# Date 2008-01-16 Time 04:52:11 PST -0800 (1200487931.64 s)
#phil __OFF__

Command line arguments: "../496.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6249
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 496

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.9914, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96037
Completeness in resolution range: 0.971532
Completeness with d_max=infinity: 0.968554

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9604

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96037
Completeness in resolution range: 0.971532
Completeness with d_max=infinity: 0.968554

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1948 [2112/2137]  1902   210   9.9%
  bin  2:  4.1948 -  3.3420 [2039/2059]  1834   205  10.1%
  bin  3:  3.3420 -  2.9232 [2004/2023]  1801   203  10.1%
  bin  4:  2.9232 -  2.6576 [1989/2019]  1797   192   9.7%
  bin  5:  2.6576 -  2.4680 [1985/2004]  1787   198  10.0%
  bin  6:  2.4680 -  2.3231 [1969/1994]  1769   200  10.2%
  bin  7:  2.3231 -  2.2071 [1941/1969]  1742   199  10.3%
  bin  8:  2.2071 -  2.1113 [1962/1998]  1768   194   9.9%
  bin  9:  2.1113 -  2.0303 [1949/1991]  1758   191   9.8%
  bin 10:  2.0303 -  1.9604 [1639/1969]  1472   167  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_496/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: 0.12 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:
        1.62 -     2.27: 38
        2.27 -     2.93: 1604
        2.93 -     3.59: 4635
        3.59 -     4.24: 9404
        4.24 -     4.90: 13285
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.615 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.640 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.736 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.774 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28961 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_496/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_496/model_refine_001.geo

CPU time processing inputs: 8.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.9914 84.6622 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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4573   r_free= 0.4599   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267718                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6787 0.99   1381  154 0.3696 0.3649      6.5474      6.5449|
|  2:  4.6787 -  3.7330 0.99   1324  146 0.3961 0.3870      6.7912      6.7389|
|  3:  3.7330 -  3.2668 0.99   1289  142 0.4237 0.4301      6.6728      6.7659|
|  4:  3.2668 -  2.9707 0.99   1283  147 0.4327 0.4422      6.5227      6.4977|
|  5:  2.9707 -  2.7593 0.99   1291  140 0.4877 0.4522      6.3682      6.3404|
|  6:  2.7593 -  2.5975 0.99   1278  142 0.4851 0.5402      6.2794       6.261|
|  7:  2.5975 -  2.4680 0.99   1275  137 0.4891 0.4929      6.2282      6.2069|
|  8:  2.4680 -  2.3610 0.98   1255  146 0.4933 0.4908      6.1815      6.1777|
|  9:  2.3610 -  2.2705 0.98   1257  137 0.5118 0.5152      6.1222      6.1472|
| 10:  2.2705 -  2.1924 1.00   1267  143 0.4939 0.4976      6.0955      6.1115|
| 11:  2.1924 -  2.1240 0.97   1249  135 0.5074 0.5247      6.0399      6.0793|
| 12:  2.1240 -  2.0635 0.98   1244  142 0.4973 0.5075       5.974      6.0133|
| 13:  2.0635 -  2.0093 1.00   1257  138 0.4989 0.5038      5.8828      5.8474|
| 14:  2.0093 -  1.9604 0.77    980  110 0.5372 0.4462      5.8803      5.7343|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6787  1381   154  0.70  34.36   0.83     0.75      70790.06|
|  2:  4.6787 -  3.7330  1324   146  0.71  34.59   0.91     0.83     104816.26|
|  3:  3.7330 -  3.2668  1289   142  0.61  42.88   0.95     0.81     112968.24|
|  4:  3.2668 -  2.9707  1283   147  0.52  50.15   0.95     0.71     103293.76|
|  5:  2.9707 -  2.7593  1291   140  0.42  58.05   0.90     0.61      82825.03|
|  6:  2.7593 -  2.5975  1278   142  0.39  60.40   0.92     0.54      72917.42|
|  7:  2.5975 -  2.4680  1275   137  0.37  62.04   0.92     0.52      66046.91|
|  8:  2.4680 -  2.3610  1255   146  0.37  62.41   0.94     0.54      59845.95|
|  9:  2.3610 -  2.2705  1257   137  0.38  61.54   0.91     0.55      53111.27|
| 10:  2.2705 -  2.1924  1267   143  0.39  60.58   0.97     0.57      47622.50|
| 11:  2.1924 -  2.1240  1249   135  0.36  62.95   0.98     0.55      45142.53|
| 12:  2.1240 -  2.0635  1244   142  0.39  61.03   1.00     0.61      40826.69|
| 13:  2.0635 -  2.0093  1257   138  0.41  59.17   0.96     0.65      32847.83|
| 14:  2.0093 -  1.9604   980   110  0.50  51.96   0.96     0.71      22557.68|
|alpha:            min =        0.52 max =            0.83 mean =         0.64|
|beta:             min =    22557.68 max =       112968.24 mean =     66465.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.25|
|phase err.(test): min =        0.00 max =           89.97 mean =        54.56|
|-----------------------------------------------------------------------------|

