# Date 2008-01-16 Time 01:22:37 PST -0800 (1200475357.71 s)
#phil __OFF__

Command line arguments: "../404.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21933
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 404

-------------------------------------------------------------------------------
  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: (69.5475, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.98041
Completeness in resolution range: 0.961471
Completeness with d_max=infinity: 0.958507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9804

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.98041
Completeness in resolution range: 0.961471
Completeness with d_max=infinity: 0.958507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.2373 [2143/2167]  1924   219  10.2%
  bin  2:  4.2373 -  3.3760 [2050/2070]  1848   202   9.9%
  bin  3:  3.3760 -  2.9530 [2032/2051]  1834   198   9.7%
  bin  4:  2.9530 -  2.6847 [1994/2024]  1789   205  10.3%
  bin  5:  2.6847 -  2.4932 [2003/2022]  1802   201  10.0%
  bin  6:  2.4932 -  2.3468 [1997/2022]  1796   201  10.1%
  bin  7:  2.3468 -  2.2297 [1982/2010]  1785   197   9.9%
  bin  8:  2.2297 -  2.1329 [1955/1991]  1760   195  10.0%
  bin  9:  2.1329 -  2.0510 [1960/2002]  1766   194   9.9%
  bin 10:  2.0510 -  1.9804 [1473/2015]  1326   147  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_404/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 10
        2.19 -     2.87: 1200
        2.87 -     3.54: 4458
        3.54 -     4.22: 9243
        4.22 -     4.90: 13515
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.510 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.888 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.942 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.957 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28421 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_404/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_404/model_refine_001.geo

CPU time processing inputs: 9.75


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  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: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4650   r_free= 0.4489   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.263870                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.7259 0.99   1394  152 0.3826 0.3630      6.5669      6.5073|
|  2:  4.7259 -  3.7709 0.99   1329  154 0.3618 0.3679      6.7061      6.7604|
|  3:  3.7709 -  3.3001 0.99   1307  143 0.4107 0.3730      6.6314      6.5977|
|  4:  3.3001 -  3.0010 0.99   1304  140 0.4547 0.4482      6.5164      6.4821|
|  5:  3.0010 -  2.7874 0.99   1292  147 0.4896 0.4510      6.3572      6.3508|
|  6:  2.7874 -  2.6240 0.99   1300  145 0.4887 0.5277      6.2664      6.2207|
|  7:  2.6240 -  2.4932 0.99   1271  144 0.5019 0.4997      6.2313      6.1717|
|  8:  2.4932 -  2.3852 0.98   1270  136 0.5162 0.4744      6.1856      6.1966|
|  9:  2.3852 -  2.2937 0.98   1282  148 0.5097 0.5275      6.1041      6.1672|
| 10:  2.2937 -  2.2148 1.00   1275  139 0.5425 0.4566      6.1313      6.0419|
| 11:  2.2148 -  2.1457 0.97   1267  134 0.5173 0.4937      6.0423      6.0548|
| 12:  2.1457 -  2.0846 0.98   1247  145 0.5219 0.4870      5.9724      6.0034|
| 13:  2.0846 -  2.0298 1.00   1271  138 0.5150 0.4794      5.8926      5.8246|
| 14:  2.0298 -  1.9804 0.63    821   94 0.5390 0.5265      5.8828      5.7665|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.7259  1394   152  0.72  32.70   0.80     0.75      65210.22|
|  2:  4.7259 -  3.7709  1329   154  0.74  31.71   0.89     0.81      89548.37|
|  3:  3.7709 -  3.3001  1307   143  0.66  38.96   0.86     0.76      95993.97|
|  4:  3.3001 -  3.0010  1304   140  0.57  46.50   0.80     0.65      87408.12|
|  5:  3.0010 -  2.7874  1292   147  0.46  55.03   0.76     0.54      75874.15|
|  6:  2.7874 -  2.6240  1300   145  0.42  58.11   0.73     0.48      69108.29|
|  7:  2.6240 -  2.4932  1271   144  0.39  60.59   0.75     0.46      64546.57|
|  8:  2.4932 -  2.3852  1270   136  0.40  59.96   0.72     0.46      56749.77|
|  9:  2.3852 -  2.2937  1282   148  0.41  58.79   0.74     0.49      50347.35|
| 10:  2.2937 -  2.2148  1275   139  0.42  58.20   0.74     0.50      44020.20|
| 11:  2.2148 -  2.1457  1267   134  0.41  59.07   0.76     0.51      42935.04|
| 12:  2.1457 -  2.0846  1247   145  0.39  60.56   0.77     0.49      39108.20|
| 13:  2.0846 -  2.0298  1271   138  0.38  61.53   0.74     0.46      34572.10|
| 14:  2.0298 -  1.9804   821    94  0.40  60.05   0.73     0.43      28193.48|
|alpha:            min =        0.43 max =            0.81 mean =         0.56|
|beta:             min =    28193.48 max =        95993.97 mean =     61387.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.55|
|phase err.(test): min =        0.00 max =           89.70 mean =        52.84|
|-----------------------------------------------------------------------------|

============================== 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 = 10.606203             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.296   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.931640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.401   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      182 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1513 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2642 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3927 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5111 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6613 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7675 |
|-----------------------------------------------------------------------------|
|-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 |       53.647 |
| 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 |       1.904 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    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 = 11.778)------------------------------------------|
|    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: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4729   r_free= 0.4519   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.267368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4563   r_free= 0.4374   ksol= 0.35   Bsol= 18.34   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.09,8.73,10.28,0.00,0.00,0.00); trace/3= 8.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.257280                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.645772              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.873   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.864300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.514   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4563      final r-factor (work) = 0.3633          |
| start r-factor (free) = 0.4374      final r-factor (free) = 0.3801          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.7322 = 8.65 * 0.50 * 6.2655 + 1.00 * 53.6471                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7071 = 8.65 * 0.50 * 6.1482 + 1.00 * 0.1293                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3633      final r-factor (work) = 0.3126          |
| start r-factor (free) = 0.3801      final r-factor (free) = 0.3630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3282 = 0.86 * 1.00 * 6.1482 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2223 = 0.86 * 1.00 * 6.0251 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.00   12.41    None  None   None       |
|    all(noH): 2823   0      0.00    69.00   12.41    None  None   None       |
|    Sol.    : 438    0      0.00    69.00   27.15    None  None   None       |
|    Mac.    : 2385   0      0.00    59.96   9.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.900: 1117   |   5:    34.500 -  41.400:   83        |
|      1:     6.900 -  13.800:  771   |   6:    41.400 -  48.300:   43        |
|      2:    13.800 -  20.700:  438   |   7:    48.300 -  55.200:   33        |
|      3:    20.700 -  27.600:  199   |   8:    55.200 -  62.100:   14        |
