# Date 2008-01-16 Time 06:35:37 PST -0800 (1200494137.24 s)
#phil __OFF__

Command line arguments: "../1204.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24501
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1204

-------------------------------------------------------------------------------
  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: (71.655, 48.1033, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 48.1033, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 2.00132
Completeness in resolution range: 0.946146
Completeness with d_max=infinity: 0.943275

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2108
                             d_min =   2.0013

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: (71.655, 48.1033, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2108 2.00132
Completeness in resolution range: 0.946146
Completeness with d_max=infinity: 0.943275

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2112 -  4.2826 [2180/2209]  1962   218  10.0%
  bin  2:  4.2826 -  3.4119 [2072/2095]  1866   206   9.9%
  bin  3:  3.4119 -  2.9843 [2064/2086]  1855   209  10.1%
  bin  4:  2.9843 -  2.7131 [2048/2067]  1850   198   9.7%
  bin  5:  2.7131 -  2.5196 [2044/2073]  1832   212  10.4%
  bin  6:  2.5196 -  2.3716 [2011/2052]  1815   196   9.7%
  bin  7:  2.3716 -  2.2532 [1996/2031]  1794   202  10.1%
  bin  8:  2.2532 -  2.1554 [2001/2039]  1803   198   9.9%
  bin  9:  2.1554 -  2.0727 [1998/2030]  1794   204  10.2%
  bin 10:  2.0727 -  2.0013 [1175/2022]  1059   116   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1204/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 5
        1.93 -     2.68: 87
        2.68 -     3.42: 4348
        3.42 -     4.16: 9189
        4.16 -     4.90: 14142
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.194 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.608 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.685 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.793 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27766 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_1204/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1204/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 71.655 48.10325 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4524   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.268811                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7768 0.99   1411  155 0.3654 0.3893      6.5437      6.5371|
|  2:  4.7768 -  3.8111 0.99   1360  150 0.3999 0.4095       6.851      6.8004|
|  3:  3.8111 -  3.3351 0.99   1330  155 0.4272 0.3747      6.6681      6.5905|
|  4:  3.3351 -  3.0328 0.99   1331  145 0.4495 0.4225       6.511      6.4799|
|  5:  3.0328 -  2.8169 0.99   1309  146 0.4754 0.4732      6.3615      6.4028|
|  6:  2.8169 -  2.6518 0.98   1303  145 0.4821 0.4351      6.2595      6.1313|
|  7:  2.6518 -  2.5196 0.99   1321  147 0.4943 0.4290      6.2397      6.1805|
|  8:  2.5196 -  2.4104 0.99   1288  144 0.4866 0.4546      6.1349      6.1551|
|  9:  2.4104 -  2.3179 0.98   1298  143 0.5035 0.4795      6.1191        6.09|
| 10:  2.3179 -  2.2382 0.98   1279  138 0.4692 0.4303      6.0686      6.0399|
| 11:  2.2382 -  2.1684 0.98   1284  145 0.5129 0.4711      6.0486      6.0179|
| 12:  2.1684 -  2.1066 0.99   1270  140 0.4913 0.5137      5.9542      5.9944|
| 13:  2.1066 -  2.0512 0.97   1298  144 0.4814 0.4279      5.8503      5.8135|
| 14:  2.0512 -  2.0013 0.42    548   62 0.4766 0.4565      5.8025      5.7344|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2112 -  4.7768  1411   155  0.70  34.37   0.82     0.74      72143.53|
|  2:  4.7768 -  3.8111  1360   150  0.72  33.17   0.90     0.80      94288.53|
|  3:  3.8111 -  3.3351  1330   155  0.63  41.16   0.88     0.78     101752.62|
|  4:  3.3351 -  3.0328  1331   145  0.55  47.89   0.88     0.71      91387.51|
|  5:  3.0328 -  2.8169  1309   146  0.48  53.68   0.87     0.66      74559.37|
|  6:  2.8169 -  2.6518  1303   145  0.48  53.32   0.89     0.64      58207.02|
|  7:  2.6518 -  2.5196  1321   147  0.50  51.90   0.90     0.65      50320.55|
|  8:  2.5196 -  2.4104  1288   144  0.48  53.63   0.89     0.66      46741.25|
|  9:  2.4104 -  2.3179  1298   143  0.47  54.78   0.90     0.65      45042.89|
| 10:  2.3179 -  2.2382  1279   138  0.47  54.78   0.94     0.66      42288.77|
| 11:  2.2382 -  2.1684  1284   145  0.46  55.70   0.91     0.66      39094.08|
| 12:  2.1684 -  2.1066  1270   140  0.45  56.49   0.94     0.66      36237.94|
| 13:  2.1066 -  2.0512  1298   144  0.42  58.12   0.90     0.62      31573.07|
| 14:  2.0512 -  2.0013   548    62  0.40  59.68   0.96     0.56      26712.25|
|alpha:            min =        0.56 max =            0.80 mean =         0.68|
|beta:             min =    26712.25 max =       101752.62 mean =     59642.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.03|
|phase err.(test): min =        0.00 max =           89.92 mean =        49.81|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.002263             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.755   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.899958              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.782   (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 |  1.194 -  1.564:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.564 -  1.935:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.935 -  2.306:        4 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.306 -  2.676:       83 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.676 -  3.047:     2111 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.047 -  3.417:     2237 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.417 -  3.788:     3935 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.788 -  4.159:     5254 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.159 -  4.529:     6307 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.529 -  4.900:     7835 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.194 |       0.300 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4524   r_free= 0.4308   ksol= 0.00   Bsol= 0.00   scale= 0.880    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.268811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4431   r_free= 0.4203   ksol= 0.28   Bsol= 38.13   scale= 0.918   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,4.65,-2.21,0.00,-0.00,-0.00); trace/3= 0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.263217                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.770089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.473   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.961314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.635   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4431      final r-factor (work) = 0.3594          |
| start r-factor (free) = 0.4203      final r-factor (free) = 0.3888          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6184 = 8.77 * 0.50 * 6.2588 + 1.00 * 0.1733                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0468 = 8.77 * 0.50 * 6.1399 + 1.00 * 0.1230                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3594      final r-factor (work) = 0.3291          |
| start r-factor (free) = 0.3888      final r-factor (free) = 0.3943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9086 = 0.96 * 1.00 * 6.1399 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8615 = 0.96 * 1.00 * 6.0726 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.30   18.37    None  None   None       |
|    all(noH): 2823   0      0.00    95.30   18.37    None  None   None       |
|    Sol.    : 438    0      0.00    95.30   36.40    None  None   None       |
|    Mac.    : 2385   0      0.00    86.36   15.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.530:  891   |   5:    47.648 -  57.177:   76        |
|      1:     9.530 -  19.059:  904   |   6:    57.177 -  66.707:   41        |
|      2:    19.059 -  28.589:  482   |   7:    66.707 -  76.237:   24        |
|      3:    28.589 -  38.118:  258   |   8:    76.237 -  85.766:    5        |
|      4:    38.118 -  47.648:  137   |   9:    85.766 -  95.296:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3291 r_free = 0.3943             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3289 r_free = 0.3939             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3289   r_free= 0.3939   ksol= 0.28   Bsol= 38.13   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,4.65,-2.21,0.00,-0.00,-0.00); trace/3= 0.74                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.074380                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3281   r_free= 0.3924   ksol= 0.31   Bsol= 60.20   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,2.73,-0.54,0.00,-0.00,-0.00); trace/3= 0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.075756                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.569384             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.902  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.963066              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.525   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3281      final r-factor (work) = 0.2661          |
