# Date 2008-01-16 Time 02:39:16 PST -0800 (1200479956.62 s)
#phil __OFF__

Command line arguments: "../921.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 = 12617
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 921

-------------------------------------------------------------------------------
  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: (70.9525, 47.1647, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.01196
Completeness in resolution range: 0.974383
Completeness with d_max=infinity: 0.971339

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0120

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: (70.9525, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.01196
Completeness in resolution range: 0.974383
Completeness with d_max=infinity: 0.971339

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1646 -  4.3047 [2112/2136]  1899   213  10.1%
  bin  2:  4.3047 -  3.4297 [2031/2051]  1829   202   9.9%
  bin  3:  3.4297 -  3.0000 [2000/2019]  1802   198   9.9%
  bin  4:  3.0000 -  2.7275 [1981/2011]  1780   201  10.1%
  bin  5:  2.7275 -  2.5329 [1977/1996]  1779   198  10.0%
  bin  6:  2.5329 -  2.3842 [1964/1989]  1765   199  10.1%
  bin  7:  2.3842 -  2.2652 [1938/1966]  1749   189   9.8%
  bin  8:  2.2652 -  2.1669 [1950/1986]  1754   196  10.1%
  bin  9:  2.1669 -  2.0837 [1940/1982]  1746   194  10.0%
  bin 10:  2.0837 -  2.0120 [1696/1968]  1527   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_921/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2162
        3.04 -     3.66: 4580
        3.66 -     4.28: 8878
        4.28 -     4.90: 12239
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.007 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.087 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.228 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27865 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_921/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_921/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 = 70.9525 47.16465 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4488   r_free= 0.4361   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.245611                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.8010 0.99   1376  152 0.3699 0.3393      6.5531      6.4297|
|  2:  4.8010 -  3.8309 0.99   1315  148 0.3451 0.3686      6.6858      6.7915|
|  3:  3.8309 -  3.3526 0.99   1294  144 0.3973 0.3722      6.6111      6.5816|
|  4:  3.3526 -  3.0488 0.99   1285  142 0.4331 0.3774      6.4914       6.369|
|  5:  3.0488 -  2.8318 0.99   1270  141 0.4653 0.4520      6.3397      6.3716|
|  6:  2.8318 -  2.6658 0.99   1285  141 0.4748 0.5236      6.2584      6.1785|
|  7:  2.6658 -  2.5329 0.99   1264  144 0.4958 0.4816      6.2218      6.1924|
|  8:  2.5329 -  2.4231 0.98   1260  136 0.4986 0.4504      6.1646      6.1407|
|  9:  2.4231 -  2.3302 0.98   1259  141 0.4919 0.5188      6.1012      6.1275|
| 10:  2.3302 -  2.2501 1.00   1252  141 0.5087 0.4800      6.1132      6.0712|
| 11:  2.2501 -  2.1799 0.97   1258  137 0.4935 0.4799      6.0197      6.0659|
| 12:  2.1799 -  2.1178 0.98   1246  139 0.5090 0.4876      5.9862      5.9949|
| 13:  2.1178 -  2.0622 0.99   1251  139 0.5102 0.4733       5.891       5.847|
| 14:  2.0622 -  2.0120 0.81   1015  114 0.5161 0.4911      5.8555      5.7425|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.8010  1376   152  0.75  30.21   0.80     0.77      55889.06|
|  2:  4.8010 -  3.8309  1315   148  0.77  29.34   0.90     0.81      78548.20|
|  3:  3.8309 -  3.3526  1294   144  0.69  36.15   0.85     0.77      83140.81|
|  4:  3.3526 -  3.0488  1285   142  0.62  42.46   0.81     0.67      75869.49|
|  5:  3.0488 -  2.8318  1270   141  0.53  49.51   0.76     0.60      65731.01|
|  6:  2.8318 -  2.6658  1285   141  0.49  52.84   0.74     0.55      61314.57|
|  7:  2.6658 -  2.5329  1264   144  0.46  55.39   0.73     0.51      56895.05|
|  8:  2.5329 -  2.4231  1260   136  0.45  56.33   0.75     0.51      51782.33|
|  9:  2.4231 -  2.3302  1259   141  0.46  55.35   0.73     0.51      46780.05|
| 10:  2.3302 -  2.2501  1252   141  0.46  55.14   0.75     0.53      41941.10|
| 11:  2.2501 -  2.1799  1258   137  0.45  56.02   0.75     0.52      39063.88|
| 12:  2.1799 -  2.1178  1246   139  0.45  56.54   0.75     0.53      36277.00|
