# Date 2008-01-16 Time 02:17:11 PST -0800 (1200478631.64 s)
#phil __OFF__

Command line arguments: "../771.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5286
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 771

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 84.6622, 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: 3.36, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96117
Completeness in resolution range: 0.949217
Completeness with d_max=infinity: 0.946374

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9645
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9645 1.96117
Completeness in resolution range: 0.949217
Completeness with d_max=infinity: 0.946374

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9649 -  4.1971 [2168/2197]  1954   214   9.9%
  bin  2:  4.1971 -  3.3435 [2073/2089]  1863   210  10.1%
  bin  3:  3.3435 -  2.9245 [2049/2068]  1843   206  10.1%
  bin  4:  2.9245 -  2.6587 [2046/2076]  1848   198   9.7%
  bin  5:  2.6587 -  2.4691 [2038/2057]  1834   204  10.0%
  bin  6:  2.4691 -  2.3241 [2014/2050]  1806   208  10.3%
  bin  7:  2.3241 -  2.2081 [1985/2018]  1784   201  10.1%
  bin  8:  2.2081 -  2.1122 [2002/2036]  1806   196   9.8%
  bin  9:  2.1122 -  2.0311 [1983/2011]  1784   199  10.0%
  bin 10:  2.0311 -  1.9612 [1231/2035]  1108   123  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_771/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 29
        2.42 -     3.04: 2217
        3.04 -     3.66: 4752
        3.66 -     4.28: 9121
        4.28 -     4.90: 12475
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.804 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.844 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.932 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  22 " - " O   HOH Z 320 "  2.069 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28589 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_771/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_771/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 84.6622 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4555   r_free= 0.4481   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.253676                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6815 0.99   1403  157 0.3802 0.3806      6.5525      6.5748|
|  2:  4.6815 -  3.7348 0.99   1359  145 0.3654 0.3575      6.7233      6.6991|
|  3:  3.7348 -  3.2683 0.99   1321  154 0.4148 0.3690      6.6212      6.6808|
|  4:  3.2683 -  2.9721 0.99   1332  147 0.4266 0.4178       6.481      6.4491|
|  5:  2.9721 -  2.7605 0.99   1312  143 0.4753 0.4637      6.3397       6.326|
|  6:  2.7605 -  2.5986 0.99   1300  145 0.4757 0.5137      6.2482      6.2522|
|  7:  2.5986 -  2.4691 0.99   1315  141 0.5007 0.4650      6.2413      6.1824|
|  8:  2.4691 -  2.3620 0.98   1273  151 0.5133 0.4957      6.1501      6.1614|
|  9:  2.3620 -  2.2714 0.98   1299  148 0.4949 0.4843      6.1061      6.0859|
| 10:  2.2714 -  2.1933 0.98   1280  134 0.5122 0.5240      6.0924      6.1133|
| 11:  2.1933 -  2.1249 1.00   1281  141 0.5139 0.4867      6.0346      5.9961|
| 12:  2.1249 -  2.0643 0.97   1265  139 0.4902 0.5148      5.9462      6.0025|
| 13:  2.0643 -  2.0101 0.98   1284  143 0.5246 0.5263      5.8735      5.8037|
| 14:  2.0101 -  1.9612 0.47    606   71 0.5383 0.5651      5.8452      5.8037|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6815  1403   157  0.70  34.09   0.81     0.74      68744.48|
|  2:  4.6815 -  3.7348  1359   145  0.73  32.27   0.90     0.81      91670.37|
|  3:  3.7348 -  3.2683  1321   154  0.64  40.27   0.86     0.78      97147.14|
|  4:  3.2683 -  2.9721  1332   147  0.58  45.37   0.84     0.69      87145.08|
|  5:  2.9721 -  2.7605  1312   143  0.48  53.85   0.76     0.57      74734.91|
|  6:  2.7605 -  2.5986  1300   145  0.45  56.12   0.75     0.52      65409.93|
|  7:  2.5986 -  2.4691  1315   141  0.44  56.81   0.75     0.50      59035.38|
|  8:  2.4691 -  2.3620  1273   151  0.43  57.46   0.73     0.52      53184.48|
|  9:  2.3620 -  2.2714  1299   148  0.44  56.58   0.76     0.52      47559.00|
| 10:  2.2714 -  2.1933  1280   134  0.42  58.17   0.77     0.51      44123.35|
| 11:  2.1933 -  2.1249  1281   141  0.40  59.97   0.79     0.49      41744.75|
| 12:  2.1249 -  2.0643  1265   139  0.36  62.77   0.77     0.45      41285.19|
| 13:  2.0643 -  2.0101  1284   143  0.31  67.22   0.75     0.39      37086.64|
| 14:  2.0101 -  1.9612   606    71  0.28  69.52   0.72     0.31      31818.73|
|alpha:            min =        0.31 max =            0.81 mean =         0.57|
|beta:             min =    31818.73 max =        97147.14 mean =     61526.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.72|
|phase err.(test): min =        0.00 max =           89.97 mean =        53.00|
|-----------------------------------------------------------------------------|

============================== 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 = 10.482346             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.601   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.947190              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.650   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      707 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1523 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2672 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3944 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5150 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6599 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7771 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.368 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.819 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4625   r_free= 0.4544   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.257887                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4463   r_free= 0.4368   ksol= 0.37   Bsol= 20.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.05,7.90,9.45,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.249932                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.815556              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.373   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.858627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.121   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4463      final r-factor (work) = 0.3581          |
| start r-factor (free) = 0.4368      final r-factor (free) = 0.3784          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.9414 = 8.82 * 0.50 * 6.2556 + 1.00 * 53.3682                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2055 = 8.82 * 0.50 * 6.1434 + 1.00 * 0.1266                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3581      final r-factor (work) = 0.3072          |
| start r-factor (free) = 0.3784      final r-factor (free) = 0.3546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2896 = 0.86 * 1.00 * 6.1434 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1861 = 0.86 * 1.00 * 6.0237 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    52.11   11.24    None  None   None       |
|    all(noH): 2823   0      0.00    52.11   11.24    None  None   None       |
|    Sol.    : 438    0      0.00    51.51   24.07    None  None   None       |
|    Mac.    : 2385   0      0.00    52.11   8.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.211:  850   |   5:    26.057 -  31.268:  107        |
|      1:     5.211 -  10.423:  793   |   6:    31.268 -  36.479:   83        |
|      2:    10.423 -  15.634:  456   |   7:    36.479 -  41.690:   47        |
|      3:    15.634 -  20.845:  296   |   8:    41.690 -  46.902:   10        |
