# Date 2008-01-16 Time 05:03:26 PST -0800 (1200488606.87 s)
#phil __OFF__

Command line arguments: "../577.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5731
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 577

-------------------------------------------------------------------------------
  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: (69.8988, 47.6339, 86.39, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (69.8988, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99058
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9906

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: (69.8988, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99058
Completeness in resolution range: 0.963314
Completeness with d_max=infinity: 0.960292

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2586 [2136/2164]  1922   214  10.0%
  bin  2:  4.2586 -  3.3932 [2042/2061]  1839   203   9.9%
  bin  3:  3.3932 -  2.9681 [2035/2055]  1831   204  10.0%
  bin  4:  2.9681 -  2.6984 [2005/2030]  1808   197   9.8%
  bin  5:  2.6984 -  2.5060 [1999/2018]  1795   204  10.2%
  bin  6:  2.5060 -  2.3589 [1970/2017]  1776   194   9.8%
  bin  7:  2.3589 -  2.2411 [1972/2004]  1774   198  10.0%
  bin  8:  2.2411 -  2.1439 [1963/1999]  1763   200  10.2%
  bin  9:  2.1439 -  2.0616 [1945/1975]  1749   196  10.1%
  bin 10:  2.0616 -  1.9906 [1522/2012]  1373   149   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_577/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2174
        3.04 -     3.66: 4667
        3.66 -     4.28: 8957
        4.28 -     4.90: 12338
  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 "  2.165 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.211 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  70 " - " O   HOH Z 296 "  2.221 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28149 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_577/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_577/model_refine_001.geo

CPU time processing inputs: 9.60


============================ 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 = 69.89875 47.63395 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3304   r_free= 0.3206   ksol= 0.00   Bsol= 0.00   scale= 0.961    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.085597                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7494 0.99   1389  154 0.2888 0.3063      6.3652      6.3627|
|  2:  4.7494 -  3.7900 0.99   1329  150 0.2627 0.2468       6.495      6.4682|
|  3:  3.7900 -  3.3169 0.99   1312  148 0.2858 0.2709      6.3972      6.3769|
|  4:  3.3169 -  3.0164 0.99   1305  134 0.3081 0.2708      6.2806        6.12|
|  5:  3.0164 -  2.8017 0.99   1285  148 0.3391 0.2921      6.1668      6.0852|
|  6:  2.8017 -  2.6374 0.98   1283  143 0.3432 0.3508       6.077      5.9926|
|  7:  2.6374 -  2.5060 0.99   1292  145 0.3485 0.3207      6.0511      5.9234|
|  8:  2.5060 -  2.3974 0.98   1274  138 0.3589 0.3896      6.0143      6.0765|
|  9:  2.3974 -  2.3054 0.98   1272  146 0.3653 0.3695       5.961      5.9584|
| 10:  2.3054 -  2.2261 0.97   1243  136 0.3795 0.3701      5.9766       5.904|
| 11:  2.2261 -  2.1567 0.99   1274  144 0.3643 0.3363      5.8776      5.8837|
| 12:  2.1567 -  2.0953 0.98   1276  141 0.3842 0.3923      5.8536      5.9299|
| 13:  2.0953 -  2.0402 0.97   1256  134 0.4035 0.3495      5.7894      5.7257|
| 14:  2.0402 -  1.9906 0.67    840   98 0.3644 0.4302      5.6969      5.7124|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7494  1389   154  0.77  28.23   0.86     0.78      49040.25|
|  2:  4.7494 -  3.7900  1329   150  0.83  22.85   0.97     0.90      49241.56|
|  3:  3.7900 -  3.3169  1312   148  0.81  25.38   0.98     0.94      44695.08|
|  4:  3.3169 -  3.0164  1305   134  0.79  27.52   0.97     0.93      37122.55|
|  5:  3.0164 -  2.8017  1285   148  0.74  32.05   0.98     0.90      31739.01|
|  6:  2.8017 -  2.6374  1283   143  0.72  34.19   0.99     0.88      28985.85|
|  7:  2.6374 -  2.5060  1292   145  0.71  34.91   0.99     0.88      27521.28|
|  8:  2.5060 -  2.3974  1274   138  0.69  36.77   1.00     0.87      27301.09|
|  9:  2.3974 -  2.3054  1272   146  0.66  38.92   1.00     0.88      26189.25|
| 10:  2.3054 -  2.2261  1243   136  0.66  38.96   1.02     0.88      24616.20|
| 11:  2.2261 -  2.1567  1274   144  0.66  39.09   1.03     0.91      23359.79|
| 12:  2.1567 -  2.0953  1276   141  0.65  40.48   1.03     0.91      22332.14|
| 13:  2.0953 -  2.0402  1256   134  0.61  43.20   1.00     0.86      21112.07|
| 14:  2.0402 -  1.9906   840    98  0.58  45.79   1.03     0.77      19148.28|
|alpha:            min =        0.77 max =            0.94 mean =         0.88|
|beta:             min =    19148.28 max =        49241.56 mean =     31408.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.71|
|phase err.(work): min =        0.00 max =           89.97 mean =        34.48|
|phase err.(test): min =        0.00 max =           89.56 mean =        34.94|
|-----------------------------------------------------------------------------|

============================== 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 = 6.673494              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.485   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665001              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.865   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      181 |
| 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:     1860 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2807 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4595 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4362 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5616 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6722 |
|-----------------------------------------------------------------------------|
|-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 |   4.113    4.900  1.806 |       0.158 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3304   r_free= 0.3206   ksol= 0.00   Bsol= 0.00   scale= 0.961    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.085597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3146   r_free= 0.3036   ksol= 0.31   Bsol= 45.42   scale= 0.970   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,3.53,-1.80,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.059451                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.218233              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.419   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.381061              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.674   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3146      final r-factor (work) = 0.1833          |
| start r-factor (free) = 0.3036      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0274 = 6.22 * 0.50 * 6.0679 + 1.00 * 0.1617                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9891 = 6.22 * 0.50 * 5.7577 + 1.00 * 0.0878                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1833      final r-factor (work) = 0.1657          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.2052          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2001 = 0.38 * 1.00 * 5.7577 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0925 = 0.38 * 1.00 * 5.4631 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.31   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    72.31   17.02    None  None   None       |
|    Sol.    : 438    0      6.17    72.31   39.00    None  None   None       |
|    Mac.    : 2385   0      0.00    69.68   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.231:  417   |   5:    36.154 -  43.384:  114        |
|      1:     7.231 -  14.461: 1324   |   6:    43.384 -  50.615:   90        |
|      2:    14.461 -  21.692:  474   |   7:    50.615 -  57.846:   74        |
|      3:    21.692 -  28.923:  163   |   8:    57.846 -  65.076:   34        |
