# Date 2008-01-16 Time 05:51:36 PST -0800 (1200491496.59 s)
#phil __OFF__

Command line arguments: "../906.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29237
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 906

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.78, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99103
Completeness in resolution range: 0.967549
Completeness with d_max=infinity: 0.964595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9910

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99103
Completeness in resolution range: 0.967549
Completeness with d_max=infinity: 0.964595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2603 [2117/2143]  1907   210   9.9%
  bin  2:  4.2603 -  3.3942 [2048/2067]  1842   206  10.1%
  bin  3:  3.3942 -  2.9689 [2013/2032]  1809   204  10.1%
  bin  4:  2.9689 -  2.6991 [1997/2027]  1803   194   9.7%
  bin  5:  2.6991 -  2.5066 [1981/2000]  1784   197   9.9%
  bin  6:  2.5066 -  2.3594 [1972/1997]  1769   203  10.3%
  bin  7:  2.3594 -  2.2417 [1967/1995]  1769   198  10.1%
  bin  8:  2.2417 -  2.1444 [1955/1991]  1764   191   9.8%
  bin  9:  2.1444 -  2.0620 [1966/2008]  1771   195   9.9%
  bin 10:  2.0620 -  1.9910 [1573/1986]  1412   161  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_906/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2200
        3.04 -     3.66: 4647
        3.66 -     4.28: 9013
        4.28 -     4.90: 12334
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.091 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.364 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28199 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_906/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_906/model_refine_001.geo

CPU time processing inputs: 7.97


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2308   r_free= 0.2325   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.729731                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7517 0.99   1383  154 0.2526 0.2435      6.2553      6.1774|
|  2:  4.7517 -  3.7913 0.99   1333  146 0.1766 0.1765      6.0891      6.0919|
|  3:  3.7913 -  3.3179 0.99   1292  144 0.1876 0.1749      5.9598      6.0493|
|  4:  3.3179 -  3.0172 0.99   1291  147 0.1966 0.2164      5.8678      5.9041|
|  5:  3.0172 -  2.8024 0.99   1292  142 0.2227 0.2231      5.7644      5.8484|
|  6:  2.8024 -  2.6381 0.99   1281  143 0.2287 0.2334      5.7084      5.6874|
|  7:  2.6381 -  2.5066 0.99   1273  135 0.2409 0.2271      5.7048      5.7124|
|  8:  2.5066 -  2.3979 0.98   1265  150 0.2460 0.2325      5.6533      5.6018|
|  9:  2.3979 -  2.3060 0.98   1271  137 0.2382 0.2568      5.5885      5.6135|
| 10:  2.3060 -  2.2267 0.99   1260  140 0.2450 0.2678      5.5766      5.6546|
| 11:  2.2267 -  2.1572 0.98   1257  136 0.2572 0.2656      5.5587      5.6318|
| 12:  2.1572 -  2.0957 0.97   1248  142 0.2580 0.2455       5.521      5.5397|
| 13:  2.0957 -  2.0407 1.00   1256  140 0.2622 0.2775      5.4386      5.4026|
| 14:  2.0407 -  1.9910 0.71    928  103 0.2490 0.2811      5.3453      5.3046|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7517  1383   154  0.82  22.98   0.87     0.83      33578.22|
|  2:  4.7517 -  3.7913  1333   146  0.90  16.19   1.00     0.94      26142.78|
|  3:  3.7913 -  3.3179  1292   144  0.89  17.43   1.02     1.00      21387.40|
|  4:  3.3179 -  3.0172  1291   147  0.88  18.61   1.02     1.00      18366.73|
|  5:  3.0172 -  2.8024  1292   142  0.84  22.34   1.02     0.99      15706.59|
|  6:  2.8024 -  2.6381  1281   143  0.85  21.87   1.04     0.99      13093.19|
|  7:  2.6381 -  2.5066  1273   135  0.85  21.54   1.04     1.01      11590.97|
|  8:  2.5066 -  2.3979  1265   150  0.84  22.63   1.05     1.02      10957.58|
|  9:  2.3979 -  2.3060  1271   137  0.84  22.72   1.08     1.03      10591.26|
| 10:  2.3060 -  2.2267  1260   140  0.82  24.66   1.09     1.04      10634.28|
| 11:  2.2267 -  2.1572  1257   136  0.82  24.95   1.11     1.04      10207.71|
| 12:  2.1572 -  2.0957  1248   142  0.83  24.19   1.09     1.07       9459.70|
| 13:  2.0957 -  2.0407  1256   140  0.82  24.93   1.10     1.07       7766.69|
| 14:  2.0407 -  1.9910   928   103  0.85  22.51   1.09     1.03       5757.97|
|alpha:            min =        0.83 max =            1.07 mean =         1.00|
|beta:             min =     5757.97 max =        33578.22 mean =     15026.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.98 mean =        21.93|
|phase err.(test): min =        0.00 max =           89.22 mean =        21.66|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.629082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.325   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.375947              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.263   (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 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      187 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2013 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1821 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2826 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4652 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4361 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5607 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6727 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.138 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2308   r_free= 0.2325   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.729731                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2125   r_free= 0.2159   ksol= 0.32   Bsol= 49.91   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,-2.89,-1.48,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.691481                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.417728              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.618   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191272              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.000   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2125      final r-factor (work) = 0.1371          |
| start r-factor (free) = 0.2159      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1007 = 2.42 * 0.50 * 5.7414 + 1.00 * 0.1601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6127 = 2.42 * 0.50 * 5.4229 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1371      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0435 = 0.19 * 1.00 * 5.4229 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0252 = 0.19 * 1.00 * 5.2028 + 1.00 * 0.0301                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.41   16.46    None  None   None       |
|    all(noH): 2823   0      0.00    63.41   16.46    None  None   None       |
|    Sol.    : 438    0      6.83    62.78   37.06    None  None   None       |
|    Mac.    : 2385   0      0.00    63.41   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.341:  148   |   5:    31.707 -  38.048:   91        |
|      1:     6.341 -  12.683: 1370   |   6:    38.048 -  44.390:  104        |
|      2:    12.683 -  19.024:  659   |   7:    44.390 -  50.731:   74        |
|      3:    19.024 -  25.365:  190   |   8:    50.731 -  57.072:   56        |
