# Date 2008-01-16 Time 02:26:54 PST -0800 (1200479214.41 s)
#phil __OFF__

Command line arguments: "../832.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6110
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 832

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.8686, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01057
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01057
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.3013 [2125/2152]  1912   213  10.0%
  bin  2:  4.3013 -  3.4272 [2036/2052]  1833   203  10.0%
  bin  3:  3.4272 -  2.9979 [2027/2046]  1825   202  10.0%
  bin  4:  2.9979 -  2.7255 [1993/2023]  1795   198   9.9%
  bin  5:  2.7255 -  2.5312 [1984/2003]  1785   199  10.0%
  bin  6:  2.5312 -  2.3825 [1970/2006]  1773   197  10.0%
  bin  7:  2.3825 -  2.2636 [1964/1997]  1766   198  10.1%
  bin  8:  2.2636 -  2.1654 [1950/1984]  1755   195  10.0%
  bin  9:  2.1654 -  2.0823 [1939/1967]  1744   195  10.1%
  bin 10:  2.0823 -  2.0106 [1601/2019]  1442   159   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_832/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:
        1.80 -     2.42: 13
        2.42 -     3.04: 2126
        3.04 -     3.66: 4566
        3.66 -     4.28: 8854
        4.28 -     4.90: 12279
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.797 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.017 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.017 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.145 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27833 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_832/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_832/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.8686 87.2539 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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4867   r_free= 0.4730   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.285420                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1379  153 0.3919 0.3857       6.588      6.5602|
|  2:  4.7971 -  3.8281 0.99   1325  149 0.4065 0.4390      6.8057      6.8954|
|  3:  3.8281 -  3.3502 0.99   1309  146 0.4540 0.4130      6.7079      6.6438|
|  4:  3.3502 -  3.0466 0.99   1291  136 0.4726 0.4321      6.5467      6.4576|
|  5:  3.0466 -  2.8298 0.99   1285  145 0.5226 0.4909      6.3896      6.4207|
|  6:  2.8298 -  2.6639 0.99   1278  145 0.5182 0.5077      6.2986      6.1913|
|  7:  2.6639 -  2.5312 0.99   1283  141 0.5017 0.4847      6.2406      6.1544|
|  8:  2.5312 -  2.4214 0.98   1266  142 0.5272 0.4437      6.1974      6.1618|
|  9:  2.4214 -  2.3286 0.98   1272  143 0.5313 0.6055      6.1125      6.1711|
| 10:  2.3286 -  2.2485 0.98   1248  135 0.5485 0.5129      6.1333      6.1131|
| 11:  2.2485 -  2.1784 1.00   1262  146 0.5256 0.5009      6.0368      6.0915|
| 12:  2.1784 -  2.1163 0.97   1261  134 0.5382 0.5256       5.983      6.0266|
| 13:  2.1163 -  2.0607 0.98   1260  141 0.5385 0.5224      5.8984      5.8577|
| 14:  2.0607 -  2.0106 0.72    911  103 0.5423 0.5334      5.8617      5.7561|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0896 -  4.7971  1379   153  0.68  35.99   0.79     0.70      76107.09|
|  2:  4.7971 -  3.8281  1325   149  0.70  35.60   0.87     0.74     107436.30|
|  3:  3.8281 -  3.3502  1309   146  0.60  43.60   0.80     0.69     112516.04|
|  4:  3.3502 -  3.0466  1291   136  0.53  49.62   0.79     0.60      96016.79|
|  5:  3.0466 -  2.8298  1285   145  0.45  55.79   0.72     0.52      77276.28|
|  6:  2.8298 -  2.6639  1278   145  0.45  56.36   0.71     0.50      65637.13|
|  7:  2.6639 -  2.5312  1283   141  0.42  58.21   0.74     0.47      60298.83|
|  8:  2.5312 -  2.4214  1266   142  0.38  61.46   0.73     0.44      58200.60|
|  9:  2.4214 -  2.3286  1272   143  0.32  66.20   0.69     0.37      56963.00|
| 10:  2.3286 -  2.2485  1248   135  0.31  67.02   0.70     0.36      53418.89|
| 11:  2.2485 -  2.1784  1262   146  0.30  67.52   0.74     0.36      49025.82|
| 12:  2.1784 -  2.1163  1261   134  0.30  67.55   0.74     0.37      44849.74|
| 13:  2.1163 -  2.0607  1260   141  0.27  70.03   0.71     0.32      39289.95|
| 14:  2.0607 -  2.0106   911   103  0.20  75.26   0.71     0.21      33122.61|
|alpha:            min =        0.21 max =            0.74 mean =         0.48|
|beta:             min =    33122.61 max =       112516.04 mean =     67498.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           90.00 mean =        57.24|
|phase err.(test): min =        0.00 max =           89.96 mean =        57.42|
|-----------------------------------------------------------------------------|

============================== 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 = 13.700020             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.769   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.389685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.489   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1473 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2566 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3846 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4980 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6492 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7598 |
|-----------------------------------------------------------------------------|
|-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 |       54.487 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.709 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    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 = 12.292)------------------------------------------|
|    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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4918   r_free= 0.4744   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.287252                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4794   r_free= 0.4632   ksol= 0.30   Bsol= 20.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.20,11.47,8.61,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.278780                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.671577             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.834   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.247758              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.429   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4794      final r-factor (work) = 0.3982          |
| start r-factor (free) = 0.4632      final r-factor (free) = 0.4091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 94.3219 = 12.67 * 0.50 * 6.2873 + 1.00 * 54.4867                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.4280 = 12.67 * 0.50 * 6.2011 + 1.00 * 0.1393                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3982      final r-factor (work) = 0.3530          |
| start r-factor (free) = 0.4091      final r-factor (free) = 0.3952          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7522 = 1.25 * 1.00 * 6.2011 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6536 = 1.25 * 1.00 * 6.1174 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.12  14.27    None  None   None       |
|    all(noH): 2823   0      0.00    110.12  14.27    None  None   None       |
|    Sol.    : 438    0      0.00    110.12  28.11    None  None   None       |
|    Mac.    : 2385   0      0.00    73.81   11.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.012: 1482   |   5:    55.060 -  66.072:   28        |
|      1:    11.012 -  22.024:  733   |   6:    66.072 -  77.084:   16        |
|      2:    22.024 -  33.036:  356   |   7:    77.084 -  88.096:    3        |
|      3:    33.036 -  44.048:  137   |   8:    88.096 -  99.107:    0        |
|      4:    44.048 -  55.060:   65   |   9:    99.107 - 110.119:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3530 r_free = 0.3952             target_work(ml) = 6.098         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3523 r_free = 0.3946             target_work(ml) = 6.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3523   r_free= 0.3946   ksol= 0.30   Bsol= 20.00   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.20,11.47,8.61,0.00,0.00,0.00); trace/3= 8.76                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.097370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3498   r_free= 0.3888   ksol= 0.32   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,7.41,5.07,0.00,0.00,0.00); trace/3= 5.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.098888                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.489681              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.078  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.456561              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.816  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3498      final r-factor (work) = 0.2776          |