|      4:    28.923 -  36.154:  116   |   9:    65.076 -  72.307:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1657 r_free = 0.2052             target_work(ml) = 5.473         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1655 r_free = 0.2049             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1655   r_free= 0.2049   ksol= 0.31   Bsol= 45.42   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,3.53,-1.80,0.00,-0.00,-0.00); trace/3= -0.51                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.471636                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1617   r_free= 0.2008   ksol= 0.32   Bsol= 58.52   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-0.28,-1.47,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.453818                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.948369              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.748   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.153327              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.297   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1617      final r-factor (work) = 0.1313          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4070 = 1.95 * 0.50 * 5.4601 + 1.00 * 0.0878                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2768 = 1.95 * 0.50 * 5.3615 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8341 = 0.15 * 1.00 * 5.3615 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8219 = 0.15 * 1.00 * 5.2504 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.02   16.57    None  None   None       |
|    all(noH): 2823   0      0.00    74.02   16.57    None  None   None       |
|    Sol.    : 438    0      5.44    70.90   37.71    None  None   None       |
|    Mac.    : 2385   0      0.00    74.02   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.402:  423   |   5:    37.008 -  44.409:  112        |
|      1:     7.402 -  14.803: 1430   |   6:    44.409 -  51.811:   91        |
|      2:    14.803 -  22.205:  425   |   7:    51.811 -  59.212:   58        |
|      3:    22.205 -  29.606:  131   |   8:    59.212 -  66.614:   27        |
|      4:    29.606 -  37.008:  118   |   9:    66.614 -  74.015:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1279 r_free = 0.1628             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1627             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1627   ksol= 0.32   Bsol= 58.52   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-0.28,-1.47,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.233219                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1621   ksol= 0.32   Bsol= 54.56   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.18,-1.17,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.231234                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.468347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.932  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.510661              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.471   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9077 = 1.47 * 0.50 * 5.2493 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8664 = 1.47 * 0.50 * 5.1940 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6622 = 0.51 * 1.00 * 5.1940 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6448 = 0.51 * 1.00 * 5.1617 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    78.47   16.65    None  None   None       |
|    all(noH): 2823   0      1.01    78.47   16.65    None  None   None       |
|    Sol.    : 438    0      5.26    71.07   38.82    None  None   None       |
|    Mac.    : 2385   0      1.01    78.47   12.57    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:     1.013 -   8.759:  796   |   5:    39.742 -  47.487:  114        |
|      1:     8.759 -  16.505: 1199   |   6:    47.487 -  55.233:   80        |
|      2:    16.505 -  24.250:  318   |   7:    55.233 -  62.979:   56        |
|      3:    24.250 -  31.996:  125   |   8:    62.979 -  70.724:   19        |
|      4:    31.996 -  39.742:  111   |   9:    70.724 -  78.470:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1161 r_free = 0.1563             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1562             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1562   ksol= 0.32   Bsol= 54.56   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.18,-1.17,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164591                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1561   ksol= 0.32   Bsol= 54.56   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.31,-0.94,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.824502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.954  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.371222              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.887  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1159      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7620 = 1.82 * 0.50 * 5.1618 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7548 = 1.82 * 0.50 * 5.1489 + 1.00 * 0.0576                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0692 = 1.37 * 1.00 * 5.1489 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0604 = 1.37 * 1.00 * 5.1417 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.61   16.62    None  None   None       |
|    all(noH): 2823   0      0.00    84.61   16.62    None  None   None       |
|    Sol.    : 438    0      5.42    73.70   39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    84.61   12.42    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 -   8.461:  790   |   5:    42.303 -  50.764:  112        |
|      1:     8.461 -  16.921: 1248   |   6:    50.764 -  59.225:   85        |
|      2:    16.921 -  25.382:  296   |   7:    59.225 -  67.686:   38        |
|      3:    25.382 -  33.843:  137   |   8:    67.686 -  76.146:   12        |
|      4:    33.843 -  42.303:  100   |   9:    76.146 -  84.607:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1571             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1572             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1572   ksol= 0.32   Bsol= 54.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.31,-0.94,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1570   ksol= 0.32   Bsol= 54.87   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.15,-0.67,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146241                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.437635              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.525  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.887890              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.449  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7544 = 1.44 * 0.50 * 5.1429 + 1.00 * 0.0576                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7539 = 1.44 * 0.50 * 5.1524 + 1.00 * 0.0503                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 45.8043 = 8.89 * 1.00 * 5.1524 + 1.00 * 0.0099                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 45.8225 = 8.89 * 1.00 * 5.1543 + 1.00 * 0.0116                              |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.11  16.79    None  None   None       |
|    all(noH): 2823   0      0.00    106.11  16.79    None  None   None       |
|    Sol.    : 438    0      5.06    91.74   40.72    None  None   None       |
|    Mac.    : 2385   0      0.00    106.11  12.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.611: 1331   |   5:    53.057 -  63.668:   80        |
|      1:    10.611 -  21.223:  914   |   6:    63.668 -  74.279:   46        |
|      2:    21.223 -  31.834:  187   |   7:    74.279 -  84.891:   11        |
|      3:    31.834 -  42.445:  128   |   8:    84.891 -  95.502:    5        |