| 13:  2.1178 -  2.0622  1251   139  0.44  56.98   0.73     0.51      31243.62|
| 14:  2.0622 -  2.0120  1015   114  0.49  52.92   0.72     0.51      23941.05|
|alpha:            min =        0.51 max =            0.81 mean =         0.60|
|beta:             min =    23941.05 max =        83140.81 mean =     54102.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.66|
|phase err.(test): min =        0.00 max =           89.93 mean =        48.78|
|-----------------------------------------------------------------------------|

============================== 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 = 9.118277              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.144   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.768569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.059   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1475 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2575 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3847 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5012 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6480 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7626 |
|-----------------------------------------------------------------------------|
|-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 |       54.392 |
| 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 |       1.633 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    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 = 12.255)------------------------------------------|
|    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 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4551   r_free= 0.4360   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.250147                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4400   r_free= 0.4203   ksol= 0.35   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,7.70,10.43,0.00,0.00,0.00); trace/3= 8.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.239807                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.445885              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.328   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.734419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.791   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4400      final r-factor (work) = 0.3328          |
| start r-factor (free) = 0.4203      final r-factor (free) = 0.3562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.8039 = 8.45 * 0.50 * 6.2544 + 1.00 * 54.3919                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8718 = 8.45 * 0.50 * 6.0955 + 1.00 * 0.1308                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3328      final r-factor (work) = 0.2772          |
| start r-factor (free) = 0.3562      final r-factor (free) = 0.3141          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4911 = 0.73 * 1.00 * 6.0955 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3794 = 0.73 * 1.00 * 5.9452 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.60   11.18    None  None   None       |
|    all(noH): 2823   0      0.00    86.60   11.18    None  None   None       |
|    Sol.    : 438    0      0.00    86.60   28.44    None  None   None       |
|    Mac.    : 2385   0      0.00    64.70   8.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.661: 1603   |   5:    43.302 -  51.963:   57        |
|      1:     8.661 -  17.321:  681   |   6:    51.963 -  60.623:   19        |
|      2:    17.321 -  25.981:  218   |   7:    60.623 -  69.284:    6        |
|      3:    25.981 -  34.642:  145   |   8:    69.284 -  77.944:    1        |
|      4:    34.642 -  43.302:   92   |   9:    77.944 -  86.605:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2772 r_free = 0.3141             target_work(ml) = 5.896         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2766 r_free = 0.3151             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2766   r_free= 0.3151   ksol= 0.35   Bsol= 50.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,7.70,10.43,0.00,0.00,0.00); trace/3= 8.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.894460                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2730   r_free= 0.3108   ksol= 0.32   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.24,4.53,6.77,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.895386                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.530436              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.618   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347669              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.860  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2730      final r-factor (work) = 0.1886          |
