# Date 2008-01-16 Time 06:14:52 PST -0800 (1200492892.21 s)
#phil __OFF__

Command line arguments: "../1066.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10278
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1066

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.6339, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.03017
Completeness in resolution range: 0.976959
Completeness with d_max=infinity: 0.97385

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   2.0302

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.03017
Completeness in resolution range: 0.976959
Completeness with d_max=infinity: 0.97385

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2595 -  4.3434 [2110/2133]  1897   213  10.1%
  bin  2:  4.3434 -  3.4607 [2025/2045]  1824   201   9.9%
  bin  3:  3.4607 -  3.0271 [2002/2021]  1804   198   9.9%
  bin  4:  3.0271 -  2.7521 [1967/1997]  1767   200  10.2%
  bin  5:  2.7521 -  2.5558 [1976/1995]  1778   198  10.0%
  bin  6:  2.5558 -  2.4058 [1953/1978]  1756   197  10.1%
  bin  7:  2.4058 -  2.2857 [1942/1970]  1751   191   9.8%
  bin  8:  2.2857 -  2.1865 [1938/1974]  1745   193  10.0%
  bin  9:  2.1865 -  2.1026 [1938/1980]  1742   196  10.1%
  bin 10:  2.1026 -  2.0302 [1738/1958]  1566   172   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1066/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2137
        3.04 -     3.66: 4553
        3.66 -     4.28: 8782
        4.28 -     4.90: 12065
  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 "  1.825 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.964 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.005 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.005 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27549 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_1066/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1066/model_refine_001.geo

CPU time processing inputs: 9.84


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.63395 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4632   r_free= 0.4581   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.269020                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8441 0.99   1374  152 0.3570 0.3570      6.5219      6.4481|
|  2:  4.8441 -  3.8655 0.99   1308  149 0.3918 0.4048      6.8076      6.8799|
|  3:  3.8655 -  3.3829 0.99   1294  142 0.4317 0.3775      6.6786      6.6164|
|  4:  3.3829 -  3.0764 0.99   1286  139 0.4471 0.4514      6.5295      6.4537|
|  5:  3.0764 -  2.8574 0.99   1264  145 0.4826 0.4550      6.3615      6.3703|
|  6:  2.8574 -  2.6899 0.99   1279  138 0.4873 0.5060      6.2747      6.2055|
|  7:  2.6899 -  2.5558 0.99   1265  145 0.4988 0.5037      6.2404      6.1832|
|  8:  2.5558 -  2.4451 0.98   1257  135 0.5113 0.4759      6.1905      6.1834|
|  9:  2.4451 -  2.3513 0.98   1249  143 0.5131 0.5044      6.1152      6.1599|
| 10:  2.3513 -  2.2704 1.00   1246  138 0.5290 0.5017      6.1208      6.1297|
| 11:  2.2704 -  2.1996 0.97   1262  139 0.5264 0.5529      6.0405      6.0929|
| 12:  2.1996 -  2.1369 0.98   1237  139 0.5219 0.5386      5.9909       6.033|
| 13:  2.1369 -  2.0808 1.00   1257  138 0.5282 0.5152      5.9069      5.8677|
| 14:  2.0808 -  2.0302 0.84   1052  117 0.5205 0.5430      5.8492      5.7768|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8441  1374   152  0.74  30.78   0.82     0.77      59318.34|
|  2:  4.8441 -  3.8655  1308   149  0.74  31.66   0.89     0.81      91682.47|
|  3:  3.8655 -  3.3829  1294   142  0.65  39.98   0.88     0.78      97940.98|
|  4:  3.3829 -  3.0764  1286   139  0.56  47.39   0.89     0.68      90754.75|
|  5:  3.0764 -  2.8574  1264   145  0.46  54.98   0.88     0.60      73555.11|
|  6:  2.8574 -  2.6899  1279   138  0.42  58.27   0.87     0.54      68019.32|
|  7:  2.6899 -  2.5558  1265   145  0.39  60.69   0.88     0.52      63210.40|
|  8:  2.5558 -  2.4451  1257   135  0.37  62.02   0.87     0.50      58885.37|
|  9:  2.4451 -  2.3513  1249   143  0.34  64.36   0.89     0.49      55919.18|
| 10:  2.3513 -  2.2704  1246   138  0.33  65.28   0.91     0.47      51311.57|
| 11:  2.2704 -  2.1996  1262   139  0.31  67.11   0.88     0.45      49263.58|
| 12:  2.1996 -  2.1369  1237   139  0.31  66.72   0.88     0.45      44608.90|
| 13:  2.1369 -  2.0808  1257   138  0.31  66.97   0.88     0.45      38005.49|
| 14:  2.0808 -  2.0302  1052   117  0.34  64.53   0.89     0.45      29953.20|
|alpha:            min =        0.45 max =            0.81 mean =         0.57|
|beta:             min =    29953.20 max =        97940.98 mean =     62917.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.37|
|phase err.(test): min =        0.00 max =           90.00 mean =        55.53|
|-----------------------------------------------------------------------------|

