =    1.796
peak=    4.123 closest distance to " O   HOH Z 389 " =    1.852
peak=    4.121 closest distance to " O   HOH Z 128 " =    2.029
peak=    4.109 closest distance to " CG1BVAL A  72 " =    1.583
peak=    4.099 closest distance to " NZ  LYS A 117 " =    3.124
peak=    4.098 closest distance to " O   HOH Z 102 " =    1.275
peak=    4.094 closest distance to " O   HOH Z 326 " =    1.643
peak=    4.083 closest distance to " O   HOH Z 133 " =    1.412
peak=    4.063 closest distance to " O   HOH Z 260 " =    1.339
peak=    4.063 closest distance to " O   HOH Z  63 " =    1.983
peak=    4.031 closest distance to " CB  TYR A 169 " =    0.850
peak=    3.997 closest distance to " O   HOH Z 298 " =    1.857
peak=    3.995 closest distance to " CB  ARG A 190 " =    1.708
peak=    3.993 closest distance to " O   HOH Z 134 " =    1.711
peak=    3.978 closest distance to " O   HOH Z 236 " =    1.947
peak=    3.966 closest distance to " O   HOH Z 427 " =    2.702
peak=    3.963 closest distance to " O   HOH Z 357 " =    1.984
peak=    3.954 closest distance to " CB  PRO A  54 " =    0.791
peak=    3.946 closest distance to " O   HOH Z  97 " =    2.446
peak=    3.943 closest distance to " CB  ARG A  79 " =    1.373
peak=    3.934 closest distance to " CB  ASN A 148 " =    1.560
peak=    3.928 closest distance to " O   HOH Z 154 " =    1.430
peak=    3.921 closest distance to " O   HOH Z 156 " =    3.222
peak=    3.921 closest distance to " O   HOH Z 132 " =    1.985
peak=    3.907 closest distance to " O   HOH Z 145 " =    2.114
peak=    3.906 closest distance to " O   HOH Z 214 " =    0.946
peak=    3.903 closest distance to " O   HOH Z 279 " =    2.073
peak=    3.901 closest distance to " O   HOH Z  43 " =    2.226
peak=    3.890 closest distance to " ND2 ASN A 187 " =    1.665
peak=    3.874 closest distance to " CD  ARG A 269 " =    0.981
peak=    3.872 closest distance to " O   HOH Z 369 " =    2.085
peak=    3.870 closest distance to " O   HOH Z 232 " =    2.279
peak=    3.863 closest distance to " O   HOH Z   6 " =    2.199
peak=    3.860 closest distance to " NZ  LYS A 119 " =    1.717
peak=    3.856 closest distance to " CG AARG A 275 " =    0.944
peak=    3.853 closest distance to " O   HOH Z 408 " =    1.552
peak=    3.847 closest distance to " NH2AARG A 190 " =    1.243
peak=    3.845 closest distance to " OE1 GLN A  11 " =    1.813
peak=    3.842 closest distance to " O   HOH Z 303 " =    1.986
peak=    3.834 closest distance to " CB  ARG A 139 " =    1.112
peak=    3.827 closest distance to " N   ASN A  39 " =    1.264
peak=    3.825 closest distance to " CA  THR A 221 " =    0.936
peak=    3.823 closest distance to " O   HOH Z  66 " =    2.304
peak=    3.797 closest distance to " O   HOH Z 344 " =    2.788
peak=    3.792 closest distance to " OD2 ASP A 286 " =    2.694
peak=    3.788 closest distance to " O   HOH Z 406 " =    1.641
peak=    3.772 closest distance to " O   HOH Z  67 " =    1.828
peak=    3.771 closest distance to " O   HOH Z 276 " =    1.364
peak=    3.770 closest distance to " CB  VAL A 202 " =    1.563
peak=    3.764 closest distance to " O   HOH Z 214 " =    2.284
peak=    3.758 closest distance to " O   HOH Z 132 " =    2.699
peak=    3.756 closest distance to " O   HOH Z  78 " =    1.676
peak=    3.755 closest distance to " CB  TRP A 179 " =    1.225
peak=    3.747 closest distance to " O   HOH Z  88 " =    3.194
peak=    3.740 closest distance to " O   HOH Z 203 " =    1.784
peak=    3.739 closest distance to " O   HOH Z 173 " =    2.094
peak=    3.738 closest distance to " NE2 GLN A  11 " =    1.083
peak=    3.730 closest distance to " O   HOH Z 207 " =    1.763
peak=    3.722 closest distance to " CB  LEU A 228 " =    1.183
peak=    3.719 closest distance to " O   HOH Z 416 " =    2.908
peak=    3.718 closest distance to " CA  ASP A 191 " =    0.901
peak=    3.701 closest distance to " O   HOH Z 163 " =    2.020
peak=    3.697 closest distance to " O   HOH Z 374 " =    2.504
peak=    3.692 closest distance to " CB  PRO A 198 " =    1.117
peak=    3.687 closest distance to " CB  ASN A  39 " =    0.895
peak=    3.684 closest distance to " CD  PRO A  54 " =    1.111
peak=    3.682 closest distance to " O   HOH Z 183 " =    1.525
peak=    3.682 closest distance to " O   HOH Z 423 " =    1.947
peak=    3.679 closest distance to " CD  ARG A 139 " =    1.414
peak=    3.676 closest distance to " O   HOH Z 194 " =    1.934
peak=    3.668 closest distance to " NH2AARG A 145 " =    2.210
peak=    3.650 closest distance to " OD1 ASP A 238 " =    0.910
peak=    3.641 closest distance to " O   HOH Z 358 " =    2.165
peak=    3.631 closest distance to " CG2 THR A 221 " =    1.134
peak=    3.613 closest distance to " O   HOH Z 291 " =    1.565
peak=    3.605 closest distance to " O   HOH Z 118 " =    1.116
peak=    3.604 closest distance to " OD1 ASN A  69 " =    2.484
peak=    3.604 closest distance to " CG2BVAL A  41 " =    0.913
peak=    3.595 closest distance to " O   SER A  26 " =    1.679
peak=    3.592 closest distance to " O   HOH Z  54 " =    2.290
peak=    3.590 closest distance to " O   HOH Z 421 " =    1.543
peak=    3.585 closest distance to " O   HOH Z 261 " =    1.588
peak=    3.581 closest distance to " O   HOH Z  44 " =    1.994
