# Date 2008-01-16 Time 05:33:53 PST -0800 (1200490433.40 s)
#phil __OFF__

Command line arguments: "../785.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24423
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 785

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 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: (70.6012, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99102
Completeness in resolution range: 0.972786
Completeness with d_max=infinity: 0.969704

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9910

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99102
Completeness in resolution range: 0.972786
Completeness with d_max=infinity: 0.969704

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2600 [2104/2128]  1894   210  10.0%
  bin  2:  4.2600 -  3.3941 [2038/2057]  1834   204  10.0%
  bin  3:  3.3941 -  2.9688 [2007/2026]  1803   204  10.2%
  bin  4:  2.9688 -  2.6991 [1990/2020]  1796   194   9.7%
  bin  5:  2.6991 -  2.5066 [1977/1996]  1779   198  10.0%
  bin  6:  2.5066 -  2.3594 [1946/1971]  1752   194  10.0%
  bin  7:  2.3594 -  2.2416 [1966/1994]  1765   201  10.2%
  bin  8:  2.2416 -  2.1443 [1946/1982]  1755   191   9.8%
  bin  9:  2.1443 -  2.0620 [1939/1981]  1747   192   9.9%
  bin 10:  2.0620 -  1.9910 [1676/1982]  1505   171  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_785/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2204
        3.04 -     3.66: 4653
        3.66 -     4.28: 9042
        4.28 -     4.90: 12357
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.222 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.379 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28260 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_785/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_785/model_refine_001.geo