|      4:    20.845 -  26.057:  176   |   9:    46.902 -  52.113:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3072 r_free = 0.3546             target_work(ml) = 5.999         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3067 r_free = 0.3549             target_work(ml) = 5.998         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3067   r_free= 0.3549   ksol= 0.37   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.05,7.90,9.45,0.00,0.00,0.00); trace/3= 8.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.998187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3022   r_free= 0.3506   ksol= 0.33   Bsol= 28.92   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.77,6.11,0.00,0.00,0.00); trace/3= 4.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.997826                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.571182              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.310   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428166              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.394  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3022      final r-factor (work) = 0.2181          |
| start r-factor (free) = 0.3506      final r-factor (free) = 0.2748          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8995 = 4.57 * 0.50 * 6.0263 + 1.00 * 0.1259                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4494 = 4.57 * 0.50 * 5.8548 + 1.00 * 0.0678                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2181      final r-factor (work) = 0.1966          |
| start r-factor (free) = 0.2748      final r-factor (free) = 0.2492          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5718 = 0.43 * 1.00 * 5.8548 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4414 = 0.43 * 1.00 * 5.6789 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    59.37   11.77    None  None   None       |
|    all(noH): 2823   0      0.00    59.37   11.77    None  None   None       |
|    Sol.    : 438    0      1.02    59.37   30.98    None  None   None       |
|    Mac.    : 2385   0      0.00    57.43   8.24     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 -   5.937: 1134   |   5:    29.685 -  35.622:  109        |
|      1:     5.937 -  11.874:  842   |   6:    35.622 -  41.559:  110        |
|      2:    11.874 -  17.811:  290   |   7:    41.559 -  47.495:   67        |
|      3:    17.811 -  23.748:  122   |   8:    47.495 -  53.432:   26        |
|      4:    23.748 -  29.685:  114   |   9:    53.432 -  59.369:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1966 r_free = 0.2492             target_work(ml) = 5.634         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1963 r_free = 0.2487             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1963   r_free= 0.2487   ksol= 0.33   Bsol= 28.92   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,3.77,6.11,0.00,0.00,0.00); trace/3= 4.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.633089                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1954   r_free= 0.2474   ksol= 0.32   Bsol= 37.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.56,2.55,3.98,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.630711                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.594138              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.685  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.914274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.534  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1954      final r-factor (work) = 0.1438          |
| start r-factor (free) = 0.2474      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2823 = 3.59 * 0.50 * 5.6840 + 1.00 * 0.0678                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9617 = 3.59 * 0.50 * 5.5075 + 1.00 * 0.0644                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1438      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1782          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5526 = 1.91 * 1.00 * 5.5075 + 1.00 * 0.0097                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1736 = 1.91 * 1.00 * 5.3076 + 1.00 * 0.0134                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.23   12.86    None  None   None       |
|    all(noH): 2823   0      0.00    78.23   12.86    None  None   None       |
|    Sol.    : 438    0      2.18    77.62   37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    78.23   8.37     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 -   7.823: 1547   |   5:    39.115 -  46.938:   89        |
|      1:     7.823 -  15.646:  630   |   6:    46.938 -  54.761:   75        |
|      2:    15.646 -  23.469:  185   |   7:    54.761 -  62.584:   52        |
|      3:    23.469 -  31.292:   97   |   8:    62.584 -  70.407:   27        |
|      4:    31.292 -  39.115:  112   |   9:    70.407 -  78.230:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1310 r_free = 0.1782             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1309 r_free = 0.1780             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1780   ksol= 0.32   Bsol= 37.05   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.56,2.55,3.98,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274261                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1778   ksol= 0.32   Bsol= 41.01   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,2.38,3.23,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.272862                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.168020              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.312  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.459097              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.995  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1778      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8184 = 2.17 * 0.50 * 5.3081 + 1.00 * 0.0644                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7357 = 2.17 * 0.50 * 5.2360 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4172 = 0.46 * 1.00 * 5.2360 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3951 = 0.46 * 1.00 * 5.1916 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.38   12.56    None  None   None       |
|    all(noH): 2823   0      0.00    84.38   12.56    None  None   None       |
|    Sol.    : 438    0      2.15    73.79   36.02    None  None   None       |
|    Mac.    : 2385   0      0.00    84.38   8.25     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 -   8.438: 1654   |   5:    42.189 -  50.627:   96        |
|      1:     8.438 -  16.876:  591   |   6:    50.627 -  59.065:   49        |
|      2:    16.876 -  25.314:  159   |   7:    59.065 -  67.503:   34        |
|      3:    25.314 -  33.751:  111   |   8:    67.503 -  75.940:   15        |
|      4:    33.751 -  42.189:  111   |   9:    75.940 -  84.378:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1622             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1620             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1620   ksol= 0.32   Bsol= 41.01   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,2.38,3.23,0.00,0.00,0.00); trace/3= 2.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180380                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1620   ksol= 0.32   Bsol= 41.01   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.38,3.04,0.00,0.00,0.00); trace/3= 2.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180330                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.214533              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.428  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.290751              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.794  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8079 = 2.21 * 0.50 * 5.1912 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7774 = 2.21 * 0.50 * 5.1626 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5127 = 0.29 * 1.00 * 5.1626 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5086 = 0.29 * 1.00 * 5.1526 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.52   12.25    None  None   None       |
|    all(noH): 2823   0      0.00    85.52   12.25    None  None   None       |
|    Sol.    : 438    0      1.92    71.62   34.71    None  None   None       |
|    Mac.    : 2385   0      0.00    85.52   8.13     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.552: 1690   |   5:    42.758 -  51.309:   88        |
|      1:     8.552 -  17.103:  581   |   6:    51.309 -  59.861:   45        |
|      2:    17.103 -  25.655:  152   |   7:    59.861 -  68.412:   26        |
|      3:    25.655 -  34.206:  129   |   8:    68.412 -  76.964:    9        |
