# Date 2008-01-16 Time 06:35:49 PST -0800 (1200494149.34 s)
#phil __OFF__

Command line arguments: "../1207.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7412
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1207

-------------------------------------------------------------------------------
  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, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2734 2.0311
Completeness in resolution range: 0.973173
Completeness with d_max=infinity: 0.970089

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2734
                             d_min =   2.0311

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, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2734 2.0311
Completeness in resolution range: 0.973173
Completeness with d_max=infinity: 0.970089

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2738 -  4.3454 [2112/2139]  1902   210   9.9%
  bin  2:  4.3454 -  3.4623 [2030/2046]  1826   204  10.0%
  bin  3:  3.4623 -  3.0285 [2005/2024]  1802   203  10.1%
  bin  4:  3.0285 -  2.7534 [1987/2017]  1793   194   9.8%
  bin  5:  2.7534 -  2.5570 [1961/1980]  1761   200  10.2%
  bin  6:  2.5570 -  2.4069 [1962/1987]  1769   193   9.8%
  bin  7:  2.4069 -  2.2868 [1968/2000]  1772   196  10.0%
  bin  8:  2.2868 -  2.1875 [1933/1965]  1737   196  10.1%
  bin  9:  2.1875 -  2.1035 [1940/1982]  1746   194  10.0%
  bin 10:  2.1035 -  2.0311 [1691/1989]  1522   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1207/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: 0.13 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:
        1.33 -     2.04: 3
        2.04 -     2.76: 338
        2.76 -     3.47: 4472
        3.47 -     4.19: 9125
        4.19 -     4.90: 13596
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.327 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.702 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.061 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A 245 " - " O   HOH Z 202 "  2.148 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27529 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_1207/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1207/model_refine_001.geo

CPU time processing inputs: 9.00


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


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


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


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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4852   r_free= 0.4669   ksol= 0.00   Bsol= 0.00   scale= 0.855    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.290732                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2738 -  4.8463 0.99   1374  153 0.3808 0.3904      6.5711      6.5356|
|  2:  4.8463 -  3.8672 0.99   1320  145 0.4344 0.4474      6.8905      6.8883|
|  3:  3.8672 -  3.3845 0.99   1300  145 0.4668 0.4091       6.731      6.6499|
|  4:  3.3845 -  3.0778 0.99   1286  144 0.4855 0.4673      6.5624      6.5077|
|  5:  3.0778 -  2.8587 0.99   1271  140 0.5138 0.4753      6.3904      6.3967|
|  6:  2.8587 -  2.6911 0.99   1277  143 0.5111 0.4904      6.2928      6.2384|
|  7:  2.6911 -  2.5570 0.99   1256  141 0.5226 0.4671      6.2492      6.1718|
|  8:  2.5570 -  2.4462 0.98   1268  140 0.5192 0.4629      6.1935      6.1907|
|  9:  2.4462 -  2.3524 0.98   1269  138 0.5249 0.5336      6.1218      6.1676|
| 10:  2.3524 -  2.2715 0.99   1236  137 0.5202 0.5027      6.1247      6.0987|
| 11:  2.2715 -  2.2006 0.99   1265  147 0.5348 0.5371      6.0519      6.1033|
| 12:  2.2006 -  2.1379 0.97   1249  129 0.5353 0.5116      5.9899      6.0015|
| 13:  2.1379 -  2.0818 0.99   1237  141 0.5196 0.5052      5.8913      5.8753|
| 14:  2.0818 -  2.0311 0.80   1022  116 0.5189 0.5147      5.8399      5.7699|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2738 -  4.8463  1374   153  0.69  34.83   0.81     0.73      74725.27|
|  2:  4.8463 -  3.8672  1320   145  0.70  35.54   0.87     0.77     106675.67|
|  3:  3.8672 -  3.3845  1300   145  0.60  44.03   0.85     0.73     115461.11|
|  4:  3.3845 -  3.0778  1286   144  0.50  52.19   0.86     0.63     105491.75|
|  5:  3.0778 -  2.8587  1271   140  0.41  59.07   0.85     0.56      83786.91|
|  6:  2.8587 -  2.6911  1277   143  0.40  59.71   0.85     0.53      69945.54|
|  7:  2.6911 -  2.5570  1256   141  0.38  61.22   0.87     0.51      62383.94|
|  8:  2.5570 -  2.4462  1268   140  0.37  62.31   0.86     0.50      59488.53|
|  9:  2.4462 -  2.3524  1269   138  0.34  64.54   0.87     0.48      55850.95|
| 10:  2.3524 -  2.2715  1236   137  0.35  63.66   0.91     0.49      50317.97|
| 11:  2.2715 -  2.2006  1265   147  0.33  65.06   0.88     0.49      46901.71|
| 12:  2.2006 -  2.1379  1249   129  0.33  65.57   0.88     0.48      43593.18|
| 13:  2.1379 -  2.0818  1237   141  0.30  67.79   0.88     0.43      38861.88|
| 14:  2.0818 -  2.0311  1022   116  0.29  68.59   0.88     0.38      31950.97|
|alpha:            min =        0.38 max =            0.77 mean =         0.56|
|beta:             min =    31950.97 max =       115461.11 mean =     68429.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.01|
|phase err.(test): min =        0.00 max =           89.97 mean =        56.99|
|-----------------------------------------------------------------------------|