CPU time processing inputs: 9.01


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1962   r_free= 0.1967   ksol= 0.00   Bsol= 0.00   scale= 1.014    |
|                                                                             |
| 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:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.547379                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7512 0.99   1376  153 0.2429 0.2401      6.2298      6.1686|
|  2:  4.7512 -  3.7911 0.99   1322  146 0.1527 0.1512      5.9593      5.9474|
|  3:  3.7911 -  3.3178 0.99   1297  145 0.1580 0.1503       5.796      5.9054|
|  4:  3.3178 -  3.0171 0.99   1280  144 0.1623 0.1771      5.6783      5.7179|
|  5:  3.0171 -  2.8024 0.99   1281  142 0.1801 0.1686      5.5595      5.5842|
|  6:  2.8024 -  2.6381 0.99   1280  138 0.1870 0.1890      5.5137      5.4808|
|  7:  2.6381 -  2.5066 0.99   1270  142 0.1967 0.1838      5.5105      5.4915|
|  8:  2.5066 -  2.3979 0.98   1261  145 0.1999 0.1899      5.4616      5.4342|
|  9:  2.3979 -  2.3059 0.98   1260  137 0.1955 0.2089      5.3979      5.4186|
| 10:  2.3059 -  2.2266 0.99   1238  141 0.1992 0.2206      5.3764      5.4373|
| 11:  2.2266 -  2.1572 0.98   1266  135 0.2016 0.1999      5.3226      5.3564|
| 12:  2.1572 -  2.0957 0.97   1236  139 0.1999 0.1979      5.2973      5.3333|
| 13:  2.0957 -  2.0407 1.00   1249  144 0.2085 0.2133      5.2267      5.2162|
| 14:  2.0407 -  1.9910 0.79   1014  108 0.2021 0.2304       5.156      5.1366|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7512  1376   153  0.83  22.58   0.88     0.83      32516.22|
|  2:  4.7512 -  3.7911  1322   146  0.91  14.85   1.00     0.95      21874.79|
|  3:  3.7911 -  3.3178  1297   145  0.91  14.05   1.03     1.02      15013.41|
|  4:  3.3178 -  3.0171  1280   144  0.91  14.49   1.04     1.02      11865.94|
|  5:  3.0171 -  2.8024  1281   142  0.90  16.59   1.04     1.02       9455.08|
|  6:  2.8024 -  2.6381  1280   138  0.90  16.21   1.06     1.03       7832.57|
|  7:  2.6381 -  2.5066  1270   142  0.90  16.34   1.06     1.04       7000.98|
|  8:  2.5066 -  2.3979  1261   145  0.89  17.38   1.07     1.06       6848.94|
|  9:  2.3979 -  2.3059  1260   137  0.89  17.66   1.10     1.06       6558.63|
| 10:  2.3059 -  2.2266  1238   141  0.88  18.78   1.11     1.07       6402.23|
| 11:  2.2266 -  2.1572  1266   135  0.88  18.63   1.12     1.09       5922.28|
| 12:  2.1572 -  2.0957  1236   139  0.89  17.85   1.12     1.12       5507.60|
| 13:  2.0957 -  2.0407  1249   144  0.88  18.82   1.13     1.11       4710.14|
| 14:  2.0407 -  1.9910  1014   108  0.89  17.91   1.11     1.07       3738.49|
|alpha:            min =        0.83 max =            1.12 mean =         1.03|
|beta:             min =     3738.49 max =        32516.22 mean =     10672.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        17.30|
|phase err.(test): min =        0.00 max =           88.72 mean =        17.05|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.567044              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.377   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.304956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.765   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      188 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2016 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1826 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2827 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4665 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4377 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5611 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6746 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.134 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1962   r_free= 0.1967   ksol= 0.00   Bsol= 0.00   scale= 1.014    |
|                                                                             |
| 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:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.547379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1751   r_free= 0.1764   ksol= 0.32   Bsol= 47.80   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.82,-1.43,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.499023                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.371784              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.653   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.153037              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.615   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1751      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1764      final r-factor (free) = 0.1456          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8100 = 2.37 * 0.50 * 5.6079 + 1.00 * 0.1596                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3052 = 2.37 * 0.50 * 5.2628 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1456      final r-factor (free) = 0.1453          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8118 = 0.15 * 1.00 * 5.2628 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8375 = 0.15 * 1.00 * 5.1291 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.84   16.26    None  None   None       |
|    all(noH): 2823   0      0.00    75.84   16.26    None  None   None       |
|    Sol.    : 438    0      5.04    62.38   36.83    None  None   None       |
|    Mac.    : 2385   0      0.00    75.84   12.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.584:  306   |   5:    37.918 -  45.502:  120        |
|      1:     7.584 -  15.167: 1609   |   6:    45.502 -  53.085:   82        |
|      2:    15.167 -  22.751:  408   |   7:    53.085 -  60.669:   43        |
|      3:    22.751 -  30.334:  143   |   8:    60.669 -  68.252:    4        |
|      4:    30.334 -  37.918:  107   |   9:    68.252 -  75.836:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1453             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1451             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1451   ksol= 0.32   Bsol= 47.80   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.82,-1.43,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127386                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1448   ksol= 0.33   Bsol= 47.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.71,-1.62,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.129906                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.633290              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.382  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.611   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1448      final r-factor (free) = 0.1473          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8185 = 2.63 * 0.50 * 5.1300 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7869 = 2.63 * 0.50 * 5.0993 + 1.00 * 0.0729                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1473      final r-factor (free) = 0.1487          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4921 = 0.28 * 1.00 * 5.0993 + 1.00 * 0.0408                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4538 = 0.28 * 1.00 * 5.0824 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    72.56   16.62    None  None   None       |
|    all(noH): 2823   0      1.65    72.56   16.62    None  None   None       |
|    Sol.    : 438    0      4.78    66.65   37.49    None  None   None       |
|    Mac.    : 2385   0      1.65    72.56   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.653 -   8.744:  674   |   5:    37.106 -  44.197:  115        |
|      1:     8.744 -  15.835: 1270   |   6:    44.197 -  51.287:   80        |
|      2:    15.835 -  22.925:  355   |   7:    51.287 -  58.378:   70        |
|      3:    22.925 -  30.016:  121   |   8:    58.378 -  65.468:   22        |
|      4:    30.016 -  37.106:  112   |   9:    65.468 -  72.559:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1487             target_work(ml) = 5.090         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1488             target_work(ml) = 5.090         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1488   ksol= 0.33   Bsol= 47.80   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.71,-1.62,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090123                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1488   ksol= 0.33   Bsol= 47.80   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.38,-1.40,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090276                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.329670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.139  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.262582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.777  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1488      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9954 = 2.33 * 0.50 * 5.0844 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9957 = 2.33 * 0.50 * 5.0918 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1506      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3443 = 0.26 * 1.00 * 5.0918 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3456 = 0.26 * 1.00 * 5.0960 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    73.88   16.50    None  None   None       |
|    all(noH): 2823   0      1.23    73.88   16.50    None  None   None       |
|    Sol.    : 438    0      5.49    66.88   37.31    None  None   None       |
|    Mac.    : 2385   0      1.23    73.88   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.230 -   8.495:  645   |   5:    37.554 -  44.819:  115        |
|      1:     8.495 -  15.760: 1288   |   6:    44.819 -  52.084:   86        |
|      2:    15.760 -  23.025:  366   |   7:    52.084 -  59.349:   58        |
|      3:    23.025 -  30.290:  130   |   8:    59.349 -  66.613:   20        |