| start r-factor (free) = 0.3108      final r-factor (free) = 0.2300          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6254 = 3.53 * 0.50 * 5.9452 + 1.00 * 0.1308                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1881 = 3.53 * 0.50 * 5.7332 + 1.00 * 0.0678                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1886      final r-factor (work) = 0.1714          |
| start r-factor (free) = 0.2300      final r-factor (free) = 0.2153          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0067 = 0.35 * 1.00 * 5.7332 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9731 = 0.35 * 1.00 * 5.5240 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.45   11.27    None  None   None       |
|    all(noH): 2823   0      0.00    85.45   11.27    None  None   None       |
|    Sol.    : 438    0      0.00    85.45   31.57    None  None   None       |
|    Mac.    : 2385   0      0.00    64.70   7.55     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.546: 1712   |   5:    42.728 -  51.273:   76        |
|      1:     8.546 -  17.091:  556   |   6:    51.273 -  59.818:   22        |
|      2:    17.091 -  25.637:  175   |   7:    59.818 -  68.364:    8        |
|      3:    25.637 -  34.182:  140   |   8:    68.364 -  76.909:    1        |
|      4:    34.182 -  42.728:  132   |   9:    76.909 -  85.455:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1714 r_free = 0.2153             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1713 r_free = 0.2157             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1713   r_free= 0.2157   ksol= 0.32   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.24,4.53,6.77,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.495329                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1704   r_free= 0.2159   ksol= 0.32   Bsol= 64.50   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.56,5.01,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.496581                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.509936              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.829  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.123284              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.955   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1704      final r-factor (work) = 0.1359          |
| start r-factor (free) = 0.2159      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0085 = 2.51 * 0.50 * 5.5304 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8391 = 2.51 * 0.50 * 5.3960 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1359      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1720          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0779 = 1.12 * 1.00 * 5.3960 + 1.00 * 0.0167                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9228 = 1.12 * 1.00 * 5.2598 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.38   12.11    None  None   None       |
|    all(noH): 2823   0      0.00    79.38   12.11    None  None   None       |
|    Sol.    : 438    0      0.00    79.38   36.26    None  None   None       |
|    Mac.    : 2385   0      0.00    72.05   7.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.938: 1623   |   5:    39.691 -  47.629:   87        |
|      1:     7.938 -  15.876:  596   |   6:    47.629 -  55.568:   85        |
|      2:    15.876 -  23.815:  169   |   7:    55.568 -  63.506:   49        |
|      3:    23.815 -  31.753:  108   |   8:    63.506 -  71.444:   13        |