| start r-factor (free) = 0.3924      final r-factor (free) = 0.3167          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.2235 = 10.57 * 0.50 * 6.0742 + 1.00 * 0.1230                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.7697 = 10.57 * 0.50 * 5.9879 + 1.00 * 0.1254                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2661      final r-factor (work) = 0.2449          |
| start r-factor (free) = 0.3167      final r-factor (free) = 0.3068          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7847 = 0.96 * 1.00 * 5.9879 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6463 = 0.96 * 1.00 * 5.8454 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.55   18.44    None  None   None       |
|    all(noH): 2823   0      0.00    93.55   18.44    None  None   None       |
|    Sol.    : 438    0      0.00    93.55   40.38    None  None   None       |
|    Mac.    : 2385   0      0.00    92.68   14.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.355:  991   |   5:    46.777 -  56.132:   98        |
|      1:     9.355 -  18.711:  846   |   6:    56.132 -  65.487:   67        |
|      2:    18.711 -  28.066:  394   |   7:    65.487 -  74.843:   25        |
|      3:    28.066 -  37.421:  230   |   8:    74.843 -  84.198:   16        |
|      4:    37.421 -  46.777:  149   |   9:    84.198 -  93.554:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2449 r_free = 0.3068             target_work(ml) = 5.835         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2446 r_free = 0.3067             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2446   r_free= 0.3067   ksol= 0.31   Bsol= 60.20   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,2.73,-0.54,0.00,-0.00,-0.00); trace/3= 0.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.834384                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2446   r_free= 0.3060   ksol= 0.33   Bsol= 71.16   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,1.58,-0.04,0.00,-0.00,-0.00); trace/3= 0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.834827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.762799              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.005   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.346698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.536  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2446      final r-factor (work) = 0.2023          |
| start r-factor (free) = 0.3060      final r-factor (free) = 0.2582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0468 = 4.76 * 0.50 * 5.8459 + 1.00 * 0.1254                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7690 = 4.76 * 0.50 * 5.7526 + 1.00 * 0.0698                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2023      final r-factor (work) = 0.1868          |
| start r-factor (free) = 0.2582      final r-factor (free) = 0.2434          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7639 = 1.35 * 1.00 * 5.7526 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5886 = 1.35 * 1.00 * 5.6217 + 1.00 * 0.0179                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.47  18.57    None  None   None       |
|    all(noH): 2823   0      0.00    107.47  18.57    None  None   None       |
|    Sol.    : 438    0      2.87    104.79  45.87    None  None   None       |
|    Mac.    : 2385   0      0.00    107.47  13.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.747: 1282   |   5:    53.733 -  64.480:   90        |
|      1:    10.747 -  21.493:  823   |   6:    64.480 -  75.226:   55        |
|      2:    21.493 -  32.240:  241   |   7:    75.226 -  85.973:   38        |
|      3:    32.240 -  42.986:  151   |   8:    85.973 -  96.719:   14        |
|      4:    42.986 -  53.733:  121   |   9:    96.719 - 107.466:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1868 r_free = 0.2434             target_work(ml) = 5.598         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1867 r_free = 0.2435             target_work(ml) = 5.598         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1867   r_free= 0.2435   ksol= 0.33   Bsol= 71.16   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,1.58,-0.04,0.00,-0.00,-0.00); trace/3= 0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.598216                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1870   r_free= 0.2431   ksol= 0.33   Bsol= 83.47   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,0.68,-0.22,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.598243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.860676              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.478  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.744857              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.697  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1870      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2431      final r-factor (free) = 0.2018          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5490 = 5.86 * 0.50 * 5.6236 + 1.00 * 0.0699                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2349 = 5.86 * 0.50 * 5.5093 + 1.00 * 0.0908                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1504      final r-factor (work) = 0.1389          |
| start r-factor (free) = 0.2018      final r-factor (free) = 0.1892          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1214 = 0.74 * 1.00 * 5.5093 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0191 = 0.74 * 1.00 * 5.3762 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.83  17.71    None  None   None       |
|    all(noH): 2823   0      0.00    113.83  17.71    None  None   None       |
|    Sol.    : 438    0      4.51    113.57  46.08    None  None   None       |
|    Mac.    : 2385   0      0.00    113.83  12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.384: 1484   |   5:    56.918 -  68.301:   90        |
|      1:    11.384 -  22.767:  769   |   6:    68.301 -  79.685:   48        |
|      2:    22.767 -  34.151:  177   |   7:    79.685 -  91.068:   24        |
|      3:    34.151 -  45.534:  118   |   8:    91.068 - 102.451:   12        |
|      4:    45.534 -  56.918:   97   |   9:   102.451 - 113.835:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1389 r_free = 0.1892             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1389 r_free = 0.1891             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1389   r_free= 0.1891   ksol= 0.33   Bsol= 83.47   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,0.68,-0.22,0.00,-0.00,-0.00); trace/3= -0.10                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.337084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1894   ksol= 0.33   Bsol= 81.20   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,0.01,-0.16,0.00,-0.00,-0.00); trace/3= -0.35                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.338661                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.842386              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.117  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.183721              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.223  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1394      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1894      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7332 = 2.84 * 0.50 * 5.3775 + 1.00 * 0.0908                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6218 = 2.84 * 0.50 * 5.3133 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1756          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9906 = 0.18 * 1.00 * 5.3133 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9823 = 0.18 * 1.00 * 5.2873 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    111.89  16.89    None  None   None       |
|    all(noH): 2823   0      0.68    111.89  16.89    None  None   None       |
|    Sol.    : 438    0      4.21    111.89  43.31    None  None   None       |
|    Mac.    : 2385   0      0.68    108.31  12.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.677 -  11.798: 1626   |   5:    56.282 -  67.403:   77        |
|      1:    11.798 -  22.919:  674   |   6:    67.403 -  78.524:   41        |
|      2:    22.919 -  34.040:  158   |   7:    78.524 -  89.645:   20        |