============================== 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 = 19.973935             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.947   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.197939              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.573   (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 |  1.327 -  1.684:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.684 -  2.041:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.041 -  2.399:        5 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.399 -  2.756:      333 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.756 -  3.113:     2222 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.113 -  3.471:     2250 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.471 -  3.828:     4236 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.828 -  4.185:     4889 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.185 -  4.543:     6089 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.543 -  4.900:     7507 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.327 |       0.223 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    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: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4852   r_free= 0.4669   ksol= 0.00   Bsol= 0.00   scale= 0.855    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.290732                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4800   r_free= 0.4604   ksol= 0.27   Bsol= 58.45   scale= 0.897   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,3.33,0.51,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.288249                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.051736             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.633   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.469160              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.223   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4800      final r-factor (work) = 0.3625          |
| start r-factor (free) = 0.4604      final r-factor (free) = 0.4026          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.7528 = 17.05 * 0.50 * 6.2848 + 1.00 * 0.1691                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.7227 = 17.05 * 0.50 * 6.1636 + 1.00 * 0.1723                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3625      final r-factor (work) = 0.3292          |
| start r-factor (free) = 0.4026      final r-factor (free) = 0.4060          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0617 = 1.47 * 1.00 * 6.1636 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9446 = 1.47 * 1.00 * 6.0623 + 1.00 * 0.0381                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.61  19.06    None  None   None       |
|    all(noH): 2823   0      0.00    115.61  19.06    None  None   None       |
|    Sol.    : 438    0      0.00    115.61  40.26    None  None   None       |
|    Mac.    : 2385   0      0.00    95.44   15.16    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 -  11.561: 1142   |   5:    57.804 -  69.365:   77        |
|      1:    11.561 -  23.122:  854   |   6:    69.365 -  80.926:   31        |
|      2:    23.122 -  34.683:  401   |   7:    80.926 -  92.487:   10        |
|      3:    34.683 -  46.244:  206   |   8:    92.487 - 104.048:    2        |
|      4:    46.244 -  57.804:   99   |   9:   104.048 - 115.609:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3292 r_free = 0.4060             target_work(ml) = 6.067         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3289 r_free = 0.4051             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3289   r_free= 0.4051   ksol= 0.27   Bsol= 58.45   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,3.33,0.51,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.066331                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3280   r_free= 0.4036   ksol= 0.31   Bsol= 77.14   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,2.43,1.16,0.00,0.00,0.00); trace/3= 1.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.067247                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.725821             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.437   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.331482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.726   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3280      final r-factor (work) = 0.2611          |
| start r-factor (free) = 0.4036      final r-factor (free) = 0.3170          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.7622 = 12.73 * 0.50 * 6.0647 + 1.00 * 0.1731                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2117 = 12.73 * 0.50 * 5.9874 + 1.00 * 0.1143                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2611      final r-factor (work) = 0.2443          |
| start r-factor (free) = 0.3170      final r-factor (free) = 0.3064          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9987 = 1.33 * 1.00 * 5.9874 + 1.00 * 0.0265                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8044 = 1.33 * 1.00 * 5.8349 + 1.00 * 0.0353                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.88  19.04    None  None   None       |
|    all(noH): 2823   0      0.00    114.88  19.04    None  None   None       |
|    Sol.    : 438    0      0.00    114.88  41.72    None  None   None       |
|    Mac.    : 2385   0      0.00    95.76   14.87    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 -  11.488: 1145   |   5:    57.442 -  68.930:   79        |
|      1:    11.488 -  22.977:  858   |   6:    68.930 -  80.419:   35        |
|      2:    22.977 -  34.465:  393   |   7:    80.419 -  91.907:   11        |
|      3:    34.465 -  45.954:  202   |   8:    91.907 - 103.395:    2        |
|      4:    45.954 -  57.442:   97   |   9:   103.395 - 114.884:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2443 r_free = 0.3064             target_work(ml) = 5.822         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2441 r_free = 0.3068             target_work(ml) = 5.822         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2441   r_free= 0.3068   ksol= 0.31   Bsol= 77.14   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.11,2.43,1.16,0.00,0.00,0.00); trace/3= 1.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.822062                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2441   r_free= 0.3070   ksol= 0.33   Bsol= 78.23   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.13,1.42,0.72,0.00,0.00,0.00); trace/3= 0.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.822058                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.227267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.068  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.430853              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.481   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2441      final r-factor (work) = 0.1980          |
| start r-factor (free) = 0.3070      final r-factor (free) = 0.2539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1129 = 8.23 * 0.50 * 5.8339 + 1.00 * 0.1143                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7021 = 8.23 * 0.50 * 5.7384 + 1.00 * 0.0964                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1980      final r-factor (work) = 0.1738          |
| start r-factor (free) = 0.2539      final r-factor (free) = 0.2201          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4968 = 0.43 * 1.00 * 5.7384 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4280 = 0.43 * 1.00 * 5.5762 + 1.00 * 0.0255                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.94  17.40    None  None   None       |
|    all(noH): 2823   0      0.00    104.94  17.40    None  None   None       |
|    Sol.    : 438    0      4.12    104.94  43.30    None  None   None       |
|    Mac.    : 2385   0      0.00    84.84   12.65    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 -  10.494: 1296   |   5:    52.469 -  62.963:   86        |
|      1:    10.494 -  20.988:  860   |   6:    62.963 -  73.457:   48        |
|      2:    20.988 -  31.482:  229   |   7:    73.457 -  83.951:   22        |
|      3:    31.482 -  41.975:  158   |   8:    83.951 -  94.445:    6        |
|      4:    41.975 -  52.469:  116   |   9:    94.445 - 104.938:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1738 r_free = 0.2201             target_work(ml) = 5.512         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1736 r_free = 0.2198             target_work(ml) = 5.511         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1736   r_free= 0.2198   ksol= 0.33   Bsol= 78.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.13,1.42,0.72,0.00,0.00,0.00); trace/3= 0.67                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.511341                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1735   r_free= 0.2194   ksol= 0.34   Bsol= 81.35   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.32,0.31,0.00,0.00,0.00); trace/3= -0.07                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.510171                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.488600              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.515  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.308190              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.569   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1735      final r-factor (work) = 0.1534          |
| start r-factor (free) = 0.2194      final r-factor (free) = 0.1987          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0375 = 2.49 * 0.50 * 5.5782 + 1.00 * 0.0966                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8548 = 2.49 * 0.50 * 5.4545 + 1.00 * 0.0677                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1534      final r-factor (work) = 0.1459          |
| start r-factor (free) = 0.1987      final r-factor (free) = 0.1987          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6047 = 2.31 * 1.00 * 5.4545 + 1.00 * 0.0146                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4509 = 2.31 * 1.00 * 5.3826 + 1.00 * 0.0268                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.91  17.91    None  None   None       |