|      4:    31.753 -  39.691:   88   |   9:    71.444 -  79.382:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1274 r_free = 0.1720             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1274 r_free = 0.1721             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1721   ksol= 0.32   Bsol= 64.50   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.56,5.01,0.00,0.00,0.00); trace/3= 3.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.247997                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1721   ksol= 0.33   Bsol= 64.50   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.22,4.59,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247785                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.477943              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 137.365  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.422  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1185          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5845 = 2.48 * 0.50 * 5.2602 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5334 = 2.48 * 0.50 * 5.2161 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1185      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1798 = 0.22 * 1.00 * 5.2161 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2034 = 0.22 * 1.00 * 5.2007 + 1.00 * 0.0416                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.70   11.52    None  None   None       |
|    all(noH): 2823   0      0.00    75.70   11.52    None  None   None       |
|    Sol.    : 438    0      0.77    75.70   33.90    None  None   None       |
|    Mac.    : 2385   0      0.00    72.54   7.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.570: 1650   |   5:    37.849 -  45.418:   80        |
|      1:     7.570 -  15.140:  589   |   6:    45.418 -  52.988:   90        |
|      2:    15.140 -  22.709:  154   |   7:    52.988 -  60.558:   33        |
|      3:    22.709 -  30.279:  106   |   8:    60.558 -  68.128:   13        |
|      4:    30.279 -  37.849:  100   |   9:    68.128 -  75.697:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1632             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1632             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1632   ksol= 0.33   Bsol= 64.50   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.22,4.59,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.191958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1632   ksol= 0.33   Bsol= 64.50   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.22,4.59,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.191979                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.738069              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.859  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.927624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.557   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7906 = 3.74 * 0.50 * 5.2004 + 1.00 * 0.0709                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7506 = 3.74 * 0.50 * 5.1674 + 1.00 * 0.0925                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8060 = 0.93 * 1.00 * 5.1674 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7918 = 0.93 * 1.00 * 5.1517 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.06   11.59    None  None   None       |
|    all(noH): 2823   0      0.00    76.06   11.59    None  None   None       |
|    Sol.    : 438    0      0.76    76.06   34.50    None  None   None       |
|    Mac.    : 2385   0      0.00    74.34   7.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.607: 1646   |   5:    38.032 -  45.639:   77        |
|      1:     7.607 -  15.213:  577   |   6:    45.639 -  53.245:   89        |
|      2:    15.213 -  22.819:  163   |   7:    53.245 -  60.852:   33        |
|      3:    22.819 -  30.426:  104   |   8:    60.852 -  68.458:   17        |
|      4:    30.426 -  38.032:  108   |   9:    68.458 -  76.065:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1614             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1615             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1615   ksol= 0.33   Bsol= 64.50   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,3.22,4.59,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155171                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.8010 0.99   1376  152 0.1013 0.1404      5.4169      5.5659|
|  2:  4.8010 -  3.8309 0.99   1315  148 0.0859 0.1172      5.4573      5.6899|
|  3:  3.8309 -  3.3526 0.99   1294  144 0.1047 0.1460      5.4837      5.8177|