peak=    3.577 closest distance to " O   HOH Z 280 " =    2.391
peak=    3.571 closest distance to " OG BSER A 210 " =    1.201
peak=    3.569 closest distance to " O   HOH Z 163 " =    1.494
peak=    3.568 closest distance to " O   HOH Z 147 " =    1.711
peak=    3.568 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.561 closest distance to " CG  ARG A  66 " =    0.966
peak=    3.557 closest distance to " O   HOH Z 346 " =    1.494
peak=    3.555 closest distance to " O   HOH Z 345 " =    1.732
peak=    3.554 closest distance to " O   HOH Z  59 " =    1.791
peak=    3.542 closest distance to " CD2 LEU A 297 " =    0.946
peak=    3.539 closest distance to " O   HOH Z  21 " =    1.889
peak=    3.539 closest distance to " O   HOH Z 433 " =    1.573
peak=    3.534 closest distance to " O   HOH Z 394 " =    1.569
peak=    3.533 closest distance to " O   HOH Z  71 " =    1.302
peak=    3.533 closest distance to " O   HOH Z  19 " =    1.644
peak=    3.522 closest distance to " O   ALA A 165 " =    1.286
peak=    3.518 closest distance to " O   HOH Z 284 " =    2.885
peak=    3.517 closest distance to " O   HOH Z 434 " =    1.558
peak=    3.512 closest distance to " O   HOH Z  40 " =    1.858
peak=    3.505 closest distance to " CG  GLN A  58 " =    2.380
peak=    3.504 closest distance to " CA  ARG A 195 " =    1.242
peak=    3.503 closest distance to " CD2 TRP A 179 " =    1.351
peak=    3.503 closest distance to " CD  LYS A 166 " =    1.345
peak=    3.491 closest distance to " CD  LYS A 119 " =    1.466
peak=    3.486 closest distance to " O   HOH Z  10 " =    1.755
peak=    3.483 closest distance to " CB  ALA A 100 " =    1.276
peak=    3.482 closest distance to " OG  SER A  62 " =    2.962
peak=    3.480 closest distance to " CA  ASP A 140 " =    1.147
peak=    3.477 closest distance to " O   HOH Z 287 " =    1.732
peak=    3.470 closest distance to " O   HOH Z  54 " =    1.565
peak=    3.470 closest distance to " CA  LYS A 117 " =    1.282
peak=    3.467 closest distance to " O   HOH Z  20 " =    1.462
peak=    3.464 closest distance to " O   HOH Z 250 " =    1.387
peak=    3.457 closest distance to " O   HOH Z 386 " =    2.279
peak=    3.454 closest distance to " CA  ARG A  36 " =    1.071
peak=    3.453 closest distance to " NZ  LYS A  76 " =    1.152
peak=    3.447 closest distance to " O   HOH Z 255 " =    1.517
peak=    3.445 closest distance to " NH1BARG A 145 " =    1.113
peak=    3.445 closest distance to " CB  SER A  62 " =    0.841
peak=    3.445 closest distance to " OE1 GLN A  58 " =    5.930
peak=    3.433 closest distance to " O   HOH Z 166 " =    3.312
peak=    3.432 closest distance to " CB  MET A  47 " =    1.209
peak=    3.432 closest distance to " OG BSER A 164 " =    2.522
peak=    3.422 closest distance to " O   HOH Z 336 " =    1.629
peak=    3.421 closest distance to " O   HOH Z 365 " =    2.729
peak=    3.421 closest distance to " CD BLYS A 290 " =    1.201
peak=    3.420 closest distance to " CB  GLN A  88 " =    1.118
peak=    3.420 closest distance to " CA  VAL A  41 " =    0.867
peak=    3.419 closest distance to " CA  ASN A 176 " =    1.120
peak=    3.412 closest distance to " CG  PRO A 243 " =    1.237
peak=    3.411 closest distance to " CD2 HIS A  81 " =    1.182
peak=    3.409 closest distance to " CE  LYS A 119 " =    1.085
peak=    3.401 closest distance to " O   HOH Z 281 " =    4.247
peak=    3.392 closest distance to " O   HOH Z 273 " =    2.629
peak=    3.392 closest distance to " O   HOH Z 404 " =    1.548
peak=    3.390 closest distance to " CG  GLN A  89 " =    1.487
peak=    3.384 closest distance to " O   HOH Z 128 " =    2.158
peak=    3.384 closest distance to " O   HOH Z 419 " =    1.507
peak=    3.384 closest distance to " CA  ASN A 217 " =    1.365
peak=    3.382 closest distance to " O   HOH Z 215 " =    1.615
peak=    3.380 closest distance to " O   HOH Z  50 " =    1.318
peak=    3.375 closest distance to " O   HOH Z 106 " =    1.596
peak=    3.372 closest distance to " CB  ARG A  66 " =    1.227
peak=    3.367 closest distance to " O   HOH Z 345 " =    2.760
peak=    3.361 closest distance to " O   HOH Z 427 " =    3.015
peak=    3.359 closest distance to " CD2 PHE A 225 " =    1.128
peak=    3.357 closest distance to " OD2 ASP A 298 " =    4.003
peak=    3.357 closest distance to " CA  LEU A 282 " =    1.200
peak=    3.350 closest distance to " CB  ARG A 259 " =    1.940
peak=    3.350 closest distance to " O   HOH Z 227 " =    1.746
peak=    3.349 closest distance to " O   HOH Z 250 " =    1.786
peak=    3.349 closest distance to " O   HOH Z 295 " =    1.501
peak=    3.344 closest distance to " CA  GLY A 211 " =    1.130
peak=    3.344 closest distance to " CB  ALA A 291 " =    1.221
peak=    3.340 closest distance to " O   HOH Z 334 " =    1.581
peak=    3.340 closest distance to " OG1 THR A 294 " =    2.294
peak=    3.333 closest distance to " O   HOH Z  30 " =    1.748
peak=    3.332 closest distance to " CG1 VAL A 153 " =    1.100
peak=    3.326 closest distance to " O   HOH Z 155 " =    2.780
peak=    3.317 closest distance to " CG  MET A  93 " =    1.021
peak=    3.317 closest distance to " O   HOH Z  35 " =    2.423
peak=    3.315 closest distance to " O   GLY A  91 " =    1.344