============================== 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 = 11.120776             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.266   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.378897              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.952   (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 |  1.615 -  1.944:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.944 -  2.272:       29 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.272 -  2.601:       64 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.601 -  2.929:     1540 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.929 -  3.258:     1981 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.258 -  3.586:     2654 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.586 -  3.915:     4797 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.915 -  4.243:     4607 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.243 -  4.572:     6051 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.572 -  4.900:     7234 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.615 |       0.523 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4573   r_free= 0.4599   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4459   r_free= 0.4468   ksol= 0.35   Bsol= 24.35   scale= 0.939   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.37,2.09,1.33,0.00,0.00,0.00); trace/3= 0.02                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.261991                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.718385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.235   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.235164              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.868   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4459      final r-factor (work) = 0.3321          |
| start r-factor (free) = 0.4468      final r-factor (free) = 0.3589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.4576 = 8.72 * 0.50 * 6.2569 + 1.00 * 0.1826                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8260 = 8.72 * 0.50 * 6.1223 + 1.00 * 0.1379                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3321      final r-factor (work) = 0.3005          |
| start r-factor (free) = 0.3589      final r-factor (free) = 0.3764          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5680 = 1.24 * 1.00 * 6.1223 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4123 = 1.24 * 1.00 * 5.9854 + 1.00 * 0.0194                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.94   18.78    None  None   None       |
|    all(noH): 2823   0      0.00    93.94   18.78    None  None   None       |
|    Sol.    : 438    0      0.86    93.94   38.80    None  None   None       |
|    Mac.    : 2385   0      0.00    90.28   15.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.394:  849   |   5:    46.968 -  56.362:   99        |
|      1:     9.394 -  18.787:  905   |   6:    56.362 -  65.756:   47        |
|      2:    18.787 -  28.181:  475   |   7:    65.756 -  75.150:   20        |
|      3:    28.181 -  37.575:  270   |   8:    75.150 -  84.543:   10        |
|      4:    37.575 -  46.968:  145   |   9:    84.543 -  93.937:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3005 r_free = 0.3764             target_work(ml) = 5.997         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2999 r_free = 0.3765             target_work(ml) = 5.996         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2999   r_free= 0.3765   ksol= 0.35   Bsol= 24.35   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.37,2.09,1.33,0.00,0.00,0.00); trace/3= 0.02                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.995986                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2972   r_free= 0.3748   ksol= 0.33   Bsol= 40.85   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-0.06,-0.06,-0.00,-0.00,-0.00); trace/3= -0.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.993367                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.949054              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.891   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.299985              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.701  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2972      final r-factor (work) = 0.2371          |
| start r-factor (free) = 0.3748      final r-factor (free) = 0.3080          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9442 = 4.95 * 0.50 * 5.9835 + 1.00 * 0.1379                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6892 = 4.95 * 0.50 * 5.9089 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2371      final r-factor (work) = 0.2265          |
| start r-factor (free) = 0.3080      final r-factor (free) = 0.2895          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7919 = 0.30 * 1.00 * 5.9089 + 1.00 * 0.0193                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7562 = 0.30 * 1.00 * 5.7915 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.33   17.72    None  None   None       |
|    all(noH): 2823   0      0.00    92.33   17.72    None  None   None       |
|    Sol.    : 438    0      4.10    92.33   38.01    None  None   None       |
|    Mac.    : 2385   0      0.00    88.78   14.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.233:  823   |   5:    46.166 -  55.399:   79        |
|      1:     9.233 -  18.467: 1086   |   6:    55.399 -  64.633:   42        |
|      2:    18.467 -  27.700:  398   |   7:    64.633 -  73.866:   14        |
|      3:    27.700 -  36.933:  207   |   8:    73.866 -  83.099:    7        |
|      4:    36.933 -  46.166:  165   |   9:    83.099 -  92.332:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2265 r_free = 0.2895             target_work(ml) = 5.765         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2263 r_free = 0.2898             target_work(ml) = 5.765         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2263   r_free= 0.2898   ksol= 0.33   Bsol= 40.85   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-0.06,-0.06,-0.00,-0.00,-0.00); trace/3= -0.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.764586                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2261   r_free= 0.2895   ksol= 0.33   Bsol= 40.85   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.06,-0.92,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.763752                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.390382              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.585   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.291835              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.371   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2261      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2895      final r-factor (free) = 0.2139          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7801 = 4.39 * 0.50 * 5.7913 + 1.00 * 0.0672                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4340 = 4.39 * 0.50 * 5.6329 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1648      final r-factor (work) = 0.1467          |
| start r-factor (free) = 0.2139      final r-factor (free) = 0.1967          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6535 = 0.29 * 1.00 * 5.6329 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5882 = 0.29 * 1.00 * 5.4136 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    87.18   17.27    None  None   None       |
|    all(noH): 2823   0      1.63    87.18   17.27    None  None   None       |
|    Sol.    : 438    0      6.22    85.09   40.67    None  None   None       |
|    Mac.    : 2385   0      1.63    87.18   12.98    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:     1.630 -  10.185: 1065   |   5:    44.404 -  52.958:  114        |
|      1:    10.185 -  18.739: 1031   |   6:    52.958 -  61.513:   73        |
|      2:    18.739 -  27.294:  245   |   7:    61.513 -  70.068:   35        |
|      3:    27.294 -  35.849:  141   |   8:    70.068 -  78.622:    8        |
|      4:    35.849 -  44.404:  109   |   9:    78.622 -  87.177:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1467 r_free = 0.1967             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1464 r_free = 0.1959             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1959   ksol= 0.33   Bsol= 40.85   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.06,-0.92,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.367395                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1951   ksol= 0.32   Bsol= 38.74   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.07,-1.35,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.364244                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.888989              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.515   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.206893              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.913  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1467      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.1951      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1841 = 1.89 * 0.50 * 5.4160 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0633 = 1.89 * 0.50 * 5.3065 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.1743      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1062 = 0.21 * 1.00 * 5.3065 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0902 = 0.21 * 1.00 * 5.2314 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    87.41   17.00    None  None   None       |