|      4:    34.206 -  42.758:  100   |   9:    76.964 -  85.515:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1579             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1578             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1578   ksol= 0.32   Bsol= 41.01   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.37,2.38,3.04,0.00,0.00,0.00); trace/3= 2.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149215                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6815 0.99   1403  157 0.0983 0.1273      5.3769       5.535|
|  2:  4.6815 -  3.7348 0.99   1359  145 0.0867 0.1173      5.4376      5.6622|
|  3:  3.7348 -  3.2683 0.99   1321  154 0.1081 0.1563      5.4833      5.8476|
|  4:  3.2683 -  2.9721 0.99   1332  147 0.1209 0.1516      5.4543      5.5966|
|  5:  2.9721 -  2.7605 0.99   1312  143 0.1305 0.1678      5.3158      5.4864|
|  6:  2.7605 -  2.5986 0.99   1300  145 0.1213 0.1815      5.1977      5.4834|
|  7:  2.5986 -  2.4691 0.99   1315  141 0.1255 0.1655      5.1719      5.3732|
|  8:  2.4691 -  2.3620 0.98   1273  151 0.1165 0.1729      5.0571      5.3233|
|  9:  2.3620 -  2.2714 0.98   1299  148 0.1156 0.1835      5.0332       5.322|
| 10:  2.2714 -  2.1933 0.98   1280  134 0.1128 0.1700       4.967      5.2138|
| 11:  2.1933 -  2.1249 1.00   1281  141 0.1167 0.1760      4.9543      5.2801|
| 12:  2.1249 -  2.0643 0.97   1265  139 0.1100 0.1622      4.8777      5.0968|
| 13:  2.0643 -  2.0101 0.98   1284  143 0.1202 0.1794      4.7868      5.0548|
| 14:  2.0101 -  1.9612 0.47    606   71 0.1027 0.1599      4.6363      4.8927|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6815  1403   157  0.94   8.82   0.98     0.96       7053.57|
|  2:  4.6815 -  3.7348  1359   145  0.95   7.94   1.02     1.01       8919.46|
|  3:  3.7348 -  3.2683  1321   154  0.93  11.68   1.03     1.02      10611.78|
|  4:  3.2683 -  2.9721  1332   147  0.92  13.67   1.01     0.99      10330.55|
|  5:  2.9721 -  2.7605  1312   143  0.90  16.00   0.99     0.96       8092.17|
|  6:  2.7605 -  2.5986  1300   145  0.90  15.66   0.99     0.96       6866.77|
|  7:  2.5986 -  2.4691  1315   141  0.91  15.41   0.99     0.96       6214.78|
|  8:  2.4691 -  2.3620  1273   151  0.90  15.59   0.99     0.97       5264.70|
|  9:  2.3620 -  2.2714  1299   148  0.91  15.37   1.01     1.00       5100.13|
| 10:  2.2714 -  2.1933  1280   134  0.90  15.81   1.00     0.97       4448.94|
| 11:  2.1933 -  2.1249  1281   141  0.90  16.36   1.00     0.97       4451.10|
| 12:  2.1249 -  2.0643  1265   139  0.91  15.19   1.02     1.01       4049.07|
| 13:  2.0643 -  2.0101  1284   143  0.90  16.35   1.01     1.00       3240.51|
| 14:  2.0101 -  1.9612   606    71  0.92  14.28   0.99     0.97       2383.43|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2383.43 max =        10611.78 mean =      6407.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.08|
|phase err.(test): min =        0.00 max =           87.48 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1578   ksol= 0.32   Bsol= 43.60   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,-0.22,0.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149232                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1578   ksol= 0.32   Bsol= 43.60   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,-0.22,0.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149232                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9649 -  4.6815 0.99   1403  157 0.0983 0.1273      5.3771      5.5351|
|  2:  4.6815 -  3.7348 0.99   1359  145 0.0866 0.1173      5.4375      5.6621|
|  3:  3.7348 -  3.2683 0.99   1321  154 0.1081 0.1563      5.4833      5.8476|
|  4:  3.2683 -  2.9721 0.99   1332  147 0.1209 0.1516      5.4544      5.5967|
|  5:  2.9721 -  2.7605 0.99   1312  143 0.1305 0.1678      5.3158      5.4865|
|  6:  2.7605 -  2.5986 0.99   1300  145 0.1213 0.1815      5.1978      5.4834|
|  7:  2.5986 -  2.4691 0.99   1315  141 0.1255 0.1655      5.1719      5.3732|
|  8:  2.4691 -  2.3620 0.98   1273  151 0.1165 0.1729      5.0571      5.3233|
|  9:  2.3620 -  2.2714 0.98   1299  148 0.1156 0.1835      5.0332       5.322|
| 10:  2.2714 -  2.1933 0.98   1280  134 0.1128 0.1700       4.967      5.2138|
| 11:  2.1933 -  2.1249 1.00   1281  141 0.1167 0.1760      4.9543      5.2801|
| 12:  2.1249 -  2.0643 0.97   1265  139 0.1100 0.1622      4.8777      5.0968|
| 13:  2.0643 -  2.0101 0.98   1284  143 0.1202 0.1794      4.7868      5.0548|
| 14:  2.0101 -  1.9612 0.47    606   71 0.1027 0.1599      4.6363      4.8927|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9649 -  4.6815  1403   157  0.94   8.82   0.98     0.96       7057.31|
|  2:  4.6815 -  3.7348  1359   145  0.95   7.94   1.02     1.01       8919.84|
|  3:  3.7348 -  3.2683  1321   154  0.93  11.68   1.03     1.02      10609.95|
|  4:  3.2683 -  2.9721  1332   147  0.92  13.67   1.01     0.99      10330.67|
|  5:  2.9721 -  2.7605  1312   143  0.90  16.00   0.99     0.96       8092.51|
|  6:  2.7605 -  2.5986  1300   145  0.90  15.66   0.99     0.96       6867.05|
|  7:  2.5986 -  2.4691  1315   141  0.91  15.41   0.99     0.96       6215.05|
|  8:  2.4691 -  2.3620  1273   151  0.90  15.59   0.99     0.97       5264.83|
|  9:  2.3620 -  2.2714  1299   148  0.91  15.37   1.01     1.00       5100.21|
| 10:  2.2714 -  2.1933  1280   134  0.90  15.81   1.00     0.97       4448.97|
| 11:  2.1933 -  2.1249  1281   141  0.90  16.36   1.00     0.97       4451.16|
| 12:  2.1249 -  2.0643  1265   139  0.91  15.19   1.02     1.01       4049.12|
| 13:  2.0643 -  2.0101  1284   143  0.90  16.35   1.01     1.00       3240.57|
| 14:  2.0101 -  1.9612   606    71  0.92  14.28   0.99     0.97       2383.47|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2383.47 max =        10609.95 mean =      6407.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.08|
|phase err.(test): min =        0.00 max =           87.47 mean =        13.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.691)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.60    88.11   14.85    None  None   None       |
|    all(noH): 2823   0      2.60    88.11   14.85    None  None   None       |
|    Sol.    : 438    0      4.51    74.22   37.31    None  None   None       |
|    Mac.    : 2385   0      2.60    88.11   10.73    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:     2.597 -  11.149: 1690   |   5:    45.355 -  53.906:   88        |
|      1:    11.149 -  19.700:  581   |   6:    53.906 -  62.458:   45        |
|      2:    19.700 -  28.252:  152   |   7:    62.458 -  71.009:   26        |
|      3:    28.252 -  36.803:  129   |   8:    71.009 -  79.561:    9        |
|      4:    36.803 -  45.355:  100   |   9:    79.561 -  88.112:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.417 - 5.603
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 318
   mapped sites are within: 0.734 - 5.603

peak=   11.346 closest distance to " CB  VAL A 230 " =    1.460
peak=    8.869 closest distance to " CG2 VAL A 296 " =    1.287
peak=    6.152 closest distance to " CG  LEU A   5 " =    1.238
peak=    5.973 closest distance to " NH2 ARG A  56 " =    2.184
peak=    5.815 closest distance to " O   HOH Z 278 " =    1.210
peak=    5.733 closest distance to " CD2 LEU A   5 " =    1.265
peak=    5.716 closest distance to " NE2 GLN A  11 " =    1.164
peak=    5.149 closest distance to " CD1AILE A 234 " =    1.021
peak=    5.133 closest distance to " CG  LEU A 228 " =    1.202
peak=    4.952 closest distance to " O   HOH Z 193 " =    1.755
peak=    4.930 closest distance to " O   HOH Z 144 " =    1.756
peak=    4.930 closest distance to " CB  GLN A 223 " =    1.439
peak=    4.893 closest distance to " O   HOH Z 126 " =    1.945
peak=    4.884 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.824 closest distance to " O   HOH Z 202 " =    1.330
peak=    4.800 closest distance to " CB  SER A  63 " =    1.306
peak=    4.750 closest distance to " O   HOH Z 124 " =    1.455
peak=    4.748 closest distance to " O   HOH Z 232 " =    2.262
peak=    4.707 closest distance to " O   HOH Z 427 " =    2.879
peak=    4.663 closest distance to " CB  ARG A 275 " =    0.872
peak=    4.634 closest distance to " O   PRO A 198 " =    1.559