| start r-factor (free) = 0.3888      final r-factor (free) = 0.3334          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0246 = 7.49 * 0.50 * 6.1112 + 1.00 * 0.1391                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4960 = 7.49 * 0.50 * 5.9840 + 1.00 * 0.0870                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2776      final r-factor (work) = 0.2606          |
| start r-factor (free) = 0.3334      final r-factor (free) = 0.3131          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7529 = 0.46 * 1.00 * 5.9840 + 1.00 * 0.0209                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7071 = 0.46 * 1.00 * 5.8905 + 1.00 * 0.0178                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.59  13.18    None  None   None       |
|    all(noH): 2823   0      0.00    107.59  13.18    None  None   None       |
|    Sol.    : 438    0      0.00    107.59  30.30    None  None   None       |
|    Mac.    : 2385   0      0.00    83.65   10.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.759: 1647   |   5:    53.793 -  64.551:   28        |
|      1:    10.759 -  21.517:  661   |   6:    64.551 -  75.310:    9        |
|      2:    21.517 -  32.276:  259   |   7:    75.310 -  86.068:    3        |
|      3:    32.276 -  43.034:  141   |   8:    86.068 -  96.827:    1        |
|      4:    43.034 -  53.793:   72   |   9:    96.827 - 107.585:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2606 r_free = 0.3131             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2602 r_free = 0.3137             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2602   r_free= 0.3137   ksol= 0.32   Bsol= 50.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,7.41,5.07,0.00,0.00,0.00); trace/3= 5.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.873430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2595   r_free= 0.3130   ksol= 0.30   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.19,4.88,3.67,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.874219                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.748951              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.224  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.327325              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.971  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2595      final r-factor (work) = 0.2011          |
| start r-factor (free) = 0.3130      final r-factor (free) = 0.2403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1298 = 3.75 * 0.50 * 5.8912 + 1.00 * 0.0870                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8890 = 3.75 * 0.50 * 5.7698 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2011      final r-factor (work) = 0.1844          |
| start r-factor (free) = 0.2403      final r-factor (free) = 0.2224          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9019 = 0.33 * 1.00 * 5.7698 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8479 = 0.33 * 1.00 * 5.5869 + 1.00 * 0.0192                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.68   13.38    None  None   None       |
|    all(noH): 2823   0      0.00    98.68   13.38    None  None   None       |
|    Sol.    : 438    0      0.00    98.68   35.03    None  None   None       |
|    Mac.    : 2385   0      0.00    75.83   9.40     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 -   9.868: 1651   |   5:    49.342 -  59.210:   82        |
|      1:     9.868 -  19.737:  610   |   6:    59.210 -  69.079:   24        |
|      2:    19.737 -  29.605:  207   |   7:    69.079 -  78.947:    9        |
|      3:    29.605 -  39.473:  134   |   8:    78.947 -  88.815:    1        |
|      4:    39.473 -  49.342:  104   |   9:    88.815 -  98.684:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1844 r_free = 0.2224             target_work(ml) = 5.561         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1842 r_free = 0.2224             target_work(ml) = 5.560         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1842   r_free= 0.2224   ksol= 0.30   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.19,4.88,3.67,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.560256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1836   r_free= 0.2224   ksol= 0.31   Bsol= 65.79   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,3.06,2.97,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.559073                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.179411              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.012   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.473588              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.482   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1836      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2224      final r-factor (free) = 0.1921          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1645 = 2.18 * 0.50 * 5.5890 + 1.00 * 0.0741                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0168 = 2.18 * 0.50 * 5.4628 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1514      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.1921      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6067 = 0.47 * 1.00 * 5.4628 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5878 = 0.47 * 1.00 * 5.3652 + 1.00 * 0.0469                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.10   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    95.10   13.57    None  None   None       |
|    Sol.    : 438    0      0.83    95.10   37.50    None  None   None       |
|    Mac.    : 2385   0      0.00    88.92   9.17     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 -   9.510: 1647   |   5:    47.551 -  57.061:   86        |
|      1:     9.510 -  19.021:  613   |   6:    57.061 -  66.572:   50        |
|      2:    19.021 -  28.531:  172   |   7:    66.572 -  76.082:   16        |
|      3:    28.531 -  38.041:  119   |   8:    76.082 -  85.592:    6        |
|      4:    38.041 -  47.551:  112   |   9:    85.592 -  95.102:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.1884             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1445 r_free = 0.1885             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1445   r_free= 0.1885   ksol= 0.31   Bsol= 65.79   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.44,3.06,2.97,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.357086                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1884   ksol= 0.33   Bsol= 66.76   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.43,2.64,3.04,0.00,0.00,0.00); trace/3= 2.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.357649                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.798736              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.073  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.805219              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.124   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1884      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2556 = 3.80 * 0.50 * 5.3658 + 1.00 * 0.0640                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1323 = 3.80 * 0.50 * 5.2899 + 1.00 * 0.0848                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1706      final r-factor (free) = 0.1693          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2735 = 0.81 * 1.00 * 5.2899 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2190 = 0.81 * 1.00 * 5.2199 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.83   13.55    None  None   None       |
|    all(noH): 2823   0      0.00    91.83   13.55    None  None   None       |
|    Sol.    : 438    0      1.52    91.83   38.72    None  None   None       |
|    Mac.    : 2385   0      0.00    87.05   8.93     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 -   9.183: 1650   |   5:    45.916 -  55.099:   84        |
|      1:     9.183 -  18.366:  612   |   6:    55.099 -  64.282:   64        |
|      2:    18.366 -  27.549:  151   |   7:    64.282 -  73.465:   33        |