|    all(noH): 2823   0      0.00    114.91  17.91    None  None   None       |
|    Sol.    : 438    0      3.83    114.91  48.08    None  None   None       |
|    Mac.    : 2385   0      0.00    109.27  12.36    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 -  11.492: 1500   |   5:    57.457 -  68.949:   70        |
|      1:    11.492 -  22.983:  738   |   6:    68.949 -  80.440:   63        |
|      2:    22.983 -  34.474:  182   |   7:    80.440 -  91.932:   31        |
|      3:    34.474 -  45.966:  118   |   8:    91.932 - 103.423:   13        |
|      4:    45.966 -  57.457:  103   |   9:   103.423 - 114.915:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1459 r_free = 0.1987             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1458 r_free = 0.1987             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1987   ksol= 0.34   Bsol= 81.35   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.32,0.31,0.00,0.00,0.00); trace/3= -0.07                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.379205                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.1988   ksol= 0.33   Bsol= 87.29   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,0.10,0.43,0.00,0.00,0.00); trace/3= -0.10                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.380627                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.937149              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.206  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.866516              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.040   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1462      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.1988      final r-factor (free) = 0.1886          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2813 = 1.94 * 0.50 * 5.3827 + 1.00 * 0.0677                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2487 = 1.94 * 0.50 * 5.3539 + 1.00 * 0.0631                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1378      final r-factor (work) = 0.1359          |
| start r-factor (free) = 0.1886      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6596 = 0.87 * 1.00 * 5.3539 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6275 = 0.87 * 1.00 * 5.3221 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    120.53  17.24    None  None   None       |
|    all(noH): 2823   0      0.00    120.53  17.24    None  None   None       |
|    Sol.    : 438    0      3.85    120.53  46.77    None  None   None       |
|    Mac.    : 2385   0      0.00    113.23  11.82    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 -  12.053: 1646   |   5:    60.265 -  72.318:   66        |
|      1:    12.053 -  24.106:  660   |   6:    72.318 -  84.370:   54        |
|      2:    24.106 -  36.159:  152   |   7:    84.370 -  96.423:   14        |
|      3:    36.159 -  48.212:  117   |   8:    96.423 - 108.476:   10        |
|      4:    48.212 -  60.265:   99   |   9:   108.476 - 120.529:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1359 r_free = 0.1866             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1359 r_free = 0.1865             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1359   r_free= 0.1865   ksol= 0.33   Bsol= 87.29   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,0.10,0.43,0.00,0.00,0.00); trace/3= -0.10                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.314574                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2738 -  4.8463 0.99   1374  153 0.1073 0.1399      5.4648        5.61|
|  2:  4.8463 -  3.8672 0.99   1320  145 0.0923 0.1102      5.5035      5.6458|
|  3:  3.8672 -  3.3845 0.99   1300  145 0.1177 0.1677      5.5736      5.9401|
|  4:  3.3845 -  3.0778 0.99   1286  144 0.1449 0.1917      5.6133      5.7921|
|  5:  3.0778 -  2.8587 0.99   1271  140 0.1687 0.1999      5.5473      5.7003|
|  6:  2.8587 -  2.6911 0.99   1277  143 0.1582 0.2356      5.4319      5.6736|
|  7:  2.6911 -  2.5570 0.99   1256  141 0.1571 0.2066        5.37      5.5732|
|  8:  2.5570 -  2.4462 0.98   1268  140 0.1505 0.2156      5.2924      5.5634|
|  9:  2.4462 -  2.3524 0.98   1269  138 0.1560 0.2165      5.2614      5.4751|
| 10:  2.3524 -  2.2715 0.99   1236  137 0.1432 0.2082      5.1762      5.3953|
| 11:  2.2715 -  2.2006 0.99   1265  147 0.1447 0.2057       5.136      5.3925|
| 12:  2.2006 -  2.1379 0.97   1249  129 0.1366 0.2090      5.0589      5.4147|
| 13:  2.1379 -  2.0818 0.99   1237  141 0.1415 0.2070       4.985      5.1885|
| 14:  2.0818 -  2.0311 0.80   1022  116 0.1326 0.2140      4.8523      5.1446|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2738 -  4.8463  1374   153  0.93  10.69   0.94     0.92       8834.57|
|  2:  4.8463 -  3.8672  1320   145  0.95   9.04   0.99     0.98      10407.79|
|  3:  3.8672 -  3.3845  1300   145  0.92  12.86   1.01     1.00      12559.03|
|  4:  3.3845 -  3.0778  1286   144  0.90  16.42   1.00     0.97      14070.69|
|  5:  3.0778 -  2.8587  1271   140  0.86  20.41   0.99     0.97      13034.99|
|  6:  2.8587 -  2.6911  1277   143  0.87  19.77   0.97     0.94      10563.54|
|  7:  2.6911 -  2.5570  1256   141  0.86  20.15   0.98     0.94       9557.64|
|  8:  2.5570 -  2.4462  1268   140  0.87  19.39   0.98     0.94       8337.11|
|  9:  2.4462 -  2.3524  1269   138  0.87  20.06   0.97     0.91       7590.93|
| 10:  2.3524 -  2.2715  1236   137  0.87  19.29   0.97     0.92       6578.51|
| 11:  2.2715 -  2.2006  1265   147  0.87  19.95   0.96     0.89       6159.99|
| 12:  2.2006 -  2.1379  1249   129  0.88  18.75   0.97     0.95       5722.65|
| 13:  2.1379 -  2.0818  1237   141  0.87  19.28   0.95     0.93       4895.01|
| 14:  2.0818 -  2.0311  1022   116  0.88  18.08   0.92     0.88       3595.82|
|alpha:            min =        0.88 max =            1.00 mean =         0.94|
|beta:             min =     3595.82 max =        14070.69 mean =      8812.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.83 mean =        17.35|
|phase err.(test): min =        0.00 max =           89.82 mean =        16.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1357   r_free= 0.1864   ksol= 0.33   Bsol= 82.64   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,0.07,0.61,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.314541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1357   r_free= 0.1864   ksol= 0.33   Bsol= 82.64   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,0.07,0.61,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.314541                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2738 -  4.8463 0.99   1374  153 0.1070 0.1401      5.4637      5.6106|
|  2:  4.8463 -  3.8672 0.99   1320  145 0.0923 0.1098      5.5032      5.6437|
|  3:  3.8672 -  3.3845 0.99   1300  145 0.1177 0.1677      5.5735      5.9404|
|  4:  3.3845 -  3.0778 0.99   1286  144 0.1451 0.1917       5.614      5.7929|
|  5:  3.0778 -  2.8587 0.99   1271  140 0.1689 0.2003      5.5478      5.7008|
|  6:  2.8587 -  2.6911 0.99   1277  143 0.1582 0.2352       5.432      5.6724|
|  7:  2.6911 -  2.5570 0.99   1256  141 0.1571 0.2069        5.37      5.5737|
|  8:  2.5570 -  2.4462 0.98   1268  140 0.1505 0.2156      5.2925      5.5634|
|  9:  2.4462 -  2.3524 0.98   1269  138 0.1559 0.2165      5.2613      5.4753|
| 10:  2.3524 -  2.2715 0.99   1236  137 0.1432 0.2086      5.1766      5.3957|
| 11:  2.2715 -  2.2006 0.99   1265  147 0.1447 0.2059      5.1359      5.3926|
| 12:  2.2006 -  2.1379 0.97   1249  129 0.1365 0.2091      5.0589      5.4152|
| 13:  2.1379 -  2.0818 0.99   1237  141 0.1416 0.2070       4.985      5.1883|
| 14:  2.0818 -  2.0311 0.80   1022  116 0.1327 0.2138      4.8517      5.1441|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2738 -  4.8463  1374   153  0.93  10.71   0.95     0.92       8858.85|
|  2:  4.8463 -  3.8672  1320   145  0.94   9.04   1.00     0.98      10403.41|
|  3:  3.8672 -  3.3845  1300   145  0.92  12.84   1.02     1.00      12540.01|
|  4:  3.3845 -  3.0778  1286   144  0.90  16.43   1.01     0.98      14080.97|
|  5:  3.0778 -  2.8587  1271   140  0.86  20.41   1.00     0.97      13037.05|
|  6:  2.8587 -  2.6911  1277   143  0.87  19.77   0.98     0.94      10567.23|
|  7:  2.6911 -  2.5570  1256   141  0.86  20.15   0.99     0.95       9553.77|
|  8:  2.5570 -  2.4462  1268   140  0.87  19.40   0.98     0.95       8337.98|
|  9:  2.4462 -  2.3524  1269   138  0.87  20.07   0.98     0.92       7594.63|
| 10:  2.3524 -  2.2715  1236   137  0.87  19.29   0.98     0.93       6582.49|
| 11:  2.2715 -  2.2006  1265   147  0.87  19.96   0.97     0.90       6165.58|
| 12:  2.2006 -  2.1379  1249   129  0.88  18.76   0.98     0.96       5726.25|
| 13:  2.1379 -  2.0818  1237   141  0.87  19.27   0.97     0.95       4890.97|
| 14:  2.0818 -  2.0311  1022   116  0.88  18.07   0.94     0.89       3587.72|
|alpha:            min =        0.89 max =            1.00 mean =         0.95|
|beta:             min =     3587.72 max =        14080.97 mean =      8814.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.81 mean =        17.35|
|phase err.(test): min =        0.00 max =           89.83 mean =        16.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.587)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.13    120.66  17.38    None  None   None       |
|    all(noH): 2823   0      0.13    120.66  17.38    None  None   None       |
|    Sol.    : 438    0      3.98    120.66  46.91    None  None   None       |
|    Mac.    : 2385   0      0.13    113.37  11.95    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:     0.135 -  12.188: 1646   |   5:    60.399 -  72.452:   66        |
|      1:    12.188 -  24.241:  660   |   6:    72.452 -  84.505:   54        |
|      2:    24.241 -  36.294:  152   |   7:    84.505 -  96.558:   14        |
|      3:    36.294 -  48.346:  117   |   8:    96.558 - 108.611:   10        |
|      4:    48.346 -  60.399:   99   |   9:   108.611 - 120.664:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 349         
Filter by distance & map next to the model:
   mapped sites are within: 0.635 - 5.023
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 349
   mapped sites are within: 0.715 - 5.023