peak=    3.312 closest distance to " NH1AARG A 145 " =    1.120
peak=    3.311 closest distance to " O   HOH Z 266 " =    1.618
peak=    3.306 closest distance to " O   HOH Z 362 " =    3.549
peak=    3.302 closest distance to " CH2 TRP A 274 " =    1.956
peak=    3.299 closest distance to " O   HOH Z 126 " =    1.615
peak=    3.298 closest distance to " O   HOH Z 261 " =    2.049
peak=    3.292 closest distance to " O   HOH Z 337 " =    3.680
peak=    3.290 closest distance to " CD2 LEU A 255 " =    1.105
peak=    3.290 closest distance to " O   HOH Z 383 " =    2.017
peak=    3.288 closest distance to " CD  ARG A 195 " =    0.911
peak=    3.283 closest distance to " CB  VAL A 265 " =    1.222
peak=    3.282 closest distance to " O   HOH Z 108 " =    2.071
peak=    3.281 closest distance to " O   HOH Z 261 " =    2.068
peak=    3.281 closest distance to " CG2 ILE A 120 " =    1.255
peak=    3.280 closest distance to " NZ  LYS A 117 " =    1.294
peak=    3.278 closest distance to " CB  GLN A 103 " =    0.893
peak=    3.271 closest distance to " O   HOH Z 234 " =    1.852
peak=    3.269 closest distance to " O   SER A 164 " =    1.393
peak=    3.268 closest distance to " CZ AARG A 102 " =    1.778
peak=    3.267 closest distance to " NE AARG A 275 " =    1.225
peak=    3.267 closest distance to " O   MET A 105 " =    1.907
peak=    3.265 closest distance to " CG2 VAL A 197 " =    1.093
peak=    3.264 closest distance to " CB  PHE A  16 " =    1.070
peak=    3.263 closest distance to " CA  ASP A 124 " =    0.702
peak=    3.259 closest distance to " CG2 ILE A  20 " =    1.425
peak=    3.258 closest distance to " OG BSER A 258 " =    3.407
peak=    3.257 closest distance to " CD1 LEU A 300 " =    1.298
peak=    3.253 closest distance to " CA  ASP A 162 " =    1.144
peak=    3.253 closest distance to " CA  MET A  40 " =    1.035
peak=    3.250 closest distance to " O   HOH Z 438 " =    2.354
peak=    3.247 closest distance to " CB  ALA A  34 " =    0.976
peak=    3.245 closest distance to " O   HOH Z 248 " =    1.518
peak=    3.233 closest distance to " CA  GLY A  80 " =    1.111
peak=    3.233 closest distance to " O   THR A 251 " =    1.303
peak=    3.232 closest distance to " OH  TYR A  30 " =    1.081
peak=    3.232 closest distance to " OG  SER A  22 " =    2.703
peak=    3.227 closest distance to " O   HOH Z 217 " =    1.264
peak=    3.225 closest distance to " O   HOH Z 282 " =    1.958
peak=    3.224 closest distance to " O   HOH Z 215 " =    1.547
peak=    3.218 closest distance to " NE2 GLN A  58 " =    4.382
peak=    3.212 closest distance to " O   HOH Z  48 " =    1.621
peak=    3.210 closest distance to " O   HOH Z  64 " =    1.460
peak=    3.209 closest distance to " CG  GLN A  77 " =    1.990
peak=    3.203 closest distance to " CG  GLN A  58 " =    2.497
peak=    3.203 closest distance to " O   ALA A 158 " =    1.242
peak=    3.202 closest distance to " O   HOH Z 197 " =    1.922
peak=    3.200 closest distance to " CB  PRO A 163 " =    3.910
peak=    3.193 closest distance to " O   HOH Z 361 " =    2.442
peak=    3.193 closest distance to " CA  GLN A 223 " =    0.798
peak=    3.192 closest distance to " CE  MET A 188 " =    2.090
peak=    3.191 closest distance to " O   HOH Z 132 " =    3.194
peak=    3.187 closest distance to " O   HOH Z  30 " =    1.252
peak=    3.185 closest distance to " OD1 ASP A 253 " =    1.956
peak=    3.185 closest distance to " CD1 LEU A 228 " =    1.682
peak=    3.182 closest distance to " O   TRP A 274 " =    1.716
peak=    3.182 closest distance to " O   HOH Z 303 " =    1.573
peak=    3.182 closest distance to " CA  ILE A  33 " =    1.341
peak=    3.180 closest distance to " O   HOH Z 285 " =    2.054
peak=    3.180 closest distance to " CD  ARG A 159 " =    0.762
peak=    3.178 closest distance to " O   HOH Z 125 " =    2.301
peak=    3.177 closest distance to " CA  ALA A 233 " =    1.333
peak=    3.177 closest distance to " O   HOH Z 313 " =    2.237
peak=    3.175 closest distance to " O   HOH Z 299 " =    2.220
peak=    3.169 closest distance to " O   HOH Z 148 " =    3.044
peak=    3.167 closest distance to " N   ARG A 156 " =    1.409
peak=    3.166 closest distance to " CB  ARG A 102 " =    0.747
peak=    3.162 closest distance to " CA  ALA A  51 " =    0.823
peak=    3.160 closest distance to " O   HOH Z 166 " =    1.424
peak=    3.159 closest distance to " O   HOH Z 359 " =    2.017
peak=    3.156 closest distance to " O   HOH Z 114 " =    1.244
peak=    3.155 closest distance to " CG1 ILE A 120 " =    0.991
peak=    3.155 closest distance to " O   HOH Z 135 " =    1.796
peak=    3.154 closest distance to " CB  ALA A 248 " =    1.294
peak=    3.152 closest distance to " CB  TRP A 150 " =    1.655
peak=    3.150 closest distance to " CA  ALA A  84 " =    1.246
peak=    3.148 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.146 closest distance to " O   HOH Z  85 " =    1.915
peak=    3.145 closest distance to " CE1 TYR A 186 " =    1.176
peak=    3.144 closest distance to " CG  GLU A 277 " =    2.209
peak=    3.141 closest distance to " O   HOH Z 380 " =    1.912
peak=    3.136 closest distance to " CD1 ILE A 106 " =    0.912
peak=    3.133 closest distance to " O   HOH Z 382 " =    1.335