|      3:    34.040 -  45.161:  116   |   8:    89.645 - 100.767:    8        |
|      4:    45.161 -  56.282:   99   |   9:   100.767 - 111.888:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1295 r_free = 0.1756             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1756             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1756   ksol= 0.33   Bsol= 81.20   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,0.01,-0.16,0.00,-0.00,-0.00); trace/3= -0.35                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.272893                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7768 0.99   1411  155 0.1034 0.1324      5.4332      5.5914|
|  2:  4.7768 -  3.8111 0.99   1360  150 0.0880 0.1116      5.4647      5.6686|
|  3:  3.8111 -  3.3351 0.99   1330  155 0.1144 0.1621      5.5354      5.8692|
|  4:  3.3351 -  3.0328 0.99   1331  145 0.1449 0.1821       5.583      5.7374|
|  5:  3.0328 -  2.8169 0.99   1309  146 0.1580 0.1964      5.4872       5.667|
|  6:  2.8169 -  2.6518 0.98   1303  145 0.1526 0.2177      5.3776       5.564|
|  7:  2.6518 -  2.5196 0.99   1321  147 0.1485 0.2030      5.3143      5.5843|
|  8:  2.5196 -  2.4104 0.99   1288  144 0.1436 0.1881      5.2134      5.3944|
|  9:  2.4104 -  2.3179 0.98   1298  143 0.1426 0.2025      5.1821      5.4044|
| 10:  2.3179 -  2.2382 0.98   1279  138 0.1379 0.1991       5.117      5.3556|
| 11:  2.2382 -  2.1684 0.98   1284  145 0.1357 0.1977      5.0727      5.3725|
| 12:  2.1684 -  2.1066 0.99   1270  140 0.1295 0.1798      4.9943      5.1882|
| 13:  2.1066 -  2.0512 0.97   1298  144 0.1392 0.2011      4.9225       5.163|
| 14:  2.0512 -  2.0013 0.42    548   62 0.1292 0.1987      4.7965       5.038|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2112 -  4.7768  1411   155  0.93   9.96   0.96     0.93       8235.70|
|  2:  4.7768 -  3.8111  1360   150  0.95   8.69   1.00     0.98       9712.47|
|  3:  3.8111 -  3.3351  1330   155  0.92  12.52   1.01     1.00      11739.40|
|  4:  3.3351 -  3.0328  1331   145  0.90  16.03   1.00     0.97      12822.14|
|  5:  3.0328 -  2.8169  1309   146  0.87  19.32   1.00     0.98      11521.49|
|  6:  2.8169 -  2.6518  1303   145  0.88  18.96   0.98     0.96       9497.37|
|  7:  2.6518 -  2.5196  1321   147  0.88  18.41   0.99     0.94       8195.79|
|  8:  2.5196 -  2.4104  1288   144  0.88  18.39   0.99     0.96       7131.28|
|  9:  2.4104 -  2.3179  1298   143  0.88  18.36   0.99     0.94       6439.84|
| 10:  2.3179 -  2.2382  1279   138  0.88  18.24   0.98     0.94       5858.83|
| 11:  2.2382 -  2.1684  1284   145  0.88  18.66   0.98     0.93       5475.83|
| 12:  2.1684 -  2.1066  1270   140  0.89  17.57   0.98     0.96       4978.40|
| 13:  2.1066 -  2.0512  1298   144  0.88  18.94   0.98     0.98       4238.14|
| 14:  2.0512 -  2.0013   548    62  0.89  17.45   0.96     0.93       3269.26|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     3269.26 max =        12822.14 mean =      8024.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.42|
|phase err.(test): min =        0.00 max =           88.45 mean =        15.73|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1757   ksol= 0.32   Bsol= 72.89   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,-0.22,-0.00,-0.00,-0.00,-0.00); trace/3= -0.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.272680                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.21 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1757   ksol= 0.32   Bsol= 72.89   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,-0.22,-0.00,-0.00,-0.00,-0.00); trace/3= -0.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.272680                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2112 -  4.7768 0.99   1411  155 0.1031 0.1326       5.431      5.5886|
|  2:  4.7768 -  3.8111 0.99   1360  150 0.0877 0.1108      5.4615      5.6631|
|  3:  3.8111 -  3.3351 0.99   1330  155 0.1143 0.1619      5.5339      5.8696|
|  4:  3.3351 -  3.0328 0.99   1331  145 0.1448 0.1821      5.5837      5.7374|
|  5:  3.0328 -  2.8169 0.99   1309  146 0.1583 0.1972      5.4883       5.669|
|  6:  2.8169 -  2.6518 0.98   1303  145 0.1526 0.2171       5.378      5.5621|
|  7:  2.6518 -  2.5196 0.99   1321  147 0.1485 0.2033      5.3146      5.5846|
|  8:  2.5196 -  2.4104 0.99   1288  144 0.1435 0.1885      5.2138       5.395|
|  9:  2.4104 -  2.3179 0.98   1298  143 0.1423 0.2025      5.1819      5.4038|
| 10:  2.3179 -  2.2382 0.98   1279  138 0.1380 0.1999      5.1176      5.3581|
| 11:  2.2382 -  2.1684 0.98   1284  145 0.1356 0.1980      5.0727      5.3726|
| 12:  2.1684 -  2.1066 0.99   1270  140 0.1293 0.1809      4.9952      5.1915|
| 13:  2.1066 -  2.0512 0.97   1298  144 0.1393 0.2008      4.9232      5.1637|
| 14:  2.0512 -  2.0013 0.42    548   62 0.1289 0.1974      4.7949      5.0334|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2112 -  4.7768  1411   155  0.93   9.95   0.96     0.93       8215.85|
|  2:  4.7768 -  3.8111  1360   150  0.95   8.65   1.00     0.98       9648.06|
|  3:  3.8111 -  3.3351  1330   155  0.92  12.46   1.01     1.00      11660.31|
|  4:  3.3351 -  3.0328  1331   145  0.90  16.04   1.00     0.97      12832.14|
|  5:  3.0328 -  2.8169  1309   146  0.87  19.32   1.00     0.97      11518.90|
|  6:  2.8169 -  2.6518  1303   145  0.88  18.95   0.98     0.95       9505.37|
|  7:  2.6518 -  2.5196  1321   147  0.88  18.41   0.98     0.94       8198.74|
|  8:  2.5196 -  2.4104  1288   144  0.88  18.42   0.99     0.96       7145.72|
|  9:  2.4104 -  2.3179  1298   143  0.88  18.36   0.99     0.93       6444.67|
| 10:  2.3179 -  2.2382  1279   138  0.88  18.26   0.98     0.94       5870.97|
| 11:  2.2382 -  2.1684  1284   145  0.88  18.67   0.98     0.93       5485.04|
| 12:  2.1684 -  2.1066  1270   140  0.89  17.61   0.98     0.96       4999.76|
| 13:  2.1066 -  2.0512  1298   144  0.88  18.93   0.98     0.98       4237.67|
| 14:  2.0512 -  2.0013   548    62  0.89  17.41   0.96     0.93       3252.44|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     3252.44 max =        12832.14 mean =      8017.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        16.41|
|phase err.(test): min =        0.00 max =           88.64 mean =        15.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.65    111.87  16.87    None  None   None       |
|    all(noH): 2823   0      0.65    111.87  16.87    None  None   None       |
|    Sol.    : 438    0      4.19    111.87  43.28    None  None   None       |
|    Mac.    : 2385   0      0.65    108.29  12.02    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:     0.654 -  11.775: 1626   |   5:    56.260 -  67.381:   77        |
|      1:    11.775 -  22.897:  674   |   6:    67.381 -  78.502:   41        |
|      2:    22.897 -  34.018:  158   |   7:    78.502 -  89.623:   20        |
|      3:    34.018 -  45.139:  116   |   8:    89.623 - 100.744:    8        |
|      4:    45.139 -  56.260:   99   |   9:   100.744 - 111.865:    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)= 342         
Filter by distance & map next to the model:
   mapped sites are within: 0.535 - 4.898
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 342
   mapped sites are within: 0.733 - 4.898

peak=    7.699 closest distance to " O   HOH Z  41 " =    1.174
peak=    7.408 closest distance to " O   HOH Z 400 " =    0.987
peak=    5.783 closest distance to " O   HOH Z 120 " =    1.070
peak=    5.711 closest distance to " O   HOH Z 210 " =    1.397
peak=    5.319 closest distance to " CB  GLN A 223 " =    1.440
peak=    5.317 closest distance to " O   HOH Z 111 " =    2.032
peak=    5.311 closest distance to " O   HOH Z 341 " =    1.229
peak=    5.173 closest distance to " CG  PRO A 213 " =    1.337
peak=    5.167 closest distance to " CB  SER A  63 " =    1.283
peak=    5.006 closest distance to " OE1 GLN A  88 " =    0.928
peak=    4.980 closest distance to " CG  PRO A  54 " =    1.355
peak=    4.913 closest distance to " CG  PRO A 280 " =    0.885
peak=    4.854 closest distance to " O   HOH Z 232 " =    2.271
peak=    4.834 closest distance to " O   HOH Z 433 " =    1.984
peak=    4.819 closest distance to " O   PRO A 198 " =    1.584
peak=    4.761 closest distance to " CA  TYR A  30 " =    1.037
peak=    4.699 closest distance to " O   HOH Z 209 " =    2.352
peak=    4.689 closest distance to " O   HOH Z 418 " =    2.036
peak=    4.582 closest distance to " O   HOH Z 133 " =    2.196
peak=    4.519 closest distance to " O   HOH Z 134 " =    2.110
peak=    4.461 closest distance to " O   HOH Z  15 " =    2.153
peak=    4.394 closest distance to " CB  TRP A 266 " =    0.988
peak=    4.373 closest distance to " O   HOH Z 214 " =    1.560
peak=    4.321 closest distance to " CG1 ILE A  33 " =    1.329
peak=    4.310 closest distance to " CB  PRO A  54 " =    0.840
peak=    4.303 closest distance to " CG  PRO A 198 " =    1.258