|      4:    25.365 -  31.707:  115   |   9:    57.072 -  63.414:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1265 r_free = 0.1561             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1260 r_free = 0.1558             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1558   ksol= 0.32   Bsol= 49.91   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,-2.89,-1.48,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.206357                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1545   ksol= 0.33   Bsol= 51.06   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.91,-1.78,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205621                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.116788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.209  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203013              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.077   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5667 = 2.12 * 0.50 * 5.2056 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5163 = 2.12 * 0.50 * 5.1529 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1506      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0961 = 0.20 * 1.00 * 5.1529 + 1.00 * 0.0500                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0461 = 0.20 * 1.00 * 5.1180 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.94    70.94   16.70    None  None   None       |
|    all(noH): 2823   0      1.94    70.94   16.70    None  None   None       |
|    Sol.    : 438    0      5.22    66.06   37.31    None  None   None       |
|    Mac.    : 2385   0      1.94    70.94   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.937 -   8.837:  650   |   5:    36.438 -  43.338:  120        |
|      1:     8.837 -  15.737: 1273   |   6:    43.338 -  50.238:   86        |
|      2:    15.737 -  22.637:  364   |   7:    50.238 -  57.138:   70        |
|      3:    22.637 -  29.538:  129   |   8:    57.138 -  64.038:   22        |
|      4:    29.538 -  36.438:  104   |   9:    64.038 -  70.938:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1506             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1506             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1506   ksol= 0.33   Bsol= 51.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.91,-1.78,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117894                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1506   ksol= 0.33   Bsol= 51.06   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.61,-1.61,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117768                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.864796              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.613  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.379861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.143  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1506      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8348 = 1.86 * 0.50 * 5.1183 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8274 = 1.86 * 0.50 * 5.1152 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9501 = 0.38 * 1.00 * 5.1152 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9519 = 0.38 * 1.00 * 5.1176 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.15    75.41   16.76    None  None   None       |
|    all(noH): 2823   0      1.15    75.41   16.76    None  None   None       |
|    Sol.    : 438    0      5.71    67.91   37.94    None  None   None       |
|    Mac.    : 2385   0      1.15    75.41   12.87    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:     1.146 -   8.573:  643   |   5:    38.280 -  45.706:  124        |
|      1:     8.573 -  16.000: 1292   |   6:    45.706 -  53.133:   83        |
|      2:    16.000 -  23.426:  361   |   7:    53.133 -  60.560:   60        |
|      3:    23.426 -  30.853:  132   |   8:    60.560 -  67.986:   17        |
|      4:    30.853 -  38.280:  107   |   9:    67.986 -  75.413:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1541             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1542             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1542   ksol= 0.33   Bsol= 51.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-2.61,-1.61,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122238                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1542   ksol= 0.32   Bsol= 51.06   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.39,-1.43,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.122264                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.902276              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.431  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.887  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9262 = 1.90 * 0.50 * 5.1183 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9278 = 1.90 * 0.50 * 5.1196 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2979 = 0.45 * 1.00 * 5.1196 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2990 = 0.45 * 1.00 * 5.1210 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    80.09   16.72    None  None   None       |
|    all(noH): 2823   0      0.78    80.09   16.72    None  None   None       |
|    Sol.    : 438    0      6.23    70.77   38.27    None  None   None       |
|    Mac.    : 2385   0      0.78    80.09   12.76    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:     0.779 -   8.711:  725   |   5:    40.437 -  48.368:  105        |
|      1:     8.711 -  16.642: 1275   |   6:    48.368 -  56.300:   88        |
|      2:    16.642 -  24.574:  325   |   7:    56.300 -  64.231:   39        |
|      3:    24.574 -  32.505:  132   |   8:    64.231 -  72.163:   15        |
|      4:    32.505 -  40.437:  114   |   9:    72.163 -  80.094:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1080 r_free = 0.1559             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1080 r_free = 0.1560             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1560   ksol= 0.32   Bsol= 51.06   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.39,-1.43,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123157                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1560   ksol= 0.32   Bsol= 51.06   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.18,-1.24,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123228                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.797196              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.790  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213707              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.940  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1079      final r-factor (work) = 0.1060          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2216 = 2.80 * 0.50 * 5.1218 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2208 = 2.80 * 0.50 * 5.1153 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1060      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1016 = 0.21 * 1.00 * 5.1153 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1010 = 0.21 * 1.00 * 5.1168 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    79.57   16.33    None  None   None       |
|    all(noH): 2823   0      1.22    79.57   16.33    None  None   None       |
|    Sol.    : 438    0      6.05    70.54   37.00    None  None   None       |
|    Mac.    : 2385   0      1.22    79.57   12.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.218 -   9.054:  848   |   5:    40.395 -  48.230:  107        |
|      1:     9.054 -  16.889: 1189   |   6:    48.230 -  56.066:   78        |
|      2:    16.889 -  24.724:  297   |   7:    56.066 -  63.901:   28        |
|      3:    24.724 -  32.560:  132   |   8:    63.901 -  71.736:    9        |
|      4:    32.560 -  40.395:  131   |   9:    71.736 -  79.572:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1555             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1067 r_free = 0.1555             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1555   ksol= 0.32   Bsol= 51.06   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.18,-1.24,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114399                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7517 0.99   1383  154 0.0982 0.1323      5.3768      5.5375|
|  2:  4.7517 -  3.7913 0.99   1333  146 0.0848 0.1106      5.4352      5.6245|