|      4:    42.445 -  53.057:  117   |   9:    95.502 - 106.113:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1590             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1590             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1590   ksol= 0.32   Bsol= 54.87   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.15,-0.67,-0.00,-0.00,-0.00); trace/3= -1.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158110                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7494 0.99   1389  154 0.0980 0.1277      5.3778      5.5149|
|  2:  4.7494 -  3.7900 0.99   1329  150 0.0831 0.1039      5.4123      5.6026|
|  3:  3.7900 -  3.3169 0.99   1312  148 0.1031 0.1464      5.4582      5.8326|
|  4:  3.3169 -  3.0164 0.99   1305  134 0.1219 0.1620      5.4592       5.642|
|  5:  3.0164 -  2.8017 0.99   1285  148 0.1314 0.1687      5.3421      5.5248|
|  6:  2.8017 -  2.6374 0.98   1283  143 0.1270 0.2013      5.2468      5.5007|
|  7:  2.6374 -  2.5060 0.99   1292  145 0.1243 0.1708      5.1749      5.3618|
|  8:  2.5060 -  2.3974 0.98   1274  138 0.1167 0.1748      5.0994      5.3809|
|  9:  2.3974 -  2.3054 0.98   1272  146 0.1197 0.1869      5.0446      5.3452|
| 10:  2.3054 -  2.2261 0.97   1243  136 0.1155 0.1706       5.001      5.1974|
| 11:  2.2261 -  2.1567 0.99   1274  144 0.1171 0.1832      4.9586      5.3048|
| 12:  2.1567 -  2.0953 0.98   1276  141 0.1122 0.1675      4.8943      5.1664|
| 13:  2.0953 -  2.0402 0.97   1256  134 0.1142 0.1734      4.8131      5.0669|
| 14:  2.0402 -  1.9906 0.67    840   98 0.1082 0.1880      4.7258      5.0174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7494  1389   154  0.94   9.13   0.97     0.94       7078.30|
|  2:  4.7494 -  3.7900  1329   150  0.95   7.69   1.01     0.99       8527.10|
|  3:  3.7900 -  3.3169  1312   148  0.94  10.83   1.02     1.02       9990.18|
|  4:  3.3169 -  3.0164  1305   134  0.92  13.58   1.01     0.99      10386.48|
|  5:  3.0164 -  2.8017  1285   148  0.90  16.20   0.99     0.96       8699.42|
|  6:  2.8017 -  2.6374  1283   143  0.90  16.67   0.98     0.95       7545.70|
|  7:  2.6374 -  2.5060  1292   145  0.90  15.81   0.98     0.95       6379.24|
|  8:  2.5060 -  2.3974  1274   138  0.91  15.48   0.99     0.95       5752.72|
|  9:  2.3974 -  2.3054  1272   146  0.90  16.16   0.99     0.95       5181.20|
| 10:  2.3054 -  2.2261  1243   136  0.90  16.30   0.98     0.94       4804.26|
| 11:  2.2261 -  2.1567  1274   144  0.90  16.09   0.98     0.94       4484.57|
| 12:  2.1567 -  2.0953  1276   141  0.91  15.70   0.99     0.98       4122.47|
| 13:  2.0953 -  2.0402  1256   134  0.90  16.45   0.97     0.96       3573.51|
| 14:  2.0402 -  1.9906   840    98  0.91  15.75   0.95     0.91       2895.91|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2895.91 max =        10386.48 mean =      6506.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.32|
|phase err.(test): min =        0.00 max =           87.70 mean =        13.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1588   ksol= 0.32   Bsol= 56.92   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.93,-0.42,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1588   ksol= 0.32   Bsol= 56.92   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.93,-0.42,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158158                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7494 0.99   1389  154 0.0981 0.1280      5.3791      5.5172|
|  2:  4.7494 -  3.7900 0.99   1329  150 0.0833 0.1039      5.4144      5.6043|
|  3:  3.7900 -  3.3169 0.99   1312  148 0.1032 0.1465      5.4588      5.8327|
|  4:  3.3169 -  3.0164 0.99   1305  134 0.1218 0.1618      5.4586      5.6415|
|  5:  3.0164 -  2.8017 0.99   1285  148 0.1313 0.1686      5.3411      5.5239|
|  6:  2.8017 -  2.6374 0.98   1283  143 0.1269 0.2010       5.246      5.4993|
|  7:  2.6374 -  2.5060 0.99   1292  145 0.1243 0.1709      5.1744       5.362|
|  8:  2.5060 -  2.3974 0.98   1274  138 0.1167 0.1747      5.0994      5.3803|
|  9:  2.3974 -  2.3054 0.98   1272  146 0.1196 0.1869      5.0447      5.3455|
| 10:  2.3054 -  2.2261 0.97   1243  136 0.1155 0.1707      5.0011      5.1975|
| 11:  2.2261 -  2.1567 0.99   1274  144 0.1170 0.1831      4.9584      5.3047|
| 12:  2.1567 -  2.0953 0.98   1276  141 0.1122 0.1674       4.894      5.1662|
| 13:  2.0953 -  2.0402 0.97   1256  134 0.1142 0.1734      4.8129      5.0666|
| 14:  2.0402 -  1.9906 0.67    840   98 0.1082 0.1879      4.7257      5.0169|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7494  1389   154  0.94   9.15   0.97     0.94       7111.38|
|  2:  4.7494 -  3.7900  1329   150  0.95   7.71   1.01     0.99       8556.58|
|  3:  3.7900 -  3.3169  1312   148  0.94  10.85   1.03     1.02      10009.51|
|  4:  3.3169 -  3.0164  1305   134  0.92  13.58   1.01     0.99      10375.55|
|  5:  3.0164 -  2.8017  1285   148  0.90  16.18   1.00     0.97       8680.72|
|  6:  2.8017 -  2.6374  1283   143  0.90  16.65   0.99     0.96       7530.58|
|  7:  2.6374 -  2.5060  1292   145  0.90  15.81   0.99     0.96       6371.25|
|  8:  2.5060 -  2.3974  1274   138  0.91  15.48   1.00     0.96       5751.10|
|  9:  2.3974 -  2.3054  1272   146  0.90  16.16   1.00     0.96       5181.77|
| 10:  2.3054 -  2.2261  1243   136  0.90  16.30   0.99     0.95       4803.45|
| 11:  2.2261 -  2.1567  1274   144  0.90  16.08   0.99     0.95       4482.99|
| 12:  2.1567 -  2.0953  1276   141  0.91  15.69   1.00     0.99       4119.12|
| 13:  2.0953 -  2.0402  1256   134  0.90  16.45   0.99     0.97       3570.58|
| 14:  2.0402 -  1.9906   840    98  0.91  15.75   0.97     0.92       2893.69|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2893.69 max =        10375.55 mean =      6508.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.32|
|phase err.(test): min =        0.00 max =           87.66 mean =        13.80|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.000)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.12  16.79    None  None   None       |
|    all(noH): 2823   0      0.00    106.12  16.79    None  None   None       |
|    Sol.    : 438    0      5.07    91.75   40.73    None  None   None       |
|    Mac.    : 2385   0      0.00    106.12  12.39    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 -  10.614: 1331   |   5:    53.060 -  63.671:   80        |
|      1:    10.614 -  21.226:  914   |   6:    63.671 -  74.282:   46        |
|      2:    21.226 -  31.837:  187   |   7:    74.282 -  84.894:   11        |
|      3:    31.837 -  42.448:  128   |   8:    84.894 -  95.505:    5        |
|      4:    42.448 -  53.060:  117   |   9:    95.505 - 106.116:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.532 - 4.512
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 287 from: 291
   mapped sites are within: 0.713 - 4.512

peak=    5.605 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.482 closest distance to " CG  PRO A  54 " =    1.320
peak=    5.335 closest distance to " CB  ARG A 275 " =    0.962
peak=    5.200 closest distance to " NH2 ARG A  56 " =    2.347
peak=    5.108 closest distance to " CG  PRO A  90 " =    1.182
peak=    5.081 closest distance to " CG  PRO A 213 " =    1.195
peak=    5.005 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.872 closest distance to " CA  TYR A  30 " =    0.929
peak=    4.857 closest distance to " O   HOH Z 232 " =    2.343
peak=    4.758 closest distance to " CB  ARG A 190 " =    1.721
peak=    4.699 closest distance to " CB  SER A  63 " =    1.205
peak=    4.631 closest distance to " CB  PRO A  54 " =    0.932
peak=    4.527 closest distance to " CB  GLN A 183 " =    1.313
peak=    4.511 closest distance to " C   PRO A 198 " =    1.509
peak=    4.466 closest distance to " O   HOH Z 234 " =    3.796
peak=    4.446 closest distance to " CB  GLU A 128 " =    1.158
peak=    4.446 closest distance to " O   HOH Z 402 " =    1.510
peak=    4.418 closest distance to " O   HOH Z 403 " =    1.757
peak=    4.412 closest distance to " O   HOH Z 298 " =    1.817
peak=    4.409 closest distance to " CB  TYR A 169 " =    0.781
peak=    4.387 closest distance to " O   HOH Z 126 " =    1.957