|      4:    27.600 -  34.500:  123   |   9:    62.100 -  69.000:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3126 r_free = 0.3630             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3122 r_free = 0.3635             target_work(ml) = 6.000         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3122   r_free= 0.3635   ksol= 0.35   Bsol= 18.34   scale= 1.114   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.09,8.73,10.28,0.00,0.00,0.00); trace/3= 8.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.999972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3078   r_free= 0.3581   ksol= 0.31   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,4.57,6.63,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.999891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.908957              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.482   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.395700              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.445  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3078      final r-factor (work) = 0.2185          |
| start r-factor (free) = 0.3581      final r-factor (free) = 0.2681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9024 = 3.91 * 0.50 * 6.0237 + 1.00 * 0.1293                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5046 = 3.91 * 0.50 * 5.8509 + 1.00 * 0.0692                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2185      final r-factor (work) = 0.1992          |
| start r-factor (free) = 0.2681      final r-factor (free) = 0.2527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3300 = 0.40 * 1.00 * 5.8509 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2494 = 0.40 * 1.00 * 5.6563 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.32   12.26    None  None   None       |
|    all(noH): 2823   0      0.00    72.32   12.26    None  None   None       |
|    Sol.    : 438    0      0.00    72.32   31.07    None  None   None       |
|    Mac.    : 2385   0      0.00    61.20   8.80     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 -   7.232: 1307   |   5:    36.162 -  43.395:   97        |
|      1:     7.232 -  14.465:  743   |   6:    43.395 -  50.627:   47        |
|      2:    14.465 -  21.697:  285   |   7:    50.627 -  57.859:   27        |
|      3:    21.697 -  28.930:  153   |   8:    57.859 -  65.092:    5        |
|      4:    28.930 -  36.162:  158   |   9:    65.092 -  72.324:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1992 r_free = 0.2527             target_work(ml) = 5.627         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1991 r_free = 0.2526             target_work(ml) = 5.627         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1991   r_free= 0.2526   ksol= 0.31   Bsol= 20.00   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,4.57,6.63,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.626927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1973   r_free= 0.2520   ksol= 0.33   Bsol= 43.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.78,4.47,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.627366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.982293              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.845  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 11.598464             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.339  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1973      final r-factor (work) = 0.1483          |
| start r-factor (free) = 0.2520      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5196 = 2.98 * 0.50 * 5.6672 + 1.00 * 0.0689                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2718 = 2.98 * 0.50 * 5.5050 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1483      final r-factor (work) = 0.1350          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 63.8608 = 11.60 * 1.00 * 5.5050 + 1.00 * 0.0112                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 61.7930 = 11.60 * 1.00 * 5.3263 + 1.00 * 0.0159                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.44   13.38    None  None   None       |
|    all(noH): 2823   0      0.00    85.44   13.38    None  None   None       |
|    Sol.    : 438    0      1.01    85.44   38.86    None  None   None       |
|    Mac.    : 2385   0      0.00    82.09   8.70     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 -   8.544: 1566   |   5:    42.720 -  51.264:  103        |
|      1:     8.544 -  17.088:  629   |   6:    51.264 -  59.808:   70        |
|      2:    17.088 -  25.632:  183   |   7:    59.808 -  68.352:   48        |
|      3:    25.632 -  34.176:  111   |   8:    68.352 -  76.896:   15        |
|      4:    34.176 -  42.720:   93   |   9:    76.896 -  85.440:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1350 r_free = 0.1875             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1349 r_free = 0.1873             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1349   r_free= 0.1873   ksol= 0.33   Bsol= 43.90   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.78,4.47,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.301358                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1350   r_free= 0.1872   ksol= 0.32   Bsol= 43.90   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.47,4.25,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.300162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.650177              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.909  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.979516              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.204  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1350      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1872      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4577 = 1.65 * 0.50 * 5.3263 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4021 = 1.65 * 0.50 * 5.2710 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1714          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1788 = 0.98 * 1.00 * 5.2710 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1531 = 0.98 * 1.00 * 5.2357 + 1.00 * 0.0247                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.98   13.00    None  None   None       |
|    all(noH): 2823   0      0.00    88.98   13.00    None  None   None       |
|    Sol.    : 438    0      1.06    87.74   38.06    None  None   None       |
|    Mac.    : 2385   0      0.00    88.98   8.40     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 -   8.898: 1688   |   5:    44.491 -  53.389:   90        |
|      1:     8.898 -  17.796:  562   |   6:    53.389 -  62.288:   52        |
|      2:    17.796 -  26.695:  156   |   7:    62.288 -  71.186:   43        |
|      3:    26.695 -  35.593:  117   |   8:    71.186 -  80.084:   10        |
|      4:    35.593 -  44.491:  101   |   9:    80.084 -  88.982:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1714             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1713             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1713   ksol= 0.32   Bsol= 43.90   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.47,4.25,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1712   ksol= 0.32   Bsol= 49.15   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.50,4.26,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225212                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.421701              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.907  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.813362              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.626   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1712      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3927 = 2.42 * 0.50 * 5.2357 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3537 = 2.42 * 0.50 * 5.1963 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1149      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2421 = 0.81 * 1.00 * 5.1963 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2174 = 0.81 * 1.00 * 5.1681 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.67   12.73    None  None   None       |
|    all(noH): 2823   0      0.00    90.67   12.73    None  None   None       |
|    Sol.    : 438    0      1.25    87.84   37.40    None  None   None       |
