# Date 2008-01-16 Time 06:10:09 PST -0800 (1200492609.23 s)
#phil __OFF__

Command line arguments: "../1031.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10217
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1031

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.93, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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: (71.3037, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.0026
Completeness in resolution range: 0.96081
Completeness with d_max=infinity: 0.95785

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   2.0026

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.0026
Completeness in resolution range: 0.96081
Completeness with d_max=infinity: 0.95785

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.2854 [2145/2169]  1931   214  10.0%
  bin  2:  4.2854 -  3.4141 [2043/2063]  1838   205  10.0%
  bin  3:  3.4141 -  2.9862 [2040/2059]  1834   206  10.1%
  bin  4:  2.9862 -  2.7149 [2010/2040]  1812   198   9.9%
  bin  5:  2.7149 -  2.5212 [2005/2024]  1805   200  10.0%
  bin  6:  2.5212 -  2.3731 [1974/1999]  1774   200  10.1%
  bin  7:  2.3731 -  2.2547 [1989/2017]  1789   200  10.1%
  bin  8:  2.2547 -  2.1568 [1981/2017]  1786   195   9.8%
  bin  9:  2.1568 -  2.0740 [1949/1991]  1754   195  10.0%
  bin 10:  2.0740 -  2.0026 [1453/2009]  1307   146  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1031/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2167
        3.04 -     3.66: 4591
        3.66 -     4.28: 8881
        4.28 -     4.90: 12229
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.032 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.294 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27873 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_1031/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1031/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.93 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3416   r_free= 0.3318   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.078882                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.7798 0.99   1393  155 0.2886 0.2693      6.3652      6.2643|
|  2:  4.7798 -  3.8135 0.99   1337  150 0.2684 0.2531      6.4851      6.4425|
|  3:  3.8135 -  3.3373 0.99   1314  141 0.2994 0.2693       6.385      6.3722|
|  4:  3.3373 -  3.0348 0.99   1298  150 0.3059 0.3281       6.255      6.2426|
|  5:  3.0348 -  2.8187 0.99   1296  146 0.3586 0.3421      6.1619       6.176|
|  6:  2.8187 -  2.6535 0.99   1302  134 0.3438 0.3514      6.0468      5.9844|
|  7:  2.6535 -  2.5212 0.99   1280  147 0.3751 0.3764      6.0528      6.1272|
|  8:  2.5212 -  2.4119 0.98   1272  144 0.3830 0.3404      6.0265      5.9598|
|  9:  2.4119 -  2.3194 0.98   1266  140 0.3848 0.3595      5.9547      5.9395|
| 10:  2.3194 -  2.2396 1.00   1288  145 0.3960 0.3688      5.9672      5.9196|
| 11:  2.2396 -  2.1698 0.98   1267  138 0.4078 0.4138       5.914      5.9779|
| 12:  2.1698 -  2.1079 0.98   1253  141 0.3992 0.4093      5.8399      5.9165|
| 13:  2.1079 -  2.0526 0.99   1287  136 0.4047 0.3844      5.7439      5.6714|
| 14:  2.0526 -  2.0026 0.61    777   92 0.3855 0.4148      5.6955      5.7036|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.7798  1393   155  0.81  24.50   0.85     0.82      38344.95|
|  2:  4.7798 -  3.8135  1337   150  0.85  21.48   0.96     0.91      44901.86|
|  3:  3.8135 -  3.3373  1314   141  0.80  26.58   0.97     0.91      46244.01|
|  4:  3.3373 -  3.0348  1298   150  0.76  29.76   0.97     0.88      42222.00|
|  5:  3.0348 -  2.8187  1296   146  0.69  36.31   0.97     0.85      36548.96|
|  6:  2.8187 -  2.6535  1302   134  0.69  36.77   0.97     0.84      32433.54|
|  7:  2.6535 -  2.5212  1280   147  0.67  38.26   0.97     0.83      30683.58|
|  8:  2.5212 -  2.4119  1272   144  0.67  38.36   0.97     0.85      28166.41|
|  9:  2.4119 -  2.3194  1266   140  0.67  37.93   0.98     0.86      25863.47|
| 10:  2.3194 -  2.2396  1288   145  0.65  39.73   1.03     0.85      24093.77|
| 11:  2.2396 -  2.1698  1267   138  0.64  40.89   0.99     0.85      24156.40|
| 12:  2.1698 -  2.1079  1253   141  0.63  41.83   1.01     0.85      23204.07|
| 13:  2.1079 -  2.0526  1287   136  0.60  43.87   1.00     0.84      20601.16|
| 14:  2.0526 -  2.0026   777    92  0.62  42.58   1.02     0.80      17196.36|
|alpha:            min =        0.80 max =            0.91 mean =         0.85|
|beta:             min =    17196.36 max =        46244.01 mean =     31596.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.97 mean =        35.28|
|phase err.(test): min =        0.00 max =           89.82 mean =        34.80|
|-----------------------------------------------------------------------------|

============================== 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 = 5.114577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.927   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.747723              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.980   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      174 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1993 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1809 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2782 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4578 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4303 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5575 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6654 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.137 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    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: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3416   r_free= 0.3318   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.078882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3281   r_free= 0.3216   ksol= 0.32   Bsol= 69.25   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-3.37,2.18,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.057117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.583908              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.883   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.423406              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.662   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3281      final r-factor (work) = 0.1816          |
| start r-factor (free) = 0.3216      final r-factor (free) = 0.2041          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0493 = 4.58 * 0.50 * 6.0594 + 1.00 * 0.1615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3103 = 4.58 * 0.50 * 5.7719 + 1.00 * 0.0813                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1816      final r-factor (work) = 0.1666          |
| start r-factor (free) = 0.2041      final r-factor (free) = 0.2087          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4504 = 0.42 * 1.00 * 5.7719 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3470 = 0.42 * 1.00 * 5.4573 + 1.00 * 0.0364                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.65   16.81    None  None   None       |
|    all(noH): 2823   0      0.00    64.65   16.81    None  None   None       |
|    Sol.    : 438    0      4.14    64.65   38.19    None  None   None       |
|    Mac.    : 2385   0      0.00    63.97   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.465:  279   |   5:    32.325 -  38.790:   89        |
|      1:     6.465 -  12.930: 1184   |   6:    38.790 -  45.255:  108        |
|      2:    12.930 -  19.395:  657   |   7:    45.255 -  51.720:   84        |
|      3:    19.395 -  25.860:  237   |   8:    51.720 -  58.185:   53        |