peak=    3.125 closest distance to " O   HOH Z 245 " =    1.383
peak=    3.121 closest distance to " O   HOH Z 327 " =    1.757
peak=    3.118 closest distance to " CB  ALA A   9 " =    1.449
peak=    3.110 closest distance to " OD1 ASN A  60 " =    1.259
peak=    3.102 closest distance to " N   SER A 135 " =    1.284
peak=    3.100 closest distance to " CA  ALA A 160 " =    0.863
peak=    3.098 closest distance to " CB  PHE A 204 " =    1.134
peak=    3.097 closest distance to " O   HOH Z 112 " =    1.549
peak=    3.096 closest distance to " CZ  PHE A  38 " =    1.489
peak=    3.088 closest distance to " NE1 TRP A 274 " =    0.924
peak=    3.085 closest distance to " CD  GLN A 194 " =    1.610
peak=    3.082 closest distance to " CD2 LEU A  83 " =    1.540
peak=    3.073 closest distance to " O   HOH Z  51 " =    1.471
peak=    3.067 closest distance to " CB  GLN A 194 " =    0.832
peak=    3.052 closest distance to " O   HOH Z 327 " =    2.638
peak=    3.044 closest distance to " O   HOH Z 368 " =    2.431
peak=    3.020 closest distance to " O   HOH Z 387 " =    2.548
peak=    3.017 closest distance to " O   HOH Z 128 " =    1.707
peak=    3.016 closest distance to " O   HOH Z 217 " =    1.835

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 226         
Filter by distance & map next to the model:
   mapped sites are within: 0.412 - 5.361
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 226
   mapped sites are within: 0.707 - 5.361

peak=   -4.551 closest distance to " O   HOH Z 266 " =    4.028
peak=   -4.477 closest distance to " O   HOH Z  13 " =    1.325
peak=   -4.427 closest distance to " C   HIS A 108 " =    1.150
peak=   -4.369 closest distance to " OXT GLY A 302 " =    2.873
peak=   -4.360 closest distance to " O   HOH Z 290 " =    0.810
peak=   -4.352 closest distance to " CA  SER A 164 " =    2.029
peak=   -4.197 closest distance to " O   HOH Z 234 " =    4.139
peak=   -4.129 closest distance to " OG ASER A 134 " =    1.351
peak=   -4.087 closest distance to " CG  LYS A 193 " =    2.374
peak=   -4.068 closest distance to " O   HOH Z  11 " =    1.654
peak=   -4.032 closest distance to " O   TRP A  92 " =    1.878
peak=   -4.019 closest distance to " O   HOH Z 292 " =    4.433
peak=   -3.997 closest distance to " NH2 ARG A  79 " =    1.903
peak=   -3.978 closest distance to " CD  ARG A 156 " =    1.962
peak=   -3.968 closest distance to " ND2 ASN A 187 " =    1.458
peak=   -3.967 closest distance to " O   HOH Z 138 " =    0.883
peak=   -3.964 closest distance to " OG  SER A  62 " =    1.299
peak=   -3.940 closest distance to " CD1 LEU A 101 " =    2.509
peak=   -3.887 closest distance to " CD  GLN A  58 " =    0.936
peak=   -3.881 closest distance to " SG  CYS A 254 " =    3.343
peak=   -3.875 closest distance to " O   HOH Z 377 " =    1.028
peak=   -3.867 closest distance to " CH2 TRP A 179 " =    1.299
peak=   -3.828 closest distance to " C   ALA A 158 " =    1.150
peak=   -3.826 closest distance to " O   HOH Z 423 " =    2.349
peak=   -3.823 closest distance to " O   HOH Z  52 " =    1.774
peak=   -3.821 closest distance to " O   VAL A  67 " =    2.681
peak=   -3.816 closest distance to " N   ALA A  43 " =    2.694
peak=   -3.813 closest distance to " CB  CYS A 254 " =    2.662
peak=   -3.810 closest distance to " OG  SER A  97 " =    2.088
peak=   -3.809 closest distance to " O   HOH Z 377 " =    1.908
peak=   -3.806 closest distance to " CE  MET A 105 " =    1.843
peak=   -3.795 closest distance to " N   GLN A  58 " =    1.707
peak=   -3.794 closest distance to " CD2 LEU A 300 " =    2.857
peak=   -3.792 closest distance to " CZ  TYR A 169 " =    1.945
peak=   -3.789 closest distance to " O   HOH Z  93 " =    1.202
peak=   -3.785 closest distance to " N   SER A 276 " =    1.334
peak=   -3.759 closest distance to " CE2 TYR A  30 " =    2.773
peak=   -3.750 closest distance to " O   HOH Z 418 " =    1.205
peak=   -3.741 closest distance to " O   HOH Z  92 " =    1.489
peak=   -3.722 closest distance to " N   ALA A 248 " =    1.791
peak=   -3.716 closest distance to " CD1 PHE A  59 " =    2.000
peak=   -3.713 closest distance to " O   HOH Z  71 " =    1.254
peak=   -3.697 closest distance to " O   HOH Z 407 " =    3.233
peak=   -3.696 closest distance to " ND2 ASN A  45 " =    0.955
peak=   -3.683 closest distance to " O   GLY A 196 " =    0.986
peak=   -3.673 closest distance to " O   VAL A  67 " =    2.899
peak=   -3.652 closest distance to " OD1 ASN A  39 " =    2.221
peak=   -3.652 closest distance to " O   HOH Z 150 " =    1.409
peak=   -3.650 closest distance to " O   SER A 146 " =    0.918
peak=   -3.644 closest distance to " O   HOH Z  17 " =    1.308
peak=   -3.623 closest distance to " O   HOH Z  10 " =    1.523
peak=   -3.622 closest distance to " OD1 ASP A 200 " =    1.230
peak=   -3.605 closest distance to " CB  ALA A 291 " =    2.343
peak=   -3.599 closest distance to " O   HOH Z  97 " =    1.464
peak=   -3.599 closest distance to " CG  GLU A  53 " =    1.390
peak=   -3.594 closest distance to " C   THR A 279 " =    1.141
peak=   -3.593 closest distance to " CG  LEU A  83 " =    1.913
peak=   -3.580 closest distance to " CD  GLN A  88 " =    0.771
peak=   -3.578 closest distance to " CA  GLY A 133 " =    1.761