|  4:  3.3526 -  3.0488 0.99   1285  142 0.1170 0.1604      5.4351      5.6033|
|  5:  3.0488 -  2.8318 0.99   1270  141 0.1311 0.1681      5.3363      5.5507|
|  6:  2.8318 -  2.6658 0.99   1285  141 0.1185 0.2047      5.2203      5.5276|
|  7:  2.6658 -  2.5329 0.99   1264  144 0.1284 0.1655      5.1896       5.354|
|  8:  2.5329 -  2.4231 0.98   1260  136 0.1178 0.1764       5.099      5.4079|
|  9:  2.4231 -  2.3302 0.98   1259  141 0.1165 0.1850      5.0603      5.3233|
| 10:  2.3302 -  2.2501 1.00   1252  141 0.1141 0.1722      4.9943      5.2494|
| 11:  2.2501 -  2.1799 0.97   1258  137 0.1131 0.1795      4.9619      5.2493|
| 12:  2.1799 -  2.1178 0.98   1246  139 0.1127 0.1791      4.8916      5.2508|
| 13:  2.1178 -  2.0622 0.99   1251  139 0.1099 0.1686       4.798      5.0545|
| 14:  2.0622 -  2.0120 0.81   1015  114 0.1025 0.1804      4.6728      4.9748|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.8010  1376   152  0.94   9.73   0.97     0.95       8091.64|
|  2:  4.8010 -  3.8309  1315   148  0.95   8.46   1.00     0.99       9744.17|
|  3:  3.8309 -  3.3526  1294   144  0.93  11.26   1.01     1.01      10692.91|
|  4:  3.3526 -  3.0488  1285   142  0.92  13.27   1.00     0.98      10025.09|
|  5:  3.0488 -  2.8318  1270   141  0.90  15.77   0.99     0.96       8545.43|
|  6:  2.8318 -  2.6658  1285   141  0.90  16.31   0.98     0.95       7419.38|
|  7:  2.6658 -  2.5329  1264   144  0.90  16.22   0.98     0.95       6579.24|
|  8:  2.5329 -  2.4231  1260   136  0.91  15.50   0.98     0.95       5701.95|
|  9:  2.4231 -  2.3302  1259   141  0.90  15.99   0.99     0.95       5397.08|
| 10:  2.3302 -  2.2501  1252   141  0.90  16.31   0.99     0.95       4773.69|
| 11:  2.2501 -  2.1799  1258   137  0.90  16.67   0.98     0.94       4685.73|
| 12:  2.1799 -  2.1178  1246   139  0.91  15.80   1.00     0.98       4106.97|
| 13:  2.1178 -  2.0622  1251   139  0.90  16.13   0.98     0.96       3469.97|
| 14:  2.0622 -  2.0120  1015   114  0.92  14.56   0.96     0.92       2631.13|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2631.13 max =        10692.91 mean =      6656.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.14 mean =        13.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1614   ksol= 0.32   Bsol= 61.97   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.38,0.98,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155002                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1614   ksol= 0.32   Bsol= 61.97   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.38,0.98,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.155002                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.8010 0.99   1376  152 0.1009 0.1404      5.4115      5.5622|
|  2:  4.8010 -  3.8309 0.99   1315  148 0.0856 0.1168      5.4543       5.686|
|  3:  3.8309 -  3.3526 0.99   1294  144 0.1046 0.1461      5.4823      5.8178|
|  4:  3.3526 -  3.0488 0.99   1285  142 0.1172 0.1606      5.4362      5.6043|
|  5:  3.0488 -  2.8318 0.99   1270  141 0.1313 0.1682      5.3381      5.5524|
|  6:  2.8318 -  2.6658 0.99   1285  141 0.1187 0.2051       5.222      5.5291|
|  7:  2.6658 -  2.5329 0.99   1264  144 0.1285 0.1658      5.1911      5.3554|
|  8:  2.5329 -  2.4231 0.98   1260  136 0.1179 0.1765      5.0999      5.4085|
|  9:  2.4231 -  2.3302 0.98   1259  141 0.1165 0.1850      5.0607      5.3232|
| 10:  2.3302 -  2.2501 1.00   1252  141 0.1141 0.1723      4.9947      5.2502|
| 11:  2.2501 -  2.1799 0.97   1258  137 0.1131 0.1793      4.9621       5.249|
| 12:  2.1799 -  2.1178 0.98   1246  139 0.1127 0.1791      4.8916      5.2507|
| 13:  2.1178 -  2.0622 0.99   1251  139 0.1099 0.1687      4.7981      5.0548|
| 14:  2.0622 -  2.0120 0.81   1015  114 0.1025 0.1804      4.6731       4.975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.8010  1376   152  0.94   9.70   0.97     0.95       8008.36|
|  2:  4.8010 -  3.8309  1315   148  0.95   8.42   1.00     0.99       9685.22|
|  3:  3.8309 -  3.3526  1294   144  0.93  11.23   1.02     1.01      10665.74|
|  4:  3.3526 -  3.0488  1285   142  0.92  13.29   1.00     0.98      10041.59|
|  5:  3.0488 -  2.8318  1270   141  0.90  15.78   1.00     0.97       8574.97|
|  6:  2.8318 -  2.6658  1285   141  0.90  16.33   0.98     0.95       7444.56|
|  7:  2.6658 -  2.5329  1264   144  0.90  16.24   0.98     0.96       6599.78|