peak=    4.320 closest distance to " CG  PRO A 243 " =    1.117
peak=    4.282 closest distance to " CA  ARG A  36 " =    1.105
peak=    4.279 closest distance to " CD  ARG A 269 " =    1.030
peak=    4.276 closest distance to " O   HOH Z  43 " =    2.065
peak=    4.251 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.244 closest distance to " NZ  LYS A 117 " =    3.246
peak=    4.238 closest distance to " O   HOH Z 369 " =    2.351
peak=    4.191 closest distance to " O   HOH Z 209 " =    2.242
peak=    4.184 closest distance to " O   HOH Z 203 " =    1.873
peak=    4.149 closest distance to " CZ  PHE A 218 " =    1.087
peak=    4.146 closest distance to " CB  GLU A 152 " =    1.117
peak=    4.140 closest distance to " O   HOH Z 142 " =    1.546
peak=    4.138 closest distance to " O   HOH Z 272 " =    1.873
peak=    4.113 closest distance to " CB  LEU A 228 " =    1.107
peak=    4.106 closest distance to " CB  ARG A  79 " =    1.289
peak=    4.104 closest distance to " O   HOH Z 287 " =    1.979
peak=    4.043 closest distance to " O   HOH Z 303 " =    2.136
peak=    4.041 closest distance to " O   HOH Z 427 " =    3.051
peak=    4.040 closest distance to " O   SER A  87 " =    2.214
peak=    4.032 closest distance to " CA  ALA A  21 " =    1.260
peak=    4.030 closest distance to " O   HOH Z 189 " =    2.391
peak=    4.029 closest distance to " O   HOH Z  97 " =    1.973
peak=    4.028 closest distance to " O   HOH Z  15 " =    2.152
peak=    4.024 closest distance to " OD1 ASN A  69 " =    2.428
peak=    4.012 closest distance to " CG  ARG A  66 " =    2.536
peak=    4.004 closest distance to " O   HOH Z  78 " =    1.728
peak=    3.992 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.965 closest distance to " CA  ALA A  51 " =    0.923
peak=    3.960 closest distance to " O   HOH Z 423 " =    1.947
peak=    3.945 closest distance to " O   HOH Z  40 " =    1.997
peak=    3.939 closest distance to " CG2 ILE A 120 " =    1.071
peak=    3.933 closest distance to " O   HOH Z 316 " =    3.102
peak=    3.910 closest distance to " CA  ARG A 195 " =    1.309
peak=    3.904 closest distance to " O   HOH Z 265 " =    2.205
peak=    3.892 closest distance to " O   HOH Z  44 " =    1.919
peak=    3.890 closest distance to " O   HOH Z 280 " =    2.984
peak=    3.882 closest distance to " CD2 LEU A 297 " =    0.914
peak=    3.882 closest distance to " O   HOH Z 193 " =    1.818
peak=    3.880 closest distance to " O   HOH Z 346 " =    1.642
peak=    3.871 closest distance to " O   HOH Z 291 " =    1.502
peak=    3.863 closest distance to " CB  ARG A  79 " =    0.905
peak=    3.860 closest distance to " O   HOH Z 158 " =    3.059
peak=    3.853 closest distance to " CA  ASN A 176 " =    1.250
peak=    3.843 closest distance to " CB  VAL A 202 " =    1.519
peak=    3.836 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.834 closest distance to " NH2 ARG A 156 " =    1.124
peak=    3.832 closest distance to " NE2 GLN A  11 " =    0.944
peak=    3.830 closest distance to " O   HOH Z 102 " =    1.275
peak=    3.817 closest distance to " CB  VAL A 265 " =    1.186
peak=    3.814 closest distance to " O   HOH Z 128 " =    2.025
peak=    3.808 closest distance to " CB  GLU A 277 " =    3.679
peak=    3.805 closest distance to " O   HOH Z 133 " =    2.745
peak=    3.800 closest distance to " CB  TRP A 266 " =    0.996
peak=    3.797 closest distance to " O   HOH Z 368 " =    2.105
peak=    3.797 closest distance to " CE  LYS A  76 " =    0.843
peak=    3.796 closest distance to " O   HOH Z 279 " =    2.176
peak=    3.795 closest distance to " CG2 VAL A 257 " =    0.910
peak=    3.780 closest distance to " O   HOH Z 371 " =    3.323
peak=    3.773 closest distance to " O   HOH Z 134 " =    1.314
peak=    3.768 closest distance to " O   HOH Z  80 " =    1.760
peak=    3.768 closest distance to " CB  TRP A 179 " =    1.392
peak=    3.766 closest distance to " O   HOH Z 214 " =    2.256
peak=    3.765 closest distance to " CA  ALA A 160 " =    0.877
peak=    3.764 closest distance to " O   HOH Z  63 " =    1.950
peak=    3.764 closest distance to " CB  SER A  62 " =    0.851
peak=    3.764 closest distance to " ND2 ASN A 187 " =    1.486
peak=    3.762 closest distance to " NH2BARG A 145 " =    2.157
peak=    3.753 closest distance to " O   HOH Z 389 " =    1.932
peak=    3.751 closest distance to " CA  ASN A 215 " =    1.097
peak=    3.748 closest distance to " O   HOH Z  59 " =    2.331
peak=    3.744 closest distance to " CD1 LEU A 300 " =    1.239
peak=    3.743 closest distance to " CD BLYS A 290 " =    1.007
peak=    3.738 closest distance to " O   HOH Z 426 " =    1.573
peak=    3.736 closest distance to " CB  SER A   3 " =    1.279
peak=    3.735 closest distance to " CD2 TRP A 179 " =    1.355
peak=    3.735 closest distance to " O   HOH Z 412 " =    3.774
peak=    3.730 closest distance to " NE2 GLN A  77 " =    3.283
peak=    3.727 closest distance to " O   HOH Z 421 " =    1.723
peak=    3.720 closest distance to " CA  THR A 221 " =    0.937
peak=    3.715 closest distance to " O   THR A 220 " =    1.179
peak=    3.713 closest distance to " CD1 LEU A  96 " =    0.713
peak=    3.705 closest distance to " CB  ASP A 140 " =    0.975
peak=    3.700 closest distance to " CG1BVAL A  72 " =    1.748
peak=    3.697 closest distance to " O   HOH Z 185 " =    1.759
peak=    3.687 closest distance to " N   ASN A  39 " =    1.279
peak=    3.686 closest distance to " CB  ALA A 248 " =    1.347
peak=    3.682 closest distance to " O   HOH Z 258 " =    2.160
peak=    3.675 closest distance to " O   HOH Z 180 " =    2.276
peak=    3.672 closest distance to " O   HOH Z 126 " =    1.540
peak=    3.665 closest distance to " O   ASN A  74 " =    1.675
peak=    3.665 closest distance to " O   HOH Z 357 " =    2.020
peak=    3.654 closest distance to " O   THR A 251 " =    1.144
peak=    3.649 closest distance to " O   HOH Z 247 " =    1.404
peak=    3.644 closest distance to " O   HOH Z  21 " =    1.813
peak=    3.642 closest distance to " O   HOH Z 132 " =    2.634
peak=    3.635 closest distance to " CB  PRO A 198 " =    1.092
peak=    3.633 closest distance to " O   HOH Z  61 " =    1.575
peak=    3.627 closest distance to " CD  LYS A 166 " =    1.359
peak=    3.622 closest distance to " CD  ARG A 159 " =    0.814
peak=    3.621 closest distance to " O   HOH Z 183 " =    1.480
peak=    3.610 closest distance to " C   ILE A 106 " =    1.904
peak=    3.602 closest distance to " O   HOH Z 108 " =    2.841
peak=    3.601 closest distance to " O   HOH Z 147 " =    1.794
peak=    3.600 closest distance to " O   HOH Z  68 " =    1.857
peak=    3.598 closest distance to " CB  MET A  47 " =    0.921
peak=    3.595 closest distance to " CA  LYS A 117 " =    1.283
peak=    3.587 closest distance to " O   HOH Z 402 " =    2.877
peak=    3.585 closest distance to " OE1 GLU A   2 " =    2.149
peak=    3.580 closest distance to " C   GLY A  80 " =    1.070
peak=    3.578 closest distance to " O   HOH Z 365 " =    2.851
peak=    3.574 closest distance to " OD2 ASP A 298 " =    3.918
peak=    3.570 closest distance to " CB  ASN A  39 " =    0.857
peak=    3.550 closest distance to " OD2 ASP A 286 " =    2.834
peak=    3.548 closest distance to " O   HOH Z 245 " =    1.316
peak=    3.542 closest distance to " O   HOH Z 227 " =    1.727
peak=    3.542 closest distance to " CA  ALA A 248 " =    1.255
peak=    3.538 closest distance to " O   HOH Z 285 " =    3.020
peak=    3.537 closest distance to " O   HOH Z 403 " =    1.340
peak=    3.531 closest distance to " CG2BVAL A  41 " =    0.790
peak=    3.523 closest distance to " CG  GLN A  58 " =    2.706
peak=    3.521 closest distance to " O   HOH Z 361 " =    3.304
peak=    3.519 closest distance to " CG1 VAL A 153 " =    0.932
peak=    3.519 closest distance to " O   HOH Z 163 " =    1.534
peak=    3.517 closest distance to " O   HOH Z  66 " =    2.091
peak=    3.504 closest distance to " OG1 THR A 294 " =    2.382
peak=    3.504 closest distance to " CG2 THR A 221 " =    1.157
peak=    3.500 closest distance to " CG2 VAL A 197 " =    1.145
