# Date 2008-01-16 Time 06:29:21 PST -0800 (1200493761.89 s)
#phil __OFF__

Command line arguments: "../1161.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20841
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1161

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.1647, 86.822, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 2.01038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2319
                             d_min =   2.0104

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2319 2.01038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2323 -  4.3018 [2110/2135]  1900   210  10.0%
  bin  2:  4.3018 -  3.4272 [2038/2058]  1833   205  10.1%
  bin  3:  3.4272 -  2.9978 [2006/2025]  1803   203  10.1%
  bin  4:  2.9978 -  2.7254 [1987/2017]  1795   192   9.7%
  bin  5:  2.7254 -  2.5310 [1983/2002]  1787   196   9.9%
  bin  6:  2.5310 -  2.3824 [1965/1990]  1764   201  10.2%
  bin  7:  2.3824 -  2.2634 [1947/1975]  1747   200  10.3%
  bin  8:  2.2634 -  2.1652 [1959/1995]  1765   194   9.9%
  bin  9:  2.1652 -  2.0821 [1950/1992]  1761   189   9.7%
  bin 10:  2.0821 -  2.0104 [1644/1967]  1475   169  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1161/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:
        1.66 -     2.31: 4
        2.31 -     2.96: 1643
        2.96 -     3.61: 4450
        3.61 -     4.25: 9071
        4.25 -     4.90: 12723
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.663 3.040 -x+1/2,-y+1,z+1/2
  " 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 208 " - " O   HOH Z 342 "  2.242 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27886 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_1161/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1161/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.16465 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3296   r_free= 0.3203   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.053847                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7980 0.99   1380  154 0.2854 0.2634      6.3439      6.2519|
|  2:  4.7980 -  3.8282 0.99   1324  145 0.2565 0.2453      6.4569      6.4096|
|  3:  3.8282 -  3.3502 0.99   1287  143 0.2801 0.2726      6.3398      6.3663|
|  4:  3.3502 -  3.0465 0.99   1284  147 0.3042 0.2821      6.2444      6.1857|
|  5:  3.0465 -  2.8297 0.99   1292  140 0.3354 0.3653      6.1121      6.2368|
|  6:  2.8297 -  2.6638 0.99   1274  141 0.3470 0.3323      6.0667      5.9953|
|  7:  2.6638 -  2.5310 0.99   1277  136 0.3609 0.3196      6.0257      6.0511|
|  8:  2.5310 -  2.4213 0.98   1254  148 0.3679 0.3495      6.0035      5.9714|
|  9:  2.4213 -  2.3284 0.98   1255  137 0.3657 0.3609      5.9312      5.9664|
| 10:  2.3284 -  2.2483 1.00   1268  141 0.3650 0.3679      5.9168       5.938|
| 11:  2.2483 -  2.1782 0.97   1250  137 0.3912 0.3945      5.9128      5.9572|
| 12:  2.1782 -  2.1161 0.98   1240  142 0.3890 0.3880      5.8181      5.9022|
| 13:  2.1161 -  2.0605 1.00   1258  136 0.3934 0.4002      5.7608       5.703|
| 14:  2.0605 -  2.0104 0.77    987  112 0.3785 0.3542       5.675      5.6047|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.7980  1380   154  0.80  25.32   0.85     0.81      39598.62|
|  2:  4.7980 -  3.8282  1324   145  0.85  21.45   0.97     0.90      42800.51|
|  3:  3.8282 -  3.3502  1287   143  0.81  25.49   0.97     0.92      43443.69|
|  4:  3.3502 -  3.0465  1284   147  0.78  28.65   0.97     0.90      40072.38|
|  5:  3.0465 -  2.8297  1292   140  0.70  35.77   0.97     0.86      36019.47|
|  6:  2.8297 -  2.6638  1274   141  0.70  35.74   0.98     0.85      31461.21|
|  7:  2.6638 -  2.5310  1277   136  0.68  36.95   0.97     0.85      29205.12|
|  8:  2.5310 -  2.4213  1254   148  0.68  37.16   0.99     0.87      27144.32|
|  9:  2.4213 -  2.3284  1255   137  0.68  37.73   0.99     0.86      26089.09|
| 10:  2.3284 -  2.2483  1268   141  0.65  40.09   1.03     0.85      25332.18|
| 11:  2.2483 -  2.1782  1250   137  0.63  41.95   1.02     0.84      24968.82|
| 12:  2.1782 -  2.1161  1240   142  0.64  40.79   1.00     0.88      22768.60|
| 13:  2.1161 -  2.0605  1258   136  0.66  39.40   1.00     0.90      18186.31|
| 14:  2.0605 -  2.0104   987   112  0.72  34.59   1.00     0.90      12231.43|
|alpha:            min =        0.81 max =            0.92 mean =         0.87|
|beta:             min =    12231.43 max =        43443.69 mean =     30396.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.97 mean =        34.22|
|phase err.(test): min =        0.00 max =           89.96 mean =        33.68|
|-----------------------------------------------------------------------------|

============================== 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 = 4.483664              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.835   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.720098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.649   (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 |  1.663 -  1.987:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.987 -  2.310:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.310 -  2.634:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.634 -  2.958:     1604 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.958 -  3.281:     1893 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.281 -  3.605:     2557 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.605 -  3.929:     4685 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.929 -  4.253:     4386 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.253 -  4.576:     5795 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.576 -  4.900:     6928 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| 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  1.663 |       0.153 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3296   r_free= 0.3203   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.053847                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3172   r_free= 0.3090   ksol= 0.32   Bsol= 64.54   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,-1.98,-1.08,-0.00,-0.00,-0.00); trace/3= -0.44                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.033060                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.081741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.076   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.413181              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.347   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3172      final r-factor (work) = 0.1888          |
| start r-factor (free) = 0.3090      final r-factor (free) = 0.2088          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4871 = 4.08 * 0.50 * 6.0388 + 1.00 * 0.1626                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8321 = 4.08 * 0.50 * 5.7629 + 1.00 * 0.0708                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1888      final r-factor (work) = 0.1752          |
| start r-factor (free) = 0.2088      final r-factor (free) = 0.2120          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3881 = 0.41 * 1.00 * 5.7629 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3898 = 0.41 * 1.00 * 5.5008 + 1.00 * 0.1170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.76  16.74    None  None   None       |
|    all(noH): 2823   0      0.00    102.76  16.74    None  None   None       |
|    Sol.    : 438    0      5.10    64.05   37.99    None  None   None       |
|    Mac.    : 2385   0      0.00    102.76  12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.276:  971   |   5:    51.381 -  61.657:   73        |
|      1:    10.276 -  20.552: 1224   |   6:    61.657 -  71.933:    4        |
|      2:    20.552 -  30.828:  252   |   7:    71.933 -  82.209:    0        |
|      3:    30.828 -  41.105:  159   |   8:    82.209 -  92.485:    0        |