peak=    8.581 closest distance to " O   HOH Z 400 " =    1.249
peak=    7.952 closest distance to " O   HOH Z  41 " =    1.391
peak=    6.848 closest distance to " O   HOH Z  82 " =    1.131
peak=    5.499 closest distance to " O   HOH Z 210 " =    1.435
peak=    5.428 closest distance to " O   HOH Z 117 " =    1.365
peak=    5.264 closest distance to " O   HOH Z  54 " =    1.531
peak=    5.243 closest distance to " CB  GLN A 223 " =    1.450
peak=    5.140 closest distance to " O   HOH Z 341 " =    1.523
peak=    5.036 closest distance to " CB  SER A  63 " =    1.325
peak=    4.866 closest distance to " OE1 GLN A  88 " =    0.962
peak=    4.771 closest distance to " O   HOH Z 425 " =    1.699
peak=    4.759 closest distance to " CG  PRO A  54 " =    1.426
peak=    4.704 closest distance to " CG  PRO A 280 " =    0.958
peak=    4.686 closest distance to " O   HOH Z 111 " =    2.093
peak=    4.662 closest distance to " O   GLN A  11 " =    1.009
peak=    4.631 closest distance to " CG  PRO A 213 " =    1.355
peak=    4.613 closest distance to " O   HOH Z 418 " =    2.201
peak=    4.593 closest distance to " CA  TYR A  30 " =    0.996
peak=    4.554 closest distance to " CB  GLN A 183 " =    1.217
peak=    4.533 closest distance to " CD  ARG A 269 " =    0.819
peak=    4.510 closest distance to " O   HOH Z 422 " =    1.064
peak=    4.503 closest distance to " O   HOH Z  49 " =    1.228
peak=    4.488 closest distance to " O   HOH Z 394 " =    1.710
peak=    4.468 closest distance to " O   HOH Z 412 " =    3.533
peak=    4.387 closest distance to " CG  PRO A 198 " =    1.220
peak=    4.367 closest distance to " O   HOH Z 126 " =    1.700
peak=    4.364 closest distance to " O   HOH Z   7 " =    1.599
peak=    4.361 closest distance to " NE2 HIS A 115 " =    1.156
peak=    4.346 closest distance to " O   PRO A 198 " =    1.624
peak=    4.339 closest distance to " O   HOH Z 234 " =    3.992
peak=    4.332 closest distance to " O   HOH Z 176 " =    1.900
peak=    4.328 closest distance to " O   HOH Z 196 " =    2.416
peak=    4.280 closest distance to " N   SER A 164 " =    1.016
peak=    4.279 closest distance to " O   HOH Z 134 " =    2.036
peak=    4.277 closest distance to " CB  PRO A  54 " =    0.955
peak=    4.259 closest distance to " O  BHOH Z 338 " =    0.914
peak=    4.239 closest distance to " CB  GLU A 128 " =    1.056
peak=    4.219 closest distance to " O   HOH Z 214 " =    1.680
peak=    4.206 closest distance to " CD1 LEU A 300 " =    1.156
peak=    4.202 closest distance to " CA  ALA A  51 " =    0.974
peak=    4.198 closest distance to " CB  VAL A 202 " =    1.507
peak=    4.174 closest distance to " CG2BVAL A  41 " =    0.917
peak=    4.171 closest distance to " CZ  PHE A 218 " =    1.131
peak=    4.148 closest distance to " CB  TRP A 179 " =    1.517
peak=    4.135 closest distance to " O   THR A 251 " =    1.229
peak=    4.133 closest distance to " CD  ARG A  66 " =    2.507
peak=    4.129 closest distance to " CA  ARG A 195 " =    1.096
peak=    4.104 closest distance to " O   HOH Z 232 " =    2.281
peak=    4.098 closest distance to " CB  ASN A 148 " =    1.513
peak=    4.093 closest distance to " O   HOH Z 133 " =    2.625
peak=    4.079 closest distance to " O   HOH Z 404 " =    1.517
peak=    4.077 closest distance to " O   HOH Z 377 " =    1.582
peak=    4.069 closest distance to " O   HOH Z 389 " =    2.062
peak=    4.067 closest distance to " O   HOH Z 434 " =    1.833
peak=    4.054 closest distance to " O   HOH Z 437 " =    1.800
peak=    4.052 closest distance to " CB  ASP A 124 " =    0.854
peak=    4.036 closest distance to " CB  TRP A 266 " =    1.050
peak=    4.021 closest distance to " CB  LEU A 228 " =    1.189
peak=    4.015 closest distance to " CB  ARG A 275 " =    0.807
peak=    3.998 closest distance to " CG1 VAL A 153 " =    1.173
peak=    3.994 closest distance to " CD  ARG A 159 " =    0.856
peak=    3.992 closest distance to " CA  ALA A 160 " =    1.040
peak=    3.987 closest distance to " CG  LEU A 167 " =    1.051
peak=    3.975 closest distance to " CG AARG A 275 " =    1.214
peak=    3.936 closest distance to " N   ILE A  33 " =    0.954
peak=    3.935 closest distance to " O   ALA A 165 " =    1.353
peak=    3.926 closest distance to " CA  ARG A 102 " =    1.199
peak=    3.911 closest distance to " O   HOH Z 369 " =    1.981
peak=    3.901 closest distance to " CA  ILE A 106 " =    0.857
peak=    3.883 closest distance to " CG  PRO A 243 " =    1.144
peak=    3.877 closest distance to " CB  ARG A 190 " =    1.816
peak=    3.876 closest distance to " O   HOH Z 357 " =    2.236
peak=    3.857 closest distance to " O   HOH Z 298 " =    2.006
peak=    3.849 closest distance to " CB  GLU A 152 " =    1.164
peak=    3.846 closest distance to " O   HOH Z  15 " =    2.274
peak=    3.846 closest distance to " NE2 GLN A  11 " =    1.121
peak=    3.841 closest distance to " O   HOH Z  44 " =    1.914
peak=    3.824 closest distance to " NH1AARG A 145 " =    1.260
peak=    3.816 closest distance to " CD ALYS A 290 " =    1.038
peak=    3.783 closest distance to " CB  MET A  47 " =    0.996
peak=    3.760 closest distance to " CB  PRO A  54 " =    1.413
peak=    3.749 closest distance to " O   HOH Z  54 " =    1.505
peak=    3.748 closest distance to " CB  PRO A 198 " =    0.907
peak=    3.746 closest distance to " CG1 ILE A  33 " =    1.259
peak=    3.743 closest distance to " CA  TYR A  30 " =    1.100
peak=    3.738 closest distance to " O   HOH Z 301 " =    1.495
peak=    3.734 closest distance to " CA  GLU A 152 " =    0.930
peak=    3.728 closest distance to " O   HOH Z 395 " =    1.434
peak=    3.727 closest distance to " CB  ASN A 142 " =    1.005
peak=    3.716 closest distance to " O   HOH Z  78 " =    1.121
peak=    3.711 closest distance to " CB  GLU A 277 " =    3.879
peak=    3.709 closest distance to " CD1 LEU A  96 " =    0.772
peak=    3.684 closest distance to " CG2 THR A 221 " =    1.080
peak=    3.683 closest distance to " CA  ASP A 191 " =    0.910
peak=    3.678 closest distance to " NH2 ARG A 156 " =    1.215
peak=    3.658 closest distance to " CB  SER A  62 " =    0.837
peak=    3.656 closest distance to " CA  ALA A 100 " =    1.153
peak=    3.656 closest distance to " O   HOH Z 171 " =    3.954
peak=    3.654 closest distance to " CZ  PHE A 192 " =    1.020
peak=    3.648 closest distance to " CB  ASN A  39 " =    0.856
peak=    3.641 closest distance to " CG  ARG A 138 " =    1.329
peak=    3.637 closest distance to " O   HOH Z 406 " =    1.752
peak=    3.636 closest distance to " O   GLY A  91 " =    1.181
peak=    3.636 closest distance to " O   HOH Z  95 " =    1.967
peak=    3.633 closest distance to " CA  ARG A 156 " =    0.989
peak=    3.631 closest distance to " CB  ASP A 140 " =    0.928
peak=    3.628 closest distance to " O   HOH Z 316 " =    3.144
peak=    3.624 closest distance to " CA  GLY A 196 " =    1.020
peak=    3.623 closest distance to " O   HOH Z 200 " =    1.535
peak=    3.612 closest distance to " O   HOH Z  78 " =    2.146
peak=    3.605 closest distance to " O   ASN A  74 " =    1.650
peak=    3.598 closest distance to " CB  MET A  40 " =    0.792
peak=    3.593 closest distance to " CB  VAL A 265 " =    1.348
peak=    3.586 closest distance to " O   HOH Z 139 " =    4.968
peak=    3.579 closest distance to " OD1 ASN A 301 " =    1.147