|      4:    30.290 -  37.554:  111   |   9:    66.613 -  73.878:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1512             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1513             target_work(ml) = 5.099         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1513   ksol= 0.33   Bsol= 47.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.38,-1.40,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099181                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1513   ksol= 0.33   Bsol= 47.80   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.19,-1.23,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099287                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.393339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 168.743  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.618466              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.355  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6154 = 1.39 * 0.50 * 5.0969 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6135 = 1.39 * 0.50 * 5.1123 + 1.00 * 0.0519                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1692 = 0.62 * 1.00 * 5.1123 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1720 = 0.62 * 1.00 * 5.1150 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.29    77.73   16.56    None  None   None       |
|    all(noH): 2823   0      0.29    77.73   16.56    None  None   None       |
|    Sol.    : 438    0      6.16    68.04   38.10    None  None   None       |
|    Mac.    : 2385   0      0.29    77.73   12.61    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:     0.292 -   8.036:  592   |   5:    39.009 -  46.753:  119        |
|      1:     8.036 -  15.779: 1351   |   6:    46.753 -  54.496:   89        |
|      2:    15.779 -  23.522:  362   |   7:    54.496 -  62.239:   45        |
|      3:    23.522 -  31.266:  132   |   8:    62.239 -  69.983:   19        |
|      4:    31.266 -  39.009:  109   |   9:    69.983 -  77.726:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1541             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1542             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1542   ksol= 0.33   Bsol= 47.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.19,-1.23,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120741                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1542   ksol= 0.33   Bsol= 47.80   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.00,-1.07,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120847                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.512510              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 169.000  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.142161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.444  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4786 = 2.51 * 0.50 * 5.1157 + 1.00 * 0.0519                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4802 = 2.51 * 0.50 * 5.1078 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1058      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.2737 = 5.14 * 1.00 * 5.1078 + 1.00 * 0.0085                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.2510 = 5.14 * 1.00 * 5.1031 + 1.00 * 0.0101                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.81   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    91.81   16.76    None  None   None       |
|    Sol.    : 438    0      5.78    79.38   39.51    None  None   None       |
|    Mac.    : 2385   0      0.00    91.81   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.181:  953   |   5:    45.904 -  55.085:   99        |
|      1:     9.181 -  18.362: 1178   |   6:    55.085 -  64.265:   65        |
|      2:    18.362 -  27.542:  236   |   7:    64.265 -  73.446:   27        |
|      3:    27.542 -  36.723:  139   |   8:    73.446 -  82.627:    4        |
|      4:    36.723 -  45.904:  116   |   9:    82.627 -  91.807:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1055 r_free = 0.1554             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1055 r_free = 0.1554             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1554   ksol= 0.33   Bsol= 47.80   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.00,-1.07,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106928                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7512 0.99   1376  153 0.0963 0.1290       5.364      5.5101|
|  2:  4.7512 -  3.7911 0.99   1322  146 0.0814 0.1071      5.4038      5.5925|
|  3:  3.7911 -  3.3178 0.99   1297  145 0.0997 0.1504      5.4372      5.8594|
|  4:  3.3178 -  3.0171 0.99   1280  144 0.1155 0.1498      5.4303      5.5634|
|  5:  3.0171 -  2.8024 0.99   1281  142 0.1247 0.1779      5.2976       5.556|
|  6:  2.8024 -  2.6381 0.99   1280  138 0.1140 0.1744      5.1827      5.3883|
|  7:  2.6381 -  2.5066 0.99   1270  142 0.1187 0.1593      5.1207      5.3699|
|  8:  2.5066 -  2.3979 0.98   1261  145 0.1073 0.1687      5.0163      5.3149|
|  9:  2.3979 -  2.3059 0.98   1260  137 0.1091 0.1725       4.993      5.2588|
| 10:  2.3059 -  2.2266 0.99   1238  141 0.1012 0.1734      4.9165      5.2292|
| 11:  2.2266 -  2.1572 0.98   1266  135 0.1077 0.1734      4.9155      5.2316|
| 12:  2.1572 -  2.0957 0.97   1236  139 0.1044 0.1643      4.8442      5.2008|
| 13:  2.0957 -  2.0407 1.00   1249  144 0.1048 0.1719      4.7713      5.0568|
| 14:  2.0407 -  1.9910 0.79   1014  108 0.1011 0.1793      4.6458      4.9347|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7512  1376   153  0.94   9.14   0.98     0.95       7033.42|
|  2:  4.7512 -  3.7911  1322   146  0.95   7.68   1.01     1.00       8685.40|
|  3:  3.7911 -  3.3178  1297   145  0.94  10.70   1.02     1.01       9777.71|
|  4:  3.3178 -  3.0171  1280   144  0.92  13.21   1.01     0.99      10027.78|
|  5:  3.0171 -  2.8024  1281   142  0.90  15.54   0.99     0.96       8070.05|
|  6:  2.8024 -  2.6381  1280   138  0.91  15.34   0.98     0.96       6881.82|
|  7:  2.6381 -  2.5066  1270   142  0.91  15.22   0.98     0.96       5819.79|
|  8:  2.5066 -  2.3979  1261   145  0.92  14.16   0.99     0.97       4856.89|
|  9:  2.3979 -  2.3059  1260   137  0.92  14.57   0.99     0.96       4695.97|
| 10:  2.3059 -  2.2266  1238   141  0.91  14.66   0.99     0.94       4062.15|
| 11:  2.2266 -  2.1572  1266   135  0.90  16.25   0.99     0.95       4306.02|
| 12:  2.1572 -  2.0957  1236   139  0.92  14.26   0.99     0.97       3709.74|
| 13:  2.0957 -  2.0407  1249   144  0.91  15.55   0.99     0.98       3326.43|
| 14:  2.0407 -  1.9910  1014   108  0.92  14.35   0.96     0.92       2492.99|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2492.99 max =        10027.78 mean =      6069.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.22 mean =        13.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1552   ksol= 0.32   Bsol= 48.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.72,-0.81,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1552   ksol= 0.32   Bsol= 48.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.87,-1.72,-0.81,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7512 0.99   1376  153 0.0962 0.1290      5.3619      5.5091|
|  2:  4.7512 -  3.7911 0.99   1322  146 0.0816 0.1073      5.4052      5.5937|
|  3:  3.7911 -  3.3178 0.99   1297  145 0.0997 0.1504      5.4377      5.8591|
|  4:  3.3178 -  3.0171 0.99   1280  144 0.1155 0.1498      5.4296      5.5629|
|  5:  3.0171 -  2.8024 0.99   1281  142 0.1245 0.1777      5.2966      5.5546|
|  6:  2.8024 -  2.6381 0.99   1280  138 0.1138 0.1743       5.182      5.3875|
|  7:  2.6381 -  2.5066 0.99   1270  142 0.1187 0.1593      5.1203      5.3699|
|  8:  2.5066 -  2.3979 0.98   1261  145 0.1073 0.1686       5.016       5.314|
|  9:  2.3979 -  2.3059 0.98   1260  137 0.1090 0.1727      4.9929      5.2591|
| 10:  2.3059 -  2.2266 0.99   1238  141 0.1012 0.1734      4.9166      5.2289|
| 11:  2.2266 -  2.1572 0.98   1266  135 0.1077 0.1733      4.9154      5.2313|
| 12:  2.1572 -  2.0957 0.97   1236  139 0.1044 0.1643      4.8441      5.2006|
| 13:  2.0957 -  2.0407 1.00   1249  144 0.1048 0.1718      4.7711      5.0562|
| 14:  2.0407 -  1.9910 0.79   1014  108 0.1011 0.1793      4.6458      4.9348|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7512  1376   153  0.94   9.12   0.98     0.95       6997.15|
|  2:  4.7512 -  3.7911  1322   146  0.95   7.69   1.02     1.00       8681.03|
|  3:  3.7911 -  3.3178  1297   145  0.94  10.71   1.03     1.02       9786.82|
|  4:  3.3178 -  3.0171  1280   144  0.92  13.20   1.01     1.00      10013.97|
|  5:  3.0171 -  2.8024  1281   142  0.90  15.53   1.00     0.97       8057.31|
|  6:  2.8024 -  2.6381  1280   138  0.91  15.33   0.99     0.97       6869.57|
|  7:  2.6381 -  2.5066  1270   142  0.91  15.22   1.00     0.97       5812.05|
|  8:  2.5066 -  2.3979  1261   145  0.92  14.16   1.00     0.98       4853.19|
|  9:  2.3979 -  2.3059  1260   137  0.92  14.57   1.01     0.98       4695.43|
| 10:  2.3059 -  2.2266  1238   141  0.91  14.66   1.00     0.96       4062.16|
| 11:  2.2266 -  2.1572  1266   135  0.90  16.25   1.00     0.97       4304.11|
| 12:  2.1572 -  2.0957  1236   139  0.92  14.25   1.01     0.99       3707.25|
| 13:  2.0957 -  2.0407  1249   144  0.91  15.55   1.01     1.00       3324.44|
| 14:  2.0407 -  1.9910  1014   108  0.92  14.35   0.98     0.94       2493.45|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2493.45 max =        10013.97 mean =      6062.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.55|
|phase err.(test): min =        0.00 max =           89.24 mean =        13.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.930)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.81   16.76    None  None   None       |
|    all(noH): 2823   0      0.00    91.81   16.76    None  None   None       |
|    Sol.    : 438    0      5.78    79.38   39.52    None  None   None       |
|    Mac.    : 2385   0      0.00    91.81   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.184:  953   |   5:    45.907 -  55.087:   99        |
|      1:     9.184 -  18.365: 1178   |   6:    55.087 -  64.268:   65        |
|      2:    18.365 -  27.545:  236   |   7:    64.268 -  73.449:   27        |
|      3:    27.545 -  36.726:  139   |   8:    73.449 -  82.630:    4        |
|      4:    36.726 -  45.907:  116   |   9:    82.630 -  91.810:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.598 - 5.454
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 288
   mapped sites are within: 0.715 - 5.454