peak=    4.615 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.557 closest distance to " CB  ASN A 148 " =    1.371
peak=    4.547 closest distance to " OD1 ASN A  69 " =    2.632
peak=    4.514 closest distance to " CB  SER A   3 " =    1.410
peak=    4.494 closest distance to " CB  GLU A 152 " =    1.215
peak=    4.488 closest distance to " O   HOH Z 316 " =    2.920
peak=    4.453 closest distance to " CB  TYR A 169 " =    0.859
peak=    4.443 closest distance to " O   HOH Z 263 " =    1.520
peak=    4.394 closest distance to " CG  PRO A 198 " =    1.290
peak=    4.393 closest distance to " O   HOH Z 132 " =    0.936
peak=    4.322 closest distance to " O   HOH Z 298 " =    1.795
peak=    4.321 closest distance to " CB  VAL A 230 " =    1.155
peak=    4.296 closest distance to " CD2 LEU A 228 " =    1.213
peak=    4.285 closest distance to " O   HOH Z 411 " =    3.813
peak=    4.252 closest distance to " O   HOH Z 368 " =    2.049
peak=    4.212 closest distance to " O   HOH Z 272 " =    1.870
peak=    4.210 closest distance to " O   HOH Z 203 " =    1.656
peak=    4.207 closest distance to " O   HOH Z 236 " =    1.861
peak=    4.204 closest distance to " O   HOH Z 108 " =    1.297
peak=    4.202 closest distance to " CB  VAL A 265 " =    1.247
peak=    4.189 closest distance to " CB  VAL A 296 " =    1.080
peak=    4.159 closest distance to " CB  GLU A 128 " =    1.078
peak=    4.132 closest distance to " O   HOH Z 303 " =    2.070
peak=    4.121 closest distance to " O   HOH Z 260 " =    1.260
peak=    4.104 closest distance to " O   SER A  87 " =    2.356
peak=    4.097 closest distance to " CA  ALA A  21 " =    1.142
peak=    4.094 closest distance to " OD2 ASP A 286 " =    2.767
peak=    4.080 closest distance to " O   HOH Z  97 " =    2.044
peak=    4.073 closest distance to " O   HOH Z 128 " =    1.993
peak=    4.068 closest distance to " O   HOH Z 425 " =    1.372
peak=    4.059 closest distance to " O   HOH Z 234 " =    3.657
peak=    4.048 closest distance to " O   HOH Z  48 " =    1.545
peak=    4.042 closest distance to " O   HOH Z  78 " =    1.762
peak=    4.027 closest distance to " O   HOH Z 371 " =    3.082
peak=    3.983 closest distance to " ND2 ASN A 187 " =    1.622
peak=    3.978 closest distance to " O   HOH Z  61 " =    1.599
peak=    3.974 closest distance to " O   HOH Z 158 " =    2.903
peak=    3.972 closest distance to " O   HOH Z 369 " =    1.883
peak=    3.933 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.925 closest distance to " O   HOH Z   9 " =    2.180
peak=    3.924 closest distance to " CA  VAL A  41 " =    0.875
peak=    3.875 closest distance to " O   HOH Z  59 " =    1.937
peak=    3.851 closest distance to " CG  GLN A  88 " =    1.078
peak=    3.836 closest distance to " O   HOH Z 133 " =    1.609
peak=    3.835 closest distance to " CG  ARG A  66 " =    2.596
peak=    3.833 closest distance to " O   HOH Z 193 " =    1.881
peak=    3.822 closest distance to " O   HOH Z 346 " =    1.512
peak=    3.821 closest distance to " CB  GLN A  88 " =    1.235
peak=    3.819 closest distance to " CB  ASN A 148 " =    1.911
peak=    3.813 closest distance to " O   HOH Z 344 " =    2.760
peak=    3.812 closest distance to " O   HOH Z  93 " =    2.496
peak=    3.803 closest distance to " CA  ALA A  51 " =    0.980
peak=    3.801 closest distance to " CG1BVAL A  72 " =    1.533
peak=    3.797 closest distance to " CB  TRP A 266 " =    0.997
peak=    3.794 closest distance to " O   HOH Z 392 " =    3.109
peak=    3.787 closest distance to " O   HOH Z  88 " =    3.141
peak=    3.779 closest distance to " O   HOH Z 189 " =    2.653
peak=    3.777 closest distance to " OG BSER A 164 " =    2.183
peak=    3.772 closest distance to " O   HOH Z 247 " =    1.254
peak=    3.769 closest distance to " CB  TRP A 179 " =    1.334
peak=    3.768 closest distance to " CA  THR A 221 " =    0.884
peak=    3.759 closest distance to " O   HOH Z 250 " =    1.320
peak=    3.758 closest distance to " CG2 VAL A 257 " =    0.922
peak=    3.756 closest distance to " O   HOH Z 236 " =    1.564
peak=    3.754 closest distance to " O   TRP A 274 " =    1.924
peak=    3.753 closest distance to " CB  PRO A  54 " =    0.741
peak=    3.753 closest distance to " O   HOH Z   3 " =    1.754
peak=    3.747 closest distance to " OE1 GLU A   2 " =    2.155
peak=    3.746 closest distance to " CA  TYR A  30 " =    0.970
peak=    3.743 closest distance to " O   MET A 105 " =    1.743
peak=    3.742 closest distance to " CB  VAL A 202 " =    1.602
peak=    3.732 closest distance to " N   PHE A 130 " =    1.366
peak=    3.723 closest distance to " O   HOH Z  55 " =    2.262
peak=    3.718 closest distance to " O   HOH Z 389 " =    1.793
peak=    3.717 closest distance to " CG  PRO A 243 " =    1.196
peak=    3.715 closest distance to " CB  SER A 216 " =    0.795
peak=    3.692 closest distance to " O   HOH Z 193 " =    1.694
peak=    3.686 closest distance to " O   HOH Z 134 " =    1.384
peak=    3.686 closest distance to " CA  ALA A 248 " =    1.350
peak=    3.684 closest distance to " CA  THR A 264 " =    0.777
peak=    3.678 closest distance to " CB  ARG A  79 " =    1.421
peak=    3.663 closest distance to " O   HOH Z 345 " =    3.343
peak=    3.662 closest distance to " CB  ASN A 187 " =    1.248
peak=    3.661 closest distance to " CB  GLU A 277 " =    3.511
peak=    3.656 closest distance to " O   HOH Z 273 " =    2.685
peak=    3.651 closest distance to " O   HOH Z 329 " =    3.738
peak=    3.647 closest distance to " CA  LEU A 282 " =    1.110
peak=    3.631 closest distance to " NH2 ARG A 156 " =    1.071
peak=    3.627 closest distance to " CG BARG A 102 " =    1.851
peak=    3.621 closest distance to " NZ  LYS A 117 " =    3.157
peak=    3.621 closest distance to " O   HOH Z 426 " =    1.480
peak=    3.611 closest distance to " CG  LEU A 167 " =    1.162
peak=    3.611 closest distance to " O   HOH Z 108 " =    1.991
peak=    3.606 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.604 closest distance to " CD BLYS A 290 " =    1.132
peak=    3.604 closest distance to " CB  ARG A 139 " =    0.981
peak=    3.603 closest distance to " CB  LEU A 143 " =    1.150
peak=    3.597 closest distance to " O   HOH Z 209 " =    2.334
peak=    3.596 closest distance to " C   LYS A 290 " =    1.327
peak=    3.589 closest distance to " O   HOH Z 227 " =    1.702
peak=    3.587 closest distance to " O   HOH Z 403 " =    1.669
peak=    3.586 closest distance to " O   HOH Z 280 " =    1.671
peak=    3.569 closest distance to " CG1 ILE A  33 " =    1.341
peak=    3.564 closest distance to " O   HOH Z 295 " =    1.534
peak=    3.557 closest distance to " O   HOH Z 180 " =    2.126
peak=    3.547 closest distance to " CG2 THR A 221 " =    1.096
peak=    3.546 closest distance to " C   ALA A 299 " =    0.989
peak=    3.543 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.532 closest distance to " CA  VAL A 126 " =    1.010
peak=    3.530 closest distance to " CD2 LEU A 255 " =    1.399
peak=    3.526 closest distance to " CD1 ILE A  33 " =    1.604
peak=    3.521 closest distance to " CB  LEU A 228 " =    1.343
peak=    3.517 closest distance to " O   HOH Z 423 " =    1.799
peak=    3.516 closest distance to " O   HOH Z 112 " =    1.519
peak=    3.514 closest distance to " CA  ALA A 158 " =    1.139
peak=    3.513 closest distance to " NE2 GLN A  58 " =    5.603
peak=    3.512 closest distance to " CD1 LEU A 300 " =    1.213
peak=    3.503 closest distance to " O   HOH Z  54 " =    1.552
peak=    3.501 closest distance to " O   HOH Z 227 " =    2.142
peak=    3.497 closest distance to " O   HOH Z  37 " =    1.271
peak=    3.496 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.491 closest distance to " O   HOH Z 322 " =    1.914
peak=    3.489 closest distance to " O   HOH Z 344 " =    1.225
peak=    3.485 closest distance to " O   HOH Z  44 " =    1.755
peak=    3.478 closest distance to " O   HOH Z 284 " =    1.575
peak=    3.475 closest distance to " O   HOH Z 261 " =    2.092
peak=    3.473 closest distance to " CB BVAL A  41 " =    1.240
peak=    3.472 closest distance to " O   HOH Z 126 " =    1.572
peak=    3.472 closest distance to " O   HOH Z 276 " =    1.252
peak=    3.471 closest distance to " O   ALA A 158 " =    1.332