|      3:    27.549 -  36.732:  121   |   8:    73.465 -  82.648:    8        |
|      4:    36.732 -  45.916:   93   |   9:    82.648 -  91.831:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1693             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1207 r_free = 0.1692             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1692   ksol= 0.33   Bsol= 66.76   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.43,2.64,3.04,0.00,0.00,0.00); trace/3= 2.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.214209                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1379  153 0.1013 0.1338       5.417      5.5539|
|  2:  4.7971 -  3.8281 0.99   1325  149 0.0869 0.1143      5.4644      5.6737|
|  3:  3.8281 -  3.3502 0.99   1309  146 0.1119 0.1557      5.5299      5.8996|
|  4:  3.3502 -  3.0466 0.99   1291  136 0.1275 0.1654       5.501      5.6651|
|  5:  3.0466 -  2.8298 0.99   1285  145 0.1445 0.1729      5.4137      5.5544|
|  6:  2.8298 -  2.6639 0.99   1278  145 0.1354 0.2155      5.3071      5.5836|
|  7:  2.6639 -  2.5312 0.99   1283  141 0.1349 0.1869      5.2401       5.448|
|  8:  2.5312 -  2.4214 0.98   1266  142 0.1305 0.1877      5.1761      5.4413|
|  9:  2.4214 -  2.3286 0.98   1272  143 0.1324 0.1975      5.1131      5.3581|
| 10:  2.3286 -  2.2485 0.98   1248  135 0.1289 0.1883      5.0816      5.3182|
| 11:  2.2485 -  2.1784 1.00   1262  146 0.1270 0.1954       5.023      5.3378|
| 12:  2.1784 -  2.1163 0.97   1261  134 0.1214 0.1790      4.9442      5.2411|
| 13:  2.1163 -  2.0607 0.98   1260  141 0.1235 0.1801      4.8587      5.0913|
| 14:  2.0607 -  2.0106 0.72    911  103 0.1182 0.1904      4.7413      5.0174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0896 -  4.7971  1379   153  0.94   9.80   0.96     0.94       8128.68|
|  2:  4.7971 -  3.8281  1325   149  0.95   8.52   1.00     0.98       9654.90|
|  3:  3.8281 -  3.3502  1309   146  0.93  11.88   1.02     1.02      11346.80|
|  4:  3.3502 -  3.0466  1291   136  0.92  14.21   1.00     0.98      11101.82|
|  5:  3.0466 -  2.8298  1285   145  0.89  17.50   1.00     0.98       9929.64|
|  6:  2.8298 -  2.6639  1278   145  0.89  17.79   0.98     0.94       8502.87|
|  7:  2.6639 -  2.5312  1283   141  0.89  17.12   0.98     0.96       7285.27|
|  8:  2.5312 -  2.4214  1266   142  0.89  17.15   0.98     0.94       6559.62|
|  9:  2.4214 -  2.3286  1272   143  0.89  17.67   0.99     0.94       5896.51|
| 10:  2.3286 -  2.2485  1248   135  0.88  17.81   0.99     0.94       5584.27|
| 11:  2.2485 -  2.1784  1262   146  0.89  17.58   0.98     0.94       5087.21|
| 12:  2.1784 -  2.1163  1261   134  0.90  16.80   0.99     0.97       4558.94|
| 13:  2.1163 -  2.0607  1260   141  0.89  16.97   0.97     0.95       3752.68|
| 14:  2.0607 -  2.0106   911   103  0.90  16.12   0.95     0.91       2859.07|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2859.07 max =        11346.80 mean =      7285.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.41|
|phase err.(test): min =        0.00 max =           87.99 mean =        14.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1691   ksol= 0.32   Bsol= 66.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.11,0.72,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.214046                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1691   ksol= 0.32   Bsol= 66.92   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.11,0.72,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.214046                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1379  153 0.1013 0.1338      5.4169      5.5544|
|  2:  4.7971 -  3.8281 0.99   1325  149 0.0869 0.1141      5.4639       5.672|
|  3:  3.8281 -  3.3502 0.99   1309  146 0.1119 0.1557        5.53       5.901|
|  4:  3.3502 -  3.0466 0.99   1291  136 0.1275 0.1653      5.5012      5.6652|
|  5:  3.0466 -  2.8298 0.99   1285  145 0.1446 0.1729      5.4141      5.5543|
|  6:  2.8298 -  2.6639 0.99   1278  145 0.1353 0.2151      5.3067      5.5821|
|  7:  2.6639 -  2.5312 0.99   1283  141 0.1349 0.1872      5.2401      5.4489|
|  8:  2.5312 -  2.4214 0.98   1266  142 0.1304 0.1875      5.1763      5.4412|
|  9:  2.4214 -  2.3286 0.98   1272  143 0.1322 0.1974      5.1129      5.3585|
| 10:  2.3286 -  2.2485 0.98   1248  135 0.1288 0.1886      5.0816      5.3189|
| 11:  2.2485 -  2.1784 1.00   1262  146 0.1270 0.1951      5.0226      5.3367|
| 12:  2.1784 -  2.1163 0.97   1261  134 0.1214 0.1788      4.9441      5.2415|
| 13:  2.1163 -  2.0607 0.98   1260  141 0.1235 0.1801      4.8579      5.0908|
| 14:  2.0607 -  2.0106 0.72    911  103 0.1182 0.1899      4.7403       5.015|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0896 -  4.7971  1379   153  0.94   9.81   0.97     0.94       8137.35|
|  2:  4.7971 -  3.8281  1325   149  0.95   8.52   1.00     0.98       9647.04|
|  3:  3.8281 -  3.3502  1309   146  0.93  11.88   1.02     1.02      11343.55|
|  4:  3.3502 -  3.0466  1291   136  0.92  14.21   1.00     0.98      11105.84|
|  5:  3.0466 -  2.8298  1285   145  0.89  17.49   1.00     0.98       9926.53|
|  6:  2.8298 -  2.6639  1278   145  0.89  17.78   0.98     0.94       8496.51|
|  7:  2.6639 -  2.5312  1283   141  0.89  17.12   0.99     0.96       7284.40|
|  8:  2.5312 -  2.4214  1266   142  0.89  17.16   0.99     0.95       6564.29|
|  9:  2.4214 -  2.3286  1272   143  0.89  17.66   0.99     0.95       5898.70|
| 10:  2.3286 -  2.2485  1248   135  0.88  17.81   0.99     0.95       5584.73|
| 11:  2.2485 -  2.1784  1262   146  0.89  17.57   0.99     0.94       5085.48|
| 12:  2.1784 -  2.1163  1261   134  0.90  16.80   1.00     0.98       4557.74|
| 13:  2.1163 -  2.0607  1260   141  0.89  16.94   0.98     0.96       3742.59|
| 14:  2.0607 -  2.0106   911   103  0.90  16.07   0.96     0.92       2844.32|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2844.32 max =        11343.55 mean =      7283.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.41|
|phase err.(test): min =        0.00 max =           87.96 mean =        14.67|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.292)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.51    94.34   16.06    None  None   None       |
|    all(noH): 2823   0      2.51    94.34   16.06    None  None   None       |
|    Sol.    : 438    0      4.03    94.34   41.23    None  None   None       |
|    Mac.    : 2385   0      2.51    89.56   11.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.510 -  11.693: 1650   |   5:    48.425 -  57.608:   84        |
|      1:    11.693 -  20.876:  612   |   6:    57.608 -  66.791:   64        |
|      2:    20.876 -  30.059:  151   |   7:    66.791 -  75.975:   33        |
|      3:    30.059 -  39.242:  121   |   8:    75.975 -  85.158:    8        |
|      4:    39.242 -  48.425:   93   |   9:    85.158 -  94.341:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.257 - 5.412
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 325
   mapped sites are within: 0.707 - 5.412

peak=    8.993 closest distance to " CG2 VAL A 230 " =    1.352
peak=    6.317 closest distance to " O   HOH Z 210 " =    1.386
peak=    6.240 closest distance to " CD1AILE A 234 " =    1.214
peak=    6.182 closest distance to " O   HOH Z 120 " =    1.203
peak=    5.982 closest distance to " NH2 ARG A  56 " =    2.339
peak=    5.944 closest distance to " CG  LEU A   5 " =    1.165
peak=    5.458 closest distance to " CB  VAL A 296 " =    1.039
peak=    5.070 closest distance to " CB  VAL A 230 " =    1.235
peak=    5.069 closest distance to " CG  LEU A 228 " =    1.233
peak=    4.969 closest distance to " CB  GLN A 223 " =    1.387
peak=    4.948 closest distance to " CB  SER A  63 " =    1.259
peak=    4.911 closest distance to " O   HOH Z 433 " =    1.800
peak=    4.682 closest distance to " O   HOH Z  49 " =    1.369
peak=    4.649 closest distance to " O   HOH Z 232 " =    2.309
peak=    4.612 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.599 closest distance to " O   HOH Z 248 " =    1.712
peak=    4.593 closest distance to " O   HOH Z 412 " =    3.646
peak=    4.592 closest distance to " O   HOH Z 102 " =    1.435
peak=    4.573 closest distance to " CG  PRO A  54 " =    1.231
peak=    4.500 closest distance to " NE2 GLN A  11 " =    1.117
peak=    4.455 closest distance to " O   HOH Z 402 " =    1.604
peak=    4.452 closest distance to " O   HOH Z 425 " =    1.612
peak=    4.440 closest distance to " O   HOH Z 403 " =    1.847
peak=    4.414 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.405 closest distance to " O   HOH Z 128 " =    1.534