peak=    5.583 closest distance to " CG  PRO A  54 " =    1.261
peak=    5.462 closest distance to " NH2 ARG A  56 " =    2.239
peak=    5.255 closest distance to " O   HOH Z 126 " =    1.902
peak=    5.183 closest distance to " CB  SER A  63 " =    1.205
peak=    5.139 closest distance to " O   HOH Z 232 " =    2.358
peak=    5.081 closest distance to " CB  ARG A 275 " =    0.919
peak=    5.070 closest distance to " CB  GLN A 223 " =    1.436
peak=    4.892 closest distance to " NE2 GLN A  11 " =    1.046
peak=    4.866 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.771 closest distance to " O   HOH Z 142 " =    1.680
peak=    4.690 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.663 closest distance to " C   PRO A 198 " =    1.499
peak=    4.654 closest distance to " O   HOH Z 298 " =    1.924
peak=    4.647 closest distance to " O   HOH Z  78 " =    1.709
peak=    4.565 closest distance to " CB  PRO A  54 " =    0.920
peak=    4.516 closest distance to " O   HOH Z 236 " =    1.990
peak=    4.510 closest distance to " OD1 ASN A  69 " =    2.552
peak=    4.481 closest distance to " CB  TYR A 169 " =    0.765
peak=    4.479 closest distance to " CB  GLU A 152 " =    1.192
peak=    4.410 closest distance to " O   HOH Z 369 " =    2.200
peak=    4.402 closest distance to " O   HOH Z  15 " =    2.182
peak=    4.362 closest distance to " CB  LEU A 228 " =    1.106
peak=    4.354 closest distance to " O   HOH Z 427 " =    2.933
peak=    4.326 closest distance to " O   HOH Z 193 " =    1.843
peak=    4.324 closest distance to " CB  ARG A  79 " =    1.362
peak=    4.288 closest distance to " CG  PRO A  90 " =    1.061
peak=    4.278 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.262 closest distance to " O   HOH Z 203 " =    1.741
peak=    4.244 closest distance to " O   HOH Z 234 " =    3.693
peak=    4.225 closest distance to " CB  ASN A 148 " =    1.412
peak=    4.220 closest distance to " O   HOH Z 158 " =    3.000
peak=    4.157 closest distance to " O   HOH Z 250 " =    1.474
peak=    4.117 closest distance to " CB  GLU A 128 " =    1.083
peak=    4.103 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.086 closest distance to " O   HOH Z 316 " =    3.134
peak=    4.081 closest distance to " CB  ASP A 140 " =    0.975
peak=    4.077 closest distance to " O   HOH Z 303 " =    2.048
peak=    4.058 closest distance to " O   HOH Z  61 " =    1.606
peak=    4.026 closest distance to " O   HOH Z 344 " =    3.206
peak=    4.024 closest distance to " ND2 ASN A 187 " =    1.354
peak=    3.999 closest distance to " CA  ASN A 215 " =    1.208
peak=    3.995 closest distance to " O   HOH Z  43 " =    1.895
peak=    3.984 closest distance to " CG2 VAL A 257 " =    0.906
peak=    3.982 closest distance to " O   HOH Z 403 " =    1.676
peak=    3.976 closest distance to " O   HOH Z 261 " =    2.286
peak=    3.945 closest distance to " NZ  LYS A 117 " =    3.260
peak=    3.943 closest distance to " O   HOH Z  40 " =    1.715
peak=    3.941 closest distance to " CB  TRP A 266 " =    0.978
peak=    3.941 closest distance to " O   HOH Z 346 " =    1.685
peak=    3.922 closest distance to " O   HOH Z 392 " =    3.199
peak=    3.911 closest distance to " O   HOH Z 425 " =    2.087
peak=    3.906 closest distance to " CG  PRO A 243 " =    1.059
peak=    3.893 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.882 closest distance to " CB  VAL A 265 " =    1.260
peak=    3.873 closest distance to " CG  ARG A  66 " =    2.518
peak=    3.867 closest distance to " CB  SER A   3 " =    1.309
peak=    3.865 closest distance to " O   HOH Z 245 " =    1.292
peak=    3.859 closest distance to " O   HOH Z 193 " =    1.659
peak=    3.846 closest distance to " O   HOH Z  54 " =    2.431
peak=    3.830 closest distance to " CB  GLU A 277 " =    3.582
peak=    3.827 closest distance to " CZ  PHE A 218 " =    1.018
peak=    3.826 closest distance to " O   HOH Z 189 " =    2.253
peak=    3.813 closest distance to " CD2 LEU A 297 " =    0.890
peak=    3.800 closest distance to " O   HOH Z 214 " =    2.058
peak=    3.794 closest distance to " O   HOH Z 389 " =    1.913
peak=    3.791 closest distance to " O   HOH Z  66 " =    2.119
peak=    3.790 closest distance to " O   HOH Z 280 " =    2.963
peak=    3.787 closest distance to " CB  TRP A 179 " =    1.379
peak=    3.783 closest distance to " CB  VAL A 202 " =    1.551
peak=    3.765 closest distance to " O   HOH Z 426 " =    1.617
peak=    3.745 closest distance to " CG2 THR A 221 " =    1.113
peak=    3.741 closest distance to " O   HOH Z 132 " =    2.488
peak=    3.738 closest distance to " CD1 LEU A 300 " =    1.239
peak=    3.735 closest distance to " CG1 ILE A  33 " =    1.229
peak=    3.732 closest distance to " O   MET A 105 " =    1.827
peak=    3.727 closest distance to " CB  SER A 212 " =    1.081
peak=    3.725 closest distance to " O   SER A  87 " =    2.314
peak=    3.721 closest distance to " CA  THR A 221 " =    1.012
peak=    3.707 closest distance to " O   HOH Z 402 " =    1.413
peak=    3.705 closest distance to " NH1AARG A 145 " =    1.139
peak=    3.703 closest distance to " CD  ARG A 159 " =    0.746
peak=    3.685 closest distance to " OD2 ASP A 286 " =    2.842
peak=    3.678 closest distance to " O   HOH Z 147 " =    1.773
peak=    3.671 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.665 closest distance to " CB  ALA A 291 " =    1.419
peak=    3.654 closest distance to " CD BLYS A 290 " =    1.088
peak=    3.646 closest distance to " O   HOH Z 368 " =    2.061
peak=    3.641 closest distance to " O   HOH Z 305 " =    3.571
peak=    3.641 closest distance to " O   HOH Z 209 " =    2.375
peak=    3.619 closest distance to " CB  TYR A 169 " =    0.715
peak=    3.618 closest distance to " O   HOH Z  59 " =    1.984
peak=    3.617 closest distance to " CA  ALA A  21 " =    1.184
peak=    3.616 closest distance to " CD1 ILE A 106 " =    0.757
peak=    3.611 closest distance to " O   HOH Z 291 " =    1.549
peak=    3.610 closest distance to " CA  ARG A  36 " =    1.045
peak=    3.608 closest distance to " O   HOH Z 180 " =    2.228
peak=    3.605 closest distance to " O   HOH Z  10 " =    1.836
peak=    3.604 closest distance to " O   HOH Z 133 " =    1.553
peak=    3.592 closest distance to " N   ARG A 156 " =    1.293
peak=    3.589 closest distance to " OG BSER A 164 " =    2.305
peak=    3.582 closest distance to " O   HOH Z 423 " =    1.845
peak=    3.575 closest distance to " CB  ARG A 139 " =    0.932
peak=    3.573 closest distance to " O   HOH Z 371 " =    3.255
peak=    3.567 closest distance to " CG2 ILE A 120 " =    1.081
peak=    3.563 closest distance to " O   HOH Z 213 " =    1.719
peak=    3.557 closest distance to " NH2 ARG A 156 " =    1.170
peak=    3.552 closest distance to " O   HOH Z 298 " =    2.567
peak=    3.551 closest distance to " NH2BARG A 145 " =    2.108
peak=    3.547 closest distance to " CA  ALA A  51 " =    0.902
peak=    3.546 closest distance to " CA  ARG A 195 " =    1.182
peak=    3.541 closest distance to " CA  MET A  40 " =    1.115
peak=    3.540 closest distance to " O   HOH Z 172 " =    3.469
peak=    3.539 closest distance to " O   HOH Z   1 " =    1.937
peak=    3.535 closest distance to " O   HOH Z  19 " =    2.487
peak=    3.533 closest distance to " O   HOH Z 368 " =    3.654
peak=    3.533 closest distance to " CA  ALA A 158 " =    1.221
peak=    3.532 closest distance to " O   HOH Z  61 " =    1.500
peak=    3.510 closest distance to " O   HOH Z  97 " =    1.964
peak=    3.508 closest distance to " CA  THR A 264 " =    0.872
peak=    3.506 closest distance to " CB  ASN A 142 " =    1.077
peak=    3.478 closest distance to " O   HOH Z  21 " =    1.766
peak=    3.475 closest distance to " ND2 ASN A 110 " =    1.717
peak=    3.463 closest distance to " O   HOH Z  54 " =    1.692
peak=    3.462 closest distance to " CD2 LEU A 255 " =    1.421
peak=    3.458 closest distance to " O   HOH Z  40 " =    1.429
peak=    3.457 closest distance to " ND1 HIS A  81 " =    1.616
peak=    3.450 closest distance to " O   HOH Z 391 " =    2.901
peak=    3.448 closest distance to " O   HOH Z 281 " =    4.075
peak=    3.447 closest distance to " CB  HIS A 108 " =    0.828
peak=    3.445 closest distance to " CB  SER A 216 " =    0.863
peak=    3.443 closest distance to " OE1 GLU A   2 " =    2.249
peak=    3.442 closest distance to " O   HOH Z 108 " =    2.499
peak=    3.440 closest distance to " O   HOH Z 175 " =    2.164
peak=    3.436 closest distance to " CB  MET A  47 " =    1.025
peak=    3.434 closest distance to " CD  ARG A  66 " =    2.409
peak=    3.429 closest distance to " O   HOH Z 407 " =    2.516
peak=    3.428 closest distance to " O   HOH Z 148 " =    3.330
peak=    3.426 closest distance to " O   HOH Z 313 " =    1.908
peak=    3.425 closest distance to " O   HOH Z 193 " =    2.080
peak=    3.424 closest distance to " CA  ALA A 291 " =    0.846
peak=    3.420 closest distance to " O   HOH Z 185 " =    1.754
peak=    3.420 closest distance to " CE1 TYR A 186 " =    1.268