|    all(noH): 2823   0      1.29    87.41   17.00    None  None   None       |
|    Sol.    : 438    0      4.87    81.05   40.42    None  None   None       |
|    Mac.    : 2385   0      1.29    87.41   12.70    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:     1.294 -   9.906: 1022   |   5:    44.354 -  52.966:  102        |
|      1:     9.906 -  18.518: 1108   |   6:    52.966 -  61.577:   79        |
|      2:    18.518 -  27.130:  233   |   7:    61.577 -  70.189:   36        |
|      3:    27.130 -  35.742:  123   |   8:    70.189 -  78.801:    6        |
|      4:    35.742 -  44.354:  111   |   9:    78.801 -  87.413:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1243 r_free = 0.1695             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1241 r_free = 0.1692             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1692   ksol= 0.32   Bsol= 38.74   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.07,-1.35,-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: 5.216195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1692   ksol= 0.32   Bsol= 38.74   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.07,-1.35,-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: 5.216195                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.339353              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445394              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.697  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1241      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1695 = 2.34 * 0.50 * 5.2310 + 1.00 * 0.0510                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1164 = 2.34 * 0.50 * 5.1785 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3143 = 0.45 * 1.00 * 5.1785 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2988 = 0.45 * 1.00 * 5.1419 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.69    91.58   16.98    None  None   None       |
|    all(noH): 2823   0      0.69    91.58   16.98    None  None   None       |
|    Sol.    : 438    0      5.73    84.26   40.83    None  None   None       |
|    Mac.    : 2385   0      0.69    91.58   12.59    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:     0.695 -   9.784: 1024   |   5:    46.139 -  55.228:  104        |
|      1:     9.784 -  18.873: 1129   |   6:    55.228 -  64.317:   68        |
|      2:    18.873 -  27.961:  230   |   7:    64.317 -  73.406:   31        |
|      3:    27.961 -  37.050:  123   |   8:    73.406 -  82.495:    5        |
|      4:    37.050 -  46.139:  105   |   9:    82.495 -  91.584:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1583             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1583             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1583   ksol= 0.32   Bsol= 38.74   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.07,-1.35,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140050                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6787 0.99   1381  154 0.1005 0.1245      5.3774      5.5167|
|  2:  4.6787 -  3.7330 0.99   1324  146 0.0854 0.1145      5.4454      5.6499|
|  3:  3.7330 -  3.2668 0.99   1289  142 0.1095 0.1467      5.5081       5.856|
|  4:  3.2668 -  2.9707 0.99   1283  147 0.1262 0.1621      5.4795      5.6167|
|  5:  2.9707 -  2.7593 0.99   1291  140 0.1311 0.1748      5.3116      5.5334|
|  6:  2.7593 -  2.5975 0.99   1278  142 0.1160 0.1655      5.1873      5.3571|
|  7:  2.5975 -  2.4680 0.99   1275  137 0.1248 0.1670      5.1436      5.3955|
|  8:  2.4680 -  2.3610 0.98   1255  146 0.1172 0.1707      5.0609       5.342|
|  9:  2.3610 -  2.2705 0.98   1257  137 0.1151 0.1633      5.0215      5.2297|
| 10:  2.2705 -  2.1924 1.00   1267  143 0.1109 0.1936      4.9587      5.2918|
| 11:  2.1924 -  2.1240 0.97   1249  135 0.1115 0.1748      4.9501      5.2573|
| 12:  2.1240 -  2.0635 0.98   1244  142 0.1132 0.1694      4.8915      5.1811|
| 13:  2.0635 -  2.0093 1.00   1257  138 0.1100 0.1873      4.7891      5.1112|
| 14:  2.0093 -  1.9604 0.77    980  110 0.1039 0.1660      4.6677      4.8975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6787  1381   154  0.94   8.69   0.99     0.96       6541.89|
|  2:  4.6787 -  3.7330  1324   146  0.95   8.02   1.03     1.03       9113.02|
|  3:  3.7330 -  3.2668  1289   142  0.93  11.36   1.04     1.03      10711.73|
|  4:  3.2668 -  2.9707  1283   147  0.92  13.76   1.03     1.01      10495.21|
|  5:  2.9707 -  2.7593  1291   140  0.90  15.41   1.00     0.98       7777.72|
|  6:  2.7593 -  2.5975  1278   142  0.91  15.10   1.00     0.98       6691.26|
|  7:  2.5975 -  2.4680  1275   137  0.91  15.44   1.00     0.97       5897.67|
|  8:  2.4680 -  2.3610  1255   146  0.91  14.99   1.01     0.99       5103.12|
|  9:  2.3610 -  2.2705  1257   137  0.92  14.58   1.02     1.00       4840.97|
| 10:  2.2705 -  2.1924  1267   143  0.90  15.39   1.01     0.98       4379.82|
| 11:  2.1924 -  2.1240  1249   135  0.89  16.85   1.02     0.98       4558.58|
| 12:  2.1240 -  2.0635  1244   142  0.91  15.34   1.02     1.00       4037.80|
| 13:  2.0635 -  2.0093  1257   138  0.90  15.93   1.03     1.02       3369.43|
| 14:  2.0093 -  1.9604   980   110  0.92  14.23   1.01     0.98       2561.76|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2561.76 max =        10711.73 mean =      6238.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.87|
|phase err.(test): min =        0.00 max =           89.27 mean =        13.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1586   ksol= 0.32   Bsol= 38.90   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.05,-1.33,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1586   ksol= 0.32   Bsol= 38.90   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.05,-1.33,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140979                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6787 0.99   1381  154 0.0990 0.1269      5.3657      5.5202|
|  2:  4.6787 -  3.7330 0.99   1324  146 0.0871 0.1157      5.4565      5.6681|
|  3:  3.7330 -  3.2668 0.99   1289  142 0.1097 0.1463      5.5125      5.8495|
|  4:  3.2668 -  2.9707 0.99   1283  147 0.1268 0.1631      5.4809      5.6212|
|  5:  2.9707 -  2.7593 0.99   1291  140 0.1316 0.1743      5.3172      5.5313|
|  6:  2.7593 -  2.5975 0.99   1278  142 0.1161 0.1669      5.1909      5.3618|
|  7:  2.5975 -  2.4680 0.99   1275  137 0.1250 0.1676      5.1464      5.3993|
|  8:  2.4680 -  2.3610 0.98   1255  146 0.1169 0.1704      5.0611      5.3406|
|  9:  2.3610 -  2.2705 0.98   1257  137 0.1147 0.1641      5.0202       5.234|
| 10:  2.2705 -  2.1924 1.00   1267  143 0.1104 0.1932      4.9585      5.2888|
| 11:  2.1924 -  2.1240 0.97   1249  135 0.1111 0.1744      4.9485      5.2571|
| 12:  2.1240 -  2.0635 0.98   1244  142 0.1132 0.1687      4.8911      5.1786|
| 13:  2.0635 -  2.0093 1.00   1257  138 0.1100 0.1870      4.7888      5.1117|
| 14:  2.0093 -  1.9604 0.77    980  110 0.1037 0.1661      4.6675      4.8985|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6787  1381   154  0.94   8.65   0.99     0.96       6668.64|
|  2:  4.6787 -  3.7330  1324   146  0.95   8.09   1.03     1.03       9241.41|
|  3:  3.7330 -  3.2668  1289   142  0.93  11.43   1.04     1.03      10851.67|
|  4:  3.2668 -  2.9707  1283   147  0.92  13.81   1.03     1.01      10546.49|
|  5:  2.9707 -  2.7593  1291   140  0.90  15.52   1.01     0.98       7863.49|
|  6:  2.7593 -  2.5975  1278   142  0.91  15.19   1.00     0.98       6768.33|
|  7:  2.5975 -  2.4680  1275   137  0.90  15.52   1.00     0.97       5951.49|
|  8:  2.4680 -  2.3610  1255   146  0.91  15.02   1.01     0.99       5132.00|
|  9:  2.3610 -  2.2705  1257   137  0.92  14.60   1.02     1.00       4843.76|
| 10:  2.2705 -  2.1924  1267   143  0.90  15.40   1.01     0.98       4386.91|
| 11:  2.1924 -  2.1240  1249   135  0.89  16.82   1.02     0.98       4547.86|
| 12:  2.1240 -  2.0635  1244   142  0.91  15.33   1.02     1.00       4035.88|
| 13:  2.0635 -  2.0093  1257   138  0.90  15.92   1.03     1.02       3369.13|
| 14:  2.0093 -  1.9604   980   110  0.92  14.25   1.01     0.98       2566.15|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2566.15 max =        10851.67 mean =      6289.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.90|
|phase err.(test): min =        0.00 max =           89.86 mean =        13.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    91.56   16.95    None  None   None       |
|    all(noH): 2823   0      0.67    91.56   16.95    None  None   None       |
|    Sol.    : 438    0      5.71    84.24   40.81    None  None   None       |
|    Mac.    : 2385   0      0.67    91.56   12.57    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:     0.672 -   9.761: 1024   |   5:    46.116 -  55.205:  104        |
|      1:     9.761 -  18.849: 1129   |   6:    55.205 -  64.294:   68        |
|      2:    18.849 -  27.938:  230   |   7:    64.294 -  73.383:   31        |
|      3:    27.938 -  37.027:  123   |   8:    73.383 -  82.472:    5        |
|      4:    37.027 -  46.116:  105   |   9:    82.472 -  91.561:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 5.034
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 323
   mapped sites are within: 0.741 - 5.034