peak=   -3.577 closest distance to " O   HOH Z 138 " =    1.218
peak=   -3.567 closest distance to " O   HOH Z 165 " =    2.056
peak=   -3.566 closest distance to " CG2 THR A   4 " =    1.844
peak=   -3.565 closest distance to " CB  ALA A 161 " =    2.564
peak=   -3.564 closest distance to " CB  PHE A 208 " =    2.229
peak=   -3.560 closest distance to " O   ALA A 256 " =    1.388
peak=   -3.544 closest distance to " CD  ARG A 139 " =    1.665
peak=   -3.544 closest distance to " O   HOH Z 118 " =    2.942
peak=   -3.544 closest distance to " O   PRO A 198 " =    1.242
peak=   -3.521 closest distance to " OG BSER A 134 " =    1.747
peak=   -3.516 closest distance to " CD1 LEU A 228 " =    2.215
peak=   -3.508 closest distance to " OG BSER A 134 " =    1.321
peak=   -3.494 closest distance to " O   HOH Z  63 " =    1.145
peak=   -3.486 closest distance to " O   SER A  26 " =    1.196
peak=   -3.486 closest distance to " CD2 LEU A 237 " =    2.717
peak=   -3.486 closest distance to " C   ASN A 285 " =    2.256
peak=   -3.484 closest distance to " CD1 PHE A 130 " =    2.243
peak=   -3.483 closest distance to " O   HOH Z 313 " =    0.994
peak=   -3.482 closest distance to " CA  TRP A 274 " =    1.667
peak=   -3.479 closest distance to " O   HOH Z 151 " =    1.406
peak=   -3.474 closest distance to " N   ALA A 248 " =    2.068
peak=   -3.466 closest distance to " C   GLY A  80 " =    2.350
peak=   -3.457 closest distance to " O   PRO A 198 " =    1.289
peak=   -3.452 closest distance to " NH2 ARG A  66 " =    4.822
peak=   -3.448 closest distance to " OG  SER A   3 " =    1.700
peak=   -3.446 closest distance to " O   VAL A 174 " =    1.973
peak=   -3.445 closest distance to " CA  ASN A 148 " =    1.688
peak=   -3.433 closest distance to " O   ALA A   1 " =    1.916
peak=   -3.431 closest distance to " O   HOH Z 388 " =    2.077
peak=   -3.431 closest distance to " OE2 GLU A   2 " =    1.556
peak=   -3.430 closest distance to " O   HOH Z 116 " =    1.093
peak=   -3.419 closest distance to " CG  ASP A 132 " =    2.253
peak=   -3.415 closest distance to " O   HOH Z 265 " =    1.907
peak=   -3.415 closest distance to " O   SER A 210 " =    1.821
peak=   -3.406 closest distance to " O   ALA A 161 " =    1.571
peak=   -3.400 closest distance to " O   ASN A 187 " =    1.454
peak=   -3.398 closest distance to " O   HOH Z 396 " =    1.739
peak=   -3.397 closest distance to " CD  GLN A  58 " =    1.251
peak=   -3.394 closest distance to " C   SER A 206 " =    1.644
peak=   -3.392 closest distance to " CD  ARG A 195 " =    5.096
peak=   -3.390 closest distance to " O   HOH Z 166 " =    1.691
peak=   -3.385 closest distance to " O   HOH Z 311 " =    3.443
peak=   -3.385 closest distance to " O   HOH Z  98 " =    1.753
peak=   -3.383 closest distance to " O   HOH Z 435 " =    2.548
peak=   -3.382 closest distance to " CG  ASP A  50 " =    2.308
peak=   -3.373 closest distance to " CD1 TYR A 247 " =    2.229
peak=   -3.368 closest distance to " O   HOH Z  43 " =    1.606
peak=   -3.365 closest distance to " O   GLN A  11 " =    1.386
peak=   -3.364 closest distance to " O   HOH Z 222 " =    1.181
peak=   -3.363 closest distance to " O   HOH Z  65 " =    0.707
peak=   -3.361 closest distance to " O   HOH Z  15 " =    1.585
peak=   -3.360 closest distance to " CB  PRO A 163 " =    2.803
peak=   -3.355 closest distance to " O   HOH Z 126 " =    1.969
peak=   -3.353 closest distance to " OD1 ASP A 191 " =    1.665
peak=   -3.352 closest distance to " O   HOH Z 185 " =    2.202
peak=   -3.347 closest distance to " O   HOH Z  20 " =    1.243
peak=   -3.346 closest distance to " CB  ASP A 162 " =    2.642
peak=   -3.345 closest distance to " O   LEU A 167 " =    1.546
peak=   -3.344 closest distance to " O   HOH Z 283 " =    1.726
peak=   -3.342 closest distance to " CG  GLU A 152 " =    2.339
peak=   -3.338 closest distance to " O   VAL A 197 " =    1.058
peak=   -3.336 closest distance to " O   HOH Z 140 " =    0.846
peak=   -3.334 closest distance to " CB  ALA A 244 " =    2.030
peak=   -3.331 closest distance to " N   LEU A 281 " =    1.838
peak=   -3.329 closest distance to " OD2 ASP A 171 " =    2.311
peak=   -3.327 closest distance to " CD1 LEU A  25 " =    2.451
peak=   -3.327 closest distance to " O   HOH Z 100 " =    0.914
peak=   -3.324 closest distance to " O   HOH Z 136 " =    1.571
peak=   -3.318 closest distance to " OG  SER A  63 " =    1.403
peak=   -3.316 closest distance to " CB  ASN A  39 " =    2.285
peak=   -3.314 closest distance to " CG  GLN A  58 " =    1.314
peak=   -3.310 closest distance to " CD2 PHE A  59 " =    2.378
peak=   -3.308 closest distance to " CE3 TRP A 150 " =    2.139
peak=   -3.306 closest distance to " CD2 TRP A 274 " =    1.002
peak=   -3.304 closest distance to " CA  GLY A 241 " =    2.290
peak=   -3.303 closest distance to " CH2 TRP A 274 " =    1.056
peak=   -3.302 closest distance to " O   HOH Z 353 " =    2.325
peak=   -3.301 closest distance to " OH  TYR A 172 " =    1.664
peak=   -3.299 closest distance to " O   HOH Z 166 " =    1.575
peak=   -3.294 closest distance to " OD1 ASP A 171 " =    1.678
peak=   -3.293 closest distance to " O   SER A 273 " =    1.340
peak=   -3.292 closest distance to " O   HOH Z 281 " =    2.846