peak=    3.419 closest distance to " O   HOH Z 248 " =    1.635
peak=    3.417 closest distance to " O   HOH Z 272 " =    1.831
peak=    3.416 closest distance to " O   HOH Z 411 " =    1.778
peak=    3.414 closest distance to " O   HOH Z  93 " =    2.680
peak=    3.409 closest distance to " CG1BVAL A  72 " =    1.608
peak=    3.409 closest distance to " O   HOH Z 345 " =    3.374
peak=    3.406 closest distance to " O   HOH Z  44 " =    3.192
peak=    3.402 closest distance to " CD  ARG A 269 " =    0.915
peak=    3.398 closest distance to " O   HOH Z 359 " =    1.418
peak=    3.391 closest distance to " O   HOH Z  44 " =    1.697
peak=    3.387 closest distance to " O   HOH Z   9 " =    2.112
peak=    3.378 closest distance to " CD  LYS A 119 " =    1.193
peak=    3.376 closest distance to " CB  ASN A  39 " =    0.891
peak=    3.376 closest distance to " O   HOH Z 133 " =    2.432
peak=    3.373 closest distance to " CD  GLU A 152 " =    0.735
peak=    3.367 closest distance to " CB  THR A 157 " =    1.113
peak=    3.364 closest distance to " CB  ALA A 248 " =    1.348
peak=    3.359 closest distance to " CA  ALA A  84 " =    1.325
peak=    3.359 closest distance to " O   HOH Z 417 " =    3.133
peak=    3.358 closest distance to " O   HOH Z  49 " =    2.181
peak=    3.356 closest distance to " O   HOH Z 128 " =    2.061
peak=    3.354 closest distance to " N   ASN A 127 " =    1.235
peak=    3.354 closest distance to " CG2 VAL A 197 " =    1.102
peak=    3.352 closest distance to " O   HOH Z 173 " =    1.844
peak=    3.352 closest distance to " CB  MET A  40 " =    0.830
peak=    3.351 closest distance to " O   HOH Z 421 " =    1.771
peak=    3.345 closest distance to " CG  LEU A 167 " =    1.241
peak=    3.345 closest distance to " OG  SER A  22 " =    2.693
peak=    3.345 closest distance to " O   HOH Z 383 " =    1.740
peak=    3.342 closest distance to " CG2 ILE A  20 " =    1.458
peak=    3.340 closest distance to " CB  ALA A  34 " =    0.973
peak=    3.335 closest distance to " O   HOH Z 171 " =    2.078
peak=    3.335 closest distance to " CZ2 TRP A 179 " =    1.649
peak=    3.334 closest distance to " CB  THR A  31 " =    1.758
peak=    3.332 closest distance to " O   HOH Z  64 " =    2.123
peak=    3.326 closest distance to " O   HOH Z 411 " =    3.808
peak=    3.324 closest distance to " CA  MET A 105 " =    1.026
peak=    3.322 closest distance to " O   HOH Z 166 " =    3.880
peak=    3.319 closest distance to " O   HOH Z 327 " =    1.670
peak=    3.315 closest distance to " CA  ALA A 248 " =    1.264
peak=    3.312 closest distance to " CB  GLN A  89 " =    1.333
peak=    3.312 closest distance to " CB  SER A 141 " =    1.018
peak=    3.312 closest distance to " CA  ALA A  43 " =    1.276
peak=    3.312 closest distance to " O   HOH Z 295 " =    1.542
peak=    3.308 closest distance to " O   HOH Z 403 " =    1.305
peak=    3.307 closest distance to " O   HOH Z 423 " =    2.926
peak=    3.307 closest distance to " CD  LYS A 166 " =    1.235
peak=    3.304 closest distance to " CA  PHE A 283 " =    1.338
peak=    3.303 closest distance to " O   HOH Z 290 " =    0.866
peak=    3.300 closest distance to " O   HOH Z 261 " =    1.477
peak=    3.299 closest distance to " O   HOH Z  88 " =    3.368
peak=    3.299 closest distance to " O   HOH Z 199 " =    1.500
peak=    3.297 closest distance to " O   HOH Z 128 " =    2.382
peak=    3.295 closest distance to " N   VAL A 126 " =    1.294
peak=    3.293 closest distance to " O   HOH Z 437 " =    1.231
peak=    3.293 closest distance to " CG1 ILE A 151 " =    0.971
peak=    3.288 closest distance to " O  BHOH Z 338 " =    2.255
peak=    3.288 closest distance to " CB  TYR A 116 " =    0.799
peak=    3.279 closest distance to " CB  ALA A   9 " =    1.540
peak=    3.273 closest distance to " O   HOH Z 329 " =    3.831
peak=    3.273 closest distance to " NE2 GLN A  77 " =    3.203
peak=    3.268 closest distance to " CB  SER A  26 " =    1.641
peak=    3.267 closest distance to " O   HOH Z 419 " =    1.949
peak=    3.266 closest distance to " O   HOH Z 279 " =    2.170
peak=    3.265 closest distance to " O   HOH Z 337 " =    3.689
peak=    3.265 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.265 closest distance to " CB  LEU A 255 " =    0.774
peak=    3.263 closest distance to " CB  ASN A 224 " =    0.987
peak=    3.261 closest distance to " ND1 HIS A  86 " =    1.673
peak=    3.249 closest distance to " CB  GLN A  88 " =    1.224
peak=    3.247 closest distance to " O   HOH Z 273 " =    2.792
peak=    3.243 closest distance to " O   THR A 220 " =    1.302
peak=    3.243 closest distance to " O   HOH Z 135 " =    1.635
peak=    3.242 closest distance to " O   THR A 251 " =    1.237
peak=    3.235 closest distance to " O   HOH Z 435 " =    1.901
peak=    3.229 closest distance to " CG  PRO A 213 " =    0.986
peak=    3.224 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.222 closest distance to " O   HOH Z 163 " =    1.712
peak=    3.220 closest distance to " O   HOH Z 285 " =    2.933
peak=    3.214 closest distance to " O   HOH Z 366 " =    3.313
peak=    3.212 closest distance to " CB  ILE A 120 " =    1.279
peak=    3.210 closest distance to " CA  ASP A 140 " =    1.130
peak=    3.207 closest distance to " CG1 VAL A 153 " =    0.939
peak=    3.204 closest distance to " O   HOH Z 116 " =    1.731
peak=    3.204 closest distance to " CB  ALA A 242 " =    0.973
peak=    3.202 closest distance to " CA  ASN A 176 " =    1.750
peak=    3.198 closest distance to " CB  ASN A 110 " =    1.159
peak=    3.197 closest distance to " CA  ASN A 217 " =    1.167
peak=    3.196 closest distance to " O   HOH Z 409 " =    3.040
peak=    3.193 closest distance to " CG  MET A 185 " =    1.130
peak=    3.191 closest distance to " CA  ASN A  74 " =    1.302
peak=    3.191 closest distance to " O   ALA A 158 " =    1.292
peak=    3.190 closest distance to " CB  ALA A   1 " =    4.720
peak=    3.190 closest distance to " CG  GLN A  77 " =    2.185
peak=    3.189 closest distance to " CB  ARG A 138 " =    0.943
peak=    3.187 closest distance to " CB  ASN A 215 " =    1.131
peak=    3.185 closest distance to " O   HOH Z 219 " =    2.003
peak=    3.184 closest distance to " CA  ALA A 233 " =    1.389
peak=    3.183 closest distance to " O   HOH Z 353 " =    2.717
peak=    3.172 closest distance to " O   HOH Z 341 " =    1.869
peak=    3.170 closest distance to " CG  LYS A  76 " =    0.986
peak=    3.167 closest distance to " CA  LEU A 101 " =    1.513
peak=    3.164 closest distance to " CG  GLN A  11 " =    1.570
peak=    3.163 closest distance to " O   HOH Z 374 " =    2.652
peak=    3.163 closest distance to " CB  GLN A 278 " =    0.893
peak=    3.162 closest distance to " O   ALA A 165 " =    1.462
peak=    3.159 closest distance to " O   ALA A   1 " =    1.651
peak=    3.159 closest distance to " CA  GLY A 267 " =    1.142
peak=    3.158 closest distance to " CB  ALA A 248 " =    0.887
peak=    3.157 closest distance to " O   HOH Z  71 " =    2.319
peak=    3.156 closest distance to " O   HOH Z 357 " =    1.870
peak=    3.146 closest distance to " CG BARG A 275 " =    1.452
peak=    3.138 closest distance to " O   HOH Z 261 " =    2.201
peak=    3.138 closest distance to " CA  ASN A 252 " =    1.850
peak=    3.136 closest distance to " O   HOH Z 299 " =    4.520
peak=    3.136 closest distance to " CE  LYS A  48 " =    1.040
peak=    3.133 closest distance to " O   HOH Z  85 " =    2.238
peak=    3.125 closest distance to " N   GLN A 278 " =    1.161
peak=    3.122 closest distance to " O   HOH Z 406 " =    1.534
peak=    3.122 closest distance to " O   TRP A 274 " =    1.852
peak=    3.122 closest distance to " CA  VAL A 125 " =    1.092
peak=    3.121 closest distance to " CA  SER A  87 " =    1.055
peak=    3.120 closest distance to " CB  SER A  62 " =    1.269
peak=    3.110 closest distance to " CD1AILE A 234 " =    0.948
peak=    3.106 closest distance to " CA  ARG A 102 " =    1.062
peak=    3.098 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.096 closest distance to " O   HOH Z 156 " =    2.955
peak=    3.095 closest distance to " CB  VAL A 126 " =    1.148
peak=    3.094 closest distance to " O   HOH Z 371 " =    1.693
peak=    3.092 closest distance to " CD  ARG A 219 " =    1.116
peak=    3.086 closest distance to " OG  SER A 206 " =    1.306
peak=    3.085 closest distance to " CA  SER A 146 " =    1.704
peak=    3.085 closest distance to " O   HOH Z 430 " =    5.454
peak=    3.078 closest distance to " O   HOH Z 365 " =    2.965
peak=    3.077 closest distance to " CG  GLN A  89 " =    1.493
peak=    3.073 closest distance to " CD1 ILE A 106 " =    0.919
peak=    3.070 closest distance to " O   HOH Z 336 " =    1.730
peak=    3.062 closest distance to " CG1 ILE A  49 " =    1.459
peak=    3.054 closest distance to " CA  ALA A 154 " =    0.976
peak=    3.049 closest distance to " CB  GLU A  46 " =    1.082
peak=    3.034 closest distance to " O   HOH Z 302 " =    1.902
peak=    3.010 closest distance to " O   HOH Z 258 " =    1.873