============================== 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 = 9.090456              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.761   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.601391              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.933   (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:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      172 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1965 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1802 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2751 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4515 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4267 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5475 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6590 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| 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 |       0.170 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4632   r_free= 0.4581   ksol= 0.00   Bsol= 0.00   scale= 0.874    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.269020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4559   r_free= 0.4521   ksol= 0.30   Bsol= 80.00   scale= 0.927   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,1.25,4.32,0.00,0.00,0.00); trace/3= 1.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.262330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.865170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.415   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.336188              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.560   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4559      final r-factor (work) = 0.3452          |
| start r-factor (free) = 0.4521      final r-factor (free) = 0.3695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7869 = 7.87 * 0.50 * 6.2609 + 1.00 * 0.1653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2539 = 7.87 * 0.50 * 6.1359 + 1.00 * 0.1241                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3452      final r-factor (work) = 0.3103          |
| start r-factor (free) = 0.3695      final r-factor (free) = 0.3792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2047 = 1.34 * 1.00 * 6.1359 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0456 = 1.34 * 1.00 * 6.0049 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.40  19.33    None  None   None       |
|    all(noH): 2823   0      0.00    123.40  19.33    None  None   None       |
|    Sol.    : 438    0      0.00    123.40  42.49    None  None   None       |
|    Mac.    : 2385   0      0.00    89.90   15.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.340: 1235   |   5:    61.702 -  74.042:   59        |
|      1:    12.340 -  24.681:  839   |   6:    74.042 -  86.383:   30        |
|      2:    24.681 -  37.021:  375   |   7:    86.383 -  98.723:   11        |
|      3:    37.021 -  49.362:  186   |   8:    98.723 - 111.063:    2        |
|      4:    49.362 -  61.702:   85   |   9:   111.063 - 123.404:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3103 r_free = 0.3792             target_work(ml) = 6.011         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3100 r_free = 0.3786             target_work(ml) = 6.011         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3100   r_free= 0.3786   ksol= 0.30   Bsol= 80.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,1.25,4.32,0.00,0.00,0.00); trace/3= 1.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.010879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3094   r_free= 0.3778   ksol= 0.33   Bsol= 84.73   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.75,2.37,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.011607                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.519034              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.324   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445192              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.821  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3094      final r-factor (work) = 0.2383          |
| start r-factor (free) = 0.3778      final r-factor (free) = 0.2975          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6977 = 6.52 * 0.50 * 6.0051 + 1.00 * 0.1241                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3686 = 6.52 * 0.50 * 5.9159 + 1.00 * 0.0855                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2383      final r-factor (work) = 0.2295          |
| start r-factor (free) = 0.2975      final r-factor (free) = 0.2857          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6557 = 0.45 * 1.00 * 5.9159 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6650 = 0.45 * 1.00 * 5.7759 + 1.00 * 0.0936                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.40  19.28    None  None   None       |
|    all(noH): 2823   0      0.00    123.40  19.28    None  None   None       |
|    Sol.    : 438    0      0.00    123.40  42.69    None  None   None       |
|    Mac.    : 2385   0      0.00    89.78   14.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.340: 1279   |   5:    61.702 -  74.042:   58        |
|      1:    12.340 -  24.681:  850   |   6:    74.042 -  86.382:   28        |
|      2:    24.681 -  37.021:  327   |   7:    86.382 -  98.723:   10        |
|      3:    37.021 -  49.361:  177   |   8:    98.723 - 111.063:    2        |
|      4:    49.361 -  61.702:   91   |   9:   111.063 - 123.403:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2295 r_free = 0.2857             target_work(ml) = 5.758         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2293 r_free = 0.2853             target_work(ml) = 5.757         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2293   r_free= 0.2853   ksol= 0.33   Bsol= 84.73   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.75,2.37,0.00,0.00,0.00); trace/3= 0.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.756790                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2292   r_free= 0.2853   ksol= 0.33   Bsol= 80.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-0.34,0.87,-0.00,0.00,0.00); trace/3= -0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.756923                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.017256              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.347  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.893688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.988   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2292      final r-factor (work) = 0.1946          |
| start r-factor (free) = 0.2853      final r-factor (free) = 0.2424          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7941 = 3.02 * 0.50 * 5.7725 + 1.00 * 0.0855                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6377 = 3.02 * 0.50 * 5.6848 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1946      final r-factor (work) = 0.1728          |
| start r-factor (free) = 0.2424      final r-factor (free) = 0.2278          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7875 = 1.89 * 1.00 * 5.6848 + 1.00 * 0.0223                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5271 = 1.89 * 1.00 * 5.5500 + 1.00 * 0.0172                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.02  19.22    None  None   None       |
|    all(noH): 2823   0      0.00    125.02  19.22    None  None   None       |
|    Sol.    : 438    0      3.96    125.02  48.58    None  None   None       |
|    Mac.    : 2385   0      0.00    105.71  13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.502: 1412   |   5:    62.510 -  75.012:   90        |
|      1:    12.502 -  25.004:  820   |   6:    75.012 -  87.514:   43        |
|      2:    25.004 -  37.506:  207   |   7:    87.514 - 100.016:   14        |
|      3:    37.506 -  50.008:  133   |   8:   100.016 - 112.518:    7        |
|      4:    50.008 -  62.510:   95   |   9:   112.518 - 125.020:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1728 r_free = 0.2278             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1728 r_free = 0.2276             target_work(ml) = 5.520         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1728   r_free= 0.2276   ksol= 0.33   Bsol= 80.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-0.34,0.87,-0.00,0.00,0.00); trace/3= -0.28                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.519746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2275   ksol= 0.34   Bsol= 98.38   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-1.06,0.23,-0.00,0.00,0.00); trace/3= -0.87                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.520147                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.334271              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.355339              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.754  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1731      final r-factor (work) = 0.1408          |
| start r-factor (free) = 0.2275      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0957 = 4.33 * 0.50 * 5.5531 + 1.00 * 0.0615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8629 = 4.33 * 0.50 * 5.4360 + 1.00 * 0.0824                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1408      final r-factor (work) = 0.1340          |
| start r-factor (free) = 0.1939      final r-factor (free) = 0.1816          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9487 = 0.36 * 1.00 * 5.4360 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9076 = 0.36 * 1.00 * 5.3312 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.84  18.15    None  None   None       |