|      4:    25.860 -  32.325:  113   |   9:    58.185 -  64.650:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1666 r_free = 0.2087             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1661 r_free = 0.2083             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1661   r_free= 0.2083   ksol= 0.32   Bsol= 69.25   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-3.37,2.18,-0.00,0.00,0.00); trace/3= -0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.465191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1637   r_free= 0.2059   ksol= 0.34   Bsol= 69.25   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-3.17,-0.40,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.459518                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.062082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.589   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.300206              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.260   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1637      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.2059      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4576 = 3.06 * 0.50 * 5.4709 + 1.00 * 0.0813                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2658 = 3.06 * 0.50 * 5.3550 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1295      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6238 = 0.30 * 1.00 * 5.3550 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5780 = 0.30 * 1.00 * 5.2273 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    75.20   17.11    None  None   None       |
|    all(noH): 2823   0      1.03    75.20   17.11    None  None   None       |
|    Sol.    : 438    0      5.82    75.20   39.71    None  None   None       |
|    Mac.    : 2385   0      1.03    74.88   12.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.029 -   8.446:  616   |   5:    38.112 -  45.529:   98        |
|      1:     8.446 -  15.862: 1292   |   6:    45.529 -  52.946:   89        |
|      2:    15.862 -  23.279:  377   |   7:    52.946 -  60.363:   72        |
|      3:    23.279 -  30.696:  134   |   8:    60.363 -  67.779:   32        |
|      4:    30.696 -  38.112:  103   |   9:    67.779 -  75.196:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1221 r_free = 0.1647             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1220 r_free = 0.1645             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1645   ksol= 0.34   Bsol= 69.25   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-3.17,-0.40,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.207159                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1218   r_free= 0.1639   ksol= 0.34   Bsol= 69.25   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.73,-0.74,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204792                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.549267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.346  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.138048              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.564  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7290 = 2.55 * 0.50 * 5.2265 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6706 = 2.55 * 0.50 * 5.1780 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7234 = 0.14 * 1.00 * 5.1780 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7209 = 0.14 * 1.00 * 5.1685 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    75.61   16.74    None  None   None       |
|    all(noH): 2823   0      1.74    75.61   16.74    None  None   None       |
|    Sol.    : 438    0      2.60    75.61   38.28    None  None   None       |
|    Mac.    : 2385   0      1.74    74.35   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.738 -   9.125:  789   |   5:    38.673 -  46.060:   84        |
|      1:     9.125 -  16.512: 1209   |   6:    46.060 -  53.447:   88        |
|      2:    16.512 -  23.899:  323   |   7:    53.447 -  60.834:   62        |
|      3:    23.899 -  31.286:  128   |   8:    60.834 -  68.221:   19        |
|      4:    31.286 -  38.673:  113   |   9:    68.221 -  75.607:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1584             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1583             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1583   ksol= 0.34   Bsol= 69.25   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.73,-0.74,-0.00,-0.00,-0.00); trace/3= -1.91                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1583   ksol= 0.34   Bsol= 69.25   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.51,-0.82,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.576509              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.447  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.237060              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.214  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7285 = 2.58 * 0.50 * 5.1683 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7111 = 2.58 * 0.50 * 5.1530 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.1471 = 6.24 * 1.00 * 5.1530 + 1.00 * 0.0073                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.1137 = 6.24 * 1.00 * 5.1472 + 1.00 * 0.0103                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.30   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    87.30   17.21    None  None   None       |
|    Sol.    : 438    0      3.22    84.33   40.82    None  None   None       |
|    Mac.    : 2385   0      0.00    87.30   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.730:  786   |   5:    43.648 -  52.377:   87        |
|      1:     8.730 -  17.459: 1279   |   6:    52.377 -  61.107:   81        |
|      2:    17.459 -  26.189:  283   |   7:    61.107 -  69.836:   47        |
|      3:    26.189 -  34.918:  130   |   8:    69.836 -  78.566:   16        |
|      4:    34.918 -  43.648:  107   |   9:    78.566 -  87.295:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1606             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1607             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1607   ksol= 0.34   Bsol= 69.25   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.51,-0.82,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153774                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1605   ksol= 0.32   Bsol= 63.75   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.22,-0.63,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153346                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.476192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.225  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.419663              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.459  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8722 = 1.48 * 0.50 * 5.1477 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8701 = 1.48 * 0.50 * 5.1677 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3467 = 1.42 * 1.00 * 5.1677 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3575 = 1.42 * 1.00 * 5.1751 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.40   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    88.40   17.01    None  None   None       |
|    Sol.    : 438    0      4.87    84.86   40.70    None  None   None       |
|    Mac.    : 2385   0      0.00    88.40   12.66    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 -   8.840:  867   |   5:    44.202 -  53.042:   91        |
|      1:     8.840 -  17.681: 1206   |   6:    53.042 -  61.883:   77        |
|      2:    17.681 -  26.521:  279   |   7:    61.883 -  70.723:   44        |
|      3:    26.521 -  35.362:  134   |   8:    70.723 -  79.564:   15        |
|      4:    35.362 -  44.202:  103   |   9:    79.564 -  88.404:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1636             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1636             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1636   ksol= 0.32   Bsol= 63.75   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.22,-0.63,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178146                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.7798 0.99   1393  155 0.1014 0.1321       5.421      5.5629|
|  2:  4.7798 -  3.8135 0.99   1337  150 0.0865 0.1107      5.4491      5.6284|