|      4:    41.105 -  51.381:  139   |   9:    92.485 - 102.761:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1752 r_free = 0.2120             target_work(ml) = 5.507         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1746 r_free = 0.2114             target_work(ml) = 5.505         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1746   r_free= 0.2114   ksol= 0.32   Bsol= 64.54   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,-1.98,-1.08,-0.00,-0.00,-0.00); trace/3= -0.44                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.504615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1723   r_free= 0.2076   ksol= 0.34   Bsol= 66.31   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-2.64,-1.61,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.498467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.813339              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.437   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 87.837   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1723      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.2076      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0718 = 1.81 * 0.50 * 5.5157 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9432 = 1.81 * 0.50 * 5.3924 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1286          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7556 = 0.69 * 1.00 * 5.3924 + 1.00 * 0.0496                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6291 = 0.69 * 1.00 * 5.2655 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.32    80.51   17.48    None  None   None       |
|    all(noH): 2823   0      0.32    80.51   17.48    None  None   None       |
|    Sol.    : 438    0      5.66    79.65   41.16    None  None   None       |
|    Mac.    : 2385   0      0.32    80.51   13.13    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:     0.315 -   8.334:  630   |   5:    40.411 -  48.430:  100        |
|      1:     8.334 -  16.353: 1318   |   6:    48.430 -  56.449:   82        |
|      2:    16.353 -  24.373:  340   |   7:    56.449 -  64.469:   74        |
|      3:    24.373 -  32.392:  141   |   8:    64.469 -  72.488:   26        |
|      4:    32.392 -  40.411:  105   |   9:    72.488 -  80.507:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1286 r_free = 0.1698             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1285 r_free = 0.1696             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1696   ksol= 0.34   Bsol= 66.31   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-2.64,-1.61,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1694   ksol= 0.33   Bsol= 68.30   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.40,-1.33,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248455                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.433511              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.459  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.242  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0934 = 3.43 * 0.50 * 5.2653 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0058 = 3.43 * 0.50 * 5.1978 + 1.00 * 0.0824                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2366 = 0.43 * 1.00 * 5.1978 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2229 = 0.43 * 1.00 * 5.1667 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.01   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    82.01   17.23    None  None   None       |
|    Sol.    : 438    0      0.00    80.21   40.82    None  None   None       |
|    Mac.    : 2385   0      0.57    82.01   12.90    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 -   8.201:  636   |   5:    41.004 -  49.205:   96        |
|      1:     8.201 -  16.402: 1331   |   6:    49.205 -  57.405:   84        |
|      2:    16.402 -  24.602:  339   |   7:    57.405 -  65.606:   68        |
|      3:    24.602 -  32.803:  134   |   8:    65.606 -  73.807:   22        |
|      4:    32.803 -  41.004:  106   |   9:    73.807 -  82.008:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1610             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1609             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1609   ksol= 0.33   Bsol= 68.30   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.40,-1.33,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159361                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1608   ksol= 0.33   Bsol= 68.30   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-2.10,-1.00,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.612571              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.647  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.482639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.208  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8325 = 2.61 * 0.50 * 5.1674 + 1.00 * 0.0824                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8051 = 2.61 * 0.50 * 5.1538 + 1.00 * 0.0728                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4972 = 0.48 * 1.00 * 5.1538 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4959 = 0.48 * 1.00 * 5.1514 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    85.13   16.95    None  None   None       |
|    all(noH): 2823   0      0.22    85.13   16.95    None  None   None       |
|    Sol.    : 438    0      0.47    82.83   40.01    None  None   None       |
|    Mac.    : 2385   0      0.22    85.13   12.71    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:     0.225 -   8.715:  796   |   5:    42.677 -  51.168:   92        |
|      1:     8.715 -  17.206: 1249   |   6:    51.168 -  59.658:   88        |
|      2:    17.206 -  25.696:  295   |   7:    59.658 -  68.149:   36        |
|      3:    25.696 -  34.187:  131   |   8:    68.149 -  76.639:   19        |
|      4:    34.187 -  42.677:  112   |   9:    76.639 -  85.130:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1608             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1609             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1609   ksol= 0.33   Bsol= 68.30   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-2.10,-1.00,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.151803                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1608   ksol= 0.33   Bsol= 68.30   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.96,-0.88,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.151867                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.203549              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.316  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365854              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.904  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1608      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7486 = 2.20 * 0.50 * 5.1516 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7448 = 2.20 * 0.50 * 5.1549 + 1.00 * 0.0652                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8955 = 0.37 * 1.00 * 5.1549 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8971 = 0.37 * 1.00 * 5.1601 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.23    85.43   16.66    None  None   None       |
|    all(noH): 2823   0      0.23    85.43   16.66    None  None   None       |
|    Sol.    : 438    0      2.72    83.15   39.37    None  None   None       |
|    Mac.    : 2385   0      0.23    85.43   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:     0.233 -   8.752:  838   |   5:    42.829 -  51.349:   86        |
|      1:     8.752 -  17.272: 1225   |   6:    51.349 -  59.868:   82        |
|      2:    17.272 -  25.791:  286   |   7:    59.868 -  68.387:   38        |
|      3:    25.791 -  34.310:  129   |   8:    68.387 -  76.906:   13        |
|      4:    34.310 -  42.829:  121   |   9:    76.906 -  85.426:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1619             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1619             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1619   ksol= 0.33   Bsol= 68.30   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.96,-0.88,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159907                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7980 0.99   1380  154 0.1020 0.1337      5.4155      5.5485|