|    all(noH): 2823   0      0.00    122.84  18.15    None  None   None       |
|    Sol.    : 438    0      4.67    122.84  46.49    None  None   None       |
|    Mac.    : 2385   0      0.00    102.95  12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.284: 1523   |   5:    61.418 -  73.702:   72        |
|      1:    12.284 -  24.567:  765   |   6:    73.702 -  85.985:   38        |
|      2:    24.567 -  36.851:  168   |   7:    85.985 -  98.269:   14        |
|      3:    36.851 -  49.134:  129   |   8:    98.269 - 110.552:    6        |
|      4:    49.134 -  61.418:  106   |   9:   110.552 - 122.836:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1340 r_free = 0.1816             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1338 r_free = 0.1815             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1815   ksol= 0.34   Bsol= 98.38   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-1.06,0.23,-0.00,0.00,0.00); trace/3= -0.87                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.294019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1338   r_free= 0.1814   ksol= 0.33   Bsol= 88.37   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.16,0.24,-0.00,0.00,0.00); trace/3= -0.84                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.294250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.392119              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.044  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.048278              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.662  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1338      final r-factor (work) = 0.1284          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4583 = 2.39 * 0.50 * 5.3308 + 1.00 * 0.0824                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3812 = 2.39 * 0.50 * 5.2780 + 1.00 * 0.0684                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1750      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8238 = 2.05 * 1.00 * 5.2780 + 1.00 * 0.0130                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7624 = 2.05 * 1.00 * 5.2474 + 1.00 * 0.0142                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.64  17.81    None  None   None       |
|    all(noH): 2823   0      0.00    126.64  17.81    None  None   None       |
|    Sol.    : 438    0      2.72    126.64  46.10    None  None   None       |
|    Mac.    : 2385   0      0.00    105.67  12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.664: 1619   |   5:    63.318 -  75.982:   62        |
|      1:    12.664 -  25.327:  694   |   6:    75.982 -  88.645:   33        |
|      2:    25.327 -  37.991:  160   |   7:    88.645 - 101.309:   13        |
|      3:    37.991 -  50.655:  135   |   8:   101.309 - 113.973:    7        |
|      4:    50.655 -  63.318:   98   |   9:   113.973 - 126.636:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1759             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1759             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1759   ksol= 0.33   Bsol= 88.37   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.16,0.24,-0.00,0.00,0.00); trace/3= -0.84                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247673                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8441 0.99   1374  152 0.1037 0.1372      5.4237      5.5632|
|  2:  4.8441 -  3.8655 0.99   1308  149 0.0862 0.1107      5.4552      5.6546|
|  3:  3.8655 -  3.3829 0.99   1294  142 0.1141 0.1528      5.5395       5.887|
|  4:  3.3829 -  3.0764 0.99   1286  139 0.1338 0.1855      5.5525      5.7391|
|  5:  3.0764 -  2.8574 0.99   1264  145 0.1565 0.1970        5.48      5.6516|
|  6:  2.8574 -  2.6899 0.99   1279  138 0.1429 0.2273      5.3569      5.6469|
|  7:  2.6899 -  2.5558 0.99   1265  145 0.1460 0.1878      5.2986      5.4695|
|  8:  2.5558 -  2.4451 0.98   1257  135 0.1420 0.1922      5.2312        5.47|
|  9:  2.4451 -  2.3513 0.98   1249  143 0.1347 0.2058      5.1422      5.3941|
| 10:  2.3513 -  2.2704 1.00   1246  138 0.1298 0.1895      5.0875      5.3102|
| 11:  2.2704 -  2.1996 0.97   1262  139 0.1319 0.1853      5.0584      5.2758|
| 12:  2.1996 -  2.1369 0.98   1237  139 0.1318 0.2039      5.0008      5.3654|
| 13:  2.1369 -  2.0808 1.00   1257  138 0.1254 0.1935      4.9209      5.1646|
| 14:  2.0808 -  2.0302 0.84   1052  117 0.1193 0.1999      4.7974      5.0859|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8441  1374   152  0.93   9.86   0.95     0.93       8000.45|
|  2:  4.8441 -  3.8655  1308   149  0.95   8.28   0.99     0.98       9450.08|
|  3:  3.8655 -  3.3829  1294   142  0.93  11.81   1.02     1.01      11401.32|
|  4:  3.3829 -  3.0764  1286   139  0.91  15.32   1.00     0.98      12549.32|
|  5:  3.0764 -  2.8574  1264   145  0.88  18.44   1.00     0.98      11172.84|
|  6:  2.8574 -  2.6899  1279   138  0.88  18.46   0.98     0.95       9399.55|
|  7:  2.6899 -  2.5558  1265   145  0.88  18.40   0.99     0.95       8187.06|
|  8:  2.5558 -  2.4451  1257   135  0.89  17.58   0.98     0.94       6950.50|
|  9:  2.4451 -  2.3513  1249   143  0.89  17.46   0.99     0.94       6205.68|
| 10:  2.3513 -  2.2704  1246   138  0.89  17.11   0.98     0.92       5256.26|
| 11:  2.2704 -  2.1996  1262   139  0.88  18.04   0.98     0.92       5325.10|
| 12:  2.1996 -  2.1369  1237   139  0.89  18.01   0.99     0.97       5032.01|
| 13:  2.1369 -  2.0808  1257   138  0.88  18.19   0.97     0.94       4405.99|
| 14:  2.0808 -  2.0302  1052   117  0.90  16.68   0.94     0.89       3268.83|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     3268.83 max =        12549.32 mean =      7697.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.90|
|phase err.(test): min =        0.00 max =           89.50 mean =        15.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1757   ksol= 0.33   Bsol= 81.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.96,0.44,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247595                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1757   ksol= 0.33   Bsol= 81.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.96,0.44,-0.00,0.00,0.00); trace/3= -0.61                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247595                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8441 0.99   1374  152 0.1035 0.1370      5.4209      5.5626|
|  2:  4.8441 -  3.8655 0.99   1308  149 0.0860 0.1104      5.4537      5.6518|
|  3:  3.8655 -  3.3829 0.99   1294  142 0.1141 0.1529      5.5389      5.8876|
|  4:  3.3829 -  3.0764 0.99   1286  139 0.1340 0.1856      5.5538      5.7398|
|  5:  3.0764 -  2.8574 0.99   1264  145 0.1566 0.1972      5.4809      5.6524|
|  6:  2.8574 -  2.6899 0.99   1279  138 0.1429 0.2274      5.3575      5.6475|
|  7:  2.6899 -  2.5558 0.99   1265  145 0.1461 0.1879      5.2992      5.4701|
|  8:  2.5558 -  2.4451 0.98   1257  135 0.1421 0.1922      5.2317      5.4698|
|  9:  2.4451 -  2.3513 0.98   1249  143 0.1346 0.2057      5.1422       5.394|
| 10:  2.3513 -  2.2704 1.00   1246  138 0.1298 0.1897      5.0876      5.3113|
| 11:  2.2704 -  2.1996 0.97   1262  139 0.1319 0.1850      5.0583      5.2753|
| 12:  2.1996 -  2.1369 0.98   1237  139 0.1318 0.2037      5.0007      5.3648|
| 13:  2.1369 -  2.0808 1.00   1257  138 0.1254 0.1937      4.9209      5.1648|
| 14:  2.0808 -  2.0302 0.84   1052  117 0.1193 0.2000      4.7976       5.086|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2595 -  4.8441  1374   152  0.93   9.85   0.96     0.93       7977.68|
|  2:  4.8441 -  3.8655  1308   149  0.95   8.26   1.00     0.98       9419.03|
|  3:  3.8655 -  3.3829  1294   142  0.93  11.79   1.02     1.02      11368.04|
|  4:  3.3829 -  3.0764  1286   139  0.91  15.34   1.01     0.98      12563.43|
|  5:  3.0764 -  2.8574  1264   145  0.88  18.44   1.01     0.99      11187.48|
|  6:  2.8574 -  2.6899  1279   138  0.88  18.47   0.98     0.96       9411.88|
|  7:  2.6899 -  2.5558  1265   145  0.88  18.41   0.99     0.96       8194.88|
|  8:  2.5558 -  2.4451  1257   135  0.89  17.60   0.99     0.95       6953.27|
|  9:  2.4451 -  2.3513  1249   143  0.89  17.47   1.00     0.95       6210.05|
| 10:  2.3513 -  2.2704  1246   138  0.89  17.11   0.99     0.93       5254.51|
| 11:  2.2704 -  2.1996  1262   139  0.88  18.04   0.99     0.93       5324.77|
| 12:  2.1996 -  2.1369  1237   139  0.89  18.01   1.00     0.98       5031.15|
| 13:  2.1369 -  2.0808  1257   138  0.88  18.19   0.98     0.95       4406.00|
| 14:  2.0808 -  2.0302  1052   117  0.90  16.67   0.95     0.90       3267.95|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3267.95 max =        12563.43 mean =      7694.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.90|
|phase err.(test): min =        0.00 max =           89.48 mean =        15.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.521)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.64  17.82    None  None   None       |
|    all(noH): 2823   0      0.00    126.64  17.82    None  None   None       |
|    Sol.    : 438    0      2.72    126.64  46.10    None  None   None       |
|    Mac.    : 2385   0      0.00    105.67  12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  12.667: 1619   |   5:    63.321 -  75.985:   62        |
|      1:    12.667 -  25.330:  694   |   6:    75.985 -  88.648:   33        |
|      2:    25.330 -  37.994:  160   |   7:    88.648 - 101.312:   13        |
|      3:    37.994 -  50.657:  135   |   8:   101.312 - 113.976:    7        |
|      4:    50.657 -  63.321:   98   |   9:   113.976 - 126.639:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.570 - 4.814
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 322
   mapped sites are within: 0.715 - 4.814