peak=    3.493 closest distance to " NH1AARG A 145 " =    1.184
peak=    3.492 closest distance to " CB  ALA A 291 " =    1.282
peak=    3.488 closest distance to " CB  GLU A  46 " =    1.012
peak=    3.480 closest distance to " O   HOH Z  19 " =    1.728
peak=    3.477 closest distance to " O   HOH Z 325 " =    2.211
peak=    3.474 closest distance to " ND1 HIS A  81 " =    1.572
peak=    3.470 closest distance to " CB  SER A 273 " =    0.880
peak=    3.468 closest distance to " OG BSER A 164 " =    2.369
peak=    3.467 closest distance to " CG2 ILE A  20 " =    1.374
peak=    3.459 closest distance to " CB  ASN A 215 " =    1.199
peak=    3.459 closest distance to " O   HOH Z 359 " =    1.404
peak=    3.455 closest distance to " O   HOH Z 406 " =    1.556
peak=    3.448 closest distance to " O   HOH Z 435 " =    2.950
peak=    3.444 closest distance to " CB  SER A 141 " =    1.002
peak=    3.440 closest distance to " N   TYR A 116 " =    1.533
peak=    3.433 closest distance to " O   ALA A 165 " =    1.446
peak=    3.430 closest distance to " O   HOH Z 344 " =    3.189
peak=    3.425 closest distance to " CB  TYR A 169 " =    0.757
peak=    3.422 closest distance to " CA  MET A 105 " =    1.103
peak=    3.419 closest distance to " CE1 TYR A 186 " =    1.287
peak=    3.418 closest distance to " O   HOH Z 345 " =    1.636
peak=    3.408 closest distance to " O   HOH Z 156 " =    3.406
peak=    3.398 closest distance to " O   HOH Z 261 " =    1.648
peak=    3.398 closest distance to " CB  GLN A 103 " =    0.839
peak=    3.397 closest distance to " O   HOH Z  97 " =    2.404
peak=    3.396 closest distance to " O   HOH Z 383 " =    2.173
peak=    3.395 closest distance to " N   ILE A  33 " =    1.040
peak=    3.394 closest distance to " C   TYR A 214 " =    1.504
peak=    3.390 closest distance to " CA  ASP A 140 " =    1.174
peak=    3.388 closest distance to " O   HOH Z 392 " =    2.643
peak=    3.386 closest distance to " O   HOH Z 299 " =    4.512
peak=    3.382 closest distance to " O   HOH Z 148 " =    3.343
peak=    3.378 closest distance to " CA  MET A  40 " =    1.086
peak=    3.377 closest distance to " CB  SER A  26 " =    1.759
peak=    3.374 closest distance to " O   HOH Z 171 " =    1.759
peak=    3.373 closest distance to " O   HOH Z 353 " =    2.770
peak=    3.366 closest distance to " O   HOH Z 305 " =    3.720
peak=    3.344 closest distance to " O   HOH Z  20 " =    1.372
peak=    3.344 closest distance to " O   HOH Z 345 " =    2.987
peak=    3.343 closest distance to " O   HOH Z 374 " =    2.696
peak=    3.342 closest distance to " CG AARG A 275 " =    1.156
peak=    3.341 closest distance to " O   HOH Z 173 " =    2.148
peak=    3.338 closest distance to " O   TRP A 274 " =    1.954
peak=    3.336 closest distance to " O   HOH Z 261 " =    1.791
peak=    3.330 closest distance to " CD1 ILE A 106 " =    0.853
peak=    3.330 closest distance to " O   HOH Z 141 " =    1.712
peak=    3.327 closest distance to " CA  ALA A  84 " =    1.233
peak=    3.325 closest distance to " CB  MET A  40 " =    0.836
peak=    3.324 closest distance to " N   ARG A 156 " =    1.441
peak=    3.322 closest distance to " O   HOH Z 337 " =    3.734
peak=    3.316 closest distance to " CB  ASN A 142 " =    1.187
peak=    3.314 closest distance to " O   HOH Z 135 " =    1.764
peak=    3.310 closest distance to " CG2 THR A 220 " =    0.788
peak=    3.310 closest distance to " CD  GLU A 152 " =    0.741
peak=    3.299 closest distance to " CE  LYS A  48 " =    1.038
peak=    3.299 closest distance to " CG  GLN A  11 " =    1.379
peak=    3.290 closest distance to " CA  ALA A 295 " =    1.128
peak=    3.289 closest distance to " O   HOH Z 417 " =    2.809
peak=    3.288 closest distance to " O   HOH Z 422 " =    2.629
peak=    3.285 closest distance to " CA  SER A  87 " =    1.073
peak=    3.285 closest distance to " O   ALA A 242 " =    1.064
peak=    3.276 closest distance to " O   HOH Z 294 " =    1.527
peak=    3.273 closest distance to " CB  ALA A 114 " =    0.782
peak=    3.273 closest distance to " CA  ASP A 191 " =    0.873
peak=    3.272 closest distance to " CB  ARG A 269 " =    0.753
peak=    3.271 closest distance to " CB  THR A  31 " =    1.757
peak=    3.269 closest distance to " CA  ASP A 191 " =    1.111
peak=    3.268 closest distance to " CZ  PHE A  38 " =    1.340
peak=    3.264 closest distance to " OH  TYR A  30 " =    1.154
peak=    3.263 closest distance to " CA  GLU A 152 " =    0.864
peak=    3.262 closest distance to " CE1 HIS A 108 " =    1.105
peak=    3.262 closest distance to " O   HOH Z 336 " =    1.593
peak=    3.262 closest distance to " O   HOH Z 393 " =    3.296
peak=    3.261 closest distance to " CB  PHE A  16 " =    0.975
peak=    3.261 closest distance to " NZ  LYS A  48 " =    1.274
peak=    3.258 closest distance to " O   HOH Z 298 " =    2.463
peak=    3.258 closest distance to " CB  ILE A 120 " =    1.266
peak=    3.254 closest distance to " O   HOH Z 313 " =    1.844
peak=    3.245 closest distance to " CZ3 TRP A 266 " =    1.102
peak=    3.241 closest distance to " O   ASP A 124 " =    1.321
peak=    3.240 closest distance to " CB  SER A 212 " =    1.051
peak=    3.237 closest distance to " O   HOH Z 380 " =    1.946
peak=    3.233 closest distance to " CG  MET A 185 " =    1.164
peak=    3.229 closest distance to " CA  ASP A 162 " =    1.126
peak=    3.225 closest distance to " OG BSER A 134 " =    2.853
peak=    3.224 closest distance to " N   ASN A 127 " =    1.256
peak=    3.217 closest distance to " CA  LEU A  83 " =    1.313
peak=    3.215 closest distance to " ND2 ASN A 249 " =    0.903
peak=    3.214 closest distance to " O   HOH Z 128 " =    2.214
peak=    3.212 closest distance to " CA  ALA A 291 " =    0.802
peak=    3.205 closest distance to " O   HOH Z 417 " =    2.152
peak=    3.204 closest distance to " O   HOH Z 427 " =    3.120
peak=    3.203 closest distance to " O   HOH Z 227 " =    2.193
peak=    3.203 closest distance to " O   HOH Z 437 " =    1.268
peak=    3.202 closest distance to " CB  ARG A 139 " =    0.838
peak=    3.198 closest distance to " O   HOH Z 423 " =    3.449
peak=    3.192 closest distance to " O   HOH Z 387 " =    2.957
peak=    3.188 closest distance to " O   HOH Z 109 " =    2.591
peak=    3.186 closest distance to " CG  LEU A 167 " =    1.153
peak=    3.186 closest distance to " O   HOH Z  10 " =    1.766
peak=    3.186 closest distance to " O   HOH Z 327 " =    1.634
peak=    3.186 closest distance to " CG  ARG A 219 " =    1.178
peak=    3.185 closest distance to " O   HOH Z 411 " =    1.713
peak=    3.184 closest distance to " O   HOH Z  48 " =    1.742
peak=    3.182 closest distance to " CB  TYR A 247 " =    0.959
peak=    3.181 closest distance to " CA  ASN A 217 " =    1.210
peak=    3.179 closest distance to " CZ2 TRP A 179 " =    1.677
peak=    3.177 closest distance to " O   HOH Z  62 " =    2.312
peak=    3.175 closest distance to " CD1AILE A 234 " =    0.891
peak=    3.174 closest distance to " CB  HIS A 108 " =    0.817
peak=    3.168 closest distance to " O   HOH Z  44 " =    3.498
peak=    3.166 closest distance to " CB  THR A  52 " =    0.807
peak=    3.164 closest distance to " CA  TYR A 116 " =    1.429
peak=    3.162 closest distance to " OH  TYR A 116 " =    1.079
peak=    3.158 closest distance to " OG  SER A 245 " =    1.584
peak=    3.157 closest distance to " CD  PRO A  54 " =    1.070
peak=    3.154 closest distance to " O   HOH Z  49 " =    2.417
peak=    3.153 closest distance to " CG  GLU A  37 " =    0.863
peak=    3.152 closest distance to " CG  ARG A  66 " =    0.985
peak=    3.151 closest distance to " CG1 ILE A 151 " =    0.986
peak=    3.147 closest distance to " CD  GLU A 236 " =    1.031
peak=    3.144 closest distance to " CA  VAL A  41 " =    0.943
peak=    3.135 closest distance to " NE2 GLN A  58 " =    3.118
peak=    3.130 closest distance to " CB  ALA A 227 " =    1.064
peak=    3.129 closest distance to " CD1 ILE A 199 " =    1.111
peak=    3.125 closest distance to " OG  SER A  62 " =    2.814