|  3:  3.8135 -  3.3373 0.99   1314  141 0.1060 0.1514      5.4822       5.867|
|  4:  3.3373 -  3.0348 0.99   1298  150 0.1231 0.1722      5.4773       5.636|
|  5:  3.0348 -  2.8187 0.99   1296  146 0.1386 0.1779      5.3709      5.5963|
|  6:  2.8187 -  2.6535 0.99   1302  134 0.1254 0.2057      5.2502      5.5139|
|  7:  2.6535 -  2.5212 0.99   1280  147 0.1323 0.1687      5.2068      5.3907|
|  8:  2.5212 -  2.4119 0.98   1272  144 0.1188 0.1716      5.1005      5.3439|
|  9:  2.4119 -  2.3194 0.98   1266  140 0.1204 0.1820      5.0678      5.3374|
| 10:  2.3194 -  2.2396 1.00   1288  145 0.1146 0.1794       4.984      5.2655|
| 11:  2.2396 -  2.1698 0.98   1267  138 0.1173 0.1811      4.9727      5.2926|
| 12:  2.1698 -  2.1079 0.98   1253  141 0.1154 0.1764      4.9181      5.2009|
| 13:  2.1079 -  2.0526 0.99   1287  136 0.1169 0.1856      4.8323       5.098|
| 14:  2.0526 -  2.0026 0.61    777   92 0.1091 0.1759      4.7288      4.9735|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.7798  1393   155  0.94   9.74   0.96     0.93       7895.46|
|  2:  4.7798 -  3.8135  1337   150  0.95   8.03   1.00     0.98       9332.17|
|  3:  3.8135 -  3.3373  1314   141  0.93  11.34   1.01     1.01      10430.13|
|  4:  3.3373 -  3.0348  1298   150  0.91  14.27   1.00     0.97      10924.31|
|  5:  3.0348 -  2.8187  1296   146  0.89  16.69   0.99     0.97       9173.21|
|  6:  2.8187 -  2.6535  1302   134  0.89  16.88   0.98     0.95       7791.16|
|  7:  2.6535 -  2.5212  1280   147  0.90  16.37   0.98     0.95       6792.85|
|  8:  2.5212 -  2.4119  1272   144  0.90  15.91   0.98     0.96       5708.96|
|  9:  2.4119 -  2.3194  1266   140  0.91  15.81   0.98     0.94       5345.52|
| 10:  2.3194 -  2.2396  1288   145  0.90  16.28   0.98     0.94       4711.23|
| 11:  2.2396 -  2.1698  1267   138  0.90  16.55   0.96     0.91       4481.61|
| 12:  2.1698 -  2.1079  1253   141  0.91  15.75   0.99     0.98       4310.35|
| 13:  2.1079 -  2.0526  1287   136  0.89  17.16   0.96     0.94       3722.96|
| 14:  2.0526 -  2.0026   777    92  0.91  15.60   0.94     0.91       2972.47|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     2972.47 max =        10924.31 mean =      6827.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1634   ksol= 0.32   Bsol= 63.76   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.97,-0.43,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178273                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1634   ksol= 0.32   Bsol= 63.76   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.97,-0.43,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178273                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.7798 0.99   1393  155 0.1015 0.1322      5.4217      5.5641|
|  2:  4.7798 -  3.8135 0.99   1337  150 0.0865 0.1107      5.4494      5.6282|
|  3:  3.8135 -  3.3373 0.99   1314  141 0.1060 0.1514       5.482      5.8671|
|  4:  3.3373 -  3.0348 0.99   1298  150 0.1231 0.1722      5.4773       5.636|
|  5:  3.0348 -  2.8187 0.99   1296  146 0.1386 0.1778      5.3709       5.596|
|  6:  2.8187 -  2.6535 0.99   1302  134 0.1254 0.2059      5.2504      5.5143|
|  7:  2.6535 -  2.5212 0.99   1280  147 0.1323 0.1686      5.2069      5.3907|
|  8:  2.5212 -  2.4119 0.98   1272  144 0.1188 0.1716      5.1006      5.3438|
|  9:  2.4119 -  2.3194 0.98   1266  140 0.1204 0.1821       5.068      5.3377|
| 10:  2.3194 -  2.2396 1.00   1288  145 0.1146 0.1793      4.9841      5.2644|
| 11:  2.2396 -  2.1698 0.98   1267  138 0.1174 0.1811      4.9728      5.2926|
| 12:  2.1698 -  2.1079 0.98   1253  141 0.1154 0.1764      4.9179      5.2007|
| 13:  2.1079 -  2.0526 0.99   1287  136 0.1169 0.1857      4.8325      5.0981|
| 14:  2.0526 -  2.0026 0.61    777   92 0.1090 0.1760      4.7293      4.9743|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.7798  1393   155  0.94   9.75   0.96     0.93       7910.43|
|  2:  4.7798 -  3.8135  1337   150  0.95   8.04   1.00     0.99       9339.16|
|  3:  3.8135 -  3.3373  1314   141  0.93  11.34   1.02     1.01      10427.14|
|  4:  3.3373 -  3.0348  1298   150  0.91  14.27   1.00     0.98      10923.79|
|  5:  3.0348 -  2.8187  1296   146  0.89  16.69   1.00     0.97       9175.58|
|  6:  2.8187 -  2.6535  1302   134  0.89  16.88   0.98     0.96       7791.82|
|  7:  2.6535 -  2.5212  1280   147  0.90  16.38   0.99     0.96       6793.42|
|  8:  2.5212 -  2.4119  1272   144  0.90  15.92   0.99     0.96       5710.17|
|  9:  2.4119 -  2.3194  1266   140  0.91  15.82   0.99     0.95       5346.41|
| 10:  2.3194 -  2.2396  1288   145  0.90  16.28   0.99     0.95       4709.75|
| 11:  2.2396 -  2.1698  1267   138  0.90  16.54   0.97     0.92       4478.13|
| 12:  2.1698 -  2.1079  1253   141  0.91  15.75   1.00     0.99       4307.58|
| 13:  2.1079 -  2.0526  1287   136  0.89  17.17   0.98     0.95       3723.61|
| 14:  2.0526 -  2.0026   777    92  0.91  15.61   0.96     0.92       2976.55|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2976.55 max =        10923.79 mean =      6828.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.257)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.41   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    88.41   17.02    None  None   None       |
|    Sol.    : 438    0      4.88    84.87   40.70    None  None   None       |
|    Mac.    : 2385   0      0.00    88.41   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.843:  867   |   5:    44.205 -  53.045:   91        |
|      1:     8.843 -  17.684: 1206   |   6:    53.045 -  61.886:   77        |
|      2:    17.684 -  26.524:  279   |   7:    61.886 -  70.726:   44        |
|      3:    26.524 -  35.365:  134   |   8:    70.726 -  79.567:   15        |
|      4:    35.365 -  44.205:  103   |   9:    79.567 -  88.407:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.545 - 4.763
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 295
   mapped sites are within: 0.705 - 4.763

peak=    5.574 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.534 closest distance to " O   HOH Z 111 " =    2.253
peak=    5.291 closest distance to " CG  PRO A  54 " =    1.360
peak=    5.174 closest distance to " O   HOH Z 232 " =    2.308
peak=    4.934 closest distance to " CG  PRO A 198 " =    1.223
peak=    4.881 closest distance to " CG  PRO A 213 " =    1.218
peak=    4.706 closest distance to " CB  PRO A  54 " =    0.982
peak=    4.700 closest distance to " NE2 GLN A  11 " =    1.094
peak=    4.686 closest distance to " O   HOH Z 126 " =    1.942
peak=    4.662 closest distance to " CB  LEU A 228 " =    1.126
peak=    4.661 closest distance to " O   HOH Z 298 " =    2.013
peak=    4.642 closest distance to " CB  GLN A 183 " =    1.272
peak=    4.598 closest distance to " O   HOH Z  78 " =    1.691
peak=    4.592 closest distance to " CB  ARG A 190 " =    1.665
peak=    4.554 closest distance to " CB  SER A  63 " =    1.245
peak=    4.532 closest distance to " CA  TYR A  30 " =    0.988
peak=    4.531 closest distance to " CZ  PHE A 218 " =    1.058
peak=    4.518 closest distance to " CB  ARG A 275 " =    0.949
peak=    4.474 closest distance to " CB  ARG A  79 " =    1.395
peak=    4.389 closest distance to " CB  ASN A 148 " =    1.391
peak=    4.349 closest distance to " CD  ARG A 159 " =    0.808
peak=    4.331 closest distance to " O   HOH Z 369 " =    2.170
peak=    4.318 closest distance to " O   HOH Z 189 " =    2.803
peak=    4.304 closest distance to " O   HOH Z  15 " =    2.191
peak=    4.290 closest distance to " CE  LYS A  76 " =    0.829
peak=    4.269 closest distance to " CG2 VAL A 257 " =    0.915
peak=    4.257 closest distance to " C   PRO A 198 " =    1.536
peak=    4.243 closest distance to " CB  ASP A 124 " =    0.818
peak=    4.184 closest distance to " CB  TRP A 266 " =    1.025
peak=    4.182 closest distance to " CB  GLU A 128 " =    0.989
peak=    4.182 closest distance to " O   HOH Z 142 " =    1.745
peak=    4.178 closest distance to " CD1 LEU A 300 " =    1.191
peak=    4.176 closest distance to " O   HOH Z 234 " =    3.857
peak=    4.099 closest distance to " O   HOH Z 287 " =    2.049