peak=    6.740 closest distance to " NE2 GLN A  11 " =    1.339
peak=    6.133 closest distance to " O   HOH Z 126 " =    2.092
peak=    6.080 closest distance to " O   HOH Z 144 " =    1.830
peak=    5.543 closest distance to " O   HOH Z 130 " =    0.857
peak=    5.486 closest distance to " O   HOH Z  65 " =    1.131
peak=    5.362 closest distance to " O   HOH Z   7 " =    1.501
peak=    5.349 closest distance to " CG  PRO A  54 " =    1.227
peak=    5.341 closest distance to " NH2 ARG A  56 " =    2.068
peak=    5.302 closest distance to " O   HOH Z 112 " =    1.419
peak=    5.178 closest distance to " O   HOH Z 124 " =    1.587
peak=    5.138 closest distance to " O   HOH Z  78 " =    1.643
peak=    5.097 closest distance to " O   HOH Z 427 " =    2.235
peak=    4.958 closest distance to " O   HOH Z 287 " =    1.910
peak=    4.834 closest distance to " O   HOH Z 380 " =    1.718
peak=    4.775 closest distance to " CG  PRO A 213 " =    1.258
peak=    4.766 closest distance to " O   HOH Z  28 " =    1.364
peak=    4.765 closest distance to " O   HOH Z 236 " =    1.443
peak=    4.750 closest distance to " CB  SER A   3 " =    1.345
peak=    4.688 closest distance to " O   HOH Z  63 " =    1.730
peak=    4.644 closest distance to " O   HOH Z 278 " =    1.137
peak=    4.638 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.610 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.580 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.579 closest distance to " O   HOH Z 193 " =    1.822
peak=    4.579 closest distance to " O   HOH Z 209 " =    2.255
peak=    4.535 closest distance to " O   HOH Z 419 " =    2.324
peak=    4.434 closest distance to " CB  SER A  63 " =    1.213
peak=    4.427 closest distance to " O   HOH Z  11 " =    1.361
peak=    4.424 closest distance to " O   HOH Z 371 " =    2.185
peak=    4.415 closest distance to " O   HOH Z 403 " =    1.341
peak=    4.406 closest distance to " O   HOH Z 272 " =    1.761
peak=    4.400 closest distance to " O   HOH Z 222 " =    1.014
peak=    4.396 closest distance to " CG2 VAL A 257 " =    0.901
peak=    4.383 closest distance to " CB  GLN A 223 " =    1.570
peak=    4.322 closest distance to " O   HOH Z 298 " =    1.908
peak=    4.319 closest distance to " O   HOH Z 394 " =    1.605
peak=    4.305 closest distance to " O   HOH Z 417 " =    1.425
peak=    4.290 closest distance to " CG  ARG A  66 " =    2.492
peak=    4.221 closest distance to " O   HOH Z 425 " =    1.416
peak=    4.200 closest distance to " O   HOH Z 214 " =    1.197
peak=    4.189 closest distance to " O   HOH Z 232 " =    2.123
peak=    4.182 closest distance to " CB  ARG A 139 " =    1.072
peak=    4.182 closest distance to " CG  TRP A 179 " =    2.189
peak=    4.180 closest distance to " O   SER A  87 " =    2.182
peak=    4.169 closest distance to " CB  GLN A 183 " =    1.192
peak=    4.163 closest distance to " CB  TYR A 169 " =    0.933
peak=    4.130 closest distance to " O   HOH Z 378 " =    1.072
peak=    4.111 closest distance to " O   HOH Z 423 " =    1.508
peak=    4.108 closest distance to " O   HOH Z 166 " =    1.491
peak=    4.093 closest distance to " CB  GLU A 128 " =    1.008
peak=    4.086 closest distance to " O   HOH Z 217 " =    2.989
peak=    4.080 closest distance to " O   HOH Z 352 " =    1.612
peak=    4.077 closest distance to " O   HOH Z 313 " =    1.708
peak=    4.072 closest distance to " CG  PRO A 198 " =    1.236
peak=    4.070 closest distance to " O   HOH Z   1 " =    1.802
peak=    4.062 closest distance to " CB  GLU A 152 " =    1.266
peak=    4.053 closest distance to " CG  GLN A  11 " =    2.083
peak=    4.048 closest distance to " O   HOH Z 405 " =    1.303
peak=    4.048 closest distance to " O   HOH Z 234 " =    3.567
peak=    4.047 closest distance to " O   HOH Z 302 " =    1.343
peak=    4.043 closest distance to " O   HOH Z 371 " =    1.788
peak=    4.042 closest distance to " O   HOH Z 108 " =    1.592
peak=    4.027 closest distance to " OD1 ASN A  69 " =    2.572
peak=    4.000 closest distance to " CA  TYR A  30 " =    0.978
peak=    3.998 closest distance to " OG ASER A 258 " =    3.009
peak=    3.987 closest distance to " O   HOH Z 368 " =    3.559
peak=    3.973 closest distance to " O   HOH Z  61 " =    1.674
peak=    3.946 closest distance to " O   HOH Z 261 " =    1.655
peak=    3.946 closest distance to " O   HOH Z 207 " =    1.749
peak=    3.922 closest distance to " O   HOH Z  59 " =    2.086
peak=    3.894 closest distance to " O   PRO A 198 " =    1.564
peak=    3.891 closest distance to " O   HOH Z  97 " =    1.943
peak=    3.877 closest distance to " O   HOH Z 213 " =    1.755
peak=    3.874 closest distance to " O   HOH Z 385 " =    0.862
peak=    3.866 closest distance to " CB  TRP A 179 " =    1.300
peak=    3.864 closest distance to " O   HOH Z   9 " =    2.211
peak=    3.856 closest distance to " O   HOH Z 392 " =    1.305
peak=    3.845 closest distance to " O   HOH Z  49 " =    1.146
peak=    3.841 closest distance to " O   HOH Z 286 " =    2.396
peak=    3.838 closest distance to " CG2 THR A 221 " =    1.250
peak=    3.820 closest distance to " OG BSER A  99 " =    2.202
peak=    3.805 closest distance to " OG BSER A 164 " =    2.416
peak=    3.789 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.788 closest distance to " CG1 ILE A  33 " =    1.212
peak=    3.786 closest distance to " O   HOH Z 245 " =    1.292
peak=    3.785 closest distance to " O   HOH Z  92 " =    1.289
peak=    3.784 closest distance to " O   HOH Z 227 " =    1.902
peak=    3.781 closest distance to " O   HOH Z 427 " =    1.117
peak=    3.779 closest distance to " O   HOH Z 183 " =    1.384
peak=    3.771 closest distance to " CB  VAL A 265 " =    1.390
peak=    3.758 closest distance to " CA  ALA A 299 " =    0.964
peak=    3.756 closest distance to " O   HOH Z 158 " =    2.709
peak=    3.746 closest distance to " O   HOH Z 128 " =    2.139
peak=    3.739 closest distance to " NH1BARG A 145 " =    1.322
peak=    3.731 closest distance to " O   HOH Z 215 " =    1.370
peak=    3.727 closest distance to " OD2 ASP A 286 " =    2.484
peak=    3.721 closest distance to " CA  GLY A 241 " =    3.603
peak=    3.719 closest distance to " O   HOH Z 250 " =    1.348
peak=    3.696 closest distance to " O   HOH Z 281 " =    1.741
peak=    3.692 closest distance to " O   HOH Z 425 " =    1.921
peak=    3.691 closest distance to " O   HOH Z  44 " =    3.051
peak=    3.690 closest distance to " OG  SER A  62 " =    2.979
peak=    3.690 closest distance to " O   HOH Z 435 " =    1.801
peak=    3.683 closest distance to " O   HOH Z 155 " =    1.704
peak=    3.683 closest distance to " O   HOH Z 128 " =    2.010
peak=    3.675 closest distance to " O   HOH Z 134 " =    1.295
peak=    3.672 closest distance to " O   HOH Z   1 " =    1.577
peak=    3.671 closest distance to " O   HOH Z 151 " =    1.656
peak=    3.663 closest distance to " O   HOH Z 375 " =    0.953
peak=    3.659 closest distance to " O   HOH Z 365 " =    2.686
peak=    3.658 closest distance to " O   HOH Z 260 " =    1.151
peak=    3.651 closest distance to " N   GLN A 278 " =    1.105
peak=    3.643 closest distance to " O   HOH Z 357 " =    1.827
peak=    3.636 closest distance to " O   HOH Z 371 " =    3.013
peak=    3.635 closest distance to " CB  THR A 157 " =    1.063
peak=    3.630 closest distance to " O   HOH Z 393 " =    1.310
peak=    3.623 closest distance to " CG  PRO A  90 " =    1.296
peak=    3.620 closest distance to " O   HOH Z  44 " =    1.835
peak=    3.618 closest distance to " ND2 ASN A 187 " =    1.604
peak=    3.616 closest distance to " O   HOH Z 282 " =    1.564
peak=    3.599 closest distance to " N   HIS A  86 " =    1.856
peak=    3.591 closest distance to " O   HOH Z  73 " =    1.857
peak=    3.584 closest distance to " O   HOH Z 108 " =    1.804
peak=    3.583 closest distance to " O   HOH Z  10 " =    1.725
peak=    3.583 closest distance to " O   HOH Z 175 " =    2.015
peak=    3.582 closest distance to " O   HOH Z   6 " =    2.115
peak=    3.572 closest distance to " NE2 GLN A  73 " =    3.475
peak=    3.569 closest distance to " NH2 ARG A 219 " =    1.787
peak=    3.566 closest distance to " O   GLY A 302 " =    1.700
peak=    3.565 closest distance to " CB  SER A  26 " =    1.514
peak=    3.564 closest distance to " O   HOH Z  93 " =    1.925
peak=    3.560 closest distance to " O   HOH Z 359 " =    1.340
peak=    3.559 closest distance to " CA  ASN A 215 " =    1.192
peak=    3.554 closest distance to " O   HOH Z 362 " =    1.999
peak=    3.553 closest distance to " CB  SER A 216 " =    0.744
peak=    3.545 closest distance to " CG  LEU A 167 " =    1.241
peak=    3.541 closest distance to " NE AARG A 275 " =    1.683
peak=    3.536 closest distance to " O   HOH Z 139 " =    1.302
peak=    3.527 closest distance to " CB  SER A 276 " =    1.102
peak=    3.527 closest distance to " O   HOH Z 207 " =    1.907
peak=    3.526 closest distance to " N   PHE A 130 " =    1.327
peak=    3.526 closest distance to " O   HOH Z 389 " =    1.722
peak=    3.524 closest distance to " O   HOH Z 217 " =    1.631
peak=    3.523 closest distance to " O   HOH Z 145 " =    1.225
peak=    3.523 closest distance to " O   HOH Z 119 " =    1.391
peak=    3.521 closest distance to " CB  ILE A 120 " =    1.298
peak=    3.518 closest distance to " O   HOH Z 144 " =    2.283
peak=    3.515 closest distance to " O   HOH Z 244 " =    1.659
peak=    3.514 closest distance to " O   HOH Z 355 " =    1.662
peak=    3.512 closest distance to " O   HOH Z   2 " =    1.586
peak=    3.512 closest distance to " O   HOH Z  50 " =    1.592
peak=    3.511 closest distance to " O   HOH Z 116 " =    2.597
peak=    3.509 closest distance to " NH2AARG A 190 " =    1.401
peak=    3.507 closest distance to " O   HOH Z  88 " =    2.792
peak=    3.505 closest distance to " O   HOH Z 189 " =    1.959
peak=    3.503 closest distance to " O   HOH Z 130 " =    2.616
peak=    3.502 closest distance to " O   HOH Z 344 " =    2.989
peak=    3.496 closest distance to " NE2 GLN A 278 " =    3.377
peak=    3.494 closest distance to " O   HOH Z 106 " =    2.433
peak=    3.492 closest distance to " O   HOH Z 258 " =    2.146
peak=    3.485 closest distance to " O   HOH Z 140 " =    1.528