peak=    4.297 closest distance to " CB  ARG A 275 " =    0.822
peak=    4.275 closest distance to " CD  ARG A 269 " =    0.882
peak=    4.274 closest distance to " O   HOH Z 394 " =    1.661
peak=    4.231 closest distance to " O   HOH Z 425 " =    1.657
peak=    4.224 closest distance to " O   HOH Z 234 " =    3.755
peak=    4.212 closest distance to " CZ  PHE A 218 " =    1.130
peak=    4.208 closest distance to " CA  ILE A 106 " =    0.790
peak=    4.194 closest distance to " O   HOH Z  67 " =    2.014
peak=    4.190 closest distance to " CB  GLU A 128 " =    1.071
peak=    4.172 closest distance to " CG2BVAL A  41 " =    0.957
peak=    4.172 closest distance to " CB  ARG A 190 " =    1.746
peak=    4.171 closest distance to " O   HOH Z 411 " =    3.428
peak=    4.163 closest distance to " O   HOH Z  78 " =    1.998
peak=    4.143 closest distance to " O   HOH Z  97 " =    2.040
peak=    4.135 closest distance to " CA  ASP A 191 " =    0.855
peak=    4.112 closest distance to " O   HOH Z 126 " =    1.709
peak=    4.101 closest distance to " CB  TRP A 179 " =    1.450
peak=    4.091 closest distance to " O   HOH Z  99 " =    1.610
peak=    4.086 closest distance to " O   HOH Z   7 " =    1.108
peak=    4.084 closest distance to " CB  VAL A 202 " =    1.474
peak=    4.055 closest distance to " O  BHOH Z 338 " =    0.906
peak=    4.052 closest distance to " CA  ALA A 160 " =    1.086
peak=    4.039 closest distance to " NH2 ARG A 156 " =    1.194
peak=    4.038 closest distance to " O   HOH Z 404 " =    1.621
peak=    4.020 closest distance to " O   HOH Z 357 " =    2.138
peak=    4.020 closest distance to " O   HOH Z 422 " =    0.876
peak=    3.999 closest distance to " CB  GLN A 183 " =    1.230
peak=    3.994 closest distance to " O   HOH Z  35 " =    1.877
peak=    3.980 closest distance to " O   HOH Z  40 " =    1.928
peak=    3.970 closest distance to " O   HOH Z 369 " =    2.007
peak=    3.962 closest distance to " O   HOH Z  48 " =    1.915
peak=    3.960 closest distance to " O   HOH Z 265 " =    1.930
peak=    3.960 closest distance to " O   HOH Z  54 " =    1.261
peak=    3.955 closest distance to " CB  LEU A 228 " =    1.115
peak=    3.930 closest distance to " O   HOH Z  80 " =    2.188
peak=    3.928 closest distance to " NH2BARG A 102 " =    1.041
peak=    3.911 closest distance to " N   SER A 164 " =    1.055
peak=    3.910 closest distance to " O   HOH Z 247 " =    1.380
peak=    3.905 closest distance to " CB  ASN A 148 " =    1.350
peak=    3.901 closest distance to " CG2 THR A 221 " =    1.016
peak=    3.897 closest distance to " CB  SER A 141 " =    1.022
peak=    3.897 closest distance to " CD  ARG A  66 " =    2.758
peak=    3.894 closest distance to " O   HOH Z 389 " =    1.995
peak=    3.884 closest distance to " O   HOH Z 415 " =    1.255
peak=    3.883 closest distance to " CA  VAL A  41 " =    0.816
peak=    3.849 closest distance to " CB  GLU A 152 " =    1.123
peak=    3.837 closest distance to " O   GLY A  91 " =    1.129
peak=    3.834 closest distance to " O   HOH Z  95 " =    1.882
peak=    3.833 closest distance to " CD  LYS A 166 " =    1.404
peak=    3.830 closest distance to " O   HOH Z 176 " =    2.096
peak=    3.813 closest distance to " O   HOH Z 271 " =    2.584
peak=    3.803 closest distance to " O   HOH Z  78 " =    1.140
peak=    3.797 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.793 closest distance to " CA  ALA A  51 " =    0.976
peak=    3.790 closest distance to " O   THR A 251 " =    1.335
peak=    3.788 closest distance to " O   HOH Z 196 " =    2.215
peak=    3.784 closest distance to " O   HOH Z 377 " =    1.508
peak=    3.781 closest distance to " NE2 HIS A 115 " =    1.127
peak=    3.780 closest distance to " ND1 HIS A  81 " =    1.567
peak=    3.779 closest distance to " CG  PRO A 243 " =    1.184
peak=    3.779 closest distance to " O   HOH Z 316 " =    3.118
peak=    3.776 closest distance to " CD2 LEU A 297 " =    1.084
peak=    3.760 closest distance to " O   HOH Z 301 " =    1.655
peak=    3.748 closest distance to " CA  GLY A 196 " =    0.952
peak=    3.747 closest distance to " OD1 ASN A 217 " =    1.603
peak=    3.736 closest distance to " CB  ARG A  79 " =    1.347
peak=    3.730 closest distance to " CZ3 TRP A  85 " =    0.944
peak=    3.726 closest distance to " CD1 LEU A 300 " =    1.261
peak=    3.725 closest distance to " CB  ASN A 187 " =    1.145
peak=    3.716 closest distance to " CG  GLN A  77 " =    0.776
peak=    3.692 closest distance to " O   ASP A 200 " =    1.518
peak=    3.687 closest distance to " O   HOH Z 193 " =    1.778
peak=    3.683 closest distance to " O   HOH Z 403 " =    1.864
peak=    3.683 closest distance to " O   HOH Z 298 " =    2.032
peak=    3.682 closest distance to " O   HOH Z 327 " =    1.747
peak=    3.678 closest distance to " CA  LYS A  48 " =    1.419
peak=    3.677 closest distance to " O   HOH Z 189 " =    2.536
peak=    3.677 closest distance to " O   HOH Z 118 " =    1.572
peak=    3.673 closest distance to " O   HOH Z 128 " =    2.340
peak=    3.672 closest distance to " O   HOH Z 395 " =    1.492
peak=    3.660 closest distance to " CA  ARG A 195 " =    1.107
peak=    3.659 closest distance to " CB  ASP A 124 " =    0.846
peak=    3.656 closest distance to " O   HOH Z  88 " =    1.708
peak=    3.650 closest distance to " O   HOH Z 437 " =    1.693
peak=    3.645 closest distance to " O   HOH Z 368 " =    1.966
peak=    3.638 closest distance to " CD1 LEU A 222 " =    0.828
peak=    3.635 closest distance to " O   HOH Z 174 " =    1.412
peak=    3.623 closest distance to " O   HOH Z 374 " =    2.719
peak=    3.620 closest distance to " O   HOH Z 343 " =    2.519
peak=    3.614 closest distance to " CA  ARG A 102 " =    1.276
peak=    3.614 closest distance to " CB  LEU A  83 " =    0.750
peak=    3.614 closest distance to " N   ILE A  33 " =    1.042
peak=    3.608 closest distance to " C   VAL A 265 " =    1.147
peak=    3.607 closest distance to " CD2 TRP A 179 " =    1.255
peak=    3.604 closest distance to " CB  GLN A  88 " =    1.148
peak=    3.604 closest distance to " O   HOH Z 432 " =    1.932
peak=    3.598 closest distance to " O   HOH Z 139 " =    4.898
peak=    3.597 closest distance to " CG1 VAL A 153 " =    1.062
peak=    3.595 closest distance to " O   HOH Z 132 " =    2.656
peak=    3.593 closest distance to " O   HOH Z  98 " =    1.946
peak=    3.593 closest distance to " O   HOH Z 126 " =    2.312
peak=    3.593 closest distance to " O   HOH Z 134 " =    2.439
peak=    3.591 closest distance to " CG AARG A 275 " =    1.156
peak=    3.591 closest distance to " CG2 VAL A 197 " =    1.220
peak=    3.583 closest distance to " CA  ALA A  21 " =    1.449
peak=    3.583 closest distance to " CB  ASN A  39 " =    0.846
peak=    3.581 closest distance to " N   ASN A  39 " =    1.092
peak=    3.580 closest distance to " CA  TRP A 274 " =    0.979
peak=    3.578 closest distance to " CB  GLU A 277 " =    3.836
peak=    3.577 closest distance to " CA  GLU A 152 " =    0.931
peak=    3.571 closest distance to " CD BLYS A 290 " =    1.072
peak=    3.568 closest distance to " OE1 GLN A  11 " =    2.071
peak=    3.563 closest distance to " CB  ASP A 140 " =    0.772
peak=    3.563 closest distance to " O   HOH Z 387 " =    2.844
peak=    3.561 closest distance to " CB  ILE A 120 " =    1.388
peak=    3.560 closest distance to " O   HOH Z  49 " =    0.812
peak=    3.559 closest distance to " CG  GLU A  37 " =    1.064
peak=    3.557 closest distance to " CG2 THR A  42 " =    0.855
peak=    3.555 closest distance to " CA  GLU A  46 " =    0.770
peak=    3.548 closest distance to " NE2 GLN A  11 " =    0.993
peak=    3.538 closest distance to " OD1 ASN A 301 " =    1.251
peak=    3.536 closest distance to " CB  ALA A   9 " =    1.567
peak=    3.534 closest distance to " O   HOH Z 154 " =    1.378
peak=    3.529 closest distance to " CE1 TYR A 186 " =    1.372
peak=    3.529 closest distance to " CB  GLU A 277 " =    0.733
peak=    3.527 closest distance to " O   HOH Z 193 " =    1.944
peak=    3.526 closest distance to " CG2 VAL A  78 " =    1.048
peak=    3.521 closest distance to " CG2 ILE A  20 " =    1.284
peak=    3.515 closest distance to " N   TYR A 116 " =    1.618
peak=    3.512 closest distance to " CB  SER A  62 " =    0.851
peak=    3.510 closest distance to " O   HOH Z 244 " =    1.776
peak=    3.506 closest distance to " CE  LYS A 119 " =    1.023
peak=    3.503 closest distance to " O   HOH Z  50 " =    3.743
peak=    3.499 closest distance to " NZ  LYS A 166 " =    3.237
peak=    3.492 closest distance to " O   HOH Z 215 " =    1.521
peak=    3.488 closest distance to " N   LYS A 166 " =    0.837
peak=    3.474 closest distance to " O   ALA A 165 " =    1.337
peak=    3.472 closest distance to " CG2 ILE A 151 " =    0.810
peak=    3.467 closest distance to " O   ARG A 275 " =    0.752