peak=    3.578 closest distance to " O   HOH Z 301 " =    1.917
peak=    3.571 closest distance to " OE1 GLN A  58 " =    3.602
peak=    3.567 closest distance to " CA  ALA A  21 " =    1.435
peak=    3.566 closest distance to " CA  MET A 105 " =    1.280
peak=    3.563 closest distance to " CE3 TRP A  85 " =    1.066
peak=    3.556 closest distance to " CD  ARG A 195 " =    1.099
peak=    3.556 closest distance to " O   HOH Z  32 " =    2.296
peak=    3.554 closest distance to " CB  ARG A 269 " =    0.933
peak=    3.553 closest distance to " O   HOH Z 346 " =    1.631
peak=    3.547 closest distance to " CD2 TRP A 179 " =    1.356
peak=    3.544 closest distance to " O   HOH Z 265 " =    1.983
peak=    3.542 closest distance to " O   HOH Z  47 " =    1.445
peak=    3.538 closest distance to " CD2 LEU A 255 " =    1.548
peak=    3.535 closest distance to " CA  ASP A 124 " =    0.895
peak=    3.534 closest distance to " O   HOH Z 368 " =    2.123
peak=    3.531 closest distance to " O   SER A  87 " =    2.340
peak=    3.526 closest distance to " CB  ASN A 187 " =    1.175
peak=    3.524 closest distance to " OG  SER A  28 " =    1.465
peak=    3.520 closest distance to " N   GLY A  98 " =    1.056
peak=    3.520 closest distance to " CB  ASN A 285 " =    0.785
peak=    3.518 closest distance to " O   HOH Z 146 " =    1.433
peak=    3.518 closest distance to " O   PRO A 213 " =    1.632
peak=    3.517 closest distance to " OE1 GLU A   2 " =    1.499
peak=    3.514 closest distance to " O   HOH Z 418 " =    1.229
peak=    3.502 closest distance to " CB  SER A 141 " =    1.154
peak=    3.502 closest distance to " OG  SER A 245 " =    1.673
peak=    3.500 closest distance to " O   TYR A 116 " =    1.353
peak=    3.492 closest distance to " O   ASP A 200 " =    1.573
peak=    3.490 closest distance to " O   HOH Z 435 " =    2.977
peak=    3.485 closest distance to " CA  ARG A 139 " =    1.581
peak=    3.484 closest distance to " O   HOH Z 403 " =    1.004
peak=    3.479 closest distance to " O   THR A 220 " =    1.089
peak=    3.469 closest distance to " NE2 GLN A  77 " =    3.207
peak=    3.468 closest distance to " N   THR A  52 " =    1.172
peak=    3.468 closest distance to " O   HOH Z 126 " =    2.260
peak=    3.464 closest distance to " CA  ALA A 154 " =    1.032
peak=    3.463 closest distance to " CA  ARG A  36 " =    1.076
peak=    3.463 closest distance to " CB  SER A 210 " =    1.019
peak=    3.460 closest distance to " O   HOH Z 431 " =    1.126
peak=    3.456 closest distance to " CB  GLN A 194 " =    0.973
peak=    3.453 closest distance to " CD1 LEU A 222 " =    0.780
peak=    3.449 closest distance to " O   HOH Z  88 " =    1.832
peak=    3.449 closest distance to " O   HOH Z 271 " =    2.510
peak=    3.440 closest distance to " CB  MET A 105 " =    1.134
peak=    3.438 closest distance to " CG  GLU A  37 " =    0.996
peak=    3.438 closest distance to " CG1 ILE A 120 " =    1.121
peak=    3.438 closest distance to " O   HOH Z 284 " =    2.901
peak=    3.436 closest distance to " CB  TRP A 179 " =    1.589
peak=    3.435 closest distance to " O   HOH Z 223 " =    1.038
peak=    3.432 closest distance to " O   HOH Z 150 " =    1.989
peak=    3.432 closest distance to " CB  ALA A 137 " =    1.058
peak=    3.427 closest distance to " CB  SER A  26 " =    0.838
peak=    3.426 closest distance to " N   TYR A  15 " =    0.945
peak=    3.425 closest distance to " O   HOH Z 247 " =    1.531
peak=    3.425 closest distance to " CG  GLN A  89 " =    1.482
peak=    3.421 closest distance to " CG  GLN A  11 " =    1.021
peak=    3.420 closest distance to " O   HOH Z 139 " =    1.153
peak=    3.420 closest distance to " CB  GLU A  46 " =    1.063
peak=    3.418 closest distance to " O   HOH Z 243 " =    1.074
peak=    3.412 closest distance to " CA  GLY A 267 " =    0.994
peak=    3.408 closest distance to " OE1 GLN A  11 " =    2.229
peak=    3.405 closest distance to " CG  GLN A  77 " =    0.812
peak=    3.404 closest distance to " CA  VAL A  41 " =    0.898
peak=    3.399 closest distance to " O   HOH Z  49 " =    2.112
peak=    3.398 closest distance to " CB  ARG A  79 " =    0.960
peak=    3.396 closest distance to " CG2 ILE A 120 " =    0.969
peak=    3.395 closest distance to " CA  GLU A  46 " =    0.970
peak=    3.393 closest distance to " O   HOH Z 290 " =    1.199
peak=    3.391 closest distance to " O   HOH Z 132 " =    3.120
peak=    3.385 closest distance to " O   ASN A  74 " =    1.991
peak=    3.385 closest distance to " O   HOH Z 432 " =    1.810
peak=    3.378 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.377 closest distance to " CZ3 TRP A  85 " =    0.815
peak=    3.373 closest distance to " CG2AVAL A 121 " =    2.017
peak=    3.373 closest distance to " CE1 TYR A 186 " =    1.530
peak=    3.369 closest distance to " OD1 ASN A 217 " =    1.623
peak=    3.366 closest distance to " CB  GLN A 103 " =    0.913
peak=    3.365 closest distance to " CA  TRP A 274 " =    0.912
peak=    3.364 closest distance to " CG  MET A 185 " =    1.045
peak=    3.361 closest distance to " CD  LYS A 166 " =    1.536
peak=    3.355 closest distance to " O   HOH Z 102 " =    1.519
peak=    3.355 closest distance to " N   HIS A 108 " =    1.824
peak=    3.347 closest distance to " O   HOH Z 201 " =    2.746
peak=    3.347 closest distance to " CA  LEU A  83 " =    1.496
peak=    3.343 closest distance to " O   HOH Z  80 " =    2.299
peak=    3.342 closest distance to " O   HOH Z 175 " =    3.837
peak=    3.341 closest distance to " O   HOH Z  30 " =    1.958
peak=    3.337 closest distance to " CA  CYS A 254 " =    1.441
peak=    3.336 closest distance to " N   ASN A  39 " =    1.239
peak=    3.335 closest distance to " O   HOH Z 183 " =    1.162
peak=    3.331 closest distance to " CA  LYS A  48 " =    1.386
peak=    3.330 closest distance to " CA  SER A  87 " =    0.986
peak=    3.328 closest distance to " NH2AARG A 145 " =    0.975
peak=    3.327 closest distance to " O   HOH Z  98 " =    1.913
peak=    3.325 closest distance to " O   HOH Z 374 " =    3.332
peak=    3.325 closest distance to " CB  PHE A  16 " =    1.392
peak=    3.324 closest distance to " CB  ALA A 256 " =    1.523
peak=    3.323 closest distance to " CE  LYS A  76 " =    0.805
peak=    3.319 closest distance to " O   HOH Z 344 " =    3.179
peak=    3.319 closest distance to " O   HOH Z 261 " =    1.627
peak=    3.317 closest distance to " CB  ALA A 292 " =    0.852
peak=    3.317 closest distance to " O   HOH Z 344 " =    1.964
peak=    3.316 closest distance to " O   HOH Z 174 " =    1.978
peak=    3.316 closest distance to " NH1 ARG A 269 " =    0.715
peak=    3.315 closest distance to " CB  ASN A 217 " =    1.068
peak=    3.313 closest distance to " CE3 TRP A 274 " =    3.759
peak=    3.312 closest distance to " C   VAL A 265 " =    1.080
peak=    3.312 closest distance to " CA  TRP A  92 " =    0.964
peak=    3.312 closest distance to " O   HOH Z 258 " =    2.143
peak=    3.311 closest distance to " CB  GLU A  37 " =    0.899
peak=    3.308 closest distance to " O   HOH Z  83 " =    1.135
peak=    3.303 closest distance to " O   HOH Z 146 " =    1.659
peak=    3.303 closest distance to " N   ALA A 256 " =    1.351
peak=    3.300 closest distance to " O   HOH Z 189 " =    2.833