peak=    3.483 closest distance to " N   ALA A   1 " =    2.904
peak=    3.481 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.481 closest distance to " O   HOH Z 214 " =    1.974
peak=    3.480 closest distance to " O   HOH Z  64 " =    1.949
peak=    3.475 closest distance to " O   HOH Z  15 " =    1.432
peak=    3.473 closest distance to " N   ALA A   1 " =    1.139
peak=    3.473 closest distance to " O   HOH Z  43 " =    1.945
peak=    3.470 closest distance to " O   HOH Z 368 " =    1.821
peak=    3.468 closest distance to " CA  SER A  32 " =    1.594
peak=    3.464 closest distance to " O   HOH Z 327 " =    1.875
peak=    3.464 closest distance to " O   HOH Z 432 " =    1.800
peak=    3.462 closest distance to " OD1BASN A 224 " =    2.125
peak=    3.460 closest distance to " N   ARG A 156 " =    1.282
peak=    3.459 closest distance to " O   HOH Z 173 " =    2.043
peak=    3.459 closest distance to " CG AARG A 275 " =    1.094
peak=    3.458 closest distance to " O   HOH Z  59 " =    1.399
peak=    3.452 closest distance to " O   HOH Z 303 " =    1.660
peak=    3.449 closest distance to " O   HOH Z 284 " =    1.465
peak=    3.448 closest distance to " O   HOH Z 414 " =    1.308
peak=    3.446 closest distance to " CE1 TYR A 186 " =    1.312
peak=    3.445 closest distance to " CA  THR A 264 " =    0.745
peak=    3.437 closest distance to " O   HOH Z 140 " =    1.892
peak=    3.434 closest distance to " CB  TRP A 266 " =    1.082
peak=    3.429 closest distance to " CA  ASN A 127 " =    0.953
peak=    3.427 closest distance to " O   HOH Z 188 " =    1.886
peak=    3.423 closest distance to " CA  ALA A  21 " =    1.190
peak=    3.403 closest distance to " OE2 GLU A  53 " =    2.069
peak=    3.400 closest distance to " O   HOH Z 152 " =    2.487
peak=    3.399 closest distance to " O   HOH Z  66 " =    2.084
peak=    3.399 closest distance to " CB  LEU A 228 " =    1.098
peak=    3.396 closest distance to " O   HOH Z 334 " =    1.610
peak=    3.393 closest distance to " O   HOH Z 132 " =    1.089
peak=    3.391 closest distance to " O   HOH Z 409 " =    2.098
peak=    3.391 closest distance to " CD1 ILE A 263 " =    1.288
peak=    3.390 closest distance to " CB  VAL A 202 " =    1.617
peak=    3.383 closest distance to " O   HOH Z  40 " =    2.088
peak=    3.382 closest distance to " O   HOH Z 132 " =    2.164
peak=    3.380 closest distance to " CB  ALA A  34 " =    1.167
peak=    3.372 closest distance to " O   HOH Z 112 " =    2.222
peak=    3.372 closest distance to " CG2BVAL A  41 " =    0.895
peak=    3.371 closest distance to " CB  GLU A 277 " =    3.399
peak=    3.370 closest distance to " O   GLY A 302 " =    1.912
peak=    3.369 closest distance to " O   HOH Z 133 " =    2.588
peak=    3.367 closest distance to " O   HOH Z 426 " =    1.896
peak=    3.361 closest distance to " CG  GLN A  77 " =    2.278
peak=    3.360 closest distance to " CA  PHE A 283 " =    1.353
peak=    3.355 closest distance to " O  BHOH Z  74 " =    1.406
peak=    3.352 closest distance to " CB  ARG A 102 " =    0.910
peak=    3.351 closest distance to " O   HOH Z 234 " =    1.880
peak=    3.347 closest distance to " NH2BARG A 145 " =    2.092
peak=    3.346 closest distance to " CD BLYS A 290 " =    1.113
peak=    3.346 closest distance to " O   HOH Z 422 " =    2.722
peak=    3.344 closest distance to " NZ  LYS A 117 " =    1.084
peak=    3.343 closest distance to " O   HOH Z 345 " =    3.282
peak=    3.338 closest distance to " O   HOH Z  21 " =    1.667
peak=    3.336 closest distance to " O   HOH Z  71 " =    1.269
peak=    3.335 closest distance to " O   HOH Z 343 " =    1.352
peak=    3.333 closest distance to " O   HOH Z 193 " =    2.023
peak=    3.332 closest distance to " O   HOH Z 158 " =    1.490
peak=    3.329 closest distance to " CG  MET A 185 " =    1.317
peak=    3.328 closest distance to " O   HOH Z 276 " =    1.255
peak=    3.323 closest distance to " CB  TYR A 116 " =    0.916
peak=    3.323 closest distance to " CB  LYS A 117 " =    1.152
peak=    3.322 closest distance to " OG  SER A  22 " =    2.795
peak=    3.322 closest distance to " NH1AARG A 145 " =    1.027
peak=    3.320 closest distance to " CB  LEU A 300 " =    0.986
peak=    3.319 closest distance to " CG  GLU A 277 " =    2.009
peak=    3.311 closest distance to " N   ASN A 127 " =    1.319
peak=    3.307 closest distance to " CE AMET A  47 " =    1.201
peak=    3.307 closest distance to " O   HOH Z 417 " =    2.254
peak=    3.304 closest distance to " O   HOH Z 434 " =    1.289
peak=    3.304 closest distance to " CZ AARG A 102 " =    1.885
peak=    3.303 closest distance to " CG1 VAL A 202 " =    1.972
peak=    3.302 closest distance to " O   HOH Z 386 " =    3.141
peak=    3.301 closest distance to " O   HOH Z 437 " =    2.038
peak=    3.295 closest distance to " O   HOH Z 196 " =    1.379
peak=    3.292 closest distance to " N   THR A 246 " =    1.373
peak=    3.290 closest distance to " O   HOH Z  32 " =    1.803
peak=    3.288 closest distance to " O   HOH Z 326 " =    1.306
peak=    3.285 closest distance to " CB  SER A 273 " =    0.841
peak=    3.284 closest distance to " OG BSER A 258 " =    0.844
peak=    3.283 closest distance to " O   HOH Z 336 " =    1.870
peak=    3.282 closest distance to " O   HOH Z 193 " =    1.808
peak=    3.277 closest distance to " CB  ARG A 190 " =    1.678
peak=    3.277 closest distance to " O   HOH Z 291 " =    1.941
peak=    3.275 closest distance to " CB  LEU A 143 " =    1.050
peak=    3.272 closest distance to " O   HOH Z 189 " =    1.694
peak=    3.272 closest distance to " O   HOH Z 119 " =    4.278
peak=    3.270 closest distance to " NE2 GLN A  58 " =    3.393
peak=    3.269 closest distance to " N   GLY A 196 " =    1.015
peak=    3.267 closest distance to " O   HOH Z 289 " =    1.414
peak=    3.266 closest distance to " CB  ALA A 114 " =    1.431
peak=    3.264 closest distance to " N   GLU A   2 " =    1.224
peak=    3.263 closest distance to " CA  SER A  87 " =    1.040
peak=    3.263 closest distance to " CB  ALA A  21 " =    1.826
peak=    3.262 closest distance to " N   TYR A  15 " =    1.043
peak=    3.259 closest distance to " O   HOH Z 266 " =    3.010
peak=    3.253 closest distance to " O   HOH Z 358 " =    1.244
peak=    3.252 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.251 closest distance to " O   HOH Z 135 " =    1.890
peak=    3.248 closest distance to " CG  GLN A  89 " =    1.361
peak=    3.242 closest distance to " O   ASN A 209 " =    1.559
peak=    3.238 closest distance to " OH  TYR A 116 " =    0.993
peak=    3.234 closest distance to " CA  GLU A 152 " =    1.338
peak=    3.234 closest distance to " O   HOH Z 171 " =    2.636
peak=    3.233 closest distance to " O   HOH Z 153 " =    3.590
peak=    3.233 closest distance to " CB  MET A 188 " =    1.687
peak=    3.225 closest distance to " O   HOH Z 334 " =    2.682
peak=    3.224 closest distance to " CD  ARG A  79 " =    2.275
peak=    3.220 closest distance to " O   HOH Z 171 " =    1.983
peak=    3.219 closest distance to " CB  GLU A 236 " =    1.355
peak=    3.209 closest distance to " O   HOH Z  47 " =    1.437
peak=    3.207 closest distance to " NE1 TRP A 274 " =    0.962
peak=    3.205 closest distance to " CD2 HIS A  81 " =    1.169
peak=    3.202 closest distance to " O   HOH Z 281 " =    4.433
peak=    3.201 closest distance to " O   HOH Z 287 " =    1.955
peak=    3.197 closest distance to " CB  ASP A 171 " =    0.955
peak=    3.194 closest distance to " O   HOH Z 146 " =    1.610
peak=    3.188 closest distance to " CB  ASN A  39 " =    0.808
peak=    3.188 closest distance to " CB  ARG A  79 " =    1.298
peak=    3.187 closest distance to " CE3 TRP A 274 " =    2.082
peak=    3.186 closest distance to " CB  THR A  31 " =    1.751
peak=    3.183 closest distance to " O   HOH Z 238 " =    5.034
peak=    3.182 closest distance to " CD  PRO A 243 " =    1.699
peak=    3.181 closest distance to " CA  LEU A 101 " =    1.646
peak=    3.181 closest distance to " CB  ASN A 215 " =    1.005
peak=    3.176 closest distance to " O   HOH Z 263 " =    2.474
peak=    3.168 closest distance to " O   HOH Z  88 " =    2.747
peak=    3.167 closest distance to " O   HOH Z 172 " =    2.827
peak=    3.161 closest distance to " N   VAL A 257 " =    1.616
peak=    3.160 closest distance to " CD  LYS A 166 " =    1.590
peak=    3.159 closest distance to " O   HOH Z  80 " =    1.937
peak=    3.152 closest distance to " CD  ARG A 138 " =    0.767
peak=    3.144 closest distance to " O   HOH Z 180 " =    2.089
peak=    3.144 closest distance to " CD2 LEU A 255 " =    1.013
peak=    3.142 closest distance to " O   HOH Z 181 " =    2.176
peak=    3.139 closest distance to " CA  ALA A 233 " =    1.052
peak=    3.137 closest distance to " O   HOH Z 255 " =    1.643
peak=    3.137 closest distance to " O   HOH Z 291 " =    1.565
peak=    3.136 closest distance to " CB  VAL A 265 " =    2.287
peak=    3.136 closest distance to " O   SER A  26 " =    1.503
peak=    3.133 closest distance to " O   HOH Z 251 " =    1.634
peak=    3.122 closest distance to " O   HOH Z 273 " =    2.814
peak=    3.118 closest distance to " CA  ALA A 160 " =    0.937
peak=    3.111 closest distance to " CB  ALA A 291 " =    1.490
peak=    3.110 closest distance to " O   GLY A 147 " =    1.531
peak=    3.108 closest distance to " O   HOH Z 128 " =    1.907
peak=    3.086 closest distance to " CB  ARG A 138 " =    0.891
peak=    3.085 closest distance to " O   HOH Z 423 " =    2.083
peak=    3.083 closest distance to " O   HOH Z 227 " =    2.152
peak=    3.082 closest distance to " O   HOH Z 365 " =    1.673
peak=    3.078 closest distance to " O   HOH Z  30 " =    1.600
peak=    3.073 closest distance to " O   HOH Z  94 " =    2.020
peak=    3.073 closest distance to " O   HOH Z 379 " =    1.797
peak=    3.064 closest distance to " O   HOH Z 409 " =    1.759
peak=    3.060 closest distance to " O   HOH Z 423 " =    1.713
peak=    3.055 closest distance to " O   HOH Z 115 " =    1.423
peak=    3.052 closest distance to " ND1 HIS A  81 " =    1.574
peak=    3.048 closest distance to " O   HOH Z   9 " =    2.068
peak=    3.031 closest distance to " O   HOH Z 189 " =    2.046
peak=    3.011 closest distance to " O   HOH Z 134 " =    2.080