peak=    3.464 closest distance to " CB  GLU A 175 " =    1.461
peak=    3.461 closest distance to " CB  MET A 105 " =    1.096
peak=    3.455 closest distance to " O   HOH Z 245 " =    1.396
peak=    3.454 closest distance to " O   SER A  87 " =    2.386
peak=    3.454 closest distance to " CG1 ILE A 120 " =    1.075
peak=    3.448 closest distance to " O   HOH Z 344 " =    3.169
peak=    3.448 closest distance to " O   HOH Z  21 " =    1.870
peak=    3.447 closest distance to " CA  GLN A 223 " =    0.889
peak=    3.445 closest distance to " O   HOH Z  49 " =    1.830
peak=    3.443 closest distance to " O   HOH Z 435 " =    3.055
peak=    3.440 closest distance to " O   HOH Z 150 " =    1.847
peak=    3.440 closest distance to " O   HOH Z 406 " =    1.604
peak=    3.430 closest distance to " O   HOH Z  88 " =    3.639
peak=    3.428 closest distance to " NZ  LYS A 117 " =    3.020
peak=    3.425 closest distance to " O   HOH Z 243 " =    0.898
peak=    3.425 closest distance to " CA  SER A  87 " =    0.811
peak=    3.419 closest distance to " C   ASN A 209 " =    1.178
peak=    3.416 closest distance to " CD2 LEU A 255 " =    1.350
peak=    3.415 closest distance to " CB  ASN A 142 " =    1.028
peak=    3.414 closest distance to " O   HOH Z 303 " =    2.267
peak=    3.412 closest distance to " O   HOH Z 104 " =    2.736
peak=    3.411 closest distance to " NH2BARG A 145 " =    1.973
peak=    3.410 closest distance to " CD  PRO A  54 " =    0.916
peak=    3.410 closest distance to " CB  PRO A 198 " =    0.877
peak=    3.403 closest distance to " O   HOH Z 258 " =    2.191
peak=    3.402 closest distance to " NH1AARG A 145 " =    1.098
peak=    3.400 closest distance to " CA  LEU A  83 " =    1.466
peak=    3.400 closest distance to " CB  TYR A 169 " =    0.864
peak=    3.398 closest distance to " CB  ALA A 242 " =    0.936
peak=    3.395 closest distance to " N   PHE A 130 " =    1.263
peak=    3.393 closest distance to " O   HOH Z  61 " =    1.683
peak=    3.391 closest distance to " CB  ILE A 199 " =    1.088
peak=    3.391 closest distance to " O   ALA A 158 " =    1.292
peak=    3.389 closest distance to " CB  ARG A 269 " =    1.004
peak=    3.388 closest distance to " CB  PHE A  16 " =    1.344
peak=    3.387 closest distance to " O   HOH Z 327 " =    2.333
peak=    3.387 closest distance to " CE3 TRP A  85 " =    1.010
peak=    3.383 closest distance to " NE2 GLN A  77 " =    3.209
peak=    3.378 closest distance to " O   HOH Z 415 " =    1.680
peak=    3.376 closest distance to " CG1 VAL A 174 " =    1.211
peak=    3.376 closest distance to " O   HOH Z 431 " =    1.176
peak=    3.375 closest distance to " O   HOH Z 234 " =    1.795
peak=    3.375 closest distance to " CB  VAL A 265 " =    1.315
peak=    3.371 closest distance to " CB  ASN A 285 " =    0.779
peak=    3.371 closest distance to " O   HOH Z 185 " =    1.942
peak=    3.363 closest distance to " O   HOH Z 324 " =    1.553
peak=    3.362 closest distance to " O   HOH Z  57 " =    2.012
peak=    3.361 closest distance to " CA  ARG A 139 " =    1.570
peak=    3.361 closest distance to " O   HOH Z 368 " =    4.318
peak=    3.355 closest distance to " CB  PHE A 283 " =    0.876
peak=    3.350 closest distance to " O   HOH Z 336 " =    1.695
peak=    3.349 closest distance to " CB  ALA A 256 " =    1.541
peak=    3.349 closest distance to " O   HOH Z 362 " =    3.154
peak=    3.345 closest distance to " CA  ALA A 100 " =    1.200
peak=    3.344 closest distance to " O   SER A 276 " =    1.229
peak=    3.332 closest distance to " CA  ASP A 132 " =    1.286
peak=    3.329 closest distance to " OG  SER A 245 " =    1.688
peak=    3.322 closest distance to " CB  ALA A  51 " =    0.743
peak=    3.321 closest distance to " CZ  PHE A  38 " =    1.397
peak=    3.320 closest distance to " CA  THR A 294 " =    1.503
peak=    3.318 closest distance to " O   HOH Z 284 " =    2.982
peak=    3.317 closest distance to " O   HOH Z 180 " =    2.197
peak=    3.316 closest distance to " O   HOH Z  22 " =    2.519
peak=    3.314 closest distance to " O   HOH Z 373 " =    1.692
peak=    3.312 closest distance to " O   HOH Z 325 " =    3.972
peak=    3.310 closest distance to " O   HOH Z 287 " =    1.867
peak=    3.307 closest distance to " O   HOH Z 281 " =    4.857
peak=    3.307 closest distance to " CB  SER A  26 " =    0.811
peak=    3.303 closest distance to " CD  ARG A  56 " =    1.289
peak=    3.303 closest distance to " O   HOH Z 352 " =    1.900
peak=    3.299 closest distance to " CA  ILE A  33 " =    1.505
peak=    3.294 closest distance to " CB  GLN A 103 " =    0.932
peak=    3.293 closest distance to " NH2BARG A 145 " =    1.203
peak=    3.291 closest distance to " O   HOH Z 163 " =    1.778
peak=    3.288 closest distance to " O   HOH Z  30 " =    2.100
peak=    3.286 closest distance to " O   HOH Z 423 " =    3.235
peak=    3.285 closest distance to " CA  TYR A 116 " =    1.476
peak=    3.281 closest distance to " CG2AVAL A 121 " =    2.120
peak=    3.276 closest distance to " O   HOH Z  32 " =    1.919
peak=    3.274 closest distance to " CA  ASP A 124 " =    0.813
peak=    3.274 closest distance to " CD1 LEU A  96 " =    0.754
peak=    3.273 closest distance to " O   HOH Z  11 " =    1.168
peak=    3.272 closest distance to " CG2 THR A 220 " =    0.734
peak=    3.271 closest distance to " CA  VAL A 125 " =    1.067
peak=    3.270 closest distance to " CG  LEU A 167 " =    1.041
peak=    3.270 closest distance to " NH1 ARG A  14 " =    1.228
peak=    3.269 closest distance to " CA  ASP A 162 " =    1.197
peak=    3.269 closest distance to " O   HOH Z  54 " =    1.414
peak=    3.264 closest distance to " OD1 ASN A  69 " =    2.496
peak=    3.263 closest distance to " CA  ALA A 295 " =    1.031
peak=    3.258 closest distance to " OG  SER A  97 " =    3.480
peak=    3.251 closest distance to " CB  MET A  47 " =    0.970
peak=    3.250 closest distance to " CB  GLN A 194 " =    0.937
peak=    3.248 closest distance to " C   ASN A 110 " =    0.891
peak=    3.245 closest distance to " O   HOH Z 420 " =    2.234
peak=    3.244 closest distance to " N   ASN A 252 " =    1.272
peak=    3.243 closest distance to " O   HOH Z 132 " =    2.867
peak=    3.242 closest distance to " O   HOH Z 435 " =    1.827
peak=    3.242 closest distance to " O   ASN A  74 " =    1.547
peak=    3.242 closest distance to " CA  ASN A 217 " =    1.355
peak=    3.241 closest distance to " CB  SER A  28 " =    1.073
peak=    3.236 closest distance to " O   HOH Z 128 " =    2.135
peak=    3.232 closest distance to " N   TYR A  15 " =    0.764
peak=    3.230 closest distance to " CB  ALA A 100 " =    1.559
peak=    3.230 closest distance to " NE2 GLN A 278 " =    2.505
peak=    3.228 closest distance to " CB  SER A 216 " =    0.828
peak=    3.226 closest distance to " CA  SER A  32 " =    1.650
peak=    3.223 closest distance to " CB  ALA A 291 " =    1.256
peak=    3.221 closest distance to " N   ARG A 156 " =    1.441
peak=    3.216 closest distance to " O   HOH Z 298 " =    4.324
peak=    3.214 closest distance to " OE1 GLN A  58 " =    3.352
peak=    3.213 closest distance to " CD  LYS A 119 " =    1.729
peak=    3.210 closest distance to " CB  GLU A  37 " =    0.876
peak=    3.195 closest distance to " O   HOH Z 214 " =    2.694
peak=    3.193 closest distance to " CA  ARG A  36 " =    1.066
peak=    3.193 closest distance to " O   HOH Z 417 " =    3.083
peak=    3.192 closest distance to " CA  GLY A  98 " =    0.992
peak=    3.192 closest distance to " NH2AARG A 190 " =    1.180
peak=    3.190 closest distance to " CA  GLN A  88 " =    1.307
peak=    3.185 closest distance to " O   HOH Z   4 " =    1.123
peak=    3.184 closest distance to " CB  ASN A 148 " =    2.087
peak=    3.184 closest distance to " CH2 TRP A 274 " =    2.375
peak=    3.181 closest distance to " O   HOH Z 345 " =    3.500
peak=    3.180 closest distance to " O   HOH Z 313 " =    2.096
peak=    3.180 closest distance to " OG  SER A  28 " =    1.352
peak=    3.180 closest distance to " O   HOH Z 405 " =    4.314
peak=    3.179 closest distance to " O   HOH Z 426 " =    1.406
peak=    3.176 closest distance to " O   HOH Z 294 " =    1.623
peak=    3.174 closest distance to " O   HOH Z 423 " =    1.680
peak=    3.172 closest distance to " CB  GLU A  46 " =    1.136
peak=    3.170 closest distance to " CE1 HIS A 108 " =    1.077
peak=    3.168 closest distance to " CD2 HIS A  81 " =    1.330
peak=    3.168 closest distance to " CG2 VAL A 257 " =    0.976
peak=    3.167 closest distance to " O   HOH Z 272 " =    1.912
peak=    3.164 closest distance to " O   VAL A  72 " =    3.349
peak=    3.161 closest distance to " N   ASN A 127 " =    1.227
peak=    3.159 closest distance to " N   ALA A 256 " =    1.131
peak=    3.157 closest distance to " CG  LEU A 237 " =    1.141
peak=    3.156 closest distance to " O   HOH Z 133 " =    1.374