peak=    5.818 closest distance to " O   HOH Z 210 " =    1.216
peak=    5.618 closest distance to " CB  GLN A 223 " =    1.455
peak=    4.982 closest distance to " CZ  PHE A 218 " =    1.150
peak=    4.916 closest distance to " CG  PRO A  54 " =    1.403
peak=    4.896 closest distance to " CB  ARG A 190 " =    1.564
peak=    4.710 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.691 closest distance to " O   HOH Z 369 " =    2.182
peak=    4.669 closest distance to " CB  SER A  63 " =    1.248
peak=    4.628 closest distance to " O   HOH Z 232 " =    2.214
peak=    4.614 closest distance to " CD  ARG A 269 " =    0.941
peak=    4.602 closest distance to " O   HOH Z 412 " =    3.757
peak=    4.467 closest distance to " CA  ALA A  51 " =    0.953
peak=    4.450 closest distance to " CB  GLN A 183 " =    1.278
peak=    4.405 closest distance to " O   HOH Z 425 " =    1.492
peak=    4.356 closest distance to " O   HOH Z  49 " =    1.381
peak=    4.353 closest distance to " CZ3 TRP A 266 " =    1.181
peak=    4.339 closest distance to " CB  VAL A 202 " =    1.571
peak=    4.339 closest distance to " CA  TYR A  30 " =    0.980
peak=    4.311 closest distance to " O   PRO A 198 " =    1.575
peak=    4.310 closest distance to " CZ  PHE A  38 " =    1.272
peak=    4.288 closest distance to " O   HOH Z 207 " =    1.314
peak=    4.288 closest distance to " O   HOH Z 113 " =    1.984
peak=    4.284 closest distance to " O   HOH Z 368 " =    2.178
peak=    4.268 closest distance to " OE1 GLN A  88 " =    0.840
peak=    4.239 closest distance to " O   HOH Z  54 " =    1.065
peak=    4.172 closest distance to " CA  ARG A 195 " =    1.181
peak=    4.140 closest distance to " CD2 TRP A 179 " =    1.271
peak=    4.133 closest distance to " O   HOH Z 189 " =    2.927
peak=    4.118 closest distance to " CG  PRO A 213 " =    1.183
peak=    4.116 closest distance to " CA  ARG A  36 " =    1.128
peak=    4.113 closest distance to " CA  GLU A 152 " =    0.906
peak=    4.110 closest distance to " O   HOH Z 214 " =    1.396
peak=    4.090 closest distance to " O   HOH Z 287 " =    1.856
peak=    4.083 closest distance to " CG  ARG A 138 " =    1.299
peak=    4.076 closest distance to " CB  GLU A 277 " =    3.876
peak=    4.072 closest distance to " CG  PRO A 243 " =    1.140
peak=    4.059 closest distance to " CB  GLU A 128 " =    1.036
peak=    4.057 closest distance to " CB  ARG A 275 " =    0.994
peak=    4.052 closest distance to " O   HOH Z 248 " =    1.661
peak=    4.038 closest distance to " CA  ALA A 160 " =    0.974
peak=    4.038 closest distance to " CB  TRP A 266 " =    1.149
peak=    4.036 closest distance to " O   HOH Z 298 " =    2.139
peak=    4.005 closest distance to " O   ASN A  74 " =    1.605
peak=    3.972 closest distance to " O   HOH Z 126 " =    1.658
peak=    3.958 closest distance to " CA  VAL A 125 " =    1.344
peak=    3.956 closest distance to " O   HOH Z 176 " =    1.722
peak=    3.953 closest distance to " CB  VAL A 265 " =    1.307
peak=    3.949 closest distance to " CB  ASN A  39 " =    0.902
peak=    3.944 closest distance to " CG2 THR A 221 " =    1.005
peak=    3.939 closest distance to " CB  ASP A 124 " =    0.860
peak=    3.929 closest distance to " O   HOH Z 234 " =    4.024
peak=    3.926 closest distance to " CD1 LEU A  96 " =    0.809
peak=    3.924 closest distance to " CA  ALA A 154 " =    1.051
peak=    3.921 closest distance to " O   HOH Z  19 " =    2.123
peak=    3.881 closest distance to " CD  ARG A  66 " =    2.571
peak=    3.865 closest distance to " O   TYR A 116 " =    1.387
peak=    3.856 closest distance to " O   HOH Z 346 " =    1.698
peak=    3.856 closest distance to " O   HOH Z 427 " =    3.238
peak=    3.829 closest distance to " CD  LYS A 166 " =    1.439
peak=    3.821 closest distance to " O   HOH Z 402 " =    1.480
peak=    3.807 closest distance to " CB  SER A  62 " =    0.862
peak=    3.802 closest distance to " O   HOH Z  80 " =    1.988
peak=    3.801 closest distance to " ND2 ASN A 187 " =    1.481
peak=    3.801 closest distance to " CG AARG A 275 " =    1.265
peak=    3.799 closest distance to " NH1AARG A 145 " =    1.262
peak=    3.787 closest distance to " CG2AVAL A 121 " =    2.149
peak=    3.777 closest distance to " O   HOH Z 406 " =    1.673
peak=    3.774 closest distance to " O   HOH Z 214 " =    2.384
peak=    3.770 closest distance to " N   HIS A 108 " =    1.847
peak=    3.768 closest distance to " NE2 GLN A  11 " =    1.074
peak=    3.763 closest distance to " CB  LEU A 228 " =    1.100
peak=    3.759 closest distance to " O   HOH Z 265 " =    2.204
peak=    3.754 closest distance to " CD2 LEU A 255 " =    1.712
peak=    3.751 closest distance to " CB  ASP A 140 " =    0.980
peak=    3.746 closest distance to " CG  GLU A  37 " =    0.932
peak=    3.740 closest distance to " CG1 VAL A 153 " =    1.077
peak=    3.737 closest distance to " NH2 ARG A  56 " =    1.052
peak=    3.732 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.726 closest distance to " N   TYR A  15 " =    0.889
peak=    3.725 closest distance to " CB  ARG A  79 " =    1.205
peak=    3.718 closest distance to " O   SER A  87 " =    2.422
peak=    3.717 closest distance to " O   THR A 220 " =    1.072
peak=    3.714 closest distance to " O   HOH Z 193 " =    1.832
peak=    3.710 closest distance to " CA  ARG A 139 " =    1.356
peak=    3.705 closest distance to " NE2 GLN A  77 " =    3.448
peak=    3.701 closest distance to " O   HOH Z 361 " =    3.409
peak=    3.686 closest distance to " CG1 ILE A  33 " =    1.224
peak=    3.683 closest distance to " CG  GLN A  11 " =    1.344
peak=    3.673 closest distance to " O   HOH Z 183 " =    1.352
peak=    3.654 closest distance to " O   HOH Z 130 " =    1.042
peak=    3.653 closest distance to " CB  TRP A 179 " =    1.350
peak=    3.652 closest distance to " O   THR A 251 " =    1.181
peak=    3.648 closest distance to " O   HOH Z 133 " =    3.104
peak=    3.648 closest distance to " O   HOH Z 366 " =    2.757
peak=    3.639 closest distance to " O   HOH Z 353 " =    2.697
peak=    3.639 closest distance to " CG2BVAL A  41 " =    0.907
peak=    3.638 closest distance to " N   ARG A 156 " =    1.611
peak=    3.636 closest distance to " CB  ARG A 138 " =    0.992
peak=    3.630 closest distance to " CD1 LEU A 300 " =    1.123
peak=    3.627 closest distance to " CA  ARG A 156 " =    1.110
peak=    3.627 closest distance to " CA  MET A 105 " =    1.121
peak=    3.627 closest distance to " O   HOH Z 193 " =    2.210
peak=    3.622 closest distance to " OG  SER A 245 " =    1.705
peak=    3.620 closest distance to " CA  GLU A  46 " =    0.914
peak=    3.614 closest distance to " CA  ALA A 100 " =    1.007
peak=    3.606 closest distance to " OG  SER A  28 " =    1.614
peak=    3.599 closest distance to " O   THR A 182 " =    1.489
peak=    3.598 closest distance to " O   HOH Z  43 " =    1.915
peak=    3.598 closest distance to " O   HOH Z 131 " =    2.415
peak=    3.596 closest distance to " CA  ASP A 162 " =    1.059
peak=    3.593 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.593 closest distance to " O   HOH Z 213 " =    1.926
peak=    3.593 closest distance to " OE1 GLN A  11 " =    2.162
peak=    3.588 closest distance to " O   HOH Z 142 " =    1.701
peak=    3.588 closest distance to " O   HOH Z 261 " =    1.775
peak=    3.587 closest distance to " CG2 VAL A 197 " =    1.175
peak=    3.581 closest distance to " O   ALA A 165 " =    1.482
peak=    3.577 closest distance to " CB  PRO A  54 " =    0.943
peak=    3.572 closest distance to " O   HOH Z  21 " =    1.914
peak=    3.571 closest distance to " O   HOH Z  40 " =    1.574
peak=    3.569 closest distance to " O   ASP A 124 " =    1.226
peak=    3.569 closest distance to " O   HOH Z 199 " =    1.554
peak=    3.566 closest distance to " O   HOH Z 433 " =    1.390
peak=    3.559 closest distance to " O   HOH Z 261 " =    1.498
peak=    3.556 closest distance to " CA  ASP A 124 " =    0.842
peak=    3.551 closest distance to " CB  GLN A  89 " =    1.277
peak=    3.550 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.541 closest distance to " O   HOH Z 325 " =    2.338
peak=    3.538 closest distance to " O   HOH Z 273 " =    1.176
peak=    3.535 closest distance to " O   HOH Z 417 " =    3.053
peak=    3.531 closest distance to " CB  ASN A 148 " =    1.405
peak=    3.516 closest distance to " O   HOH Z 258 " =    1.870
peak=    3.516 closest distance to " CG2 VAL A 257 " =    0.754
peak=    3.515 closest distance to " CE1 HIS A 115 " =    1.031
peak=    3.514 closest distance to " O   HOH Z  38 " =    2.396
peak=    3.513 closest distance to " O   HOH Z 171 " =    3.938
peak=    3.504 closest distance to " OG1 THR A  82 " =    0.904
peak=    3.500 closest distance to " N   ASN A  39 " =    1.366
peak=    3.499 closest distance to " O   HOH Z  88 " =    3.905
peak=    3.494 closest distance to " CG2 ILE A 234 " =    0.965
peak=    3.494 closest distance to " CZ  PHE A 192 " =    1.040
peak=    3.488 closest distance to " CB  ASN A 285 " =    0.956
peak=    3.485 closest distance to " NH2AARG A 145 " =    1.116
peak=    3.485 closest distance to " O   HOH Z 124 " =    1.906
peak=    3.482 closest distance to " CB  GLU A  37 " =    0.841
peak=    3.479 closest distance to " O   HOH Z 316 " =    3.144
peak=    3.472 closest distance to " O   HOH Z 148 " =    3.509
peak=    3.471 closest distance to " CA  ALA A 291 " =    0.839
peak=    3.468 closest distance to " O   HOH Z  78 " =    1.739
peak=    3.461 closest distance to " NE2 GLN A  58 " =    4.814
peak=    3.458 closest distance to " CB  ALA A 114 " =    0.715
peak=    3.457 closest distance to " CB  LEU A  83 " =    0.805
peak=    3.454 closest distance to " O   HOH Z  76 " =    1.196
peak=    3.452 closest distance to " O   HOH Z   9 " =    2.204
peak=    3.449 closest distance to " O   HOH Z 285 " =    2.423
peak=    3.446 closest distance to " O   HOH Z 345 " =    3.852
peak=    3.437 closest distance to " CA  ARG A 102 " =    1.191
peak=    3.435 closest distance to " CG  LEU A 167 " =    1.141
peak=    3.428 closest distance to " O   HOH Z 368 " =    4.281