peak=    3.468 closest distance to " OG  SER A  22 " =    2.781
peak=    3.467 closest distance to " NH1AARG A 145 " =    0.991
peak=    3.463 closest distance to " O   HOH Z 135 " =    1.843
peak=    3.459 closest distance to " N   SER A 135 " =    1.316
peak=    3.458 closest distance to " O   HOH Z  10 " =    1.808
peak=    3.458 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.457 closest distance to " O   HOH Z 374 " =    2.460
peak=    3.456 closest distance to " NH1 ARG A 138 " =    1.210
peak=    3.456 closest distance to " O   HOH Z 175 " =    2.058
peak=    3.454 closest distance to " O   HOH Z 151 " =    1.683
peak=    3.454 closest distance to " O   HOH Z  43 " =    2.228
peak=    3.452 closest distance to " O   HOH Z 145 " =    1.804
peak=    3.452 closest distance to " O   HOH Z 116 " =    1.706
peak=    3.451 closest distance to " CB  MET A  40 " =    0.853
peak=    3.450 closest distance to " CA  SER A  87 " =    0.936
peak=    3.450 closest distance to " O   HOH Z   9 " =    1.984
peak=    3.446 closest distance to " O   HOH Z 271 " =    1.930
peak=    3.444 closest distance to " CG2 ILE A 120 " =    1.287
peak=    3.443 closest distance to " O   HOH Z 222 " =    2.405
peak=    3.439 closest distance to " ND1 HIS A  86 " =    1.659
peak=    3.438 closest distance to " N   ARG A 156 " =    1.301
peak=    3.434 closest distance to " O   HOH Z  21 " =    1.777
peak=    3.433 closest distance to " O   HOH Z  68 " =    1.994
peak=    3.426 closest distance to " O   HOH Z 209 " =    2.372
peak=    3.424 closest distance to " O   HOH Z 171 " =    2.250
peak=    3.417 closest distance to " CG  MET A 185 " =    1.213
peak=    3.415 closest distance to " O   HOH Z  61 " =    1.611
peak=    3.413 closest distance to " N   TRP A 177 " =    1.658
peak=    3.412 closest distance to " OG  SER A  97 " =    2.642
peak=    3.411 closest distance to " O   HOH Z 132 " =    2.577
peak=    3.410 closest distance to " O   HOH Z 151 " =    1.730
peak=    3.409 closest distance to " CB  ILE A 234 " =    0.896
peak=    3.407 closest distance to " O   HOH Z 172 " =    3.675
peak=    3.399 closest distance to " CD  ARG A 269 " =    1.065
peak=    3.394 closest distance to " O   HOH Z 419 " =    1.696
peak=    3.386 closest distance to " O   HOH Z 248 " =    1.782
peak=    3.385 closest distance to " N   ASN A  39 " =    1.157
peak=    3.381 closest distance to " O   HOH Z 334 " =    1.444
peak=    3.377 closest distance to " CG  MET A 185 " =    1.043
peak=    3.376 closest distance to " O   HOH Z 411 " =    1.812
peak=    3.374 closest distance to " O   GLN A  58 " =    1.529
peak=    3.368 closest distance to " O   HOH Z 357 " =    1.856
peak=    3.368 closest distance to " O   HOH Z 164 " =    2.066
peak=    3.361 closest distance to " OG1 THR A 294 " =    2.362
peak=    3.361 closest distance to " O   HOH Z  50 " =    1.513
peak=    3.360 closest distance to " CB  VAL A 268 " =    0.812
peak=    3.360 closest distance to " CB  LEU A 255 " =    0.865
peak=    3.358 closest distance to " O   HOH Z  40 " =    1.916
peak=    3.354 closest distance to " CB  ASN A 142 " =    1.008
peak=    3.353 closest distance to " CB  ALA A 291 " =    1.383
peak=    3.351 closest distance to " O   HOH Z 130 " =    2.258
peak=    3.351 closest distance to " O   HOH Z 281 " =    4.546
peak=    3.340 closest distance to " O   HOH Z 422 " =    2.618
peak=    3.338 closest distance to " NH1 ARG A  14 " =    0.962
peak=    3.335 closest distance to " O   HOH Z 216 " =    2.351
peak=    3.327 closest distance to " O   HOH Z 214 " =    1.991
peak=    3.326 closest distance to " O   HOH Z 255 " =    1.712
peak=    3.324 closest distance to " CB  THR A  31 " =    1.695
peak=    3.324 closest distance to " O   HOH Z 355 " =    1.782
peak=    3.323 closest distance to " ND1 HIS A  81 " =    1.535
peak=    3.321 closest distance to " O   HOH Z 303 " =    1.724
peak=    3.317 closest distance to " O   HOH Z 207 " =    1.726
peak=    3.316 closest distance to " CD  ARG A 159 " =    0.736
peak=    3.308 closest distance to " CA  ASP A 140 " =    1.205
peak=    3.307 closest distance to " O   HOH Z 407 " =    2.455
peak=    3.305 closest distance to " O   HOH Z   1 " =    1.618
peak=    3.298 closest distance to " CB  LYS A 117 " =    1.184
peak=    3.297 closest distance to " NH2 ARG A 219 " =    1.801
peak=    3.297 closest distance to " CB  TYR A  30 " =    1.528
peak=    3.290 closest distance to " CE  LYS A  76 " =    0.927
peak=    3.289 closest distance to " CA  GLY A 267 " =    0.962
peak=    3.287 closest distance to " CA  PHE A 283 " =    1.272
peak=    3.283 closest distance to " O   HOH Z 313 " =    1.731
peak=    3.282 closest distance to " CA  LYS A 117 " =    1.242
peak=    3.281 closest distance to " CA  ALA A 154 " =    1.107
peak=    3.280 closest distance to " CA  ASN A  74 " =    1.168
peak=    3.280 closest distance to " CB  SER A  62 " =    1.260
peak=    3.279 closest distance to " CA  GLN A 194 " =    1.219
peak=    3.278 closest distance to " CD  LYS A 166 " =    1.319
peak=    3.277 closest distance to " CA  ASP A 191 " =    0.735
peak=    3.277 closest distance to " O   ALA A   1 " =    1.528
peak=    3.276 closest distance to " NE2 GLN A  58 " =    4.122
peak=    3.276 closest distance to " O   HOH Z 279 " =    2.108
peak=    3.276 closest distance to " CB  SER A 212 " =    1.177
peak=    3.266 closest distance to " O   HOH Z 368 " =    3.560
peak=    3.266 closest distance to " O   HOH Z  30 " =    1.179
peak=    3.265 closest distance to " CD1 ILE A 106 " =    1.114
peak=    3.265 closest distance to " CA  ALA A 295 " =    1.019
peak=    3.262 closest distance to " O   HOH Z 286 " =    2.309
peak=    3.262 closest distance to " CB  THR A 157 " =    1.012
peak=    3.260 closest distance to " O   HOH Z  59 " =    2.083
peak=    3.255 closest distance to " O  BHOH Z 338 " =    2.507
peak=    3.255 closest distance to " O   HOH Z  68 " =    1.541
peak=    3.254 closest distance to " O   HOH Z 189 " =    2.896
peak=    3.254 closest distance to " CB  ASP A 140 " =    0.734
peak=    3.244 closest distance to " CB  ALA A 248 " =    0.991
peak=    3.244 closest distance to " O   HOH Z 109 " =    2.613
peak=    3.242 closest distance to " CA  GLY A 211 " =    1.203
peak=    3.242 closest distance to " O   HOH Z  40 " =    2.326
peak=    3.240 closest distance to " O   THR A  31 " =    1.545
peak=    3.237 closest distance to " CB  ALA A   9 " =    1.590
peak=    3.233 closest distance to " O   HOH Z 423 " =    2.812
peak=    3.231 closest distance to " CD1 LEU A 228 " =    1.594
peak=    3.231 closest distance to " O   HOH Z 359 " =    3.781
peak=    3.229 closest distance to " O   ALA A   1 " =    1.704
peak=    3.226 closest distance to " O   HOH Z  48 " =    1.477
peak=    3.221 closest distance to " CG  MET A 188 " =    1.307
peak=    3.220 closest distance to " O   SER A  26 " =    1.575
peak=    3.215 closest distance to " CB  TRP A 150 " =    1.511
peak=    3.209 closest distance to " O   HOH Z 409 " =    3.180
peak=    3.208 closest distance to " N   VAL A 126 " =    1.202
peak=    3.206 closest distance to " CB  ALA A   1 " =    1.201
peak=    3.206 closest distance to " O   HOH Z 213 " =    2.266
peak=    3.204 closest distance to " O   HOH Z 272 " =    2.496
peak=    3.204 closest distance to " OG  SER A  62 " =    3.081
peak=    3.204 closest distance to " O   HOH Z 367 " =    3.534
peak=    3.200 closest distance to " CB  GLN A 278 " =    0.823
peak=    3.199 closest distance to " CG2 ILE A  20 " =    1.563
peak=    3.198 closest distance to " CZ2 TRP A 274 " =    1.641
peak=    3.195 closest distance to " CB  ALA A 295 " =    1.313
peak=    3.193 closest distance to " NH2BARG A 145 " =    2.103
peak=    3.185 closest distance to " O   HOH Z  11 " =    1.644
peak=    3.185 closest distance to " O   HOH Z 245 " =    1.410
peak=    3.184 closest distance to " OD1 ASP A 286 " =    1.564
peak=    3.181 closest distance to " CA  ARG A  56 " =    2.027
peak=    3.178 closest distance to " NZ  LYS A  76 " =    1.229
peak=    3.174 closest distance to " CB  PRO A 198 " =    0.954
peak=    3.172 closest distance to " CB  ILE A  20 " =    1.427
peak=    3.171 closest distance to " O   HOH Z 291 " =    1.559
peak=    3.170 closest distance to " O   HOH Z 163 " =    1.856