peak=    4.083 closest distance to " CD  ARG A 269 " =    0.927
peak=    4.054 closest distance to " CG  LEU A 167 " =    1.249
peak=    4.048 closest distance to " NH1AARG A 145 " =    1.321
peak=    4.036 closest distance to " O   HOH Z 303 " =    2.123
peak=    4.035 closest distance to " O   HOH Z 250 " =    1.532
peak=    4.026 closest distance to " CA  ARG A 195 " =    1.272
peak=    4.020 closest distance to " O   HOH Z 427 " =    3.124
peak=    4.014 closest distance to " O   HOH Z  78 " =    2.145
peak=    3.988 closest distance to " CB  TYR A 169 " =    0.748
peak=    3.957 closest distance to " CG  PRO A 243 " =    1.048
peak=    3.935 closest distance to " O   HOH Z  53 " =    2.518
peak=    3.934 closest distance to " O   HOH Z 180 " =    2.138
peak=    3.924 closest distance to " CA  ALA A  51 " =    0.937
peak=    3.909 closest distance to " CB  ASN A  39 " =    0.935
peak=    3.907 closest distance to " ND2 ASN A 187 " =    1.377
peak=    3.906 closest distance to " O   HOH Z 158 " =    3.095
peak=    3.902 closest distance to " CB  VAL A 202 " =    1.620
peak=    3.896 closest distance to " CB  VAL A 265 " =    1.230
peak=    3.863 closest distance to " CB  ALA A 104 " =    0.725
peak=    3.862 closest distance to " CB  GLU A  46 " =    0.964
peak=    3.850 closest distance to " OD1 ASN A  69 " =    2.645
peak=    3.840 closest distance to " CD BLYS A 290 " =    0.976
peak=    3.838 closest distance to " O   HOH Z 316 " =    3.112
peak=    3.832 closest distance to " CB  GLU A 277 " =    3.751
peak=    3.825 closest distance to " O   HOH Z 214 " =    2.144
peak=    3.825 closest distance to " ND2 ASN A 249 " =    0.835
peak=    3.824 closest distance to " O   HOH Z 411 " =    3.849
peak=    3.824 closest distance to " O   HOH Z 261 " =    1.905
peak=    3.820 closest distance to " CA  SER A  87 " =    1.029
peak=    3.815 closest distance to " CB  ASN A 142 " =    1.030
peak=    3.801 closest distance to " O   HOH Z  21 " =    1.821
peak=    3.800 closest distance to " CB  ASP A 140 " =    1.031
peak=    3.796 closest distance to " CA  ARG A  36 " =    1.115
peak=    3.787 closest distance to " CZ  PHE A  38 " =    1.259
peak=    3.783 closest distance to " NZ  LYS A 117 " =    3.289
peak=    3.765 closest distance to " O   THR A 251 " =    1.206
peak=    3.762 closest distance to " CD  ARG A  66 " =    2.334
peak=    3.761 closest distance to " O   HOH Z 368 " =    2.110
peak=    3.754 closest distance to " NE2 HIS A 207 " =    1.221
peak=    3.749 closest distance to " O   HOH Z 346 " =    1.692
peak=    3.748 closest distance to " CD  LYS A 166 " =    1.289
peak=    3.744 closest distance to " O  BHOH Z 338 " =    2.380
peak=    3.737 closest distance to " CA  ASN A 215 " =    1.161
peak=    3.730 closest distance to " CA  THR A 264 " =    0.890
peak=    3.730 closest distance to " CB  SER A 210 " =    0.805
peak=    3.728 closest distance to " CB  SER A 212 " =    1.164
peak=    3.728 closest distance to " O   HOH Z 133 " =    2.449
peak=    3.722 closest distance to " ND2 ASN A 249 " =    1.945
peak=    3.721 closest distance to " O   HOH Z 265 " =    2.388
peak=    3.707 closest distance to " CG2 THR A 221 " =    1.006
peak=    3.706 closest distance to " CB  ASN A 187 " =    1.358
peak=    3.694 closest distance to " O   HOH Z 193 " =    1.940
peak=    3.688 closest distance to " O   HOH Z 392 " =    3.056
peak=    3.685 closest distance to " O   HOH Z 126 " =    1.967
peak=    3.681 closest distance to " CA  ALA A 160 " =    0.966
peak=    3.671 closest distance to " O   HOH Z 313 " =    1.896
peak=    3.671 closest distance to " O   TYR A 116 " =    1.304
peak=    3.671 closest distance to " CB  GLU A 152 " =    1.171
peak=    3.667 closest distance to " N   ASN A 127 " =    1.275
peak=    3.667 closest distance to " CB  MET A  40 " =    0.793
peak=    3.661 closest distance to " O   HOH Z 291 " =    1.612
peak=    3.655 closest distance to " CB  SER A 216 " =    0.903
peak=    3.642 closest distance to " CB  TYR A 116 " =    0.785
peak=    3.628 closest distance to " CA  ASP A 124 " =    0.706
peak=    3.614 closest distance to " CG1 ILE A  33 " =    1.252
peak=    3.612 closest distance to " CA  MET A 105 " =    1.038
peak=    3.611 closest distance to " CD1 LEU A  96 " =    0.739
peak=    3.605 closest distance to " CA  MET A  40 " =    1.202
peak=    3.605 closest distance to " O   HOH Z 368 " =    3.686
peak=    3.604 closest distance to " CG1 VAL A 153 " =    0.990
peak=    3.603 closest distance to " CD2 LEU A 297 " =    0.871
peak=    3.597 closest distance to " O   THR A 220 " =    1.202
peak=    3.591 closest distance to " O   HOH Z 185 " =    1.919
peak=    3.590 closest distance to " CZ3 TRP A 266 " =    1.141
peak=    3.583 closest distance to " CD2 TRP A 179 " =    1.315
peak=    3.579 closest distance to " CA  THR A 221 " =    1.029
peak=    3.577 closest distance to " O   HOH Z 272 " =    1.834
peak=    3.567 closest distance to " CA  ALA A 158 " =    1.222
peak=    3.566 closest distance to " O   HOH Z   1 " =    2.039
peak=    3.566 closest distance to " CB  LEU A  83 " =    0.795
peak=    3.558 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.557 closest distance to " CA  ALA A 154 " =    0.999
peak=    3.556 closest distance to " O   HOH Z 371 " =    2.931
peak=    3.552 closest distance to " O   HOH Z  10 " =    1.796
peak=    3.547 closest distance to " N   ASN A  39 " =    1.329
peak=    3.544 closest distance to " O   HOH Z 209 " =    2.331
peak=    3.539 closest distance to " CG2 ILE A 120 " =    1.097
peak=    3.536 closest distance to " O   HOH Z 285 " =    2.538
peak=    3.521 closest distance to " CB  ASN A 110 " =    1.132
peak=    3.517 closest distance to " CB  ALA A 114 " =    0.750
peak=    3.516 closest distance to " O   HOH Z 403 " =    1.474
peak=    3.516 closest distance to " CB  ALA A  34 " =    0.947
peak=    3.511 closest distance to " O   HOH Z 172 " =    3.387
peak=    3.504 closest distance to " O   HOH Z 329 " =    4.068
peak=    3.502 closest distance to " N   ARG A 156 " =    1.412
peak=    3.497 closest distance to " CZ  PHE A 192 " =    0.945
peak=    3.495 closest distance to " O   HOH Z 423 " =    1.814
peak=    3.495 closest distance to " O   HOH Z 353 " =    2.650
peak=    3.494 closest distance to " O   HOH Z 359 " =    1.404
peak=    3.488 closest distance to " CE1 PHE A 218 " =    1.018
peak=    3.487 closest distance to " NH2 ARG A 156 " =    1.187
peak=    3.487 closest distance to " CB  ALA A 291 " =    1.175
peak=    3.483 closest distance to " CB  SER A   3 " =    1.331
peak=    3.478 closest distance to " CE1 TYR A 186 " =    1.371
peak=    3.478 closest distance to " O   HOH Z  88 " =    3.855
peak=    3.475 closest distance to " O   HOH Z  59 " =    1.965
peak=    3.471 closest distance to " O   HOH Z  43 " =    1.872
peak=    3.470 closest distance to " CB  PRO A  90 " =    1.146
peak=    3.469 closest distance to " C   ILE A 106 " =    1.935
peak=    3.469 closest distance to " CB  MET A  47 " =    0.981
peak=    3.459 closest distance to " O   HOH Z 166 " =    3.875
peak=    3.446 closest distance to " OG BSER A 164 " =    2.361
peak=    3.445 closest distance to " O   HOH Z 426 " =    1.802
peak=    3.438 closest distance to " O   HOH Z 280 " =    3.014
peak=    3.422 closest distance to " O   HOH Z 167 " =    1.760
peak=    3.422 closest distance to " CB  ILE A 120 " =    1.264
peak=    3.420 closest distance to " O   HOH Z  40 " =    1.900
peak=    3.417 closest distance to " CB  TYR A 169 " =    0.713
peak=    3.411 closest distance to " O   HOH Z 391 " =    2.918
peak=    3.410 closest distance to " OD1 ASP A 171 " =    1.238
peak=    3.407 closest distance to " O   ASN A  74 " =    1.477
peak=    3.407 closest distance to " CG2AVAL A  72 " =    1.743
peak=    3.405 closest distance to " CB  THR A  82 " =    1.406
peak=    3.404 closest distance to " CA  VAL A 125 " =    1.138
peak=    3.400 closest distance to " O   HOH Z 406 " =    1.582
peak=    3.399 closest distance to " O   HOH Z 135 " =    1.696
peak=    3.398 closest distance to " CG  GLU A  37 " =    0.862