|    Mac.    : 2385   0      0.00    90.67   8.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.067: 1749   |   5:    45.334 -  54.401:   85        |
|      1:     9.067 -  18.134:  523   |   6:    54.401 -  63.468:   47        |
|      2:    18.134 -  27.201:  153   |   7:    63.468 -  72.535:   38        |
|      3:    27.201 -  36.267:  116   |   8:    72.535 -  81.602:   10        |
|      4:    36.267 -  45.334:   99   |   9:    81.602 -  90.669:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1603             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1603             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1603   ksol= 0.32   Bsol= 49.15   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.50,4.26,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162463                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.7259 0.99   1394  152 0.0999 0.1277      5.3908       5.529|
|  2:  4.7259 -  3.7709 0.99   1329  154 0.0841 0.1094      5.4283      5.6285|
|  3:  3.7709 -  3.3001 0.99   1307  143 0.1058 0.1493      5.4806      5.8431|
|  4:  3.3001 -  3.0010 0.99   1304  140 0.1231 0.1778      5.4641       5.658|
|  5:  3.0010 -  2.7874 0.99   1292  147 0.1332 0.1646       5.342      5.5398|
|  6:  2.7874 -  2.6240 0.99   1300  145 0.1224 0.2070      5.2245      5.5385|
|  7:  2.6240 -  2.4932 0.99   1271  144 0.1319 0.1665       5.209       5.352|
|  8:  2.4932 -  2.3852 0.98   1270  136 0.1211 0.1631      5.1124      5.3502|
|  9:  2.3852 -  2.2937 0.98   1282  148 0.1215 0.1956      5.0603      5.3588|
| 10:  2.2937 -  2.2148 1.00   1275  139 0.1170 0.1606      4.9856      5.1858|
| 11:  2.2148 -  2.1457 0.97   1267  134 0.1179 0.1841      4.9774      5.2893|
| 12:  2.1457 -  2.0846 0.98   1247  145 0.1209 0.1749      4.9236      5.2619|
| 13:  2.0846 -  2.0298 1.00   1271  138 0.1137 0.1742      4.8002      5.0397|
| 14:  2.0298 -  1.9804 0.63    821   94 0.0962 0.1689      4.6271      4.9004|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.7259  1394   152  0.94   9.39   0.98     0.95       7371.22|
|  2:  4.7259 -  3.7709  1329   154  0.95   7.94   1.02     1.01       9049.00|
|  3:  3.7709 -  3.3001  1307   143  0.93  11.26   1.04     1.03      10404.61|
|  4:  3.3001 -  3.0010  1304   140  0.92  13.60   1.02     1.01      10490.97|
|  5:  3.0010 -  2.7874  1292   147  0.90  15.87   1.01     0.98       8552.79|
|  6:  2.7874 -  2.6240  1300   145  0.89  16.66   0.98     0.96       7443.92|
|  7:  2.6240 -  2.4932  1271   144  0.90  16.20   0.99     0.95       6584.43|
|  8:  2.4932 -  2.3852  1270   136  0.90  15.75   0.99     0.97       5747.49|
|  9:  2.3852 -  2.2937  1282   148  0.91  15.58   1.00     0.97       5262.89|
| 10:  2.2937 -  2.2148  1275   139  0.89  16.73   1.00     0.97       4694.92|
| 11:  2.2148 -  2.1457  1267   134  0.89  16.89   1.00     0.96       4781.99|
| 12:  2.1457 -  2.0846  1247   145  0.90  16.82   1.01     1.01       4329.54|
| 13:  2.0846 -  2.0298  1271   138  0.91  15.63   1.00     0.97       3365.05|
| 14:  2.0298 -  1.9804   821    94  0.93  13.42   0.99     0.96       2374.67|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2374.67 max =        10490.97 mean =      6602.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1602   ksol= 0.32   Bsol= 52.17   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.48,1.31,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162470                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1602   ksol= 0.32   Bsol= 52.17   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.48,1.31,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162470                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.7259 0.99   1394  152 0.1000 0.1278      5.3909      5.5294|
|  2:  4.7259 -  3.7709 0.99   1329  154 0.0841 0.1094      5.4287      5.6287|
|  3:  3.7709 -  3.3001 0.99   1307  143 0.1058 0.1493      5.4808      5.8433|
|  4:  3.3001 -  3.0010 0.99   1304  140 0.1231 0.1778      5.4641       5.658|
|  5:  3.0010 -  2.7874 0.99   1292  147 0.1332 0.1646      5.3419      5.5396|
|  6:  2.7874 -  2.6240 0.99   1300  145 0.1224 0.2070      5.2244      5.5383|
|  7:  2.6240 -  2.4932 0.99   1271  144 0.1319 0.1666       5.209      5.3522|
|  8:  2.4932 -  2.3852 0.98   1270  136 0.1211 0.1631      5.1124      5.3501|
|  9:  2.3852 -  2.2937 0.98   1282  148 0.1215 0.1955      5.0603      5.3586|
| 10:  2.2937 -  2.2148 1.00   1275  139 0.1170 0.1607      4.9855      5.1863|
| 11:  2.2148 -  2.1457 0.97   1267  134 0.1179 0.1840      4.9774      5.2891|
| 12:  2.1457 -  2.0846 0.98   1247  145 0.1209 0.1749      4.9235      5.2617|
| 13:  2.0846 -  2.0298 1.00   1271  138 0.1137 0.1741         4.8      5.0395|
| 14:  2.0298 -  1.9804 0.63    821   94 0.0962 0.1687      4.6269      4.8999|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.7259  1394   152  0.94   9.40   0.98     0.95       7376.15|
|  2:  4.7259 -  3.7709  1329   154  0.95   7.95   1.02     1.01       9055.55|
|  3:  3.7709 -  3.3001  1307   143  0.93  11.26   1.04     1.03      10410.20|
|  4:  3.3001 -  3.0010  1304   140  0.92  13.60   1.02     1.01      10490.75|
|  5:  3.0010 -  2.7874  1292   147  0.90  15.87   1.01     0.98       8550.36|
|  6:  2.7874 -  2.6240  1300   145  0.89  16.66   0.99     0.96       7442.37|
|  7:  2.6240 -  2.4932  1271   144  0.90  16.20   0.99     0.96       6584.69|
|  8:  2.4932 -  2.3852  1270   136  0.90  15.75   1.00     0.98       5747.51|
|  9:  2.3852 -  2.2937  1282   148  0.91  15.59   1.01     0.97       5263.37|
| 10:  2.2937 -  2.2148  1275   139  0.89  16.74   1.01     0.97       4695.08|
| 11:  2.2148 -  2.1457  1267   134  0.89  16.89   1.00     0.96       4782.26|
| 12:  2.1457 -  2.0846  1247   145  0.90  16.82   1.01     1.01       4329.41|
| 13:  2.0846 -  2.0298  1271   138  0.91  15.62   1.00     0.98       3363.06|
| 14:  2.0298 -  1.9804   821    94  0.93  13.41   0.99     0.96       2371.94|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2371.94 max =        10490.75 mean =      6602.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.81 mean =        14.38|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.778)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.02    93.69   15.75    None  None   None       |
|    all(noH): 2823   0      3.02    93.69   15.75    None  None   None       |
|    Sol.    : 438    0      4.28    90.86   40.42    None  None   None       |
|    Mac.    : 2385   0      3.02    93.69   11.22    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:     3.025 -  12.091: 1749   |   5:    48.359 -  57.426:   85        |
|      1:    12.091 -  21.158:  523   |   6:    57.426 -  66.492:   47        |
|      2:    21.158 -  30.225:  153   |   7:    66.492 -  75.559:   38        |
|      3:    30.225 -  39.292:  116   |   8:    75.559 -  84.626:   10        |
|      4:    39.292 -  48.359:   99   |   9:    84.626 -  93.693:    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)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.219 - 4.836
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 304
   mapped sites are within: 0.716 - 4.836

peak=   10.947 closest distance to " CB  VAL A 230 " =    1.455
peak=    9.915 closest distance to " CB  VAL A 296 " =    1.569
peak=    6.295 closest distance to " CD2 LEU A   5 " =    1.192
peak=    6.021 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.711 closest distance to " O   HOH Z 130 " =    1.097
peak=    5.661 closest distance to " O   HOH Z   9 " =    1.833
peak=    5.645 closest distance to " CG  LEU A   5 " =    1.171
peak=    5.604 closest distance to " CG  PRO A  54 " =    1.357
peak=    5.398 closest distance to " O   HOH Z 142 " =    1.994
peak=    5.327 closest distance to " NH2 ARG A  56 " =    2.053
peak=    5.258 closest distance to " CG  LEU A 228 " =    1.189
peak=    4.984 closest distance to " CB  GLN A 223 " =    1.503
peak=    4.976 closest distance to " O   HOH Z 427 " =    2.827
peak=    4.831 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.789 closest distance to " CB  GLN A 183 " =    1.233
peak=    4.671 closest distance to " CB  ARG A 275 " =    0.990
peak=    4.587 closest distance to " CB  PRO A  54 " =    0.968
peak=    4.561 closest distance to " CB  ASN A 142 " =    1.088