peak=    3.156 closest distance to " CZ  PHE A 192 " =    0.999
peak=    3.155 closest distance to " CD  ARG A 195 " =    0.967
peak=    3.144 closest distance to " CB  SER A   3 " =    1.478
peak=    3.144 closest distance to " CB  SER A 212 " =    1.249
peak=    3.141 closest distance to " CA  ARG A 156 " =    1.017
peak=    3.138 closest distance to " OD2 ASP A 200 " =    1.357
peak=    3.137 closest distance to " O   HOH Z 171 " =    3.906
peak=    3.132 closest distance to " CA  ALA A 158 " =    1.122
peak=    3.130 closest distance to " O   HOH Z 365 " =    2.977
peak=    3.127 closest distance to " CG2 THR A  29 " =    1.456
peak=    3.126 closest distance to " O   HOH Z 421 " =    1.665
peak=    3.125 closest distance to " CA  THR A 221 " =    1.597
peak=    3.118 closest distance to " CA  MET A 105 " =    1.161
peak=    3.105 closest distance to " O   HOH Z 413 " =    1.880
peak=    3.100 closest distance to " CB  ALA A  43 " =    0.952
peak=    3.099 closest distance to " OD2 ASP A 298 " =    3.525
peak=    3.098 closest distance to " N   ARG A 190 " =    1.006
peak=    3.097 closest distance to " CA  GLY A 267 " =    0.745
peak=    3.095 closest distance to " CB  VAL A 296 " =    1.470
peak=    3.094 closest distance to " CA  LYS A 117 " =    1.252
peak=    3.091 closest distance to " O   HOH Z   1 " =    3.212
peak=    3.090 closest distance to " CB  ARG A 156 " =    0.971
peak=    3.088 closest distance to " O   HOH Z  48 " =    1.472
peak=    3.085 closest distance to " CB  PRO A 243 " =    1.122
peak=    3.085 closest distance to " ND1 HIS A  81 " =    1.490
peak=    3.083 closest distance to " CA  GLY A 229 " =    0.856
peak=    3.081 closest distance to " CA  ASN A 170 " =    0.782
peak=    3.048 closest distance to " O   HOH Z 346 " =    1.550
peak=    3.037 closest distance to " CD1 TRP A 274 " =    1.084
peak=    3.007 closest distance to " CB  ARG A  79 " =    0.851

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.685 - 5.871
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 222
   mapped sites are within: 0.758 - 5.871

peak=   -4.585 closest distance to " CD1 PHE A  59 " =    1.971
peak=   -4.360 closest distance to " CD  GLN A 223 " =    1.579
peak=   -4.187 closest distance to " O   HOH Z 166 " =    1.457
peak=   -4.173 closest distance to " O   HOH Z 155 " =    1.642
peak=   -4.148 closest distance to " C   ASN A 285 " =    2.472
peak=   -4.147 closest distance to " O   HOH Z  19 " =    2.236
peak=   -4.083 closest distance to " CD2 LEU A 237 " =    2.627
peak=   -4.042 closest distance to " CA  GLY A 203 " =    2.408
peak=   -4.033 closest distance to " O   HOH Z 243 " =    2.149
peak=   -4.000 closest distance to " O   VAL A  67 " =    2.834
peak=   -3.997 closest distance to " C   SER A 271 " =    1.203
peak=   -3.976 closest distance to " O   HOH Z 411 " =    4.996
peak=   -3.961 closest distance to " CD  GLN A 223 " =    0.811
peak=   -3.956 closest distance to " CG  ARG A 269 " =    2.443
peak=   -3.935 closest distance to " NH2 ARG A  66 " =    1.420
peak=   -3.928 closest distance to " O   HOH Z 407 " =    0.770
peak=   -3.912 closest distance to " O   HOH Z   5 " =    1.621
peak=   -3.905 closest distance to " O   HOH Z 290 " =    1.036
peak=   -3.872 closest distance to " C   THR A 279 " =    1.080
peak=   -3.870 closest distance to " O   PRO A 198 " =    1.403
peak=   -3.868 closest distance to " CB  ALA A  10 " =    2.023
peak=   -3.866 closest distance to " O   SER A 276 " =    1.815
peak=   -3.862 closest distance to " O   HOH Z  37 " =    1.410
peak=   -3.854 closest distance to " CD  GLN A  88 " =    0.858
peak=   -3.846 closest distance to " O   HOH Z 150 " =    1.019
peak=   -3.840 closest distance to " O   HOH Z  38 " =    1.043
peak=   -3.835 closest distance to " O   HOH Z 103 " =    2.186
peak=   -3.825 closest distance to " CA  GLU A 277 " =    1.231
peak=   -3.822 closest distance to " CD  ARG A 156 " =    2.153
peak=   -3.819 closest distance to " CG1 VAL A 112 " =    2.588
peak=   -3.804 closest distance to " CB  PRO A 243 " =    2.700
peak=   -3.804 closest distance to " OXT GLY A 302 " =    3.043
peak=   -3.803 closest distance to " O   HOH Z  52 " =    1.783
peak=   -3.794 closest distance to " O   HOH Z 207 " =    1.347
peak=   -3.784 closest distance to " CD1 LEU A 167 " =    2.083
peak=   -3.783 closest distance to " OD1 ASP A 191 " =    1.618
peak=   -3.769 closest distance to " CB  SER A 146 " =    2.176
peak=   -3.761 closest distance to " OD1 ASN A 148 " =    1.538
peak=   -3.754 closest distance to " O   HOH Z 185 " =    2.415
peak=   -3.753 closest distance to " CD1 PHE A 130 " =    2.298
peak=   -3.736 closest distance to " O   HOH Z 128 " =    4.257
peak=   -3.733 closest distance to " O   ALA A   1 " =    2.093
peak=   -3.721 closest distance to " CG  PRO A 243 " =    1.519
peak=   -3.709 closest distance to " CG  ASP A 231 " =    0.758
peak=   -3.708 closest distance to " O   HOH Z   7 " =    1.050
peak=   -3.707 closest distance to " CG  MET A 105 " =    0.941
peak=   -3.705 closest distance to " O   HOH Z 184 " =    1.452
peak=   -3.705 closest distance to " O   HOH Z 418 " =    1.361
peak=   -3.700 closest distance to " O   HOH Z 414 " =    1.535
peak=   -3.691 closest distance to " O   HOH Z 109 " =    3.404
peak=   -3.680 closest distance to " O   HOH Z 388 " =    1.910
peak=   -3.674 closest distance to " N   ARG A 275 " =    1.004
peak=   -3.670 closest distance to " OE1 GLN A  88 " =    0.975
peak=   -3.661 closest distance to " CE2 TYR A  30 " =    2.733
peak=   -3.661 closest distance to " O   HOH Z 308 " =    1.414
peak=   -3.651 closest distance to " CA  GLY A 241 " =    2.387
peak=   -3.649 closest distance to " C   SER A 206 " =    1.442
peak=   -3.639 closest distance to " O   ALA A 256 " =    1.724
peak=   -3.635 closest distance to " CG2 ILE A  49 " =    2.739
peak=   -3.632 closest distance to " O   HOH Z 348 " =    2.314
peak=   -3.623 closest distance to " CG1 VAL A  78 " =    2.676
peak=   -3.614 closest distance to " O   HOH Z 377 " =    0.767
peak=   -3.613 closest distance to " O   HOH Z 151 " =    1.550
peak=   -3.610 closest distance to " O   PHE A 218 " =    1.328
peak=   -3.606 closest distance to " O   HOH Z  71 " =    1.613
peak=   -3.599 closest distance to " CD  PRO A 213 " =    2.351
peak=   -3.581 closest distance to " OD2 ASP A 171 " =    1.971
peak=   -3.581 closest distance to " O   GLY A 262 " =    2.488
peak=   -3.579 closest distance to " CA  SER A 164 " =    2.245
peak=   -3.567 closest distance to " CG  TRP A 266 " =    1.875
peak=   -3.566 closest distance to " ND2 ASN A  45 " =    1.902
peak=   -3.566 closest distance to " CD  ARG A  14 " =    3.369
peak=   -3.555 closest distance to " CA  GLY A 133 " =    2.378
peak=   -3.552 closest distance to " O   HOH Z 396 " =    1.307
peak=   -3.547 closest distance to " OG  SER A  97 " =    2.233
peak=   -3.544 closest distance to " O   HOH Z 400 " =    1.303
peak=   -3.539 closest distance to " CA  VAL A 197 " =    0.934
peak=   -3.527 closest distance to " CD2 PHE A  61 " =    1.869
peak=   -3.520 closest distance to " CB  ALA A  43 " =    2.623
peak=   -3.501 closest distance to " O   HOH Z 234 " =    4.317
peak=   -3.498 closest distance to " O   SER A 135 " =    1.750
peak=   -3.498 closest distance to " O   HOH Z 422 " =    1.242
peak=   -3.497 closest distance to " O   HOH Z  91 " =    2.133
peak=   -3.497 closest distance to " CB  ALA A 161 " =    2.694
peak=   -3.496 closest distance to " OG  SER A  87 " =    1.669
peak=   -3.495 closest distance to " O   HOH Z  17 " =    1.362
peak=   -3.490 closest distance to " O   HOH Z 351 " =    1.525
peak=   -3.487 closest distance to " CA  ASP A 298 " =    1.079
peak=   -3.484 closest distance to " CE  MET A  93 " =    2.500
peak=   -3.483 closest distance to " N   GLN A  58 " =    1.445
peak=   -3.481 closest distance to " ND2 ASN A  45 " =    0.999
peak=   -3.474 closest distance to " O   HOH Z 111 " =    1.341
peak=   -3.471 closest distance to " CA  GLY A 241 " =    3.235
peak=   -3.469 closest distance to " O   HOH Z 183 " =    1.641
peak=   -3.468 closest distance to " CD2 PHE A  59 " =    2.386
peak=   -3.463 closest distance to " CG2 THR A 221 " =    2.257
peak=   -3.459 closest distance to " NH2 ARG A  66 " =    1.026
peak=   -3.457 closest distance to " OG1 THR A  82 " =    1.699
peak=   -3.455 closest distance to " CA  ASN A 127 " =    1.083
peak=   -3.451 closest distance to " O   HOH Z 113 " =    1.908
peak=   -3.450 closest distance to " O   VAL A 174 " =    2.076
peak=   -3.449 closest distance to " OH  TYR A 169 " =    0.959
peak=   -3.441 closest distance to " O   HOH Z 118 " =    3.698
peak=   -3.428 closest distance to " O   HOH Z  58 " =    0.823
peak=   -3.426 closest distance to " O   HOH Z 369 " =    2.453
peak=   -3.416 closest distance to " O   HOH Z 136 " =    2.189
peak=   -3.412 closest distance to " O   ALA A   7 " =    1.634