peak=    4.393 closest distance to " CG  ARG A  66 " =    2.691
peak=    4.386 closest distance to " CA  ALA A  51 " =    1.058
peak=    4.370 closest distance to " O   HOH Z 431 " =    1.302
peak=    4.368 closest distance to " O   HOH Z  44 " =    2.069
peak=    4.359 closest distance to " O   PRO A 198 " =    1.533
peak=    4.327 closest distance to " O   HOH Z 234 " =    3.609
peak=    4.319 closest distance to " CG  PRO A 280 " =    0.879
peak=    4.288 closest distance to " O   ASP A 124 " =    1.313
peak=    4.287 closest distance to " O   HOH Z 144 " =    2.005
peak=    4.284 closest distance to " CB  ARG A 275 " =    0.884
peak=    4.246 closest distance to " O   HOH Z  40 " =    2.030
peak=    4.213 closest distance to " CB  PRO A  54 " =    0.821
peak=    4.193 closest distance to " O   ALA A 165 " =    1.343
peak=    4.188 closest distance to " O   HOH Z  43 " =    2.059
peak=    4.175 closest distance to " O   SER A  87 " =    2.318
peak=    4.174 closest distance to " CB  GLU A 128 " =    1.219
peak=    4.138 closest distance to " CZ  PHE A 218 " =    1.179
peak=    4.122 closest distance to " CA  ARG A 195 " =    1.207
peak=    4.079 closest distance to " O   HOH Z 369 " =    2.025
peak=    4.060 closest distance to " CD2 LEU A 228 " =    1.270
peak=    4.050 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.044 closest distance to " O   HOH Z 126 " =    2.508
peak=    4.040 closest distance to " O   HOH Z  48 " =    1.701
peak=    4.013 closest distance to " O   HOH Z  63 " =    1.813
peak=    4.012 closest distance to " CG2 THR A 221 " =    1.157
peak=    4.005 closest distance to " CZ3 TRP A  85 " =    0.944
peak=    4.000 closest distance to " O   HOH Z 261 " =    2.113
peak=    3.990 closest distance to " O   HOH Z 154 " =    1.436
peak=    3.987 closest distance to " O   HOH Z 130 " =    1.160
peak=    3.983 closest distance to " OG BSER A 164 " =    1.996
peak=    3.983 closest distance to " O   HOH Z 303 " =    2.392
peak=    3.977 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.964 closest distance to " CG  PRO A 198 " =    1.194
peak=    3.958 closest distance to " CD  LYS A 166 " =    1.426
peak=    3.955 closest distance to " CB  TRP A 179 " =    1.382
peak=    3.950 closest distance to " O   HOH Z 126 " =    1.646
peak=    3.940 closest distance to " CB  TRP A 266 " =    1.082
peak=    3.932 closest distance to " O   HOH Z 285 " =    2.759
peak=    3.930 closest distance to " CG1 VAL A 296 " =    1.168
peak=    3.915 closest distance to " O   HOH Z 134 " =    1.761
peak=    3.911 closest distance to " CB  VAL A 202 " =    1.504
peak=    3.906 closest distance to " CB BVAL A  41 " =    1.174
peak=    3.889 closest distance to " O   HOH Z  80 " =    1.989
peak=    3.888 closest distance to " CG2 ILE A 234 " =    1.060
peak=    3.886 closest distance to " O   HOH Z 146 " =    1.679
peak=    3.875 closest distance to " CB  ARG A 190 " =    1.778
peak=    3.850 closest distance to " CG2 VAL A 296 " =    0.993
peak=    3.850 closest distance to " O   HOH Z  61 " =    1.460
peak=    3.838 closest distance to " O   HOH Z  68 " =    1.929
peak=    3.836 closest distance to " O   HOH Z 417 " =    3.032
peak=    3.831 closest distance to " O   HOH Z 423 " =    1.728
peak=    3.812 closest distance to " CB  GLU A 277 " =    3.754
peak=    3.812 closest distance to " CE  LYS A 119 " =    1.199
peak=    3.787 closest distance to " O   HOH Z 265 " =    2.084
peak=    3.787 closest distance to " CG  PRO A 243 " =    1.186
peak=    3.776 closest distance to " CG1 ILE A  33 " =    1.162
peak=    3.773 closest distance to " O   HOH Z 214 " =    3.207
peak=    3.771 closest distance to " OD1 ASN A 217 " =    1.688
peak=    3.769 closest distance to " CD2 TRP A 179 " =    1.332
peak=    3.764 closest distance to " O   HOH Z 247 " =    1.538
peak=    3.754 closest distance to " CD  PRO A  54 " =    1.084
peak=    3.749 closest distance to " OE1 GLN A  11 " =    1.990
peak=    3.743 closest distance to " CB  TYR A 169 " =    0.734
peak=    3.737 closest distance to " O   HOH Z 357 " =    2.201
peak=    3.724 closest distance to " O   ASP A 200 " =    1.621
peak=    3.722 closest distance to " CB  ASP A 140 " =    0.919
peak=    3.703 closest distance to " CA  ALA A 295 " =    1.065
peak=    3.702 closest distance to " CB  GLU A 152 " =    1.075
peak=    3.701 closest distance to " O   HOH Z 196 " =    1.268
peak=    3.700 closest distance to " O   HOH Z 359 " =    1.522
peak=    3.697 closest distance to " O   HOH Z 126 " =    2.126
peak=    3.693 closest distance to " O   HOH Z 251 " =    1.503
peak=    3.685 closest distance to " O   HOH Z 394 " =    1.599
peak=    3.681 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.679 closest distance to " CE1 TYR A 186 " =    1.162
peak=    3.676 closest distance to " O   HOH Z 393 " =    3.550
peak=    3.676 closest distance to " O   HOH Z 280 " =    2.876
peak=    3.672 closest distance to " O   HOH Z 245 " =    1.344
peak=    3.662 closest distance to " O   HOH Z 298 " =    1.890
peak=    3.660 closest distance to " CA  VAL A  41 " =    0.838
peak=    3.648 closest distance to " O   HOH Z 427 " =    3.125
peak=    3.644 closest distance to " CB  ARG A  79 " =    1.371
peak=    3.644 closest distance to " O   HOH Z 258 " =    2.253
peak=    3.634 closest distance to " CA  SER A  12 " =    1.496
peak=    3.623 closest distance to " CB  ASP A 124 " =    0.707
peak=    3.621 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.618 closest distance to " CB  ASN A 148 " =    1.360
peak=    3.613 closest distance to " O   HOH Z 420 " =    5.412
peak=    3.607 closest distance to " O   HOH Z 316 " =    3.061
peak=    3.606 closest distance to " CB  ALA A 100 " =    1.373
peak=    3.604 closest distance to " CG  GLN A  77 " =    0.913
peak=    3.588 closest distance to " CA  LEU A 282 " =    1.016
peak=    3.576 closest distance to " O   HOH Z 422 " =    2.532
peak=    3.574 closest distance to " NH2 ARG A 156 " =    1.155
peak=    3.571 closest distance to " CB  GLN A  89 " =    1.163
peak=    3.568 closest distance to " CA  TYR A 116 " =    1.386
peak=    3.567 closest distance to " O   HOH Z 365 " =    2.858
peak=    3.566 closest distance to " CB  ASN A  39 " =    0.743
peak=    3.554 closest distance to " CA  ASP A 191 " =    0.927
peak=    3.551 closest distance to " O   HOH Z 155 " =    3.213
peak=    3.541 closest distance to " O   HOH Z 142 " =    1.541
peak=    3.538 closest distance to " O   ASN A  74 " =    1.580
peak=    3.537 closest distance to " CG1 VAL A 153 " =    1.012
peak=    3.536 closest distance to " O   HOH Z 383 " =    2.183
peak=    3.534 closest distance to " CG2 ILE A  20 " =    1.461
peak=    3.531 closest distance to " CA  THR A 246 " =    0.960
peak=    3.527 closest distance to " CD  ARG A 269 " =    1.029
peak=    3.527 closest distance to " CB  THR A  52 " =    0.957
peak=    3.525 closest distance to " O   HOH Z 271 " =    2.569
peak=    3.523 closest distance to " CD1 LEU A  96 " =    0.756
peak=    3.522 closest distance to " O   PRO A 213 " =    1.456
peak=    3.522 closest distance to " O   HOH Z 346 " =    1.555
peak=    3.520 closest distance to " CA  GLN A  88 " =    1.286
peak=    3.517 closest distance to " O   HOH Z 371 " =    3.211
peak=    3.513 closest distance to " O   HOH Z  99 " =    2.902
peak=    3.504 closest distance to " NH1 ARG A  14 " =    1.056
peak=    3.504 closest distance to " O   HOH Z 327 " =    1.572
peak=    3.503 closest distance to " CA  ASP A 162 " =    1.096
peak=    3.496 closest distance to " O   HOH Z 418 " =    1.361
peak=    3.495 closest distance to " O   HOH Z  56 " =    1.708
peak=    3.495 closest distance to " CA  ALA A  21 " =    1.263
peak=    3.492 closest distance to " O   HOH Z  15 " =    2.334
peak=    3.491 closest distance to " O   HOH Z 374 " =    2.852
peak=    3.491 closest distance to " O   HOH Z 199 " =    1.532
peak=    3.489 closest distance to " O  BHOH Z  74 " =    1.344
peak=    3.488 closest distance to " O   HOH Z  57 " =    1.455
peak=    3.487 closest distance to " CB  SER A  62 " =    0.880
peak=    3.486 closest distance to " CB  ASN A 142 " =    1.216
peak=    3.485 closest distance to " O   HOH Z  78 " =    1.686
peak=    3.484 closest distance to " O   HOH Z 132 " =    2.692
peak=    3.479 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.477 closest distance to " OE1 GLN A  55 " =    1.482
peak=    3.471 closest distance to " O   PRO A  90 " =    1.407
peak=    3.466 closest distance to " CB  SER A  26 " =    1.721