|  2:  4.7980 -  3.8282 0.99   1324  145 0.0862 0.1113      5.4495      5.6399|
|  3:  3.8282 -  3.3502 0.99   1287  143 0.1035 0.1524      5.4755       5.867|
|  4:  3.3502 -  3.0465 0.99   1284  147 0.1205 0.1599      5.4705      5.6152|
|  5:  3.0465 -  2.8297 0.99   1292  140 0.1363 0.1825      5.3563      5.6058|
|  6:  2.8297 -  2.6638 0.99   1274  141 0.1209 0.1908      5.2351       5.453|
|  7:  2.6638 -  2.5310 0.99   1277  136 0.1281 0.1659      5.1884      5.3986|
|  8:  2.5310 -  2.4213 0.98   1254  148 0.1158 0.1759      5.0755      5.3668|
|  9:  2.4213 -  2.3284 0.98   1255  137 0.1174 0.1714      5.0532      5.2847|
| 10:  2.3284 -  2.2483 1.00   1268  141 0.1119 0.1877      4.9725      5.2994|
| 11:  2.2483 -  2.1782 0.97   1250  137 0.1149 0.1774      4.9692      5.2545|
| 12:  2.1782 -  2.1161 0.98   1240  142 0.1135 0.1774       4.905      5.2299|
| 13:  2.1161 -  2.0605 1.00   1258  136 0.1153 0.1779      4.8222      5.1202|
| 14:  2.0605 -  2.0104 0.77    987  112 0.1079 0.1745      4.6834      4.9363|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.7980  1380   154  0.94   9.55   0.97     0.94       7744.31|
|  2:  4.7980 -  3.8282  1324   145  0.95   8.17   1.00     0.98       9397.93|
|  3:  3.8282 -  3.3502  1287   143  0.93  11.29   1.01     1.00      10619.47|
|  4:  3.3502 -  3.0465  1284   147  0.92  13.87   1.00     0.97      10767.99|
|  5:  3.0465 -  2.8297  1292   140  0.89  16.60   0.99     0.96       8936.71|
|  6:  2.8297 -  2.6638  1274   141  0.90  16.12   0.98     0.96       7572.76|
|  7:  2.6638 -  2.5310  1277   136  0.90  15.92   0.98     0.95       6483.25|
|  8:  2.5310 -  2.4213  1254   148  0.91  15.42   0.98     0.96       5474.80|
|  9:  2.4213 -  2.3284  1255   137  0.91  15.49   0.99     0.95       5189.10|
| 10:  2.3284 -  2.2483  1268   141  0.90  15.53   0.98     0.94       4469.62|
| 11:  2.2483 -  2.1782  1250   137  0.89  16.92   0.98     0.94       4652.33|
| 12:  2.1782 -  2.1161  1240   142  0.91  15.18   0.99     0.97       4156.43|
| 13:  2.1161 -  2.0605  1258   136  0.90  16.34   0.98     0.96       3613.09|
| 14:  2.0605 -  2.0104   987   112  0.91  15.02   0.95     0.91       2635.41|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2635.41 max =        10767.99 mean =      6651.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.32|
|phase err.(test): min =        0.00 max =           88.98 mean =        13.84|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1618   ksol= 0.32   Bsol= 62.01   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-1.78,-0.70,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160029                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.23 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1618   ksol= 0.32   Bsol= 62.01   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-1.78,-0.70,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160029                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2323 -  4.7980 0.99   1380  154 0.1014 0.1337      5.4114      5.5467|
|  2:  4.7980 -  3.8282 0.99   1324  145 0.0859 0.1110      5.4473      5.6371|
|  3:  3.8282 -  3.3502 0.99   1287  143 0.1033 0.1525      5.4744      5.8673|
|  4:  3.3502 -  3.0465 0.99   1284  147 0.1207 0.1598      5.4718      5.6157|
|  5:  3.0465 -  2.8297 0.99   1292  140 0.1365 0.1827       5.358      5.6075|
|  6:  2.8297 -  2.6638 0.99   1274  141 0.1211 0.1912      5.2368      5.4548|
|  7:  2.6638 -  2.5310 0.99   1277  136 0.1282 0.1660      5.1894      5.3992|
|  8:  2.5310 -  2.4213 0.98   1254  148 0.1159 0.1762      5.0763      5.3676|
|  9:  2.4213 -  2.3284 0.98   1255  137 0.1175 0.1713      5.0538      5.2846|
| 10:  2.3284 -  2.2483 1.00   1268  141 0.1119 0.1878      4.9733      5.2997|
| 11:  2.2483 -  2.1782 0.97   1250  137 0.1150 0.1776      4.9699      5.2552|
| 12:  2.1782 -  2.1161 0.98   1240  142 0.1136 0.1777      4.9055      5.2305|
| 13:  2.1161 -  2.0605 1.00   1258  136 0.1154 0.1780      4.8225      5.1205|
| 14:  2.0605 -  2.0104 0.77    987  112 0.1079 0.1746      4.6837      4.9368|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2323 -  4.7980  1380   154  0.94   9.54   0.97     0.94       7714.50|
|  2:  4.7980 -  3.8282  1324   145  0.95   8.16   1.00     0.99       9370.93|
|  3:  3.8282 -  3.3502  1287   143  0.93  11.28   1.01     1.01      10598.49|
|  4:  3.3502 -  3.0465  1284   147  0.92  13.89   1.00     0.98      10785.27|
|  5:  3.0465 -  2.8297  1292   140  0.89  16.62   0.99     0.97       8962.05|
|  6:  2.8297 -  2.6638  1274   141  0.90  16.15   0.99     0.96       7597.84|
|  7:  2.6638 -  2.5310  1277   136  0.90  15.93   0.99     0.96       6497.64|
|  8:  2.5310 -  2.4213  1254   148  0.91  15.43   0.99     0.97       5482.00|
|  9:  2.4213 -  2.3284  1255   137  0.91  15.50   0.99     0.95       5191.18|
| 10:  2.3284 -  2.2483  1268   141  0.90  15.54   0.99     0.94       4474.61|
| 11:  2.2483 -  2.1782  1250   137  0.89  16.94   0.99     0.95       4658.69|
| 12:  2.1782 -  2.1161  1240   142  0.91  15.20   0.99     0.98       4162.38|
| 13:  2.1161 -  2.0605  1258   136  0.90  16.35   0.99     0.97       3616.30|
| 14:  2.0605 -  2.0104   987   112  0.91  15.02   0.96     0.92       2637.48|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2637.48 max =        10785.27 mean =      6653.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.33|
|phase err.(test): min =        0.00 max =           89.12 mean =        13.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.23    85.42   16.66    None  None   None       |
|    all(noH): 2823   0      0.23    85.42   16.66    None  None   None       |
|    Sol.    : 438    0      2.71    83.14   39.37    None  None   None       |
|    Mac.    : 2385   0      0.23    85.42   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:     0.227 -   8.746:  838   |   5:    42.824 -  51.343:   86        |
|      1:     8.746 -  17.266: 1225   |   6:    51.343 -  59.862:   82        |
|      2:    17.266 -  25.785:  286   |   7:    59.862 -  68.381:   38        |
|      3:    25.785 -  34.304:  129   |   8:    68.381 -  76.901:   13        |
|      4:    34.304 -  42.824:  121   |   9:    76.901 -  85.420:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.503 - 4.778
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 302
   mapped sites are within: 0.703 - 4.778

peak=    5.683 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.662 closest distance to " O   HOH Z 111 " =    2.049
peak=    5.481 closest distance to " CG  PRO A  54 " =    1.310
peak=    5.022 closest distance to " O   HOH Z 232 " =    2.270
peak=    4.964 closest distance to " CB  SER A  63 " =    1.251
peak=    4.884 closest distance to " CB  PRO A  54 " =    0.949
peak=    4.743 closest distance to " O   HOH Z 126 " =    1.860
peak=    4.740 closest distance to " O   HOH Z  78 " =    1.735
peak=    4.672 closest distance to " CG  PRO A 198 " =    1.292
peak=    4.657 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.653 closest distance to " CG  PRO A 213 " =    1.204
peak=    4.627 closest distance to " CB  LEU A 228 " =    1.078
peak=    4.577 closest distance to " CB  ARG A 275 " =    0.911
peak=    4.534 closest distance to " O   HOH Z 369 " =    2.082
peak=    4.515 closest distance to " O   HOH Z 298 " =    1.996
peak=    4.471 closest distance to " C   PRO A 198 " =    1.535
peak=    4.463 closest distance to " NE2 GLN A  11 " =    1.116
peak=    4.452 closest distance to " CG  PRO A  90 " =    1.100
peak=    4.393 closest distance to " CB  ASN A 148 " =    1.432
peak=    4.354 closest distance to " CB  ARG A 190 " =    1.615
peak=    4.343 closest distance to " CB  GLU A 128 " =    1.068
peak=    4.340 closest distance to " CZ  PHE A 218 " =    1.076
peak=    4.326 closest distance to " CB  ARG A  79 " =    1.388
peak=    4.326 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.277 closest distance to " O   HOH Z 236 " =    2.097
peak=    4.239 closest distance to " O   HOH Z  15 " =    2.159
peak=    4.223 closest distance to " CB  TRP A 266 " =    0.951