peak=    3.165 closest distance to " OG  SER A  62 " =    2.836
peak=    3.163 closest distance to " CA  ASN A 176 " =    1.120
peak=    3.163 closest distance to " O   HOH Z 141 " =    1.583
peak=    3.162 closest distance to " OG BSER A 134 " =    3.104
peak=    3.160 closest distance to " CB  ARG A 190 " =    1.789
peak=    3.159 closest distance to " OD2 ASP A 200 " =    1.444
peak=    3.158 closest distance to " O   GLN A 278 " =    1.309
peak=    3.157 closest distance to " OG BSER A 258 " =    3.516
peak=    3.152 closest distance to " O   HOH Z  20 " =    1.384
peak=    3.146 closest distance to " CE  MET A  93 " =    1.468
peak=    3.144 closest distance to " OD1BASN A 224 " =    2.174
peak=    3.137 closest distance to " CD  LYS A 119 " =    1.358
peak=    3.130 closest distance to " O   HOH Z 406 " =    1.639
peak=    3.129 closest distance to " O   HOH Z  49 " =    2.378
peak=    3.127 closest distance to " OG  SER A 206 " =    1.198
peak=    3.125 closest distance to " O   HOH Z  59 " =    2.043
peak=    3.123 closest distance to " CB  ASN A 215 " =    1.055
peak=    3.123 closest distance to " O   HOH Z 353 " =    2.654
peak=    3.118 closest distance to " CA  ILE A 234 " =    0.881
peak=    3.114 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.113 closest distance to " O   HOH Z 394 " =    1.730
peak=    3.109 closest distance to " CA  ALA A 233 " =    1.390
peak=    3.107 closest distance to " O   HOH Z 251 " =    1.563
peak=    3.106 closest distance to " CG  MET A 113 " =    1.201
peak=    3.106 closest distance to " CA  ARG A  36 " =    1.051
peak=    3.103 closest distance to " OD1 ASN A  45 " =    1.414
peak=    3.099 closest distance to " O   HOH Z 438 " =    2.086
peak=    3.099 closest distance to " O   HOH Z 185 " =    2.156
peak=    3.081 closest distance to " CD2 HIS A  81 " =    1.177
peak=    3.059 closest distance to " N   GLN A 278 " =    1.012
peak=    3.056 closest distance to " O   HOH Z 152 " =    1.578
peak=    3.052 closest distance to " O   HOH Z 192 " =    1.756
peak=    3.026 closest distance to " O   HOH Z 280 " =    2.476

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.413
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 190
   mapped sites are within: 0.706 - 5.413

peak=   -5.486 closest distance to " CG2 VAL A 230 " =    0.794
peak=   -4.484 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.323 closest distance to " O   HOH Z 290 " =    1.060
peak=   -4.309 closest distance to " O   HOH Z 266 " =    4.496
peak=   -4.215 closest distance to " O   HOH Z 231 " =    1.537
peak=   -4.211 closest distance to " CB  ALA A 161 " =    2.568
peak=   -4.021 closest distance to " N   GLN A  58 " =    1.769
peak=   -4.020 closest distance to " CG  GLN A 223 " =    1.943
peak=   -3.996 closest distance to " CG2 VAL A 296 " =    1.398
peak=   -3.954 closest distance to " O   HOH Z 198 " =    2.400
peak=   -3.943 closest distance to " SG  CYS A 254 " =    3.100
peak=   -3.931 closest distance to " O   HOH Z 166 " =    1.486
peak=   -3.916 closest distance to " O   PRO A 163 " =    1.946
peak=   -3.901 closest distance to " C   HIS A 108 " =    1.217
peak=   -3.888 closest distance to " CE2 TYR A  30 " =    2.852
peak=   -3.888 closest distance to " OXT GLY A 302 " =    2.870
peak=   -3.887 closest distance to " CB  TYR A  15 " =    2.173
peak=   -3.838 closest distance to " CD1 LEU A 101 " =    2.648
peak=   -3.826 closest distance to " CG  PHE A 283 " =    2.648
peak=   -3.818 closest distance to " CB  PRO A 163 " =    2.605
peak=   -3.804 closest distance to " CG2 THR A   4 " =    1.939
peak=   -3.790 closest distance to " O   HOH Z  92 " =    1.550
peak=   -3.782 closest distance to " CG  ASP A 231 " =    0.739
peak=   -3.771 closest distance to " C   ASP A 231 " =    2.555
peak=   -3.766 closest distance to " C   ALA A 158 " =    1.248
peak=   -3.757 closest distance to " CB  PRO A 243 " =    2.620
peak=   -3.742 closest distance to " O   HOH Z 435 " =    2.773
peak=   -3.728 closest distance to " O   HOH Z 377 " =    2.095
peak=   -3.723 closest distance to " O   HOH Z  43 " =    1.773
peak=   -3.708 closest distance to " O   VAL A  67 " =    2.661
peak=   -3.678 closest distance to " O   HOH Z  98 " =    1.887
peak=   -3.665 closest distance to " CD1 LEU A 228 " =    2.256
peak=   -3.653 closest distance to " O   HOH Z 389 " =    1.800
peak=   -3.651 closest distance to " O   HOH Z 388 " =    2.029
peak=   -3.637 closest distance to " OG BSER A 134 " =    1.672
peak=   -3.636 closest distance to " OG BSER A 134 " =    1.171
peak=   -3.630 closest distance to " O   VAL A  67 " =    2.583
peak=   -3.624 closest distance to " O   HOH Z  52 " =    1.493
peak=   -3.615 closest distance to " CD  ARG A  14 " =    2.950
peak=   -3.612 closest distance to " O   HOH Z 351 " =    1.425
peak=   -3.601 closest distance to " NH2 ARG A  79 " =    1.873
peak=   -3.593 closest distance to " O   HOH Z 166 " =    1.988
peak=   -3.587 closest distance to " C   ASN A 285 " =    2.412
peak=   -3.577 closest distance to " CD  ARG A 139 " =    1.682
peak=   -3.575 closest distance to " O   PRO A 198 " =    1.237
peak=   -3.573 closest distance to " N   THR A 157 " =    1.482
peak=   -3.571 closest distance to " CB  ALA A 248 " =    1.941
peak=   -3.564 closest distance to " O   MET A  40 " =    2.645
peak=   -3.563 closest distance to " CZ3 TRP A 179 " =    1.303
peak=   -3.560 closest distance to " CB  ASN A  39 " =    2.088
peak=   -3.556 closest distance to " O   GLY A 211 " =    1.285
peak=   -3.551 closest distance to " N   SER A 276 " =    1.257
peak=   -3.538 closest distance to " NH2AARG A 275 " =    5.215
peak=   -3.532 closest distance to " O   ALA A  51 " =    1.466
peak=   -3.525 closest distance to " O   HOH Z  13 " =    1.424
peak=   -3.521 closest distance to " N   HIS A 115 " =    2.066
peak=   -3.518 closest distance to " CG  LEU A 228 " =    0.954
peak=   -3.514 closest distance to " O   HOH Z 148 " =    1.774
peak=   -3.506 closest distance to " O   HOH Z 198 " =    1.436
peak=   -3.500 closest distance to " CG  LYS A 193 " =    2.214
peak=   -3.495 closest distance to " ND2 ASN A  45 " =    0.991
peak=   -3.488 closest distance to " CE  MET A 105 " =    2.061
peak=   -3.487 closest distance to " CB  ASP A 132 " =    2.276
peak=   -3.486 closest distance to " CE2 PHE A 218 " =    2.600
peak=   -3.472 closest distance to " CD  LYS A 289 " =    2.608
peak=   -3.471 closest distance to " C   ASN A 187 " =    1.800
peak=   -3.464 closest distance to " N   ALA A 226 " =    2.046
peak=   -3.463 closest distance to " N   ALA A 248 " =    1.629
peak=   -3.454 closest distance to " CG  ASP A  50 " =    2.339
peak=   -3.448 closest distance to " OG  SER A  87 " =    1.352
peak=   -3.445 closest distance to " N   THR A 235 " =    1.248
peak=   -3.445 closest distance to " O   HOH Z  63 " =    1.042
peak=   -3.442 closest distance to " O   ALA A 161 " =    1.621
peak=   -3.441 closest distance to " O   HOH Z  97 " =    1.896
peak=   -3.441 closest distance to " OG ASER A 134 " =    1.299
peak=   -3.441 closest distance to " CD2 LEU A 300 " =    2.861
peak=   -3.438 closest distance to " CD2 LEU A 237 " =    2.701
peak=   -3.434 closest distance to " CZ  PHE A  59 " =    1.494
peak=   -3.430 closest distance to " CG  MET A 105 " =    0.932
peak=   -3.427 closest distance to " O   HOH Z 103 " =    1.870
peak=   -3.426 closest distance to " O   HOH Z 211 " =    1.565
peak=   -3.423 closest distance to " OD1 ASN A 148 " =    1.568
peak=   -3.423 closest distance to " CG  TRP A 266 " =    1.689
peak=   -3.421 closest distance to " CE BMET A  47 " =    1.765
peak=   -3.413 closest distance to " CG1 VAL A 112 " =    2.840
peak=   -3.404 closest distance to " CD1 PHE A  59 " =    1.868
peak=   -3.399 closest distance to " ND2 ASN A  60 " =    1.450
peak=   -3.394 closest distance to " OG  SER A  97 " =    2.114
peak=   -3.392 closest distance to " OG  SER A  62 " =    1.534
peak=   -3.392 closest distance to " O   HOH Z 407 " =    3.117
peak=   -3.388 closest distance to " OXT GLY A 302 " =    3.603
peak=   -3.387 closest distance to " CD  GLN A  88 " =    2.290
peak=   -3.386 closest distance to " O   PRO A 198 " =    1.300
peak=   -3.385 closest distance to " O   HOH Z 426 " =    2.295
peak=   -3.378 closest distance to " O   HOH Z 165 " =    2.030