peak=    3.463 closest distance to " OE1 GLU A   2 " =    1.754
peak=    3.460 closest distance to " O   HOH Z   4 " =    1.621
peak=    3.457 closest distance to " OG1 THR A 294 " =    2.370
peak=    3.457 closest distance to " O   HOH Z 395 " =    1.378
peak=    3.447 closest distance to " N   SER A 164 " =    1.000
peak=    3.444 closest distance to " CD1 LEU A 101 " =    1.162
peak=    3.438 closest distance to " OD1 ASN A  69 " =    2.433
peak=    3.436 closest distance to " CA  SER A  87 " =    0.977
peak=    3.436 closest distance to " CA  GLY A 267 " =    0.734
peak=    3.436 closest distance to " CZ3 TRP A 266 " =    1.128
peak=    3.435 closest distance to " O   HOH Z 174 " =    2.060
peak=    3.434 closest distance to " O   HOH Z 291 " =    1.504
peak=    3.430 closest distance to " CD1 LEU A   5 " =    1.391
peak=    3.430 closest distance to " CE1 HIS A 108 " =    1.123
peak=    3.426 closest distance to " CD2 LEU A   5 " =    1.122
peak=    3.425 closest distance to " O   HOH Z 193 " =    1.793
peak=    3.425 closest distance to " O   HOH Z 189 " =    2.870
peak=    3.422 closest distance to " CG AARG A 275 " =    1.156
peak=    3.413 closest distance to " O   HOH Z 109 " =    2.348
peak=    3.412 closest distance to " NH2BARG A 145 " =    2.054
peak=    3.411 closest distance to " O   HOH Z  90 " =    3.524
peak=    3.406 closest distance to " O   HOH Z 236 " =    1.885
peak=    3.401 closest distance to " CB  ASN A 187 " =    1.179
peak=    3.400 closest distance to " OG  SER A 276 " =    1.646
peak=    3.398 closest distance to " O   HOH Z 151 " =    1.902
peak=    3.394 closest distance to " CE  LYS A  76 " =    0.853
peak=    3.393 closest distance to " CD1 LEU A 300 " =    1.138
peak=    3.391 closest distance to " O   HOH Z 189 " =    2.914
peak=    3.384 closest distance to " O   HOH Z 272 " =    2.002
peak=    3.384 closest distance to " O   HOH Z 214 " =    1.374
peak=    3.381 closest distance to " CB  ALA A   9 " =    1.671
peak=    3.381 closest distance to " O   HOH Z 131 " =    2.349
peak=    3.378 closest distance to " CB  SER A  28 " =    1.070
peak=    3.377 closest distance to " OD2 ASP A 298 " =    3.630
peak=    3.376 closest distance to " CA  ALA A 160 " =    0.929
peak=    3.375 closest distance to " O   HOH Z 133 " =    2.320
peak=    3.373 closest distance to " O   HOH Z 193 " =    1.896
peak=    3.373 closest distance to " O   HOH Z 344 " =    3.039
peak=    3.372 closest distance to " O   HOH Z 332 " =    1.592
peak=    3.368 closest distance to " O   HOH Z 365 " =    2.470
peak=    3.367 closest distance to " O   HOH Z 301 " =    1.925
peak=    3.365 closest distance to " O   HOH Z 146 " =    1.408
peak=    3.360 closest distance to " O   HOH Z 124 " =    1.107
peak=    3.359 closest distance to " O   HOH Z 368 " =    4.200
peak=    3.357 closest distance to " CD  ARG A 195 " =    1.046
peak=    3.355 closest distance to " O   GLY A 211 " =    2.958
peak=    3.352 closest distance to " CG1 ILE A  49 " =    1.667
peak=    3.351 closest distance to " C   ASN A 209 " =    1.219
peak=    3.348 closest distance to " CB  GLN A 103 " =    0.891
peak=    3.345 closest distance to " O   HOH Z 421 " =    1.705
peak=    3.342 closest distance to " CD BLYS A 290 " =    1.105
peak=    3.342 closest distance to " O   HOH Z 176 " =    1.553
peak=    3.336 closest distance to " CD2 LEU A 297 " =    0.996
peak=    3.335 closest distance to " O   GLY A  91 " =    1.184
peak=    3.333 closest distance to " CD  ARG A  66 " =    2.574
peak=    3.330 closest distance to " O   HOH Z 327 " =    2.711
peak=    3.329 closest distance to " CD  ARG A 159 " =    0.805
peak=    3.327 closest distance to " CB  ALA A 248 " =    1.055
peak=    3.326 closest distance to " CG2 VAL A 197 " =    1.222
peak=    3.325 closest distance to " NH1AARG A 145 " =    1.287
peak=    3.321 closest distance to " O   HOH Z 203 " =    1.803
peak=    3.320 closest distance to " C   VAL A 265 " =    1.175
peak=    3.318 closest distance to " CA  LYS A 117 " =    1.306
peak=    3.315 closest distance to " C   ILE A 106 " =    1.899
peak=    3.315 closest distance to " O   HOH Z 193 " =    1.696
peak=    3.314 closest distance to " O   HOH Z 435 " =    2.781
peak=    3.313 closest distance to " CB  LEU A 228 " =    1.357
peak=    3.310 closest distance to " O   HOH Z 389 " =    2.010
peak=    3.308 closest distance to " CA  ALA A 291 " =    0.899
peak=    3.306 closest distance to " OG BSER A 134 " =    2.798
peak=    3.305 closest distance to " CA  ASP A 140 " =    1.291
peak=    3.301 closest distance to " CG  ARG A 138 " =    1.327
peak=    3.300 closest distance to " CA  VAL A 125 " =    1.384
peak=    3.299 closest distance to " CB  MET A 105 " =    1.294
peak=    3.296 closest distance to " O   ALA A 158 " =    1.243
peak=    3.293 closest distance to " CB  ASN A 285 " =    0.873
peak=    3.293 closest distance to " O   HOH Z  88 " =    3.273
peak=    3.291 closest distance to " O   HOH Z 227 " =    1.602
peak=    3.287 closest distance to " OH  TYR A 116 " =    1.254
peak=    3.286 closest distance to " CG  MET A 185 " =    1.233
peak=    3.279 closest distance to " OG  SER A 245 " =    1.564
peak=    3.277 closest distance to " O   HOH Z 128 " =    1.972
peak=    3.277 closest distance to " O   HOH Z 273 " =    3.021
peak=    3.277 closest distance to " CA  ASN A 217 " =    1.225
peak=    3.276 closest distance to " CB  VAL A 265 " =    1.295
peak=    3.274 closest distance to " O   HOH Z 329 " =    3.949
peak=    3.273 closest distance to " O   ASN A  74 " =    1.964
peak=    3.271 closest distance to " O   HOH Z 313 " =    1.797
peak=    3.270 closest distance to " O   HOH Z 236 " =    1.566
peak=    3.266 closest distance to " CA  ALA A 158 " =    1.295
peak=    3.261 closest distance to " CG  ARG A 219 " =    1.193
peak=    3.258 closest distance to " NH2 ARG A  79 " =    1.323
peak=    3.258 closest distance to " OG  SER A  22 " =    2.890
peak=    3.257 closest distance to " O   HOH Z 163 " =    1.647
peak=    3.248 closest distance to " O   HOH Z 185 " =    1.678
peak=    3.247 closest distance to " CZ  PHE A 192 " =    1.026
peak=    3.244 closest distance to " C   SER A  32 " =    1.062
peak=    3.241 closest distance to " O   HOH Z 368 " =    3.482
peak=    3.237 closest distance to " CZ  PHE A  38 " =    1.261
peak=    3.236 closest distance to " CB  ALA A 248 " =    1.382
peak=    3.234 closest distance to " CG ALYS A 290 " =    1.068
peak=    3.233 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.232 closest distance to " O   HOH Z 435 " =    1.991
peak=    3.227 closest distance to " NE2 HIS A 115 " =    1.038
peak=    3.226 closest distance to " O   HOH Z 238 " =    0.957
peak=    3.223 closest distance to " O   HOH Z 387 " =    2.956
peak=    3.221 closest distance to " O   HOH Z 158 " =    3.018
peak=    3.216 closest distance to " CB  ALA A  71 " =    1.289
peak=    3.214 closest distance to " O   HOH Z  21 " =    1.791
peak=    3.210 closest distance to " O   HOH Z 126 " =    1.828
peak=    3.207 closest distance to " CB  PHE A 204 " =    0.949
peak=    3.207 closest distance to " CD  LYS A 119 " =    1.845
peak=    3.203 closest distance to " N   ASP A 162 " =    1.320
peak=    3.197 closest distance to " O   GLU A   2 " =    1.642
peak=    3.193 closest distance to " O   HOH Z 299 " =    4.462
peak=    3.192 closest distance to " CA  ASN A 215 " =    1.105
peak=    3.191 closest distance to " O   HOH Z 117 " =    2.035
peak=    3.191 closest distance to " N   ASN A  39 " =    1.238
peak=    3.188 closest distance to " CG1 VAL A 174 " =    1.573
peak=    3.183 closest distance to " O   HOH Z 285 " =    1.700
peak=    3.177 closest distance to " CB  ASN A 215 " =    1.269
peak=    3.176 closest distance to " CA  ALA A 100 " =    1.040
peak=    3.175 closest distance to " CB  LEU A   5 " =    1.326
peak=    3.165 closest distance to " CD2 TYR A 186 " =    0.982
peak=    3.165 closest distance to " OD1 ASN A 301 " =    1.311
peak=    3.159 closest distance to " CG  LEU A 167 " =    1.093
peak=    3.158 closest distance to " O   HOH Z 130 " =    2.205
peak=    3.155 closest distance to " CG2 ILE A 120 " =    1.143
peak=    3.150 closest distance to " O   HOH Z 411 " =    1.789
peak=    3.146 closest distance to " CZ3 TRP A  92 " =    1.251
peak=    3.146 closest distance to " O   HOH Z 423 " =    3.112
peak=    3.142 closest distance to " CB  SER A   3 " =    1.463
peak=    3.136 closest distance to " CB  ARG A 138 " =    0.991
peak=    3.135 closest distance to " O   HOH Z 353 " =    2.772
peak=    3.134 closest distance to " CB  ARG A 219 " =    1.651