peak=   -3.285 closest distance to " O   MET A  40 " =    2.596
peak=   -3.283 closest distance to " O   HOH Z 193 " =    1.994
peak=   -3.280 closest distance to " CD  GLN A 223 " =    0.836
peak=   -3.278 closest distance to " CA  ASP A 298 " =    1.086
peak=   -3.277 closest distance to " O   TYR A 186 " =    1.447
peak=   -3.276 closest distance to " O   HOH Z 196 " =    1.914
peak=   -3.275 closest distance to " CB  LEU A 167 " =    2.075
peak=   -3.271 closest distance to " CB  MET A  93 " =    2.043
peak=   -3.269 closest distance to " C   ASP A 191 " =    1.402
peak=   -3.268 closest distance to " CA  GLY A  98 " =    2.203
peak=   -3.267 closest distance to " O   ALA A  34 " =    2.489
peak=   -3.257 closest distance to " OG1 THR A 178 " =    1.232
peak=   -3.257 closest distance to " O   PHE A  59 " =    2.414
peak=   -3.254 closest distance to " CG  LYS A 119 " =    2.898
peak=   -3.254 closest distance to " CB  PHE A 192 " =    1.921
peak=   -3.247 closest distance to " O   PHE A 218 " =    1.520
peak=   -3.245 closest distance to " O   HOH Z 132 " =    1.165
peak=   -3.244 closest distance to " CG  ASP A 231 " =    0.829
peak=   -3.235 closest distance to " CG2 VAL A 189 " =    2.180
peak=   -3.233 closest distance to " O   HOH Z  19 " =    2.091
peak=   -3.233 closest distance to " O   HOH Z 266 " =    4.652
peak=   -3.233 closest distance to " O   HOH Z 198 " =    2.258
peak=   -3.231 closest distance to " O   HOH Z 412 " =    4.475
peak=   -3.230 closest distance to " CD  PRO A 198 " =    1.287
peak=   -3.228 closest distance to " O   HOH Z 360 " =    2.592
peak=   -3.228 closest distance to " O   HOH Z  38 " =    1.494
peak=   -3.226 closest distance to " CB  ASP A 124 " =    2.138
peak=   -3.225 closest distance to " O   HOH Z 385 " =    3.489
peak=   -3.221 closest distance to " ND2 ASN A 209 " =    1.842
peak=   -3.218 closest distance to " CD1 LEU A  83 " =    2.256
peak=   -3.217 closest distance to " CG  ARG A 269 " =    2.223
peak=   -3.216 closest distance to " NH1 ARG A  66 " =    5.361
peak=   -3.216 closest distance to " CG  ARG A 259 " =    2.734
peak=   -3.212 closest distance to " O   LEU A 228 " =    2.346
peak=   -3.211 closest distance to " CG  GLU A 277 " =    1.158
peak=   -3.210 closest distance to " CE  MET A  93 " =    1.340
peak=   -3.207 closest distance to " NE2 GLN A 103 " =    1.588
peak=   -3.207 closest distance to " CG  GLU A 152 " =    0.993
peak=   -3.207 closest distance to " OD1 ASN A 176 " =    1.078
peak=   -3.204 closest distance to " O   SER A 135 " =    1.537
peak=   -3.203 closest distance to " N   SER A 206 " =    1.859
peak=   -3.202 closest distance to " CE3 TRP A 123 " =    1.333
peak=   -3.200 closest distance to " CD  LYS A 289 " =    2.528
peak=   -3.199 closest distance to " SD  MET A 188 " =    2.220
peak=   -3.196 closest distance to " O   HOH Z 417 " =    2.620
peak=   -3.191 closest distance to " CD2 LEU A 237 " =    2.246
peak=   -3.191 closest distance to " O   HOH Z 351 " =    1.518
peak=   -3.188 closest distance to " CB  ALA A 248 " =    1.927
peak=   -3.185 closest distance to " NH1 ARG A 195 " =    2.527
peak=   -3.182 closest distance to " O   HOH Z 100 " =    1.129
peak=   -3.181 closest distance to " O   ALA A  51 " =    1.493
peak=   -3.181 closest distance to " CB  ALA A  51 " =    1.854
peak=   -3.179 closest distance to " CB  SER A 258 " =    2.028
peak=   -3.178 closest distance to " N   GLN A  77 " =    1.501
peak=   -3.176 closest distance to " NZ  LYS A 117 " =    1.567
peak=   -3.162 closest distance to " O   HOH Z  41 " =    2.218
peak=   -3.145 closest distance to " O   HOH Z 385 " =    2.019
peak=   -3.145 closest distance to " C   LEU A 143 " =    1.855
peak=   -3.131 closest distance to " O   HOH Z  39 " =    1.011
peak=   -3.130 closest distance to " OG1 THR A  82 " =    1.448
peak=   -3.130 closest distance to " O   HOH Z 414 " =    1.453
peak=   -3.128 closest distance to " O   HOH Z 264 " =    1.764
peak=   -3.123 closest distance to " ND2 ASN A  60 " =    1.366
peak=   -3.123 closest distance to " CG  ARG A 219 " =    2.306
peak=   -3.122 closest distance to " O   ALA A 160 " =    1.438
peak=   -3.118 closest distance to " CA  VAL A 232 " =    2.490
peak=   -3.117 closest distance to " CG  PHE A 283 " =    2.683
peak=   -3.116 closest distance to " CG2 THR A 178 " =    2.106
peak=   -3.113 closest distance to " NH2 ARG A  66 " =    1.697
peak=   -3.108 closest distance to " O   HOH Z 424 " =    3.043
peak=   -3.107 closest distance to " O   HOH Z  78 " =    1.748
peak=   -3.107 closest distance to " C   GLN A 223 " =    1.196
peak=   -3.087 closest distance to " O   THR A  52 " =    1.796
peak=   -3.072 closest distance to " OG  SER A 273 " =    2.116
peak=   -3.060 closest distance to " O   HOH Z 148 " =    3.591
peak=   -3.049 closest distance to " CB  ALA A  10 " =    2.193
peak=   -3.028 closest distance to " O   HOH Z 111 " =    3.285
peak=   -3.011 closest distance to " O   HOH Z 361 " =    3.391
peak=   -3.000 closest distance to " CD2 LEU A 237 " =    2.733

================= 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 0.4458   6.258896e+00   6.251063e+00
   1_bss:  0.4416 0.4358   6.250961e+00   6.233886e+00