peak=    3.423 closest distance to " CB  PRO A  90 " =    1.251
peak=    3.421 closest distance to " CD  ARG A 195 " =    1.032
peak=    3.420 closest distance to " O   HOH Z 422 " =    2.555
peak=    3.416 closest distance to " O   HOH Z 192 " =    1.524
peak=    3.415 closest distance to " CB  ASN A 142 " =    0.923
peak=    3.410 closest distance to " ND1 HIS A  81 " =    1.734
peak=    3.410 closest distance to " N   TYR A 247 " =    1.113
peak=    3.408 closest distance to " NZ  LYS A 117 " =    2.904
peak=    3.406 closest distance to " O   ASP A 191 " =    1.423
peak=    3.403 closest distance to " CA  SER A  87 " =    1.004
peak=    3.402 closest distance to " O   HOH Z 180 " =    2.134
peak=    3.399 closest distance to " O   HOH Z 291 " =    1.465
peak=    3.397 closest distance to " ND2 ASN A 249 " =    0.874
peak=    3.393 closest distance to " CA  MET A  40 " =    1.270
peak=    3.393 closest distance to " CD1 ILE A 199 " =    0.996
peak=    3.388 closest distance to " N   ASN A 127 " =    1.283
peak=    3.387 closest distance to " CB  SER A 273 " =    1.004
peak=    3.377 closest distance to " O   HOH Z 251 " =    1.666
peak=    3.372 closest distance to " CB  ALA A  43 " =    0.885
peak=    3.371 closest distance to " N   SER A 164 " =    0.969
peak=    3.367 closest distance to " CB  PRO A 243 " =    1.444
peak=    3.367 closest distance to " O   HOH Z 271 " =    2.569
peak=    3.363 closest distance to " CB  ALA A 299 " =    0.733
peak=    3.360 closest distance to " CB  GLU A 152 " =    1.114
peak=    3.359 closest distance to " O   HOH Z 377 " =    1.235
peak=    3.357 closest distance to " O   ASP A 200 " =    1.698
peak=    3.356 closest distance to " CA  ASN A 215 " =    1.085
peak=    3.356 closest distance to " CG1 ILE A  20 " =    1.376
peak=    3.355 closest distance to " CD BLYS A 290 " =    0.937
peak=    3.351 closest distance to " O   HOH Z 389 " =    1.986
peak=    3.349 closest distance to " CB  MET A  40 " =    0.823
peak=    3.347 closest distance to " O   HOH Z 403 " =    1.537
peak=    3.341 closest distance to " O   HOH Z 394 " =    1.929
peak=    3.340 closest distance to " CB  SER A 210 " =    0.844
peak=    3.338 closest distance to " CG  MET A 185 " =    1.313
peak=    3.338 closest distance to " ND2 ASN A  69 " =    1.322
peak=    3.334 closest distance to " O   HOH Z 184 " =    1.693
peak=    3.334 closest distance to " O   HOH Z 141 " =    1.625
peak=    3.333 closest distance to " O   HOH Z 303 " =    2.351
peak=    3.328 closest distance to " CB  ALA A 291 " =    1.052
peak=    3.324 closest distance to " CA  ILE A 106 " =    0.873
peak=    3.324 closest distance to " O   HOH Z 146 " =    1.521
peak=    3.319 closest distance to " NH2AARG A 275 " =    3.403
peak=    3.318 closest distance to " OE1 GLN A  55 " =    1.363
peak=    3.315 closest distance to " O   HOH Z  54 " =    1.240
peak=    3.312 closest distance to " O   HOH Z 134 " =    1.149
peak=    3.309 closest distance to " CA  GLY A   6 " =    0.803
peak=    3.308 closest distance to " OD2 ASP A 298 " =    3.969
peak=    3.302 closest distance to " CG  MET A 188 " =    0.858
peak=    3.299 closest distance to " NH2 ARG A 156 " =    1.147
peak=    3.298 closest distance to " O   HOH Z 391 " =    3.020
peak=    3.297 closest distance to " O   HOH Z 145 " =    1.328
peak=    3.292 closest distance to " NE2 HIS A 207 " =    1.065
peak=    3.291 closest distance to " O   HOH Z 313 " =    1.586
peak=    3.290 closest distance to " CD  ARG A  66 " =    2.175
peak=    3.286 closest distance to " O   HOH Z 246 " =    1.491
peak=    3.286 closest distance to " O   THR A 294 " =    1.456
peak=    3.286 closest distance to " CA  GLY A 267 " =    1.134
peak=    3.286 closest distance to " O   HOH Z 290 " =    1.237
peak=    3.285 closest distance to " O   HOH Z 393 " =    3.031
peak=    3.281 closest distance to " O   HOH Z 116 " =    3.274
peak=    3.280 closest distance to " O   HOH Z  78 " =    2.083
peak=    3.276 closest distance to " O   HOH Z 359 " =    1.767
peak=    3.275 closest distance to " O   PRO A 213 " =    1.422
peak=    3.275 closest distance to " OD1 ASN A 217 " =    1.476
peak=    3.274 closest distance to " CA  ALA A  21 " =    1.356
peak=    3.273 closest distance to " CA  GLY A 211 " =    1.429
peak=    3.268 closest distance to " N   ASN A 252 " =    1.307
peak=    3.267 closest distance to " O   HOH Z 125 " =    3.622
peak=    3.264 closest distance to " CD2 PHE A  59 " =    1.894
peak=    3.263 closest distance to " O   HOH Z 394 " =    3.913
peak=    3.261 closest distance to " CB  ASP A 107 " =    1.264
peak=    3.260 closest distance to " OG BSER A 164 " =    2.460
peak=    3.258 closest distance to " O   HOH Z 343 " =    2.607
peak=    3.255 closest distance to " O   HOH Z 116 " =    1.867
peak=    3.255 closest distance to " O   HOH Z  63 " =    2.353
peak=    3.255 closest distance to " CZ3 TRP A  85 " =    0.943
peak=    3.245 closest distance to " N   GLU A  44 " =    1.145
peak=    3.244 closest distance to " NH1BARG A 102 " =    1.009
peak=    3.243 closest distance to " CB  SER A   3 " =    1.699
peak=    3.243 closest distance to " CA  ASP A 140 " =    1.592
peak=    3.238 closest distance to " O   HOH Z 371 " =    2.950
peak=    3.238 closest distance to " O   HOH Z 174 " =    2.398
peak=    3.237 closest distance to " CE3 TRP A  85 " =    1.092
peak=    3.234 closest distance to " CD  GLU A 152 " =    0.833
peak=    3.233 closest distance to " OE1 GLN A 223 " =    3.533
peak=    3.231 closest distance to " O   HOH Z 365 " =    2.847
peak=    3.231 closest distance to " O   HOH Z 279 " =    2.376
peak=    3.230 closest distance to " CD1 LEU A   5 " =    1.286
peak=    3.230 closest distance to " O   HOH Z 139 " =    4.769
peak=    3.224 closest distance to " O   ALA A 158 " =    1.207
peak=    3.221 closest distance to " O   HOH Z 361 " =    3.911
peak=    3.219 closest distance to " O   HOH Z 285 " =    2.121
peak=    3.218 closest distance to " CB  ASN A 173 " =    1.172
peak=    3.216 closest distance to " CA  VAL A 112 " =    1.139
peak=    3.215 closest distance to " CA  PRO A  54 " =    1.405
peak=    3.214 closest distance to " O   HOH Z  88 " =    1.976
peak=    3.214 closest distance to " O   HOH Z 117 " =    2.024
peak=    3.209 closest distance to " O   HOH Z  88 " =    3.067
peak=    3.209 closest distance to " CA  SER A  95 " =    0.935
peak=    3.206 closest distance to " O   HOH Z 280 " =    3.026
peak=    3.199 closest distance to " O   HOH Z 196 " =    1.077
peak=    3.199 closest distance to " O   HOH Z 357 " =    2.566
peak=    3.195 closest distance to " O   HOH Z 126 " =    2.199
peak=    3.192 closest distance to " CB  ALA A 242 " =    0.841
peak=    3.190 closest distance to " CH2 TRP A  70 " =    0.915
peak=    3.190 closest distance to " NH1 ARG A 269 " =    0.789
peak=    3.186 closest distance to " N   GLU A 152 " =    1.588
peak=    3.184 closest distance to " CA  TYR A 116 " =    1.360
peak=    3.184 closest distance to " CB  LEU A 300 " =    0.900
peak=    3.183 closest distance to " CB  SER A  62 " =    0.901
peak=    3.182 closest distance to " CA  SER A  12 " =    1.512
peak=    3.180 closest distance to " CA  GLN A  94 " =    0.784
peak=    3.178 closest distance to " O   HOH Z  90 " =    2.521
peak=    3.176 closest distance to " CA  GLN A 223 " =    0.952
peak=    3.175 closest distance to " O   HOH Z 383 " =    2.258
peak=    3.169 closest distance to " O   HOH Z 327 " =    1.929
peak=    3.169 closest distance to " NE AARG A 275 " =    1.386
peak=    3.168 closest distance to " CA  ALA A 233 " =    1.723
peak=    3.165 closest distance to " CB  ASN A 187 " =    1.194
peak=    3.164 closest distance to " CA  CYS A 254 " =    1.383
peak=    3.161 closest distance to " N   ALA A 104 " =    1.052
peak=    3.157 closest distance to " CG2 ILE A 151 " =    0.950
peak=    3.153 closest distance to " CB  SER A 216 " =    0.938
peak=    3.149 closest distance to " O   HOH Z 238 " =    0.738
peak=    3.146 closest distance to " CG2 VAL A 268 " =    1.036
peak=    3.145 closest distance to " CB  GLN A 103 " =    0.842
peak=    3.143 closest distance to " OG BSER A 134 " =    2.838
peak=    3.142 closest distance to " CB  TRP A 150 " =    1.355
peak=    3.132 closest distance to " O   HOH Z 134 " =    2.803
peak=    3.131 closest distance to " O   HOH Z 211 " =    1.333
peak=    3.130 closest distance to " CB  ALA A 248 " =    1.492
peak=    3.122 closest distance to " NH1 ARG A 138 " =    0.994
peak=    3.120 closest distance to " O  BHOH Z 338 " =    2.359
peak=    3.117 closest distance to " O   HOH Z 272 " =    1.867
peak=    3.115 closest distance to " O   HOH Z 420 " =    1.826
peak=    3.114 closest distance to " CB  GLU A 277 " =    0.918
peak=    3.113 closest distance to " CE3 TRP A 150 " =    1.180
peak=    3.112 closest distance to " O   HOH Z 132 " =    3.090
peak=    3.108 closest distance to " CG  GLN A  89 " =    1.434
peak=    3.106 closest distance to " CG2 ILE A  20 " =    1.326
peak=    3.106 closest distance to " N   ILE A  33 " =    0.943
peak=    3.096 closest distance to " CE1 PHE A 225 " =    0.971
peak=    3.094 closest distance to " O   HOH Z 158 " =    2.916
peak=    3.092 closest distance to " CD  PRO A  54 " =    0.935
peak=    3.089 closest distance to " CA  THR A 221 " =    0.900
peak=    3.081 closest distance to " CA  ALA A 158 " =    1.284
peak=    3.078 closest distance to " CG2 THR A  31 " =    1.155
peak=    3.077 closest distance to " CA  ALA A 129 " =    1.001
peak=    3.072 closest distance to " OE2 GLU A  53 " =    1.144
peak=    3.069 closest distance to " CG2 THR A 220 " =    0.837
peak=    3.067 closest distance to " OD1 ASP A 171 " =    1.154
peak=    3.066 closest distance to " O   THR A 251 " =    1.982
peak=    3.065 closest distance to " O   HOH Z 298 " =    4.089
peak=    3.063 closest distance to " CB  ARG A 156 " =    1.068
peak=    3.061 closest distance to " OG  SER A  62 " =    2.901
peak=    3.053 closest distance to " N   GLY A  98 " =    1.158
peak=    3.049 closest distance to " CG2 ILE A 120 " =    1.198