peak=    3.132 closest distance to " O   HOH Z 166 " =    1.677
peak=    3.132 closest distance to " CG2 VAL A 126 " =    0.845
peak=    3.131 closest distance to " CB  ALA A 291 " =    1.330
peak=    3.127 closest distance to " O   HOH Z 420 " =    2.000
peak=    3.123 closest distance to " CD1 LEU A 228 " =    1.565
peak=    3.120 closest distance to " CG2 THR A  29 " =    1.472
peak=    3.114 closest distance to " C   GLY A  80 " =    1.053
peak=    3.111 closest distance to " CG1 VAL A 257 " =    0.974
peak=    3.109 closest distance to " CB  PHE A 283 " =    0.788
peak=    3.103 closest distance to " CA  CYS A 260 " =    1.587
peak=    3.101 closest distance to " CB  ALA A  34 " =    0.762
peak=    3.099 closest distance to " O   HOH Z 433 " =    4.049
peak=    3.097 closest distance to " O   HOH Z 191 " =    4.108
peak=    3.094 closest distance to " O   HOH Z  30 " =    0.985
peak=    3.091 closest distance to " CG2 THR A 220 " =    0.731
peak=    3.090 closest distance to " O   HOH Z 394 " =    3.885
peak=    3.090 closest distance to " O   HOH Z  29 " =    1.285
peak=    3.078 closest distance to " O   HOH Z  83 " =    1.520
peak=    3.067 closest distance to " O   HOH Z 162 " =    1.723
peak=    3.060 closest distance to " CB  THR A  31 " =    1.524
peak=    3.057 closest distance to " ND1 HIS A  81 " =    1.590
peak=    3.053 closest distance to " CB  TYR A 247 " =    1.013
peak=    3.049 closest distance to " CG2BVAL A  72 " =    1.737
peak=    3.048 closest distance to " CA  ASN A  74 " =    1.216
peak=    3.041 closest distance to " O   HOH Z 281 " =    2.612
peak=    3.030 closest distance to " CA  GLU A  46 " =    0.783
peak=    3.023 closest distance to " ND2 ASN A 187 " =    1.425

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.711 - 5.426
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 208
   mapped sites are within: 0.711 - 5.426

peak=   -5.327 closest distance to " CG2 VAL A 230 " =    0.854
peak=   -4.748 closest distance to " O   HOH Z 166 " =    1.441
peak=   -4.670 closest distance to " CD  GLN A  58 " =    1.008
peak=   -4.625 closest distance to " O   VAL A  67 " =    2.938
peak=   -4.524 closest distance to " O   HOH Z 266 " =    5.426
peak=   -4.312 closest distance to " CG1 VAL A 250 " =    2.646
peak=   -4.177 closest distance to " O   HOH Z 166 " =    2.542
peak=   -4.175 closest distance to " CA  ASP A 298 " =    1.038
peak=   -4.150 closest distance to " CD1 PHE A  59 " =    2.025
peak=   -4.116 closest distance to " O   HOH Z  13 " =    1.813
peak=   -4.109 closest distance to " CA  TYR A  68 " =    2.897
peak=   -4.094 closest distance to " OXT GLY A 302 " =    2.928
peak=   -4.019 closest distance to " OD1 ASN A 148 " =    1.453
peak=   -4.018 closest distance to " CB  PRO A 243 " =    2.830
peak=   -4.017 closest distance to " O   HOH Z 252 " =    3.792
peak=   -3.959 closest distance to " O   HOH Z 351 " =    1.578
peak=   -3.959 closest distance to " CG1 VAL A 296 " =    1.109
peak=   -3.889 closest distance to " CD  ARG A  14 " =    3.300
peak=   -3.888 closest distance to " O   HOH Z  10 " =    1.667
peak=   -3.872 closest distance to " CD1 LEU A 101 " =    2.488
peak=   -3.871 closest distance to " CG  ARG A 269 " =    2.293
peak=   -3.861 closest distance to " CD  ARG A 156 " =    2.137
peak=   -3.853 closest distance to " CA  SER A 164 " =    2.229
peak=   -3.840 closest distance to " OG  SER A  97 " =    2.333
peak=   -3.839 closest distance to " CD  GLN A  88 " =    0.841
peak=   -3.820 closest distance to " CA  SER A 276 " =    1.508
peak=   -3.814 closest distance to " O   ILE A 109 " =    2.653
peak=   -3.811 closest distance to " CE3 TRP A 150 " =    2.367
peak=   -3.805 closest distance to " O   HOH Z 103 " =    2.023
peak=   -3.795 closest distance to " O   HOH Z 120 " =    0.793
peak=   -3.788 closest distance to " O   SER A 271 " =    2.105
peak=   -3.776 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.774 closest distance to " O   HOH Z 200 " =    1.270
peak=   -3.772 closest distance to " O   HOH Z  19 " =    2.321
peak=   -3.771 closest distance to " OD2 ASP A 298 " =    0.958
peak=   -3.765 closest distance to " O   HOH Z 231 " =    2.143
peak=   -3.756 closest distance to " CG1 VAL A 112 " =    2.653
peak=   -3.755 closest distance to " CG2 ILE A  49 " =    2.751
peak=   -3.748 closest distance to " O   HOH Z 283 " =    2.251
peak=   -3.729 closest distance to " CD  GLN A 223 " =    1.423
peak=   -3.722 closest distance to " OD1 ASN A 249 " =    2.453
peak=   -3.707 closest distance to " O   HOH Z 171 " =    2.302
peak=   -3.704 closest distance to " NH2 ARG A  66 " =    1.432
peak=   -3.702 closest distance to " CH2 TRP A 179 " =    1.211
peak=   -3.687 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -3.687 closest distance to " OG BSER A 210 " =    1.287
peak=   -3.682 closest distance to " N   ALA A 226 " =    2.116
peak=   -3.672 closest distance to " OG  SER A  26 " =    1.209
peak=   -3.661 closest distance to " O   HOH Z 407 " =    3.292
peak=   -3.658 closest distance to " C   SER A 206 " =    1.401
peak=   -3.642 closest distance to " CD  PRO A 213 " =    2.234
peak=   -3.641 closest distance to " O   HOH Z 184 " =    1.286
peak=   -3.636 closest distance to " O   SER A 276 " =    1.618
peak=   -3.625 closest distance to " ND2 ASN A  45 " =    1.143
peak=   -3.621 closest distance to " ND2 ASN A  45 " =    2.201
peak=   -3.618 closest distance to " CE2 TYR A  30 " =    2.740
peak=   -3.613 closest distance to " CD2 TYR A 293 " =    1.951
peak=   -3.602 closest distance to " C   HIS A 108 " =    1.158
peak=   -3.600 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.598 closest distance to " O   HOH Z 396 " =    1.723
peak=   -3.583 closest distance to " CB  ALA A  10 " =    2.130
peak=   -3.577 closest distance to " O   HOH Z 426 " =    1.819
peak=   -3.573 closest distance to " NE2 GLN A 194 " =    2.019
peak=   -3.564 closest distance to " C   ALA A 158 " =    1.309
peak=   -3.560 closest distance to " O   HOH Z  56 " =    2.163
peak=   -3.546 closest distance to " N   ALA A  43 " =    2.707
peak=   -3.542 closest distance to " O   HOH Z 150 " =    1.663
peak=   -3.541 closest distance to " OE1 GLN A  88 " =    1.159
peak=   -3.534 closest distance to " CB  PHE A 208 " =    2.413
peak=   -3.534 closest distance to " O   HOH Z 109 " =    3.560
peak=   -3.530 closest distance to " CG2 THR A 182 " =    2.449
peak=   -3.523 closest distance to " ND2BASN A 224 " =    1.907
peak=   -3.522 closest distance to " CG2 VAL A 189 " =    2.118
peak=   -3.514 closest distance to " C   ASN A 285 " =    2.488
peak=   -3.498 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.493 closest distance to " CA  VAL A 197 " =    0.969
peak=   -3.490 closest distance to " O   HOH Z  52 " =    1.876
peak=   -3.488 closest distance to " O   HOH Z 431 " =    2.506
peak=   -3.488 closest distance to " O   HOH Z 193 " =    1.536
peak=   -3.487 closest distance to " O   HOH Z 264 " =    1.804
peak=   -3.487 closest distance to " OG BSER A 134 " =    1.367
peak=   -3.477 closest distance to " O   HOH Z 234 " =    4.279
peak=   -3.475 closest distance to " O   HOH Z 275 " =    1.503
peak=   -3.473 closest distance to " O   HOH Z   6 " =    1.914
peak=   -3.471 closest distance to " OE1 GLN A 223 " =    2.469
peak=   -3.464 closest distance to " O   HOH Z 189 " =    1.954
peak=   -3.461 closest distance to " CG  ASP A 231 " =    0.843
peak=   -3.455 closest distance to " CB  ASP A 171 " =    2.261
peak=   -3.448 closest distance to " O   HOH Z 227 " =    1.126
peak=   -3.440 closest distance to " CB  PHE A 192 " =    2.045
peak=   -3.439 closest distance to " O   ASP A  27 " =    2.181
peak=   -3.438 closest distance to " CD  PRO A 243 " =    1.944
peak=   -3.432 closest distance to " O   VAL A  67 " =    2.871
peak=   -3.410 closest distance to " O   HOH Z 174 " =    1.950
peak=   -3.402 closest distance to " O   HOH Z 165 " =    1.840
peak=   -3.398 closest distance to " O   HOH Z 136 " =    2.617
peak=   -3.395 closest distance to " O   GLY A  75 " =    2.068
peak=   -3.394 closest distance to " O   HOH Z 185 " =    2.246
peak=   -3.391 closest distance to " O   HOH Z 120 " =    1.894
peak=   -3.390 closest distance to " CG1 VAL A 197 " =    2.296
peak=   -3.389 closest distance to " O   VAL A 125 " =    2.234
peak=   -3.383 closest distance to " O   HOH Z 385 " =    3.810
peak=   -3.383 closest distance to " O   HOH Z 166 " =    1.546
peak=   -3.383 closest distance to " CD2 PHE A  61 " =    2.065
peak=   -3.382 closest distance to " O   HOH Z 292 " =    4.562