peak=    3.124 closest distance to " O   HOH Z 156 " =    2.553
peak=    3.121 closest distance to " N   GLY A  98 " =    1.121
peak=    3.117 closest distance to " CB  TYR A 116 " =    0.767
peak=    3.112 closest distance to " O   HOH Z 329 " =    3.851
peak=    3.103 closest distance to " CD  LYS A 119 " =    1.286
peak=    3.102 closest distance to " O   HOH Z 130 " =    2.224
peak=    3.098 closest distance to " ND2 ASN A 110 " =    1.565
peak=    3.093 closest distance to " O   HOH Z  68 " =    1.904
peak=    3.092 closest distance to " CG  MET A 185 " =    1.040
peak=    3.084 closest distance to " CB  MET A 105 " =    0.879
peak=    3.079 closest distance to " O   HOH Z 271 " =    2.254
peak=    3.078 closest distance to " CD2 TYR A  30 " =    0.924
peak=    3.051 closest distance to " O   HOH Z   1 " =    2.400

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.877 - 5.675
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.877 - 5.675

peak=   -4.803 closest distance to " O   HOH Z 266 " =    4.898
peak=   -4.591 closest distance to " C   HIS A 108 " =    1.068
peak=   -4.321 closest distance to " CB  PRO A 243 " =    2.661
peak=   -4.288 closest distance to " CD  GLN A  58 " =    1.076
peak=   -4.220 closest distance to " OXT GLY A 302 " =    2.843
peak=   -4.215 closest distance to " CD  ARG A 156 " =    2.071
peak=   -4.153 closest distance to " O   HOH Z 372 " =    2.407
peak=   -4.147 closest distance to " O   HOH Z  10 " =    1.596
peak=   -4.121 closest distance to " CA  ASP A 298 " =    1.029
peak=   -4.098 closest distance to " O   HOH Z 231 " =    2.339
peak=   -4.027 closest distance to " SG  CYS A 254 " =    3.440
peak=   -4.005 closest distance to " O   ILE A 109 " =    2.628
peak=   -4.002 closest distance to " O   ALA A 256 " =    1.608
peak=   -3.997 closest distance to " O   VAL A  67 " =    2.714
peak=   -3.975 closest distance to " ND2 ASN A  45 " =    1.709
peak=   -3.966 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.957 closest distance to " OG BSER A 134 " =    1.263
peak=   -3.935 closest distance to " O   HOH Z 196 " =    1.977
peak=   -3.915 closest distance to " O   HOH Z  13 " =    1.771
peak=   -3.907 closest distance to " O   HOH Z 292 " =    4.590
peak=   -3.903 closest distance to " OE1 GLN A 223 " =    2.056
peak=   -3.891 closest distance to " O   HOH Z 377 " =    1.901
peak=   -3.886 closest distance to " CG  ASP A 132 " =    2.361
peak=   -3.884 closest distance to " NE2 GLN A  88 " =    1.857
peak=   -3.876 closest distance to " CG1 VAL A 250 " =    2.639
peak=   -3.862 closest distance to " O   HOH Z 166 " =    1.795
peak=   -3.848 closest distance to " OG  SER A  97 " =    2.254
peak=   -3.799 closest distance to " O   HOH Z 198 " =    2.076
peak=   -3.795 closest distance to " O   HOH Z 165 " =    1.913
peak=   -3.794 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.787 closest distance to " CD1 LEU A 101 " =    2.424
peak=   -3.785 closest distance to " CB  PHE A 192 " =    2.042
peak=   -3.730 closest distance to " O   HOH Z 348 " =    2.299
peak=   -3.728 closest distance to " CB  ASN A  39 " =    2.350
peak=   -3.722 closest distance to " N   ALA A  43 " =    2.694
peak=   -3.719 closest distance to " O   HOH Z 353 " =    2.219
peak=   -3.717 closest distance to " ND2 ASN A  45 " =    1.028
peak=   -3.717 closest distance to " CD1 LEU A  25 " =    2.474
peak=   -3.699 closest distance to " O   PRO A 163 " =    2.114
peak=   -3.695 closest distance to " CG2 ILE A 263 " =    2.350
peak=   -3.691 closest distance to " CD1 PHE A  59 " =    1.938
peak=   -3.688 closest distance to " CE3 TRP A 150 " =    2.062
peak=   -3.650 closest distance to " O   PHE A 218 " =    1.554
peak=   -3.625 closest distance to " O   HOH Z 283 " =    2.170
peak=   -3.617 closest distance to " O   SER A 210 " =    1.960
peak=   -3.616 closest distance to " NH2 ARG A  66 " =    1.958
peak=   -3.612 closest distance to " O   HOH Z 114 " =    3.290
peak=   -3.609 closest distance to " CG1 VAL A 112 " =    2.583
peak=   -3.605 closest distance to " CG2 ILE A  20 " =    2.975
peak=   -3.602 closest distance to " O   HOH Z  52 " =    1.511
peak=   -3.585 closest distance to " CD  ARG A 195 " =    5.108
peak=   -3.582 closest distance to " CD  ARG A 139 " =    1.578
peak=   -3.567 closest distance to " OG BSER A 210 " =    2.128
peak=   -3.565 closest distance to " O   HOH Z   6 " =    2.192
peak=   -3.562 closest distance to " N   TYR A  68 " =    3.134
peak=   -3.558 closest distance to " N   THR A  52 " =    1.673
peak=   -3.551 closest distance to " CG  GLU A 277 " =    1.140
peak=   -3.547 closest distance to " CD  GLN A 223 " =    1.486
peak=   -3.545 closest distance to " CE2 PHE A  61 " =    2.556
peak=   -3.541 closest distance to " C   SER A 206 " =    1.538
peak=   -3.540 closest distance to " O   HOH Z 126 " =    1.982
peak=   -3.540 closest distance to " CZ3 TRP A 179 " =    1.246
peak=   -3.534 closest distance to " O   HOH Z 407 " =    3.154
peak=   -3.530 closest distance to " C   THR A 279 " =    1.148
peak=   -3.527 closest distance to " O   HOH Z  71 " =    1.795
peak=   -3.513 closest distance to " O   ALA A  10 " =    1.747
peak=   -3.507 closest distance to " O   HOH Z 102 " =    1.533
peak=   -3.499 closest distance to " CB  PHE A  16 " =    2.542
peak=   -3.498 closest distance to " O   HOH Z 166 " =    1.644
peak=   -3.489 closest distance to " O   HOH Z 171 " =    2.077
peak=   -3.485 closest distance to " O   ALA A  34 " =    2.300
peak=   -3.484 closest distance to " ND2 ASN A 249 " =    2.472
peak=   -3.482 closest distance to " OD1 ASN A 148 " =    1.471
peak=   -3.472 closest distance to " CB  TYR A  15 " =    2.262
peak=   -3.470 closest distance to " OD1 ASN A 187 " =    1.755
peak=   -3.466 closest distance to " CA  GLY A 133 " =    2.345
peak=   -3.459 closest distance to " N   ALA A 226 " =    2.028
peak=   -3.452 closest distance to " O   ALA A 160 " =    1.477
peak=   -3.450 closest distance to " CD2 TYR A 293 " =    1.987
peak=   -3.449 closest distance to " O   HOH Z  43 " =    1.558
peak=   -3.448 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.445 closest distance to " CB  ALA A 248 " =    2.067
peak=   -3.444 closest distance to " O   HOH Z 123 " =    2.291
peak=   -3.442 closest distance to " O   HOH Z 351 " =    1.440
peak=   -3.429 closest distance to " CD2 LEU A 237 " =    2.605
peak=   -3.422 closest distance to " CZ  TYR A 169 " =    1.823
peak=   -3.420 closest distance to " CG  ASP A 231 " =    0.877
peak=   -3.418 closest distance to " N   GLN A  58 " =    1.445
peak=   -3.412 closest distance to " CG  PRO A 243 " =    1.716
peak=   -3.404 closest distance to " O   HOH Z 234 " =    4.200
peak=   -3.402 closest distance to " NH2 ARG A  66 " =    5.675
peak=   -3.398 closest distance to " OG BSER A 134 " =    1.893
peak=   -3.397 closest distance to " CE  MET A  93 " =    1.248
peak=   -3.396 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.392 closest distance to " ND2 ASN A 187 " =    1.590
peak=   -3.391 closest distance to " O   HOH Z 377 " =    1.698
peak=   -3.391 closest distance to " CG  GLU A  53 " =    1.344
peak=   -3.382 closest distance to " CD1 ILE A 239 " =    2.246
peak=   -3.382 closest distance to " CB  ALA A 291 " =    2.312
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.454
peak=   -3.366 closest distance to " O   HOH Z 177 " =    1.789
peak=   -3.364 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.362 closest distance to " N   ALA A 248 " =    1.653
peak=   -3.355 closest distance to " OG  SER A  62 " =    1.730
peak=   -3.355 closest distance to " CB  GLN A  11 " =    1.711
peak=   -3.354 closest distance to " CD2 PHE A 225 " =    1.233
peak=   -3.353 closest distance to " O   HOH Z  37 " =    1.752
peak=   -3.347 closest distance to " O   HOH Z 243 " =    2.100
peak=   -3.346 closest distance to " O   HOH Z 211 " =    1.668
peak=   -3.342 closest distance to " CD1 LEU A 228 " =    2.198
peak=   -3.339 closest distance to " NH2 ARG A  79 " =    2.085
peak=   -3.338 closest distance to " OD1 ASP A 191 " =    1.428