peak=    3.394 closest distance to " O   HOH Z 213 " =    2.141
peak=    3.393 closest distance to " CB  GLN A  88 " =    1.256
peak=    3.392 closest distance to " O   SER A  87 " =    2.256
peak=    3.391 closest distance to " O   HOH Z 171 " =    3.928
peak=    3.391 closest distance to " O   HOH Z 326 " =    2.448
peak=    3.390 closest distance to " O   HOH Z 193 " =    1.719
peak=    3.379 closest distance to " CB  GLN A  89 " =    1.254
peak=    3.368 closest distance to " CB  ALA A   1 " =    4.763
peak=    3.365 closest distance to " O   HOH Z 227 " =    1.731
peak=    3.364 closest distance to " CA  ARG A 102 " =    1.170
peak=    3.363 closest distance to " O   HOH Z 421 " =    2.225
peak=    3.361 closest distance to " O   HOH Z 294 " =    1.586
peak=    3.358 closest distance to " O   HOH Z 422 " =    2.699
peak=    3.355 closest distance to " CG  MET A 185 " =    1.215
peak=    3.337 closest distance to " CG  PHE A 204 " =    0.871
peak=    3.336 closest distance to " CD1AILE A 234 " =    0.944
peak=    3.335 closest distance to " O   HOH Z 344 " =    3.206
peak=    3.332 closest distance to " OG  SER A  22 " =    2.836
peak=    3.321 closest distance to " NH2BARG A 145 " =    2.233
peak=    3.320 closest distance to " CA  ASN A 217 " =    1.261
peak=    3.318 closest distance to " CG  ARG A 138 " =    1.123
peak=    3.318 closest distance to " CB  ALA A 248 " =    1.276
peak=    3.316 closest distance to " CA  ALA A 233 " =    1.478
peak=    3.315 closest distance to " O   HOH Z  68 " =    2.168
peak=    3.314 closest distance to " O   HOH Z 128 " =    2.489
peak=    3.312 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.311 closest distance to " N   GLY A  98 " =    1.142
peak=    3.308 closest distance to " CD  ARG A 219 " =    1.108
peak=    3.305 closest distance to " N   PHE A 130 " =    1.224
peak=    3.303 closest distance to " CA  ILE A 234 " =    1.018
peak=    3.303 closest distance to " CA  ALA A 295 " =    1.126
peak=    3.299 closest distance to " CG  ARG A 159 " =    0.935
peak=    3.297 closest distance to " CA  GLU A  46 " =    0.809
peak=    3.297 closest distance to " CB  LYS A 117 " =    1.200
peak=    3.295 closest distance to " O   HOH Z 425 " =    1.256
peak=    3.293 closest distance to " CB  ALA A 291 " =    0.803
peak=    3.283 closest distance to " C   TYR A 214 " =    1.605
peak=    3.283 closest distance to " CG2 ILE A 151 " =    0.903
peak=    3.281 closest distance to " CB  ARG A 138 " =    1.000
peak=    3.279 closest distance to " O   THR A 182 " =    1.392
peak=    3.274 closest distance to " CA  TYR A 116 " =    1.353
peak=    3.274 closest distance to " O   HOH Z 402 " =    1.388
peak=    3.273 closest distance to " CB  HIS A 108 " =    0.779
peak=    3.272 closest distance to " O   HOH Z 394 " =    4.097
peak=    3.272 closest distance to " O   HOH Z 109 " =    2.714
peak=    3.272 closest distance to " CB  ALA A 242 " =    0.830
peak=    3.271 closest distance to " O   HOH Z 409 " =    2.928
peak=    3.262 closest distance to " CB  LEU A 143 " =    1.140
peak=    3.260 closest distance to " CG  GLN A  11 " =    1.563
peak=    3.258 closest distance to " CB  ALA A 248 " =    0.991
peak=    3.256 closest distance to " O   HOH Z 383 " =    2.238
peak=    3.255 closest distance to " O   HOH Z 245 " =    1.194
peak=    3.254 closest distance to " O   HOH Z 403 " =    1.641
peak=    3.253 closest distance to " O   HOH Z 218 " =    4.698
peak=    3.250 closest distance to " O   HOH Z 116 " =    3.146
peak=    3.250 closest distance to " CB  PHE A 204 " =    0.744
peak=    3.250 closest distance to " O   HOH Z 132 " =    2.757
peak=    3.247 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.245 closest distance to " CB  SER A  22 " =    0.969
peak=    3.240 closest distance to " OG BSER A 134 " =    2.922
peak=    3.240 closest distance to " O   HOH Z 148 " =    3.448
peak=    3.239 closest distance to " OE1 GLU A 152 " =    0.856
peak=    3.238 closest distance to " O   HOH Z   9 " =    2.025
peak=    3.233 closest distance to " CB  THR A  31 " =    1.695
peak=    3.232 closest distance to " CA  GLY A 211 " =    1.295
peak=    3.230 closest distance to " CB  ASN A 215 " =    1.167
peak=    3.229 closest distance to " CG1 ILE A 151 " =    1.014
peak=    3.229 closest distance to " CB  ALA A 227 " =    1.058
peak=    3.226 closest distance to " CB  LYS A 193 " =    0.984
peak=    3.223 closest distance to " CB  THR A 235 " =    1.136
peak=    3.219 closest distance to " NE  ARG A  79 " =    1.147
peak=    3.217 closest distance to " CD1 ILE A 106 " =    0.774
peak=    3.215 closest distance to " O   ALA A 158 " =    1.300
peak=    3.212 closest distance to " O   HOH Z 365 " =    2.998
peak=    3.210 closest distance to " O   HOH Z 273 " =    2.812
peak=    3.207 closest distance to " CA  GLY A 241 " =    0.740
peak=    3.205 closest distance to " CB  SER A 141 " =    1.021
peak=    3.201 closest distance to " O   HOH Z 203 " =    1.830
peak=    3.200 closest distance to " O   HOH Z 305 " =    3.677
peak=    3.193 closest distance to " OG  SER A  28 " =    1.469
peak=    3.190 closest distance to " CA  ASN A 127 " =    1.126
peak=    3.187 closest distance to " O   HOH Z 419 " =    2.025
peak=    3.186 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.181 closest distance to " O   HOH Z 271 " =    2.825
peak=    3.181 closest distance to " NZ  LYS A  48 " =    1.349
peak=    3.181 closest distance to " ND2 ASN A 110 " =    1.640
peak=    3.180 closest distance to " O   GLN A 278 " =    1.330
peak=    3.177 closest distance to " CA  PHE A  59 " =    1.044
peak=    3.176 closest distance to " O   HOH Z 425 " =    1.957
peak=    3.175 closest distance to " CB  ALA A  43 " =    0.834
peak=    3.173 closest distance to " CG2 ILE A 239 " =    0.751
peak=    3.172 closest distance to " O   HOH Z 327 " =    2.730
peak=    3.168 closest distance to " OE1 GLU A 236 " =    1.080
peak=    3.167 closest distance to " O   HOH Z  28 " =    1.850
peak=    3.153 closest distance to " CG  MET A 113 " =    1.330
peak=    3.151 closest distance to " O   HOH Z 147 " =    1.782
peak=    3.147 closest distance to " O   HOH Z 371 " =    1.727
peak=    3.145 closest distance to " CB  VAL A 268 " =    0.829
peak=    3.144 closest distance to " CB  PHE A  16 " =    1.039
peak=    3.144 closest distance to " CB  ASN A 173 " =    1.105
peak=    3.141 closest distance to " CG2 ILE A 234 " =    0.738
peak=    3.140 closest distance to " CA  ALA A  21 " =    1.203
peak=    3.137 closest distance to " O   ASN A 209 " =    1.272
peak=    3.134 closest distance to " CB  GLN A 103 " =    0.866
peak=    3.133 closest distance to " O   HOH Z 285 " =    1.839
peak=    3.130 closest distance to " O   HOH Z 234 " =    1.778
peak=    3.128 closest distance to " NH2AARG A 275 " =    3.659
peak=    3.125 closest distance to " CB  ASP A 171 " =    0.832
peak=    3.125 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.122 closest distance to " CB  ARG A 139 " =    0.911
peak=    3.115 closest distance to " O   HOH Z 124 " =    1.832
peak=    3.114 closest distance to " O   HOH Z 128 " =    2.176
peak=    3.113 closest distance to " O   HOH Z  80 " =    1.550
peak=    3.104 closest distance to " O   HOH Z 116 " =    1.840
peak=    3.100 closest distance to " CG2BVAL A  41 " =    0.868
peak=    3.098 closest distance to " N   TYR A  15 " =    0.705
peak=    3.095 closest distance to " O   HOH Z  20 " =    1.713
peak=    3.094 closest distance to " CA  ASP A 191 " =    1.196
peak=    3.090 closest distance to " CB  TRP A 179 " =    1.477
peak=    3.086 closest distance to " CA  ALA A 100 " =    1.118
peak=    3.085 closest distance to " O   HOH Z 302 " =    2.023
peak=    3.079 closest distance to " CA  LYS A 290 " =    1.259
peak=    3.079 closest distance to " CA  ASN A 176 " =    1.754
peak=    3.076 closest distance to " CE2 TYR A 186 " =    0.846
peak=    3.065 closest distance to " CA  LEU A 282 " =    1.065
peak=    3.051 closest distance to " O   HOH Z  88 " =    2.908
peak=    3.040 closest distance to " ND1 HIS A  81 " =    1.675