peak=    4.210 closest distance to " NH2 ARG A 156 " =    1.185
peak=    4.191 closest distance to " OD1 ASN A  69 " =    2.612
peak=    4.162 closest distance to " CB  ASP A 124 " =    0.751
peak=    4.142 closest distance to " CD1 LEU A 300 " =    1.239
peak=    4.138 closest distance to " CB  TYR A 169 " =    0.738
peak=    4.107 closest distance to " O   HOH Z 234 " =    3.884
peak=    4.102 closest distance to " ND2 ASN A 187 " =    1.469
peak=    4.097 closest distance to " CG  PRO A 243 " =    1.096
peak=    4.088 closest distance to " O   HOH Z 261 " =    1.950
peak=    4.085 closest distance to " CB  ASN A 187 " =    1.364
peak=    4.070 closest distance to " CB  GLU A 152 " =    1.134
peak=    4.043 closest distance to " CD  ARG A 159 " =    0.808
peak=    4.004 closest distance to " CA  PRO A  54 " =    1.368
peak=    3.995 closest distance to " O   HOH Z 250 " =    1.557
peak=    3.979 closest distance to " CD ALYS A 290 " =    1.012
peak=    3.960 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.950 closest distance to " CG2 THR A 221 " =    1.019
peak=    3.950 closest distance to " O   THR A 251 " =    1.329
peak=    3.947 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.925 closest distance to " CB  SER A   3 " =    1.355
peak=    3.922 closest distance to " CD  ARG A 269 " =    0.929
peak=    3.921 closest distance to " CB  GLU A 277 " =    3.734
peak=    3.919 closest distance to " CB  ASP A 140 " =    0.924
peak=    3.916 closest distance to " O   HOH Z 368 " =    2.153
peak=    3.901 closest distance to " NH1AARG A 145 " =    1.262
peak=    3.875 closest distance to " CA  ALA A  51 " =    0.920
peak=    3.867 closest distance to " O   HOH Z 316 " =    3.140
peak=    3.862 closest distance to " O   HOH Z 189 " =    2.728
peak=    3.858 closest distance to " CZ  PHE A 192 " =    0.938
peak=    3.857 closest distance to " O   HOH Z 158 " =    3.047
peak=    3.851 closest distance to " O   HOH Z 346 " =    1.623
peak=    3.849 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.848 closest distance to " CG2 VAL A 257 " =    0.918
peak=    3.834 closest distance to " O   HOH Z 423 " =    1.837
peak=    3.830 closest distance to " O   HOH Z 214 " =    2.014
peak=    3.824 closest distance to " CA  THR A 264 " =    0.854
peak=    3.824 closest distance to " O   HOH Z 133 " =    2.323
peak=    3.812 closest distance to " O   HOH Z 427 " =    3.139
peak=    3.791 closest distance to " ND2 ASN A 249 " =    1.953
peak=    3.786 closest distance to " CB  ASN A  39 " =    0.923
peak=    3.780 closest distance to " O   HOH Z 272 " =    1.932
peak=    3.777 closest distance to " CG1 ILE A  33 " =    1.280
peak=    3.776 closest distance to " CD  LYS A 166 " =    1.287
peak=    3.774 closest distance to " O   HOH Z 193 " =    1.769
peak=    3.765 closest distance to " O   HOH Z  40 " =    1.874
peak=    3.762 closest distance to " O   HOH Z 193 " =    2.022
peak=    3.759 closest distance to " CA  ASP A 124 " =    0.710
peak=    3.755 closest distance to " O   HOH Z 213 " =    1.986
peak=    3.744 closest distance to " O   MET A 105 " =    1.882
peak=    3.743 closest distance to " O   HOH Z 403 " =    1.720
peak=    3.741 closest distance to " O   HOH Z 303 " =    2.141
peak=    3.738 closest distance to " CG  LEU A 167 " =    1.234
peak=    3.725 closest distance to " CD  ARG A  66 " =    2.318
peak=    3.722 closest distance to " CA  ASP A 191 " =    0.807
peak=    3.720 closest distance to " CE  LYS A  76 " =    0.838
peak=    3.718 closest distance to " CB  VAL A 265 " =    1.267
peak=    3.706 closest distance to " CA  TYR A  30 " =    1.057
peak=    3.700 closest distance to " O   HOH Z  61 " =    1.630
peak=    3.700 closest distance to " CA  MET A  40 " =    1.160
peak=    3.692 closest distance to " CB  GLU A  46 " =    0.966
peak=    3.692 closest distance to " CB  SER A 212 " =    1.152
peak=    3.690 closest distance to " O   HOH Z  63 " =    1.978
peak=    3.686 closest distance to " O   HOH Z  21 " =    1.811
peak=    3.680 closest distance to " O   HOH Z 411 " =    3.745
peak=    3.674 closest distance to " ND2 ASN A 110 " =    1.628
peak=    3.667 closest distance to " NZ  LYS A 117 " =    3.301
peak=    3.665 closest distance to " O   HOH Z 142 " =    1.598
peak=    3.663 closest distance to " N   ASN A 127 " =    1.279
peak=    3.661 closest distance to " CB  MET A  40 " =    0.803
peak=    3.657 closest distance to " O   HOH Z 265 " =    2.353
peak=    3.653 closest distance to " CA  THR A 221 " =    0.933
peak=    3.651 closest distance to " O   HOH Z 285 " =    2.813
peak=    3.649 closest distance to " O   HOH Z 280 " =    2.982
peak=    3.643 closest distance to " O   HOH Z 135 " =    1.743
peak=    3.642 closest distance to " O   HOH Z  53 " =    2.542
peak=    3.636 closest distance to " CA  ARG A  36 " =    1.158
peak=    3.635 closest distance to " O   HOH Z 197 " =    3.033
peak=    3.632 closest distance to " N   ARG A 156 " =    1.392
peak=    3.628 closest distance to " O   HOH Z 344 " =    3.317
peak=    3.625 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.620 closest distance to " O   HOH Z 171 " =    3.909
peak=    3.608 closest distance to " CD2 LEU A 297 " =    0.876
peak=    3.607 closest distance to " O   HOH Z   1 " =    2.140
peak=    3.607 closest distance to " CD  ARG A  66 " =    2.308
peak=    3.606 closest distance to " CA  ASN A 252 " =    2.097
peak=    3.602 closest distance to " O   HOH Z 426 " =    1.615
peak=    3.601 closest distance to " CG BARG A 275 " =    1.468
peak=    3.584 closest distance to " CB  TRP A 179 " =    1.503
peak=    3.577 closest distance to " CB  ILE A 120 " =    1.211
peak=    3.576 closest distance to " CB  LEU A 143 " =    1.124
peak=    3.573 closest distance to " NH2BARG A 145 " =    2.228
peak=    3.572 closest distance to " OD1 ASN A 217 " =    1.725
peak=    3.570 closest distance to " O   HOH Z 406 " =    1.687
peak=    3.568 closest distance to " O   HOH Z  88 " =    3.718
peak=    3.566 closest distance to " CB  MET A  47 " =    1.025
peak=    3.558 closest distance to " CB  SER A 216 " =    0.843
peak=    3.550 closest distance to " CD1 ILE A 106 " =    0.791
peak=    3.545 closest distance to " CG1BVAL A  72 " =    1.715
peak=    3.540 closest distance to " CA  ASN A 215 " =    1.216
peak=    3.539 closest distance to " O   HOH Z 147 " =    1.776
peak=    3.538 closest distance to " O   HOH Z 132 " =    2.772
peak=    3.538 closest distance to " O  BHOH Z 338 " =    2.392
peak=    3.532 closest distance to " O   HOH Z 425 " =    1.294
peak=    3.532 closest distance to " CB  ASN A 142 " =    0.978
peak=    3.527 closest distance to " CB  TYR A 169 " =    0.739
peak=    3.524 closest distance to " ND1 HIS A  86 " =    1.779
peak=    3.523 closest distance to " O   HOH Z 148 " =    3.336
peak=    3.513 closest distance to " CG2 ILE A 120 " =    1.063
peak=    3.511 closest distance to " N   VAL A 126 " =    1.436
peak=    3.510 closest distance to " O   HOH Z  20 " =    1.770
peak=    3.504 closest distance to " CB  ALA A 104 " =    0.727
peak=    3.504 closest distance to " O   HOH Z 368 " =    3.662
peak=    3.489 closest distance to " O   HOH Z  66 " =    2.142
peak=    3.488 closest distance to " CG1 ILE A 151 " =    1.025
peak=    3.478 closest distance to " CA  ALA A 154 " =    1.004
peak=    3.477 closest distance to " O   HOH Z  44 " =    2.264
peak=    3.476 closest distance to " CB  TYR A 116 " =    0.852
peak=    3.476 closest distance to " ND1 HIS A  81 " =    1.661
peak=    3.476 closest distance to " O   ALA A 158 " =    1.281
peak=    3.475 closest distance to " CA  SER A  87 " =    1.015
peak=    3.465 closest distance to " CA  ALA A  21 " =    1.172
peak=    3.460 closest distance to " CB  SER A 141 " =    1.003
peak=    3.458 closest distance to " O   HOH Z 305 " =    3.665
peak=    3.452 closest distance to " CA  ALA A 158 " =    1.154
peak=    3.449 closest distance to " O   HOH Z  10 " =    1.826
peak=    3.448 closest distance to " O   HOH Z 383 " =    2.084
peak=    3.443 closest distance to " O   HOH Z 291 " =    1.631
peak=    3.438 closest distance to " O   ALA A 165 " =    1.463
peak=    3.437 closest distance to " CB  ALA A   1 " =    4.778