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.768 - 5.975
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 215
   mapped sites are within: 0.768 - 5.975

peak=   -4.863 closest distance to " CG1 VAL A 250 " =    2.726
peak=   -4.491 closest distance to " CD  GLN A  58 " =    0.864
peak=   -4.341 closest distance to " CD  GLN A 223 " =    1.424
peak=   -4.305 closest distance to " O   PRO A 198 " =    1.403
peak=   -4.290 closest distance to " O   HOH Z   5 " =    1.609
peak=   -4.287 closest distance to " O   HOH Z 196 " =    2.451
peak=   -4.255 closest distance to " CB  PRO A 243 " =    2.788
peak=   -4.254 closest distance to " CD  ARG A 156 " =    2.161
peak=   -4.198 closest distance to " CD  GLN A  88 " =    0.969
peak=   -4.159 closest distance to " CG1 VAL A 112 " =    2.581
peak=   -4.157 closest distance to " CD2 TYR A 293 " =    1.896
peak=   -4.151 closest distance to " CD1 PHE A  59 " =    2.069
peak=   -4.110 closest distance to " CD  ARG A  14 " =    3.423
peak=   -4.107 closest distance to " CG  GLN A  11 " =    1.385
peak=   -4.072 closest distance to " N   ALA A  43 " =    2.760
peak=   -4.063 closest distance to " O   HOH Z 283 " =    2.500
peak=   -4.045 closest distance to " CG  ARG A 269 " =    2.374
peak=   -3.991 closest distance to " O   HOH Z 411 " =    5.547
peak=   -3.974 closest distance to " CG2 ILE A  49 " =    2.844
peak=   -3.970 closest distance to " O   HOH Z 166 " =    1.519
peak=   -3.927 closest distance to " O   HOH Z 211 " =    0.900
peak=   -3.914 closest distance to " CB  GLU A 277 " =    1.301
peak=   -3.913 closest distance to " O   HOH Z 377 " =    2.015
peak=   -3.905 closest distance to " CE2 PHE A  61 " =    2.714
peak=   -3.894 closest distance to " NE2 GLN A 194 " =    2.065
peak=   -3.874 closest distance to " CA  GLY A 241 " =    3.187
peak=   -3.867 closest distance to " CG  MET A 105 " =    1.058
peak=   -3.865 closest distance to " C   ASN A 285 " =    2.473
peak=   -3.858 closest distance to " O   HOH Z 114 " =    0.797
peak=   -3.839 closest distance to " CA  ASP A 298 " =    1.096
peak=   -3.834 closest distance to " O   GLY A 136 " =    2.390
peak=   -3.818 closest distance to " O   VAL A  67 " =    2.700
peak=   -3.774 closest distance to " O   HOH Z 185 " =    2.433
peak=   -3.750 closest distance to " OG  SER A  97 " =    2.301
peak=   -3.742 closest distance to " NE  ARG A  79 " =    1.281
peak=   -3.740 closest distance to " O   HOH Z 103 " =    1.872
peak=   -3.731 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.708 closest distance to " O   SER A 210 " =    1.894
peak=   -3.707 closest distance to " CE3 TRP A 150 " =    2.081
peak=   -3.705 closest distance to " CB  ALA A 291 " =    2.506
peak=   -3.701 closest distance to " CB  HIS A  86 " =    1.159
peak=   -3.700 closest distance to " O   HOH Z 128 " =    2.792
peak=   -3.699 closest distance to " C   GLY A  17 " =    1.252
peak=   -3.692 closest distance to " O   HOH Z 438 " =    3.210
peak=   -3.690 closest distance to " O   HOH Z 407 " =    3.632
peak=   -3.684 closest distance to " O   HOH Z 150 " =    1.569
peak=   -3.683 closest distance to " CH2 TRP A 179 " =    1.184
peak=   -3.670 closest distance to " O   HOH Z 394 " =    1.615
peak=   -3.667 closest distance to " CA  GLY A 241 " =    2.373
peak=   -3.666 closest distance to " CA  GLY A 203 " =    2.466
peak=   -3.665 closest distance to " O   HOH Z 183 " =    1.232
peak=   -3.664 closest distance to " O   HOH Z   6 " =    1.379
peak=   -3.663 closest distance to " OD1 ASN A 148 " =    1.405
peak=   -3.658 closest distance to " CA  VAL A  67 " =    2.970
peak=   -3.652 closest distance to " O   HOH Z 154 " =    1.437
peak=   -3.647 closest distance to " OD2 ASP A 171 " =    1.875
peak=   -3.640 closest distance to " O   HOH Z 150 " =    2.220
peak=   -3.640 closest distance to " O   HOH Z 357 " =    2.041
peak=   -3.640 closest distance to " CB  ALA A  10 " =    2.227
peak=   -3.638 closest distance to " O   HOH Z 368 " =    1.799
peak=   -3.617 closest distance to " CG  PRO A 198 " =    2.056
peak=   -3.616 closest distance to " O   HOH Z 193 " =    1.335
peak=   -3.614 closest distance to " O   HOH Z 216 " =    0.818
peak=   -3.597 closest distance to " CB  ALA A  43 " =    2.731
peak=   -3.595 closest distance to " CE3 TRP A  70 " =    1.844
peak=   -3.593 closest distance to " O   HOH Z 418 " =    1.313
peak=   -3.584 closest distance to " CG2 VAL A 189 " =    2.209
peak=   -3.573 closest distance to " O   HOH Z 341 " =    0.955
peak=   -3.568 closest distance to " O   HOH Z  19 " =    2.096
peak=   -3.566 closest distance to " C   HIS A 108 " =    1.044
peak=   -3.566 closest distance to " O   HOH Z  43 " =    1.478
peak=   -3.562 closest distance to " O   HOH Z 191 " =    5.975
peak=   -3.546 closest distance to " O   HOH Z 111 " =    1.577
peak=   -3.545 closest distance to " O   HOH Z  38 " =    1.698
peak=   -3.538 closest distance to " CD1 LEU A 101 " =    2.451
peak=   -3.537 closest distance to " O   HOH Z  60 " =    1.532
peak=   -3.531 closest distance to " ND2 ASN A  69 " =    1.684
peak=   -3.524 closest distance to " O   HOH Z  64 " =    1.408
peak=   -3.517 closest distance to " NE2 HIS A  86 " =    1.099
peak=   -3.510 closest distance to " CG  PRO A 243 " =    1.712
peak=   -3.509 closest distance to " CA  GLY A 241 " =    2.910
peak=   -3.490 closest distance to " O   HOH Z 351 " =    1.864
peak=   -3.488 closest distance to " O   ILE A 109 " =    2.632
peak=   -3.484 closest distance to " O   ALA A  34 " =    2.628
peak=   -3.483 closest distance to " N   ILE A 120 " =    1.020
peak=   -3.476 closest distance to " O   HOH Z  39 " =    0.977
peak=   -3.473 closest distance to " CD2 PHE A  61 " =    2.204
peak=   -3.472 closest distance to " CG  GLN A  58 " =    1.187
peak=   -3.470 closest distance to " O   HOH Z 278 " =    1.271
peak=   -3.468 closest distance to " O   HOH Z 348 " =    2.217
peak=   -3.458 closest distance to " CG2 THR A 221 " =    2.402
peak=   -3.449 closest distance to " O   TYR A 186 " =    1.888
peak=   -3.448 closest distance to " OE1 GLN A 223 " =    2.186
peak=   -3.445 closest distance to " O   HOH Z 371 " =    1.323
peak=   -3.433 closest distance to " O   HOH Z 113 " =    2.415
peak=   -3.432 closest distance to " O   HOH Z 210 " =    1.770
peak=   -3.430 closest distance to " SG ACYS A 201 " =    1.127
peak=   -3.427 closest distance to " CZ  PHE A  38 " =    2.636
peak=   -3.425 closest distance to " ND2 ASN A  45 " =    2.251
peak=   -3.422 closest distance to " CB  TRP A  85 " =    2.551
peak=   -3.421 closest distance to " O   HOH Z  52 " =    1.534
peak=   -3.418 closest distance to " CB  ASP A 132 " =    2.364
peak=   -3.418 closest distance to " O   HOH Z 426 " =    1.715
peak=   -3.410 closest distance to " CD2 HIS A 207 " =    2.163
peak=   -3.395 closest distance to " ND2 ASN A  60 " =    4.212
peak=   -3.394 closest distance to " O   PRO A 163 " =    2.108