peak=    3.032 closest distance to " OE2 GLU A  53 " =    2.004
peak=    3.028 closest distance to " O   HOH Z 361 " =    3.218
peak=    3.028 closest distance to " NE2 HIS A 115 " =    0.987

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.833 - 5.754
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.833 - 5.754

peak=   -4.611 closest distance to " CG1 VAL A 112 " =    2.673
peak=   -4.448 closest distance to " CD  ARG A  14 " =    3.434
peak=   -4.442 closest distance to " O   HOH Z 231 " =    2.259
peak=   -4.347 closest distance to " CD  ARG A 156 " =    2.089
peak=   -4.291 closest distance to " CB  PRO A 243 " =    2.658
peak=   -4.286 closest distance to " O   PRO A 198 " =    1.264
peak=   -4.281 closest distance to " CD  GLN A  58 " =    0.946
peak=   -4.216 closest distance to " O   HOH Z 266 " =    5.500
peak=   -4.184 closest distance to " N   ALA A  43 " =    2.602
peak=   -4.181 closest distance to " O   HOH Z 377 " =    2.016
peak=   -4.104 closest distance to " O   HOH Z  73 " =    2.125
peak=   -4.085 closest distance to " CE2 TYR A  30 " =    2.730
peak=   -4.073 closest distance to " CZ3 TRP A 179 " =    1.160
peak=   -4.034 closest distance to " O   VAL A  67 " =    2.698
peak=   -4.030 closest distance to " O   HOH Z  10 " =    1.544
peak=   -3.969 closest distance to " OE1 GLN A 223 " =    2.045
peak=   -3.936 closest distance to " CD1 PHE A  59 " =    1.951
peak=   -3.902 closest distance to " OG BSER A 134 " =    1.319
peak=   -3.901 closest distance to " CG1 VAL A 250 " =    2.690
peak=   -3.887 closest distance to " CD2 TYR A 293 " =    1.972
peak=   -3.885 closest distance to " C   HIS A 108 " =    1.094
peak=   -3.867 closest distance to " CG  ARG A 269 " =    2.525
peak=   -3.840 closest distance to " OD1 ASN A 148 " =    1.436
peak=   -3.831 closest distance to " CG  MET A 105 " =    0.975
peak=   -3.806 closest distance to " O   HOH Z  38 " =    1.395
peak=   -3.800 closest distance to " O   HOH Z 114 " =    3.244
peak=   -3.798 closest distance to " O   ILE A 109 " =    2.548
peak=   -3.776 closest distance to " O   HOH Z 198 " =    2.168
peak=   -3.769 closest distance to " O   HOH Z  51 " =    1.641
peak=   -3.764 closest distance to " O   HOH Z 394 " =    1.526
peak=   -3.751 closest distance to " CE2 PHE A  61 " =    2.646
peak=   -3.749 closest distance to " OG  SER A  97 " =    2.269
peak=   -3.741 closest distance to " CG2 ILE A  49 " =    2.738
peak=   -3.730 closest distance to " CB  ALA A  43 " =    2.686
peak=   -3.724 closest distance to " C   GLY A  17 " =    1.225
peak=   -3.717 closest distance to " NH2AARG A 275 " =    5.554
peak=   -3.717 closest distance to " O   HOH Z 389 " =    2.043
peak=   -3.713 closest distance to " ND2 ASN A 249 " =    2.467
peak=   -3.678 closest distance to " O   HOH Z 372 " =    2.375
peak=   -3.672 closest distance to " O   HOH Z 290 " =    1.314
peak=   -3.671 closest distance to " CG1 VAL A 112 " =    3.018
peak=   -3.657 closest distance to " O   HOH Z 196 " =    2.071
peak=   -3.654 closest distance to " CB  ALA A 291 " =    2.337
peak=   -3.638 closest distance to " O   HOH Z 407 " =    3.327
peak=   -3.630 closest distance to " CB  ASN A  39 " =    2.324
peak=   -3.617 closest distance to " O   HOH Z 351 " =    1.491
peak=   -3.612 closest distance to " CA  GLY A 241 " =    3.247
peak=   -3.611 closest distance to " CA  GLY A 203 " =    2.438
peak=   -3.609 closest distance to " CE  MET A 105 " =    2.367
peak=   -3.607 closest distance to " O   HOH Z  52 " =    1.454
peak=   -3.601 closest distance to " ND2 ASN A  45 " =    1.100
peak=   -3.595 closest distance to " CE3 TRP A 150 " =    2.151
peak=   -3.594 closest distance to " OXT GLY A 302 " =    3.025
peak=   -3.594 closest distance to " O   HOH Z 185 " =    2.312
peak=   -3.591 closest distance to " N   THR A 157 " =    1.616
peak=   -3.585 closest distance to " CD1 LEU A 101 " =    2.356
peak=   -3.581 closest distance to " O   HOH Z 166 " =    1.918
peak=   -3.578 closest distance to " O   HOH Z 426 " =    1.589
peak=   -3.577 closest distance to " O   VAL A 189 " =    2.629
peak=   -3.568 closest distance to " CB  PHE A 192 " =    2.023
peak=   -3.554 closest distance to " ND2 ASN A  45 " =    1.896
peak=   -3.553 closest distance to " O   HOH Z  60 " =    2.333
peak=   -3.530 closest distance to " CE BMET A  47 " =    1.630
peak=   -3.518 closest distance to " NH2 ARG A  79 " =    1.466
peak=   -3.518 closest distance to " O   HOH Z 435 " =    2.844
peak=   -3.513 closest distance to " CG  HIS A  86 " =    1.091
peak=   -3.500 closest distance to " OE1 GLN A  88 " =    1.160
peak=   -3.497 closest distance to " CA  GLY A 241 " =    2.339
peak=   -3.497 closest distance to " O   ALA A  10 " =    1.678
peak=   -3.492 closest distance to " O   GLY A 211 " =    1.362
peak=   -3.490 closest distance to " O   PHE A 218 " =    1.499
peak=   -3.488 closest distance to " CG1 VAL A 125 " =    1.897
peak=   -3.485 closest distance to " NE2 GLN A 194 " =    1.878
peak=   -3.479 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.470 closest distance to " O   TYR A 247 " =    2.890
peak=   -3.469 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.467 closest distance to " CG2 ILE A 263 " =    2.409
peak=   -3.462 closest distance to " O   HOH Z 353 " =    2.165
peak=   -3.448 closest distance to " ND2 ASN A  60 " =    1.514
peak=   -3.445 closest distance to " O   HOH Z 350 " =    2.038
peak=   -3.445 closest distance to " CG1AVAL A  41 " =    2.919
peak=   -3.438 closest distance to " O   PRO A 163 " =    2.146
peak=   -3.432 closest distance to " O   HOH Z 243 " =    2.106
peak=   -3.431 closest distance to " ND2 ASN A  45 " =    1.376
peak=   -3.418 closest distance to " CB  TRP A  85 " =    2.420
peak=   -3.410 closest distance to " N   THR A 264 " =    1.307
peak=   -3.407 closest distance to " C   ASN A 285 " =    2.468
peak=   -3.405 closest distance to " ND2 ASN A  60 " =    4.148
peak=   -3.402 closest distance to " O   HOH Z 126 " =    1.935
peak=   -3.395 closest distance to " CB  ALA A 291 " =    2.167
peak=   -3.395 closest distance to " O   HOH Z 232 " =    1.711
peak=   -3.395 closest distance to " CA  SER A 135 " =    1.291
peak=   -3.392 closest distance to " OD1 ASP A 191 " =    1.616
peak=   -3.391 closest distance to " O   HOH Z   6 " =    1.454
peak=   -3.386 closest distance to " O   HOH Z  43 " =    1.651
peak=   -3.382 closest distance to " O   HOH Z 128 " =    2.583
peak=   -3.376 closest distance to " ND2BASN A 224 " =    1.774
peak=   -3.376 closest distance to " C   LEU A 222 " =    0.833
peak=   -3.374 closest distance to " CD  ARG A 195 " =    5.107
peak=   -3.372 closest distance to " O   HOH Z 106 " =    1.973
peak=   -3.371 closest distance to " O   TRP A  70 " =    1.414
peak=   -3.370 closest distance to " CA  VAL A  67 " =    2.975
peak=   -3.370 closest distance to " CG2 THR A 178 " =    2.352
peak=   -3.365 closest distance to " OD2 ASP A 171 " =    1.883
peak=   -3.362 closest distance to " O   HOH Z 253 " =    4.089
peak=   -3.361 closest distance to " CD2 PHE A  61 " =    2.108
peak=   -3.354 closest distance to " O   HOH Z 102 " =    1.587
peak=   -3.349 closest distance to " CB  PRO A  54 " =    2.557
peak=   -3.347 closest distance to " N   THR A  52 " =    1.682
peak=   -3.346 closest distance to " O   HOH Z  11 " =    1.704
peak=   -3.345 closest distance to " CG  PRO A 243 " =    1.750
peak=   -3.344 closest distance to " CG  PHE A 283 " =    2.723
peak=   -3.342 closest distance to " CZ  PHE A 155 " =    1.251
peak=   -3.340 closest distance to " CA  ASP A  27 " =    2.536
peak=   -3.339 closest distance to " O   HOH Z 295 " =    1.504
peak=   -3.339 closest distance to " O   SER A  62 " =    2.289
peak=   -3.333 closest distance to " O   HOH Z  71 " =    2.079
peak=   -3.333 closest distance to " NE2 GLN A  88 " =    1.998
peak=   -3.331 closest distance to " CB  ALA A   7 " =    2.397
peak=   -3.321 closest distance to " CB  GLN A  11 " =    1.656
peak=   -3.319 closest distance to " O   HOH Z  37 " =    1.851
peak=   -3.319 closest distance to " O   HOH Z 357 " =    2.114