|  3:  3.7913 -  3.3179 0.99   1292  144 0.1012 0.1535      5.4513      5.8785|
|  4:  3.3179 -  3.0172 0.99   1291  147 0.1165 0.1477      5.4376      5.5567|
|  5:  3.0172 -  2.8024 0.99   1292  142 0.1276 0.1774      5.3064      5.5639|
|  6:  2.8024 -  2.6381 0.99   1281  143 0.1146 0.1773      5.1867      5.3997|
|  7:  2.6381 -  2.5066 0.99   1273  135 0.1192 0.1617      5.1321      5.3753|
|  8:  2.5066 -  2.3979 0.98   1265  150 0.1083 0.1702      5.0158      5.3239|
|  9:  2.3979 -  2.3060 0.98   1271  137 0.1096 0.1686      4.9949      5.2534|
| 10:  2.3060 -  2.2267 0.99   1260  140 0.1043 0.1727      4.9158      5.2255|
| 11:  2.2267 -  2.1572 0.98   1257  136 0.1076 0.1700      4.9147      5.2121|
| 12:  2.1572 -  2.0957 0.97   1248  142 0.1037 0.1600      4.8393      5.1554|
| 13:  2.0957 -  2.0407 1.00   1256  140 0.1073 0.1728      4.7626      5.0888|
| 14:  2.0407 -  1.9910 0.71    928  103 0.1025 0.1680       4.637      4.8722|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7517  1383   154  0.94   9.11   0.98     0.95       7160.41|
|  2:  4.7517 -  3.7913  1333   146  0.95   7.95   1.01     1.00       9113.96|
|  3:  3.7913 -  3.3179  1292   144  0.94  11.04   1.01     1.00      10163.67|
|  4:  3.3179 -  3.0172  1291   147  0.92  13.55   1.00     0.99      10241.87|
|  5:  3.0172 -  2.8024  1292   142  0.90  15.86   0.99     0.96       8153.39|
|  6:  2.8024 -  2.6381  1281   143  0.91  15.39   0.98     0.96       6893.61|
|  7:  2.6381 -  2.5066  1273   135  0.91  14.94   0.99     0.96       5858.99|
|  8:  2.5066 -  2.3979  1265   150  0.92  14.35   0.99     0.97       4872.11|
|  9:  2.3979 -  2.3060  1271   137  0.92  14.43   1.00     0.97       4637.76|
| 10:  2.3060 -  2.2267  1260   140  0.91  14.79   0.99     0.95       4050.87|
| 11:  2.2267 -  2.1572  1257   136  0.90  16.17   0.99     0.95       4247.82|
| 12:  2.1572 -  2.0957  1248   142  0.92  14.04   1.00     0.99       3694.67|
| 13:  2.0957 -  2.0407  1256   140  0.91  15.44   1.00     0.99       3212.69|
| 14:  2.0407 -  1.9910   928   103  0.92  14.07   0.97     0.93       2386.88|
|alpha:            min =        0.93 max =            1.00 mean =         0.97|
|beta:             min =     2386.88 max =        10241.87 mean =      6159.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.80 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.41 mean =        13.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1556   ksol= 0.32   Bsol= 51.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.99,-1.05,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114505                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1556   ksol= 0.32   Bsol= 51.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.99,-1.05,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114505                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7517 0.99   1383  154 0.0983 0.1325      5.3776      5.5384|
|  2:  4.7517 -  3.7913 0.99   1333  146 0.0848 0.1105      5.4352      5.6241|
|  3:  3.7913 -  3.3179 0.99   1292  144 0.1012 0.1535      5.4511      5.8785|
|  4:  3.3179 -  3.0172 0.99   1291  147 0.1165 0.1477      5.4375      5.5567|
|  5:  3.0172 -  2.8024 0.99   1292  142 0.1276 0.1774      5.3065      5.5639|
|  6:  2.8024 -  2.6381 0.99   1281  143 0.1146 0.1773      5.1867      5.3997|
|  7:  2.6381 -  2.5066 0.99   1273  135 0.1192 0.1617      5.1321      5.3752|
|  8:  2.5066 -  2.3979 0.98   1265  150 0.1083 0.1703      5.0158      5.3238|
|  9:  2.3979 -  2.3060 0.98   1271  137 0.1096 0.1685       4.995      5.2532|
| 10:  2.3060 -  2.2267 0.99   1260  140 0.1043 0.1727      4.9159      5.2255|
| 11:  2.2267 -  2.1572 0.98   1257  136 0.1076 0.1701      4.9149      5.2123|
| 12:  2.1572 -  2.0957 0.97   1248  142 0.1037 0.1600      4.8394      5.1555|
| 13:  2.0957 -  2.0407 1.00   1256  140 0.1074 0.1728      4.7626      5.0888|
| 14:  2.0407 -  1.9910 0.71    928  103 0.1025 0.1680      4.6371      4.8722|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7517  1383   154  0.94   9.12   0.98     0.95       7174.73|
|  2:  4.7517 -  3.7913  1333   146  0.95   7.95   1.01     1.00       9119.37|
|  3:  3.7913 -  3.3179  1292   144  0.94  11.04   1.02     1.01      10158.07|
|  4:  3.3179 -  3.0172  1291   147  0.92  13.55   1.01     0.99      10241.40|
|  5:  3.0172 -  2.8024  1292   142  0.90  15.86   0.99     0.96       8152.77|
|  6:  2.8024 -  2.6381  1281   143  0.91  15.39   0.99     0.96       6893.90|
|  7:  2.6381 -  2.5066  1273   135  0.91  14.94   0.99     0.96       5858.20|
|  8:  2.5066 -  2.3979  1265   150  0.92  14.35   0.99     0.98       4872.30|
|  9:  2.3979 -  2.3060  1271   137  0.92  14.43   1.00     0.97       4637.40|
| 10:  2.3060 -  2.2267  1260   140  0.91  14.80   1.00     0.96       4052.25|
| 11:  2.2267 -  2.1572  1257   136  0.90  16.17   1.00     0.96       4248.82|
| 12:  2.1572 -  2.0957  1248   142  0.92  14.04   1.01     0.99       3695.71|
| 13:  2.0957 -  2.0407  1256   140  0.91  15.44   1.01     1.00       3212.75|
| 14:  2.0407 -  1.9910   928   103  0.92  14.08   0.98     0.94       2387.04|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2387.04 max =        10241.40 mean =      6160.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.80 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.992)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    79.53   16.29    None  None   None       |
|    all(noH): 2823   0      1.18    79.53   16.29    None  None   None       |
|    Sol.    : 438    0      6.01    70.50   36.96    None  None   None       |
|    Mac.    : 2385   0      1.18    79.53   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.175 -   9.011:  848   |   5:    40.352 -  48.187:  107        |
|      1:     9.011 -  16.846: 1189   |   6:    48.187 -  56.023:   78        |
|      2:    16.846 -  24.681:  297   |   7:    56.023 -  63.858:   28        |
|      3:    24.681 -  32.517:  132   |   8:    63.858 -  71.694:    9        |
|      4:    32.517 -  40.352:  131   |   9:    71.694 -  79.529:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 280         
Filter by distance & map next to the model:
   mapped sites are within: 0.605 - 5.503
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 280
   mapped sites are within: 0.735 - 5.503

peak=    5.929 closest distance to " NH2 ARG A  56 " =    2.251
peak=    5.493 closest distance to " CG  PRO A  54 " =    1.278
peak=    5.348 closest distance to " O   HOH Z 126 " =    1.860
peak=    5.219 closest distance to " CB  SER A  63 " =    1.195
peak=    5.127 closest distance to " CB  GLN A 223 " =    1.459
peak=    4.956 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.788 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.738 closest distance to " C   PRO A 198 " =    1.514
peak=    4.685 closest distance to " NE2 GLN A  11 " =    1.118
peak=    4.653 closest distance to " CB  GLU A 152 " =    1.168
peak=    4.624 closest distance to " O   HOH Z  78 " =    1.699
peak=    4.611 closest distance to " CB  PRO A  54 " =    0.909
peak=    4.611 closest distance to " O   HOH Z 369 " =    2.094
peak=    4.547 closest distance to " CB  GLN A 183 " =    1.172
peak=    4.533 closest distance to " O   HOH Z 236 " =    1.917
peak=    4.511 closest distance to " CA  TYR A  30 " =    0.941
peak=    4.491 closest distance to " O   HOH Z 142 " =    1.668
peak=    4.427 closest distance to " O   HOH Z 298 " =    1.922
peak=    4.408 closest distance to " O   HOH Z  15 " =    2.175
peak=    4.407 closest distance to " ND2 ASN A 187 " =    1.486
peak=    4.406 closest distance to " CB  LEU A 228 " =    1.070
peak=    4.374 closest distance to " CB  ARG A  79 " =    1.329
peak=    4.343 closest distance to " OD1 ASN A  69 " =    2.612
peak=    4.314 closest distance to " O   HOH Z 193 " =    1.942
peak=    4.301 closest distance to " CB  ASN A 148 " =    1.512