peak=   -3.410 closest distance to " CZ3 TRP A 179 " =    1.206
peak=   -3.398 closest distance to " O   HOH Z 111 " =    1.919
peak=   -3.397 closest distance to " CA  VAL A  67 " =    3.003
peak=   -3.394 closest distance to " O   HOH Z 120 " =    1.046
peak=   -3.388 closest distance to " O   HOH Z 426 " =    1.937
peak=   -3.380 closest distance to " O   HOH Z  41 " =    2.489
peak=   -3.378 closest distance to " CG2BVAL A  41 " =    2.049
peak=   -3.377 closest distance to " O   ALA A  10 " =    1.898
peak=   -3.376 closest distance to " CD1 LEU A  25 " =    2.532
peak=   -3.373 closest distance to " CE2 PHE A  61 " =    2.675
peak=   -3.372 closest distance to " O   HOH Z  90 " =    2.044
peak=   -3.371 closest distance to " OG BSER A 164 " =    5.067
peak=   -3.358 closest distance to " O   HOH Z 331 " =    1.059
peak=   -3.356 closest distance to " O   HOH Z 117 " =    4.713
peak=   -3.352 closest distance to " CB  CYS A 254 " =    2.161
peak=   -3.348 closest distance to " CB  ALA A   9 " =    2.672
peak=   -3.345 closest distance to " O   HOH Z 200 " =    1.384
peak=   -3.345 closest distance to " CD  GLU A 236 " =    1.060
peak=   -3.334 closest distance to " CG  LEU A 101 " =    2.503
peak=   -3.334 closest distance to " CD1 LEU A 228 " =    2.514
peak=   -3.332 closest distance to " CB  ALA A 291 " =    2.591
peak=   -3.328 closest distance to " CH2 TRP A 177 " =    2.018
peak=   -3.320 closest distance to " OD1 ASP A 298 " =    2.039
peak=   -3.318 closest distance to " O   HOH Z  83 " =    1.630
peak=   -3.313 closest distance to " CE  MET A  93 " =    1.766
peak=   -3.312 closest distance to " OD2 ASP A 171 " =    2.341
peak=   -3.303 closest distance to " O   GLY A  17 " =    1.336
peak=   -3.294 closest distance to " CD  GLN A  58 " =    1.146
peak=   -3.294 closest distance to " N   ALA A 226 " =    2.128
peak=   -3.289 closest distance to " ND2 ASN A  60 " =    1.690
peak=   -3.287 closest distance to " O   GLY A 118 " =    2.271
peak=   -3.285 closest distance to " O   HOH Z   7 " =    1.662
peak=   -3.283 closest distance to " O   HOH Z 251 " =    1.894
peak=   -3.282 closest distance to " CG2BVAL A  41 " =    1.408
peak=   -3.276 closest distance to " NH2BARG A 145 " =    2.331
peak=   -3.276 closest distance to " O   HOH Z 109 " =    3.338
peak=   -3.276 closest distance to " O   HOH Z 423 " =    2.004
peak=   -3.271 closest distance to " O   HOH Z 313 " =    1.470
peak=   -3.267 closest distance to " SG  CYS A 168 " =    1.104
peak=   -3.259 closest distance to " O   HOH Z 134 " =    2.064
peak=   -3.255 closest distance to " CD2 PHE A 225 " =    1.293
peak=   -3.254 closest distance to " O   HOH Z 150 " =    1.798
peak=   -3.244 closest distance to " O   HOH Z 323 " =    1.240
peak=   -3.239 closest distance to " O   HOH Z 423 " =    1.422
peak=   -3.238 closest distance to " N   SER A 134 " =    1.237
peak=   -3.238 closest distance to " O   HOH Z 275 " =    1.668
peak=   -3.237 closest distance to " O   HOH Z 377 " =    2.224
peak=   -3.237 closest distance to " O   HOH Z 325 " =    1.820
peak=   -3.235 closest distance to " ND2 ASN A  60 " =    1.800
peak=   -3.234 closest distance to " CG2 VAL A 189 " =    2.175
peak=   -3.233 closest distance to " O   HOH Z 241 " =    1.065
peak=   -3.233 closest distance to " ND2 ASN A 127 " =    1.734
peak=   -3.232 closest distance to " CG  GLN A  58 " =    1.320
peak=   -3.232 closest distance to " O   HOH Z  60 " =    2.006
peak=   -3.225 closest distance to " O   HOH Z 210 " =    1.387
peak=   -3.223 closest distance to " O   TYR A  15 " =    1.560
peak=   -3.223 closest distance to " C   TRP A 274 " =    1.280
peak=   -3.215 closest distance to " N   GLY A 302 " =    1.895
peak=   -3.215 closest distance to " O   HOH Z  43 " =    1.350
peak=   -3.213 closest distance to " O   HOH Z 174 " =    1.683
peak=   -3.209 closest distance to " O   ASN A 301 " =    1.230
peak=   -3.206 closest distance to " O   HOH Z 259 " =    2.218
peak=   -3.206 closest distance to " CZ  ARG A  79 " =    1.786
peak=   -3.206 closest distance to " OG BSER A 210 " =    2.123
peak=   -3.200 closest distance to " OE1 GLN A  89 " =    1.862
peak=   -3.198 closest distance to " OG ASER A  12 " =    1.715
peak=   -3.197 closest distance to " O   HOH Z 292 " =    4.559
peak=   -3.194 closest distance to " O   HOH Z 275 " =    1.841
peak=   -3.193 closest distance to " CG  GLU A  53 " =    1.288
peak=   -3.190 closest distance to " O   HOH Z 113 " =    2.171
peak=   -3.190 closest distance to " CE2 PHE A  38 " =    1.992
peak=   -3.188 closest distance to " O   HOH Z 113 " =    2.074
peak=   -3.188 closest distance to " O   HOH Z  31 " =    2.207
peak=   -3.186 closest distance to " O   HOH Z  90 " =    3.487
peak=   -3.182 closest distance to " O   HOH Z 118 " =    5.642
peak=   -3.182 closest distance to " CB  ALA A 227 " =    2.442
peak=   -3.179 closest distance to " CA  VAL A 232 " =    2.404
peak=   -3.177 closest distance to " CB  PRO A 213 " =    1.626
peak=   -3.176 closest distance to " O   ASP A 171 " =    1.050
peak=   -3.172 closest distance to " O   GLN A  11 " =    1.151
peak=   -3.170 closest distance to " CB  ALA A 291 " =    2.402
peak=   -3.165 closest distance to " O   HOH Z 119 " =    3.165
peak=   -3.163 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.163 closest distance to " O   HOH Z 165 " =    1.887
peak=   -3.160 closest distance to " O   HOH Z   6 " =    1.487
peak=   -3.158 closest distance to " OD1 ASN A 301 " =    0.890
peak=   -3.151 closest distance to " CG2AVAL A  41 " =    2.754
peak=   -3.146 closest distance to " CG2 VAL A 189 " =    0.899
peak=   -3.140 closest distance to " O   HOH Z 400 " =    1.162
peak=   -3.133 closest distance to " O   HOH Z  11 " =    1.425
peak=   -3.133 closest distance to " O   HOH Z 312 " =    1.523
peak=   -3.128 closest distance to " CD2 TRP A 274 " =    2.342
peak=   -3.128 closest distance to " CG  ARG A 219 " =    2.500
peak=   -3.127 closest distance to " O   ALA A  34 " =    2.050
peak=   -3.127 closest distance to " NZ  LYS A 119 " =    1.906
peak=   -3.120 closest distance to " CG  PRO A 163 " =    1.742
peak=   -3.116 closest distance to " CB  ASP A 132 " =    2.445
peak=   -3.090 closest distance to " O   HOH Z 402 " =    1.293
peak=   -3.082 closest distance to " O   HOH Z 252 " =    4.503
peak=   -3.080 closest distance to " O   HOH Z 422 " =    1.688
peak=   -3.078 closest distance to " O   HOH Z 191 " =    5.871
peak=   -3.073 closest distance to " CA  SER A 276 " =    1.491
peak=   -3.073 closest distance to " O   TRP A  92 " =    1.968
peak=   -3.068 closest distance to " SD  MET A  40 " =    1.977
peak=   -3.066 closest distance to " CD  GLN A  11 " =    1.158
peak=   -3.056 closest distance to " OE1 GLN A  88 " =    2.001
peak=   -3.055 closest distance to " OE1 GLN A  77 " =    2.276
peak=   -3.041 closest distance to " CG1 VAL A 112 " =    2.337
peak=   -3.040 closest distance to " SG  CYS A 254 " =    3.229
peak=   -3.028 closest distance to " O   THR A  18 " =    1.697
peak=   -3.017 closest distance to " O   HOH Z 118 " =    0.794
peak=   -3.002 closest distance to " O   HOH Z 120 " =    0.940

================= 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    :  0.4524 0.4308   6.268811e+00   6.238891e+00
   1_bss:  0.4431 0.4203   6.263217e+00   6.228645e+00
   1_xyz:  0.3594 0.3888   6.121962e+00   6.169939e+00
   1_adp:  0.3291 0.3943   6.075300e+00   6.173460e+00
   1_occ:  0.3289 0.3939   6.074380e+00   6.173197e+00
   2_bss:  0.3281 0.3924   6.075756e+00   6.173521e+00
   2_xyz:  0.2661 0.3167   5.884005e+00   6.022801e+00
   2_adp:  0.2449 0.3068   5.834890e+00   5.999682e+00
   2_occ:  0.2446 0.3067   5.834384e+00   5.999715e+00
   3_bss:  0.2446 0.3060   5.834827e+00   5.999758e+00
   3_xyz:  0.2023 0.2582   5.656317e+00   5.841047e+00
   3_adp:  0.1868 0.2434   5.598307e+00   5.791384e+00
   3_occ:  0.1867 0.2435   5.598216e+00   5.791611e+00
   4_bss:  0.1870 0.2431   5.598243e+00   5.790385e+00
   4_xyz:  0.1504 0.2018   5.407499e+00   5.629565e+00
   4_adp:  0.1389 0.1892   5.337307e+00   5.563393e+00
   4_occ:  0.1389 0.1891   5.337084e+00   5.563303e+00
   5_bss:  0.1394 0.1894   5.338661e+00   5.563961e+00
   5_xyz:  0.1307 0.1804   5.287521e+00   5.518358e+00
   5_adp:  0.1295 0.1756   5.273284e+00   5.494265e+00
   5_occ:  0.1294 0.1756   5.272893e+00   5.494400e+00
   5_bss:  0.1293 0.1757   5.272680e+00   5.494149e+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:  0.283  38.129  -0.228   4.651  -2.212   0.000  -0.000  -0.000
   1_xyz:  0.283  38.129  -0.228   4.651  -2.212   0.000  -0.000  -0.000
   1_adp:  0.283  38.129  -0.228   4.651  -2.212   0.000  -0.000  -0.000
   1_occ:  0.283  38.129  -0.228   4.651  -2.212   0.000  -0.000  -0.000
   2_bss:  0.311  60.202  -0.545   2.726  -0.536   0.000  -0.000  -0.000
   2_xyz:  0.311  60.202  -0.545   2.726  -0.536   0.000  -0.000  -0.000