peak=   -3.394 closest distance to " CG1 VAL A 125 " =    1.822
peak=   -3.391 closest distance to " O   HOH Z 370 " =    2.331
peak=   -3.389 closest distance to " O   HOH Z 396 " =    1.694
peak=   -3.379 closest distance to " O   HOH Z 234 " =    4.678
peak=   -3.378 closest distance to " CG  GLU A  53 " =    1.486
peak=   -3.376 closest distance to " NE2 GLN A 240 " =    1.931
peak=   -3.375 closest distance to " O   HOH Z  78 " =    2.035
peak=   -3.364 closest distance to " O   HOH Z 298 " =    2.625
peak=   -3.363 closest distance to " O   ALA A  10 " =    1.727
peak=   -3.358 closest distance to " O   HOH Z 275 " =    1.691
peak=   -3.357 closest distance to " CZ  PHE A  38 " =    1.143
peak=   -3.356 closest distance to " CG1BVAL A  72 " =    2.515
peak=   -3.348 closest distance to " OD1 ASN A 173 " =    1.256
peak=   -3.346 closest distance to " O   HOH Z 189 " =    2.150
peak=   -3.344 closest distance to " CB  ALA A 129 " =    2.489
peak=   -3.344 closest distance to " CE1 PHE A  59 " =    2.065
peak=   -3.335 closest distance to " CB  ALA A 291 " =    2.448
peak=   -3.325 closest distance to " O   HOH Z 240 " =    3.615
peak=   -3.321 closest distance to " O   HOH Z 357 " =    2.161
peak=   -3.319 closest distance to " CE  MET A 105 " =    2.946
peak=   -3.316 closest distance to " CD1 TRP A  70 " =    1.111
peak=   -3.305 closest distance to " O   HOH Z 377 " =    1.041
peak=   -3.305 closest distance to " OD2 ASP A 270 " =    1.190
peak=   -3.302 closest distance to " CD1 LEU A   5 " =    2.534
peak=   -3.300 closest distance to " CH2 TRP A 150 " =    1.196
peak=   -3.299 closest distance to " O   HOH Z 156 " =    3.478
peak=   -3.295 closest distance to " CG  ARG A  66 " =    2.322
peak=   -3.295 closest distance to " O   HOH Z  60 " =    2.420
peak=   -3.295 closest distance to " O   HOH Z 340 " =    1.557
peak=   -3.292 closest distance to " O   HOH Z  55 " =    1.941
peak=   -3.292 closest distance to " CA  GLY A 133 " =    2.514
peak=   -3.286 closest distance to " O   HOH Z 424 " =    2.851
peak=   -3.286 closest distance to " O   HOH Z 174 " =    2.210
peak=   -3.282 closest distance to " O   HOH Z 171 " =    2.280
peak=   -3.277 closest distance to " O   HOH Z 389 " =    1.649
peak=   -3.276 closest distance to " O   HOH Z 174 " =    3.915
peak=   -3.276 closest distance to " OH  TYR A 247 " =    2.294
peak=   -3.276 closest distance to " CE  MET A  93 " =    1.820
peak=   -3.276 closest distance to " CG1 VAL A  78 " =    2.640
peak=   -3.274 closest distance to " O   HOH Z 198 " =    1.492
peak=   -3.271 closest distance to " OE1 GLN A  89 " =    1.846
peak=   -3.269 closest distance to " O   VAL A 189 " =    2.541
peak=   -3.265 closest distance to " O   SER A 276 " =    1.846
peak=   -3.262 closest distance to " O   HOH Z 407 " =    0.980
peak=   -3.259 closest distance to " CD  LYS A 289 " =    2.320
peak=   -3.256 closest distance to " O   VAL A 189 " =    1.787
peak=   -3.254 closest distance to " N   GLY A  35 " =    1.604
peak=   -3.253 closest distance to " CG  LEU A 281 " =    1.907
peak=   -3.253 closest distance to " O   HOH Z 393 " =    1.321
peak=   -3.252 closest distance to " O   HOH Z 276 " =    1.649
peak=   -3.252 closest distance to " C   LEU A 143 " =    1.209
peak=   -3.252 closest distance to " NE2 GLN A 103 " =    1.814
peak=   -3.247 closest distance to " NH2 ARG A  79 " =    1.553
peak=   -3.238 closest distance to " C   ALA A 158 " =    1.419
peak=   -3.234 closest distance to " O   HOH Z 232 " =    1.737
peak=   -3.233 closest distance to " CD2 PHE A 225 " =    1.255
peak=   -3.231 closest distance to " O   SER A 271 " =    2.226
peak=   -3.230 closest distance to " O   HOH Z  51 " =    1.432
peak=   -3.229 closest distance to " CG  PRO A 163 " =    1.889
peak=   -3.223 closest distance to " OD1 ASP A 191 " =    1.435
peak=   -3.218 closest distance to " OG BSER A 134 " =    1.485
peak=   -3.215 closest distance to " O   HOH Z  44 " =    0.768
peak=   -3.212 closest distance to " OD1 ASP A 171 " =    1.568
peak=   -3.210 closest distance to " O   HOH Z 281 " =    2.439
peak=   -3.210 closest distance to " OG1 THR A  82 " =    1.405
peak=   -3.207 closest distance to " O   PHE A 218 " =    1.407
peak=   -3.204 closest distance to " O   HOH Z 292 " =    4.910
peak=   -3.203 closest distance to " O   GLU A 152 " =    1.444
peak=   -3.199 closest distance to " C   ARG A  79 " =    2.599
peak=   -3.196 closest distance to " CB  PHE A  16 " =    2.496
peak=   -3.187 closest distance to " O   HOH Z 110 " =    1.251
peak=   -3.186 closest distance to " N   GLN A 223 " =    0.927
peak=   -3.185 closest distance to " CD2 LEU A 237 " =    2.879
peak=   -3.182 closest distance to " CE BMET A  47 " =    2.036
peak=   -3.182 closest distance to " CG1 VAL A 112 " =    2.813
peak=   -3.175 closest distance to " O   HOH Z 285 " =    1.793
peak=   -3.174 closest distance to " O   HOH Z 163 " =    5.161
peak=   -3.173 closest distance to " CG2 THR A 251 " =    1.826
peak=   -3.170 closest distance to " O   HOH Z  38 " =    1.161
peak=   -3.169 closest distance to " CG  ARG A 259 " =    1.386
peak=   -3.168 closest distance to " O   HOH Z 120 " =    4.493
peak=   -3.167 closest distance to " O   HOH Z 196 " =    1.980
peak=   -3.167 closest distance to " CB  ALA A 131 " =    2.336
peak=   -3.166 closest distance to " NH2 ARG A 159 " =    2.421
peak=   -3.159 closest distance to " O   ASP A  27 " =    2.192
peak=   -3.148 closest distance to " CG2BVAL A  41 " =    1.830
peak=   -3.146 closest distance to " ND2 ASN A  45 " =    1.200
peak=   -3.145 closest distance to " OH  TYR A 247 " =    1.782
peak=   -3.144 closest distance to " O   HOH Z 436 " =    1.554
peak=   -3.128 closest distance to " O   HOH Z 198 " =    2.315
peak=   -3.127 closest distance to " OG  SER A  63 " =    1.161
peak=   -3.126 closest distance to " CG  LEU A  83 " =    2.190
peak=   -3.124 closest distance to " CD1 ILE A 263 " =    2.027
peak=   -3.120 closest distance to " O   HOH Z 252 " =    3.781
peak=   -3.117 closest distance to " O   HOH Z  37 " =    1.511
peak=   -3.112 closest distance to " O   HOH Z 251 " =    5.093
peak=   -3.111 closest distance to " CG2 VAL A 189 " =    1.965
peak=   -3.111 closest distance to " O   HOH Z 105 " =    1.863
peak=   -3.110 closest distance to " CZ  PHE A 218 " =    1.228
peak=   -3.092 closest distance to " O   HOH Z 287 " =    1.954
peak=   -3.088 closest distance to " SD  MET A  40 " =    1.948
peak=   -3.087 closest distance to " O   HOH Z  82 " =    2.108
peak=   -3.086 closest distance to " OE1 GLU A  44 " =    1.044
peak=   -3.082 closest distance to " OG BSER A 210 " =    2.170
peak=   -3.053 closest distance to " ND2 ASN A 249 " =    2.359
peak=   -3.044 closest distance to " O   HOH Z 231 " =    1.964
peak=   -3.042 closest distance to " N   LYS A 166 " =    2.014
peak=   -3.042 closest distance to " O   HOH Z 251 " =    1.921
peak=   -3.028 closest distance to " CB  TYR A  15 " =    2.274