peak=    4.282 closest distance to " O   HOH Z 250 " =    1.513
peak=    4.280 closest distance to " O   HOH Z 303 " =    2.072
peak=    4.236 closest distance to " CB  TYR A 169 " =    0.735
peak=    4.230 closest distance to " O   HOH Z 234 " =    3.724
peak=    4.159 closest distance to " O   HOH Z 158 " =    3.001
peak=    4.136 closest distance to " O   HOH Z 261 " =    2.082
peak=    4.074 closest distance to " O   HOH Z 197 " =    3.132
peak=    4.069 closest distance to " CB  GLU A 128 " =    1.037
peak=    4.068 closest distance to " CG  PRO A  90 " =    1.092
peak=    4.060 closest distance to " CG  PRO A 243 " =    1.098
peak=    4.042 closest distance to " CB  ARG A 190 " =    1.614
peak=    4.023 closest distance to " O   HOH Z 427 " =    2.948
peak=    3.957 closest distance to " CG  PRO A 198 " =    1.294
peak=    3.929 closest distance to " CA  ASN A 215 " =    1.197
peak=    3.919 closest distance to " NH1AARG A 145 " =    1.193
peak=    3.919 closest distance to " O   HOH Z 214 " =    2.050
peak=    3.917 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.907 closest distance to " OD2 ASP A 286 " =    2.878
peak=    3.904 closest distance to " CB  GLU A 277 " =    3.619
peak=    3.894 closest distance to " CB  ASP A 140 " =    0.913
peak=    3.886 closest distance to " O   HOH Z 344 " =    3.197
peak=    3.875 closest distance to " O   HOH Z 346 " =    1.563
peak=    3.873 closest distance to " CB  SER A   3 " =    1.337
peak=    3.860 closest distance to " O   HOH Z 291 " =    1.578
peak=    3.857 closest distance to " CD1 LEU A 300 " =    1.255
peak=    3.836 closest distance to " CA  PRO A  54 " =    1.329
peak=    3.829 closest distance to " O   HOH Z 193 " =    1.751
peak=    3.826 closest distance to " CB  VAL A 202 " =    1.561
peak=    3.823 closest distance to " O   HOH Z 203 " =    1.801
peak=    3.823 closest distance to " O   HOH Z 213 " =    1.810
peak=    3.822 closest distance to " CZ  PHE A 218 " =    1.048
peak=    3.811 closest distance to " O   HOH Z  40 " =    1.743
peak=    3.807 closest distance to " O   HOH Z  10 " =    1.839
peak=    3.806 closest distance to " O   HOH Z 403 " =    1.678
peak=    3.805 closest distance to " NZ  LYS A 117 " =    3.230
peak=    3.803 closest distance to " O   HOH Z 426 " =    1.624
peak=    3.802 closest distance to " CA  ALA A  21 " =    1.202
peak=    3.802 closest distance to " O   HOH Z 389 " =    1.941
peak=    3.800 closest distance to " CB  TRP A 266 " =    0.917
peak=    3.796 closest distance to " CA  THR A 264 " =    0.885
peak=    3.787 closest distance to " NH2 ARG A 156 " =    1.190
peak=    3.784 closest distance to " CB  VAL A 265 " =    1.263
peak=    3.779 closest distance to " CG2 VAL A 257 " =    0.941
peak=    3.774 closest distance to " O   HOH Z 133 " =    1.627
peak=    3.767 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.766 closest distance to " CG2 THR A 221 " =    1.063
peak=    3.759 closest distance to " O   HOH Z 425 " =    1.945
peak=    3.759 closest distance to " CB  TRP A 179 " =    1.362
peak=    3.752 closest distance to " ND2 ASN A 110 " =    1.803
peak=    3.751 closest distance to " O   HOH Z 423 " =    1.836
peak=    3.747 closest distance to " CB  SER A 212 " =    1.142
peak=    3.742 closest distance to " O   MET A 105 " =    1.824
peak=    3.729 closest distance to " O   HOH Z   1 " =    1.932
peak=    3.726 closest distance to " O   HOH Z  66 " =    2.204
peak=    3.726 closest distance to " O   SER A  87 " =    2.278
peak=    3.721 closest distance to " CA  ALA A  51 " =    0.887
peak=    3.720 closest distance to " O   HOH Z 189 " =    2.346
peak=    3.719 closest distance to " O   HOH Z 316 " =    3.133
peak=    3.710 closest distance to " CA  THR A 221 " =    1.005
peak=    3.694 closest distance to " O   HOH Z 368 " =    1.995
peak=    3.690 closest distance to " O   HOH Z 265 " =    2.390
peak=    3.678 closest distance to " NH2BARG A 145 " =    2.087
peak=    3.678 closest distance to " O   HOH Z  21 " =    1.757
peak=    3.673 closest distance to " CG2 ILE A 120 " =    1.220
peak=    3.660 closest distance to " CD2 TRP A 179 " =    1.321
peak=    3.654 closest distance to " CG1 ILE A  33 " =    1.258
peak=    3.653 closest distance to " CD2 LEU A 297 " =    0.854
peak=    3.652 closest distance to " O   HOH Z 147 " =    1.812
peak=    3.651 closest distance to " O   HOH Z 132 " =    2.599
peak=    3.634 closest distance to " CD  ARG A 159 " =    0.753
peak=    3.622 closest distance to " O   HOH Z  63 " =    2.130
peak=    3.622 closest distance to " CB  ASN A  39 " =    0.878
peak=    3.618 closest distance to " O   HOH Z 402 " =    1.473
peak=    3.617 closest distance to " CB  TYR A 169 " =    0.751
peak=    3.617 closest distance to " O   HOH Z 305 " =    3.639
peak=    3.612 closest distance to " O   HOH Z 280 " =    2.974
peak=    3.609 closest distance to " CD  ARG A  66 " =    2.428
peak=    3.604 closest distance to " CD1 ILE A 106 " =    0.796
peak=    3.594 closest distance to " O   HOH Z 245 " =    1.323
peak=    3.593 closest distance to " ND1 HIS A  81 " =    1.610
peak=    3.592 closest distance to " CB  ASN A 142 " =    0.991
peak=    3.580 closest distance to " O   HOH Z 209 " =    2.366
peak=    3.575 closest distance to " O   HOH Z  43 " =    1.878
peak=    3.573 closest distance to " CB  MET A  40 " =    0.840
peak=    3.554 closest distance to " O   HOH Z 172 " =    3.413
peak=    3.550 closest distance to " CB  ALA A 291 " =    1.428
peak=    3.539 closest distance to " CG1BVAL A  72 " =    1.613
peak=    3.533 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.518 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.518 closest distance to " O   HOH Z 180 " =    2.124
peak=    3.512 closest distance to " CB  ARG A 139 " =    0.980
peak=    3.504 closest distance to " CA  ALA A 233 " =    1.361
peak=    3.504 closest distance to " CB  LEU A 143 " =    1.090
peak=    3.497 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.496 closest distance to " CD  LYS A 166 " =    1.231
peak=    3.495 closest distance to " O   HOH Z 234 " =    1.749
peak=    3.489 closest distance to " O   HOH Z 108 " =    2.611
peak=    3.488 closest distance to " ND1 HIS A  86 " =    1.657
peak=    3.486 closest distance to " O   HOH Z 368 " =    3.652
peak=    3.484 closest distance to " CA  ALA A  84 " =    1.343
peak=    3.476 closest distance to " O   HOH Z 135 " =    1.680
peak=    3.475 closest distance to " O   HOH Z 248 " =    1.721
peak=    3.474 closest distance to " O   HOH Z 406 " =    1.632
peak=    3.472 closest distance to " N   ASN A 127 " =    1.272
peak=    3.469 closest distance to " O   HOH Z   9 " =    2.114
peak=    3.469 closest distance to " CB  SER A 141 " =    0.981
peak=    3.468 closest distance to " O   TRP A 274 " =    1.860
peak=    3.462 closest distance to " O   HOH Z 295 " =    1.519
peak=    3.457 closest distance to " CB  SER A 216 " =    0.808
peak=    3.452 closest distance to " N   ARG A 156 " =    1.317
peak=    3.451 closest distance to " CD BLYS A 290 " =    1.131
peak=    3.451 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.449 closest distance to " O   HOH Z  54 " =    1.627
peak=    3.445 closest distance to " CB  GLN A  88 " =    1.224
peak=    3.441 closest distance to " O   HOH Z 148 " =    3.277
peak=    3.438 closest distance to " CA  MET A  40 " =    1.111
peak=    3.438 closest distance to " O   HOH Z 219 " =    2.021
peak=    3.437 closest distance to " O   HOH Z 313 " =    1.875
peak=    3.434 closest distance to " CB  ALA A   1 " =    4.712
peak=    3.433 closest distance to " CB  ILE A 120 " =    1.199
peak=    3.432 closest distance to " O   HOH Z  88 " =    3.290
peak=    3.431 closest distance to " OD1 ASN A 217 " =    1.700
peak=    3.425 closest distance to " O   HOH Z 171 " =    2.118
peak=    3.416 closest distance to " O   HOH Z  93 " =    2.722
peak=    3.411 closest distance to " O   HOH Z 199 " =    1.517