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.807 - 5.620
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.807 - 5.620

peak=   -4.874 closest distance to " O   HOH Z 266 " =    4.938
peak=   -4.577 closest distance to " CB  PRO A 243 " =    2.651
peak=   -4.564 closest distance to " CD  ARG A 156 " =    2.005
peak=   -4.444 closest distance to " CG  GLN A 223 " =    2.048
peak=   -4.404 closest distance to " SG  CYS A 254 " =    3.561
peak=   -4.401 closest distance to " O   VAL A  67 " =    2.738
peak=   -4.357 closest distance to " C   HIS A 108 " =    1.066
peak=   -4.168 closest distance to " O   HOH Z 231 " =    2.233
peak=   -4.160 closest distance to " O   HOH Z 198 " =    2.063
peak=   -4.160 closest distance to " OG BSER A 134 " =    1.204
peak=   -4.130 closest distance to " O   HOH Z 377 " =    2.087
peak=   -4.123 closest distance to " O   HOH Z 389 " =    1.882
peak=   -4.109 closest distance to " O   HOH Z 372 " =    2.408
peak=   -4.068 closest distance to " O   HOH Z  10 " =    1.510
peak=   -3.963 closest distance to " CE  MET A 105 " =    2.329
peak=   -3.952 closest distance to " CB  ALA A 161 " =    2.536
peak=   -3.946 closest distance to " ND2 ASN A  45 " =    1.771
peak=   -3.943 closest distance to " O   HOH Z 114 " =    3.155
peak=   -3.938 closest distance to " CZ  PHE A  59 " =    1.609
peak=   -3.932 closest distance to " CB  ALA A 291 " =    2.243
peak=   -3.929 closest distance to " CZ3 TRP A 179 " =    1.169
peak=   -3.923 closest distance to " CD  GLN A  58 " =    1.089
peak=   -3.915 closest distance to " CG1 VAL A 112 " =    2.856
peak=   -3.869 closest distance to " O   HOH Z 126 " =    1.892
peak=   -3.861 closest distance to " O   HOH Z 435 " =    2.804
peak=   -3.852 closest distance to " O   HOH Z 196 " =    2.028
peak=   -3.843 closest distance to " OXT GLY A 302 " =    2.843
peak=   -3.841 closest distance to " N   ALA A  43 " =    2.677
peak=   -3.837 closest distance to " CD1 PHE A  59 " =    1.859
peak=   -3.813 closest distance to " CA  VAL A  67 " =    2.908
peak=   -3.806 closest distance to " CG2 ILE A 263 " =    2.316
peak=   -3.798 closest distance to " O   HOH Z  43 " =    1.615
peak=   -3.797 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.793 closest distance to " O   HOH Z 353 " =    2.140
peak=   -3.772 closest distance to " O   PRO A 163 " =    2.042
peak=   -3.758 closest distance to " CD  ARG A 139 " =    1.547
peak=   -3.741 closest distance to " CD2 PHE A 192 " =    2.045
peak=   -3.718 closest distance to " CG  PHE A 283 " =    2.679
peak=   -3.716 closest distance to " CB  ASN A  39 " =    2.328
peak=   -3.712 closest distance to " O   HOH Z 311 " =    3.659
peak=   -3.700 closest distance to " O   HOH Z 290 " =    1.306
peak=   -3.690 closest distance to " CE2 PHE A 218 " =    2.447
peak=   -3.689 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.679 closest distance to " O   PRO A 198 " =    1.313
peak=   -3.668 closest distance to " CB  TYR A  15 " =    2.195
peak=   -3.667 closest distance to " O   HOH Z 198 " =    1.430
peak=   -3.664 closest distance to " O   HOH Z 185 " =    2.283
peak=   -3.650 closest distance to " OD1 ASP A 171 " =    1.631
peak=   -3.649 closest distance to " O   HOH Z  60 " =    2.507
peak=   -3.637 closest distance to " NH2AARG A 275 " =    5.339
peak=   -3.634 closest distance to " O   HOH Z 407 " =    3.083
peak=   -3.623 closest distance to " SG ACYS A 201 " =    1.858
peak=   -3.613 closest distance to " O   HOH Z 211 " =    1.686
peak=   -3.612 closest distance to " N   SER A 212 " =    2.037
peak=   -3.611 closest distance to " CA  GLY A 203 " =    2.322
peak=   -3.607 closest distance to " CD1 LEU A 228 " =    2.247
peak=   -3.588 closest distance to " CB  ALA A 291 " =    2.421
peak=   -3.570 closest distance to " O   SER A 135 " =    1.475
peak=   -3.567 closest distance to " C   ALA A 158 " =    1.297
peak=   -3.560 closest distance to " O   HOH Z 313 " =    1.923
peak=   -3.557 closest distance to " CG1 VAL A 250 " =    2.606
peak=   -3.557 closest distance to " NH1 ARG A 195 " =    2.610
peak=   -3.548 closest distance to " N   ASP A 286 " =    2.472
peak=   -3.548 closest distance to " OG  SER A  62 " =    1.725
peak=   -3.545 closest distance to " CG  ARG A 269 " =    2.392
peak=   -3.540 closest distance to " CD1 LEU A 101 " =    2.337
peak=   -3.540 closest distance to " OD2 ASP A 191 " =    1.531
peak=   -3.537 closest distance to " ND2 ASN A  45 " =    1.090
peak=   -3.532 closest distance to " CB  ALA A  43 " =    2.535
peak=   -3.526 closest distance to " CA  GLY A 241 " =    3.071
peak=   -3.523 closest distance to " O   HOH Z 253 " =    3.946
peak=   -3.521 closest distance to " O   HOH Z  52 " =    1.403
peak=   -3.517 closest distance to " O   PHE A 218 " =    1.585
peak=   -3.513 closest distance to " O   HOH Z 351 " =    1.518
peak=   -3.510 closest distance to " CG  ARG A  66 " =    2.426
peak=   -3.498 closest distance to " CA  ASP A 298 " =    1.045
peak=   -3.497 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.494 closest distance to " OG  SER A  97 " =    2.190
peak=   -3.492 closest distance to " O   HOH Z 292 " =    4.550
peak=   -3.490 closest distance to " OE2 GLU A   2 " =    1.899
peak=   -3.489 closest distance to " NE2 GLN A  88 " =    1.911
peak=   -3.486 closest distance to " N   GLN A  58 " =    1.613
peak=   -3.482 closest distance to " O   HOH Z  13 " =    1.693
peak=   -3.473 closest distance to " O   HOH Z  73 " =    2.175
peak=   -3.467 closest distance to " OD1 ASN A 187 " =    1.568
peak=   -3.463 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.451 closest distance to " CD  ARG A 195 " =    5.185
peak=   -3.443 closest distance to " OD1 ASN A 148 " =    1.572
peak=   -3.443 closest distance to " O   HOH Z  38 " =    1.480
peak=   -3.435 closest distance to " O   LYS A 117 " =    1.724
peak=   -3.434 closest distance to " CB  ASP A 132 " =    2.338
peak=   -3.431 closest distance to " CD2 PHE A 225 " =    1.175
peak=   -3.428 closest distance to " CB  ALA A 131 " =    2.114
peak=   -3.418 closest distance to " OG BSER A 134 " =    1.762
peak=   -3.414 closest distance to " O   HOH Z 166 " =    1.959
peak=   -3.398 closest distance to " C   LEU A 143 " =    1.116
peak=   -3.397 closest distance to " O   HOH Z 298 " =    1.290
peak=   -3.395 closest distance to " OE1 GLN A  88 " =    1.189
peak=   -3.392 closest distance to " CD1 LEU A 297 " =    2.403
peak=   -3.391 closest distance to " CG1 VAL A 112 " =    2.608