peak=    3.427 closest distance to " OD2 ASP A 286 " =    2.937
peak=    3.423 closest distance to " CD  ARG A 219 " =    1.062
peak=    3.413 closest distance to " CB  GLN A 103 " =    0.873
peak=    3.412 closest distance to " CD2 TRP A 179 " =    1.319
peak=    3.411 closest distance to " O   HOH Z 313 " =    1.874
peak=    3.410 closest distance to " O   HOH Z 133 " =    3.237
peak=    3.409 closest distance to " O   THR A 220 " =    1.251
peak=    3.409 closest distance to " O   HOH Z 172 " =    3.675
peak=    3.404 closest distance to " O   HOH Z 391 " =    2.908
peak=    3.404 closest distance to " O   HOH Z 425 " =    1.961
peak=    3.404 closest distance to " O   HOH Z 329 " =    3.839
peak=    3.402 closest distance to " CA  ALA A 295 " =    1.091
peak=    3.401 closest distance to " OG  SER A  22 " =    2.798
peak=    3.399 closest distance to " CA  MET A 105 " =    1.007
peak=    3.399 closest distance to " CB  ALA A 248 " =    0.980
peak=    3.398 closest distance to " O   HOH Z 185 " =    1.914
peak=    3.394 closest distance to " CZ  PHE A  38 " =    1.259
peak=    3.390 closest distance to " CB  ALA A 242 " =    0.848
peak=    3.386 closest distance to " O   HOH Z 359 " =    1.448
peak=    3.386 closest distance to " N   ASN A  39 " =    1.351
peak=    3.379 closest distance to " O   HOH Z 313 " =    1.708
peak=    3.377 closest distance to " O   HOH Z 203 " =    1.824
peak=    3.376 closest distance to " O   HOH Z 109 " =    2.699
peak=    3.374 closest distance to " O   HOH Z 273 " =    2.801
peak=    3.371 closest distance to " O   HOH Z 271 " =    2.878
peak=    3.359 closest distance to " O   HOH Z 128 " =    2.400
peak=    3.351 closest distance to " O   HOH Z 199 " =    1.552
peak=    3.347 closest distance to " O   HOH Z 371 " =    3.231
peak=    3.344 closest distance to " CB  LYS A 193 " =    0.970
peak=    3.344 closest distance to " CA  ALA A 160 " =    0.914
peak=    3.343 closest distance to " N   TYR A  15 " =    0.733
peak=    3.340 closest distance to " CB  GLN A  89 " =    1.273
peak=    3.337 closest distance to " OG BSER A 164 " =    2.419
peak=    3.328 closest distance to " CG2BVAL A  41 " =    0.845
peak=    3.328 closest distance to " O   HOH Z 245 " =    1.268
peak=    3.325 closest distance to " CZ  PHE A 208 " =    1.130
peak=    3.325 closest distance to " O   HOH Z 402 " =    1.428
peak=    3.320 closest distance to " O   HOH Z 128 " =    2.135
peak=    3.318 closest distance to " NE2 HIS A 207 " =    1.307
peak=    3.316 closest distance to " O   HOH Z 193 " =    2.160
peak=    3.304 closest distance to " O   HOH Z  97 " =    1.990
peak=    3.301 closest distance to " CG  GLU A  37 " =    0.878
peak=    3.297 closest distance to " CB  HIS A 108 " =    0.818
peak=    3.294 closest distance to " CB  ALA A  34 " =    0.974
peak=    3.292 closest distance to " O   HOH Z 166 " =    3.718
peak=    3.291 closest distance to " O   HOH Z 294 " =    1.587
peak=    3.291 closest distance to " CB  ALA A   9 " =    1.590
peak=    3.287 closest distance to " O   SER A  87 " =    2.333
peak=    3.283 closest distance to " O   HOH Z  62 " =    2.233
peak=    3.280 closest distance to " O   HOH Z 126 " =    1.655
peak=    3.279 closest distance to " CG2 VAL A 197 " =    1.165
peak=    3.279 closest distance to " O   TYR A 116 " =    1.289
peak=    3.276 closest distance to " O   HOH Z 295 " =    1.480
peak=    3.275 closest distance to " C   TYR A 214 " =    1.522
peak=    3.274 closest distance to " CG  ARG A 159 " =    0.929
peak=    3.273 closest distance to " CB  ALA A 291 " =    1.284
peak=    3.271 closest distance to " CB  GLN A  88 " =    1.272
peak=    3.268 closest distance to " CD1 TRP A 266 " =    1.153
peak=    3.262 closest distance to " O   HOH Z 133 " =    1.712
peak=    3.262 closest distance to " O   HOH Z 134 " =    1.364
peak=    3.260 closest distance to " N   GLY A  98 " =    1.127
peak=    3.259 closest distance to " O   HOH Z 116 " =    1.885
peak=    3.249 closest distance to " CE1 TYR A 186 " =    1.293
peak=    3.242 closest distance to " O   HOH Z 163 " =    1.614
peak=    3.240 closest distance to " CD1AILE A 234 " =    0.953
peak=    3.236 closest distance to " O   HOH Z 281 " =    4.085
peak=    3.228 closest distance to " O   HOH Z 327 " =    2.007
peak=    3.227 closest distance to " CA  ALA A 291 " =    0.830
peak=    3.226 closest distance to " NE2 HIS A 115 " =    1.007
peak=    3.225 closest distance to " O   HOH Z 188 " =    2.397
peak=    3.221 closest distance to " CB  THR A  31 " =    1.777
peak=    3.214 closest distance to " O   HOH Z 403 " =    1.358
peak=    3.214 closest distance to " CB  ARG A 139 " =    0.896
peak=    3.208 closest distance to " O   TRP A 274 " =    1.827
peak=    3.206 closest distance to " O   HOH Z  66 " =    2.117
peak=    3.203 closest distance to " CA  GLN A  88 " =    1.440
peak=    3.203 closest distance to " CA  GLU A 152 " =    0.869
peak=    3.202 closest distance to " CD2 LEU A 255 " =    1.618
peak=    3.200 closest distance to " CA  ARG A 102 " =    1.156
peak=    3.197 closest distance to " O   ASN A 209 " =    1.339
peak=    3.197 closest distance to " O   HOH Z 327 " =    2.834
peak=    3.193 closest distance to " OG BSER A 134 " =    2.981
peak=    3.191 closest distance to " CA  LEU A 282 " =    1.088
peak=    3.186 closest distance to " CA  ASN A 217 " =    1.237
peak=    3.180 closest distance to " CB  LEU A  83 " =    0.796
peak=    3.171 closest distance to " O   HOH Z  80 " =    1.558
peak=    3.168 closest distance to " CG2 ILE A 234 " =    0.878
peak=    3.167 closest distance to " NE  ARG A  79 " =    1.129
peak=    3.167 closest distance to " CA  VAL A 125 " =    1.131
peak=    3.166 closest distance to " O   HOH Z 234 " =    1.781
peak=    3.166 closest distance to " ND2 ASN A 249 " =    0.808
peak=    3.165 closest distance to " O   HOH Z 271 " =    2.337
peak=    3.164 closest distance to " CB  ARG A 138 " =    1.027
peak=    3.159 closest distance to " NZ  LYS A  76 " =    1.564
peak=    3.157 closest distance to " O   HOH Z  49 " =    2.830
peak=    3.152 closest distance to " CA  LYS A 117 " =    1.210
peak=    3.152 closest distance to " O   HOH Z 422 " =    2.715
peak=    3.150 closest distance to " O   HOH Z 149 " =    2.053
peak=    3.148 closest distance to " CB  ASN A 110 " =    1.149
peak=    3.148 closest distance to " CA  ASN A 127 " =    1.092
peak=    3.142 closest distance to " CB  ALA A 248 " =    1.256
peak=    3.140 closest distance to " NE2 GLN A  58 " =    3.717
peak=    3.140 closest distance to " CG  MET A 185 " =    1.214
peak=    3.139 closest distance to " CB  LEU A 237 " =    0.722
peak=    3.137 closest distance to " CA  ILE A  33 " =    1.686
peak=    3.137 closest distance to " O   HOH Z 175 " =    3.644
peak=    3.136 closest distance to " CG BARG A 102 " =    1.897
peak=    3.133 closest distance to " O   HOH Z 219 " =    1.678
peak=    3.130 closest distance to " CB  PRO A 163 " =    4.188
peak=    3.126 closest distance to " N   GLN A 278 " =    1.014
peak=    3.126 closest distance to " O   HOH Z 350 " =    1.659
peak=    3.126 closest distance to " CA  ALA A 233 " =    1.532
peak=    3.125 closest distance to " CA  ALA A 100 " =    1.249
peak=    3.118 closest distance to " CA  GLN A 223 " =    0.914
peak=    3.117 closest distance to " CB  ALA A 114 " =    1.061
peak=    3.116 closest distance to " CZ2 TRP A 179 " =    1.716
peak=    3.116 closest distance to " O   HOH Z  59 " =    2.235
peak=    3.113 closest distance to " CB  ASP A 140 " =    0.703
peak=    3.112 closest distance to " O   HOH Z  49 " =    2.327
peak=    3.111 closest distance to " CB  SER A 210 " =    0.834
peak=    3.108 closest distance to " OE1 GLU A 152 " =    0.857
peak=    3.107 closest distance to " CG2 ILE A 151 " =    0.769
peak=    3.102 closest distance to " N   SER A 135 " =    1.374
peak=    3.102 closest distance to " O   HOH Z 365 " =    2.987
peak=    3.096 closest distance to " NZ ALYS A 290 " =    1.102
peak=    3.095 closest distance to " CA  ILE A 106 " =    0.832
peak=    3.093 closest distance to " OD2 ASP A 200 " =    1.257
peak=    3.085 closest distance to " CB  ALA A 100 " =    1.232