peak=    3.407 closest distance to " O   HOH Z 281 " =    4.015
peak=    3.405 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.397 closest distance to " CA  ARG A  36 " =    1.085
peak=    3.395 closest distance to " O   HOH Z 371 " =    3.158
peak=    3.384 closest distance to " CD2 LEU A 255 " =    1.470
peak=    3.383 closest distance to " O   HOH Z 273 " =    2.664
peak=    3.377 closest distance to " O   HOH Z 193 " =    2.065
peak=    3.377 closest distance to " CZ2 TRP A 179 " =    1.742
peak=    3.377 closest distance to " CB  HIS A 108 " =    0.808
peak=    3.367 closest distance to " O   HOH Z 173 " =    1.813
peak=    3.365 closest distance to " OG  SER A  22 " =    2.698
peak=    3.361 closest distance to " O   HOH Z  49 " =    2.177
peak=    3.359 closest distance to " O   HOH Z  19 " =    2.558
peak=    3.357 closest distance to " CB  ALA A 248 " =    0.918
peak=    3.354 closest distance to " CA  ALA A 291 " =    0.908
peak=    3.354 closest distance to " CG  GLN A  77 " =    2.136
peak=    3.354 closest distance to " CB  MET A  47 " =    1.103
peak=    3.353 closest distance to " OG BSER A 164 " =    2.358
peak=    3.347 closest distance to " O   HOH Z 128 " =    2.081
peak=    3.346 closest distance to " O   HOH Z  49 " =    2.855
peak=    3.346 closest distance to " O   HOH Z 133 " =    2.419
peak=    3.344 closest distance to " O   HOH Z 345 " =    3.398
peak=    3.344 closest distance to " CB  ASN A 224 " =    1.067
peak=    3.343 closest distance to " O   HOH Z  59 " =    2.080
peak=    3.343 closest distance to " O   HOH Z 209 " =    2.396
peak=    3.342 closest distance to " O   HOH Z 185 " =    1.758
peak=    3.338 closest distance to " O   HOH Z 419 " =    1.972
peak=    3.337 closest distance to " N   VAL A 126 " =    1.383
peak=    3.336 closest distance to " CA  SER A  87 " =    1.017
peak=    3.336 closest distance to " O   HOH Z 411 " =    3.869
peak=    3.333 closest distance to " CB  GLN A 278 " =    0.867
peak=    3.328 closest distance to " O   HOH Z 421 " =    1.737
peak=    3.328 closest distance to " CA  ASP A 140 " =    1.184
peak=    3.327 closest distance to " CB  ALA A  34 " =    0.907
peak=    3.316 closest distance to " O   THR A 251 " =    1.280
peak=    3.316 closest distance to " CB  THR A 157 " =    1.107
peak=    3.314 closest distance to " CA  ALA A 248 " =    1.243
peak=    3.312 closest distance to " CD  ARG A 219 " =    1.067
peak=    3.310 closest distance to " CG  LYS A  76 " =    0.937
peak=    3.307 closest distance to " CG1 VAL A 153 " =    0.861
peak=    3.306 closest distance to " O   HOH Z 329 " =    3.760
peak=    3.306 closest distance to " CA  ARG A 195 " =    1.193
peak=    3.303 closest distance to " O   HOH Z 261 " =    2.170
peak=    3.299 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.292 closest distance to " CA  ALA A 154 " =    0.942
peak=    3.288 closest distance to " CD2 HIS A  81 " =    1.165
peak=    3.288 closest distance to " CB  ALA A 248 " =    1.383
peak=    3.285 closest distance to " O   HOH Z 359 " =    1.494
peak=    3.285 closest distance to " CB  TYR A 116 " =    0.843
peak=    3.284 closest distance to " O   HOH Z 383 " =    1.883
peak=    3.281 closest distance to " O   HOH Z 128 " =    2.313
peak=    3.279 closest distance to " OG1 THR A 294 " =    2.436
peak=    3.276 closest distance to " CG AARG A 275 " =    1.178
peak=    3.274 closest distance to " O   HOH Z 166 " =    3.726
peak=    3.270 closest distance to " CA  ILE A  33 " =    1.500
peak=    3.269 closest distance to " CB  GLN A  89 " =    1.256
peak=    3.269 closest distance to " O   HOH Z 175 " =    2.197
peak=    3.267 closest distance to " O  BHOH Z 338 " =    2.332
peak=    3.267 closest distance to " O   HOH Z 263 " =    1.735
peak=    3.266 closest distance to " NH2AARG A 275 " =    3.702
peak=    3.259 closest distance to " CB  ALA A   9 " =    1.548
peak=    3.247 closest distance to " CG  MET A 185 " =    1.028
peak=    3.240 closest distance to " O   HOH Z 116 " =    1.748
peak=    3.239 closest distance to " N   SER A 135 " =    1.341
peak=    3.237 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.236 closest distance to " CA  ASP A 191 " =    0.758
peak=    3.235 closest distance to " O   HOH Z 407 " =    2.432
peak=    3.231 closest distance to " CA  MET A 105 " =    0.952
peak=    3.225 closest distance to " O   ALA A 165 " =    1.448
peak=    3.223 closest distance to " CG1 ILE A 151 " =    1.024
peak=    3.222 closest distance to " O   HOH Z 433 " =    1.754
peak=    3.221 closest distance to " CA  ASN A 252 " =    1.934
peak=    3.218 closest distance to " O   HOH Z 327 " =    1.808
peak=    3.216 closest distance to " O   HOH Z 188 " =    2.230
peak=    3.215 closest distance to " CG  GLN A  58 " =    2.763
peak=    3.215 closest distance to " CA  TYR A 116 " =    1.375
peak=    3.213 closest distance to " O   HOH Z 144 " =    1.837
peak=    3.212 closest distance to " CG  MET A 113 " =    1.340
peak=    3.211 closest distance to " CG  GLN A  11 " =    1.582
peak=    3.205 closest distance to " O   HOH Z  44 " =    3.232
peak=    3.200 closest distance to " CA  ALA A 158 " =    1.177
peak=    3.199 closest distance to " OE1 GLU A   2 " =    2.245
peak=    3.197 closest distance to " O   HOH Z 435 " =    1.927
peak=    3.188 closest distance to " CZ3 TRP A 123 " =    1.255
peak=    3.183 closest distance to " O   HOH Z 411 " =    1.812
peak=    3.183 closest distance to " O   HOH Z 171 " =    3.977
peak=    3.182 closest distance to " OG  SER A  97 " =    3.606
peak=    3.179 closest distance to " CE BLYS A 290 " =    1.044
peak=    3.177 closest distance to " OD1BASN A 224 " =    2.370
peak=    3.172 closest distance to " O   HOH Z 345 " =    1.729
peak=    3.169 closest distance to " N   PHE A 130 " =    1.234
peak=    3.168 closest distance to " O   HOH Z 410 " =    1.909
peak=    3.160 closest distance to " O   HOH Z 423 " =    2.939
peak=    3.157 closest distance to " CB  PHE A  16 " =    1.061
peak=    3.153 closest distance to " O   HOH Z 358 " =    3.682
peak=    3.137 closest distance to " O   HOH Z 417 " =    3.226
peak=    3.136 closest distance to " O   ALA A 158 " =    1.286
peak=    3.136 closest distance to " N   ASN A  39 " =    1.300
peak=    3.135 closest distance to " O   HOH Z 391 " =    2.884
peak=    3.132 closest distance to " O   HOH Z  88 " =    1.671
peak=    3.132 closest distance to " O   HOH Z  97 " =    1.903
peak=    3.128 closest distance to " CB  ASN A 215 " =    1.130
peak=    3.128 closest distance to " NE2 GLN A  77 " =    3.252
peak=    3.127 closest distance to " CB  ASN A 110 " =    1.115
peak=    3.122 closest distance to " O   HOH Z 302 " =    1.958
peak=    3.117 closest distance to " O   HOH Z 384 " =    3.040
peak=    3.115 closest distance to " O   HOH Z 287 " =    2.200
peak=    3.113 closest distance to " CD  LYS A 119 " =    1.340
peak=    3.112 closest distance to " O   HOH Z 298 " =    2.550
peak=    3.102 closest distance to " N   GLN A 278 " =    1.087
peak=    3.102 closest distance to " CA  GLU A  46 " =    0.740
peak=    3.100 closest distance to " CA  SER A 146 " =    1.682
peak=    3.093 closest distance to " CG1 ILE A  49 " =    1.416
peak=    3.090 closest distance to " N   ASN A 252 " =    1.393
peak=    3.086 closest distance to " CG BARG A 102 " =    1.812
peak=    3.083 closest distance to " O   HOH Z 123 " =    2.328
peak=    3.076 closest distance to " CB  ALA A 114 " =    1.187
peak=    3.074 closest distance to " O   HOH Z 285 " =    2.961
peak=    3.065 closest distance to " O   HOH Z 430 " =    5.503
peak=    3.064 closest distance to " O   HOH Z 336 " =    1.770
peak=    3.061 closest distance to " O   ALA A   1 " =    1.694
peak=    3.061 closest distance to " O   HOH Z 258 " =    1.864
peak=    3.057 closest distance to " NZ  LYS A  76 " =    1.241
peak=    3.046 closest distance to " CB  ARG A 138 " =    1.003
peak=    3.033 closest distance to " CG2 ILE A  20 " =    1.309