peak=   -3.378 closest distance to " O   HOH Z 394 " =    1.469
peak=   -3.376 closest distance to " CG  TRP A 266 " =    1.832
peak=   -3.371 closest distance to " CA  GLY A 133 " =    1.995
peak=   -3.370 closest distance to " O   GLY A 211 " =    1.433
peak=   -3.369 closest distance to " CB  PHE A 208 " =    2.266
peak=   -3.360 closest distance to " O   HOH Z   6 " =    1.523
peak=   -3.356 closest distance to " O   ALA A 161 " =    1.719
peak=   -3.356 closest distance to " ND2 ASN A 249 " =    2.091
peak=   -3.347 closest distance to " O   SER A  95 " =    1.541
peak=   -3.347 closest distance to " N   THR A 235 " =    1.382
peak=   -3.345 closest distance to " OD1 ASP A 191 " =    1.542
peak=   -3.343 closest distance to " CZ  TYR A 169 " =    1.707
peak=   -3.338 closest distance to " OG  SER A  26 " =    1.285
peak=   -3.336 closest distance to " O   HOH Z  44 " =    2.205
peak=   -3.334 closest distance to " O   VAL A 189 " =    2.568
peak=   -3.328 closest distance to " CA  GLY A  98 " =    1.952
peak=   -3.326 closest distance to " NH2BARG A 275 " =    1.930
peak=   -3.323 closest distance to " O   HOH Z 295 " =    1.557
peak=   -3.320 closest distance to " CB  ALA A 248 " =    2.057
peak=   -3.317 closest distance to " NH1 ARG A  36 " =    2.093
peak=   -3.316 closest distance to " O   HOH Z 102 " =    1.588
peak=   -3.316 closest distance to " O   HOH Z  51 " =    1.686
peak=   -3.314 closest distance to " CG1 VAL A 125 " =    2.381
peak=   -3.310 closest distance to " CB  ALA A 248 " =    2.339
peak=   -3.301 closest distance to " O   ARG A 145 " =    1.549
peak=   -3.300 closest distance to " CB  ASP A 286 " =    2.154
peak=   -3.297 closest distance to " O   HOH Z  37 " =    1.850
peak=   -3.295 closest distance to " O   HOH Z 322 " =    1.602
peak=   -3.291 closest distance to " O   MET A  40 " =    2.729
peak=   -3.287 closest distance to " CD2 PHE A  61 " =    2.582
peak=   -3.285 closest distance to " CG  GLN A  11 " =    1.791
peak=   -3.281 closest distance to " O   HOH Z 361 " =    3.392
peak=   -3.277 closest distance to " O   HOH Z  11 " =    2.106
peak=   -3.274 closest distance to " N   ASP A 171 " =    2.392
peak=   -3.273 closest distance to " O   HOH Z 385 " =    1.902
peak=   -3.273 closest distance to " CB  PRO A 163 " =    2.489
peak=   -3.272 closest distance to " CB  ASP A 286 " =    1.830
peak=   -3.269 closest distance to " O   HOH Z  11 " =    1.715
peak=   -3.268 closest distance to " O   HOH Z 324 " =    2.117
peak=   -3.266 closest distance to " O   HOH Z 414 " =    1.673
peak=   -3.261 closest distance to " N   ALA A 226 " =    2.037
peak=   -3.261 closest distance to " NH2 ARG A  79 " =    1.979
peak=   -3.256 closest distance to " C   PHE A  59 " =    1.406
peak=   -3.256 closest distance to " CB  CYS A 201 " =    2.662
peak=   -3.255 closest distance to " O   HOH Z 385 " =    2.054
peak=   -3.243 closest distance to " CG1 VAL A 197 " =    2.274
peak=   -3.242 closest distance to " N   THR A 157 " =    1.557
peak=   -3.234 closest distance to " CD2 LEU A 300 " =    2.882
peak=   -3.229 closest distance to " OE1 GLN A 223 " =    2.008
peak=   -3.228 closest distance to " O   VAL A 174 " =    2.015
peak=   -3.222 closest distance to " CD1 LEU A 101 " =    2.867
peak=   -3.221 closest distance to " CG  GLU A 277 " =    1.197
peak=   -3.221 closest distance to " O   HOH Z 417 " =    2.503
peak=   -3.217 closest distance to " NE  ARG A  36 " =    1.942
peak=   -3.217 closest distance to " OD2 ASP A 171 " =    1.785
peak=   -3.213 closest distance to " CD2 TYR A 247 " =    2.357
peak=   -3.209 closest distance to " O   HOH Z  93 " =    2.103
peak=   -3.207 closest distance to " O   HOH Z  88 " =    2.053
peak=   -3.204 closest distance to " C   MET A 188 " =    1.392
peak=   -3.203 closest distance to " CB  TRP A  85 " =    2.490
peak=   -3.203 closest distance to " NE2 GLN A 278 " =    1.745
peak=   -3.196 closest distance to " OD2 ASP A 171 " =    2.329
peak=   -3.193 closest distance to " CG  MET A 105 " =    0.949
peak=   -3.192 closest distance to " O   HOH Z 123 " =    2.226
peak=   -3.188 closest distance to " O   HOH Z 166 " =    1.591
peak=   -3.188 closest distance to " O   ALA A  10 " =    1.655
peak=   -3.185 closest distance to " ND2 ASN A 187 " =    1.614
peak=   -3.183 closest distance to " O   HOH Z 234 " =    4.123
peak=   -3.183 closest distance to " CD  GLN A 223 " =    1.324
peak=   -3.169 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.166 closest distance to " OXT GLY A 302 " =    3.288
peak=   -3.165 closest distance to " O   TRP A  70 " =    1.485
peak=   -3.161 closest distance to " CD  GLU A 236 " =    1.043
peak=   -3.158 closest distance to " OD2 ASP A  50 " =    1.624
peak=   -3.157 closest distance to " O   HOH Z 262 " =    2.873
peak=   -3.154 closest distance to " CG2 VAL A 189 " =    2.110
peak=   -3.151 closest distance to " O   HOH Z 191 " =    5.620
peak=   -3.143 closest distance to " CG2 THR A 221 " =    2.265
peak=   -3.139 closest distance to " O   HOH Z 200 " =    3.413
peak=   -3.139 closest distance to " O   HOH Z 426 " =    1.611
peak=   -3.132 closest distance to " CB  ALA A  10 " =    2.244
peak=   -3.129 closest distance to " SD  MET A 188 " =    2.238
peak=   -3.129 closest distance to " CA  GLY A 241 " =    2.795
peak=   -3.125 closest distance to " O   HOH Z 184 " =    1.817
peak=   -3.124 closest distance to " OG BSER A 210 " =    2.235
peak=   -3.122 closest distance to " O   HOH Z 322 " =    1.340
peak=   -3.120 closest distance to " CD1 TYR A 247 " =    2.751
peak=   -3.115 closest distance to " N   LYS A 289 " =    1.579
peak=   -3.114 closest distance to " C   TRP A 274 " =    1.446
peak=   -3.106 closest distance to " O   ASN A 301 " =    1.428
peak=   -3.104 closest distance to " O   LYS A 289 " =    2.979
peak=   -3.100 closest distance to " O   HOH Z 139 " =    2.914
peak=   -3.097 closest distance to " O   HOH Z 323 " =    1.491
peak=   -3.081 closest distance to " O   HOH Z 148 " =    3.384
peak=   -3.075 closest distance to " N   PHE A  59 " =    2.103
peak=   -3.074 closest distance to " CB  ASP A 132 " =    2.374
peak=   -3.059 closest distance to " O   ASP A 171 " =    2.004
peak=   -3.050 closest distance to " O   HOH Z 193 " =    1.698
peak=   -3.043 closest distance to " CD2 LEU A 237 " =    2.637
peak=   -3.036 closest distance to " O   HOH Z 111 " =    2.227
peak=   -3.035 closest distance to " OD1 ASP A 200 " =    1.414