================= 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    :  0.4632 0.4581   6.269020e+00   6.253742e+00
   1_bss:  0.4559 0.4521   6.262330e+00   6.246060e+00
   1_xyz:  0.3452 0.3695   6.065638e+00   6.118805e+00
   1_adp:  0.3103 0.3792   6.011255e+00   6.126692e+00
   1_occ:  0.3100 0.3786   6.010879e+00   6.126917e+00
   2_bss:  0.3094 0.3778   6.011607e+00   6.127093e+00
   2_xyz:  0.2383 0.2975   5.789044e+00   5.953689e+00
   2_adp:  0.2295 0.2857   5.757563e+00   5.923224e+00
   2_occ:  0.2293 0.2853   5.756790e+00   5.922786e+00
   3_bss:  0.2292 0.2853   5.756923e+00   5.922324e+00
   3_xyz:  0.1946 0.2424   5.610138e+00   5.784301e+00
   3_adp:  0.1728 0.2278   5.519894e+00   5.727589e+00
   3_occ:  0.1728 0.2276   5.519746e+00   5.727486e+00
   4_bss:  0.1731 0.2275   5.520147e+00   5.726072e+00
   4_xyz:  0.1408 0.1939   5.351380e+00   5.586725e+00
   4_adp:  0.1340 0.1816   5.294466e+00   5.522329e+00
   4_occ:  0.1338 0.1815   5.294019e+00   5.522113e+00
   5_bss:  0.1338 0.1814   5.294250e+00   5.522509e+00
   5_xyz:  0.1284 0.1750   5.257317e+00   5.486078e+00
   5_adp:  0.1260 0.1759   5.247992e+00   5.484159e+00
   5_occ:  0.1259 0.1759   5.247673e+00   5.484006e+00
   5_bss:  0.1259 0.1757   5.247595e+00   5.483994e+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:  0.300  80.000  -1.450   1.252   4.324   0.000   0.000   0.000
   1_xyz:  0.300  80.000  -1.450   1.252   4.324   0.000   0.000   0.000
   1_adp:  0.300  80.000  -1.450   1.252   4.324   0.000   0.000   0.000
   1_occ:  0.300  80.000  -1.450   1.252   4.324   0.000   0.000   0.000
   2_bss:  0.327  84.729  -0.850   0.750   2.368   0.000   0.000   0.000
   2_xyz:  0.327  84.729  -0.850   0.750   2.368   0.000   0.000   0.000
   2_adp:  0.327  84.729  -0.850   0.750   2.368   0.000   0.000   0.000
   2_occ:  0.327  84.729  -0.850   0.750   2.368   0.000   0.000   0.000
   3_bss:  0.329  80.001  -1.385  -0.337   0.870  -0.000   0.000   0.000
   3_xyz:  0.329  80.001  -1.385  -0.337   0.870  -0.000   0.000   0.000
   3_adp:  0.329  80.001  -1.385  -0.337   0.870  -0.000   0.000   0.000
   3_occ:  0.329  80.001  -1.385  -0.337   0.870  -0.000   0.000   0.000
   4_bss:  0.340  98.378  -1.768  -1.061   0.231  -0.000   0.000   0.000
   4_xyz:  0.340  98.378  -1.768  -1.061   0.231  -0.000   0.000   0.000
   4_adp:  0.340  98.378  -1.768  -1.061   0.231  -0.000   0.000   0.000
   4_occ:  0.340  98.378  -1.768  -1.061   0.231  -0.000   0.000   0.000
   5_bss:  0.334  88.365  -1.610  -1.156   0.243  -0.000   0.000   0.000
   5_xyz:  0.334  88.365  -1.610  -1.156   0.243  -0.000   0.000   0.000
   5_adp:  0.334  88.365  -1.610  -1.156   0.243  -0.000   0.000   0.000
   5_occ:  0.334  88.365  -1.610  -1.156   0.243  -0.000   0.000   0.000
   5_bss:  0.326  81.543  -1.323  -0.964   0.443  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.385 0.4521  0.5724    62916.705
   1_bss:  54.665 0.4604  0.6169    61344.937
   1_xyz:  40.660 0.6349  0.8318    38209.759
   1_adp:  41.524 0.6238  0.8090    39709.040
   1_occ:  41.534 0.6237  0.8085    39739.616
   2_bss:  41.348 0.6260  0.7962    39626.019
   2_xyz:  31.185 0.7436  0.9177    23376.373
   2_adp:  29.343 0.7649  0.9468    21494.644
   2_occ:  29.308 0.7653  0.9468    21463.314
   3_bss:  29.212 0.7663  0.9145    21379.216
   3_xyz:  23.966 0.8222  0.9660    15128.140
   3_adp:  22.010 0.8420  0.9627    13177.532
   3_occ:  22.014 0.8420  0.9625    13168.574
   4_bss:  21.962 0.8424  0.9435    13110.848
   4_xyz:  18.595 0.8744  0.9615     9605.112
   4_adp:  16.924 0.8901  0.9561     8426.750
   4_occ:  16.921 0.8901  0.9562     8420.417
   5_bss:  16.936 0.8900  0.9568     8431.876
   5_xyz:  15.938 0.8991  0.9622     7729.819
   5_adp:  15.833 0.9002  0.9513     7705.073
   5_occ:  15.825 0.9003  0.9513     7697.084
   5_bss:  15.825 0.9003  0.9590     7694.343
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6531e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6531e-01
   1_xyz:   1.540  0.012  0.094 15.602  0.006  4.116   1.2413e-01
   1_adp:   1.540  0.012  0.094 15.602  0.006  4.116   1.2413e-01
   1_occ:   1.540  0.012  0.094 15.602  0.006  4.116   1.2413e-01
   2_bss:   1.540  0.012  0.094 15.602  0.006  4.116   1.2413e-01
   2_xyz:   1.267  0.009  0.088 14.756  0.005  4.113   8.5531e-02
   2_adp:   1.267  0.009  0.088 14.756  0.005  4.113   8.5531e-02
   2_occ:   1.267  0.009  0.088 14.756  0.005  4.113   8.5531e-02
   3_bss:   1.267  0.009  0.088 14.756  0.005  4.113   8.5531e-02
   3_xyz:   1.008  0.008  0.067 14.652  0.004  4.128   6.1484e-02
   3_adp:   1.008  0.008  0.067 14.652  0.004  4.128   6.1484e-02
   3_occ:   1.008  0.008  0.067 14.652  0.004  4.128   6.1484e-02
   4_bss:   1.008  0.008  0.067 14.652  0.004  4.128   6.1484e-02
   4_xyz:   1.194  0.011  0.085 14.902  0.004  4.117   8.2381e-02
   4_adp:   1.194  0.011  0.085 14.902  0.004  4.117   8.2381e-02
   4_occ:   1.194  0.011  0.085 14.902  0.004  4.117   8.2381e-02
   5_bss:   1.194  0.011  0.085 14.902  0.004  4.117   8.2381e-02
   5_xyz:   1.062  0.010  0.078 14.694  0.004  4.123   6.8397e-02
   5_adp:   1.062  0.010  0.078 14.694  0.004  4.123   6.8397e-02
   5_occ:   1.062  0.010  0.078 14.694  0.004  4.123   6.8397e-02
   5_bss:   1.062  0.010  0.078 14.694  0.004  4.123   6.8397e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4607e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4607e-01
   1_xyz:  10.262  0.059  0.360 84.962  0.050  2.032   1.5659e-01
   1_adp:  10.262  0.059  0.360 84.962  0.050  2.032   1.5659e-01
   1_occ:  10.262  0.059  0.360 84.962  0.050  2.032   1.5659e-01
   2_bss:  10.262  0.059  0.360 84.962  0.050  2.032   1.5659e-01
   2_xyz:   7.919  0.050  0.238 82.078  0.043  2.253   8.5197e-02
   2_adp:   7.919  0.050  0.238 82.078  0.043  2.253   8.5197e-02
   2_occ:   7.919  0.050  0.238 82.078  0.043  2.253   8.5197e-02
   3_bss:   7.919  0.050  0.238 82.078  0.043  2.253   8.5197e-02
   3_xyz:   8.151  0.053  0.285 81.418  0.036  2.353   1.0357e-01
   3_adp:   8.151  0.053  0.285 81.418  0.036  2.353   1.0357e-01
   3_occ:   8.151  0.053  0.285 81.418  0.036  2.353   1.0357e-01
   4_bss:   8.151  0.053  0.285 81.418  0.036  2.353   1.0357e-01
   4_xyz:   7.936  0.054  0.245 85.408  0.050  2.222   6.2407e-02
   4_adp:   7.936  0.054  0.245 85.408  0.050  2.222   6.2407e-02
   4_occ:   7.936  0.054  0.245 85.408  0.050  2.222   6.2407e-02
   5_bss:   7.936  0.054  0.245 85.408  0.050  2.222   6.2407e-02
   5_xyz:   7.756  0.047  0.253 81.740  0.040  2.413   4.2461e-02
   5_adp:   7.756  0.047  0.253 81.740  0.040  2.413   4.2461e-02
   5_occ:   7.756  0.047  0.253 81.740  0.040  2.413   4.2461e-02
   5_bss:   7.756  0.047  0.253 81.740  0.040  2.413   4.2461e-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: 123.40   0.00  19.33  89.90   0.00  15.08 123.40   0.00  42.49
   1_occ: 123.40   0.00  19.33  89.90   0.00  15.08 123.40   0.00  42.49
   2_bss: 123.40   0.00  19.33  89.90   0.00  15.08 123.40   0.00  42.49
   2_xyz: 123.40   0.00  19.33  89.90   0.00  15.08 123.40   0.00  42.49
   2_adp: 123.40   0.00  19.28  89.78   0.00  14.98 123.40   0.00  42.69
   2_occ: 123.40   0.00  19.28  89.78   0.00  14.98 123.40   0.00  42.69
   3_bss: 123.40   0.00  19.28  89.78   0.00  14.98 123.40   0.00  42.69
   3_xyz: 123.40   0.00  19.28  89.78   0.00  14.98 123.40   0.00  42.69
   3_adp: 125.02   0.00  19.22 105.71   0.00  13.82 125.02   3.96  48.58
   3_occ: 125.02   0.00  19.22 105.71   0.00  13.82 125.02   3.96  48.58
   4_bss: 125.02   0.00  19.22 105.71   0.00  13.82 125.02   3.96  48.58
   4_xyz: 125.02   0.00  19.22 105.71   0.00  13.82 125.02   3.96  48.58
   4_adp: 122.84   0.00  18.15 102.95   0.00  12.94 122.84   4.67  46.49
   4_occ: 122.84   0.00  18.15 102.95   0.00  12.94 122.84   4.67  46.49
   5_bss: 122.84   0.00  18.15 102.95   0.00  12.94 122.84   4.67  46.49
   5_xyz: 122.84   0.00  18.15 102.95   0.00  12.94 122.84   4.67  46.49
   5_adp: 126.64   0.00  17.81 105.67   0.00  12.62 126.64   2.72  46.10
   5_occ: 126.64   0.00  17.81 105.67   0.00  12.62 126.64   2.72  46.10
   5_bss: 126.64   0.00  17.82 105.67   0.00  12.62 126.64   2.72  46.10
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.850    0.004    0.362
   1_adp:    1.850    0.004    0.362
   1_occ:    1.850    0.004    0.362
   2_bss:    1.850    0.004    0.362
   2_xyz:    1.473    0.034    0.521
   2_adp:    1.473    0.034    0.521
   2_occ:    1.473    0.034    0.521
   3_bss:    1.473    0.034    0.521
   3_xyz:    1.416    0.035    0.636
   3_adp:    1.416    0.035    0.636
   3_occ:    1.416    0.035    0.636
   4_bss:    1.416    0.035    0.636
   4_xyz:    1.328    0.028    0.713
   4_adp:    1.328    0.028    0.713
   4_occ:    1.328    0.028    0.713
   5_bss:    1.328    0.028    0.713
   5_xyz:    1.353    0.038    0.732
   5_adp:    1.353    0.038    0.732
   5_occ:    1.353    0.038    0.732
   5_bss:    1.353    0.038    0.732
------------------------------------------------------------------------

CPU time actual refinement: 356.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1066/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_1066/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1066/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1066/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1066/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 355.85 
  Macro-tasks:
    bulk solvent and scale       = 67.21  
    individual site refinement   = 131.83 
    weights calculation          = 29.36  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 235.04 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 104.29 
    alpha_beta                      = 8.16   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.28 
    fmodel                         = 10.52  
    r_factors                      = 0.37   
    phase_errors                   = 10.41  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 249.84 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.035 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    638 calls, 104.02 s
gradients_fft:          583 calls,  99.37 s

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

# Date 2008-01-16 Time 06:21:00 PST -0800 (1200493260.78 s)
Start R-work = 0.4632, R-free = 0.4581 (no bulk solvent and anisotropic scale)
Final R-work = 0.1429, R-free = 0.1900 (no bulk solvent and anisotropic scale)

Start R-work = 0.4559, R-free = 0.4521
Final R-work = 0.1259, R-free = 0.1757