peak=    4.523 closest distance to " O   HOH Z 313 " =    1.964
peak=    4.515 closest distance to " CD1AILE A 234 " =    0.917
peak=    4.477 closest distance to " CB  ASN A 148 " =    1.364
peak=    4.467 closest distance to " CB  VAL A 265 " =    1.379
peak=    4.448 closest distance to " O   SER A  87 " =    2.307
peak=    4.380 closest distance to " O   HOH Z 369 " =    2.263
peak=    4.375 closest distance to " ND2 ASN A 187 " =    1.690
peak=    4.375 closest distance to " O   HOH Z 265 " =    2.103
peak=    4.346 closest distance to " O   HOH Z 346 " =    1.548
peak=    4.293 closest distance to " CB  ARG A  79 " =    1.465
peak=    4.285 closest distance to " O   HOH Z 425 " =    1.464
peak=    4.260 closest distance to " O   HOH Z  61 " =    1.700
peak=    4.233 closest distance to " O   HOH Z 287 " =    1.955
peak=    4.231 closest distance to " CB BVAL A  41 " =    1.255
peak=    4.225 closest distance to " O   HOH Z 248 " =    1.187
peak=    4.222 closest distance to " O   HOH Z 422 " =    2.518
peak=    4.215 closest distance to " CG  PRO A 213 " =    1.193
peak=    4.210 closest distance to " CB  VAL A 230 " =    1.167
peak=    4.206 closest distance to " O   HOH Z 130 " =    2.505
peak=    4.191 closest distance to " O   HOH Z 209 " =    2.325
peak=    4.154 closest distance to " O   HOH Z 303 " =    2.127
peak=    4.151 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.121 closest distance to " O   HOH Z 272 " =    1.807
peak=    4.080 closest distance to " CB  ARG A 190 " =    1.484
peak=    4.073 closest distance to " O   HOH Z 403 " =    1.607
peak=    4.071 closest distance to " O   HOH Z 112 " =    1.057
peak=    4.069 closest distance to " CB  GLU A 277 " =    3.564
peak=    4.058 closest distance to " CB  VAL A 202 " =    1.714
peak=    4.051 closest distance to " O   HOH Z  78 " =    1.608
peak=    4.027 closest distance to " CG  LEU A 167 " =    1.234
peak=    4.016 closest distance to " CB  TRP A 266 " =    1.100
peak=    4.012 closest distance to " O   PRO A 198 " =    1.570
peak=    3.983 closest distance to " CG  PRO A 243 " =    1.190
peak=    3.964 closest distance to " O   HOH Z 353 " =    2.582
peak=    3.963 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.962 closest distance to " O   HOH Z 126 " =    2.147
peak=    3.956 closest distance to " O   HOH Z  43 " =    1.975
peak=    3.947 closest distance to " O   HOH Z 359 " =    1.420
peak=    3.942 closest distance to " CG AARG A 275 " =    1.139
peak=    3.936 closest distance to " CB  SER A  63 " =    1.263
peak=    3.935 closest distance to " O   HOH Z   3 " =    2.023
peak=    3.919 closest distance to " O   HOH Z 193 " =    1.618
peak=    3.913 closest distance to " O   HOH Z 411 " =    3.757
peak=    3.911 closest distance to " CB  SER A   3 " =    1.307
peak=    3.884 closest distance to " CZ  PHE A 218 " =    1.159
peak=    3.883 closest distance to " O   HOH Z 234 " =    3.624
peak=    3.860 closest distance to " CA  PHE A 283 " =    1.176
peak=    3.855 closest distance to " O  BHOH Z 338 " =    2.427
peak=    3.835 closest distance to " O   HOH Z 126 " =    1.552
peak=    3.824 closest distance to " OG ASER A 258 " =    3.017
peak=    3.816 closest distance to " CD  ARG A 269 " =    1.066
peak=    3.809 closest distance to " O   HOH Z 290 " =    1.008
peak=    3.808 closest distance to " O   HOH Z  59 " =    1.709
peak=    3.807 closest distance to " O   HOH Z 214 " =    2.412
peak=    3.807 closest distance to " O   HOH Z  40 " =    1.569
peak=    3.800 closest distance to " N   PHE A 130 " =    1.315
peak=    3.789 closest distance to " O   HOH Z  30 " =    1.534
peak=    3.789 closest distance to " O   HOH Z  97 " =    2.432
peak=    3.785 closest distance to " CB  GLN A  88 " =    1.268
peak=    3.772 closest distance to " CB  ARG A  79 " =    0.897
peak=    3.768 closest distance to " O   HOH Z  10 " =    1.676
peak=    3.757 closest distance to " CG  ARG A 138 " =    1.343
peak=    3.745 closest distance to " O   HOH Z 124 " =    1.238
peak=    3.744 closest distance to " CA  TYR A  30 " =    0.945
peak=    3.744 closest distance to " O   HOH Z 380 " =    1.760
peak=    3.741 closest distance to " O   HOH Z 251 " =    1.543
peak=    3.739 closest distance to " O   HOH Z 188 " =    2.853
peak=    3.736 closest distance to " CB  SER A  26 " =    1.725
peak=    3.732 closest distance to " CA  ALA A  51 " =    0.981
peak=    3.732 closest distance to " N   ASP A 162 " =    1.162
peak=    3.725 closest distance to " O   HOH Z 402 " =    1.352
peak=    3.724 closest distance to " ND2 ASN A 249 " =    0.867
peak=    3.721 closest distance to " O   HOH Z 258 " =    2.093
peak=    3.720 closest distance to " CG2 VAL A 257 " =    0.830
peak=    3.718 closest distance to " O   HOH Z 389 " =    1.258
peak=    3.716 closest distance to " O   HOH Z 298 " =    1.655
peak=    3.712 closest distance to " CG  MET A 185 " =    1.263
peak=    3.712 closest distance to " CB  ASN A  39 " =    0.966
peak=    3.705 closest distance to " CA  LYS A 117 " =    1.211
peak=    3.705 closest distance to " OG BSER A 164 " =    2.105
peak=    3.694 closest distance to " O   HOH Z 368 " =    2.127
peak=    3.686 closest distance to " CB  LYS A 117 " =    1.204
peak=    3.686 closest distance to " CB  ASN A 215 " =    1.151
peak=    3.672 closest distance to " CB  TYR A 169 " =    0.718
peak=    3.660 closest distance to " O   HOH Z 299 " =    4.116
peak=    3.656 closest distance to " CG2 ILE A 234 " =    0.987
peak=    3.652 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.648 closest distance to " CB  PRO A  90 " =    1.122
peak=    3.640 closest distance to " O   HOH Z 286 " =    2.462
peak=    3.630 closest distance to " O   HOH Z 371 " =    2.821
peak=    3.627 closest distance to " CD2 LEU A 228 " =    1.223
peak=    3.627 closest distance to " O   HOH Z 419 " =    2.057
peak=    3.627 closest distance to " CE  LYS A  76 " =    0.897
peak=    3.623 closest distance to " CH2 TRP A 266 " =    1.089
peak=    3.620 closest distance to " NZ  LYS A 117 " =    2.955
peak=    3.620 closest distance to " O   HOH Z  85 " =    1.253
peak=    3.615 closest distance to " O   HOH Z 143 " =    1.329
peak=    3.613 closest distance to " CG BARG A 102 " =    1.868
peak=    3.611 closest distance to " CB  TRP A 179 " =    1.406
peak=    3.598 closest distance to " O   HOH Z 406 " =    1.663
peak=    3.595 closest distance to " OE2 GLU A   2 " =    1.873
peak=    3.580 closest distance to " O   HOH Z 423 " =    1.755
peak=    3.578 closest distance to " CG  GLN A  88 " =    1.121
peak=    3.577 closest distance to " CB  GLU A 152 " =    1.188
peak=    3.576 closest distance to " CD1 ILE A  33 " =    1.747
peak=    3.573 closest distance to " O   HOH Z  44 " =    1.736
peak=    3.572 closest distance to " CB  SER A 216 " =    0.814
peak=    3.564 closest distance to " O   HOH Z 130 " =    2.183
peak=    3.559 closest distance to " CG2 ILE A  20 " =    1.565
peak=    3.559 closest distance to " O   HOH Z 366 " =    2.891
peak=    3.556 closest distance to " O   PRO A 198 " =    1.292
peak=    3.555 closest distance to " O   HOH Z  88 " =    2.755
peak=    3.554 closest distance to " CD  LYS A  76 " =    1.768
peak=    3.553 closest distance to " O   HOH Z 123 " =    0.967
peak=    3.551 closest distance to " O   HOH Z 261 " =    1.779
peak=    3.547 closest distance to " CA  SER A  87 " =    1.019
peak=    3.546 closest distance to " OD1 ASN A  69 " =    2.407
peak=    3.539 closest distance to " O   HOH Z 405 " =    1.193
peak=    3.536 closest distance to " CB  ALA A 114 " =    1.445
peak=    3.531 closest distance to " NZ  LYS A  48 " =    1.177
peak=    3.527 closest distance to " O   HOH Z 368 " =    3.439
peak=    3.525 closest distance to " N   ASN A  39 " =    1.228
peak=    3.523 closest distance to " O   HOH Z 203 " =    1.704
peak=    3.523 closest distance to " CG  GLN A  58 " =    0.882
peak=    3.520 closest distance to " NH2AARG A 145 " =    1.054
peak=    3.516 closest distance to " N   ASN A 127 " =    1.346
peak=    3.515 closest distance to " O   ASP A 124 " =    1.135
peak=    3.507 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.501 closest distance to " CA  ASN A 215 " =    1.033
peak=    3.491 closest distance to " O   HOH Z 117 " =    2.047
peak=    3.480 closest distance to " O   HOH Z 180 " =    2.088