================= 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    :  0.1962 0.1967   5.547379e+00   5.558020e+00
   1_bss:  0.1751 0.1764   5.499023e+00   5.501453e+00
   1_xyz:  0.1254 0.1456   5.182169e+00   5.315289e+00
   1_adp:  0.1168 0.1453   5.130642e+00   5.319696e+00
   1_occ:  0.1163 0.1451   5.127386e+00   5.317042e+00
   2_bss:  0.1169 0.1448   5.129906e+00   5.315546e+00
   2_xyz:  0.1106 0.1473   5.102402e+00   5.324102e+00
   2_adp:  0.1067 0.1487   5.090133e+00   5.333960e+00
   2_occ:  0.1065 0.1488   5.090123e+00   5.334418e+00
   3_bss:  0.1064 0.1488   5.090276e+00   5.334453e+00
   3_xyz:  0.1068 0.1506   5.098370e+00   5.346858e+00
   3_adp:  0.1065 0.1512   5.099027e+00   5.350340e+00
   3_occ:  0.1065 0.1513   5.099181e+00   5.350743e+00
   4_bss:  0.1064 0.1513   5.099287e+00   5.350782e+00
   4_xyz:  0.1094 0.1527   5.118854e+00   5.362358e+00
   4_adp:  0.1089 0.1541   5.120696e+00   5.370158e+00
   4_occ:  0.1089 0.1542   5.120741e+00   5.370323e+00
   5_bss:  0.1088 0.1542   5.120847e+00   5.370373e+00
   5_xyz:  0.1058 0.1543   5.106025e+00   5.368470e+00
   5_adp:  0.1055 0.1554   5.106927e+00   5.372105e+00
   5_occ:  0.1055 0.1554   5.106928e+00   5.372183e+00
   5_bss:  0.1053 0.1552   5.106646e+00   5.371829e+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:  0.321  47.797  -2.579  -2.820  -1.426  -0.000  -0.000  -0.000
   1_xyz:  0.321  47.797  -2.579  -2.820  -1.426  -0.000  -0.000  -0.000
   1_adp:  0.321  47.797  -2.579  -2.820  -1.426  -0.000  -0.000  -0.000
   1_occ:  0.321  47.797  -2.579  -2.820  -1.426  -0.000  -0.000  -0.000
   2_bss:  0.326  47.797  -2.790  -2.705  -1.625  -0.000  -0.000  -0.000
   2_xyz:  0.326  47.797  -2.790  -2.705  -1.625  -0.000  -0.000  -0.000
   2_adp:  0.326  47.797  -2.790  -2.705  -1.625  -0.000  -0.000  -0.000
   2_occ:  0.326  47.797  -2.790  -2.705  -1.625  -0.000  -0.000  -0.000
   3_bss:  0.326  47.797  -2.515  -2.381  -1.395  -0.000  -0.000  -0.000
   3_xyz:  0.326  47.797  -2.515  -2.381  -1.395  -0.000  -0.000  -0.000
   3_adp:  0.326  47.797  -2.515  -2.381  -1.395  -0.000  -0.000  -0.000
   3_occ:  0.326  47.797  -2.515  -2.381  -1.395  -0.000  -0.000  -0.000
   4_bss:  0.326  47.797  -2.339  -2.186  -1.231  -0.000  -0.000  -0.000
   4_xyz:  0.326  47.797  -2.339  -2.186  -1.231  -0.000  -0.000  -0.000
   4_adp:  0.326  47.797  -2.339  -2.186  -1.231  -0.000  -0.000  -0.000
   4_occ:  0.326  47.797  -2.339  -2.186  -1.231  -0.000  -0.000  -0.000
   5_bss:  0.326  47.797  -2.159  -2.000  -1.071  -0.000  -0.000  -0.000
   5_xyz:  0.326  47.797  -2.159  -2.000  -1.071  -0.000  -0.000  -0.000
   5_adp:  0.326  47.797  -2.159  -2.000  -1.071  -0.000  -0.000  -0.000
   5_occ:  0.326  47.797  -2.159  -2.000  -1.071  -0.000  -0.000  -0.000
   5_bss:  0.321  48.899  -1.865  -1.725  -0.807  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  17.272 0.8903  1.0329    10672.779
   1_bss:  15.738 0.9028  0.9669     7819.679
   1_xyz:  12.377 0.9282  0.9798     5556.171
   1_adp:  12.518 0.9267  0.9769     5557.322
   1_occ:  12.471 0.9270  0.9768     5496.958
   2_bss:  12.458 0.9271  0.9732     5474.672
   2_xyz:  12.525 0.9269  0.9726     5591.743
   2_adp:  12.764 0.9249  0.9678     5629.591
   2_occ:  12.776 0.9248  0.9677     5635.416
   3_bss:  12.780 0.9248  0.9773     5637.867
   3_xyz:  12.988 0.9232  0.9762     5798.585
   3_adp:  13.058 0.9227  0.9707     5828.973
   3_occ:  13.068 0.9226  0.9706     5834.416
   4_bss:  13.070 0.9226  0.9769     5835.953
   4_xyz:  13.259 0.9213  0.9762     5967.297
   4_adp:  13.424 0.9199  0.9695     6043.981
   4_occ:  13.429 0.9199  0.9694     6047.407
   5_bss:  13.431 0.9199  0.9756     6049.136
   5_xyz:  13.415 0.9199  0.9757     6037.298
   5_adp:  13.511 0.9191  0.9678     6067.677
   5_occ:  13.513 0.9191  0.9677     6069.639
   5_bss:  13.508 0.9191  0.9777     6063.049
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.5959e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.5959e-01
   1_xyz:   1.020  0.008  0.077 15.397  0.004  4.113   6.4088e-02
   1_adp:   1.020  0.008  0.077 15.397  0.004  4.113   6.4088e-02
   1_occ:   1.020  0.008  0.077 15.397  0.004  4.113   6.4088e-02
   2_bss:   1.020  0.008  0.077 15.397  0.004  4.113   6.4088e-02
   2_xyz:   1.080  0.010  0.083 15.274  0.005  4.116   7.2938e-02
   2_adp:   1.080  0.010  0.083 15.274  0.005  4.116   7.2938e-02
   2_occ:   1.080  0.010  0.083 15.274  0.005  4.116   7.2938e-02
   3_bss:   1.080  0.010  0.083 15.274  0.005  4.116   7.2938e-02
   3_xyz:   1.017  0.008  0.079 15.026  0.004  4.116   6.4549e-02
   3_adp:   1.017  0.008  0.079 15.026  0.004  4.116   6.4549e-02
   3_occ:   1.017  0.008  0.079 15.026  0.004  4.116   6.4549e-02
   4_bss:   1.017  0.008  0.079 15.026  0.004  4.116   6.4549e-02
   4_xyz:   0.901  0.006  0.071 14.758  0.004  4.116   5.1944e-02
   4_adp:   0.901  0.006  0.071 14.758  0.004  4.116   5.1944e-02
   4_occ:   0.901  0.006  0.071 14.758  0.004  4.116   5.1944e-02
   5_bss:   0.901  0.006  0.071 14.758  0.004  4.116   5.1944e-02
   5_xyz:   1.011  0.008  0.079 14.941  0.004  4.117   6.3513e-02
   5_adp:   1.011  0.008  0.079 14.941  0.004  4.117   6.3513e-02
   5_occ:   1.011  0.008  0.079 14.941  0.004  4.117   6.3513e-02
   5_bss:   1.011  0.008  0.079 14.941  0.004  4.117   6.3513e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4108e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4108e-01
   1_xyz:   7.930  0.047  0.263 85.303  0.033  2.362   4.8089e-02
   1_adp:   7.930  0.047  0.263 85.303  0.033  2.362   4.8089e-02
   1_occ:   7.930  0.047  0.263 85.303  0.033  2.362   4.8089e-02
   2_bss:   7.930  0.047  0.263 85.303  0.033  2.362   4.8089e-02
   2_xyz:   6.905  0.046  0.277 83.725  0.037  2.240   5.9757e-02
   2_adp:   6.905  0.046  0.277 83.725  0.037  2.240   5.9757e-02
   2_occ:   6.905  0.046  0.277 83.725  0.037  2.240   5.9757e-02
   3_bss:   6.905  0.046  0.277 83.725  0.037  2.240   5.9757e-02
   3_xyz:   6.809  0.045  0.252 83.758  0.038  2.328   4.8574e-02
   3_adp:   6.809  0.045  0.252 83.758  0.038  2.328   4.8574e-02
   3_occ:   6.809  0.045  0.252 83.758  0.038  2.328   4.8574e-02
   4_bss:   6.809  0.045  0.252 83.758  0.038  2.328   4.8574e-02
   4_xyz:   6.858  0.039  0.222 83.407  0.037  2.364   3.0709e-02
   4_adp:   6.858  0.039  0.222 83.407  0.037  2.364   3.0709e-02
   4_occ:   6.858  0.039  0.222 83.407  0.037  2.364   3.0709e-02
   5_bss:   6.858  0.039  0.222 83.407  0.037  2.364   3.0709e-02
   5_xyz:   6.730  0.044  0.248 83.345  0.036  2.311   4.7277e-02
   5_adp:   6.730  0.044  0.248 83.345  0.036  2.311   4.7277e-02
   5_occ:   6.730  0.044  0.248 83.345  0.036  2.311   4.7277e-02
   5_bss:   6.730  0.044  0.248 83.345  0.036  2.311   4.7277e-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:  75.84   0.00  16.26  75.84   0.00  12.49  62.38   5.04  36.83
   1_occ:  75.84   0.00  16.26  75.84   0.00  12.49  62.38   5.04  36.83
   2_bss:  75.84   0.00  16.26  75.84   0.00  12.49  62.38   5.04  36.83
   2_xyz:  75.84   0.00  16.26  75.84   0.00  12.49  62.38   5.04  36.83
   2_adp:  72.56   1.65  16.62  72.56   1.65  12.79  66.65   4.78  37.49
   2_occ:  72.56   1.65  16.62  72.56   1.65  12.79  66.65   4.78  37.49
   3_bss:  72.56   1.65  16.62  72.56   1.65  12.79  66.65   4.78  37.49
   3_xyz:  72.56   1.65  16.62  72.56   1.65  12.79  66.65   4.78  37.49
   3_adp:  73.88   1.23  16.50  73.88   1.23  12.68  66.88   5.49  37.31
   3_occ:  73.88   1.23  16.50  73.88   1.23  12.68  66.88   5.49  37.31
   4_bss:  73.88   1.23  16.50  73.88   1.23  12.68  66.88   5.49  37.31
   4_xyz:  73.88   1.23  16.50  73.88   1.23  12.68  66.88   5.49  37.31
   4_adp:  77.73   0.29  16.56  77.73   0.29  12.61  68.04   6.16  38.10
   4_occ:  77.73   0.29  16.56  77.73   0.29  12.61  68.04   6.16  38.10
   5_bss:  77.73   0.29  16.56  77.73   0.29  12.61  68.04   6.16  38.10
   5_xyz:  77.73   0.29  16.56  77.73   0.29  12.61  68.04   6.16  38.10
   5_adp:  91.81   0.00  16.76  91.81   0.00  12.58  79.38   5.78  39.51
   5_occ:  91.81   0.00  16.76  91.81   0.00  12.58  79.38   5.78  39.51
   5_bss:  91.81   0.00  16.76  91.81   0.00  12.59  79.38   5.78  39.52
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.488    0.006    0.138
   1_adp:    0.488    0.006    0.138
   1_occ:    0.488    0.006    0.138
   2_bss:    0.488    0.006    0.138
   2_xyz:    0.579    0.013    0.157
   2_adp:    0.579    0.013    0.157
   2_occ:    0.579    0.013    0.157
   3_bss:    0.579    0.013    0.157
   3_xyz:    0.737    0.011    0.162
   3_adp:    0.737    0.011    0.162
   3_occ:    0.737    0.011    0.162
   4_bss:    0.737    0.011    0.162
   4_xyz:    0.817    0.005    0.165
   4_adp:    0.817    0.005    0.165
   4_occ:    0.817    0.005    0.165
   5_bss:    0.817    0.005    0.165
   5_xyz:    0.870    0.006    0.168
   5_adp:    0.870    0.006    0.168
   5_occ:    0.870    0.006    0.168
   5_bss:    0.870    0.006    0.168
------------------------------------------------------------------------

CPU time actual refinement: 322.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_785/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_785/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_785/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_785/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_785/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.55 
  Macro-tasks:
    bulk solvent and scale       = 39.90  
    individual site refinement   = 126.85 
    weights calculation          = 29.39  
    collect and process          = 6.73   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 202.96 
  Micro-tasks:
    mask                            = 0.56   
    f_calc                          = 103.47 
    alpha_beta                      = 8.54   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 107.17 
    fmodel                         = 6.71   
    r_factors                      = 0.15   
    phase_errors                   = 12.22  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 240.33 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.628 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    640 calls, 103.07 s
gradients_fft:          585 calls,  96.00 s

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

# Date 2008-01-16 Time 05:39:29 PST -0800 (1200490769.36 s)
Start R-work = 0.1962, R-free = 0.1967 (no bulk solvent and anisotropic scale)
Final R-work = 0.1281, R-free = 0.1726 (no bulk solvent and anisotropic scale)

Start R-work = 0.1751, R-free = 0.1764
Final R-work = 0.1053, R-free = 0.1552