peak=    3.085 closest distance to " O   HOH Z 201 " =    3.157
peak=    3.084 closest distance to " CB  ALA A 227 " =    1.083
peak=    3.083 closest distance to " OH  TYR A 214 " =    1.185
peak=    3.080 closest distance to " CB  TRP A 150 " =    1.339
peak=    3.079 closest distance to " CA  THR A 221 " =    1.448
peak=    3.070 closest distance to " CE2 TYR A 186 " =    0.894
peak=    3.064 closest distance to " OG  SER A 206 " =    1.246
peak=    3.063 closest distance to " O   HOH Z  88 " =    2.979
peak=    3.055 closest distance to " CB  GLU A 152 " =    1.462
peak=    3.050 closest distance to " O  BHOH Z  74 " =    1.313
peak=    3.038 closest distance to " CD  LYS A 119 " =    1.318
peak=    3.025 closest distance to " CG2 ILE A  20 " =    1.222
peak=    3.011 closest distance to " O   HOH Z 213 " =    2.873

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.803 - 5.574
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.803 - 5.574

peak=   -4.422 closest distance to " CB  PRO A 243 " =    2.642
peak=   -4.415 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -4.280 closest distance to " N   ALA A  43 " =    2.630
peak=   -4.199 closest distance to " CD  ARG A 156 " =    2.103
peak=   -4.189 closest distance to " O   VAL A  67 " =    2.699
peak=   -4.178 closest distance to " O   HOH Z  10 " =    1.612
peak=   -4.169 closest distance to " O   HOH Z 266 " =    5.216
peak=   -4.146 closest distance to " CD  ARG A  14 " =    3.446
peak=   -4.116 closest distance to " CZ3 TRP A 179 " =    1.116
peak=   -4.114 closest distance to " O   PRO A 198 " =    1.295
peak=   -4.098 closest distance to " O   HOH Z 290 " =    1.219
peak=   -4.075 closest distance to " O   HOH Z 231 " =    2.262
peak=   -4.075 closest distance to " O   HOH Z 377 " =    1.862
peak=   -4.046 closest distance to " CE2 TYR A  30 " =    2.813
peak=   -4.044 closest distance to " CD  GLN A  58 " =    0.933
peak=   -3.981 closest distance to " OE1 GLN A 223 " =    1.886
peak=   -3.979 closest distance to " O   HOH Z  73 " =    2.127
peak=   -3.944 closest distance to " CG1 VAL A 250 " =    2.681
peak=   -3.934 closest distance to " CA  GLY A 241 " =    3.172
peak=   -3.919 closest distance to " O   HOH Z 118 " =    3.512
peak=   -3.915 closest distance to " O   HOH Z 389 " =    1.999
peak=   -3.888 closest distance to " O   ILE A 109 " =    2.599
peak=   -3.874 closest distance to " NH2AARG A 275 " =    5.574
peak=   -3.864 closest distance to " O   HOH Z  52 " =    1.469
peak=   -3.855 closest distance to " CD2 TYR A 293 " =    2.036
peak=   -3.842 closest distance to " O   HOH Z 394 " =    1.493
peak=   -3.830 closest distance to " OD1 ASN A 148 " =    1.560
peak=   -3.800 closest distance to " OG  SER A  97 " =    2.249
peak=   -3.767 closest distance to " C   HIS A 108 " =    1.109
peak=   -3.756 closest distance to " O   HOH Z 196 " =    2.012
peak=   -3.748 closest distance to " CD1 PHE A  59 " =    1.904
peak=   -3.745 closest distance to " O   HOH Z  38 " =    1.214
peak=   -3.737 closest distance to " CD  GLN A 223 " =    1.441
peak=   -3.732 closest distance to " O   HOH Z 372 " =    2.526
peak=   -3.725 closest distance to " CG  ARG A 269 " =    2.518
peak=   -3.724 closest distance to " C   ASN A 187 " =    1.899
peak=   -3.716 closest distance to " CG1 VAL A 112 " =    2.930
peak=   -3.708 closest distance to " CD2 PHE A  61 " =    2.566
peak=   -3.699 closest distance to " C   ASN A 285 " =    2.570
peak=   -3.695 closest distance to " OG BSER A 134 " =    1.253
peak=   -3.662 closest distance to " O   HOH Z 353 " =    2.130
peak=   -3.645 closest distance to " O   HOH Z  60 " =    2.530
peak=   -3.645 closest distance to " CB  ALA A 291 " =    2.339
peak=   -3.642 closest distance to " O   HOH Z 426 " =    1.672
peak=   -3.634 closest distance to " CD1 ILE A 151 " =    2.430
peak=   -3.618 closest distance to " CA  GLY A 241 " =    2.320
peak=   -3.609 closest distance to " OXT GLY A 302 " =    2.993
peak=   -3.603 closest distance to " O   ALA A  10 " =    1.716
peak=   -3.602 closest distance to " CB  ALA A 291 " =    2.203
peak=   -3.599 closest distance to " CD1 LEU A 101 " =    2.440
peak=   -3.599 closest distance to " CB  ALA A  43 " =    2.628
peak=   -3.589 closest distance to " O   HOH Z 198 " =    2.266
peak=   -3.585 closest distance to " O   HOH Z 185 " =    2.386
peak=   -3.580 closest distance to " CD1 LEU A 228 " =    2.438
peak=   -3.568 closest distance to " ND2 ASN A  45 " =    1.878
peak=   -3.566 closest distance to " CG  MET A 105 " =    0.955
peak=   -3.552 closest distance to " O   HOH Z 407 " =    3.410
peak=   -3.550 closest distance to " ND2 ASN A  45 " =    1.096
peak=   -3.541 closest distance to " O   HOH Z  43 " =    1.540
peak=   -3.538 closest distance to " CG2 ILE A  49 " =    2.780
peak=   -3.535 closest distance to " O   PRO A 163 " =    2.166
peak=   -3.531 closest distance to " CE  MET A 105 " =    2.300
peak=   -3.530 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.521 closest distance to " C   ALA A 158 " =    1.345
peak=   -3.517 closest distance to " O   HOH Z 166 " =    1.812
peak=   -3.517 closest distance to " OD2 ASP A 171 " =    1.858
peak=   -3.514 closest distance to " NH2 ARG A  79 " =    1.545
peak=   -3.503 closest distance to " CA  GLY A 203 " =    2.398
peak=   -3.486 closest distance to " O   HOH Z 114 " =    1.402
peak=   -3.484 closest distance to " CE BMET A  47 " =    2.005
peak=   -3.475 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.473 closest distance to " CE3 TRP A 150 " =    2.122
peak=   -3.473 closest distance to " N   ALA A 226 " =    2.195
peak=   -3.468 closest distance to " CB  ASN A  39 " =    2.323
peak=   -3.467 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.460 closest distance to " O   HOH Z  37 " =    1.881
peak=   -3.459 closest distance to " ND2BASN A 224 " =    1.755
peak=   -3.452 closest distance to " O   HOH Z 241 " =    1.300
peak=   -3.451 closest distance to " CD  ARG A 195 " =    5.129
peak=   -3.448 closest distance to " O   HOH Z 351 " =    1.493
peak=   -3.447 closest distance to " ND2 ASN A 249 " =    2.379
peak=   -3.443 closest distance to " CG  PHE A 283 " =    2.798
peak=   -3.441 closest distance to " CE2 PHE A 218 " =    2.462
peak=   -3.441 closest distance to " O   GLY A 211 " =    1.450
peak=   -3.437 closest distance to " O   HOH Z 435 " =    2.734
peak=   -3.428 closest distance to " CB  PRO A  54 " =    2.527
peak=   -3.426 closest distance to " O   HOH Z 232 " =    1.740
peak=   -3.411 closest distance to " O   HOH Z  51 " =    1.666
peak=   -3.407 closest distance to " O   HOH Z 396 " =    1.787
peak=   -3.404 closest distance to " CG  ARG A  66 " =    2.320
peak=   -3.403 closest distance to " C   LEU A 143 " =    1.172
peak=   -3.401 closest distance to " N   THR A 157 " =    1.629
peak=   -3.390 closest distance to " O   HOH Z 311 " =    3.796
peak=   -3.390 closest distance to " O   HOH Z 393 " =    1.430
peak=   -3.389 closest distance to " OE1 GLN A  88 " =    1.237
peak=   -3.387 closest distance to " O   HOH Z  19 " =    2.525
peak=   -3.383 closest distance to " O   HOH Z 275 " =    1.563
peak=   -3.381 closest distance to " ND2 ASN A  60 " =    1.388
peak=   -3.381 closest distance to " N   THR A  18 " =    1.283
peak=   -3.379 closest distance to " CD  PRO A 213 " =    2.242
peak=   -3.378 closest distance to " CG2 ILE A 263 " =    2.400
peak=   -3.376 closest distance to " CG  GLU A  53 " =    1.471
peak=   -3.373 closest distance to " O   HOH Z 252 " =    4.195
peak=   -3.368 closest distance to " NE2 GLN A 194 " =    1.831
peak=   -3.362 closest distance to " O   GLY A 203 " =    2.365
peak=   -3.351 closest distance to " O   HOH Z 106 " =    1.957
peak=   -3.350 closest distance to " O   HOH Z 295 " =    1.511
peak=   -3.346 closest distance to " CA  GLY A 241 " =    2.840
peak=   -3.346 closest distance to " O   HOH Z 243 " =    2.054
peak=   -3.344 closest distance to " CG1 VAL A 125 " =    1.983
peak=   -3.341 closest distance to " CG2 VAL A 189 " =    2.159
peak=   -3.341 closest distance to " CG1 VAL A 197 " =    2.303
peak=   -3.332 closest distance to " O   HOH Z 253 " =    4.201
peak=   -3.330 closest distance to " CG2 THR A 221 " =    2.230