peak=    3.479 closest distance to " CE1 TYR A 186 " =    1.286
peak=    3.479 closest distance to " O   HOH Z  80 " =    1.527
peak=    3.473 closest distance to " O   HOH Z 193 " =    1.526
peak=    3.464 closest distance to " O   HOH Z  22 " =    2.048
peak=    3.463 closest distance to " CB  ALA A   9 " =    1.561
peak=    3.460 closest distance to " CB  GLN A  89 " =    1.291
peak=    3.455 closest distance to " CA  ASN A 127 " =    1.025
peak=    3.450 closest distance to " CD  LYS A 166 " =    1.335
peak=    3.446 closest distance to " N   ALA A 256 " =    0.967
peak=    3.443 closest distance to " CB  GLU A 128 " =    1.020
peak=    3.438 closest distance to " OE2 GLU A  53 " =    2.009
peak=    3.437 closest distance to " CE3 TRP A 150 " =    0.992
peak=    3.436 closest distance to " O   ASN A  74 " =    1.548
peak=    3.434 closest distance to " CG2 ILE A 120 " =    1.264
peak=    3.432 closest distance to " CB  ASN A 187 " =    1.093
peak=    3.429 closest distance to " CB  ASP A 124 " =    0.773
peak=    3.429 closest distance to " O   HOH Z 329 " =    4.140
peak=    3.428 closest distance to " NH1AARG A 145 " =    1.174
peak=    3.425 closest distance to " CG1 ILE A 151 " =    1.122
peak=    3.419 closest distance to " CG1BVAL A  72 " =    1.604
peak=    3.417 closest distance to " CB  THR A  52 " =    0.964
peak=    3.416 closest distance to " N   SER A 135 " =    1.329
peak=    3.413 closest distance to " O   HOH Z 172 " =    3.402
peak=    3.413 closest distance to " CG1 ILE A  49 " =    1.482
peak=    3.412 closest distance to " O   HOH Z 261 " =    1.747
peak=    3.405 closest distance to " O   HOH Z   1 " =    1.710
peak=    3.403 closest distance to " NZ  LYS A 119 " =    2.729
peak=    3.400 closest distance to " O   HOH Z  40 " =    2.429
peak=    3.398 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.396 closest distance to " CA  ASN A 217 " =    1.214
peak=    3.392 closest distance to " O   HOH Z 392 " =    3.070
peak=    3.391 closest distance to " NH2AARG A 275 " =    3.500
peak=    3.391 closest distance to " O   HOH Z  59 " =    2.199
peak=    3.391 closest distance to " O   HOH Z 158 " =    3.194
peak=    3.389 closest distance to " O   HOH Z 437 " =    1.654
peak=    3.389 closest distance to " CA  LYS A 290 " =    1.206
peak=    3.386 closest distance to " CA  ARG A  36 " =    1.033
peak=    3.386 closest distance to " O   HOH Z 126 " =    1.830
peak=    3.382 closest distance to " O   HOH Z 303 " =    2.563
peak=    3.381 closest distance to " O   HOH Z  88 " =    3.129
peak=    3.379 closest distance to " O   HOH Z   2 " =    1.501
peak=    3.376 closest distance to " CA  GLY A 267 " =    0.902
peak=    3.373 closest distance to " O   HOH Z 196 " =    1.407
peak=    3.372 closest distance to " CB  SER A 212 " =    1.292
peak=    3.372 closest distance to " CA  ARG A 195 " =    1.170
peak=    3.372 closest distance to " O   HOH Z 421 " =    2.115
peak=    3.372 closest distance to " O   HOH Z 273 " =    3.023
peak=    3.371 closest distance to " NE  ARG A  56 " =    3.511
peak=    3.368 closest distance to " CB  PHE A 204 " =    1.074
peak=    3.366 closest distance to " CA  ALA A 129 " =    1.477
peak=    3.366 closest distance to " OG BSER A  99 " =    2.187
peak=    3.366 closest distance to " O   HOH Z 193 " =    1.120
peak=    3.364 closest distance to " N   GLN A 278 " =    1.444
peak=    3.362 closest distance to " O   HOH Z  68 " =    2.181
peak=    3.360 closest distance to " OG  SER A  62 " =    2.858
peak=    3.352 closest distance to " O   HOH Z 128 " =    2.081
peak=    3.346 closest distance to " O   HOH Z 327 " =    1.963
peak=    3.343 closest distance to " O   HOH Z 425 " =    2.106
peak=    3.343 closest distance to " CG  LEU A 281 " =    0.988
peak=    3.329 closest distance to " O   HOH Z 175 " =    2.040
peak=    3.326 closest distance to " O   HOH Z 305 " =    3.411
peak=    3.325 closest distance to " O   HOH Z 250 " =    1.356
peak=    3.322 closest distance to " CB  THR A  31 " =    1.581
peak=    3.320 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.318 closest distance to " C   ALA A 299 " =    0.914
peak=    3.316 closest distance to " OE1 GLU A   2 " =    1.873
peak=    3.316 closest distance to " O   HOH Z 417 " =    1.086
peak=    3.315 closest distance to " O   HOH Z 371 " =    3.326
peak=    3.311 closest distance to " CB  LEU A  83 " =    0.716
peak=    3.306 closest distance to " CB  GLU A  46 " =    0.961
peak=    3.304 closest distance to " CG  MET A 113 " =    1.063
peak=    3.303 closest distance to " O   HOH Z 193 " =    1.650
peak=    3.302 closest distance to " NH1 ARG A 138 " =    1.166
peak=    3.302 closest distance to " CB  ALA A 248 " =    1.378
peak=    3.299 closest distance to " O   HOH Z 153 " =    3.772
peak=    3.298 closest distance to " CA  ALA A 158 " =    1.349
peak=    3.297 closest distance to " CG2 VAL A 197 " =    1.122
peak=    3.296 closest distance to " O   HOH Z 322 " =    1.941
peak=    3.286 closest distance to " CG  LYS A 119 " =    1.088
peak=    3.282 closest distance to " NE2 GLN A  73 " =    1.367
peak=    3.277 closest distance to " O   HOH Z 423 " =    1.385
peak=    3.273 closest distance to " CB  THR A 157 " =    1.201
peak=    3.272 closest distance to " N   SER A 146 " =    1.773
peak=    3.269 closest distance to " CA  ILE A 234 " =    1.038
peak=    3.262 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.261 closest distance to " NE2 GLN A  77 " =    3.090
peak=    3.259 closest distance to " O   THR A 182 " =    1.436
peak=    3.255 closest distance to " CB  LEU A 300 " =    0.908
peak=    3.252 closest distance to " CG1 VAL A 153 " =    0.919
peak=    3.251 closest distance to " CB  LEU A 228 " =    1.311
peak=    3.248 closest distance to " O   HOH Z  59 " =    1.974
peak=    3.247 closest distance to " CB  GLN A 278 " =    0.951
peak=    3.245 closest distance to " O   HOH Z  92 " =    2.338
peak=    3.242 closest distance to " CA  TRP A 150 " =    0.862
peak=    3.241 closest distance to " CB  ALA A 248 " =    1.142
peak=    3.240 closest distance to " O   HOH Z  61 " =    1.523
peak=    3.239 closest distance to " CA  ASP A 162 " =    0.997
peak=    3.239 closest distance to " CD1 LEU A  96 " =    0.726
peak=    3.237 closest distance to " CB  ASP A 140 " =    1.007
peak=    3.237 closest distance to " O   HOH Z  21 " =    1.825
peak=    3.224 closest distance to " CD2 LEU A 297 " =    0.975
peak=    3.223 closest distance to " O   HOH Z 280 " =    3.012
peak=    3.221 closest distance to " O   HOH Z 233 " =    1.815
peak=    3.210 closest distance to " O   HOH Z 357 " =    2.020
peak=    3.209 closest distance to " NE2 HIS A 207 " =    1.218
peak=    3.208 closest distance to " CA  ALA A 160 " =    0.936
peak=    3.207 closest distance to " O   HOH Z 145 " =    2.074
peak=    3.205 closest distance to " CZ  PHE A  38 " =    1.129
peak=    3.204 closest distance to " O   HOH Z 325 " =    2.102
peak=    3.193 closest distance to " CD2 TYR A 186 " =    1.079
peak=    3.193 closest distance to " O   HOH Z   1 " =    1.703
peak=    3.193 closest distance to " O   GLY A  57 " =    2.529
peak=    3.190 closest distance to " O   PHE A 192 " =    1.410
peak=    3.189 closest distance to " O   HOH Z 189 " =    2.719
peak=    3.188 closest distance to " O   HOH Z   4 " =    1.454
peak=    3.185 closest distance to " O   HOH Z  65 " =    0.864
peak=    3.180 closest distance to " CB  ALA A 227 " =    1.134
peak=    3.172 closest distance to " CA  ARG A 102 " =    1.128
peak=    3.165 closest distance to " CA  LEU A 282 " =    1.165
peak=    3.164 closest distance to " N   CYS A 260 " =    0.754
peak=    3.163 closest distance to " CB  THR A 235 " =    1.280
peak=    3.162 closest distance to " O   HOH Z 130 " =    1.933
peak=    3.159 closest distance to " OG  SER A  62 " =    2.706
peak=    3.155 closest distance to " CG1 ILE A 120 " =    1.137
peak=    3.153 closest distance to " CB  SER A  62 " =    1.104
peak=    3.150 closest distance to " O   HOH Z 357 " =    2.651
peak=    3.150 closest distance to " CE  LYS A  48 " =    1.095
peak=    3.146 closest distance to " NH2BARG A 145 " =    2.077
peak=    3.138 closest distance to " CB  VAL A 268 " =    0.847
peak=    3.137 closest distance to " O   HOH Z 213 " =    2.110
peak=    3.134 closest distance to " O   HOH Z 222 " =    2.263