peak=   -3.377 closest distance to " CG  PRO A 163 " =    2.579
peak=   -3.372 closest distance to " O   HOH Z 292 " =    4.449
peak=   -3.371 closest distance to " CD  GLN A  88 " =    0.842
peak=   -3.371 closest distance to " N   ALA A  43 " =    2.402
peak=   -3.355 closest distance to " NZ  LYS A 119 " =    3.336
peak=   -3.355 closest distance to " CG1 VAL A 296 " =    1.450
peak=   -3.353 closest distance to " CG2 VAL A 112 " =    2.573
peak=   -3.352 closest distance to " O   HOH Z 185 " =    2.268
peak=   -3.352 closest distance to " O   VAL A 153 " =    2.281
peak=   -3.342 closest distance to " C   GLN A 205 " =    2.005
peak=   -3.336 closest distance to " C   MET A 188 " =    1.571
peak=   -3.334 closest distance to " O   GLY A 196 " =    1.145
peak=   -3.333 closest distance to " O   HOH Z 423 " =    2.193
peak=   -3.332 closest distance to " O   HOH Z 111 " =    4.533
peak=   -3.327 closest distance to " O   HOH Z  47 " =    1.503
peak=   -3.326 closest distance to " CZ  TYR A 169 " =    1.682
peak=   -3.314 closest distance to " O   HOH Z 132 " =    0.857
peak=   -3.312 closest distance to " O   HOH Z 191 " =    5.413
peak=   -3.311 closest distance to " CE  LYS A  76 " =    2.823
peak=   -3.308 closest distance to " CB  ALA A  43 " =    2.442
peak=   -3.306 closest distance to " O   HOH Z 348 " =    1.858
peak=   -3.305 closest distance to " O   HOH Z  71 " =    0.998
peak=   -3.305 closest distance to " CG1 VAL A 112 " =    2.628
peak=   -3.301 closest distance to " OG  SER A   3 " =    1.644
peak=   -3.300 closest distance to " O   HOH Z  11 " =    1.909
peak=   -3.298 closest distance to " CB  ASP A 132 " =    2.198
peak=   -3.296 closest distance to " OD1 ASP A 191 " =    1.606
peak=   -3.285 closest distance to " C   LEU A 143 " =    1.160
peak=   -3.284 closest distance to " O   HOH Z 353 " =    2.131
peak=   -3.282 closest distance to " O   HOH Z 210 " =    1.050
peak=   -3.280 closest distance to " O   HOH Z 417 " =    2.727
peak=   -3.276 closest distance to " CD1 ILE A 199 " =    2.450
peak=   -3.272 closest distance to " OE1 GLN A  88 " =    1.090
peak=   -3.268 closest distance to " O   ASP A 231 " =    2.378
peak=   -3.261 closest distance to " O   HOH Z 411 " =    3.755
peak=   -3.261 closest distance to " CA  SER A 146 " =    2.315
peak=   -3.260 closest distance to " CG2 ILE A 263 " =    2.289
peak=   -3.258 closest distance to " O   HOH Z 281 " =    2.856
peak=   -3.252 closest distance to " CA  ASP A 298 " =    1.046
peak=   -3.250 closest distance to " O   HOH Z 174 " =    2.424
peak=   -3.247 closest distance to " O   HOH Z 436 " =    1.481
peak=   -3.245 closest distance to " C   GLN A 240 " =    2.363
peak=   -3.242 closest distance to " CG1 VAL A 197 " =    2.273
peak=   -3.240 closest distance to " O   HOH Z 118 " =    2.646
peak=   -3.237 closest distance to " O   HOH Z 222 " =    1.422
peak=   -3.236 closest distance to " O   HOH Z 298 " =    1.202
peak=   -3.235 closest distance to " N   PHE A  59 " =    2.151
peak=   -3.228 closest distance to " N   ALA A   9 " =    1.533
peak=   -3.221 closest distance to " CG1 VAL A 230 " =    1.780
peak=   -3.220 closest distance to " O   HOH Z  19 " =    2.238
peak=   -3.212 closest distance to " CB  ALA A  51 " =    1.748
peak=   -3.212 closest distance to " O   ALA A   8 " =    1.829
peak=   -3.211 closest distance to " CA  GLY A 133 " =    1.935
peak=   -3.202 closest distance to " O   HOH Z  44 " =    2.063
peak=   -3.199 closest distance to " O   HOH Z  90 " =    2.780
peak=   -3.197 closest distance to " CA  TYR A  30 " =    2.885
peak=   -3.196 closest distance to " OG1 THR A 178 " =    1.209
peak=   -3.195 closest distance to " O   HOH Z 377 " =    0.706
peak=   -3.195 closest distance to " NH2 ARG A  66 " =    2.098
peak=   -3.194 closest distance to " O   HOH Z  93 " =    1.580
peak=   -3.193 closest distance to " CE3 TRP A 274 " =    2.468
peak=   -3.193 closest distance to " CA  GLY A 133 " =    2.221
peak=   -3.189 closest distance to " O   HOH Z 385 " =    1.958
peak=   -3.189 closest distance to " O   HOH Z 313 " =    1.741
peak=   -3.185 closest distance to " O   HOH Z 385 " =    2.227
peak=   -3.183 closest distance to " O   HOH Z 423 " =    1.105
peak=   -3.177 closest distance to " OG  SER A 206 " =    1.659
peak=   -3.173 closest distance to " CA  ASN A 127 " =    1.100
peak=   -3.171 closest distance to " CD2 TYR A 293 " =    2.126
peak=   -3.168 closest distance to " CD2 LEU A 237 " =    2.815
peak=   -3.164 closest distance to " CB  PHE A 192 " =    1.754
peak=   -3.161 closest distance to " CD  GLU A 152 " =    2.590
peak=   -3.156 closest distance to " O   HOH Z 309 " =    2.442
peak=   -3.152 closest distance to " O   HOH Z 168 " =    1.792
peak=   -3.150 closest distance to " O   HOH Z  97 " =    0.913
peak=   -3.146 closest distance to " O   SER A 210 " =    1.951
peak=   -3.145 closest distance to " CG  GLU A 277 " =    1.136
peak=   -3.143 closest distance to " O   HOH Z 228 " =    1.498
peak=   -3.142 closest distance to " O   HOH Z 140 " =    1.905
peak=   -3.141 closest distance to " NH1AARG A 275 " =    1.881
peak=   -3.134 closest distance to " O   HOH Z  98 " =    1.515
peak=   -3.132 closest distance to " O   GLY A 203 " =    2.351
peak=   -3.131 closest distance to " O   HOH Z 369 " =    2.095
peak=   -3.122 closest distance to " O   HOH Z 283 " =    1.545
peak=   -3.114 closest distance to " O   HOH Z 234 " =    4.167
peak=   -3.091 closest distance to " O   SER A  22 " =    2.237
peak=   -3.084 closest distance to " N   GLN A  77 " =    1.560
peak=   -3.084 closest distance to " O   HOH Z  60 " =    2.216
peak=   -3.052 closest distance to " O   HOH Z 417 " =    2.647
peak=   -3.050 closest distance to " O   HOH Z 128 " =    4.085
peak=   -3.045 closest distance to " CB  TYR A 172 " =    2.187
peak=   -3.037 closest distance to " CE  MET A  93 " =    1.082
peak=   -3.023 closest distance to " NH2 ARG A 156 " =    1.146

================= 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    :  0.4555 0.4481   6.253676e+00   6.245749e+00
   1_bss:  0.4463 0.4368   6.249932e+00   6.236712e+00
   1_xyz:  0.3581 0.3784   6.107272e+00   6.144862e+00
   1_adp:  0.3072 0.3546   5.998731e+00   6.098121e+00
   1_occ:  0.3067 0.3549   5.998187e+00   6.098984e+00
   2_bss:  0.3022 0.3506   5.997826e+00   6.096645e+00
   2_xyz:  0.2181 0.2748   5.725005e+00   5.897893e+00
   2_adp:  0.1966 0.2492   5.634318e+00   5.818696e+00
   2_occ:  0.1963 0.2487   5.633089e+00   5.818074e+00
   3_bss:  0.1954 0.2474   5.630711e+00   5.814520e+00
   3_xyz:  0.1438 0.1891   5.349559e+00   5.565194e+00
   3_adp:  0.1310 0.1782   5.274882e+00   5.504382e+00
   3_occ:  0.1309 0.1780   5.274261e+00   5.503576e+00
   4_bss:  0.1309 0.1778   5.272862e+00   5.501581e+00
   4_xyz:  0.1191 0.1650   5.197221e+00   5.434661e+00
   4_adp:  0.1170 0.1622   5.180998e+00   5.416654e+00
   4_occ:  0.1169 0.1620   5.180380e+00   5.416044e+00
   5_bss:  0.1168 0.1620   5.180330e+00   5.415986e+00
   5_xyz:  0.1121 0.1587   5.151793e+00   5.397400e+00
   5_adp:  0.1122 0.1579   5.149755e+00   5.393080e+00
   5_occ:  0.1121 0.1578   5.149215e+00   5.392463e+00
   5_bss:  0.1121 0.1578   5.149232e+00   5.392468e+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:  0.375  20.000   7.052   7.901   9.453   0.000   0.000   0.000
   1_xyz:  0.375  20.000   7.052   7.901   9.453   0.000   0.000   0.000
   1_adp:  0.375  20.000   7.052   7.901   9.453   0.000   0.000   0.000
   1_occ:  0.375  20.000   7.052   7.901   9.453   0.000   0.000   0.000
   2_bss:  0.330  28.917   3.500   3.774   6.107   0.000   0.000   0.000
   2_xyz:  0.330  28.917   3.500   3.774   6.107   0.000   0.000   0.000
   2_adp:  0.330  28.917   3.500   3.774   6.107   0.000   0.000   0.000
   2_occ:  0.330  28.917   3.500   3.774   6.107   0.000   0.000   0.000
   3_bss:  0.317  37.049   2.560   2.554   3.976   0.000   0.000   0.000
   3_xyz:  0.317  37.049   2.560   2.554   3.976   0.000   0.000   0.000
   3_adp:  0.317  37.049   2.560   2.554   3.976   0.000   0.000   0.000
   3_occ:  0.317  37.049   2.560   2.554   3.976   0.000   0.000   0.000
   4_bss:  0.320  41.006   2.416   2.382   3.233   0.000   0.000   0.000
   4_xyz:  0.320  41.006   2.416   2.382   3.233   0.000   0.000   0.000