peak=    3.298 closest distance to " O   HOH Z  48 " =    1.933
peak=    3.295 closest distance to " ND1 HIS A  81 " =    1.603
peak=    3.293 closest distance to " CG2 ILE A  20 " =    1.465
peak=    3.292 closest distance to " CA  TYR A 116 " =    1.482
peak=    3.292 closest distance to " O   HOH Z 421 " =    1.637
peak=    3.289 closest distance to " CG2 THR A  42 " =    0.961
peak=    3.287 closest distance to " CB  LEU A  83 " =    0.815
peak=    3.286 closest distance to " CA  GLY A  35 " =    0.867
peak=    3.286 closest distance to " CA  GLY A   6 " =    0.832
peak=    3.282 closest distance to " NZ  LYS A 181 " =    0.728
peak=    3.280 closest distance to " NH2AARG A 275 " =    3.350
peak=    3.275 closest distance to " CB  PHE A 283 " =    0.865
peak=    3.275 closest distance to " N   ASN A 252 " =    1.351
peak=    3.275 closest distance to " O   HOH Z 197 " =    5.023
peak=    3.274 closest distance to " CG2 VAL A 197 " =    1.302
peak=    3.274 closest distance to " O   HOH Z 193 " =    1.908
peak=    3.273 closest distance to " CA  ASP A 162 " =    1.087
peak=    3.273 closest distance to " CD  LYS A 289 " =    1.098
peak=    3.272 closest distance to " O   HOH Z 215 " =    1.473
peak=    3.272 closest distance to " O   HOH Z 287 " =    1.831
peak=    3.271 closest distance to " CH2 TRP A 266 " =    1.074
peak=    3.271 closest distance to " CB  SER A 216 " =    0.987
peak=    3.266 closest distance to " CA  ASN A 215 " =    1.111
peak=    3.260 closest distance to " CG  ARG A 269 " =    1.286
peak=    3.257 closest distance to " CB  ALA A 114 " =    0.787
peak=    3.257 closest distance to " O   HOH Z 141 " =    1.739
peak=    3.257 closest distance to " CA  GLN A  88 " =    1.500
peak=    3.250 closest distance to " NZ  LYS A 117 " =    3.012
peak=    3.249 closest distance to " CA  ASP A 191 " =    1.034
peak=    3.245 closest distance to " CB  ALA A  10 " =    1.310
peak=    3.245 closest distance to " CG2 VAL A 126 " =    0.895
peak=    3.244 closest distance to " O   HOH Z 172 " =    2.463
peak=    3.238 closest distance to " O   HOH Z 373 " =    1.642
peak=    3.238 closest distance to " CB  ALA A  43 " =    1.036
peak=    3.237 closest distance to " CE1 PHE A 225 " =    1.043
peak=    3.237 closest distance to " C   ASN A 209 " =    1.203
peak=    3.232 closest distance to " CA  SER A  32 " =    1.690
peak=    3.230 closest distance to " CA  VAL A 125 " =    1.265
peak=    3.229 closest distance to " CA  ALA A 299 " =    1.036
peak=    3.224 closest distance to " CG2 ILE A 151 " =    0.822
peak=    3.223 closest distance to " OG  SER A  22 " =    2.876
peak=    3.222 closest distance to " N   TYR A 116 " =    1.759
peak=    3.219 closest distance to " O   HOH Z 435 " =    1.775
peak=    3.218 closest distance to " OD1 ASN A 148 " =    2.083
peak=    3.216 closest distance to " N   VAL A 126 " =    1.661
peak=    3.216 closest distance to " O   HOH Z 238 " =    2.593
peak=    3.215 closest distance to " O   HOH Z 415 " =    1.275
peak=    3.215 closest distance to " O   GLY A  75 " =    3.441
peak=    3.214 closest distance to " CB  ALA A 248 " =    1.311
peak=    3.212 closest distance to " CB  PRO A  90 " =    1.254
peak=    3.207 closest distance to " CA  ASN A 217 " =    1.371
peak=    3.207 closest distance to " NH1 ARG A  14 " =    1.336
peak=    3.207 closest distance to " N   SER A 271 " =    1.253
peak=    3.206 closest distance to " CD1 LEU A   5 " =    1.319
peak=    3.199 closest distance to " CA  SER A  12 " =    1.582
peak=    3.198 closest distance to " O   HOH Z 327 " =    1.747
peak=    3.197 closest distance to " NE2 GLN A 278 " =    2.352
peak=    3.197 closest distance to " N   LYS A 166 " =    0.968
peak=    3.184 closest distance to " CA  GLN A 223 " =    0.862
peak=    3.183 closest distance to " O   HOH Z 343 " =    2.358
peak=    3.181 closest distance to " N   GLN A 278 " =    1.255
peak=    3.180 closest distance to " CD  GLU A 152 " =    0.844
peak=    3.177 closest distance to " CB  ARG A 156 " =    1.081
peak=    3.177 closest distance to " NE2 GLN A  58 " =    4.531
peak=    3.177 closest distance to " ND2 ASN A 187 " =    1.348
peak=    3.175 closest distance to " CA  GLY A 229 " =    0.892
peak=    3.174 closest distance to " CB  GLN A  89 " =    1.151
peak=    3.171 closest distance to " OG1 THR A  82 " =    1.088
peak=    3.170 closest distance to " CG  LYS A  76 " =    1.190
peak=    3.170 closest distance to " O   HOH Z 417 " =    3.055
peak=    3.169 closest distance to " CB  GLU A 175 " =    1.443
peak=    3.168 closest distance to " O   HOH Z 403 " =    1.560
peak=    3.167 closest distance to " CG2 ILE A 239 " =    1.035
peak=    3.167 closest distance to " N   PHE A 130 " =    1.200
peak=    3.164 closest distance to " O   HOH Z 374 " =    2.869
peak=    3.162 closest distance to " O   HOH Z 222 " =    2.845
peak=    3.158 closest distance to " O   HOH Z 362 " =    3.110
peak=    3.154 closest distance to " ND2 ASN A 176 " =    0.855
peak=    3.154 closest distance to " CB  TYR A 116 " =    1.362
peak=    3.154 closest distance to " N   VAL A 265 " =    1.162
peak=    3.153 closest distance to " O   HOH Z 339 " =    2.094
peak=    3.152 closest distance to " O   ASP A 124 " =    1.298
peak=    3.148 closest distance to " O   HOH Z  58 " =    1.560
peak=    3.147 closest distance to " O   HOH Z  44 " =    3.313
peak=    3.146 closest distance to " ND2 ASN A 301 " =    0.961
peak=    3.146 closest distance to " CA  GLN A  11 " =    1.132
peak=    3.145 closest distance to " CA  THR A 246 " =    1.059
peak=    3.145 closest distance to " CD  LYS A 119 " =    1.520
peak=    3.142 closest distance to " NH2BARG A 190 " =    1.957
peak=    3.137 closest distance to " CB  SER A   3 " =    1.697
peak=    3.132 closest distance to " OE1 GLU A  46 " =    1.510
peak=    3.132 closest distance to " OG ASER A 134 " =    1.257
peak=    3.125 closest distance to " CB  LYS A 193 " =    1.126
peak=    3.124 closest distance to " N   CYS A 260 " =    0.813
peak=    3.121 closest distance to " CE1 TYR A  30 " =    0.844
peak=    3.119 closest distance to " CB  ALA A  34 " =    0.717
peak=    3.118 closest distance to " CE2 PHE A 204 " =    1.031
peak=    3.118 closest distance to " O   HOH Z 195 " =    4.050
peak=    3.115 closest distance to " CB  ALA A 291 " =    1.265
peak=    3.109 closest distance to " NH1 ARG A 138 " =    1.027
peak=    3.108 closest distance to " CA  ALA A 291 " =    0.904
peak=    3.108 closest distance to " CG1 VAL A 257 " =    1.006
peak=    3.095 closest distance to " OG  SER A  97 " =    3.458
peak=    3.093 closest distance to " O   HOH Z 134 " =    2.262
peak=    3.087 closest distance to " N   GLY A 111 " =    1.300
peak=    3.079 closest distance to " O   HOH Z 261 " =    1.282
peak=    3.075 closest distance to " O   HOH Z 271 " =    2.124
peak=    3.074 closest distance to " O   HOH Z 358 " =    1.425
peak=    3.068 closest distance to " O   HOH Z 106 " =    3.506
peak=    3.063 closest distance to " CE1 HIS A 108 " =    1.040
peak=    3.063 closest distance to " O   PRO A 280 " =    0.908
peak=    3.062 closest distance to " CB  SER A  28 " =    1.243
peak=    3.045 closest distance to " CB  ASN A 215 " =    1.138
peak=    3.038 closest distance to " OG  SER A 273 " =    0.950
peak=    3.028 closest distance to " O   HOH Z 128 " =    2.450