peak=    3.131 closest distance to " O   HOH Z  40 " =    1.483
peak=    3.128 closest distance to " CA  MET A 105 " =    0.972
peak=    3.128 closest distance to " CA  THR A 264 " =    0.888
peak=    3.127 closest distance to " CA  ALA A 233 " =    1.050
peak=    3.125 closest distance to " O   HOH Z 285 " =    2.348
peak=    3.124 closest distance to " O   HOH Z 259 " =    2.264
peak=    3.119 closest distance to " O   HOH Z  48 " =    1.630
peak=    3.112 closest distance to " CD1 LEU A 228 " =    2.005
peak=    3.112 closest distance to " CA  ASP A 191 " =    1.266
peak=    3.110 closest distance to " O   LEU A 228 " =    1.889
peak=    3.110 closest distance to " O   HOH Z 260 " =    1.590
peak=    3.105 closest distance to " CG  GLN A  55 " =    2.380
peak=    3.100 closest distance to " CB  ALA A 104 " =    0.736
peak=    3.090 closest distance to " CB  VAL A 250 " =    1.095
peak=    3.070 closest distance to " CB  ALA A   1 " =    4.836
peak=    3.069 closest distance to " O   ALA A 158 " =    1.392
peak=    3.061 closest distance to " O   HOH Z  89 " =    2.174
peak=    3.056 closest distance to " O   HOH Z 132 " =    3.712
peak=    3.052 closest distance to " CG  LYS A 289 " =    1.274
peak=    3.043 closest distance to " O   HOH Z 272 " =    2.245
peak=    3.039 closest distance to " O   HOH Z 344 " =    2.900

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.722 - 5.515
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.722 - 5.515

peak=   -4.640 closest distance to " OG BSER A 134 " =    1.265
peak=   -4.502 closest distance to " CG2 VAL A 230 " =    0.722
peak=   -4.472 closest distance to " CD  ARG A 156 " =    2.051
peak=   -4.357 closest distance to " CD  ARG A  14 " =    3.197
peak=   -4.229 closest distance to " C   HIS A 108 " =    1.212
peak=   -4.220 closest distance to " CZ2 TRP A  92 " =    2.856
peak=   -4.176 closest distance to " CG  GLN A  58 " =    1.047
peak=   -4.127 closest distance to " O   HOH Z 266 " =    5.456
peak=   -4.121 closest distance to " CB  PRO A 243 " =    2.700
peak=   -4.071 closest distance to " O   VAL A  67 " =    2.481
peak=   -4.043 closest distance to " CB  PHE A 192 " =    1.897
peak=   -4.036 closest distance to " CD  GLN A 223 " =    2.239
peak=   -3.981 closest distance to " O   HOH Z 394 " =    1.533
peak=   -3.927 closest distance to " CG2 VAL A 202 " =    2.708
peak=   -3.896 closest distance to " O   HOH Z 211 " =    1.302
peak=   -3.888 closest distance to " O   HOH Z 290 " =    1.199
peak=   -3.864 closest distance to " O   HOH Z 231 " =    2.044
peak=   -3.855 closest distance to " CB  ALA A  43 " =    2.570
peak=   -3.849 closest distance to " O   HOH Z 351 " =    1.517
peak=   -3.844 closest distance to " O   PRO A 163 " =    2.027
peak=   -3.841 closest distance to " CE BMET A  47 " =    1.149
peak=   -3.826 closest distance to " O   HOH Z 185 " =    2.236
peak=   -3.819 closest distance to " O   HOH Z 131 " =    4.127
peak=   -3.818 closest distance to " O   PRO A 198 " =    1.193
peak=   -3.765 closest distance to " N   THR A 157 " =    1.441
peak=   -3.758 closest distance to " O   HOH Z  11 " =    1.785
peak=   -3.756 closest distance to " N   ALA A  43 " =    2.555
peak=   -3.753 closest distance to " CD1 LEU A 255 " =    2.763
peak=   -3.743 closest distance to " O   HOH Z 193 " =    1.315
peak=   -3.721 closest distance to " O   HOH Z 429 " =    1.984
peak=   -3.719 closest distance to " CA  ASN A 127 " =    1.184
peak=   -3.697 closest distance to " CA  VAL A  67 " =    2.959
peak=   -3.677 closest distance to " CB  ALA A 161 " =    2.482
peak=   -3.675 closest distance to " CE2 PHE A 218 " =    2.568
peak=   -3.670 closest distance to " OG  SER A  62 " =    4.328
peak=   -3.653 closest distance to " O   HOH Z 100 " =    1.093
peak=   -3.643 closest distance to " CE2 TYR A  30 " =    2.676
peak=   -3.640 closest distance to " O   HOH Z 359 " =    3.093
peak=   -3.637 closest distance to " CB  ALA A 114 " =    2.456
peak=   -3.631 closest distance to " NH2 ARG A  79 " =    2.051
peak=   -3.616 closest distance to " O   HOH Z 286 " =    1.671
peak=   -3.615 closest distance to " CG1 VAL A 112 " =    2.860
peak=   -3.615 closest distance to " ND2 ASN A 249 " =    2.369
peak=   -3.609 closest distance to " CE1 PHE A  59 " =    1.973
peak=   -3.599 closest distance to " O   HOH Z  44 " =    2.323
peak=   -3.599 closest distance to " N   ALA A 226 " =    2.002
peak=   -3.592 closest distance to " CG2 VAL A 296 " =    1.982
peak=   -3.588 closest distance to " CD1 LEU A 101 " =    2.270
peak=   -3.588 closest distance to " OH  TYR A 172 " =    1.798
peak=   -3.574 closest distance to " O   HOH Z 114 " =    3.022
peak=   -3.570 closest distance to " OG  SER A  97 " =    2.230
peak=   -3.566 closest distance to " OG  SER A  87 " =    1.359
peak=   -3.563 closest distance to " CE  MET A 105 " =    2.401
peak=   -3.555 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.552 closest distance to " CD1 ILE A 199 " =    2.438
peak=   -3.548 closest distance to " O   HOH Z 166 " =    2.046
peak=   -3.542 closest distance to " CD  PRO A 213 " =    2.030
peak=   -3.538 closest distance to " O   HOH Z 191 " =    5.515
peak=   -3.531 closest distance to " O   HOH Z 357 " =    2.064
peak=   -3.530 closest distance to " CA  GLY A 241 " =    2.378
peak=   -3.526 closest distance to " NE2 GLN A  11 " =    1.884
peak=   -3.525 closest distance to " CG  TRP A 266 " =    1.926
peak=   -3.523 closest distance to " N   THR A  52 " =    1.731
peak=   -3.515 closest distance to " O   HOH Z 243 " =    1.995
peak=   -3.504 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.499 closest distance to " CA  GLY A 133 " =    1.940
peak=   -3.498 closest distance to " O   HOH Z  73 " =    2.399
peak=   -3.491 closest distance to " CD2 TYR A 293 " =    1.940
peak=   -3.483 closest distance to " O   SER A  22 " =    2.331
peak=   -3.480 closest distance to " ND2 ASN A 187 " =    1.518
peak=   -3.478 closest distance to " OD2 ASP A 171 " =    2.228
peak=   -3.469 closest distance to " C   MET A 188 " =    1.453
peak=   -3.463 closest distance to " CD2 LEU A   5 " =    1.123
peak=   -3.458 closest distance to " CZ2 TRP A 274 " =    0.957
peak=   -3.457 closest distance to " CG  LEU A   5 " =    0.963
peak=   -3.446 closest distance to " ND2 ASN A 252 " =    1.857
peak=   -3.445 closest distance to " OXT GLY A 302 " =    2.967
peak=   -3.444 closest distance to " CD2 HIS A 207 " =    2.282
peak=   -3.442 closest distance to " CB  PRO A 280 " =    2.150
peak=   -3.436 closest distance to " ND2 ASN A  45 " =    2.026
peak=   -3.431 closest distance to " N   ALA A 248 " =    1.634
peak=   -3.429 closest distance to " O   HOH Z  43 " =    1.890
peak=   -3.428 closest distance to " CD2 LEU A 237 " =    2.682
peak=   -3.422 closest distance to " O   HOH Z 102 " =    1.608
peak=   -3.420 closest distance to " CD2 TYR A 247 " =    2.478
peak=   -3.419 closest distance to " O   HOH Z 389 " =    2.214
peak=   -3.418 closest distance to " O   HOH Z 421 " =    3.097
peak=   -3.417 closest distance to " O   HOH Z 295 " =    1.641
peak=   -3.415 closest distance to " O   HOH Z 352 " =    1.462
peak=   -3.412 closest distance to " O   PHE A 218 " =    1.480
peak=   -3.411 closest distance to " ND2 ASN A  45 " =    1.236
peak=   -3.394 closest distance to " CA  GLY A 203 " =    2.476
peak=   -3.391 closest distance to " O   HOH Z 281 " =    2.822
peak=   -3.390 closest distance to " OD2 ASP A 191 " =    1.303
peak=   -3.384 closest distance to " O   HOH Z 165 " =    2.082
peak=   -3.381 closest distance to " OD1 ASN A  39 " =    2.163
peak=   -3.380 closest distance to " O   HOH Z  52 " =    1.325
peak=   -3.376 closest distance to " CB  PRO A 163 " =    2.398
peak=   -3.372 closest distance to " O   HOH Z 389 " =    1.430
peak=   -3.369 closest distance to " OD1 ASN A 187 " =    1.695
peak=   -3.364 closest distance to " O   HOH Z 103 " =    1.786
peak=   -3.364 closest distance to " CD  LYS A 289 " =    2.344
peak=   -3.361 closest distance to " O   HOH Z 134 " =    4.039
peak=   -3.349 closest distance to " OE2 GLU A 152 " =    1.300
peak=   -3.344 closest distance to " CG1 VAL A 250 " =    2.681
peak=   -3.343 closest distance to " O   HOH Z 166 " =    2.053
peak=   -3.341 closest distance to " O   ALA A  10 " =    1.813