   2_adp:  0.311  60.202  -0.545   2.726  -0.536   0.000  -0.000  -0.000
   2_occ:  0.311  60.202  -0.545   2.726  -0.536   0.000  -0.000  -0.000
   3_bss:  0.326  71.160  -0.344   1.580  -0.045   0.000  -0.000  -0.000
   3_xyz:  0.326  71.160  -0.344   1.580  -0.045   0.000  -0.000  -0.000
   3_adp:  0.326  71.160  -0.344   1.580  -0.045   0.000  -0.000  -0.000
   3_occ:  0.326  71.160  -0.344   1.580  -0.045   0.000  -0.000  -0.000
   4_bss:  0.330  83.471  -0.757   0.684  -0.219   0.000  -0.000  -0.000
   4_xyz:  0.330  83.471  -0.757   0.684  -0.219   0.000  -0.000  -0.000
   4_adp:  0.330  83.471  -0.757   0.684  -0.219   0.000  -0.000  -0.000
   4_occ:  0.330  83.471  -0.757   0.684  -0.219   0.000  -0.000  -0.000
   5_bss:  0.332  81.204  -0.891   0.006  -0.157   0.000  -0.000  -0.000
   5_xyz:  0.332  81.204  -0.891   0.006  -0.157   0.000  -0.000  -0.000
   5_adp:  0.332  81.204  -0.891   0.006  -0.157   0.000  -0.000  -0.000
   5_occ:  0.332  81.204  -0.891   0.006  -0.157   0.000  -0.000  -0.000
   5_bss:  0.323  72.891  -0.885  -0.223  -0.003  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.009 0.5225  0.6804    59652.280
   1_bss:  49.193 0.5312  0.7089    56512.055
   1_xyz:  44.617 0.5869  0.7707    45646.076
   1_adp:  44.986 0.5819  0.7578    46099.370
   1_occ:  44.966 0.5821  0.7576    46049.809
   2_bss:  44.812 0.5840  0.7581    45822.026
   2_xyz:  34.646 0.7040  0.8899    28081.457
   2_adp:  33.090 0.7222  0.8892    26258.273
   2_occ:  33.076 0.7223  0.8890    26238.519
   3_bss:  32.987 0.7234  0.8868    26169.208
   3_xyz:  26.400 0.7960  0.9522    17468.535
   3_adp:  24.464 0.8169  0.9518    15670.231
   3_occ:  24.464 0.8169  0.9518    15675.336
   4_bss:  24.378 0.8177  0.9362    15575.167
   4_xyz:  19.961 0.8610  0.9650    10581.112
   4_adp:  18.098 0.8791  0.9645     9219.663
   4_occ:  18.093 0.8792  0.9644     9218.220
   5_bss:  18.108 0.8790  0.9565     9243.409
   5_xyz:  16.977 0.8895  0.9615     8347.755
   5_adp:  16.349 0.8955  0.9580     8023.868
   5_occ:  16.349 0.8955  0.9580     8025.560
   5_bss:  16.347 0.8955  0.9568     8018.328
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7335e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7335e-01
   1_xyz:   1.520  0.012  0.093 15.926  0.005  4.109   1.2297e-01
   1_adp:   1.520  0.012  0.093 15.926  0.005  4.109   1.2297e-01
   1_occ:   1.520  0.012  0.093 15.926  0.005  4.109   1.2297e-01
   2_bss:   1.520  0.012  0.093 15.926  0.005  4.109   1.2297e-01
   2_xyz:   1.504  0.012  0.093 15.501  0.006  4.116   1.2544e-01
   2_adp:   1.504  0.012  0.093 15.501  0.006  4.116   1.2544e-01
   2_occ:   1.504  0.012  0.093 15.501  0.006  4.116   1.2544e-01
   3_bss:   1.504  0.012  0.093 15.501  0.006  4.116   1.2544e-01
   3_xyz:   1.072  0.009  0.075 14.651  0.004  4.128   6.9812e-02
   3_adp:   1.072  0.009  0.075 14.651  0.004  4.128   6.9812e-02
   3_occ:   1.072  0.009  0.075 14.651  0.004  4.128   6.9812e-02
   4_bss:   1.072  0.009  0.075 14.651  0.004  4.128   6.9812e-02
   4_xyz:   1.236  0.012  0.085 15.121  0.004  4.114   9.0781e-02
   4_adp:   1.236  0.012  0.085 15.121  0.004  4.114   9.0781e-02
   4_occ:   1.236  0.012  0.085 15.121  0.004  4.114   9.0781e-02
   5_bss:   1.236  0.012  0.085 15.121  0.004  4.114   9.0781e-02
   5_xyz:   1.095  0.009  0.077 14.828  0.004  4.121   7.0508e-02
   5_adp:   1.095  0.009  0.077 14.828  0.004  4.121   7.0508e-02
   5_occ:   1.095  0.009  0.077 14.828  0.004  4.121   7.0508e-02
   5_bss:   1.095  0.009  0.077 14.828  0.004  4.121   7.0508e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.194   2.4533e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.194   2.4533e-01
   1_xyz:   9.466  0.069  0.302 88.440  0.031  1.970   1.0264e-01
   1_adp:   9.466  0.069  0.302 88.440  0.031  1.970   1.0264e-01
   1_occ:   9.466  0.069  0.302 88.440  0.031  1.970   1.0264e-01
   2_bss:   9.466  0.069  0.302 88.440  0.031  1.970   1.0264e-01
   2_xyz:   8.508  0.052  0.309 86.231  0.034  2.163   1.9679e-01
   2_adp:   8.508  0.052  0.309 86.231  0.034  2.163   1.9679e-01
   2_occ:   8.508  0.052  0.309 86.231  0.034  2.163   1.9679e-01
   3_bss:   8.508  0.052  0.309 86.231  0.034  2.163   1.9679e-01
   3_xyz:   7.781  0.040  0.233 82.657  0.029  2.275   7.3491e-02
   3_adp:   7.781  0.040  0.233 82.657  0.029  2.275   7.3491e-02
   3_occ:   7.781  0.040  0.233 82.657  0.029  2.275   7.3491e-02
   4_bss:   7.781  0.040  0.233 82.657  0.029  2.275   7.3491e-02
   4_xyz:   8.380  0.078  0.237 85.911  0.042  2.160   6.4680e-02
   4_adp:   8.380  0.078  0.237 85.911  0.042  2.160   6.4680e-02
   4_occ:   8.380  0.078  0.237 85.911  0.042  2.160   6.4680e-02
   5_bss:   8.380  0.078  0.237 85.911  0.042  2.160   6.4680e-02
   5_xyz:   7.969  0.051  0.242 81.801  0.039  2.283   4.5405e-02
   5_adp:   7.969  0.051  0.242 81.801  0.039  2.283   4.5405e-02
   5_occ:   7.969  0.051  0.242 81.801  0.039  2.283   4.5405e-02
   5_bss:   7.969  0.051  0.242 81.801  0.039  2.283   4.5405e-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:  95.30   0.00  18.37  86.36   0.00  15.06  95.30   0.00  36.40
   1_occ:  95.30   0.00  18.37  86.36   0.00  15.06  95.30   0.00  36.40
   2_bss:  95.30   0.00  18.37  86.36   0.00  15.06  95.30   0.00  36.40
   2_xyz:  95.30   0.00  18.37  86.36   0.00  15.06  95.30   0.00  36.40
   2_adp:  93.55   0.00  18.44  92.68   0.00  14.42  93.55   0.00  40.38
   2_occ:  93.55   0.00  18.44  92.68   0.00  14.42  93.55   0.00  40.38
   3_bss:  93.55   0.00  18.44  92.68   0.00  14.42  93.55   0.00  40.38
   3_xyz:  93.55   0.00  18.44  92.68   0.00  14.42  93.55   0.00  40.38
   3_adp: 107.47   0.00  18.57 107.47   0.00  13.56 104.79   2.87  45.87
   3_occ: 107.47   0.00  18.57 107.47   0.00  13.56 104.79   2.87  45.87
   4_bss: 107.47   0.00  18.57 107.47   0.00  13.56 104.79   2.87  45.87
   4_xyz: 107.47   0.00  18.57 107.47   0.00  13.56 104.79   2.87  45.87
   4_adp: 113.83   0.00  17.71 113.83   0.00  12.50 113.57   4.51  46.08
   4_occ: 113.83   0.00  17.71 113.83   0.00  12.50 113.57   4.51  46.08
   5_bss: 113.83   0.00  17.71 113.83   0.00  12.50 113.57   4.51  46.08
   5_xyz: 113.83   0.00  17.71 113.83   0.00  12.50 113.57   4.51  46.08
   5_adp: 111.89   0.68  16.89 108.31   0.68  12.04 111.89   4.21  43.31
   5_occ: 111.89   0.68  16.89 108.31   0.68  12.04 111.89   4.21  43.31
   5_bss: 111.87   0.65  16.87 108.29   0.65  12.02 111.87   4.19  43.28
------------------------------------------------------------------------
 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:    2.157    0.022    0.332
   1_adp:    2.157    0.022    0.332
   1_occ:    2.157    0.022    0.332
   2_bss:    2.157    0.022    0.332
   2_xyz:    1.769    0.060    0.591
   2_adp:    1.769    0.060    0.591
   2_occ:    1.769    0.060    0.591
   3_bss:    1.769    0.060    0.591
   3_xyz:    1.628    0.047    0.692
   3_adp:    1.628    0.047    0.692
   3_occ:    1.628    0.047    0.692
   4_bss:    1.628    0.047    0.692
   4_xyz:    1.643    0.070    0.800
   4_adp:    1.643    0.070    0.800
   4_occ:    1.643    0.070    0.800
   5_bss:    1.643    0.070    0.800
   5_xyz:    1.647    0.080    0.825
   5_adp:    1.647    0.080    0.825
   5_occ:    1.647    0.080    0.825
   5_bss:    1.647    0.080    0.825
------------------------------------------------------------------------

CPU time actual refinement: 341.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1204/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_1204/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1204/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1204/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1204/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.91 
  Macro-tasks:
    bulk solvent and scale       = 48.16  
    individual site refinement   = 133.38 
    weights calculation          = 29.44  
    collect and process          = 6.44   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.55 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 106.30 
    alpha_beta                      = 8.04   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 113.83 
    fmodel                         = 8.19   
    r_factors                      = 0.22   
    phase_errors                   = 10.81  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 251.10 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.870 micro seconds
Total CPU time: 5.91 minutes
from_scatterers_fft:    636 calls, 105.99 s
gradients_fft:          581 calls, 101.26 s

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

# Date 2008-01-16 Time 06:41:30 PST -0800 (1200494490.69 s)
Start R-work = 0.4524, R-free = 0.4308 (no bulk solvent and anisotropic scale)
Final R-work = 0.1452, R-free = 0.1903 (no bulk solvent and anisotropic scale)

Start R-work = 0.4431, R-free = 0.4203
Final R-work = 0.1293, R-free = 0.1757