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.206
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 211
   mapped sites are within: 0.730 - 5.206

peak=   -4.722 closest distance to " CD  GLN A 223 " =    1.469
peak=   -4.462 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -4.281 closest distance to " O   HOH Z 418 " =    1.222
peak=   -4.269 closest distance to " O   PRO A 198 " =    1.343
peak=   -4.171 closest distance to " CA  GLY A 203 " =    2.454
peak=   -4.147 closest distance to " C   ASN A 285 " =    2.444
peak=   -4.144 closest distance to " OD1 ASN A 148 " =    1.337
peak=   -4.135 closest distance to " CD  GLN A  58 " =    0.901
peak=   -4.107 closest distance to " O   HOH Z 407 " =    0.800
peak=   -4.105 closest distance to " CD2 LEU A 237 " =    2.667
peak=   -4.092 closest distance to " CB  PRO A 243 " =    2.807
peak=   -4.069 closest distance to " O   HOH Z 400 " =    0.931
peak=   -4.067 closest distance to " O   HOH Z 183 " =    1.200
peak=   -4.044 closest distance to " CA  GLU A 277 " =    1.210
peak=   -4.027 closest distance to " O   HOH Z 166 " =    1.418
peak=   -4.025 closest distance to " CE2 PHE A  61 " =    2.684
peak=   -4.016 closest distance to " O   HOH Z 203 " =    1.058
peak=   -4.006 closest distance to " CD  ARG A  14 " =    3.246
peak=   -4.005 closest distance to " CG  ARG A 269 " =    2.503
peak=   -3.998 closest distance to " O   HOH Z 400 " =    1.611
peak=   -3.978 closest distance to " O   HOH Z  19 " =    2.155
peak=   -3.968 closest distance to " O   SER A 135 " =    1.781
peak=   -3.967 closest distance to " O   HOH Z 438 " =    3.106
peak=   -3.961 closest distance to " O   HOH Z 411 " =    5.206
peak=   -3.923 closest distance to " O   HOH Z 155 " =    1.651
peak=   -3.870 closest distance to " O   HOH Z  52 " =    1.656
peak=   -3.865 closest distance to " O   HOH Z 388 " =    1.822
peak=   -3.857 closest distance to " O   HOH Z 103 " =    2.125
peak=   -3.855 closest distance to " N   ARG A 275 " =    1.073
peak=   -3.849 closest distance to " O   HOH Z 231 " =    2.376
peak=   -3.814 closest distance to " CG  PRO A 243 " =    1.583
peak=   -3.792 closest distance to " CB  ALA A 291 " =    2.472
peak=   -3.775 closest distance to " CD  ARG A 156 " =    2.143
peak=   -3.756 closest distance to " O   HOH Z 166 " =    2.412
peak=   -3.738 closest distance to " N   ALA A  43 " =    2.810
peak=   -3.734 closest distance to " CA  ASP A 298 " =    1.103
peak=   -3.718 closest distance to " CG  MET A 105 " =    0.912
peak=   -3.701 closest distance to " O   HOH Z   5 " =    1.477
peak=   -3.690 closest distance to " CB  ALA A  10 " =    2.071
peak=   -3.685 closest distance to " O   SER A 206 " =    1.341
peak=   -3.675 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.663 closest distance to " CD  GLN A  88 " =    0.888
peak=   -3.654 closest distance to " O   SER A 276 " =    1.903
peak=   -3.643 closest distance to " CB  ALA A   9 " =    2.692
peak=   -3.635 closest distance to " O   HOH Z 243 " =    2.186
peak=   -3.631 closest distance to " CA  GLY A 241 " =    3.214
peak=   -3.627 closest distance to " CG  GLN A  11 " =    1.220
peak=   -3.626 closest distance to " CE3 TRP A 150 " =    2.007
peak=   -3.620 closest distance to " CZ  TYR A 169 " =    1.915
peak=   -3.614 closest distance to " CG1 VAL A 112 " =    2.578
peak=   -3.613 closest distance to " O   HOH Z 308 " =    1.212
peak=   -3.609 closest distance to " O   HOH Z  41 " =    2.708
peak=   -3.607 closest distance to " O   HOH Z 275 " =    1.702
peak=   -3.600 closest distance to " O   HOH Z 185 " =    2.603
peak=   -3.598 closest distance to " O   HOH Z  70 " =    2.215
peak=   -3.586 closest distance to " C   GLY A  17 " =    1.290
peak=   -3.577 closest distance to " CD  GLN A  58 " =    1.107
peak=   -3.577 closest distance to " O   HOH Z 283 " =    2.128
peak=   -3.572 closest distance to " CG2 VAL A 202 " =    2.263
peak=   -3.570 closest distance to " O   HOH Z  38 " =    1.041
peak=   -3.563 closest distance to " N   ALA A 226 " =    2.209
peak=   -3.555 closest distance to " NH2 ARG A  66 " =    1.721
peak=   -3.554 closest distance to " OD2 ASP A 171 " =    1.897
peak=   -3.550 closest distance to " O   HOH Z  37 " =    1.544
peak=   -3.549 closest distance to " CG2 ILE A  49 " =    2.729
peak=   -3.546 closest distance to " O   VAL A  67 " =    2.748
peak=   -3.531 closest distance to " CZ  PHE A 155 " =    1.368
peak=   -3.517 closest distance to " CG  PRO A 163 " =    1.729
peak=   -3.517 closest distance to " ND2 ASN A  45 " =    1.999
peak=   -3.504 closest distance to " N   VAL A  41 " =    2.047
peak=   -3.498 closest distance to " CD1 LEU A  25 " =    2.503
peak=   -3.494 closest distance to " O   HOH Z 114 " =    3.945
peak=   -3.492 closest distance to " OE1 GLN A 223 " =    2.173
peak=   -3.485 closest distance to " CE  MET A  93 " =    1.797
peak=   -3.481 closest distance to " OD1 ASP A 191 " =    1.444
peak=   -3.479 closest distance to " CE  MET A  93 " =    2.490
peak=   -3.479 closest distance to " O   HOH Z 109 " =    3.458
peak=   -3.478 closest distance to " O   HOH Z 105 " =    2.009
peak=   -3.476 closest distance to " C   HIS A 108 " =    1.135
peak=   -3.474 closest distance to " O   HOH Z 216 " =    1.711
peak=   -3.470 closest distance to " O   HOH Z 200 " =    1.262
peak=   -3.456 closest distance to " NH2 ARG A 159 " =    2.361
peak=   -3.448 closest distance to " O   HOH Z 331 " =    1.281
peak=   -3.444 closest distance to " O   HOH Z  32 " =    2.171
peak=   -3.444 closest distance to " O   HOH Z 256 " =    2.297
peak=   -3.443 closest distance to " O   HOH Z 128 " =    2.671
peak=   -3.441 closest distance to " CD2 PHE A  61 " =    2.088
peak=   -3.440 closest distance to " CD1 LEU A 167 " =    2.058
peak=   -3.439 closest distance to " CG  LEU A 101 " =    2.463
peak=   -3.428 closest distance to " CA  GLY A 241 " =    2.342
peak=   -3.427 closest distance to " O   HOH Z 186 " =    3.676
peak=   -3.425 closest distance to " CG  GLU A  53 " =    1.439
peak=   -3.422 closest distance to " N   SER A 134 " =    1.157
peak=   -3.421 closest distance to " CG  LEU A  83 " =    2.152
peak=   -3.414 closest distance to " O   HOH Z   6 " =    1.325
peak=   -3.410 closest distance to " O   HOH Z 207 " =    1.615
peak=   -3.409 closest distance to " NE2 GLN A 278 " =    2.015
peak=   -3.403 closest distance to " CE2 TYR A  30 " =    2.685
peak=   -3.401 closest distance to " O   ILE A 109 " =    2.649
peak=   -3.398 closest distance to " NE  ARG A  79 " =    1.252
peak=   -3.397 closest distance to " OG  SER A  62 " =    4.750
peak=   -3.391 closest distance to " CE3 TRP A 274 " =    2.222
peak=   -3.389 closest distance to " O   HOH Z 113 " =    2.175
peak=   -3.387 closest distance to " O   HOH Z 111 " =    1.928
peak=   -3.385 closest distance to " CD2 TYR A 293 " =    1.874
peak=   -3.377 closest distance to " CG  LEU A 281 " =    1.907
peak=   -3.374 closest distance to " O   HOH Z 394 " =    1.743
peak=   -3.373 closest distance to " O   HOH Z 369 " =    2.438
peak=   -3.372 closest distance to " O   HOH Z 396 " =    1.495
peak=   -3.368 closest distance to " OG  SER A  63 " =    1.164
peak=   -3.367 closest distance to " O   HOH Z 156 " =    3.623
peak=   -3.365 closest distance to " O   HOH Z 150 " =    1.807
peak=   -3.362 closest distance to " O   VAL A 174 " =    2.150
peak=   -3.361 closest distance to " O   HOH Z 298 " =    2.744
peak=   -3.360 closest distance to " CG1 VAL A 189 " =    2.496
peak=   -3.360 closest distance to " O   HOH Z 134 " =    2.169
peak=   -3.358 closest distance to " O   HOH Z 221 " =    1.313
peak=   -3.358 closest distance to " CB  THR A  18 " =    1.290
peak=   -3.357 closest distance to " O   HOH Z 234 " =    4.567
peak=   -3.351 closest distance to " OH  TYR A 169 " =    1.022
peak=   -3.350 closest distance to " OE1 GLN A  88 " =    0.968
peak=   -3.349 closest distance to " O   HOH Z 403 " =    0.928
peak=   -3.349 closest distance to " O   HOH Z 348 " =    2.084
peak=   -3.346 closest distance to " CD  GLN A  77 " =    0.939
peak=   -3.342 closest distance to " CG  GLU A  44 " =    2.406
peak=   -3.339 closest distance to " O   HOH Z 184 " =    1.420
peak=   -3.336 closest distance to " O   HOH Z  53 " =    1.935
peak=   -3.332 closest distance to " O   HOH Z  58 " =    0.915
peak=   -3.329 closest distance to " CB  SER A 146 " =    2.161
peak=   -3.326 closest distance to " O   HOH Z  54 " =    1.143
peak=   -3.326 closest distance to " O   PHE A 218 " =    1.240
peak=   -3.320 closest distance to " O   HOH Z 340 " =    1.218
peak=   -3.318 closest distance to " O   HOH Z 198 " =    1.672
peak=   -3.314 closest distance to " CA  VAL A 197 " =    0.977
peak=   -3.311 closest distance to " SD  MET A  93 " =    1.816
peak=   -3.307 closest distance to " O   HOH Z  60 " =    2.011
peak=   -3.306 closest distance to " O   GLN A  11 " =    1.275
peak=   -3.305 closest distance to " CD1 LEU A   5 " =    2.580
peak=   -3.300 closest distance to " O   HOH Z  90 " =    3.277
peak=   -3.295 closest distance to " NE2 GLN A 194 " =    2.164
peak=   -3.291 closest distance to " O   HOH Z 400 " =    1.360
peak=   -3.287 closest distance to " CA  GLY A 133 " =    2.556
peak=   -3.284 closest distance to " N   ASP A 272 " =    1.372
peak=   -3.284 closest distance to " CE3 TRP A  70 " =    1.989
peak=   -3.275 closest distance to " O   SER A 271 " =    2.205
peak=   -3.267 closest distance to " CG1 VAL A 125 " =    1.981
peak=   -3.265 closest distance to " N   ASP A 191 " =    1.284
peak=   -3.264 closest distance to " ND2BASN A 224 " =    2.025
peak=   -3.261 closest distance to " O   HOH Z 165 " =    1.688
peak=   -3.260 closest distance to " O   HOH Z 128 " =    4.372
peak=   -3.250 closest distance to " O   HOH Z 292 " =    4.646
peak=   -3.249 closest distance to " ND2 ASN A  60 " =    2.067
peak=   -3.247 closest distance to " SD  MET A 105 " =    2.517
peak=   -3.247 closest distance to " N   ILE A 120 " =    1.039
peak=   -3.244 closest distance to " O   HOH Z 365 " =    0.982
peak=   -3.239 closest distance to " O   HOH Z 377 " =    2.231
peak=   -3.233 closest distance to " CH2 TRP A 177 " =    2.064
peak=   -3.231 closest distance to " O   HOH Z 377 " =    0.730
peak=   -3.225 closest distance to " O   HOH Z 290 " =    1.176
peak=   -3.220 closest distance to " O   HOH Z 251 " =    5.104
peak=   -3.214 closest distance to " CB  PHE A 130 " =    1.211
peak=   -3.208 closest distance to " O   HOH Z  60 " =    1.822
peak=   -3.208 closest distance to " O   HOH Z 426 " =    1.740
peak=   -3.206 closest distance to " O   ASP A 171 " =    1.173
peak=   -3.203 closest distance to " CG2AVAL A  41 " =    2.780
peak=   -3.199 closest distance to " CA  ASN A 127 " =    0.999
peak=   -3.198 closest distance to " O   HOH Z 114 " =    1.695
peak=   -3.191 closest distance to " O   HOH Z 326 " =    4.832
peak=   -3.187 closest distance to " CB  PRO A  54 " =    2.686
peak=   -3.184 closest distance to " N   TYR A  68 " =    2.851
peak=   -3.178 closest distance to " O   HOH Z 113 " =    2.259
peak=   -3.178 closest distance to " O   HOH Z 368 " =    1.771
peak=   -3.169 closest distance to " CG  GLN A  58 " =    1.279
peak=   -3.169 closest distance to " N   GLN A  58 " =    1.420
peak=   -3.168 closest distance to " CG2BVAL A  41 " =    1.595
peak=   -3.162 closest distance to " O   HOH Z   7 " =    1.566
peak=   -3.160 closest distance to " NE2 GLN A  58 " =    2.883
peak=   -3.157 closest distance to " CB  TRP A 274 " =    2.509
peak=   -3.157 closest distance to " O   HOH Z 378 " =    1.453
peak=   -3.156 closest distance to " O   GLU A  44 " =    1.638
peak=   -3.156 closest distance to " O   LEU A 101 " =    2.473
peak=   -3.154 closest distance to " O   HOH Z 118 " =    1.570
peak=   -3.150 closest distance to " C   THR A 264 " =    1.383
peak=   -3.148 closest distance to " O   HOH Z 151 " =    1.518
peak=   -3.148 closest distance to " O   HOH Z 422 " =    1.075
peak=   -3.143 closest distance to " CD2 HIS A 115 " =    1.163
peak=   -3.140 closest distance to " CD  LYS A 289 " =    2.322
peak=   -3.135 closest distance to " O   HOH Z 250 " =    1.945
peak=   -3.135 closest distance to " CG  ARG A 259 " =    2.533
peak=   -3.133 closest distance to " CD2 PHE A 225 " =    1.418
peak=   -3.131 closest distance to " OD1 ASP A 171 " =    1.454
peak=   -3.129 closest distance to " CB  ALA A  43 " =    2.875
peak=   -3.127 closest distance to " CG  ASN A  45 " =    0.846
peak=   -3.127 closest distance to " O   HOH Z 325 " =    1.953
peak=   -3.117 closest distance to " O   HOH Z  82 " =    1.572
peak=   -3.115 closest distance to " CG1 VAL A  78 " =    2.697
peak=   -3.110 closest distance to " O   LEU A 282 " =    1.696
peak=   -3.099 closest distance to " O   HOH Z 174 " =    1.823
peak=   -3.091 closest distance to " O   HOH Z 164 " =    2.582
peak=   -3.087 closest distance to " C   ALA A 158 " =    1.381
peak=   -3.081 closest distance to " CD2 TRP A  85 " =    1.172
peak=   -3.078 closest distance to " CG1BVAL A  72 " =    2.501
peak=   -3.072 closest distance to " OG BSER A 210 " =    2.230
peak=   -3.055 closest distance to " CB  ASP A 132 " =    2.427
peak=   -3.054 closest distance to " CA  GLY A 136 " =    1.740
peak=   -3.046 closest distance to " CB  VAL A 250 " =    2.949
peak=   -3.002 closest distance to " CD1 LEU A 101 " =    2.442