   4_adp:  0.320  41.006   2.416   2.382   3.233   0.000   0.000   0.000
   4_occ:  0.320  41.006   2.416   2.382   3.233   0.000   0.000   0.000
   5_bss:  0.324  41.006   2.374   2.381   3.036   0.000   0.000   0.000
   5_xyz:  0.324  41.006   2.374   2.381   3.036   0.000   0.000   0.000
   5_adp:  0.324  41.006   2.374   2.381   3.036   0.000   0.000   0.000
   5_occ:  0.324  41.006   2.374   2.381   3.036   0.000   0.000   0.000
   5_bss:  0.325  43.604  -0.223  -0.216   0.439   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.745 0.4868  0.5685    61526.251
   1_bss:  52.984 0.4811  0.7075    58419.542
   1_xyz:  42.101 0.6164  0.8934    40866.933
   1_adp:  37.989 0.6662  0.9855    35006.549
   1_occ:  38.101 0.6648  0.9832    35125.454
   2_bss:  37.829 0.6679  0.8652    34758.637
   2_xyz:  28.316 0.7753  0.9723    19922.484
   2_adp:  25.017 0.8114  0.9976    16471.912
   2_occ:  24.982 0.8117  0.9977    16420.369
   3_bss:  24.783 0.8135  0.9493    16203.236
   3_xyz:  17.974 0.8805  0.9894     9178.402
   3_adp:  16.516 0.8939  0.9926     8164.033
   3_occ:  16.497 0.8941  0.9925     8147.460
   4_bss:  16.441 0.8946  0.9796     8116.667
   4_xyz:  14.980 0.9069  0.9860     6979.780
   4_adp:  14.525 0.9109  0.9865     6732.484
   4_occ:  14.513 0.9110  0.9865     6723.968
   5_bss:  14.510 0.9111  0.9836     6725.490
   5_xyz:  14.160 0.9138  0.9837     6469.179
   5_adp:  14.040 0.9149  0.9828     6416.626
   5_occ:  14.029 0.9150  0.9827     6407.410
   5_bss:  14.029 0.9150  0.9827     6407.706
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3368e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3368e+01
   1_xyz:   1.573  0.012  0.102 18.252  0.006  4.119   1.2657e-01
   1_adp:   1.573  0.012  0.102 18.252  0.006  4.119   1.2657e-01
   1_occ:   1.573  0.012  0.102 18.252  0.006  4.119   1.2657e-01
   2_bss:   1.573  0.012  0.102 18.252  0.006  4.119   1.2657e-01
   2_xyz:   1.015  0.007  0.072 16.273  0.004  4.121   6.7815e-02
   2_adp:   1.015  0.007  0.072 16.273  0.004  4.121   6.7815e-02
   2_occ:   1.015  0.007  0.072 16.273  0.004  4.121   6.7815e-02
   3_bss:   1.015  0.007  0.072 16.273  0.004  4.121   6.7815e-02
   3_xyz:   1.045  0.006  0.079 15.989  0.004  4.109   6.4377e-02
   3_adp:   1.045  0.006  0.079 15.989  0.004  4.109   6.4377e-02
   3_occ:   1.045  0.006  0.079 15.989  0.004  4.109   6.4377e-02
   4_bss:   1.045  0.006  0.079 15.989  0.004  4.109   6.4377e-02
   4_xyz:   0.968  0.006  0.077 16.002  0.004  4.111   5.9795e-02
   4_adp:   0.968  0.006  0.077 16.002  0.004  4.111   5.9795e-02
   4_occ:   0.968  0.006  0.077 16.002  0.004  4.111   5.9795e-02
   5_bss:   0.968  0.006  0.077 16.002  0.004  4.111   5.9795e-02
   5_xyz:   0.995  0.006  0.078 15.846  0.004  4.110   6.0982e-02
   5_adp:   0.995  0.006  0.078 15.846  0.004  4.110   6.0982e-02
   5_occ:   0.995  0.006  0.078 15.846  0.004  4.110   6.0982e-02
   5_bss:   0.995  0.006  0.078 15.846  0.004  4.110   6.0982e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9186e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9186e+00
   1_xyz:  13.258  0.149  0.439 85.677  0.043  2.285   8.9638e-02
   1_adp:  13.258  0.149  0.439 85.677  0.043  2.285   8.9638e-02
   1_occ:  13.258  0.149  0.439 85.677  0.043  2.285   8.9638e-02
   2_bss:  13.258  0.149  0.439 85.677  0.043  2.285   8.9638e-02
   2_xyz:   6.364  0.061  0.271 86.019  0.033  2.287   5.2222e-02
   2_adp:   6.364  0.061  0.271 86.019  0.033  2.287   5.2222e-02
   2_occ:   6.364  0.061  0.271 86.019  0.033  2.287   5.2222e-02
   3_bss:   6.364  0.061  0.271 86.019  0.033  2.287   5.2222e-02
   3_xyz:   7.304  0.051  0.445 87.319  0.030  2.316   4.7358e-02
   3_adp:   7.304  0.051  0.445 87.319  0.030  2.316   4.7358e-02
   3_occ:   7.304  0.051  0.445 87.319  0.030  2.316   4.7358e-02
   4_bss:   7.304  0.051  0.445 87.319  0.030  2.316   4.7358e-02
   4_xyz:   7.497  0.043  0.467 83.028  0.034  2.339   3.9906e-02
   4_adp:   7.497  0.043  0.467 83.028  0.034  2.339   3.9906e-02
   4_occ:   7.497  0.043  0.467 83.028  0.034  2.339   3.9906e-02
   5_bss:   7.497  0.043  0.467 83.028  0.034  2.339   3.9906e-02
   5_xyz:   7.013  0.035  0.506 84.020  0.033  2.300   3.8595e-02
   5_adp:   7.013  0.035  0.506 84.020  0.033  2.300   3.8595e-02
   5_occ:   7.013  0.035  0.506 84.020  0.033  2.300   3.8595e-02
   5_bss:   7.013  0.035  0.506 84.020  0.033  2.300   3.8595e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  52.11   0.00  11.24  52.11   0.00   8.89  51.51   0.00  24.07
   1_occ:  52.11   0.00  11.24  52.11   0.00   8.89  51.51   0.00  24.07
   2_bss:  52.11   0.00  11.24  52.11   0.00   8.89  51.51   0.00  24.07
   2_xyz:  52.11   0.00  11.24  52.11   0.00   8.89  51.51   0.00  24.07
   2_adp:  59.37   0.00  11.77  57.43   0.00   8.24  59.37   1.02  30.98
   2_occ:  59.37   0.00  11.77  57.43   0.00   8.24  59.37   1.02  30.98
   3_bss:  59.37   0.00  11.77  57.43   0.00   8.24  59.37   1.02  30.98
   3_xyz:  59.37   0.00  11.77  57.43   0.00   8.24  59.37   1.02  30.98
   3_adp:  78.23   0.00  12.86  78.23   0.00   8.37  77.62   2.18  37.32
   3_occ:  78.23   0.00  12.86  78.23   0.00   8.37  77.62   2.18  37.32
   4_bss:  78.23   0.00  12.86  78.23   0.00   8.37  77.62   2.18  37.32
   4_xyz:  78.23   0.00  12.86  78.23   0.00   8.37  77.62   2.18  37.32
   4_adp:  84.38   0.00  12.56  84.38   0.00   8.25  73.79   2.15  36.02
   4_occ:  84.38   0.00  12.56  84.38   0.00   8.25  73.79   2.15  36.02
   5_bss:  84.38   0.00  12.56  84.38   0.00   8.25  73.79   2.15  36.02
   5_xyz:  84.38   0.00  12.56  84.38   0.00   8.25  73.79   2.15  36.02
   5_adp:  85.52   0.00  12.25  85.52   0.00   8.13  71.62   1.92  34.71
   5_occ:  85.52   0.00  12.25  85.52   0.00   8.13  71.62   1.92  34.71
   5_bss:  88.11   2.60  14.85  88.11   2.60  10.73  74.22   4.51  37.31
------------------------------------------------------------------------
 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:    1.199    0.019    0.403
   1_adp:    1.199    0.019    0.403
   1_occ:    1.199    0.019    0.403
   2_bss:    1.199    0.019    0.403
   2_xyz:    1.462    0.019    0.542
   2_adp:    1.462    0.019    0.542
   2_occ:    1.462    0.019    0.542
   3_bss:    1.462    0.019    0.542
   3_xyz:    1.464    0.011    0.604
   3_adp:    1.464    0.011    0.604
   3_occ:    1.464    0.011    0.604
   4_bss:    1.464    0.011    0.604
   4_xyz:    1.649    0.046    0.627
   4_adp:    1.649    0.046    0.627
   4_occ:    1.649    0.046    0.627
   5_bss:    1.649    0.046    0.627
   5_xyz:    1.733    0.046    0.638
   5_adp:    1.733    0.046    0.638
   5_occ:    1.733    0.046    0.638
   5_bss:    1.733    0.046    0.638
------------------------------------------------------------------------

CPU time actual refinement: 338.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_771/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/trial/run_771/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_771/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_771/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_771/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.14 
  Macro-tasks:
    bulk solvent and scale       = 42.42  
    individual site refinement   = 142.65 
    weights calculation          = 32.30  
    collect and process          = 6.66   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 224.12 
  Micro-tasks:
    mask                            = 1.68   
    f_calc                          = 104.72 
    alpha_beta                      = 8.43   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 111.72 
    fmodel                         = 7.62   
    r_factors                      = 0.17   
    phase_errors                   = 11.51  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 247.34 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.684 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    662 calls, 104.21 s
gradients_fft:          608 calls,  99.50 s

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

# Date 2008-01-16 Time 02:23:03 PST -0800 (1200478983.26 s)
Start R-work = 0.4555, R-free = 0.4481 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1748 (no bulk solvent and anisotropic scale)

Start R-work = 0.4463, R-free = 0.4368
Final R-work = 0.1121, R-free = 0.1578