peak=   -3.338 closest distance to " CE3 TRP A 150 " =    2.093
peak=   -3.336 closest distance to " CB  PRO A 213 " =    2.228
peak=   -3.329 closest distance to " O   HOH Z  65 " =    1.370
peak=   -3.328 closest distance to " O   HOH Z 140 " =    1.687
peak=   -3.319 closest distance to " CE2 TRP A  70 " =    2.175
peak=   -3.319 closest distance to " O   HOH Z 236 " =    1.388
peak=   -3.308 closest distance to " O   HOH Z 313 " =    1.594
peak=   -3.307 closest distance to " CG  MET A 105 " =    0.933
peak=   -3.307 closest distance to " CA  GLY A  35 " =    2.100
peak=   -3.304 closest distance to " CD2 PHE A 225 " =    1.137
peak=   -3.299 closest distance to " O   HOH Z 139 " =    3.076
peak=   -3.297 closest distance to " OG  SER A  63 " =    1.207
peak=   -3.294 closest distance to " C   GLN A 205 " =    1.841
peak=   -3.291 closest distance to " O   HOH Z 350 " =    1.732
peak=   -3.291 closest distance to " CB  ALA A 291 " =    2.209
peak=   -3.288 closest distance to " NE2 GLN A 278 " =    1.697
peak=   -3.287 closest distance to " N   GLN A  58 " =    2.111
peak=   -3.280 closest distance to " CZ  ARG A 259 " =    0.995
peak=   -3.279 closest distance to " CB  SER A 210 " =    1.135
peak=   -3.276 closest distance to " CB  ALA A  10 " =    2.328
peak=   -3.273 closest distance to " O   HOH Z 318 " =    2.124
peak=   -3.273 closest distance to " N   SER A 276 " =    1.375
peak=   -3.272 closest distance to " O   HOH Z 345 " =    2.054
peak=   -3.271 closest distance to " O   HOH Z  51 " =    1.162
peak=   -3.269 closest distance to " O   HOH Z 238 " =    1.063
peak=   -3.267 closest distance to " O   MET A  40 " =    2.811
peak=   -3.265 closest distance to " O   HOH Z  90 " =    2.578
peak=   -3.264 closest distance to " O   VAL A 189 " =    2.578
peak=   -3.263 closest distance to " O   SER A 210 " =    1.806
peak=   -3.263 closest distance to " CZ3 TRP A 179 " =    1.276
peak=   -3.261 closest distance to " O   HOH Z 384 " =    2.227
peak=   -3.254 closest distance to " CA  GLY A  98 " =    1.829
peak=   -3.250 closest distance to " O   SER A 271 " =    2.056
peak=   -3.249 closest distance to " O   HOH Z 198 " =    1.783
peak=   -3.243 closest distance to " OE1 GLN A 183 " =    1.532
peak=   -3.243 closest distance to " CZ  TYR A 169 " =    1.790
peak=   -3.242 closest distance to " O   ASP A  27 " =    1.937
peak=   -3.238 closest distance to " CE  LYS A  76 " =    2.702
peak=   -3.232 closest distance to " CG1 VAL A 125 " =    1.988
peak=   -3.224 closest distance to " NH2AARG A 275 " =    5.056
peak=   -3.217 closest distance to " O   HOH Z 111 " =    1.967
peak=   -3.217 closest distance to " O   HOH Z 407 " =    2.907
peak=   -3.215 closest distance to " O   HOH Z 285 " =    2.149
peak=   -3.215 closest distance to " O   HOH Z 371 " =    2.220
peak=   -3.210 closest distance to " O   ARG A 145 " =    1.518
peak=   -3.208 closest distance to " CB  ASP A 132 " =    2.410
peak=   -3.202 closest distance to " NE2 GLN A 278 " =    1.773
peak=   -3.199 closest distance to " O   SER A 276 " =    1.584
peak=   -3.197 closest distance to " O   HOH Z 359 " =    1.570
peak=   -3.196 closest distance to " CB  ASP A 231 " =    2.396
peak=   -3.196 closest distance to " O   HOH Z 346 " =    1.752
peak=   -3.194 closest distance to " OE1 GLN A  88 " =    1.047
peak=   -3.194 closest distance to " O   HOH Z 411 " =    1.412
peak=   -3.193 closest distance to " O   HOH Z 149 " =    2.198
peak=   -3.189 closest distance to " O   HOH Z 231 " =    1.450
peak=   -3.187 closest distance to " O   HOH Z  11 " =    2.184
peak=   -3.186 closest distance to " CB  GLN A  55 " =    1.259
peak=   -3.181 closest distance to " O   TRP A  70 " =    1.488
peak=   -3.179 closest distance to " CG2 ILE A 151 " =    2.486
peak=   -3.176 closest distance to " O   HOH Z 166 " =    1.554
peak=   -3.174 closest distance to " N   HIS A 115 " =    2.178
peak=   -3.172 closest distance to " O   HOH Z 111 " =    4.386
peak=   -3.172 closest distance to " O   HOH Z 377 " =    1.000
peak=   -3.168 closest distance to " O   PRO A 198 " =    1.336
peak=   -3.168 closest distance to " C   ASN A 285 " =    2.256
peak=   -3.163 closest distance to " O   SER A 135 " =    1.430
peak=   -3.160 closest distance to " O   HOH Z 423 " =    2.251
peak=   -3.142 closest distance to " CG1 VAL A 197 " =    2.333
peak=   -3.141 closest distance to " O   GLN A 240 " =    2.479
peak=   -3.136 closest distance to " O   GLY A  80 " =    2.520
peak=   -3.136 closest distance to " NE2 GLN A  88 " =    2.046
peak=   -3.133 closest distance to " CB  ASN A  39 " =    2.234
peak=   -3.133 closest distance to " CB  ALA A 291 " =    2.237
peak=   -3.131 closest distance to " O   GLN A 240 " =    2.105
peak=   -3.131 closest distance to " O   HOH Z 250 " =    1.668
peak=   -3.130 closest distance to " NH2 ARG A 219 " =    1.684
peak=   -3.129 closest distance to " CE1 HIS A  81 " =    1.652
peak=   -3.129 closest distance to " C   LEU A 222 " =    0.910
peak=   -3.126 closest distance to " OD1 ASN A 301 " =    1.987
peak=   -3.122 closest distance to " CB  ALA A  64 " =    2.753
peak=   -3.108 closest distance to " CG  PHE A 283 " =    2.637
peak=   -3.108 closest distance to " CA  GLY A  57 " =    2.164
peak=   -3.105 closest distance to " O   HOH Z   9 " =    3.031
peak=   -3.103 closest distance to " CG  GLN A  88 " =    0.874
peak=   -3.097 closest distance to " O   HOH Z 124 " =    3.711
peak=   -3.091 closest distance to " O   HOH Z 252 " =    3.975
peak=   -3.091 closest distance to " O   HOH Z 216 " =    1.419
peak=   -3.079 closest distance to " OG  SER A 245 " =    1.407
peak=   -3.075 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.072 closest distance to " O   GLY A  75 " =    1.839
peak=   -3.068 closest distance to " O   HOH Z 412 " =    4.093
peak=   -3.066 closest distance to " O   HOH Z 134 " =    3.585
peak=   -3.062 closest distance to " O   HOH Z 410 " =    2.204
peak=   -3.040 closest distance to " O   HOH Z  89 " =    2.804
peak=   -3.029 closest distance to " O   HOH Z 244 " =    2.017
peak=   -3.010 closest distance to " CD2 PHE A  61 " =    2.032

================= 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    :  0.4650 0.4489   6.263870e+00   6.242198e+00
   1_bss:  0.4563 0.4374   6.257280e+00   6.230297e+00
   1_xyz:  0.3633 0.3801   6.111772e+00   6.134047e+00
   1_adp:  0.3126 0.3630   6.001047e+00   6.092274e+00
   1_occ:  0.3122 0.3635   5.999972e+00   6.093868e+00
   2_bss:  0.3078 0.3581   5.999891e+00   6.091860e+00
   2_xyz:  0.2185 0.2681   5.703809e+00   5.865020e+00
   2_adp:  0.1992 0.2527   5.626846e+00   5.802918e+00
   2_occ:  0.1991 0.2526   5.626927e+00   5.803794e+00
   3_bss:  0.1973 0.2520   5.627366e+00   5.803077e+00
   3_xyz:  0.1483 0.1956   5.371577e+00   5.583575e+00
   3_adp:  0.1350 0.1875   5.301960e+00   5.534403e+00
   3_occ:  0.1349 0.1873   5.301358e+00   5.533751e+00
   4_bss:  0.1350 0.1872   5.300162e+00   5.531347e+00
   4_xyz:  0.1250 0.1754   5.241981e+00   5.478760e+00
   4_adp:  0.1230 0.1714   5.225740e+00   5.459288e+00
   4_occ:  0.1228 0.1713   5.225284e+00   5.458997e+00
   5_bss:  0.1228 0.1712   5.225212e+00   5.458996e+00
   5_xyz:  0.1149 0.1620   5.171474e+00   5.417567e+00
   5_adp:  0.1139 0.1603   5.162633e+00   5.407144e+00
   5_occ:  0.1139 0.1603   5.162463e+00   5.407046e+00
   5_bss:  0.1139 0.1602   5.162470e+00   5.407049e+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:  0.354  18.342   7.088   8.728  10.281   0.000   0.000   0.000
   1_xyz:  0.354  18.342   7.088   8.728  10.281   0.000   0.000   0.000
   1_adp:  0.354  18.342   7.088   8.728  10.281   0.000   0.000   0.000
   1_occ:  0.354  18.342   7.088   8.728  10.281   0.000   0.000   0.000
   2_bss:  0.314  20.000   3.658   4.574   6.629   0.000   0.000   0.000
   2_xyz:  0.314  20.000   3.658   4.574   6.629   0.000   0.000   0.000
   2_adp:  0.314  20.000   3.658   4.574   6.629   0.000   0.000   0.000
   2_occ:  0.314  20.000   3.658   4.574   6.629   0.000   0.000   0.000
   3_bss:  0.330  43.896   2.150   2.778   4.473   0.000   0.000   0.000
   3_xyz:  0.330  43.896   2.150   2.778   4.473   0.000   0.000   0.000
   3_adp:  0.330  43.896   2.150   2.778   4.473   0.000   0.000   0.000
   3_occ:  0.330  43.896   2.150   2.778   4.473   0.000   0.000   0.000