|  8:  2.5329 -  2.4231  1260   136  0.91  15.52   0.98     0.96       5711.48|
|  9:  2.4231 -  2.3302  1259   141  0.90  16.00   1.00     0.95       5403.77|
| 10:  2.3302 -  2.2501  1252   141  0.90  16.31   0.99     0.95       4775.12|
| 11:  2.2501 -  2.1799  1258   137  0.90  16.67   0.99     0.95       4686.24|
| 12:  2.1799 -  2.1178  1246   139  0.91  15.81   1.00     0.99       4107.39|
| 13:  2.1178 -  2.0622  1251   139  0.90  16.13   0.99     0.97       3471.34|
| 14:  2.0622 -  2.0120  1015   114  0.92  14.57   0.97     0.93       2632.45|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2632.45 max =        10665.74 mean =      6651.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.12 mean =        13.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.73    79.79   15.32    None  None   None       |
|    all(noH): 2823   0      3.73    79.79   15.32    None  None   None       |
|    Sol.    : 438    0      4.49    79.79   38.23    None  None   None       |
|    Mac.    : 2385   0      3.73    78.07   11.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.727 -  11.333: 1646   |   5:    41.759 -  49.366:   77        |
|      1:    11.333 -  18.940:  577   |   6:    49.366 -  56.972:   89        |
|      2:    18.940 -  26.546:  163   |   7:    56.972 -  64.579:   33        |
|      3:    26.546 -  34.153:  104   |   8:    64.579 -  72.185:   17        |
|      4:    34.153 -  41.759:  108   |   9:    72.185 -  79.792:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.306 - 4.874
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 313
   mapped sites are within: 0.702 - 4.874

peak=   10.328 closest distance to " CG2 VAL A 230 " =    1.402
peak=    6.321 closest distance to " NH2 ARG A  56 " =    2.259
peak=    6.075 closest distance to " CG  LEU A   5 " =    1.159
peak=    5.943 closest distance to " CG  LEU A 228 " =    1.152
peak=    5.524 closest distance to " CB  VAL A 296 " =    1.073
peak=    5.378 closest distance to " CB  GLN A 223 " =    1.481
peak=    5.110 closest distance to " CB  GLN A 183 " =    1.287
peak=    5.092 closest distance to " NE2 GLN A  11 " =    1.129
peak=    5.007 closest distance to " O   HOH Z 232 " =    2.332
peak=    4.957 closest distance to " CD2 LEU A   5 " =    1.166
peak=    4.815 closest distance to " CB  VAL A 230 " =    1.176
peak=    4.638 closest distance to " O   HOH Z 142 " =    1.667
peak=    4.602 closest distance to " CB  SER A  63 " =    1.260
peak=    4.569 closest distance to " O   HOH Z 369 " =    2.138
peak=    4.551 closest distance to " CG2 VAL A 296 " =    0.971
peak=    4.501 closest distance to " O   HOH Z 303 " =    2.109
peak=    4.475 closest distance to " CB  ARG A  79 " =    1.504
peak=    4.458 closest distance to " O   HOH Z 427 " =    3.075
peak=    4.410 closest distance to " O   HOH Z 126 " =    1.922
peak=    4.356 closest distance to " O   HOH Z 298 " =    1.918
peak=    4.344 closest distance to " CB  ARG A 190 " =    1.594
peak=    4.331 closest distance to " O   HOH Z  61 " =    1.681
peak=    4.257 closest distance to " O   HOH Z 265 " =    2.197
peak=    4.245 closest distance to " CZ  PHE A 218 " =    1.133
peak=    4.241 closest distance to " O   SER A  87 " =    2.337
peak=    4.226 closest distance to " O   HOH Z 368 " =    2.299
peak=    4.214 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.202 closest distance to " CB  GLU A 152 " =    1.191
peak=    4.178 closest distance to " O   HOH Z 158 " =    3.182
peak=    4.164 closest distance to " CB  ASP A 140 " =    1.048
peak=    4.124 closest distance to " C   PRO A 198 " =    1.543
peak=    4.111 closest distance to " O   HOH Z 236 " =    2.028
peak=    4.104 closest distance to " O   HOH Z 248 " =    1.644
peak=    4.100 closest distance to " CA  TYR A  30 " =    0.984
peak=    4.089 closest distance to " CB  TYR A 169 " =    0.702
peak=    4.071 closest distance to " O   HOH Z 234 " =    3.681
peak=    4.066 closest distance to " CB  TRP A 266 " =    1.024
peak=    4.045 closest distance to " CB  GLU A 277 " =    3.679
peak=    4.030 closest distance to " CA  ALA A  51 " =    0.929
peak=    4.010 closest distance to " O   HOH Z 423 " =    1.784
peak=    4.000 closest distance to " O   HOH Z 126 " =    1.602
peak=    3.998 closest distance to " O   HOH Z  78 " =    1.645
peak=    3.995 closest distance to " O   HOH Z 403 " =    1.626