peak=   -3.316 closest distance to " CG  GLU A 277 " =    1.177
peak=   -3.314 closest distance to " O   HOH Z 348 " =    2.247
peak=   -3.313 closest distance to " CB  ALA A 129 " =    2.428
peak=   -3.298 closest distance to " C   SER A 206 " =    1.474
peak=   -3.295 closest distance to " OH  TYR A 247 " =    2.152
peak=   -3.292 closest distance to " O   HOH Z 298 " =    2.491
peak=   -3.290 closest distance to " C   GLY A  13 " =    0.958
peak=   -3.290 closest distance to " O   HOH Z 393 " =    1.380
peak=   -3.289 closest distance to " O   HOH Z 275 " =    1.587
peak=   -3.284 closest distance to " CD1 LEU A   5 " =    2.626
peak=   -3.279 closest distance to " ND2 ASN A 249 " =    2.219
peak=   -3.278 closest distance to " O   HOH Z 176 " =    0.895
peak=   -3.277 closest distance to " O   HOH Z 177 " =    1.710
peak=   -3.277 closest distance to " O   HOH Z 292 " =    1.860
peak=   -3.275 closest distance to " CG  TRP A 266 " =    1.845
peak=   -3.275 closest distance to " O   HOH Z 313 " =    1.952
peak=   -3.274 closest distance to " CB  ALA A 114 " =    2.608
peak=   -3.274 closest distance to " CG  ARG A  66 " =    2.219
peak=   -3.273 closest distance to " CA  GLY A 241 " =    2.876
peak=   -3.271 closest distance to " CB  ALA A 100 " =    2.217
peak=   -3.270 closest distance to " CG  LEU A  83 " =    1.971
peak=   -3.265 closest distance to " CB  ALA A   9 " =    2.516
peak=   -3.260 closest distance to " NH2 ARG A 159 " =    2.321
peak=   -3.259 closest distance to " N   ALA A 248 " =    1.640
peak=   -3.248 closest distance to " O   HOH Z 114 " =    1.472
peak=   -3.244 closest distance to " CB  ALA A 248 " =    2.495
peak=   -3.242 closest distance to " O   HOH Z 359 " =    3.158
peak=   -3.241 closest distance to " CD  ARG A  79 " =    1.148
peak=   -3.241 closest distance to " CD  GLU A 236 " =    1.118
peak=   -3.237 closest distance to " O   HOH Z 311 " =    3.872
peak=   -3.237 closest distance to " C   PHE A  59 " =    1.297
peak=   -3.235 closest distance to " C   ALA A 158 " =    1.465
peak=   -3.232 closest distance to " O   HOH Z 111 " =    2.148
peak=   -3.231 closest distance to " O   TYR A 186 " =    1.702
peak=   -3.230 closest distance to " O   HOH Z 198 " =    1.514
peak=   -3.229 closest distance to " CB  PHE A  16 " =    2.508
peak=   -3.222 closest distance to " CD2 TYR A 293 " =    2.130
peak=   -3.217 closest distance to " O   HOH Z 189 " =    1.966
peak=   -3.212 closest distance to " CD2 LEU A 222 " =    2.190
peak=   -3.209 closest distance to " CB  PRO A 163 " =    2.551
peak=   -3.205 closest distance to " C   LEU A 143 " =    1.250
peak=   -3.204 closest distance to " OG  SER A 206 " =    1.895
peak=   -3.200 closest distance to " OD1 ASP A 171 " =    1.575
peak=   -3.199 closest distance to " N   SER A 276 " =    1.314
peak=   -3.198 closest distance to " O   HOH Z 216 " =    1.645
peak=   -3.198 closest distance to " CB  ASN A 252 " =    1.551
peak=   -3.197 closest distance to " CG1BVAL A  41 " =    2.740
peak=   -3.195 closest distance to " O   HOH Z 322 " =    1.295
peak=   -3.194 closest distance to " N   LYS A 166 " =    2.008
peak=   -3.190 closest distance to " CD2 PHE A  59 " =    2.542
peak=   -3.189 closest distance to " C   MET A 188 " =    1.375
peak=   -3.186 closest distance to " O   HOH Z 396 " =    1.722
peak=   -3.182 closest distance to " N   SER A 212 " =    1.862
peak=   -3.181 closest distance to " O   GLY A 203 " =    2.357
peak=   -3.181 closest distance to " CA  GLY A  98 " =    1.972
peak=   -3.178 closest distance to " CZ  PHE A  59 " =    1.676
peak=   -3.171 closest distance to " CZ  TYR A 169 " =    1.762
peak=   -3.168 closest distance to " O   HOH Z 417 " =    2.860
peak=   -3.167 closest distance to " CG2 VAL A 189 " =    2.157
peak=   -3.166 closest distance to " O   HOH Z 191 " =    5.754
peak=   -3.163 closest distance to " CE3 TRP A 274 " =    2.483
peak=   -3.161 closest distance to " CB  ASP A 286 " =    2.057
peak=   -3.158 closest distance to " O   HOH Z 134 " =    2.900
peak=   -3.155 closest distance to " O   HOH Z 207 " =    2.203
peak=   -3.152 closest distance to " O   ALA A  34 " =    2.502
peak=   -3.149 closest distance to " O   HOH Z 281 " =    2.608
peak=   -3.147 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.145 closest distance to " O   HOH Z 298 " =    1.242
peak=   -3.141 closest distance to " CB  ALA A 248 " =    2.121
peak=   -3.141 closest distance to " O   SER A 135 " =    1.411
peak=   -3.137 closest distance to " O   VAL A 189 " =    1.572
peak=   -3.134 closest distance to " N   ALA A 226 " =    2.242
peak=   -3.134 closest distance to " CD1 LEU A 228 " =    2.431
peak=   -3.128 closest distance to " O   ALA A 180 " =    1.448
peak=   -3.127 closest distance to " O   HOH Z 252 " =    4.270
peak=   -3.126 closest distance to " CG1 VAL A 197 " =    2.329
peak=   -3.117 closest distance to " CD2 TYR A 247 " =    2.426
peak=   -3.113 closest distance to " CB  ALA A  10 " =    2.283
peak=   -3.113 closest distance to " CA  GLY A 133 " =    2.334
peak=   -3.107 closest distance to " CE3 TRP A  70 " =    1.819
peak=   -3.100 closest distance to " O   HOH Z 174 " =    2.693
peak=   -3.097 closest distance to " O   HOH Z  90 " =    1.667
peak=   -3.096 closest distance to " OD1 ASN A 187 " =    1.555
peak=   -3.087 closest distance to " SD  MET A 188 " =    2.319
peak=   -3.086 closest distance to " NE1 TRP A  70 " =    1.134
peak=   -3.078 closest distance to " CB  TYR A  15 " =    2.253
peak=   -3.074 closest distance to " OH  TYR A 247 " =    1.811
peak=   -3.029 closest distance to " CG  PRO A 163 " =    2.410

================= 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    :  0.3416 0.3318   6.078882e+00   6.064219e+00
   1_bss:  0.3281 0.3216   6.057117e+00   6.039869e+00
   1_xyz:  0.1816 0.2041   5.520650e+00   5.611017e+00
   1_adp:  0.1666 0.2087   5.466977e+00   5.638548e+00
   1_occ:  0.1661 0.2083   5.465191e+00   5.637809e+00
   2_bss:  0.1637 0.2059   5.459518e+00   5.632742e+00
   2_xyz:  0.1295 0.1705   5.255198e+00   5.463492e+00
   2_adp:  0.1221 0.1647   5.207724e+00   5.426136e+00
   2_occ:  0.1220 0.1645   5.207159e+00   5.425640e+00
   3_bss:  0.1218 0.1639   5.204792e+00   5.421732e+00
   3_xyz:  0.1145 0.1605   5.166943e+00   5.401982e+00
   3_adp:  0.1148 0.1584   5.160864e+00   5.390118e+00
   3_occ:  0.1147 0.1583   5.160944e+00   5.390635e+00
   4_bss:  0.1147 0.1583   5.160827e+00   5.390518e+00
   4_xyz:  0.1127 0.1592   5.155439e+00   5.395567e+00
   4_adp:  0.1114 0.1606   5.153748e+00   5.403304e+00
   4_occ:  0.1113 0.1607   5.153774e+00   5.403480e+00
   5_bss:  0.1112 0.1605   5.153346e+00   5.403283e+00
   5_xyz:  0.1148 0.1629   5.177470e+00   5.419249e+00
   5_adp:  0.1148 0.1636   5.178086e+00   5.422119e+00
   5_occ:  0.1148 0.1636   5.178146e+00   5.422341e+00
   5_bss:  0.1147 0.1634   5.178273e+00   5.422407e+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:  0.323  69.247  -0.444  -3.365   2.182  -0.000   0.000   0.000
   1_xyz:  0.323  69.247  -0.444  -3.365   2.182  -0.000   0.000   0.000
   1_adp:  0.323  69.247  -0.444  -3.365   2.182  -0.000   0.000   0.000
   1_occ:  0.323  69.247  -0.444  -3.365   2.182  -0.000   0.000   0.000
   2_bss:  0.337  69.247  -2.028  -3.165  -0.400  -0.000  -0.000  -0.000
   2_xyz:  0.337  69.247  -2.028  -3.165  -0.400  -0.000  -0.000  -0.000
   2_adp:  0.337  69.247  -2.028  -3.165  -0.400  -0.000  -0.000  -0.000
   2_occ:  0.337  69.247  -2.028  -3.165  -0.400  -0.000  -0.000  -0.000
   3_bss:  0.337  69.247  -2.253  -2.728  -0.744  -0.000  -0.000  -0.000
   3_xyz:  0.337  69.247  -2.253  -2.728  -0.744  -0.000  -0.000  -0.000
   3_adp:  0.337  69.247  -2.253  -2.728  -0.744  -0.000  -0.000  -0.000
   3_occ:  0.337  69.247  -2.253  -2.728  -0.744  -0.000  -0.000  -0.000
   4_bss:  0.337  69.247  -2.282  -2.511  -0.817  -0.000  -0.000  -0.000
   4_xyz:  0.337  69.247  -2.282  -2.511  -0.817  -0.000  -0.000  -0.000
   4_adp:  0.337  69.247  -2.282  -2.511  -0.817  -0.000  -0.000  -0.000
   4_occ:  0.337  69.247  -2.282  -2.511  -0.817  -0.000  -0.000  -0.000