peak=    3.028 closest distance to " CB  TRP A 150 " =    1.389

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.608 - 5.400
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.769 - 5.400

peak=   -4.757 closest distance to " O   HOH Z 266 " =    4.928
peak=   -4.518 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.482 closest distance to " CB  PRO A 243 " =    2.629
peak=   -4.444 closest distance to " O   HOH Z 290 " =    1.252
peak=   -4.413 closest distance to " O   VAL A  67 " =    2.741
peak=   -4.360 closest distance to " CG  GLN A 223 " =    1.969
peak=   -4.084 closest distance to " C   HIS A 108 " =    1.123
peak=   -4.066 closest distance to " O   HOH Z 389 " =    1.898
peak=   -4.057 closest distance to " N   ALA A  43 " =    2.590
peak=   -4.048 closest distance to " CD  ARG A  14 " =    3.531
peak=   -4.048 closest distance to " CZ3 TRP A 179 " =    1.129
peak=   -4.037 closest distance to " O   HOH Z 198 " =    2.116
peak=   -3.994 closest distance to " O   ILE A 109 " =    2.592
peak=   -3.980 closest distance to " CD  GLN A  58 " =    0.993
peak=   -3.977 closest distance to " O   HOH Z 377 " =    2.059
peak=   -3.943 closest distance to " O   HOH Z 372 " =    2.469
peak=   -3.940 closest distance to " O   HOH Z 126 " =    1.878
peak=   -3.935 closest distance to " OG BSER A 134 " =    1.206
peak=   -3.920 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -3.915 closest distance to " CG  ARG A 269 " =    2.375
peak=   -3.902 closest distance to " O   HOH Z  10 " =    1.531
peak=   -3.892 closest distance to " O   HOH Z 435 " =    2.800
peak=   -3.871 closest distance to " O   HOH Z 231 " =    2.236
peak=   -3.868 closest distance to " CD1 PHE A  59 " =    1.858
peak=   -3.866 closest distance to " CD  ARG A 139 " =    1.616
peak=   -3.849 closest distance to " O   HOH Z 114 " =    3.260
peak=   -3.816 closest distance to " O   HOH Z 353 " =    2.163
peak=   -3.788 closest distance to " ND2 ASN A  45 " =    1.843
peak=   -3.783 closest distance to " CG  PHE A 283 " =    2.815
peak=   -3.771 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.761 closest distance to " O   HOH Z 311 " =    3.685
peak=   -3.757 closest distance to " O   HOH Z  52 " =    1.352
peak=   -3.756 closest distance to " CZ  PHE A  59 " =    1.599
peak=   -3.743 closest distance to " O   HOH Z 185 " =    2.320
peak=   -3.743 closest distance to " NH2AARG A 275 " =    5.400
peak=   -3.730 closest distance to " O   HOH Z  43 " =    1.534
peak=   -3.721 closest distance to " CG  ASP A 231 " =    0.791
peak=   -3.709 closest distance to " CG1 VAL A 112 " =    2.641
peak=   -3.702 closest distance to " O   HOH Z 198 " =    1.300
peak=   -3.701 closest distance to " CD2 PHE A 192 " =    2.063
peak=   -3.698 closest distance to " O   VAL A  67 " =    2.740
peak=   -3.680 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.676 closest distance to " OG  SER A  97 " =    2.219
peak=   -3.666 closest distance to " OD1 ASP A 171 " =    1.625
peak=   -3.664 closest distance to " CG2 ILE A 263 " =    2.313
peak=   -3.664 closest distance to " N   SER A 212 " =    2.025
peak=   -3.658 closest distance to " O   HOH Z 313 " =    2.002
peak=   -3.641 closest distance to " CD1 LEU A 228 " =    2.322
peak=   -3.634 closest distance to " O   PRO A 163 " =    2.085
peak=   -3.633 closest distance to " CZ  TYR A 169 " =    1.681
peak=   -3.630 closest distance to " CE2 TYR A  30 " =    2.756
peak=   -3.619 closest distance to " CB  ALA A 291 " =    2.325
peak=   -3.606 closest distance to " O   HOH Z 196 " =    2.069
peak=   -3.605 closest distance to " N   GLN A  58 " =    1.542
peak=   -3.600 closest distance to " OXT GLY A 302 " =    2.837
peak=   -3.597 closest distance to " SG ACYS A 201 " =    1.963
peak=   -3.593 closest distance to " C   ASN A 285 " =    2.495
peak=   -3.593 closest distance to " CE2 PHE A 218 " =    2.418
peak=   -3.584 closest distance to " NH1 ARG A 195 " =    2.531
peak=   -3.573 closest distance to " CB  ALA A 291 " =    2.212
peak=   -3.565 closest distance to " CG1 VAL A 250 " =    2.665
peak=   -3.562 closest distance to " O   GLY A 211 " =    1.467
peak=   -3.558 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.546 closest distance to " OG BSER A 134 " =    1.753
peak=   -3.542 closest distance to " CG  ARG A  66 " =    2.378
peak=   -3.538 closest distance to " O   HOH Z 407 " =    3.178
peak=   -3.536 closest distance to " CD1 LEU A 297 " =    2.347
peak=   -3.531 closest distance to " CB  PRO A 163 " =    2.500
peak=   -3.521 closest distance to " CG1 VAL A 197 " =    2.256
peak=   -3.514 closest distance to " C   ALA A 158 " =    1.330
peak=   -3.504 closest distance to " CB  CYS A 201 " =    2.675
peak=   -3.499 closest distance to " OD1 ASN A 148 " =    1.619
peak=   -3.478 closest distance to " O   VAL A 189 " =    2.593
peak=   -3.475 closest distance to " ND2 ASN A  45 " =    1.106
peak=   -3.474 closest distance to " NH2 ARG A  79 " =    1.630
peak=   -3.473 closest distance to " O   HOH Z  60 " =    2.611
peak=   -3.470 closest distance to " CB  ALA A  43 " =    2.504
peak=   -3.462 closest distance to " CA  ASP A 298 " =    1.084
peak=   -3.459 closest distance to " CD1 LEU A 101 " =    2.365
peak=   -3.457 closest distance to " O   HOH Z 292 " =    4.566
peak=   -3.453 closest distance to " CB  ASN A  39 " =    2.327
peak=   -3.445 closest distance to " CA  GLY A 241 " =    3.062
peak=   -3.428 closest distance to " CD2 PHE A  61 " =    2.488
peak=   -3.421 closest distance to " O   HOH Z  38 " =    1.476
peak=   -3.421 closest distance to " CD1 ILE A 239 " =    2.154
peak=   -3.416 closest distance to " CA  GLY A 203 " =    2.353
peak=   -3.404 closest distance to " CB  ASP A 132 " =    2.303
peak=   -3.396 closest distance to " N   THR A 235 " =    1.323
peak=   -3.381 closest distance to " O   HOH Z  73 " =    2.205
peak=   -3.379 closest distance to " CD2 LEU A 300 " =    2.891
peak=   -3.379 closest distance to " CE BMET A  47 " =    2.124
peak=   -3.378 closest distance to " OG  SER A  62 " =    1.591
peak=   -3.373 closest distance to " O   HOH Z 394 " =    1.414
peak=   -3.373 closest distance to " CD  ARG A 195 " =    5.226
peak=   -3.371 closest distance to " NH2 ARG A  79 " =    1.948
peak=   -3.370 closest distance to " O   LYS A 117 " =    1.728
peak=   -3.365 closest distance to " N   ALA A 226 " =    2.091
peak=   -3.345 closest distance to " C   LEU A 143 " =    1.167
peak=   -3.344 closest distance to " CG1 VAL A 230 " =    2.084
peak=   -3.342 closest distance to " OE1 GLN A  88 " =    1.251
peak=   -3.335 closest distance to " O   HOH Z 253 " =    3.925
peak=   -3.331 closest distance to " CG  TRP A 266 " =    1.826
peak=   -3.324 closest distance to " CB  ASP A 286 " =    2.110
peak=   -3.320 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.318 closest distance to " O   HOH Z 348 " =    2.251
peak=   -3.318 closest distance to " CE  MET A 105 " =    2.272
peak=   -3.317 closest distance to " CB  LEU A  83 " =    2.404
peak=   -3.314 closest distance to " O   HOH Z 377 " =    0.771
peak=   -3.311 closest distance to " C   MET A 188 " =    1.417
peak=   -3.311 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.310 closest distance to " O   HOH Z  11 " =    1.742
peak=   -3.309 closest distance to " O   HOH Z  37 " =    1.966
peak=   -3.307 closest distance to " O   HOH Z  13 " =    1.544
peak=   -3.305 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.304 closest distance to " O   HOH Z 385 " =    2.111
peak=   -3.299 closest distance to " O   HOH Z 174 " =    2.484
peak=   -3.298 closest distance to " O   HOH Z  76 " =    1.891
peak=   -3.298 closest distance to " CA  GLY A  98 " =    1.940
peak=   -3.298 closest distance to " O   HOH Z 417 " =    2.476
peak=   -3.293 closest distance to " O   HOH Z   6 " =    1.491
peak=   -3.291 closest distance to " ND2 ASN A 249 " =    2.125
peak=   -3.290 closest distance to " CB  TYR A  15 " =    2.163