peak=   -3.380 closest distance to " OG1 THR A  82 " =    1.472
peak=   -3.376 closest distance to " CG  GLU A 277 " =    1.177
peak=   -3.372 closest distance to " OD1 ASN A 187 " =    1.580
peak=   -3.369 closest distance to " CD1 LEU A  25 " =    2.456
peak=   -3.361 closest distance to " O   HOH Z 384 " =    2.001
peak=   -3.358 closest distance to " O   HOH Z 301 " =    2.483
peak=   -3.357 closest distance to " CD1 TYR A 247 " =    2.373
peak=   -3.357 closest distance to " OH  TYR A 247 " =    2.005
peak=   -3.352 closest distance to " NH2 ARG A 159 " =    2.476
peak=   -3.351 closest distance to " CD2 LEU A 167 " =    1.743
peak=   -3.348 closest distance to " CG  ASP A  50 " =    2.200
peak=   -3.345 closest distance to " OE1 GLN A  88 " =    0.845
peak=   -3.343 closest distance to " O   HOH Z 231 " =    1.885
peak=   -3.342 closest distance to " CB  ALA A 291 " =    2.454
peak=   -3.338 closest distance to " OH  TYR A 247 " =    1.913
peak=   -3.338 closest distance to " CA  SER A  62 " =    2.663
peak=   -3.332 closest distance to " O   HOH Z 196 " =    1.994
peak=   -3.329 closest distance to " O   HOH Z 216 " =    1.570
peak=   -3.329 closest distance to " CD1 ILE A 151 " =    2.380
peak=   -3.326 closest distance to " O   HOH Z 377 " =    1.209
peak=   -3.325 closest distance to " NH1 ARG A 195 " =    1.100
peak=   -3.325 closest distance to " CG  MET A 105 " =    0.848
peak=   -3.324 closest distance to " CA  GLY A 203 " =    2.294
peak=   -3.323 closest distance to " O   HOH Z 340 " =    1.633
peak=   -3.319 closest distance to " O   HOH Z 151 " =    1.160
peak=   -3.317 closest distance to " O   HOH Z 177 " =    1.778
peak=   -3.312 closest distance to " OE2 GLU A 277 " =    2.878
peak=   -3.312 closest distance to " CD  ARG A 139 " =    1.524
peak=   -3.310 closest distance to " O   HOH Z 109 " =    1.148
peak=   -3.308 closest distance to " CA  GLY A 133 " =    2.458
peak=   -3.304 closest distance to " O   HOH Z 111 " =    1.321
peak=   -3.303 closest distance to " O   HOH Z 210 " =    0.711
peak=   -3.302 closest distance to " CD1 LEU A 167 " =    2.168
peak=   -3.300 closest distance to " CE2 PHE A  61 " =    2.545
peak=   -3.297 closest distance to " O   HOH Z 133 " =    1.361
peak=   -3.293 closest distance to " CG2 VAL A 112 " =    2.527
peak=   -3.290 closest distance to " O   HOH Z  33 " =    1.965
peak=   -3.290 closest distance to " O   HOH Z 259 " =    1.663
peak=   -3.282 closest distance to " O   HOH Z  78 " =    1.699
peak=   -3.279 closest distance to " O   HOH Z 388 " =    1.923
peak=   -3.269 closest distance to " O   HOH Z 259 " =    4.230
peak=   -3.267 closest distance to " O   ALA A  34 " =    2.550
peak=   -3.262 closest distance to " N   SER A   3 " =    2.287
peak=   -3.260 closest distance to " C   THR A 279 " =    1.170
peak=   -3.253 closest distance to " OD1 ASN A 173 " =    1.429
peak=   -3.252 closest distance to " C   LEU A 143 " =    1.188
peak=   -3.252 closest distance to " CD1 ILE A 263 " =    2.129
peak=   -3.251 closest distance to " N   THR A 235 " =    1.220
peak=   -3.250 closest distance to " O   THR A  18 " =    1.482
peak=   -3.249 closest distance to " CG  GLU A  53 " =    1.678
peak=   -3.242 closest distance to " O   HOH Z 156 " =    3.632
peak=   -3.240 closest distance to " O   HOH Z 367 " =    3.822
peak=   -3.239 closest distance to " O   HOH Z 285 " =    1.638
peak=   -3.239 closest distance to " CB  ASP A 132 " =    2.310
peak=   -3.237 closest distance to " O   SER A  95 " =    1.934
peak=   -3.236 closest distance to " ND2 ASN A  60 " =    1.881
peak=   -3.234 closest distance to " NE2 GLN A 103 " =    1.787
peak=   -3.223 closest distance to " C   GLY A  17 " =    1.248
peak=   -3.216 closest distance to " O   HOH Z  43 " =    1.577
peak=   -3.212 closest distance to " O   HOH Z  60 " =    2.063
peak=   -3.210 closest distance to " OG1 THR A  82 " =    1.352
peak=   -3.209 closest distance to " CD2 PHE A 225 " =    1.246
peak=   -3.207 closest distance to " OH  TYR A 169 " =    0.963
peak=   -3.201 closest distance to " O   HOH Z  58 " =    1.300
peak=   -3.197 closest distance to " CB  TRP A  85 " =    2.584
peak=   -3.196 closest distance to " O   HOH Z 423 " =    2.253
peak=   -3.192 closest distance to " ND2 ASN A  45 " =    1.399
peak=   -3.192 closest distance to " O   HOH Z 120 " =    1.191
peak=   -3.189 closest distance to " CB  MET A 188 " =    1.731
peak=   -3.185 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.180 closest distance to " CE  MET A 105 " =    2.507
peak=   -3.180 closest distance to " O   HOH Z 308 " =    1.589
peak=   -3.174 closest distance to " O   HOH Z 113 " =    2.345
peak=   -3.171 closest distance to " CG  TRP A 266 " =    1.772
peak=   -3.160 closest distance to " O   HOH Z 238 " =    1.190
peak=   -3.155 closest distance to " OE1 GLN A  88 " =    1.021
peak=   -3.151 closest distance to " O   HOH Z 150 " =    1.614
peak=   -3.144 closest distance to " O   HOH Z 136 " =    1.093
peak=   -3.143 closest distance to " O   HOH Z 110 " =    1.535
peak=   -3.140 closest distance to " CG  ARG A 219 " =    2.642
peak=   -3.138 closest distance to " OG  SER A  63 " =    1.188
peak=   -3.134 closest distance to " CA  HIS A  86 " =    2.245
peak=   -3.133 closest distance to " CB  SER A 146 " =    2.151
peak=   -3.124 closest distance to " O   ASN A 187 " =    1.727
peak=   -3.119 closest distance to " CD  GLN A  88 " =    0.997
peak=   -3.118 closest distance to " CD1 LEU A 228 " =    2.336
peak=   -3.117 closest distance to " O   HOH Z 350 " =    1.831
peak=   -3.115 closest distance to " O   HOH Z 378 " =    1.454
peak=   -3.113 closest distance to " CA  ASN A 127 " =    1.039
peak=   -3.111 closest distance to " CG  GLN A  11 " =    1.637
peak=   -3.108 closest distance to " CG1 VAL A 112 " =    2.749
peak=   -3.105 closest distance to " OG  SER A 141 " =    1.707
peak=   -3.099 closest distance to " N   ILE A 120 " =    1.040
peak=   -3.094 closest distance to " O   HOH Z  30 " =    0.922
peak=   -3.090 closest distance to " O   HOH Z 139 " =    3.360
peak=   -3.087 closest distance to " O   HOH Z 353 " =    2.247
peak=   -3.083 closest distance to " O   HOH Z  17 " =    1.366
peak=   -3.074 closest distance to " NZ  LYS A 119 " =    2.018
peak=   -3.069 closest distance to " CA  GLY A 241 " =    3.244
peak=   -3.066 closest distance to " OG  SER A  87 " =    1.629
peak=   -3.063 closest distance to " O   HOH Z 246 " =    1.431
peak=   -3.051 closest distance to " ND2 ASN A  60 " =    1.583
peak=   -3.044 closest distance to " O   SER A 258 " =    2.233

================= 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    :  0.4867 0.4730   6.285420e+00   6.265615e+00
   1_bss:  0.4794 0.4632   6.278780e+00   6.258523e+00
   1_xyz:  0.3982 0.4091   6.181642e+00   6.190484e+00
   1_adp:  0.3530 0.3952   6.098457e+00   6.163509e+00
   1_occ:  0.3523 0.3946   6.097370e+00   6.164048e+00
   2_bss:  0.3498 0.3888   6.098888e+00   6.162747e+00
   2_xyz:  0.2776 0.3334   5.915754e+00   6.046840e+00
   2_adp:  0.2606 0.3131   5.873442e+00   6.009607e+00
   2_occ:  0.2602 0.3137   5.873430e+00   6.011040e+00
   3_bss:  0.2595 0.3130   5.874219e+00   6.010551e+00
   3_xyz:  0.2011 0.2403   5.632396e+00   5.783457e+00
   3_adp:  0.1844 0.2224   5.560645e+00   5.719885e+00
   3_occ:  0.1842 0.2224   5.560256e+00   5.720358e+00
   4_bss:  0.1836 0.2224   5.559073e+00   5.719257e+00
   4_xyz:  0.1514 0.1921   5.388334e+00   5.580968e+00
   4_adp:  0.1446 0.1884   5.357299e+00   5.562086e+00
   4_occ:  0.1445 0.1885   5.357086e+00   5.562084e+00
   5_bss:  0.1447 0.1884   5.357649e+00   5.561495e+00
   5_xyz:  0.1244 0.1706   5.234209e+00   5.464963e+00
   5_adp:  0.1207 0.1693   5.214475e+00   5.453646e+00
   5_occ:  0.1207 0.1692   5.214209e+00   5.453407e+00
   5_bss:  0.1206 0.1691   5.214046e+00   5.453229e+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:  0.300  20.000   6.200  11.467   8.614   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.200  11.467   8.614   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.200  11.467   8.614   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.200  11.467   8.614   0.000   0.000   0.000
   2_bss:  0.319  50.000   3.031   7.405   5.075   0.000   0.000   0.000
   2_xyz:  0.319  50.000   3.031   7.405   5.075   0.000   0.000   0.000
   2_adp:  0.319  50.000   3.031   7.405   5.075   0.000   0.000   0.000
   2_occ:  0.319  50.000   3.031   7.405   5.075   0.000   0.000   0.000
   3_bss:  0.304  50.000   2.192   4.884   3.666   0.000   0.000   0.000
   3_xyz:  0.304  50.000   2.192   4.884   3.666   0.000   0.000   0.000