peak=   -3.323 closest distance to " NH1 ARG A 195 " =    2.615
peak=   -3.323 closest distance to " O   HOH Z 377 " =    1.297
peak=   -3.320 closest distance to " CG  PRO A 243 " =    1.760
peak=   -3.318 closest distance to " O   HOH Z 211 " =    1.569
peak=   -3.314 closest distance to " C   SER A 206 " =    1.471
peak=   -3.312 closest distance to " NE2 GLN A 103 " =    1.765
peak=   -3.311 closest distance to " CB  ALA A   9 " =    2.523
peak=   -3.311 closest distance to " CD  ARG A  79 " =    1.117
peak=   -3.311 closest distance to " CD1 LEU A  83 " =    2.695
peak=   -3.309 closest distance to " CZ  TYR A 169 " =    1.750
peak=   -3.308 closest distance to " N   SER A 212 " =    1.997
peak=   -3.304 closest distance to " O   HOH Z 313 " =    2.020
peak=   -3.303 closest distance to " O   HOH Z 298 " =    2.557
peak=   -3.302 closest distance to " O   HOH Z 176 " =    0.878
peak=   -3.296 closest distance to " CB  TRP A  85 " =    2.371
peak=   -3.296 closest distance to " CD2 PHE A  59 " =    2.583
peak=   -3.296 closest distance to " SD BMET A  47 " =    0.956
peak=   -3.293 closest distance to " NH2 ARG A 159 " =    2.290
peak=   -3.290 closest distance to " O   HOH Z 177 " =    1.687
peak=   -3.289 closest distance to " NE2 GLN A  88 " =    1.997
peak=   -3.288 closest distance to " CB  ASP A 286 " =    2.082
peak=   -3.284 closest distance to " CG  GLU A 277 " =    1.111
peak=   -3.283 closest distance to " CG2 ILE A  20 " =    2.922
peak=   -3.281 closest distance to " O   HOH Z 198 " =    1.436
peak=   -3.274 closest distance to " O   HOH Z 348 " =    2.307
peak=   -3.271 closest distance to " O   VAL A 153 " =    2.304
peak=   -3.269 closest distance to " CE3 TRP A  70 " =    1.855
peak=   -3.269 closest distance to " O   HOH Z   6 " =    1.498
peak=   -3.262 closest distance to " OG BSER A 134 " =    1.861
peak=   -3.261 closest distance to " OD1 ASP A 191 " =    1.622
peak=   -3.255 closest distance to " CG  TRP A 266 " =    1.823
peak=   -3.253 closest distance to " OG  SER A  62 " =    1.706
peak=   -3.249 closest distance to " CD  GLN A  88 " =    0.836
peak=   -3.248 closest distance to " CB  ASP A 132 " =    2.319
peak=   -3.246 closest distance to " CD2 PHE A 192 " =    1.997
peak=   -3.241 closest distance to " O   HOH Z 264 " =    1.789
peak=   -3.239 closest distance to " CB  PRO A 163 " =    2.543
peak=   -3.234 closest distance to " O   HOH Z 234 " =    4.477
peak=   -3.231 closest distance to " OD1 ASP A 171 " =    1.577
peak=   -3.225 closest distance to " O   HOH Z 259 " =    2.187
peak=   -3.219 closest distance to " NH2 ARG A  66 " =    2.118
peak=   -3.218 closest distance to " O   VAL A  67 " =    2.770
peak=   -3.217 closest distance to " O   HOH Z 189 " =    1.968
peak=   -3.217 closest distance to " CD1 ILE A 239 " =    2.054
peak=   -3.212 closest distance to " O   HOH Z 193 " =    1.755
peak=   -3.208 closest distance to " O   HOH Z  13 " =    1.467
peak=   -3.207 closest distance to " CA  GLY A  98 " =    2.077
peak=   -3.201 closest distance to " O   HOH Z 111 " =    2.049
peak=   -3.198 closest distance to " SG ACYS A 201 " =    2.106
peak=   -3.198 closest distance to " CA  SER A 135 " =    1.276
peak=   -3.196 closest distance to " O   HOH Z 417 " =    2.597
peak=   -3.194 closest distance to " O   VAL A 125 " =    2.367
peak=   -3.194 closest distance to " CG  LEU A 101 " =    2.372
peak=   -3.193 closest distance to " CG  PRO A 163 " =    2.401
peak=   -3.190 closest distance to " O   LEU A 101 " =    2.897
peak=   -3.187 closest distance to " CZ  PHE A  59 " =    1.728
peak=   -3.187 closest distance to " O   GLY A 196 " =    1.269
peak=   -3.184 closest distance to " O   HOH Z 128 " =    2.581
peak=   -3.183 closest distance to " CB  ALA A  10 " =    2.213
peak=   -3.172 closest distance to " OD1 ASN A 187 " =    1.572
peak=   -3.170 closest distance to " CD  ARG A 139 " =    1.630
peak=   -3.168 closest distance to " O   HOH Z  11 " =    1.818
peak=   -3.166 closest distance to " O   ALA A  34 " =    2.149
peak=   -3.166 closest distance to " CD2 LEU A 237 " =    2.880
peak=   -3.165 closest distance to " C   GLY A  13 " =    0.939
peak=   -3.164 closest distance to " NH2 ARG A  79 " =    1.934
peak=   -3.161 closest distance to " CB  ALA A 248 " =    2.503
peak=   -3.158 closest distance to " O   HOH Z  90 " =    1.640
peak=   -3.148 closest distance to " CB  TYR A  15 " =    2.234
peak=   -3.148 closest distance to " SD  MET A 188 " =    2.402
peak=   -3.144 closest distance to " O   HOH Z  76 " =    1.956
peak=   -3.140 closest distance to " N   LYS A 166 " =    2.062
peak=   -3.138 closest distance to " O   HOH Z 350 " =    1.696
peak=   -3.133 closest distance to " CD1 LEU A 297 " =    2.517
peak=   -3.129 closest distance to " N   SER A   3 " =    2.031
peak=   -3.118 closest distance to " C   MET A 188 " =    1.369
peak=   -3.117 closest distance to " O   HOH Z 113 " =    2.267
peak=   -3.116 closest distance to " O   HOH Z 399 " =    2.198
peak=   -3.103 closest distance to " O   HOH Z  51 " =    1.421
peak=   -3.099 closest distance to " CE  MET A  93 " =    1.823
peak=   -3.098 closest distance to " O   HOH Z 281 " =    2.567
peak=   -3.097 closest distance to " CB  ASP A 132 " =    2.362
peak=   -3.083 closest distance to " O   TRP A  70 " =    1.485
peak=   -3.082 closest distance to " O   HOH Z 123 " =    2.421
peak=   -3.082 closest distance to " NH1AARG A 102 " =    1.265
peak=   -3.063 closest distance to " O   HOH Z 139 " =    2.949
peak=   -3.060 closest distance to " ND2 ASN A  60 " =    1.937
peak=   -3.057 closest distance to " CE  MET A 105 " =    2.303
peak=   -3.042 closest distance to " O   HOH Z 323 " =    1.446
peak=   -3.037 closest distance to " O   HOH Z 380 " =    5.112
peak=   -3.018 closest distance to " O   PRO A 198 " =    1.361

================= 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    :  0.3296 0.3203   6.053847e+00   6.048654e+00
   1_bss:  0.3172 0.3090   6.033060e+00   6.022637e+00
   1_xyz:  0.1888 0.2088   5.559640e+00   5.646524e+00
   1_adp:  0.1752 0.2120   5.507034e+00   5.666148e+00
   1_occ:  0.1746 0.2114   5.504615e+00   5.664281e+00
   2_bss:  0.1723 0.2076   5.498467e+00   5.657149e+00
   2_xyz:  0.1367 0.1757   5.298480e+00   5.496221e+00
   2_adp:  0.1286 0.1698   5.249193e+00   5.464298e+00
   2_occ:  0.1285 0.1696   5.248897e+00   5.464077e+00
   3_bss:  0.1285 0.1694   5.248455e+00   5.462226e+00
   3_xyz:  0.1151 0.1625   5.171765e+00   5.418358e+00
   3_adp:  0.1138 0.1610   5.159641e+00   5.406333e+00
   3_occ:  0.1138 0.1609   5.159361e+00   5.406291e+00
   4_bss:  0.1136 0.1608   5.159295e+00   5.406054e+00
   4_xyz:  0.1120 0.1613   5.154089e+00   5.405548e+00
   4_adp:  0.1115 0.1608   5.151628e+00   5.404227e+00
   4_occ:  0.1114 0.1609   5.151803e+00   5.404551e+00
   5_bss:  0.1114 0.1608   5.151867e+00   5.404535e+00
   5_xyz:  0.1123 0.1622   5.160913e+00   5.413667e+00
   5_adp:  0.1124 0.1619   5.159909e+00   5.411734e+00
   5_occ:  0.1123 0.1619   5.159907e+00   5.411832e+00
   5_bss:  0.1123 0.1618   5.160029e+00   5.412071e+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:  0.317  64.539   1.753  -1.981  -1.082  -0.000  -0.000  -0.000
   1_xyz:  0.317  64.539   1.753  -1.981  -1.082  -0.000  -0.000  -0.000
   1_adp:  0.317  64.539   1.753  -1.981  -1.082  -0.000  -0.000  -0.000
   1_occ:  0.317  64.539   1.753  -1.981  -1.082  -0.000  -0.000  -0.000
   2_bss:  0.336  66.314  -1.307  -2.636  -1.613  -0.000  -0.000  -0.000
   2_xyz:  0.336  66.314  -1.307  -2.636  -1.613  -0.000  -0.000  -0.000
   2_adp:  0.336  66.314  -1.307  -2.636  -1.613  -0.000  -0.000  -0.000
   2_occ:  0.336  66.314  -1.307  -2.636  -1.613  -0.000  -0.000  -0.000
   3_bss:  0.330  68.296  -1.834  -2.404  -1.325  -0.000  -0.000  -0.000
   3_xyz:  0.330  68.296  -1.834  -2.404  -1.325  -0.000  -0.000  -0.000
   3_adp:  0.330  68.296  -1.834  -2.404  -1.325  -0.000  -0.000  -0.000
   3_occ:  0.330  68.296  -1.834  -2.404  -1.325  -0.000  -0.000  -0.000
   4_bss:  0.330  68.296  -1.782  -2.103  -1.003  -0.000  -0.000  -0.000
   4_xyz:  0.330  68.296  -1.782  -2.103  -1.003  -0.000  -0.000  -0.000