peak=   -3.278 closest distance to " O   ALA A 161 " =    1.716
peak=   -3.275 closest distance to " O   ARG A 145 " =    1.630
peak=   -3.274 closest distance to " O   HOH Z 241 " =    1.302
peak=   -3.269 closest distance to " O   HOH Z 298 " =    2.578
peak=   -3.269 closest distance to " O   HOH Z 295 " =    1.527
peak=   -3.269 closest distance to " N   THR A 157 " =    1.592
peak=   -3.266 closest distance to " N   ASP A 171 " =    2.349
peak=   -3.264 closest distance to " NE2 GLN A 278 " =    1.737
peak=   -3.258 closest distance to " O   HOH Z 222 " =    1.226
peak=   -3.257 closest distance to " NH2BARG A 275 " =    1.866
peak=   -3.254 closest distance to " O   HOH Z 377 " =    1.256
peak=   -3.252 closest distance to " O   HOH Z 426 " =    1.602
peak=   -3.250 closest distance to " O   HOH Z 111 " =    2.100
peak=   -3.250 closest distance to " CE3 TRP A 274 " =    2.478
peak=   -3.249 closest distance to " CG  PHE A 283 " =    2.673
peak=   -3.249 closest distance to " NE2 GLN A 194 " =    1.739
peak=   -3.248 closest distance to " NE2 GLN A  88 " =    1.898
peak=   -3.247 closest distance to " O   HOH Z 166 " =    1.512
peak=   -3.238 closest distance to " N   PHE A  59 " =    2.103
peak=   -3.237 closest distance to " O   GLY A 196 " =    1.089
peak=   -3.232 closest distance to " CB  ASN A  69 " =    1.190
peak=   -3.226 closest distance to " CG  GLU A 152 " =    0.821
peak=   -3.224 closest distance to " OG  SER A  26 " =    1.191
peak=   -3.222 closest distance to " O   HOH Z 166 " =    1.846
peak=   -3.221 closest distance to " OD2 ASP A 171 " =    1.843
peak=   -3.219 closest distance to " CB  ALA A 248 " =    2.043
peak=   -3.214 closest distance to " O   VAL A 174 " =    2.042
peak=   -3.211 closest distance to " O   SER A 135 " =    1.494
peak=   -3.202 closest distance to " CA  GLY A 133 " =    2.049
peak=   -3.195 closest distance to " CG2 THR A 221 " =    2.238
peak=   -3.191 closest distance to " N   ALA A 248 " =    1.588
peak=   -3.190 closest distance to " CA  GLY A 241 " =    2.794
peak=   -3.187 closest distance to " O   HOH Z 298 " =    1.243
peak=   -3.186 closest distance to " OE2 GLU A   2 " =    1.772
peak=   -3.184 closest distance to " O   PHE A 218 " =    1.644
peak=   -3.184 closest distance to " O   HOH Z 322 " =    1.537
peak=   -3.178 closest distance to " O   HOH Z 114 " =    1.588
peak=   -3.176 closest distance to " O   HOH Z  93 " =    2.104
peak=   -3.175 closest distance to " SD  MET A 188 " =    2.252
peak=   -3.166 closest distance to " O   HOH Z 234 " =    4.185
peak=   -3.164 closest distance to " CD2 TYR A 293 " =    2.031
peak=   -3.163 closest distance to " ND2 ASN A  60 " =    1.398
peak=   -3.161 closest distance to " O   TRP A  70 " =    1.517
peak=   -3.161 closest distance to " O   HOH Z 148 " =    1.841
peak=   -3.159 closest distance to " CD  GLU A 236 " =    1.011
peak=   -3.158 closest distance to " CB  ALA A 248 " =    2.448
peak=   -3.158 closest distance to " CD1 ILE A 239 " =    2.545
peak=   -3.157 closest distance to " O   HOH Z 317 " =    1.573
peak=   -3.157 closest distance to " O   HOH Z  51 " =    1.346
peak=   -3.156 closest distance to " O   HOH Z 323 " =    1.310
peak=   -3.156 closest distance to " O   HOH Z 282 " =    1.185
peak=   -3.150 closest distance to " O   HOH Z 244 " =    2.078
peak=   -3.150 closest distance to " CB  ASP A 132 " =    2.372
peak=   -3.148 closest distance to " O   HOH Z 359 " =    3.102
peak=   -3.147 closest distance to " CB  CYS A 254 " =    2.415
peak=   -3.145 closest distance to " O   HOH Z 174 " =    3.047
peak=   -3.145 closest distance to " OD1 ASN A 187 " =    1.556
peak=   -3.144 closest distance to " O   HOH Z  51 " =    1.586
peak=   -3.141 closest distance to " O   HOH Z  88 " =    2.126
peak=   -3.138 closest distance to " O   ALA A  10 " =    1.664
peak=   -3.132 closest distance to " CH2 TRP A 177 " =    2.088
peak=   -3.130 closest distance to " CB  TRP A  85 " =    2.402
peak=   -3.130 closest distance to " O   HOH Z 184 " =    1.811
peak=   -3.130 closest distance to " O   MET A  40 " =    2.734
peak=   -3.126 closest distance to " CD1 ILE A 199 " =    2.525
peak=   -3.125 closest distance to " O   HOH Z 128 " =    2.569
peak=   -3.123 closest distance to " O   ALA A 292 " =    1.979
peak=   -3.118 closest distance to " O   GLN A 240 " =    2.399
peak=   -3.116 closest distance to " CD2 LEU A 237 " =    2.693
peak=   -3.111 closest distance to " O   HOH Z  44 " =    2.187
peak=   -3.107 closest distance to " CG  PRO A 163 " =    2.600
peak=   -3.104 closest distance to " O   LYS A 289 " =    2.993
peak=   -3.102 closest distance to " OD2 ASP A  50 " =    2.243
peak=   -3.100 closest distance to " O   HOH Z 281 " =    2.674
peak=   -3.094 closest distance to " CE  LYS A  76 " =    2.835
peak=   -3.070 closest distance to " O   HOH Z 266 " =    4.796
peak=   -3.064 closest distance to " CZ  PHE A  38 " =    2.199
peak=   -3.046 closest distance to " CG2 VAL A 189 " =    2.112
peak=   -3.041 closest distance to " O   HOH Z  41 " =    2.538
peak=   -3.015 closest distance to " CD  GLN A  88 " =    0.769
peak=   -3.010 closest distance to " O   HOH Z  60 " =    1.651

================= 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    :  0.2308 0.2325   5.729731e+00   5.743213e+00
   1_bss:  0.2125 0.2159   5.691481e+00   5.700456e+00
   1_xyz:  0.1371 0.1547   5.263782e+00   5.377583e+00
   1_adp:  0.1265 0.1561   5.209435e+00   5.394399e+00
   1_occ:  0.1260 0.1558   5.206357e+00   5.391658e+00
   2_bss:  0.1259 0.1545   5.205621e+00   5.388929e+00
   2_xyz:  0.1138 0.1506   5.132782e+00   5.352366e+00
   2_adp:  0.1107 0.1506   5.118036e+00   5.351012e+00
   2_occ:  0.1105 0.1506   5.117894e+00   5.351321e+00
   3_bss:  0.1105 0.1506   5.117768e+00   5.350994e+00
   3_xyz:  0.1098 0.1532   5.122588e+00   5.364564e+00
   3_adp:  0.1090 0.1541   5.121916e+00   5.369704e+00
   3_occ:  0.1089 0.1542   5.122238e+00   5.370376e+00
   4_bss:  0.1088 0.1542   5.122264e+00   5.370314e+00
   4_xyz:  0.1083 0.1555   5.123339e+00   5.377632e+00
   4_adp:  0.1080 0.1559   5.122800e+00   5.379046e+00
   4_occ:  0.1080 0.1560   5.123157e+00   5.379745e+00
   5_bss:  0.1079 0.1560   5.123228e+00   5.379748e+00
   5_xyz:  0.1060 0.1563   5.114558e+00   5.379411e+00
   5_adp:  0.1067 0.1555   5.114377e+00   5.375137e+00
   5_occ:  0.1067 0.1555   5.114399e+00   5.375304e+00
   5_bss:  0.1066 0.1556   5.114505e+00   5.375354e+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:  0.319  49.905  -1.371  -2.894  -1.476  -0.000  -0.000  -0.000
   1_xyz:  0.319  49.905  -1.371  -2.894  -1.476  -0.000  -0.000  -0.000
   1_adp:  0.319  49.905  -1.371  -2.894  -1.476  -0.000  -0.000  -0.000
   1_occ:  0.319  49.905  -1.371  -2.894  -1.476  -0.000  -0.000  -0.000
   2_bss:  0.328  51.060  -2.428  -2.913  -1.780  -0.000  -0.000  -0.000
   2_xyz:  0.328  51.060  -2.428  -2.913  -1.780  -0.000  -0.000  -0.000
   2_adp:  0.328  51.060  -2.428  -2.913  -1.780  -0.000  -0.000  -0.000
   2_occ:  0.328  51.060  -2.428  -2.913  -1.780  -0.000  -0.000  -0.000
   3_bss:  0.326  51.060  -2.456  -2.606  -1.611  -0.000  -0.000  -0.000
   3_xyz:  0.326  51.060  -2.456  -2.606  -1.611  -0.000  -0.000  -0.000
   3_adp:  0.326  51.060  -2.456  -2.606  -1.611  -0.000  -0.000  -0.000
   3_occ:  0.326  51.060  -2.456  -2.606  -1.611  -0.000  -0.000  -0.000
   4_bss:  0.323  51.060  -2.332  -2.386  -1.435  -0.000  -0.000  -0.000
   4_xyz:  0.323  51.060  -2.332  -2.386  -1.435  -0.000  -0.000  -0.000
   4_adp:  0.323  51.060  -2.332  -2.386  -1.435  -0.000  -0.000  -0.000
   4_occ:  0.323  51.060  -2.332  -2.386  -1.435  -0.000  -0.000  -0.000
   5_bss:  0.322  51.060  -2.162  -2.181  -1.244  -0.000  -0.000  -0.000
   5_xyz:  0.322  51.060  -2.162  -2.181  -1.244  -0.000  -0.000  -0.000
   5_adp:  0.322  51.060  -2.162  -2.181  -1.244  -0.000  -0.000  -0.000