================= 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    :  0.4852 0.4669   6.290732e+00   6.268713e+00
   1_bss:  0.4800 0.4604   6.288249e+00   6.262110e+00
   1_xyz:  0.3625 0.4026   6.113134e+00   6.171646e+00
   1_adp:  0.3292 0.4060   6.066990e+00   6.177552e+00
   1_occ:  0.3289 0.4051   6.066331e+00   6.176826e+00
   2_bss:  0.3280 0.4036   6.067247e+00   6.176447e+00
   2_xyz:  0.2611 0.3170   5.867281e+00   6.014252e+00
   2_adp:  0.2443 0.3064   5.822455e+00   5.987280e+00
   2_occ:  0.2441 0.3068   5.822062e+00   5.988183e+00
   3_bss:  0.2441 0.3070   5.822058e+00   5.988173e+00
   3_xyz:  0.1980 0.2539   5.634552e+00   5.820940e+00
   3_adp:  0.1738 0.2201   5.511914e+00   5.703691e+00
   3_occ:  0.1736 0.2198   5.511341e+00   5.703009e+00
   4_bss:  0.1735 0.2194   5.510171e+00   5.700190e+00
   4_xyz:  0.1534 0.1987   5.406711e+00   5.610371e+00
   4_adp:  0.1459 0.1987   5.379166e+00   5.599974e+00
   4_occ:  0.1458 0.1987   5.379205e+00   5.600184e+00
   5_bss:  0.1462 0.1988   5.380627e+00   5.602024e+00
   5_xyz:  0.1378 0.1886   5.329458e+00   5.557685e+00
   5_adp:  0.1359 0.1866   5.314809e+00   5.544077e+00
   5_occ:  0.1359 0.1865   5.314574e+00   5.543985e+00
   5_bss:  0.1357 0.1864   5.314541e+00   5.543987e+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:  0.274  58.445  -0.999   3.330   0.507   0.000   0.000   0.000
   1_xyz:  0.274  58.445  -0.999   3.330   0.507   0.000   0.000   0.000
   1_adp:  0.274  58.445  -0.999   3.330   0.507   0.000   0.000   0.000
   1_occ:  0.274  58.445  -0.999   3.330   0.507   0.000   0.000   0.000
   2_bss:  0.315  77.143   0.114   2.427   1.157   0.000   0.000   0.000
   2_xyz:  0.315  77.143   0.114   2.427   1.157   0.000   0.000   0.000
   2_adp:  0.315  77.143   0.114   2.427   1.157   0.000   0.000   0.000
   2_occ:  0.315  77.143   0.114   2.427   1.157   0.000   0.000   0.000
   3_bss:  0.332  78.232  -0.127   1.423   0.719   0.000   0.000   0.000
   3_xyz:  0.332  78.232  -0.127   1.423   0.719   0.000   0.000   0.000
   3_adp:  0.332  78.232  -0.127   1.423   0.719   0.000   0.000   0.000
   3_occ:  0.332  78.232  -0.127   1.423   0.719   0.000   0.000   0.000
   4_bss:  0.335  81.347  -0.827   0.318   0.311   0.000   0.000   0.000
   4_xyz:  0.335  81.347  -0.827   0.318   0.311   0.000   0.000   0.000
   4_adp:  0.335  81.347  -0.827   0.318   0.311   0.000   0.000   0.000
   4_occ:  0.335  81.347  -0.827   0.318   0.311   0.000   0.000   0.000
   5_bss:  0.334  87.291  -0.842   0.102   0.430   0.000   0.000   0.000
   5_xyz:  0.334  87.291  -0.842   0.102   0.430   0.000   0.000   0.000
   5_adp:  0.334  87.291  -0.842   0.102   0.430   0.000   0.000   0.000
   5_occ:  0.334  87.291  -0.842   0.102   0.430   0.000   0.000   0.000
   5_bss:  0.326  82.640  -0.685   0.071   0.614   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.008 0.4325  0.5570    68426.842
   1_bss:  56.316 0.4403  0.5901    66372.268
   1_xyz:  45.797 0.5715  0.7479    46145.950
   1_adp:  46.180 0.5666  0.7290    47031.241
   1_occ:  46.162 0.5668  0.7289    46988.154
   2_bss:  46.090 0.5676  0.7383    46825.469
   2_xyz:  33.958 0.7126  0.9047    27537.859
   2_adp:  32.295 0.7321  0.9191    25630.261
   2_occ:  32.316 0.7319  0.9186    25671.299
   3_bss:  32.277 0.7323  0.9019    25611.713
   3_xyz:  25.571 0.8052  0.9581    16575.299
   3_adp:  21.554 0.8468  0.9660    12572.086
   3_occ:  21.530 0.8470  0.9660    12548.606
   4_bss:  21.454 0.8476  0.9421    12433.081
   4_xyz:  18.959 0.8718  0.9556    10075.015
   4_adp:  18.600 0.8755  0.9434     9931.061
   4_occ:  18.605 0.8754  0.9432     9930.891
   5_bss:  18.649 0.8751  0.9417     9987.704
   5_xyz:  17.681 0.8836  0.9475     9059.214
   5_adp:  17.273 0.8874  0.9376     8809.776
   5_occ:  17.268 0.8875  0.9377     8812.280
   5_bss:  17.269 0.8874  0.9455     8813.843
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6914e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6914e-01
   1_xyz:   1.734  0.014  0.108 16.652  0.007  4.124   1.7235e-01
   1_adp:   1.734  0.014  0.108 16.652  0.007  4.124   1.7235e-01
   1_occ:   1.734  0.014  0.108 16.652  0.007  4.124   1.7235e-01
   2_bss:   1.734  0.014  0.108 16.652  0.007  4.124   1.7235e-01
   2_xyz:   1.450  0.011  0.094 15.405  0.006  4.110   1.1432e-01
   2_adp:   1.450  0.011  0.094 15.405  0.006  4.110   1.1432e-01
   2_occ:   1.450  0.011  0.094 15.405  0.006  4.110   1.1432e-01
   3_bss:   1.450  0.011  0.094 15.405  0.006  4.110   1.1432e-01
   3_xyz:   1.287  0.012  0.086 15.166  0.005  4.132   9.6385e-02
   3_adp:   1.287  0.012  0.086 15.166  0.005  4.132   9.6385e-02
   3_occ:   1.287  0.012  0.086 15.166  0.005  4.132   9.6385e-02
   4_bss:   1.287  0.012  0.086 15.166  0.005  4.132   9.6385e-02
   4_xyz:   1.067  0.009  0.077 14.748  0.004  4.132   6.7721e-02
   4_adp:   1.067  0.009  0.077 14.748  0.004  4.132   6.7721e-02
   4_occ:   1.067  0.009  0.077 14.748  0.004  4.132   6.7721e-02
   5_bss:   1.067  0.009  0.077 14.748  0.004  4.132   6.7721e-02
   5_xyz:   1.034  0.009  0.075 14.565  0.003  4.117   6.3072e-02
   5_adp:   1.034  0.009  0.075 14.565  0.003  4.117   6.3072e-02
   5_occ:   1.034  0.009  0.075 14.565  0.003  4.117   6.3072e-02
   5_bss:   1.034  0.009  0.075 14.565  0.003  4.117   6.3072e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.327   2.4657e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.327   2.4657e-01
   1_xyz:  11.092  0.102  0.342 87.350  0.049  1.834   1.7574e-01
   1_adp:  11.092  0.102  0.342 87.350  0.049  1.834   1.7574e-01
   1_occ:  11.092  0.102  0.342 87.350  0.049  1.834   1.7574e-01
   2_bss:  11.092  0.102  0.342 87.350  0.049  1.834   1.7574e-01
   2_xyz:   9.037  0.049  0.266 88.144  0.044  2.131   9.8267e-02
   2_adp:   9.037  0.049  0.266 88.144  0.044  2.131   9.8267e-02
   2_occ:   9.037  0.049  0.266 88.144  0.044  2.131   9.8267e-02
   3_bss:   9.037  0.049  0.266 88.144  0.044  2.131   9.8267e-02
   3_xyz:   9.173  0.074  0.239 82.741  0.037  2.132   7.3207e-02
   3_adp:   9.173  0.074  0.239 82.741  0.037  2.132   7.3207e-02
   3_occ:   9.173  0.074  0.239 82.741  0.037  2.132   7.3207e-02
   4_bss:   9.173  0.074  0.239 82.741  0.037  2.132   7.3207e-02
   4_xyz:   8.418  0.048  0.232 87.186  0.043  2.242   4.6519e-02
   4_adp:   8.418  0.048  0.232 87.186  0.043  2.242   4.6519e-02
   4_occ:   8.418  0.048  0.232 87.186  0.043  2.242   4.6519e-02
   5_bss:   8.418  0.048  0.232 87.186  0.043  2.242   4.6519e-02
   5_xyz:   8.630  0.060  0.223 79.999  0.039  2.326   3.7439e-02
   5_adp:   8.630  0.060  0.223 79.999  0.039  2.326   3.7439e-02
   5_occ:   8.630  0.060  0.223 79.999  0.039  2.326   3.7439e-02
   5_bss:   8.630  0.060  0.223 79.999  0.039  2.326   3.7439e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 115.61   0.00  19.06  95.44   0.00  15.16 115.61   0.00  40.26
   1_occ: 115.61   0.00  19.06  95.44   0.00  15.16 115.61   0.00  40.26
   2_bss: 115.61   0.00  19.06  95.44   0.00  15.16 115.61   0.00  40.26
   2_xyz: 115.61   0.00  19.06  95.44   0.00  15.16 115.61   0.00  40.26
   2_adp: 114.88   0.00  19.04  95.76   0.00  14.87 114.88   0.00  41.72
   2_occ: 114.88   0.00  19.04  95.76   0.00  14.87 114.88   0.00  41.72
   3_bss: 114.88   0.00  19.04  95.76   0.00  14.87 114.88   0.00  41.72
   3_xyz: 114.88   0.00  19.04  95.76   0.00  14.87 114.88   0.00  41.72
   3_adp: 104.94   0.00  17.40  84.84   0.00  12.65 104.94   4.12  43.30
   3_occ: 104.94   0.00  17.40  84.84   0.00  12.65 104.94   4.12  43.30
   4_bss: 104.94   0.00  17.40  84.84   0.00  12.65 104.94   4.12  43.30
   4_xyz: 104.94   0.00  17.40  84.84   0.00  12.65 104.94   4.12  43.30
   4_adp: 114.91   0.00  17.91 109.27   0.00  12.36 114.91   3.83  48.08
   4_occ: 114.91   0.00  17.91 109.27   0.00  12.36 114.91   3.83  48.08
   5_bss: 114.91   0.00  17.91 109.27   0.00  12.36 114.91   3.83  48.08
   5_xyz: 114.91   0.00  17.91 109.27   0.00  12.36 114.91   3.83  48.08
   5_adp: 120.53   0.00  17.24 113.23   0.00  11.82 120.53   3.85  46.77
   5_occ: 120.53   0.00  17.24 113.23   0.00  11.82 120.53   3.85  46.77
   5_bss: 120.66   0.13  17.38 113.37   0.13  11.95 120.66   3.98  46.91
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.783    0.034    0.485
   1_adp:    1.783    0.034    0.485
   1_occ:    1.783    0.034    0.485
   2_bss:    1.783    0.034    0.485
   2_xyz:    1.746    0.049    0.674
   2_adp:    1.746    0.049    0.674
   2_occ:    1.746    0.049    0.674
   3_bss:    1.746    0.049    0.674
   3_xyz:    1.647    0.072    0.810
   3_adp:    1.647    0.072    0.810
   3_occ:    1.647    0.072    0.810
   4_bss:    1.647    0.072    0.810
   4_xyz:    1.675    0.078    0.852
   4_adp:    1.675    0.078    0.852
   4_occ:    1.675    0.078    0.852
   5_bss:    1.675    0.078    0.852
   5_xyz:    1.643    0.068    0.886
   5_adp:    1.643    0.068    0.886
   5_occ:    1.643    0.068    0.886
   5_bss:    1.643    0.068    0.886
------------------------------------------------------------------------

CPU time actual refinement: 348.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1207/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_1207/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1207/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1207/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1207/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.00 
  Macro-tasks:
    bulk solvent and scale       = 58.81  
    individual site refinement   = 137.81 
    weights calculation          = 30.08  
    collect and process          = 6.56   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 233.37 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 103.02 
    alpha_beta                      = 8.28   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 113.03 
    fmodel                         = 9.47   
    r_factors                      = 0.35   
    phase_errors                   = 10.57  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 248.46 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.891 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    632 calls, 102.66 s
gradients_fft:          579 calls,  99.72 s

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

# Date 2008-01-16 Time 06:41:50 PST -0800 (1200494510.97 s)
Start R-work = 0.4852, R-free = 0.4669 (no bulk solvent and anisotropic scale)
Final R-work = 0.1505, R-free = 0.1998 (no bulk solvent and anisotropic scale)

Start R-work = 0.4800, R-free = 0.4604
Final R-work = 0.1357, R-free = 0.1864