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.756 - 5.616
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.756 - 5.616

peak=   -4.372 closest distance to " O   HOH Z 385 " =    1.273
peak=   -4.351 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.296 closest distance to " CD  ARG A  14 " =    3.221
peak=   -4.270 closest distance to " O   HOH Z  13 " =    1.391
peak=   -4.264 closest distance to " O   HOH Z 290 " =    1.172
peak=   -4.256 closest distance to " CA  GLY A  98 " =    1.831
peak=   -4.243 closest distance to " N   GLN A  58 " =    1.736
peak=   -4.202 closest distance to " C   HIS A 108 " =    1.150
peak=   -4.198 closest distance to " O   HOH Z 409 " =    3.252
peak=   -4.177 closest distance to " O   PRO A 198 " =    1.330
peak=   -4.096 closest distance to " O   HOH Z  65 " =    0.848
peak=   -4.089 closest distance to " O   HOH Z  43 " =    1.806
peak=   -4.051 closest distance to " CB  PRO A 243 " =    2.537
peak=   -4.049 closest distance to " CG  PHE A 283 " =    2.553
peak=   -4.040 closest distance to " O   HOH Z 377 " =    1.884
peak=   -4.006 closest distance to " O   SER A 135 " =    1.491
peak=   -3.973 closest distance to " OG BSER A 134 " =    1.298
peak=   -3.954 closest distance to " O   HOH Z 250 " =    1.479
peak=   -3.946 closest distance to " CG  GLN A  88 " =    0.855
peak=   -3.921 closest distance to " O   HOH Z  24 " =    1.194
peak=   -3.897 closest distance to " CG1 VAL A 112 " =    3.036
peak=   -3.895 closest distance to " O   HOH Z 438 " =    0.947
peak=   -3.890 closest distance to " O   HOH Z 298 " =    1.212
peak=   -3.865 closest distance to " O   SER A  95 " =    1.294
peak=   -3.858 closest distance to " CD1 LEU A 255 " =    2.867
peak=   -3.839 closest distance to " CZ  PHE A  59 " =    1.434
peak=   -3.814 closest distance to " O   VAL A  67 " =    2.732
peak=   -3.798 closest distance to " OD2 ASP A 191 " =    1.405
peak=   -3.794 closest distance to " O   HOH Z 166 " =    1.311
peak=   -3.765 closest distance to " CB  ALA A 291 " =    2.142
peak=   -3.762 closest distance to " O   HOH Z 351 " =    1.639
peak=   -3.757 closest distance to " O   HOH Z 266 " =    4.357
peak=   -3.740 closest distance to " O   MET A  40 " =    2.683
peak=   -3.738 closest distance to " CD1 LEU A 101 " =    2.307
peak=   -3.725 closest distance to " CD2 LEU A 237 " =    2.300
peak=   -3.724 closest distance to " CB  ALA A 248 " =    1.999
peak=   -3.715 closest distance to " C   ASN A 285 " =    2.287
peak=   -3.702 closest distance to " C   LEU A 143 " =    1.118
peak=   -3.693 closest distance to " CG  ASP A 231 " =    0.756
peak=   -3.693 closest distance to " CE3 TRP A 123 " =    1.357
peak=   -3.690 closest distance to " O   SER A  22 " =    2.545
peak=   -3.688 closest distance to " O   VAL A 189 " =    2.431
peak=   -3.682 closest distance to " O   HOH Z  60 " =    1.864
peak=   -3.678 closest distance to " O   ALA A 161 " =    1.702
peak=   -3.673 closest distance to " O   PRO A 243 " =    2.430
peak=   -3.673 closest distance to " O   HOH Z 185 " =    2.008
peak=   -3.661 closest distance to " OG  SER A   3 " =    1.630
peak=   -3.660 closest distance to " O   HOH Z 231 " =    1.807
peak=   -3.647 closest distance to " O   HOH Z  47 " =    1.523
peak=   -3.645 closest distance to " CA  GLY A 133 " =    1.922
peak=   -3.642 closest distance to " O   VAL A  67 " =    2.705
peak=   -3.637 closest distance to " CG2 THR A   4 " =    1.800
peak=   -3.632 closest distance to " O   PRO A 198 " =    1.194
peak=   -3.630 closest distance to " O   HOH Z 198 " =    1.929
peak=   -3.626 closest distance to " O   HOH Z 234 " =    3.822
peak=   -3.620 closest distance to " OG  SER A  97 " =    2.069
peak=   -3.606 closest distance to " CB  TYR A  15 " =    2.169
peak=   -3.606 closest distance to " CG  MET A 105 " =    0.890
peak=   -3.605 closest distance to " OXT GLY A 302 " =    2.840
peak=   -3.601 closest distance to " O   HOH Z  28 " =    1.923
peak=   -3.599 closest distance to " CE3 TRP A 274 " =    2.404
peak=   -3.589 closest distance to " C   PRO A  90 " =    1.510
peak=   -3.588 closest distance to " OD1 ASP A 191 " =    1.439
peak=   -3.587 closest distance to " NH2 ARG A  79 " =    1.889
peak=   -3.583 closest distance to " CB  ASN A  39 " =    2.281
peak=   -3.578 closest distance to " O   HOH Z  93 " =    1.910
peak=   -3.571 closest distance to " O   HOH Z  37 " =    1.528
peak=   -3.555 closest distance to " OG  SER A  87 " =    1.286
peak=   -3.551 closest distance to " O   HOH Z 263 " =    2.884
peak=   -3.534 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.528 closest distance to " OG  SER A 245 " =    1.211
peak=   -3.507 closest distance to " CG1BVAL A  41 " =    2.987
peak=   -3.496 closest distance to " CB  ALA A   7 " =    1.944
peak=   -3.494 closest distance to " O   VAL A 153 " =    2.271
peak=   -3.492 closest distance to " CG  GLN A  58 " =    1.443
peak=   -3.487 closest distance to " O   HOH Z  88 " =    2.286
peak=   -3.481 closest distance to " O   SER A 146 " =    0.950
peak=   -3.475 closest distance to " O   HOH Z 131 " =    3.951
peak=   -3.472 closest distance to " O   HOH Z 412 " =    5.616
peak=   -3.470 closest distance to " O   HOH Z 213 " =    1.234
peak=   -3.469 closest distance to " O   HOH Z 102 " =    1.678
peak=   -3.460 closest distance to " O   HOH Z 426 " =    2.233
peak=   -3.453 closest distance to " CD2 TYR A 293 " =    1.900
peak=   -3.453 closest distance to " N   GLN A 122 " =    1.466
peak=   -3.449 closest distance to " CE2 TYR A  30 " =    2.775
peak=   -3.449 closest distance to " ND2 ASN A  45 " =    1.075
peak=   -3.449 closest distance to " OG  SER A  87 " =    1.861
peak=   -3.446 closest distance to " CZ  TYR A 169 " =    1.748
peak=   -3.442 closest distance to " O   PRO A 163 " =    1.186
peak=   -3.439 closest distance to " CG  GLN A 223 " =    1.512
peak=   -3.439 closest distance to " O   HOH Z 313 " =    1.871
peak=   -3.427 closest distance to " N   VAL A  72 " =    1.491
peak=   -3.405 closest distance to " OD1 ASN A 148 " =    1.581
peak=   -3.401 closest distance to " OE1 GLU A 277 " =    2.173
peak=   -3.396 closest distance to " O   HOH Z 385 " =    1.055
peak=   -3.394 closest distance to " CG  ARG A 219 " =    2.592