   1_xyz:  0.2899 0.3187   5.926353e+00   6.005391e+00
   1_adp:  0.2643 0.3316   5.877519e+00   6.030282e+00
   1_occ:  0.2636 0.3311   5.876035e+00   6.028554e+00
   2_bss:  0.2598 0.3272   5.870258e+00   6.023909e+00
   2_xyz:  0.1992 0.2533   5.637665e+00   5.828847e+00
   2_adp:  0.1832 0.2365   5.566646e+00   5.762626e+00
   2_occ:  0.1830 0.2367   5.566713e+00   5.762855e+00
   3_bss:  0.1834 0.2360   5.565319e+00   5.760842e+00
   3_xyz:  0.1462 0.1941   5.369169e+00   5.585772e+00
   3_adp:  0.1386 0.1852   5.322977e+00   5.537055e+00
   3_occ:  0.1385 0.1852   5.322921e+00   5.537332e+00
   4_bss:  0.1390 0.1856   5.325649e+00   5.538628e+00
   4_xyz:  0.1251 0.1696   5.231771e+00   5.449457e+00
   4_adp:  0.1218 0.1689   5.214677e+00   5.437810e+00
   4_occ:  0.1217 0.1688   5.214556e+00   5.437962e+00
   5_bss:  0.1217 0.1688   5.214417e+00   5.438077e+00
   5_xyz:  0.1139 0.1638   5.169994e+00   5.408822e+00
   5_adp:  0.1144 0.1605   5.163560e+00   5.393199e+00
   5_occ:  0.1143 0.1605   5.163458e+00   5.393789e+00
   5_bss:  0.1146 0.1608   5.165399e+00   5.395330e+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:  0.312  20.789  -2.782   1.882   2.254   0.000   0.000   0.000
   1_xyz:  0.312  20.789  -2.782   1.882   2.254   0.000   0.000   0.000
   1_adp:  0.312  20.789  -2.782   1.882   2.254   0.000   0.000   0.000
   1_occ:  0.312  20.789  -2.782   1.882   2.254   0.000   0.000   0.000
   2_bss:  0.329  50.000  -2.763  -0.210  -0.316  -0.000  -0.000  -0.000
   2_xyz:  0.329  50.000  -2.763  -0.210  -0.316  -0.000  -0.000  -0.000
   2_adp:  0.329  50.000  -2.763  -0.210  -0.316  -0.000  -0.000  -0.000
   2_occ:  0.329  50.000  -2.763  -0.210  -0.316  -0.000  -0.000  -0.000
   3_bss:  0.319  44.138  -2.636  -0.826  -1.127  -0.000  -0.000  -0.000
   3_xyz:  0.319  44.138  -2.636  -0.826  -1.127  -0.000  -0.000  -0.000
   3_adp:  0.319  44.138  -2.636  -0.826  -1.127  -0.000  -0.000  -0.000
   3_occ:  0.319  44.138  -2.636  -0.826  -1.127  -0.000  -0.000  -0.000
   4_bss:  0.320  44.138  -2.749  -1.363  -1.667  -0.000  -0.000  -0.000
   4_xyz:  0.320  44.138  -2.749  -1.363  -1.667  -0.000  -0.000  -0.000
   4_adp:  0.320  44.138  -2.749  -1.363  -1.667  -0.000  -0.000  -0.000
   4_occ:  0.320  44.138  -2.749  -1.363  -1.667  -0.000  -0.000  -0.000
   5_bss:  0.322  46.795  -2.604  -1.432  -1.690  -0.000  -0.000  -0.000
   5_xyz:  0.322  46.795  -2.604  -1.432  -1.690  -0.000  -0.000  -0.000
   5_adp:  0.322  46.795  -2.604  -1.432  -1.690  -0.000  -0.000  -0.000
   5_occ:  0.322  46.795  -2.604  -1.432  -1.690  -0.000  -0.000  -0.000
   5_bss:  0.325  46.727  -2.481  -1.395  -1.588  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.561 0.4495  0.6044    63615.474
   1_bss:  53.970 0.4680  0.6401    59370.799
   1_xyz:  33.182 0.7222  0.9429    26872.836
   1_adp:  34.759 0.7030  0.9266    28893.340
   1_occ:  34.653 0.7041  0.9273    28736.083
   2_bss:  34.241 0.7086  0.8857    28134.743
   2_xyz:  25.552 0.8040  0.9679    16628.191
   2_adp:  22.908 0.8326  0.9779    14168.602
   2_occ:  22.935 0.8324  0.9774    14195.229
   3_bss:  22.819 0.8334  0.9632    14054.232
   3_xyz:  18.494 0.8752  0.9911     9563.067
   3_adp:  17.327 0.8865  0.9915     8726.907
   3_occ:  17.333 0.8865  0.9913     8734.229
   4_bss:  17.372 0.8862  0.9774     8784.372
   4_xyz:  15.542 0.9020  0.9845     7285.558
   4_adp:  15.224 0.9050  0.9801     7137.854
   4_occ:  15.226 0.9050  0.9800     7140.672
   5_bss:  15.223 0.9050  0.9810     7146.139
   5_xyz:  14.610 0.9101  0.9827     6680.748
   5_adp:  14.233 0.9133  0.9799     6483.879
   5_occ:  14.238 0.9132  0.9798     6493.232
   5_bss:  14.279 0.9130  0.9802     6550.075
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9780e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9780e-01
   1_xyz:   1.598  0.013  0.098 16.757  0.007  4.112   1.4319e-01
   1_adp:   1.598  0.013  0.098 16.757  0.007  4.112   1.4319e-01
   1_occ:   1.598  0.013  0.098 16.757  0.007  4.112   1.4319e-01
   2_bss:   1.598  0.013  0.098 16.757  0.007  4.112   1.4319e-01
   2_xyz:   1.037  0.007  0.068 14.761  0.004  4.110   6.3115e-02
   2_adp:   1.037  0.007  0.068 14.761  0.004  4.110   6.3115e-02
   2_occ:   1.037  0.007  0.068 14.761  0.004  4.110   6.3115e-02
   3_bss:   1.037  0.007  0.068 14.761  0.004  4.110   6.3115e-02
   3_xyz:   0.946  0.006  0.062 14.572  0.003  4.114   5.3835e-02
   3_adp:   0.946  0.006  0.062 14.572  0.003  4.114   5.3835e-02
   3_occ:   0.946  0.006  0.062 14.572  0.003  4.114   5.3835e-02
   4_bss:   0.946  0.006  0.062 14.572  0.003  4.114   5.3835e-02
   4_xyz:   0.941  0.005  0.067 14.596  0.003  4.109   5.2123e-02
   4_adp:   0.941  0.005  0.067 14.596  0.003  4.109   5.2123e-02
   4_occ:   0.941  0.005  0.067 14.596  0.003  4.109   5.2123e-02
   5_bss:   0.941  0.005  0.067 14.596  0.003  4.109   5.2123e-02
   5_xyz:   1.016  0.007  0.071 14.817  0.004  4.110   5.9258e-02
   5_adp:   1.016  0.007  0.071 14.817  0.004  4.110   5.9258e-02
   5_occ:   1.016  0.007  0.071 14.817  0.004  4.110   5.9258e-02
   5_bss:   1.016  0.007  0.071 14.817  0.004  4.110   5.9258e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.422   2.4061e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.422   2.4061e-01