peak=   -3.337 closest distance to " C   ALA A 158 " =    1.368
peak=   -3.337 closest distance to " CD  GLU A 236 " =    1.096
peak=   -3.334 closest distance to " NH2 ARG A 159 " =    2.330
peak=   -3.331 closest distance to " NH2 ARG A  79 " =    1.591
peak=   -3.328 closest distance to " O   HOH Z 414 " =    1.619
peak=   -3.326 closest distance to " CG1 VAL A  78 " =    2.654
peak=   -3.325 closest distance to " ND2BASN A 224 " =    1.707
peak=   -3.319 closest distance to " O   HOH Z 185 " =    2.385
peak=   -3.317 closest distance to " CB  ALA A  10 " =    2.215
peak=   -3.314 closest distance to " O   HOH Z 311 " =    3.677
peak=   -3.313 closest distance to " CB  ASP A 286 " =    1.906
peak=   -3.309 closest distance to " CG2 VAL A 189 " =    2.241
peak=   -3.303 closest distance to " O   HOH Z 252 " =    3.811
peak=   -3.303 closest distance to " CZ  PHE A  59 " =    1.796
peak=   -3.303 closest distance to " OD2 ASP A 191 " =    1.532
peak=   -3.302 closest distance to " O   HOH Z 111 " =    1.640
peak=   -3.300 closest distance to " O   HOH Z 350 " =    2.086
peak=   -3.295 closest distance to " O   HOH Z 389 " =    1.796
peak=   -3.291 closest distance to " CZ2 TRP A 274 " =    1.089
peak=   -3.290 closest distance to " O   HOH Z 377 " =    1.878
peak=   -3.290 closest distance to " O   HOH Z   6 " =    1.634
peak=   -3.289 closest distance to " CA  GLY A 241 " =    3.166
peak=   -3.287 closest distance to " O   HOH Z 393 " =    1.449
peak=   -3.287 closest distance to " NH2AARG A 275 " =    5.199
peak=   -3.284 closest distance to " O   GLY A 118 " =    2.198
peak=   -3.280 closest distance to " OE2 GLU A   2 " =    1.733
peak=   -3.279 closest distance to " CB  ALA A 248 " =    2.255
peak=   -3.275 closest distance to " CG2 ILE A  49 " =    2.818
peak=   -3.272 closest distance to " CE  MET A 105 " =    2.087
peak=   -3.268 closest distance to " O   GLY A  80 " =    2.521
peak=   -3.266 closest distance to " C   LEU A 143 " =    1.031
peak=   -3.264 closest distance to " NE2 GLN A 194 " =    1.832
peak=   -3.264 closest distance to " O   HOH Z  38 " =    1.526
peak=   -3.264 closest distance to " CD2 LEU A 300 " =    2.905
peak=   -3.261 closest distance to " NH1 ARG A 195 " =    2.663
peak=   -3.244 closest distance to " OD2 ASP A 171 " =    1.827
peak=   -3.243 closest distance to " O   HOH Z 265 " =    2.262
peak=   -3.243 closest distance to " OD2 ASP A 171 " =    2.461
peak=   -3.243 closest distance to " O   HOH Z 290 " =    1.167
peak=   -3.238 closest distance to " NE2 GLN A 103 " =    1.803
peak=   -3.236 closest distance to " CA  GLY A 241 " =    2.320
peak=   -3.235 closest distance to " O   TRP A  92 " =    1.864
peak=   -3.232 closest distance to " CG  TRP A 266 " =    1.895
peak=   -3.230 closest distance to " CZ  PHE A 155 " =    1.221
peak=   -3.228 closest distance to " CB  ALA A  43 " =    2.642
peak=   -3.226 closest distance to " NE1 TRP A 266 " =    2.365
peak=   -3.225 closest distance to " CB  TRP A  85 " =    2.374
peak=   -3.221 closest distance to " O   HOH Z 252 " =    4.162
peak=   -3.220 closest distance to " N   SER A 276 " =    1.456
peak=   -3.219 closest distance to " OE1 GLN A 183 " =    1.532
peak=   -3.207 closest distance to " CE BMET A  47 " =    1.903
peak=   -3.203 closest distance to " C   MET A 188 " =    1.729
peak=   -3.198 closest distance to " O   HOH Z   9 " =    2.179
peak=   -3.197 closest distance to " O   HOH Z 280 " =    2.362
peak=   -3.197 closest distance to " O   HOH Z 128 " =    2.525
peak=   -3.192 closest distance to " CG1 VAL A 112 " =    2.842
peak=   -3.192 closest distance to " O   HOH Z 396 " =    1.768
peak=   -3.192 closest distance to " O   HOH Z 418 " =    1.413
peak=   -3.186 closest distance to " CD  ARG A  79 " =    1.188
peak=   -3.185 closest distance to " CA  VAL A 197 " =    1.006
peak=   -3.183 closest distance to " CE3 TRP A 274 " =    2.513
peak=   -3.177 closest distance to " O   ALA A   1 " =    1.918
peak=   -3.172 closest distance to " OG  SER A  63 " =    1.205
peak=   -3.166 closest distance to " NH1 ARG A  66 " =    3.822
peak=   -3.158 closest distance to " O   MET A  40 " =    2.699
peak=   -3.154 closest distance to " O   LEU A 167 " =    1.493
peak=   -3.153 closest distance to " O   HOH Z 322 " =    1.712
peak=   -3.148 closest distance to " O   VAL A 189 " =    2.571
peak=   -3.145 closest distance to " N   MET A 105 " =    2.507
peak=   -3.137 closest distance to " O   HOH Z 233 " =    2.424
peak=   -3.137 closest distance to " O   HOH Z 431 " =    1.873
peak=   -3.132 closest distance to " O   SER A 135 " =    1.510
peak=   -3.128 closest distance to " O   HOH Z 412 " =    4.806
peak=   -3.114 closest distance to " OE1 GLN A  88 " =    1.138
peak=   -3.110 closest distance to " C   GLY A 262 " =    1.935
peak=   -3.105 closest distance to " O   HOH Z 256 " =    2.426
peak=   -3.086 closest distance to " CD2 LEU A 261 " =    2.314
peak=   -3.086 closest distance to " O   HOH Z 298 " =    2.581
peak=   -3.086 closest distance to " OG1 THR A  82 " =    1.423
peak=   -3.079 closest distance to " O   GLY A  80 " =    2.573
peak=   -3.078 closest distance to " O   HOH Z 264 " =    1.791
peak=   -3.075 closest distance to " CD  PRO A 213 " =    2.143
peak=   -3.075 closest distance to " CH2 TRP A 150 " =    1.102
peak=   -3.058 closest distance to " OD2 ASP A  50 " =    2.164
peak=   -3.048 closest distance to " O   HOH Z 126 " =    1.796
peak=   -3.045 closest distance to " O   HOH Z 357 " =    2.039
peak=   -3.030 closest distance to " O   HOH Z  60 " =    2.149
peak=   -3.026 closest distance to " O   HOH Z 193 " =    1.769

================= 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    :  0.3304 0.3206   6.085597e+00   6.050163e+00
   1_bss:  0.3146 0.3036   6.059451e+00   6.017381e+00
   1_xyz:  0.1833 0.2026   5.529158e+00   5.629244e+00
   1_adp:  0.1657 0.2052   5.472689e+00   5.649726e+00
   1_occ:  0.1655 0.2049   5.471636e+00   5.649040e+00
   2_bss:  0.1617 0.2008   5.453818e+00   5.631037e+00
   2_xyz:  0.1313 0.1680   5.263452e+00   5.460811e+00
   2_adp:  0.1279 0.1628   5.234200e+00   5.426720e+00
   2_occ:  0.1276 0.1627   5.233219e+00   5.426054e+00
   3_bss:  0.1277 0.1621   5.231234e+00   5.422776e+00
   3_xyz:  0.1180 0.1562   5.172504e+00   5.385360e+00
   3_adp:  0.1161 0.1563   5.164836e+00   5.388243e+00
   3_occ:  0.1160 0.1562   5.164591e+00   5.388131e+00
   4_bss:  0.1159 0.1561   5.164308e+00   5.387975e+00
   4_xyz:  0.1120 0.1562   5.146519e+00   5.383835e+00
   4_adp:  0.1113 0.1571   5.146092e+00   5.388462e+00
   4_occ:  0.1112 0.1572   5.146160e+00   5.388796e+00
   5_bss:  0.1111 0.1570   5.146241e+00   5.388895e+00
   5_xyz:  0.1126 0.1582   5.157210e+00   5.398148e+00
   5_adp:  0.1124 0.1590   5.158150e+00   5.402340e+00
   5_occ:  0.1123 0.1590   5.158110e+00   5.402503e+00
   5_bss:  0.1122 0.1588   5.158158e+00   5.402553e+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:  0.306  45.416  -3.267   3.526  -1.796   0.000  -0.000  -0.000
   1_xyz:  0.306  45.416  -3.267   3.526  -1.796   0.000  -0.000  -0.000
   1_adp:  0.306  45.416  -3.267   3.526  -1.796   0.000  -0.000  -0.000
   1_occ:  0.306  45.416  -3.267   3.526  -1.796   0.000  -0.000  -0.000
   2_bss:  0.324  58.524  -3.088  -0.275  -1.472  -0.000  -0.000  -0.000
   2_xyz:  0.324  58.524  -3.088  -0.275  -1.472  -0.000  -0.000  -0.000
   2_adp:  0.324  58.524  -3.088  -0.275  -1.472  -0.000  -0.000  -0.000
   2_occ:  0.324  58.524  -3.088  -0.275  -1.472  -0.000  -0.000  -0.000
   3_bss:  0.323  54.561  -2.753  -1.177  -1.167  -0.000  -0.000  -0.000
   3_xyz:  0.323  54.561  -2.753  -1.177  -1.167  -0.000  -0.000  -0.000
   3_adp:  0.323  54.561  -2.753  -1.177  -1.167  -0.000  -0.000  -0.000
   3_occ:  0.323  54.561  -2.753  -1.177  -1.167  -0.000  -0.000  -0.000
   4_bss:  0.323  54.561  -2.484  -1.306  -0.942  -0.000  -0.000  -0.000
   4_xyz:  0.323  54.561  -2.484  -1.306  -0.942  -0.000  -0.000  -0.000
   4_adp:  0.323  54.561  -2.484  -1.306  -0.942  -0.000  -0.000  -0.000