   3_adp:  0.304  50.000   2.192   4.884   3.666   0.000   0.000   0.000
   3_occ:  0.304  50.000   2.192   4.884   3.666   0.000   0.000   0.000
   4_bss:  0.315  65.788   1.440   3.064   2.971   0.000   0.000   0.000
   4_xyz:  0.315  65.788   1.440   3.064   2.971   0.000   0.000   0.000
   4_adp:  0.315  65.788   1.440   3.064   2.971   0.000   0.000   0.000
   4_occ:  0.315  65.788   1.440   3.064   2.971   0.000   0.000   0.000
   5_bss:  0.327  66.757   1.435   2.640   3.036   0.000   0.000   0.000
   5_xyz:  0.327  66.757   1.435   2.640   3.036   0.000   0.000   0.000
   5_adp:  0.327  66.757   1.435   2.640   3.036   0.000   0.000   0.000
   5_occ:  0.327  66.757   1.435   2.640   3.036   0.000   0.000   0.000
   5_bss:  0.325  66.924  -0.833   0.108   0.725   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.259 0.4291  0.4839    67492.415
   1_bss:  56.666 0.4357  0.6344    66140.668
   1_xyz:  47.138 0.5549  0.7856    48425.715
   1_adp:  43.455 0.6009  0.9014    43604.474
   1_occ:  43.428 0.6012  0.9009    43573.348
   2_bss:  43.176 0.6044  0.8014    43325.823
   2_xyz:  35.972 0.6895  0.9065    30799.962
   2_adp:  33.566 0.7180  0.9229    27684.810
   2_occ:  33.640 0.7171  0.9215    27786.048
   3_bss:  33.520 0.7185  0.8739    27689.037
   3_xyz:  23.937 0.8227  0.9644    15032.220
   3_adp:  21.809 0.8448  0.9768    13001.466
   3_occ:  21.815 0.8448  0.9767    13014.444
   4_bss:  21.747 0.8454  0.9408    12948.282
   4_xyz:  18.264 0.8783  0.9604     9424.519
   4_adp:  17.704 0.8838  0.9562     9099.493
   4_occ:  17.705 0.8838  0.9561     9101.151
   5_bss:  17.682 0.8839  0.9525     9080.177
   5_xyz:  15.643 0.9014  0.9638     7436.906
   5_adp:  15.346 0.9041  0.9578     7287.306
   5_occ:  15.339 0.9041  0.9577     7284.250
   5_bss:  15.334 0.9042  0.9627     7282.469
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4487e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4487e+01
   1_xyz:   1.670  0.013  0.106 18.025  0.007  4.126   1.3926e-01
   1_adp:   1.670  0.013  0.106 18.025  0.007  4.126   1.3926e-01
   1_occ:   1.670  0.013  0.106 18.025  0.007  4.126   1.3926e-01
   2_bss:   1.670  0.013  0.106 18.025  0.007  4.126   1.3926e-01
   2_xyz:   1.252  0.009  0.083 16.191  0.004  4.112   8.7018e-02
   2_adp:   1.252  0.009  0.083 16.191  0.004  4.112   8.7018e-02
   2_occ:   1.252  0.009  0.083 16.191  0.004  4.112   8.7018e-02
   3_bss:   1.252  0.009  0.083 16.191  0.004  4.112   8.7018e-02
   3_xyz:   1.102  0.008  0.079 15.517  0.004  4.135   7.3750e-02
   3_adp:   1.102  0.008  0.079 15.517  0.004  4.135   7.3750e-02
   3_occ:   1.102  0.008  0.079 15.517  0.004  4.135   7.3750e-02
   4_bss:   1.102  0.008  0.079 15.517  0.004  4.135   7.3750e-02
   4_xyz:   1.027  0.008  0.076 15.401  0.003  4.128   6.4001e-02
   4_adp:   1.027  0.008  0.076 15.401  0.003  4.128   6.4001e-02
   4_occ:   1.027  0.008  0.076 15.401  0.003  4.128   6.4001e-02
   5_bss:   1.027  0.008  0.076 15.401  0.003  4.128   6.4001e-02
   5_xyz:   1.195  0.011  0.093 15.679  0.004  4.117   8.4786e-02
   5_adp:   1.195  0.011  0.093 15.679  0.004  4.117   8.4786e-02
   5_occ:   1.195  0.011  0.093 15.679  0.004  4.117   8.4786e-02
   5_bss:   1.195  0.011  0.093 15.679  0.004  4.117   8.4786e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0644e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0644e+00
   1_xyz:  14.982  0.160  0.457 89.284  0.040  2.272   1.0251e-01
   1_adp:  14.982  0.160  0.457 89.284  0.040  2.272   1.0251e-01
   1_occ:  14.982  0.160  0.457 89.284  0.040  2.272   1.0251e-01
   2_bss:  14.982  0.160  0.457 89.284  0.040  2.272   1.0251e-01
   2_xyz:   9.553  0.086  0.312 85.483  0.019  2.076   5.8133e-02
   2_adp:   9.553  0.086  0.312 85.483  0.019  2.076   5.8133e-02
   2_occ:   9.553  0.086  0.312 85.483  0.019  2.076   5.8133e-02
   3_bss:   9.553  0.086  0.312 85.483  0.019  2.076   5.8133e-02
   3_xyz:   7.250  0.049  0.264 87.930  0.055  2.204   1.1158e-01
   3_adp:   7.250  0.049  0.264 87.930  0.055  2.204   1.1158e-01
   3_occ:   7.250  0.049  0.264 87.930  0.055  2.204   1.1158e-01
   4_bss:   7.250  0.049  0.264 87.930  0.055  2.204   1.1158e-01
   4_xyz:   7.793  0.051  0.288 79.991  0.033  2.195   5.0423e-02
   4_adp:   7.793  0.051  0.288 79.991  0.033  2.195   5.0423e-02
   4_occ:   7.793  0.051  0.288 79.991  0.033  2.195   5.0423e-02
   5_bss:   7.793  0.051  0.288 79.991  0.033  2.195   5.0423e-02
   5_xyz:   8.001  0.057  0.584 82.922  0.035  2.304   5.9266e-02
   5_adp:   8.001  0.057  0.584 82.922  0.035  2.304   5.9266e-02
   5_occ:   8.001  0.057  0.584 82.922  0.035  2.304   5.9266e-02
   5_bss:   8.001  0.057  0.584 82.922  0.035  2.304   5.9266e-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: 110.12   0.00  14.27  73.81   0.00  11.73 110.12   0.00  28.11
   1_occ: 110.12   0.00  14.27  73.81   0.00  11.73 110.12   0.00  28.11
   2_bss: 110.12   0.00  14.27  73.81   0.00  11.73 110.12   0.00  28.11
   2_xyz: 110.12   0.00  14.27  73.81   0.00  11.73 110.12   0.00  28.11
   2_adp: 107.59   0.00  13.18  83.65   0.00  10.04 107.59   0.00  30.30
   2_occ: 107.59   0.00  13.18  83.65   0.00  10.04 107.59   0.00  30.30
   3_bss: 107.59   0.00  13.18  83.65   0.00  10.04 107.59   0.00  30.30
   3_xyz: 107.59   0.00  13.18  83.65   0.00  10.04 107.59   0.00  30.30
   3_adp:  98.68   0.00  13.38  75.83   0.00   9.40  98.68   0.00  35.03
   3_occ:  98.68   0.00  13.38  75.83   0.00   9.40  98.68   0.00  35.03
   4_bss:  98.68   0.00  13.38  75.83   0.00   9.40  98.68   0.00  35.03
   4_xyz:  98.68   0.00  13.38  75.83   0.00   9.40  98.68   0.00  35.03
   4_adp:  95.10   0.00  13.57  88.92   0.00   9.17  95.10   0.83  37.50
   4_occ:  95.10   0.00  13.57  88.92   0.00   9.17  95.10   0.83  37.50
   5_bss:  95.10   0.00  13.57  88.92   0.00   9.17  95.10   0.83  37.50
   5_xyz:  95.10   0.00  13.57  88.92   0.00   9.17  95.10   0.83  37.50
   5_adp:  91.83   0.00  13.55  87.05   0.00   8.93  91.83   1.52  38.72
   5_occ:  91.83   0.00  13.55  87.05   0.00   8.93  91.83   1.52  38.72
   5_bss:  94.34   2.51  16.06  89.56   2.51  11.44  94.34   4.03  41.23
------------------------------------------------------------------------
 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:    1.189    0.022    0.408
   1_adp:    1.189    0.022    0.408
   1_occ:    1.189    0.022    0.408
   2_bss:    1.189    0.022    0.408
   2_xyz:    1.682    0.033    0.574
   2_adp:    1.682    0.033    0.574
   2_occ:    1.682    0.033    0.574
   3_bss:    1.682    0.033    0.574
   3_xyz:    1.715    0.060    0.674
   3_adp:    1.715    0.060    0.674
   3_occ:    1.715    0.060    0.674
   4_bss:    1.715    0.060    0.674
   4_xyz:    1.845    0.051    0.730
   4_adp:    1.845    0.051    0.730
   4_occ:    1.845    0.051    0.730
   5_bss:    1.845    0.051    0.730
   5_xyz:    1.852    0.056    0.778
   5_adp:    1.852    0.056    0.778
   5_occ:    1.852    0.056    0.778
   5_bss:    1.852    0.056    0.778
------------------------------------------------------------------------

CPU time actual refinement: 338.34


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_832/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_832/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_832/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_832/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_832/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.19 
  Macro-tasks:
    bulk solvent and scale       = 43.56  
    individual site refinement   = 138.46 
    weights calculation          = 32.73  
    collect and process          = 6.57   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 221.45 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 103.05 
    alpha_beta                      = 8.15   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 113.86 
    fmodel                         = 7.36   
    r_factors                      = 0.22   
    phase_errors                   = 10.57  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 247.06 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.769 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    644 calls, 102.66 s
gradients_fft:          589 calls, 100.53 s

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

# Date 2008-01-16 Time 02:32:46 PST -0800 (1200479566.40 s)
Start R-work = 0.4867, R-free = 0.4730 (no bulk solvent and anisotropic scale)
Final R-work = 0.1369, R-free = 0.1847 (no bulk solvent and anisotropic scale)

Start R-work = 0.4794, R-free = 0.4632
Final R-work = 0.1206, R-free = 0.1691