   1_xyz:  10.854  0.109  0.391 88.191  0.057  2.145   1.3506e-01
   1_adp:  10.854  0.109  0.391 88.191  0.057  2.145   1.3506e-01
   1_occ:  10.854  0.109  0.391 88.191  0.057  2.145   1.3506e-01
   2_bss:  10.854  0.109  0.391 88.191  0.057  2.145   1.3506e-01
   2_xyz:   7.831  0.042  0.216 85.406  0.041  2.321   7.9796e-02
   2_adp:   7.831  0.042  0.216 85.406  0.041  2.321   7.9796e-02
   2_occ:   7.831  0.042  0.216 85.406  0.041  2.321   7.9796e-02
   3_bss:   7.831  0.042  0.216 85.406  0.041  2.321   7.9796e-02
   3_xyz:   7.187  0.035  0.217 81.565  0.031  2.394   5.2539e-02
   3_adp:   7.187  0.035  0.217 81.565  0.031  2.394   5.2539e-02
   3_occ:   7.187  0.035  0.217 81.565  0.031  2.394   5.2539e-02
   4_bss:   7.187  0.035  0.217 81.565  0.031  2.394   5.2539e-02
   4_xyz:   6.763  0.033  0.198 82.966  0.028  2.381   3.5062e-02
   4_adp:   6.763  0.033  0.198 82.966  0.028  2.381   3.5062e-02
   4_occ:   6.763  0.033  0.198 82.966  0.028  2.381   3.5062e-02
   5_bss:   6.763  0.033  0.198 82.966  0.028  2.381   3.5062e-02
   5_xyz:   7.018  0.036  0.236 80.783  0.023  2.316   4.5520e-02
   5_adp:   7.018  0.036  0.236 80.783  0.023  2.316   4.5520e-02
   5_occ:   7.018  0.036  0.236 80.783  0.023  2.316   4.5520e-02
   5_bss:   7.018  0.036  0.236 80.783  0.023  2.316   4.5520e-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:  68.91   0.00  18.12  60.03   0.00  14.19  68.91   2.26  39.50
   1_occ:  68.91   0.00  18.12  60.03   0.00  14.19  68.91   2.26  39.50
   2_bss:  68.91   0.00  18.12  60.03   0.00  14.19  68.91   2.26  39.50
   2_xyz:  68.91   0.00  18.12  60.03   0.00  14.19  68.91   2.26  39.50
   2_adp:  84.27   0.00  17.85  84.27   0.00  13.62  79.87   6.41  40.92
   2_occ:  84.27   0.00  17.85  84.27   0.00  13.62  79.87   6.41  40.92
   3_bss:  84.27   0.00  17.85  84.27   0.00  13.62  79.87   6.41  40.92
   3_xyz:  84.27   0.00  17.85  84.27   0.00  13.62  79.87   6.41  40.92
   3_adp:  87.79   0.00  17.70  87.79   0.00  13.22  81.08   6.46  42.10
   3_occ:  87.79   0.00  17.70  87.79   0.00  13.22  81.08   6.46  42.10
   4_bss:  87.79   0.00  17.70  87.79   0.00  13.22  81.08   6.46  42.10
   4_xyz:  87.79   0.00  17.70  87.79   0.00  13.22  81.08   6.46  42.10
   4_adp: 101.73   0.95  17.71 101.73   0.95  13.06  86.91   5.87  43.01
   4_occ: 101.73   0.95  17.71 101.73   0.95  13.06  86.91   5.87  43.01
   5_bss: 101.73   0.95  17.71 101.73   0.95  13.06  86.91   5.87  43.01
   5_xyz: 101.73   0.95  17.71 101.73   0.95  13.06  86.91   5.87  43.01
   5_adp:  94.55   1.90  16.79  94.55   1.90  12.68  87.85   5.57  39.20
   5_occ:  94.55   1.90  16.79  94.55   1.90  12.68  87.85   5.57  39.20
   5_bss:  94.48   1.84  16.72  94.48   1.84  12.61  87.78   5.50  39.13
------------------------------------------------------------------------
 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:    1.795    0.036    0.491
   1_adp:    1.795    0.036    0.491
   1_occ:    1.795    0.036    0.491
   2_bss:    1.795    0.036    0.491
   2_xyz:    1.406    0.030    0.567
   2_adp:    1.406    0.030    0.567
   2_occ:    1.406    0.030    0.567
   3_bss:    1.406    0.030    0.567
   3_xyz:    1.512    0.034    0.653
   3_adp:    1.512    0.034    0.653
   3_occ:    1.512    0.034    0.653
   4_bss:    1.512    0.034    0.653
   4_xyz:    1.591    0.072    0.692
   4_adp:    1.591    0.072    0.692
   4_occ:    1.591    0.072    0.692
   5_bss:    1.591    0.072    0.692
   5_xyz:    1.609    0.090    0.715
   5_adp:    1.609    0.090    0.715
   5_occ:    1.609    0.090    0.715
   5_bss:    1.609    0.090    0.715
------------------------------------------------------------------------

CPU time actual refinement: 330.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_451/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_451/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_451/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_451/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_451/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.59 
  Macro-tasks:
    bulk solvent and scale       = 42.85  
    individual site refinement   = 130.88 
    weights calculation          = 29.44  
    collect and process          = 6.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 209.79 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 104.22 
    alpha_beta                      = 8.07   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 111.78 
    fmodel                         = 7.24   
    r_factors                      = 0.17   
    phase_errors                   = 10.70  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 246.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.746 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    629 calls, 103.86 s
gradients_fft:          574 calls,  99.08 s

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

# Date 2008-01-16 Time 04:51:05 PST -0800 (1200487865.55 s)
Start R-work = 0.4512, R-free = 0.4458 (no bulk solvent and anisotropic scale)
Final R-work = 0.1383, R-free = 0.1812 (no bulk solvent and anisotropic scale)

Start R-work = 0.4416, R-free = 0.4358
Final R-work = 0.1146, R-free = 0.1608