   5_bss:  0.320  63.752  -2.059  -2.222  -0.632  -0.000  -0.000  -0.000
   5_xyz:  0.320  63.752  -2.059  -2.222  -0.632  -0.000  -0.000  -0.000
   5_adp:  0.320  63.752  -2.059  -2.222  -0.632  -0.000  -0.000  -0.000
   5_occ:  0.320  63.752  -2.059  -2.222  -0.632  -0.000  -0.000  -0.000
   5_bss:  0.320  63.755  -1.850  -1.971  -0.433  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.236 0.7013  0.8542    31595.922
   1_bss:  34.230 0.7116  0.8570    29344.426
   1_xyz:  18.870 0.8737  0.9995    10361.456
   1_adp:  19.639 0.8658  0.9964    10874.679
   1_occ:  19.607 0.8660  0.9960    10820.305
   2_bss:  19.406 0.8682  0.9522    10744.575
   2_xyz:  15.703 0.9007  0.9693     7462.469
   2_adp:  14.843 0.9082  0.9665     6913.369
   2_occ:  14.831 0.9083  0.9664     6902.557
   3_bss:  14.762 0.9088  0.9648     6821.534
   3_xyz:  14.278 0.9129  0.9670     6552.061
   3_adp:  13.975 0.9155  0.9642     6423.812
   3_occ:  13.990 0.9154  0.9640     6424.955
   4_bss:  13.988 0.9154  0.9653     6422.666
   4_xyz:  14.069 0.9149  0.9648     6527.417
   4_adp:  14.250 0.9133  0.9565     6583.922
   4_occ:  14.254 0.9133  0.9564     6585.093
   5_bss:  14.249 0.9133  0.9640     6573.409
   5_xyz:  14.537 0.9112  0.9624     6788.720
   5_adp:  14.602 0.9106  0.9541     6824.372
   5_occ:  14.607 0.9106  0.9540     6827.282
   5_bss:  14.611 0.9106  0.9615     6828.824
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6153e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6153e-01
   1_xyz:   1.160  0.010  0.077 15.275  0.005  4.116   8.1333e-02
   1_adp:   1.160  0.010  0.077 15.275  0.005  4.116   8.1333e-02
   1_occ:   1.160  0.010  0.077 15.275  0.005  4.116   8.1333e-02
   2_bss:   1.160  0.010  0.077 15.275  0.005  4.116   8.1333e-02
   2_xyz:   1.068  0.009  0.079 14.965  0.004  4.132   6.7113e-02
   2_adp:   1.068  0.009  0.079 14.965  0.004  4.132   6.7113e-02
   2_occ:   1.068  0.009  0.079 14.965  0.004  4.132   6.7113e-02
   3_bss:   1.068  0.009  0.079 14.965  0.004  4.132   6.7113e-02
   3_xyz:   1.064  0.010  0.082 14.913  0.004  4.116   7.0452e-02
   3_adp:   1.064  0.010  0.082 14.913  0.004  4.116   7.0452e-02
   3_occ:   1.064  0.010  0.082 14.913  0.004  4.116   7.0452e-02
   4_bss:   1.064  0.010  0.082 14.913  0.004  4.116   7.0452e-02
   4_xyz:   1.079  0.010  0.082 14.899  0.004  4.119   7.2662e-02
   4_adp:   1.079  0.010  0.082 14.899  0.004  4.119   7.2662e-02
   4_occ:   1.079  0.010  0.082 14.899  0.004  4.119   7.2662e-02
   5_bss:   1.079  0.010  0.082 14.899  0.004  4.119   7.2662e-02
   5_xyz:   0.946  0.007  0.073 14.674  0.003  4.118   5.5830e-02
   5_adp:   0.946  0.007  0.073 14.674  0.003  4.118   5.5830e-02
   5_occ:   0.946  0.007  0.073 14.674  0.003  4.118   5.5830e-02
   5_bss:   0.946  0.007  0.073 14.674  0.003  4.118   5.5830e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4373e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4373e-01
   1_xyz:  10.097  0.060  0.250 83.081  0.036  2.390   1.6947e-01
   1_adp:  10.097  0.060  0.250 83.081  0.036  2.390   1.6947e-01
   1_occ:  10.097  0.060  0.250 83.081  0.036  2.390   1.6947e-01
   2_bss:  10.097  0.060  0.250 83.081  0.036  2.390   1.6947e-01
   2_xyz:   7.756  0.038  0.245 82.953  0.036  2.337   4.9782e-02
   2_adp:   7.756  0.038  0.245 82.953  0.036  2.337   4.9782e-02
   2_occ:   7.756  0.038  0.245 82.953  0.036  2.337   4.9782e-02
   3_bss:   7.756  0.038  0.245 82.953  0.036  2.337   4.9782e-02
   3_xyz:   7.833  0.047  0.267 83.340  0.038  2.358   4.9643e-02
   3_adp:   7.833  0.047  0.267 83.340  0.038  2.358   4.9643e-02
   3_occ:   7.833  0.047  0.267 83.340  0.038  2.358   4.9643e-02
   4_bss:   7.833  0.047  0.267 83.340  0.038  2.358   4.9643e-02
   4_xyz:   7.513  0.049  0.267 83.527  0.036  2.301   5.0996e-02
   4_adp:   7.513  0.049  0.267 83.527  0.036  2.301   5.0996e-02
   4_occ:   7.513  0.049  0.267 83.527  0.036  2.301   5.0996e-02
   5_bss:   7.513  0.049  0.267 83.527  0.036  2.301   5.0996e-02
   5_xyz:   7.756  0.043  0.226 83.091  0.036  2.413   3.2040e-02
   5_adp:   7.756  0.043  0.226 83.091  0.036  2.413   3.2040e-02
   5_occ:   7.756  0.043  0.226 83.091  0.036  2.413   3.2040e-02
   5_bss:   7.756  0.043  0.226 83.091  0.036  2.413   3.2040e-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:  64.65   0.00  16.81  63.97   0.00  12.89  64.65   4.14  38.19
   1_occ:  64.65   0.00  16.81  63.97   0.00  12.89  64.65   4.14  38.19
   2_bss:  64.65   0.00  16.81  63.97   0.00  12.89  64.65   4.14  38.19
   2_xyz:  64.65   0.00  16.81  63.97   0.00  12.89  64.65   4.14  38.19
   2_adp:  75.20   1.03  17.11  74.88   1.03  12.96  75.20   5.82  39.71
   2_occ:  75.20   1.03  17.11  74.88   1.03  12.96  75.20   5.82  39.71
   3_bss:  75.20   1.03  17.11  74.88   1.03  12.96  75.20   5.82  39.71
   3_xyz:  75.20   1.03  17.11  74.88   1.03  12.96  75.20   5.82  39.71
   3_adp:  75.61   1.74  16.74  74.35   1.74  12.79  75.61   2.60  38.28
   3_occ:  75.61   1.74  16.74  74.35   1.74  12.79  75.61   2.60  38.28
   4_bss:  75.61   1.74  16.74  74.35   1.74  12.79  75.61   2.60  38.28
   4_xyz:  75.61   1.74  16.74  74.35   1.74  12.79  75.61   2.60  38.28
   4_adp:  87.30   0.00  17.21  87.30   0.00  12.87  84.33   3.22  40.82
   4_occ:  87.30   0.00  17.21  87.30   0.00  12.87  84.33   3.22  40.82
   5_bss:  87.30   0.00  17.21  87.30   0.00  12.87  84.33   3.22  40.82
   5_xyz:  87.30   0.00  17.21  87.30   0.00  12.87  84.33   3.22  40.82
   5_adp:  88.40   0.00  17.01  88.40   0.00  12.66  84.86   4.87  40.70
   5_occ:  88.40   0.00  17.01  88.40   0.00  12.66  84.86   4.87  40.70
   5_bss:  88.41   0.00  17.02  88.41   0.00  12.67  84.87   4.88  40.70
------------------------------------------------------------------------
 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:    1.011    0.010    0.319
   1_adp:    1.011    0.010    0.319
   1_occ:    1.011    0.010    0.319
   2_bss:    1.011    0.010    0.319
   2_xyz:    0.966    0.023    0.377
   2_adp:    0.966    0.023    0.377
   2_occ:    0.966    0.023    0.377
   3_bss:    0.966    0.023    0.377
   3_xyz:    1.078    0.039    0.403
   3_adp:    1.078    0.039    0.403
   3_occ:    1.078    0.039    0.403
   4_bss:    1.078    0.039    0.403
   4_xyz:    1.334    0.052    0.414
   4_adp:    1.334    0.052    0.414
   4_occ:    1.334    0.052    0.414
   5_bss:    1.334    0.052    0.414
   5_xyz:    1.361    0.026    0.416
   5_adp:    1.361    0.026    0.416
   5_occ:    1.361    0.026    0.416
   5_bss:    1.361    0.026    0.416
------------------------------------------------------------------------

CPU time actual refinement: 322.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1031/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_1031/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1031/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1031/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1031/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.43 
  Macro-tasks:
    bulk solvent and scale       = 38.67  
    individual site refinement   = 131.90 
    weights calculation          = 29.09  
    collect and process          = 6.75   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.52 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 101.45 
    alpha_beta                      = 8.40   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 110.27 
    fmodel                         = 6.51   
    r_factors                      = 0.24   
    phase_errors                   = 11.28  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 240.82 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.596 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    636 calls, 101.11 s
gradients_fft:          581 calls,  97.01 s

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

# Date 2008-01-16 Time 06:15:45 PST -0800 (1200492945.42 s)
Start R-work = 0.3416, R-free = 0.3318 (no bulk solvent and anisotropic scale)
Final R-work = 0.1354, R-free = 0.1801 (no bulk solvent and anisotropic scale)

Start R-work = 0.3281, R-free = 0.3216
Final R-work = 0.1147, R-free = 0.1634