   5_occ:  0.322  51.060  -2.162  -2.181  -1.244  -0.000  -0.000  -0.000
   5_bss:  0.323  51.017  -1.987  -1.988  -1.046  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  21.899 0.8473  1.0008    15025.736
   1_bss:  20.585 0.8585  0.9507    12312.744
   1_xyz:  13.560 0.9192  0.9877     6305.848
   1_adp:  13.940 0.9159  0.9872     6430.070
   1_occ:  13.883 0.9163  0.9871     6364.772
   2_bss:  13.833 0.9167  0.9708     6315.535
   2_xyz:  13.108 0.9224  0.9735     5911.596
   2_adp:  13.089 0.9224  0.9708     5842.613
   2_occ:  13.095 0.9224  0.9707     5846.086
   3_bss:  13.095 0.9224  0.9757     5841.714
   3_xyz:  13.322 0.9207  0.9742     6017.031
   3_adp:  13.439 0.9198  0.9687     6066.358
   3_occ:  13.451 0.9197  0.9686     6073.954
   4_bss:  13.454 0.9197  0.9746     6072.923
   4_xyz:  13.582 0.9187  0.9741     6168.354
   4_adp:  13.623 0.9183  0.9682     6180.975
   4_occ:  13.636 0.9182  0.9680     6187.962
   5_bss:  13.638 0.9182  0.9746     6188.236
   5_xyz:  13.637 0.9182  0.9746     6193.402
   5_adp:  13.541 0.9189  0.9698     6159.153
   5_occ:  13.546 0.9189  0.9697     6159.562
   5_bss:  13.549 0.9188  0.9749     6160.812
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6012e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6012e-01
   1_xyz:   0.984  0.007  0.073 15.016  0.004  4.116   5.7177e-02
   1_adp:   0.984  0.007  0.073 15.016  0.004  4.116   5.7177e-02
   1_occ:   0.984  0.007  0.073 15.016  0.004  4.116   5.7177e-02
   2_bss:   0.984  0.007  0.073 15.016  0.004  4.116   5.7177e-02
   2_xyz:   1.008  0.008  0.078 14.966  0.004  4.120   6.2489e-02
   2_adp:   1.008  0.008  0.078 14.966  0.004  4.120   6.2489e-02
   2_occ:   1.008  0.008  0.078 14.966  0.004  4.120   6.2489e-02
   3_bss:   1.008  0.008  0.078 14.966  0.004  4.120   6.2489e-02
   3_xyz:   0.966  0.007  0.075 14.852  0.004  4.121   5.8010e-02
   3_adp:   0.966  0.007  0.075 14.852  0.004  4.121   5.8010e-02
   3_occ:   0.966  0.007  0.075 14.852  0.004  4.121   5.8010e-02
   4_bss:   0.966  0.007  0.075 14.852  0.004  4.121   5.8010e-02
   4_xyz:   0.969  0.007  0.075 14.806  0.004  4.122   5.8399e-02
   4_adp:   0.969  0.007  0.075 14.806  0.004  4.122   5.8399e-02
   4_occ:   0.969  0.007  0.075 14.806  0.004  4.122   5.8399e-02
   5_bss:   0.969  0.007  0.075 14.806  0.004  4.122   5.8399e-02
   5_xyz:   1.038  0.009  0.080 14.951  0.004  4.121   6.6599e-02
   5_adp:   1.038  0.009  0.080 14.951  0.004  4.121   6.6599e-02
   5_occ:   1.038  0.009  0.080 14.951  0.004  4.121   6.6599e-02
   5_bss:   1.038  0.009  0.080 14.951  0.004  4.121   6.6599e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4150e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4150e-01
   1_xyz:   8.252  0.038  0.254 85.008  0.034  2.341   4.6292e-02
   1_adp:   8.252  0.038  0.254 85.008  0.034  2.341   4.6292e-02
   1_occ:   8.252  0.038  0.254 85.008  0.034  2.341   4.6292e-02
   2_bss:   8.252  0.038  0.254 85.008  0.034  2.341   4.6292e-02
   2_xyz:   7.326  0.039  0.244 84.233  0.039  2.318   4.4650e-02
   2_adp:   7.326  0.039  0.244 84.233  0.039  2.318   4.4650e-02
   2_occ:   7.326  0.039  0.244 84.233  0.039  2.318   4.4650e-02
   3_bss:   7.326  0.039  0.244 84.233  0.039  2.318   4.4650e-02
   3_xyz:   7.235  0.040  0.228 83.389  0.036  2.342   3.9631e-02
   3_adp:   7.235  0.040  0.228 83.389  0.036  2.342   3.9631e-02
   3_occ:   7.235  0.040  0.228 83.389  0.036  2.342   3.9631e-02
   4_bss:   7.235  0.040  0.228 83.389  0.036  2.342   3.9631e-02
   4_xyz:   7.042  0.039  0.225 83.571  0.035  2.345   4.0452e-02
   4_adp:   7.042  0.039  0.225 83.571  0.035  2.345   4.0452e-02
   4_occ:   7.042  0.039  0.225 83.571  0.035  2.345   4.0452e-02
   5_bss:   7.042  0.039  0.225 83.571  0.035  2.345   4.0452e-02
   5_xyz:   6.899  0.046  0.250 83.195  0.037  2.304   5.1177e-02
   5_adp:   6.899  0.046  0.250 83.195  0.037  2.304   5.1177e-02
   5_occ:   6.899  0.046  0.250 83.195  0.037  2.304   5.1177e-02
   5_bss:   6.899  0.046  0.250 83.195  0.037  2.304   5.1177e-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:  63.41   0.00  16.46  63.41   0.00  12.68  62.78   6.83  37.06
   1_occ:  63.41   0.00  16.46  63.41   0.00  12.68  62.78   6.83  37.06
   2_bss:  63.41   0.00  16.46  63.41   0.00  12.68  62.78   6.83  37.06
   2_xyz:  63.41   0.00  16.46  63.41   0.00  12.68  62.78   6.83  37.06
   2_adp:  70.94   1.94  16.70  70.94   1.94  12.92  66.06   5.22  37.31
   2_occ:  70.94   1.94  16.70  70.94   1.94  12.92  66.06   5.22  37.31
   3_bss:  70.94   1.94  16.70  70.94   1.94  12.92  66.06   5.22  37.31
   3_xyz:  70.94   1.94  16.70  70.94   1.94  12.92  66.06   5.22  37.31
   3_adp:  75.41   1.15  16.76  75.41   1.15  12.87  67.91   5.71  37.94
   3_occ:  75.41   1.15  16.76  75.41   1.15  12.87  67.91   5.71  37.94
   4_bss:  75.41   1.15  16.76  75.41   1.15  12.87  67.91   5.71  37.94
   4_xyz:  75.41   1.15  16.76  75.41   1.15  12.87  67.91   5.71  37.94
   4_adp:  80.09   0.78  16.72  80.09   0.78  12.76  70.77   6.23  38.27
   4_occ:  80.09   0.78  16.72  80.09   0.78  12.76  70.77   6.23  38.27
   5_bss:  80.09   0.78  16.72  80.09   0.78  12.76  70.77   6.23  38.27
   5_xyz:  80.09   0.78  16.72  80.09   0.78  12.76  70.77   6.23  38.27
   5_adp:  79.57   1.22  16.33  79.57   1.22  12.54  70.54   6.05  37.00
   5_occ:  79.57   1.22  16.33  79.57   1.22  12.54  70.54   6.05  37.00
   5_bss:  79.53   1.18  16.29  79.53   1.18  12.49  70.50   6.01  36.96
------------------------------------------------------------------------
 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:    0.688    0.003    0.188
   1_adp:    0.688    0.003    0.188
   1_occ:    0.688    0.003    0.188
   2_bss:    0.688    0.003    0.188
   2_xyz:    0.573    0.009    0.211
   2_adp:    0.573    0.009    0.211
   2_occ:    0.573    0.009    0.211
   3_bss:    0.573    0.009    0.211
   3_xyz:    0.746    0.019    0.222
   3_adp:    0.746    0.019    0.222
   3_occ:    0.746    0.019    0.222
   4_bss:    0.746    0.019    0.222
   4_xyz:    0.878    0.012    0.229
   4_adp:    0.878    0.012    0.229
   4_occ:    0.878    0.012    0.229
   5_bss:    0.878    0.012    0.229
   5_xyz:    0.937    0.017    0.231
   5_adp:    0.937    0.017    0.231
   5_occ:    0.937    0.017    0.231
   5_bss:    0.937    0.017    0.231
------------------------------------------------------------------------

CPU time actual refinement: 275.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_906/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_906/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_906/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_906/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_906/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 275.60 
  Macro-tasks:
    bulk solvent and scale       = 32.47  
    individual site refinement   = 118.89 
    weights calculation          = 24.19  
    collect and process          = 5.44   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 181.07 
  Micro-tasks:
    mask                            = 0.48   
    f_calc                          = 87.45  
    alpha_beta                      = 6.78   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 97.27  
    fmodel                         = 5.37   
    r_factors                      = 0.11   
    phase_errors                   = 9.26   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 207.87 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 3.809 micro seconds
Total CPU time: 4.79 minutes
from_scatterers_fft:    676 calls, 87.06 s
gradients_fft:          621 calls, 84.54 s

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

# Date 2008-01-16 Time 05:56:22 PST -0800 (1200491782.51 s)
Start R-work = 0.2308, R-free = 0.2325 (no bulk solvent and anisotropic scale)
Final R-work = 0.1306, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.2125, R-free = 0.2159
Final R-work = 0.1066, R-free = 0.1556