   4_bss:  0.315  43.896   1.991   2.467   4.250   0.000   0.000   0.000
   4_xyz:  0.315  43.896   1.991   2.467   4.250   0.000   0.000   0.000
   4_adp:  0.315  43.896   1.991   2.467   4.250   0.000   0.000   0.000
   4_occ:  0.315  43.896   1.991   2.467   4.250   0.000   0.000   0.000
   5_bss:  0.324  49.147   2.109   2.497   4.260   0.000   0.000   0.000
   5_xyz:  0.324  49.147   2.109   2.497   4.260   0.000   0.000   0.000
   5_adp:  0.324  49.147   2.109   2.497   4.260   0.000   0.000   0.000
   5_occ:  0.324  49.147   2.109   2.497   4.260   0.000   0.000   0.000
   5_bss:  0.323  52.172  -0.828  -0.478   1.306  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.581 0.4890  0.5615    61388.165
   1_bss:  52.211 0.4920  0.7320    58673.048
   1_xyz:  41.695 0.6213  0.8942    39681.903
   1_adp:  38.212 0.6632  0.9838    34712.959
   1_occ:  38.314 0.6618  0.9798    34788.747
   2_bss:  38.038 0.6649  0.8602    34363.521
   2_xyz:  26.692 0.7933  0.9926    18224.784
   2_adp:  24.243 0.8196  1.0096    15748.865
   2_occ:  24.285 0.8191  1.0090    15764.714
   3_bss:  24.230 0.8198  0.9465    15762.751
   3_xyz:  18.273 0.8781  0.9858     9582.953
   3_adp:  17.133 0.8885  0.9821     8697.179
   3_occ:  17.116 0.8887  0.9822     8685.496
   4_bss:  17.061 0.8891  0.9739     8627.373
   4_xyz:  15.913 0.8991  0.9790     7667.301
   4_adp:  15.433 0.9035  0.9748     7387.634
   4_occ:  15.427 0.9035  0.9748     7381.046
   5_bss:  15.423 0.9035  0.9770     7383.888
   5_xyz:  14.570 0.9105  0.9814     6735.739
   5_adp:  14.323 0.9127  0.9780     6606.766
   5_occ:  14.322 0.9126  0.9780     6601.567
   5_bss:  14.322 0.9126  0.9805     6602.363
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3647e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3647e+01
   1_xyz:   1.624  0.012  0.104 18.026  0.006  4.108   1.2930e-01
   1_adp:   1.624  0.012  0.104 18.026  0.006  4.108   1.2930e-01
   1_occ:   1.624  0.012  0.104 18.026  0.006  4.108   1.2930e-01
   2_bss:   1.624  0.012  0.104 18.026  0.006  4.108   1.2930e-01
   2_xyz:   1.071  0.007  0.077 15.933  0.004  4.121   6.9160e-02
   2_adp:   1.071  0.007  0.077 15.933  0.004  4.121   6.9160e-02
   2_occ:   1.071  0.007  0.077 15.933  0.004  4.121   6.9160e-02
   3_bss:   1.071  0.007  0.077 15.933  0.004  4.121   6.9160e-02
   3_xyz:   1.019  0.007  0.078 15.828  0.003  4.124   6.2979e-02
   3_adp:   1.019  0.007  0.078 15.828  0.003  4.124   6.2979e-02
   3_occ:   1.019  0.007  0.078 15.828  0.003  4.124   6.2979e-02
   4_bss:   1.019  0.007  0.078 15.828  0.003  4.124   6.2979e-02
   4_xyz:   0.906  0.005  0.070 15.605  0.003  4.126   5.3100e-02
   4_adp:   0.906  0.005  0.070 15.605  0.003  4.126   5.3100e-02
   4_occ:   0.906  0.005  0.070 15.605  0.003  4.126   5.3100e-02
   5_bss:   0.906  0.005  0.070 15.605  0.003  4.126   5.3100e-02
   5_xyz:   1.004  0.007  0.077 15.485  0.004  4.110   6.1799e-02
   5_adp:   1.004  0.007  0.077 15.485  0.004  4.110   6.1799e-02
   5_occ:   1.004  0.007  0.077 15.485  0.004  4.110   6.1799e-02
   5_bss:   1.004  0.007  0.077 15.485  0.004  4.110   6.1799e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9540e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9540e+00
   1_xyz:  13.096  0.159  0.393 85.968  0.033  2.162   9.3383e-02
   1_adp:  13.096  0.159  0.393 85.968  0.033  2.162   9.3383e-02
   1_occ:  13.096  0.159  0.393 85.968  0.033  2.162   9.3383e-02
   2_bss:  13.096  0.159  0.393 85.968  0.033  2.162   9.3383e-02
   2_xyz:   5.530  0.064  0.243 84.687  0.039  2.328   4.8074e-02
   2_adp:   5.530  0.064  0.243 84.687  0.039  2.328   4.8074e-02
   2_occ:   5.530  0.064  0.243 84.687  0.039  2.328   4.8074e-02
   3_bss:   5.530  0.064  0.243 84.687  0.039  2.328   4.8074e-02
   3_xyz:   8.126  0.048  0.365 88.762  0.029  2.300   5.0324e-02
   3_adp:   8.126  0.048  0.365 88.762  0.029  2.300   5.0324e-02
   3_occ:   8.126  0.048  0.365 88.762  0.029  2.300   5.0324e-02
   4_bss:   8.126  0.048  0.365 88.762  0.029  2.300   5.0324e-02
   4_xyz:   7.308  0.039  0.263 82.917  0.034  2.382   3.0428e-02
   4_adp:   7.308  0.039  0.263 82.917  0.034  2.382   3.0428e-02
   4_occ:   7.308  0.039  0.263 82.917  0.034  2.382   3.0428e-02
   5_bss:   7.308  0.039  0.263 82.917  0.034  2.382   3.0428e-02
   5_xyz:   6.186  0.046  0.306 84.372  0.038  2.316   4.3588e-02
   5_adp:   6.186  0.046  0.306 84.372  0.038  2.316   4.3588e-02
   5_occ:   6.186  0.046  0.306 84.372  0.038  2.316   4.3588e-02
   5_bss:   6.186  0.046  0.306 84.372  0.038  2.316   4.3588e-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:  69.00   0.00  12.41  59.96   0.00   9.70  69.00   0.00  27.15
   1_occ:  69.00   0.00  12.41  59.96   0.00   9.70  69.00   0.00  27.15
   2_bss:  69.00   0.00  12.41  59.96   0.00   9.70  69.00   0.00  27.15
   2_xyz:  69.00   0.00  12.41  59.96   0.00   9.70  69.00   0.00  27.15
   2_adp:  72.32   0.00  12.26  61.20   0.00   8.80  72.32   0.00  31.07
   2_occ:  72.32   0.00  12.26  61.20   0.00   8.80  72.32   0.00  31.07
   3_bss:  72.32   0.00  12.26  61.20   0.00   8.80  72.32   0.00  31.07
   3_xyz:  72.32   0.00  12.26  61.20   0.00   8.80  72.32   0.00  31.07
   3_adp:  85.44   0.00  13.38  82.09   0.00   8.70  85.44   1.01  38.86
   3_occ:  85.44   0.00  13.38  82.09   0.00   8.70  85.44   1.01  38.86
   4_bss:  85.44   0.00  13.38  82.09   0.00   8.70  85.44   1.01  38.86
   4_xyz:  85.44   0.00  13.38  82.09   0.00   8.70  85.44   1.01  38.86
   4_adp:  88.98   0.00  13.00  88.98   0.00   8.40  87.74   1.06  38.06
   4_occ:  88.98   0.00  13.00  88.98   0.00   8.40  87.74   1.06  38.06
   5_bss:  88.98   0.00  13.00  88.98   0.00   8.40  87.74   1.06  38.06
   5_xyz:  88.98   0.00  13.00  88.98   0.00   8.40  87.74   1.06  38.06
   5_adp:  90.67   0.00  12.73  90.67   0.00   8.20  87.84   1.25  37.40
   5_occ:  90.67   0.00  12.73  90.67   0.00   8.20  87.84   1.25  37.40
   5_bss:  93.69   3.02  15.75  93.69   3.02  11.22  90.86   4.28  40.42
------------------------------------------------------------------------
 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:    1.265    0.007    0.405
   1_adp:    1.265    0.007    0.405
   1_occ:    1.265    0.007    0.405
   2_bss:    1.265    0.007    0.405
   2_xyz:    1.672    0.041    0.537
   2_adp:    1.672    0.041    0.537
   2_occ:    1.672    0.041    0.537
   3_bss:    1.672    0.041    0.537
   3_xyz:    1.604    0.032    0.601
   3_adp:    1.604    0.032    0.601
   3_occ:    1.604    0.032    0.601
   4_bss:    1.604    0.032    0.601
   4_xyz:    1.685    0.059    0.624
   4_adp:    1.685    0.059    0.624
   4_occ:    1.685    0.059    0.624
   5_bss:    1.685    0.059    0.624
   5_xyz:    1.694    0.070    0.643
   5_adp:    1.694    0.070    0.643
   5_occ:    1.694    0.070    0.643
   5_bss:    1.694    0.070    0.643
------------------------------------------------------------------------

CPU time actual refinement: 350.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_404/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_404/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_404/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_404/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_404/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.42 
  Macro-tasks:
    bulk solvent and scale       = 47.67  
    individual site refinement   = 142.42 
    weights calculation          = 32.91  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 229.67 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 106.60 
    alpha_beta                      = 8.41   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.48 
    fmodel                         = 8.23   
    r_factors                      = 0.20   
    phase_errors                   = 10.53  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 254.78 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.864 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    671 calls, 106.26 s
gradients_fft:          616 calls, 103.53 s

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

# Date 2008-01-16 Time 01:28:40 PST -0800 (1200475720.58 s)
Start R-work = 0.4650, R-free = 0.4489 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1770 (no bulk solvent and anisotropic scale)

Start R-work = 0.4563, R-free = 0.4374
Final R-work = 0.1139, R-free = 0.1602