   4_adp:  0.330  68.296  -1.782  -2.103  -1.003  -0.000  -0.000  -0.000
   4_occ:  0.330  68.296  -1.782  -2.103  -1.003  -0.000  -0.000  -0.000
   5_bss:  0.330  68.296  -1.756  -1.964  -0.880  -0.000  -0.000  -0.000
   5_xyz:  0.330  68.296  -1.756  -1.964  -0.880  -0.000  -0.000  -0.000
   5_adp:  0.330  68.296  -1.756  -1.964  -0.880  -0.000  -0.000  -0.000
   5_occ:  0.330  68.296  -1.756  -1.964  -0.880  -0.000  -0.000  -0.000
   5_bss:  0.318  62.009  -1.629  -1.782  -0.697  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.170 0.7137  0.8697    30395.018
   1_bss:  33.178 0.7235  0.8737    28024.746
   1_xyz:  19.718 0.8657  1.0009    11031.394
   1_adp:  20.320 0.8593  0.9966    11415.538
   1_occ:  20.279 0.8596  0.9964    11340.968
   2_bss:  20.068 0.8616  0.9491    11161.133
   2_xyz:  16.194 0.8968  0.9675     7847.271
   2_adp:  15.391 0.9038  0.9649     7291.070
   2_occ:  15.385 0.9039  0.9648     7283.523
   3_bss:  15.360 0.9040  0.9642     7249.342
   3_xyz:  14.488 0.9111  0.9679     6671.638
   3_adp:  14.169 0.9139  0.9622     6527.361
   3_occ:  14.170 0.9139  0.9620     6525.761
   4_bss:  14.169 0.9139  0.9696     6522.482
   4_xyz:  14.139 0.9143  0.9703     6512.754
   4_adp:  14.122 0.9144  0.9637     6516.320
   4_occ:  14.130 0.9143  0.9635     6517.633
   5_bss:  14.131 0.9143  0.9668     6517.293
   5_xyz:  14.303 0.9130  0.9652     6657.632
   5_adp:  14.268 0.9133  0.9584     6649.457
   5_occ:  14.273 0.9133  0.9583     6650.688
   5_bss:  14.283 0.9132  0.9636     6653.000
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6259e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6259e-01
   1_xyz:   1.109  0.009  0.073 15.075  0.004  4.118   7.0812e-02
   1_adp:   1.109  0.009  0.073 15.075  0.004  4.118   7.0812e-02
   1_occ:   1.109  0.009  0.073 15.075  0.004  4.118   7.0812e-02
   2_bss:   1.109  0.009  0.073 15.075  0.004  4.118   7.0812e-02
   2_xyz:   0.961  0.007  0.071 14.273  0.004  4.131   5.4116e-02
   2_adp:   0.961  0.007  0.071 14.273  0.004  4.131   5.4116e-02
   2_occ:   0.961  0.007  0.071 14.273  0.004  4.131   5.4116e-02
   3_bss:   0.961  0.007  0.071 14.273  0.004  4.131   5.4116e-02
   3_xyz:   1.168  0.012  0.087 14.652  0.005  4.114   8.2437e-02
   3_adp:   1.168  0.012  0.087 14.652  0.005  4.114   8.2437e-02
   3_occ:   1.168  0.012  0.087 14.652  0.005  4.114   8.2437e-02
   4_bss:   1.168  0.012  0.087 14.652  0.005  4.114   8.2437e-02
   4_xyz:   1.091  0.010  0.081 14.621  0.004  4.117   7.2786e-02
   4_adp:   1.091  0.010  0.081 14.621  0.004  4.117   7.2786e-02
   4_occ:   1.091  0.010  0.081 14.621  0.004  4.117   7.2786e-02
   5_bss:   1.091  0.010  0.081 14.621  0.004  4.117   7.2786e-02
   5_xyz:   1.037  0.009  0.079 14.488  0.004  4.118   6.5244e-02
   5_adp:   1.037  0.009  0.079 14.488  0.004  4.118   6.5244e-02
   5_occ:   1.037  0.009  0.079 14.488  0.004  4.118   6.5244e-02
   5_bss:   1.037  0.009  0.079 14.488  0.004  4.118   6.5244e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.663   2.4373e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.663   2.4373e-01
   1_xyz:   9.098  0.047  0.236 85.706  0.029  2.289   1.2075e-01
   1_adp:   9.098  0.047  0.236 85.706  0.029  2.289   1.2075e-01
   1_occ:   9.098  0.047  0.236 85.706  0.029  2.289   1.2075e-01
   2_bss:   9.098  0.047  0.236 85.706  0.029  2.289   1.2075e-01
   2_xyz:   7.788  0.043  0.220 81.349  0.039  2.387   4.7403e-02
   2_adp:   7.788  0.043  0.220 81.349  0.039  2.387   4.7403e-02
   2_occ:   7.788  0.043  0.220 81.349  0.039  2.387   4.7403e-02
   3_bss:   7.788  0.043  0.220 81.349  0.039  2.387   4.7403e-02
   3_xyz:   7.702  0.056  0.259 82.937  0.042  2.308   6.0940e-02
   3_adp:   7.702  0.056  0.259 82.937  0.042  2.308   6.0940e-02
   3_occ:   7.702  0.056  0.259 82.937  0.042  2.308   6.0940e-02
   4_bss:   7.702  0.056  0.259 82.937  0.042  2.308   6.0940e-02
   4_xyz:   7.850  0.049  0.251 82.964  0.040  2.356   5.1808e-02
   4_adp:   7.850  0.049  0.251 82.964  0.040  2.356   5.1808e-02
   4_occ:   7.850  0.049  0.251 82.964  0.040  2.356   5.1808e-02
   5_bss:   7.850  0.049  0.251 82.964  0.040  2.356   5.1808e-02
   5_xyz:   7.740  0.046  0.234 83.497  0.040  2.370   4.3595e-02
   5_adp:   7.740  0.046  0.234 83.497  0.040  2.370   4.3595e-02
   5_occ:   7.740  0.046  0.234 83.497  0.040  2.370   4.3595e-02
   5_bss:   7.740  0.046  0.234 83.497  0.040  2.370   4.3595e-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: 102.76   0.00  16.74 102.76   0.00  12.83  64.05   5.10  37.99
   1_occ: 102.76   0.00  16.74 102.76   0.00  12.83  64.05   5.10  37.99
   2_bss: 102.76   0.00  16.74 102.76   0.00  12.83  64.05   5.10  37.99
   2_xyz: 102.76   0.00  16.74 102.76   0.00  12.83  64.05   5.10  37.99
   2_adp:  80.51   0.32  17.48  80.51   0.32  13.13  79.65   5.66  41.16
   2_occ:  80.51   0.32  17.48  80.51   0.32  13.13  79.65   5.66  41.16
   3_bss:  80.51   0.32  17.48  80.51   0.32  13.13  79.65   5.66  41.16
   3_xyz:  80.51   0.32  17.48  80.51   0.32  13.13  79.65   5.66  41.16
   3_adp:  82.01   0.00  17.23  82.01   0.57  12.90  80.21   0.00  40.82
   3_occ:  82.01   0.00  17.23  82.01   0.57  12.90  80.21   0.00  40.82
   4_bss:  82.01   0.00  17.23  82.01   0.57  12.90  80.21   0.00  40.82
   4_xyz:  82.01   0.00  17.23  82.01   0.57  12.90  80.21   0.00  40.82
   4_adp:  85.13   0.22  16.95  85.13   0.22  12.71  82.83   0.47  40.01
   4_occ:  85.13   0.22  16.95  85.13   0.22  12.71  82.83   0.47  40.01
   5_bss:  85.13   0.22  16.95  85.13   0.22  12.71  82.83   0.47  40.01
   5_xyz:  85.13   0.22  16.95  85.13   0.22  12.71  82.83   0.47  40.01
   5_adp:  85.43   0.23  16.66  85.43   0.23  12.49  83.15   2.72  39.37
   5_occ:  85.43   0.23  16.66  85.43   0.23  12.49  83.15   2.72  39.37
   5_bss:  85.42   0.23  16.66  85.42   0.23  12.49  83.14   2.71  39.37
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.173    0.002    0.313
   1_adp:    1.173    0.002    0.313
   1_occ:    1.173    0.002    0.313
   2_bss:    1.173    0.002    0.313
   2_xyz:    0.889    0.014    0.359
   2_adp:    0.889    0.014    0.359
   2_occ:    0.889    0.014    0.359
   3_bss:    0.889    0.014    0.359
   3_xyz:    0.837    0.023    0.386
   3_adp:    0.837    0.023    0.386
   3_occ:    0.837    0.023    0.386
   4_bss:    0.837    0.023    0.386
   4_xyz:    0.948    0.067    0.407
   4_adp:    0.948    0.067    0.407
   4_occ:    0.948    0.067    0.407
   5_bss:    0.948    0.067    0.407
   5_xyz:    1.054    0.048    0.414
   5_adp:    1.054    0.048    0.414
   5_occ:    1.054    0.048    0.414
   5_bss:    1.054    0.048    0.414
------------------------------------------------------------------------

CPU time actual refinement: 327.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1161/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_1161/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1161/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1161/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1161/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.04 
  Macro-tasks:
    bulk solvent and scale       = 39.89  
    individual site refinement   = 137.96 
    weights calculation          = 28.51  
    collect and process          = 6.62   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.09 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 103.17 
    alpha_beta                      = 7.96   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 113.21 
    fmodel                         = 6.44   
    r_factors                      = 0.22   
    phase_errors                   = 11.24  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 244.87 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.583 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    654 calls, 102.72 s
gradients_fft:          599 calls,  98.94 s

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

# Date 2008-01-16 Time 06:35:01 PST -0800 (1200494101.50 s)
Start R-work = 0.3296, R-free = 0.3203 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1786 (no bulk solvent and anisotropic scale)

Start R-work = 0.3172, R-free = 0.3090
Final R-work = 0.1123, R-free = 0.1618