peak=   -3.393 closest distance to " O   HOH Z 384 " =    3.077
peak=   -3.383 closest distance to " O   ASN A 127 " =    1.545
peak=   -3.380 closest distance to " O   HOH Z 359 " =    3.329
peak=   -3.374 closest distance to " OG ASER A 134 " =    1.019
peak=   -3.362 closest distance to " CB  PHE A 192 " =    1.665
peak=   -3.357 closest distance to " C   ALA A 114 " =    2.038
peak=   -3.356 closest distance to " ND2 ASN A  60 " =    1.427
peak=   -3.356 closest distance to " O   HOH Z  15 " =    1.496
peak=   -3.355 closest distance to " O   HOH Z 316 " =    1.902
peak=   -3.344 closest distance to " O   HOH Z 143 " =    2.221
peak=   -3.343 closest distance to " O   HOH Z 137 " =    1.462
peak=   -3.338 closest distance to " O   HOH Z 388 " =    2.006
peak=   -3.337 closest distance to " CE  MET A 105 " =    2.220
peak=   -3.337 closest distance to " CE2 PHE A 218 " =    2.440
peak=   -3.336 closest distance to " O   HOH Z 393 " =    3.113
peak=   -3.334 closest distance to " CB  ILE A  33 " =    2.841
peak=   -3.332 closest distance to " O   HOH Z  64 " =    1.188
peak=   -3.324 closest distance to " OD1 ASP A 171 " =    1.502
peak=   -3.321 closest distance to " CA  GLY A 241 " =    2.086
peak=   -3.320 closest distance to " CG  GLU A 152 " =    1.351
peak=   -3.318 closest distance to " O   HOH Z  63 " =    2.436
peak=   -3.311 closest distance to " CG  ARG A 219 " =    2.335
peak=   -3.308 closest distance to " OG ASER A 216 " =    1.233
peak=   -3.304 closest distance to " O   HOH Z  51 " =    0.985
peak=   -3.303 closest distance to " O   ALA A  51 " =    1.295
peak=   -3.294 closest distance to " C   GLN A 205 " =    1.958
peak=   -3.291 closest distance to " CG1 VAL A 230 " =    1.826
peak=   -3.288 closest distance to " CZ  ARG A  66 " =    0.956
peak=   -3.286 closest distance to " CD1 LEU A 228 " =    2.099
peak=   -3.283 closest distance to " O   PRO A 163 " =    1.752
peak=   -3.277 closest distance to " N   ALA A   1 " =    1.442
peak=   -3.277 closest distance to " OE1 GLN A  88 " =    1.198
peak=   -3.271 closest distance to " O   HOH Z 211 " =    1.109
peak=   -3.267 closest distance to " N   ARG A  14 " =    1.089
peak=   -3.266 closest distance to " CA  GLY A  57 " =    2.025
peak=   -3.259 closest distance to " CB  ALA A  43 " =    2.165
peak=   -3.256 closest distance to " ND2 ASN A  39 " =    1.617
peak=   -3.255 closest distance to " CB  ASP A 132 " =    2.280
peak=   -3.253 closest distance to " CZ2 TRP A 274 " =    0.982
peak=   -3.251 closest distance to " O   PHE A 218 " =    1.397
peak=   -3.250 closest distance to " O   HOH Z 427 " =    1.557
peak=   -3.246 closest distance to " O   HOH Z  90 " =    2.478
peak=   -3.242 closest distance to " ND2 ASN A 209 " =    1.781
peak=   -3.241 closest distance to " N   ALA A 248 " =    1.515
peak=   -3.240 closest distance to " CG  ASN A 301 " =    2.043
peak=   -3.232 closest distance to " OD2 ASP A 171 " =    2.184
peak=   -3.229 closest distance to " N   ASN A 127 " =    1.987
peak=   -3.223 closest distance to " N   THR A 157 " =    1.522
peak=   -3.222 closest distance to " OG  SER A  26 " =    1.185
peak=   -3.219 closest distance to " ND2 ASN A 252 " =    1.495
peak=   -3.219 closest distance to " CB  CYS A 201 " =    2.396
peak=   -3.217 closest distance to " CB  ALA A  51 " =    1.849
peak=   -3.215 closest distance to " O   HOH Z 211 " =    1.561
peak=   -3.213 closest distance to " CG2 THR A 178 " =    2.058
peak=   -3.212 closest distance to " O   ILE A 109 " =    2.480
peak=   -3.212 closest distance to " O   HOH Z 137 " =    1.417
peak=   -3.210 closest distance to " O   HOH Z  52 " =    1.185
peak=   -3.201 closest distance to " CD2 LEU A 237 " =    2.606
peak=   -3.201 closest distance to " O   HOH Z 222 " =    0.951
peak=   -3.201 closest distance to " O   HOH Z 298 " =    2.401
peak=   -3.196 closest distance to " O   HOH Z 415 " =    1.506
peak=   -3.193 closest distance to " CD  ARG A 139 " =    1.639
peak=   -3.192 closest distance to " CD  GLN A 223 " =    1.344
peak=   -3.192 closest distance to " OE1 GLN A 223 " =    1.957
peak=   -3.186 closest distance to " CZ3 TRP A 179 " =    1.297
peak=   -3.184 closest distance to " NE  ARG A  36 " =    1.868
peak=   -3.184 closest distance to " OG1 THR A 246 " =    1.246
peak=   -3.179 closest distance to " O   HOH Z 364 " =    2.418
peak=   -3.178 closest distance to " OD2 ASP A  50 " =    1.520
peak=   -3.175 closest distance to " O   HOH Z 191 " =    5.388
peak=   -3.154 closest distance to " O   ALA A   1 " =    1.248
peak=   -3.151 closest distance to " NE2 GLN A 194 " =    2.686
peak=   -3.149 closest distance to " ND2BASN A 224 " =    1.706
peak=   -3.148 closest distance to " CA  ASP A  27 " =    2.305
peak=   -3.145 closest distance to " OG  SER A 206 " =    1.735
peak=   -3.139 closest distance to " OG BSER A 134 " =    1.580
peak=   -3.138 closest distance to " O   GLY A  80 " =    2.397
peak=   -3.133 closest distance to " O   HOH Z 397 " =    1.096
peak=   -3.125 closest distance to " O   HOH Z 126 " =    1.891
peak=   -3.122 closest distance to " O   SER A  26 " =    1.151
peak=   -3.121 closest distance to " O   HOH Z 326 " =    1.536
peak=   -3.121 closest distance to " CD1 PHE A  59 " =    2.036
peak=   -3.120 closest distance to " O   HOH Z 111 " =    4.586
peak=   -3.120 closest distance to " CE1 TYR A 169 " =    2.485
peak=   -3.117 closest distance to " O   HOH Z 372 " =    2.433
peak=   -3.112 closest distance to " NH1 ARG A  56 " =    2.476
peak=   -3.108 closest distance to " CE  MET A  93 " =    1.100
peak=   -3.104 closest distance to " OD2 ASP A  27 " =    1.516
peak=   -3.104 closest distance to " CG  ARG A  66 " =    2.237
peak=   -3.089 closest distance to " O   ASP A 162 " =    2.198
peak=   -3.082 closest distance to " O   HOH Z 129 " =    4.467
peak=   -3.065 closest distance to " O   HOH Z 231 " =    1.298
peak=   -3.065 closest distance to " O   HOH Z 318 " =    1.903
peak=   -3.058 closest distance to " OE2 GLU A 152 " =    1.105
peak=   -3.057 closest distance to " OD1 ASP A 200 " =    1.314
peak=   -3.040 closest distance to " O   HOH Z 222 " =    2.581
peak=   -3.018 closest distance to " O   HOH Z  88 " =    2.313