   4_occ:  0.323  54.561  -2.484  -1.306  -0.942  -0.000  -0.000  -0.000
   5_bss:  0.323  54.871  -2.186  -1.150  -0.669  -0.000  -0.000  -0.000
   5_xyz:  0.323  54.871  -2.186  -1.150  -0.669  -0.000  -0.000  -0.000
   5_adp:  0.323  54.871  -2.186  -1.150  -0.669  -0.000  -0.000  -0.000
   5_occ:  0.323  54.871  -2.186  -1.150  -0.669  -0.000  -0.000  -0.000
   5_bss:  0.322  56.915  -1.909  -0.934  -0.417  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  34.527 0.7100  0.8799    31407.543
   1_bss:  33.361 0.7215  0.8744    27889.658
   1_xyz:  19.746 0.8646  0.9938    10663.029
   1_adp:  20.427 0.8570  0.9814    11006.963
   1_occ:  20.419 0.8571  0.9812    10994.924
   2_bss:  19.802 0.8632  0.9539    10525.646
   2_xyz:  15.764 0.9000  0.9732     7274.080
   2_adp:  14.960 0.9071  0.9701     6881.810
   2_occ:  14.948 0.9072  0.9700     6870.326
   3_bss:  14.876 0.9078  0.9685     6820.363
   3_xyz:  14.030 0.9148  0.9724     6324.393
   3_adp:  14.066 0.9147  0.9649     6363.429
   3_occ:  14.059 0.9147  0.9648     6360.463
   4_bss:  14.053 0.9148  0.9695     6359.581
   4_xyz:  13.962 0.9155  0.9701     6308.211
   4_adp:  14.050 0.9149  0.9622     6348.697
   4_occ:  14.053 0.9148  0.9621     6352.799
   5_bss:  14.056 0.9148  0.9707     6354.933
   5_xyz:  14.185 0.9139  0.9699     6455.928
   5_adp:  14.264 0.9132  0.9610     6503.786
   5_occ:  14.266 0.9132  0.9609     6505.572
   5_bss:  14.267 0.9132  0.9697     6507.184
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6171e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6171e-01
   1_xyz:   1.288  0.011  0.080 15.242  0.005  4.113   8.7840e-02
   1_adp:   1.288  0.011  0.080 15.242  0.005  4.113   8.7840e-02
   1_occ:   1.288  0.011  0.080 15.242  0.005  4.113   8.7840e-02
   2_bss:   1.288  0.011  0.080 15.242  0.005  4.113   8.7840e-02
   2_xyz:   0.953  0.006  0.070 14.535  0.004  4.122   5.3735e-02
   2_adp:   0.953  0.006  0.070 14.535  0.004  4.122   5.3735e-02
   2_occ:   0.953  0.006  0.070 14.535  0.004  4.122   5.3735e-02
   3_bss:   0.953  0.006  0.070 14.535  0.004  4.122   5.3735e-02
   3_xyz:   0.938  0.006  0.071 14.524  0.004  4.127   5.3101e-02
   3_adp:   0.938  0.006  0.071 14.524  0.004  4.127   5.3101e-02
   3_occ:   0.938  0.006  0.071 14.524  0.004  4.127   5.3101e-02
   4_bss:   0.938  0.006  0.071 14.524  0.004  4.127   5.3101e-02
   4_xyz:   0.983  0.007  0.076 14.543  0.004  4.130   5.7635e-02
   4_adp:   0.983  0.007  0.076 14.543  0.004  4.130   5.7635e-02
   4_occ:   0.983  0.007  0.076 14.543  0.004  4.130   5.7635e-02
   5_bss:   0.983  0.007  0.076 14.543  0.004  4.130   5.7635e-02
   5_xyz:   0.906  0.006  0.070 14.343  0.003  4.130   5.0279e-02
   5_adp:   0.906  0.006  0.070 14.343  0.003  4.130   5.0279e-02
   5_occ:   0.906  0.006  0.070 14.343  0.003  4.130   5.0279e-02
   5_bss:   0.906  0.006  0.070 14.343  0.003  4.130   5.0279e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4187e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4187e-01
   1_xyz:   8.236  0.054  0.302 87.374  0.034  2.243   9.9827e-02
   1_adp:   8.236  0.054  0.302 87.374  0.034  2.243   9.9827e-02
   1_occ:   8.236  0.054  0.302 87.374  0.034  2.243   9.9827e-02
   2_bss:   8.236  0.054  0.302 87.374  0.034  2.243   9.9827e-02
   2_xyz:   6.638  0.039  0.205 82.105  0.043  2.376   3.9675e-02
   2_adp:   6.638  0.039  0.205 82.105  0.043  2.376   3.9675e-02
   2_occ:   6.638  0.039  0.205 82.105  0.043  2.376   3.9675e-02
   3_bss:   6.638  0.039  0.205 82.105  0.043  2.376   3.9675e-02
   3_xyz:   7.134  0.041  0.228 83.065  0.034  2.396   3.6033e-02
   3_adp:   7.134  0.041  0.228 83.065  0.034  2.396   3.6033e-02
   3_occ:   7.134  0.041  0.228 83.065  0.034  2.396   3.6033e-02
   4_bss:   7.134  0.041  0.228 83.065  0.034  2.396   3.6033e-02
   4_xyz:   7.420  0.045  0.243 81.411  0.036  2.344   3.8646e-02
   4_adp:   7.420  0.045  0.243 81.411  0.036  2.344   3.8646e-02
   4_occ:   7.420  0.045  0.243 81.411  0.036  2.344   3.8646e-02
   5_bss:   7.420  0.045  0.243 81.411  0.036  2.344   3.8646e-02
   5_xyz:   6.735  0.043  0.220 81.738  0.032  2.409   3.0051e-02
   5_adp:   6.735  0.043  0.220 81.738  0.032  2.409   3.0051e-02
   5_occ:   6.735  0.043  0.220 81.738  0.032  2.409   3.0051e-02
   5_bss:   6.735  0.043  0.220 81.738  0.032  2.409   3.0051e-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:  72.31   0.00  17.02  69.68   0.00  12.98  72.31   6.17  39.00
   1_occ:  72.31   0.00  17.02  69.68   0.00  12.98  72.31   6.17  39.00
   2_bss:  72.31   0.00  17.02  69.68   0.00  12.98  72.31   6.17  39.00
   2_xyz:  72.31   0.00  17.02  69.68   0.00  12.98  72.31   6.17  39.00
   2_adp:  74.02   0.00  16.57  74.02   0.00  12.69  70.90   5.44  37.71
   2_occ:  74.02   0.00  16.57  74.02   0.00  12.69  70.90   5.44  37.71
   3_bss:  74.02   0.00  16.57  74.02   0.00  12.69  70.90   5.44  37.71
   3_xyz:  74.02   0.00  16.57  74.02   0.00  12.69  70.90   5.44  37.71
   3_adp:  78.47   1.01  16.65  78.47   1.01  12.57  71.07   5.26  38.82
   3_occ:  78.47   1.01  16.65  78.47   1.01  12.57  71.07   5.26  38.82
   4_bss:  78.47   1.01  16.65  78.47   1.01  12.57  71.07   5.26  38.82
   4_xyz:  78.47   1.01  16.65  78.47   1.01  12.57  71.07   5.26  38.82
   4_adp:  84.61   0.00  16.62  84.61   0.00  12.42  73.70   5.42  39.50
   4_occ:  84.61   0.00  16.62  84.61   0.00  12.42  73.70   5.42  39.50
   5_bss:  84.61   0.00  16.62  84.61   0.00  12.42  73.70   5.42  39.50
   5_xyz:  84.61   0.00  16.62  84.61   0.00  12.42  73.70   5.42  39.50
   5_adp: 106.11   0.00  16.79 106.11   0.00  12.39  91.74   5.06  40.72
   5_occ: 106.11   0.00  16.79 106.11   0.00  12.39  91.74   5.06  40.72
   5_bss: 106.12   0.00  16.79 106.12   0.00  12.39  91.75   5.07  40.73
------------------------------------------------------------------------
 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:    1.060    0.014    0.392
   1_adp:    1.060    0.014    0.392
   1_occ:    1.060    0.014    0.392
   2_bss:    1.060    0.014    0.392
   2_xyz:    0.983    0.015    0.412
   2_adp:    0.983    0.015    0.412
   2_occ:    0.983    0.015    0.412
   3_bss:    0.983    0.015    0.412
   3_xyz:    0.990    0.023    0.450
   3_adp:    0.990    0.023    0.450
   3_occ:    0.990    0.023    0.450
   4_bss:    0.990    0.023    0.450
   4_xyz:    0.978    0.015    0.463
   4_adp:    0.978    0.015    0.463
   4_occ:    0.978    0.015    0.463
   5_bss:    0.978    0.015    0.463
   5_xyz:    1.039    0.014    0.469
   5_adp:    1.039    0.014    0.469
   5_occ:    1.039    0.014    0.469
   5_bss:    1.039    0.014    0.469
------------------------------------------------------------------------

CPU time actual refinement: 344.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_577/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_577/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_577/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_577/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_577/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.39 
  Macro-tasks:
    bulk solvent and scale       = 37.81  
    individual site refinement   = 151.81 
    weights calculation          = 28.62  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 224.91 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 111.17 
    alpha_beta                      = 8.34   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 123.67 
    fmodel                         = 6.47   
    r_factors                      = 0.18   
    phase_errors                   = 10.96  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 263.40 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.698 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    699 calls, 110.81 s
gradients_fft:          644 calls, 108.29 s

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

# Date 2008-01-16 Time 05:09:23 PST -0800 (1200488963.52 s)
Start R-work = 0.3304, R-free = 0.3206 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.3146, R-free = 0.3036
Final R-work = 0.1122, R-free = 0.1588