================= 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    :  0.4573 0.4599   6.267718e+00   6.260922e+00
   1_bss:  0.4459 0.4468   6.261991e+00   6.244057e+00
   1_xyz:  0.3321 0.3589   6.048107e+00   6.108098e+00
   1_adp:  0.3005 0.3764   5.996630e+00   6.130364e+00
   1_occ:  0.2999 0.3765   5.995986e+00   6.130155e+00
   2_bss:  0.2972 0.3748   5.993367e+00   6.127293e+00
   2_xyz:  0.2371 0.3080   5.808425e+00   5.982285e+00
   2_adp:  0.2265 0.2895   5.765042e+00   5.936477e+00
   2_occ:  0.2263 0.2898   5.764586e+00   5.936802e+00
   3_bss:  0.2261 0.2895   5.763752e+00   5.936080e+00
   3_xyz:  0.1648 0.2139   5.470607e+00   5.674461e+00
   3_adp:  0.1467 0.1967   5.369692e+00   5.591823e+00
   3_occ:  0.1464 0.1959   5.367395e+00   5.588698e+00
   4_bss:  0.1467 0.1951   5.364244e+00   5.583442e+00
   4_xyz:  0.1280 0.1743   5.243568e+00   5.471327e+00
   4_adp:  0.1243 0.1695   5.217153e+00   5.444054e+00
   4_occ:  0.1241 0.1692   5.216195e+00   5.442700e+00
   5_bss:  0.1241 0.1692   5.216195e+00   5.442700e+00
   5_xyz:  0.1142 0.1593   5.150431e+00   5.389708e+00
   5_adp:  0.1120 0.1583   5.140446e+00   5.385350e+00
   5_occ:  0.1119 0.1583   5.140050e+00   5.384830e+00
   5_bss:  0.1121 0.1586   5.140979e+00   5.386673e+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:  0.350  24.350  -3.370   2.091   1.334   0.000   0.000   0.000
   1_xyz:  0.350  24.350  -3.370   2.091   1.334   0.000   0.000   0.000
   1_adp:  0.350  24.350  -3.370   2.091   1.334   0.000   0.000   0.000
   1_occ:  0.350  24.350  -3.370   2.091   1.334   0.000   0.000   0.000
   2_bss:  0.333  40.852  -1.896  -0.056  -0.061  -0.000  -0.000  -0.000
   2_xyz:  0.333  40.852  -1.896  -0.056  -0.061  -0.000  -0.000  -0.000
   2_adp:  0.333  40.852  -1.896  -0.056  -0.061  -0.000  -0.000  -0.000
   2_occ:  0.333  40.852  -1.896  -0.056  -0.061  -0.000  -0.000  -0.000
   3_bss:  0.333  40.852  -2.053  -1.058  -0.923  -0.000  -0.000  -0.000
   3_xyz:  0.333  40.852  -2.053  -1.058  -0.923  -0.000  -0.000  -0.000
   3_adp:  0.333  40.852  -2.053  -1.058  -0.923  -0.000  -0.000  -0.000
   3_occ:  0.333  40.852  -2.053  -1.058  -0.923  -0.000  -0.000  -0.000
   4_bss:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   4_xyz:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   4_adp:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   4_occ:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   5_bss:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   5_xyz:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   5_adp:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   5_occ:  0.318  38.745  -2.300  -2.074  -1.349  -0.000  -0.000  -0.000
   5_bss:  0.316  38.901  -2.277  -2.051  -1.325  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.278 0.4677  0.6401    66462.634
   1_bss:  52.651 0.4865  0.6670    61475.277
   1_xyz:  38.293 0.6640  0.8747    36463.504
   1_adp:  40.062 0.6419  0.8503    38987.277
   1_occ:  40.079 0.6417  0.8491    38988.340
   2_bss:  39.806 0.6447  0.8354    38546.254
   2_xyz:  31.653 0.7385  0.9386    24863.186
   2_adp:  28.926 0.7699  0.9605    21895.704
   2_occ:  28.944 0.7697  0.9598    21902.132
   3_bss:  28.871 0.7704  0.9370    21784.569
   3_xyz:  20.630 0.8556  0.9996    11688.807
   3_adp:  18.407 0.8772  1.0035     9876.939
   3_occ:  18.327 0.8779  1.0037     9774.462
   4_bss:  18.184 0.8789  0.9839     9592.331
   4_xyz:  15.651 0.9011  0.9949     7466.173
   4_adp:  14.964 0.9073  0.9931     7128.163
   4_occ:  14.938 0.9075  0.9931     7099.278
   5_bss:  14.938 0.9075  0.9931     7099.278
   5_xyz:  13.967 0.9151  0.9972     6313.869
   5_adp:  13.843 0.9163  0.9931     6249.166
   5_occ:  13.834 0.9163  0.9931     6238.452
   5_bss:  13.873 0.9161  0.9932     6289.823
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8263e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8263e-01
   1_xyz:   1.610  0.012  0.104 15.756  0.006  4.103   1.3786e-01
   1_adp:   1.610  0.012  0.104 15.756  0.006  4.103   1.3786e-01
   1_occ:   1.610  0.012  0.104 15.756  0.006  4.103   1.3786e-01
   2_bss:   1.610  0.012  0.104 15.756  0.006  4.103   1.3786e-01
   2_xyz:   1.105  0.007  0.078 14.268  0.005  4.113   6.7605e-02
   2_adp:   1.105  0.007  0.078 14.268  0.005  4.113   6.7605e-02
   2_occ:   1.105  0.007  0.078 14.268  0.005  4.113   6.7605e-02
   3_bss:   1.105  0.007  0.078 14.268  0.005  4.113   6.7605e-02
   3_xyz:   1.055  0.008  0.070 14.620  0.004  4.106   6.8659e-02
   3_adp:   1.055  0.008  0.070 14.620  0.004  4.106   6.8659e-02
   3_occ:   1.055  0.008  0.070 14.620  0.004  4.106   6.8659e-02
   4_bss:   1.055  0.008  0.070 14.620  0.004  4.106   6.8659e-02
   4_xyz:   0.925  0.005  0.065 14.388  0.004  4.108   5.1354e-02
   4_adp:   0.925  0.005  0.065 14.388  0.004  4.108   5.1354e-02
   4_occ:   0.925  0.005  0.065 14.388  0.004  4.108   5.1354e-02
   5_bss:   0.925  0.005  0.065 14.388  0.004  4.108   5.1354e-02
   5_xyz:   1.005  0.006  0.071 14.636  0.004  4.112   5.9198e-02
   5_adp:   1.005  0.006  0.071 14.636  0.004  4.112   5.9198e-02
   5_occ:   1.005  0.006  0.071 14.636  0.004  4.112   5.9198e-02
   5_bss:   1.005  0.006  0.071 14.636  0.004  4.112   5.9198e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.615   2.3720e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.615   2.3720e-01
   1_xyz:  10.198  0.068  0.425 88.453  0.036  2.024   1.4985e-01
   1_adp:  10.198  0.068  0.425 88.453  0.036  2.024   1.4985e-01
   1_occ:  10.198  0.068  0.425 88.453  0.036  2.024   1.4985e-01
   2_bss:  10.198  0.068  0.425 88.453  0.036  2.024   1.4985e-01
   2_xyz:   8.496  0.064  0.230 80.775  0.031  2.309   7.5203e-02
   2_adp:   8.496  0.064  0.230 80.775  0.031  2.309   7.5203e-02
   2_occ:   8.496  0.064  0.230 80.775  0.031  2.309   7.5203e-02
   3_bss:   8.496  0.064  0.230 80.775  0.031  2.309   7.5203e-02
   3_xyz:   7.006  0.055  0.230 80.787  0.027  2.259   1.1465e-01
   3_adp:   7.006  0.055  0.230 80.787  0.027  2.259   1.1465e-01
   3_occ:   7.006  0.055  0.230 80.787  0.027  2.259   1.1465e-01
   4_bss:   7.006  0.055  0.230 80.787  0.027  2.259   1.1465e-01
   4_xyz:   6.860  0.041  0.191 84.136  0.034  2.350   5.0475e-02
   4_adp:   6.860  0.041  0.191 84.136  0.034  2.350   5.0475e-02
   4_occ:   6.860  0.041  0.191 84.136  0.034  2.350   5.0475e-02
   5_bss:   6.860  0.041  0.191 84.136  0.034  2.350   5.0475e-02
   5_xyz:   6.583  0.040  0.213 84.610  0.035  2.257   4.4617e-02
   5_adp:   6.583  0.040  0.213 84.610  0.035  2.257   4.4617e-02
   5_occ:   6.583  0.040  0.213 84.610  0.035  2.257   4.4617e-02
   5_bss:   6.583  0.040  0.213 84.610  0.035  2.257   4.4617e-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:  93.94   0.00  18.78  90.28   0.00  15.10  93.94   0.86  38.80
   1_occ:  93.94   0.00  18.78  90.28   0.00  15.10  93.94   0.86  38.80
   2_bss:  93.94   0.00  18.78  90.28   0.00  15.10  93.94   0.86  38.80
   2_xyz:  93.94   0.00  18.78  90.28   0.00  15.10  93.94   0.86  38.80
   2_adp:  92.33   0.00  17.72  88.78   0.00  14.00  92.33   4.10  38.01
   2_occ:  92.33   0.00  17.72  88.78   0.00  14.00  92.33   4.10  38.01
   3_bss:  92.33   0.00  17.72  88.78   0.00  14.00  92.33   4.10  38.01
   3_xyz:  92.33   0.00  17.72  88.78   0.00  14.00  92.33   4.10  38.01
   3_adp:  87.18   1.63  17.27  87.18   1.63  12.98  85.09   6.22  40.67
   3_occ:  87.18   1.63  17.27  87.18   1.63  12.98  85.09   6.22  40.67
   4_bss:  87.18   1.63  17.27  87.18   1.63  12.98  85.09   6.22  40.67
   4_xyz:  87.18   1.63  17.27  87.18   1.63  12.98  85.09   6.22  40.67
   4_adp:  87.41   1.29  17.00  87.41   1.29  12.70  81.05   4.87  40.42
   4_occ:  87.41   1.29  17.00  87.41   1.29  12.70  81.05   4.87  40.42
   5_bss:  87.41   1.29  17.00  87.41   1.29  12.70  81.05   4.87  40.42
   5_xyz:  87.41   1.29  17.00  87.41   1.29  12.70  81.05   4.87  40.42
   5_adp:  91.58   0.69  16.98  91.58   0.69  12.59  84.26   5.73  40.83
   5_occ:  91.58   0.69  16.98  91.58   0.69  12.59  84.26   5.73  40.83
   5_bss:  91.56   0.67  16.95  91.56   0.67  12.57  84.24   5.71  40.81
------------------------------------------------------------------------
 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:    1.932    0.036    0.400
   1_adp:    1.932    0.036    0.400
   1_occ:    1.932    0.036    0.400
   2_bss:    1.932    0.036    0.400
   2_xyz:    1.462    0.039    0.515
   2_adp:    1.462    0.039    0.515
   2_occ:    1.462    0.039    0.515
   3_bss:    1.462    0.039    0.515
   3_xyz:    1.530    0.077    0.684
   3_adp:    1.530    0.077    0.684
   3_occ:    1.530    0.077    0.684
   4_bss:    1.530    0.077    0.684
   4_xyz:    1.504    0.056    0.717
   4_adp:    1.504    0.056    0.717
   4_occ:    1.504    0.056    0.717
   5_bss:    1.504    0.056    0.717
   5_xyz:    1.451    0.074    0.747
   5_adp:    1.451    0.074    0.747
   5_occ:    1.451    0.074    0.747
   5_bss:    1.451    0.074    0.747
------------------------------------------------------------------------

CPU time actual refinement: 299.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_496/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_496/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_496/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_496/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_496/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 299.46 
  Macro-tasks:
    bulk solvent and scale       = 36.98  
    individual site refinement   = 126.86 
    weights calculation          = 25.62  
    collect and process          = 5.48   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 195.03 
  Micro-tasks:
    mask                            = 1.96   
    f_calc                          = 96.19  
    alpha_beta                      = 7.16   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 105.12 
    fmodel                         = 6.19   
    r_factors                      = 0.26   
    phase_errors                   = 8.67   
    foms                           = 0.11   
    TOTAL for micro-tasks          = 226.64 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.162 micro seconds
Total CPU time: 5.19 minutes
from_scatterers_fft:    671 calls, 95.99 s
gradients_fft:          616 calls, 92.90 s

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

# Date 2008-01-16 Time 04:57:21 PST -0800 (1200488241.85 s)
Start R-work = 0.4573, R-free = 0.4599 (no bulk solvent and anisotropic scale)
Final R-work = 0.1363, R-free = 0.1785 (no bulk solvent and anisotropic scale)

Start R-work = 0.4459, R-free = 0.4468
Final R-work = 0.1121, R-free = 0.1586