peak=    3.980 closest distance to " O   HOH Z 411 " =    3.810
peak=    3.971 closest distance to " O   HOH Z 346 " =    1.615
peak=    3.967 closest distance to " CB  GLU A 128 " =    1.044
peak=    3.956 closest distance to " CB  ASN A 148 " =    1.440
peak=    3.950 closest distance to " CG  PRO A 213 " =    1.154
peak=    3.942 closest distance to " O   HOH Z  19 " =    2.277
peak=    3.932 closest distance to " CG  MET A 185 " =    1.206
peak=    3.928 closest distance to " O   HOH Z 425 " =    1.399
peak=    3.908 closest distance to " O   HOH Z  43 " =    1.998
peak=    3.907 closest distance to " O   HOH Z 214 " =    2.288
peak=    3.887 closest distance to " CB  ASN A 142 " =    1.129
peak=    3.886 closest distance to " CA  ARG A 195 " =    1.220
peak=    3.885 closest distance to " CB  VAL A 202 " =    1.589
peak=    3.878 closest distance to " O   HOH Z 422 " =    2.705
peak=    3.873 closest distance to " OG  SER A  97 " =    3.037
peak=    3.867 closest distance to " OD1 ASN A  69 " =    2.656
peak=    3.867 closest distance to " ND2 ASN A 187 " =    1.477
peak=    3.861 closest distance to " O   HOH Z  44 " =    2.223
peak=    3.858 closest distance to " CB  GLU A  46 " =    0.964
peak=    3.844 closest distance to " O   HOH Z 261 " =    1.950
peak=    3.843 closest distance to " CG1 ILE A  49 " =    1.518
peak=    3.830 closest distance to " NH1AARG A 145 " =    1.246
peak=    3.823 closest distance to " OG BSER A 164 " =    2.271
peak=    3.810 closest distance to " O   HOH Z 280 " =    2.938
peak=    3.809 closest distance to " CB  ALA A   9 " =    1.631
peak=    3.808 closest distance to " O   HOH Z 313 " =    1.825
peak=    3.786 closest distance to " O   HOH Z 171 " =    3.880
peak=    3.776 closest distance to " O   HOH Z 197 " =    2.906
peak=    3.766 closest distance to " O   HOH Z 272 " =    1.906
peak=    3.765 closest distance to " CG1 VAL A 296 " =    1.186
peak=    3.762 closest distance to " O  BHOH Z 338 " =    2.332
peak=    3.758 closest distance to " ND2 ASN A 249 " =    1.895
peak=    3.734 closest distance to " O   HOH Z 213 " =    1.837
peak=    3.731 closest distance to " CD  ARG A 159 " =    0.747
peak=    3.728 closest distance to " CD  LYS A 166 " =    1.311
peak=    3.727 closest distance to " O   HOH Z  80 " =    1.690
peak=    3.719 closest distance to " O   HOH Z 316 " =    3.130
peak=    3.716 closest distance to " O   HOH Z  63 " =    1.940
peak=    3.716 closest distance to " O   HOH Z 193 " =    2.120
peak=    3.716 closest distance to " CB  VAL A 265 " =    1.324
peak=    3.713 closest distance to " CB  THR A  82 " =    1.362
peak=    3.706 closest distance to " N   PHE A 130 " =    1.263
peak=    3.685 closest distance to " CB  THR A  31 " =    1.608
peak=    3.683 closest distance to " O   HOH Z 180 " =    2.157
peak=    3.679 closest distance to " CA  ALA A 295 " =    1.097
peak=    3.678 closest distance to " CD  ARG A  66 " =    2.632
peak=    3.677 closest distance to " CG  PRO A 243 " =    1.137
peak=    3.674 closest distance to " CD2 LEU A 228 " =    1.074
peak=    3.673 closest distance to " CB BVAL A  41 " =    1.158
peak=    3.670 closest distance to " O   MET A 105 " =    1.907
peak=    3.655 closest distance to " O   HOH Z 193 " =    1.915
peak=    3.635 closest distance to " O   HOH Z 147 " =    1.805
peak=    3.610 closest distance to " O   HOH Z  21 " =    1.737
peak=    3.608 closest distance to " O   HOH Z  59 " =    2.332
peak=    3.603 closest distance to " O   HOH Z 285 " =    2.548
peak=    3.596 closest distance to " O   HOH Z 406 " =    1.505
peak=    3.595 closest distance to " CB  ALA A 104 " =    0.746
peak=    3.595 closest distance to " O   HOH Z 359 " =    1.511
peak=    3.592 closest distance to " CA  ALA A 291 " =    0.898
peak=    3.592 closest distance to " CA  ALA A 158 " =    1.255
peak=    3.590 closest distance to " O   HOH Z 251 " =    1.489
peak=    3.590 closest distance to " O   HOH Z 130 " =    2.256
peak=    3.589 closest distance to " O   HOH Z 402 " =    1.479
peak=    3.587 closest distance to " O   HOH Z 371 " =    3.080
peak=    3.586 closest distance to " CB  ASN A  39 " =    0.911
peak=    3.582 closest distance to " CG2 VAL A 257 " =    0.832
peak=    3.581 closest distance to " CD1 LEU A  96 " =    0.706
peak=    3.581 closest distance to " O   HOH Z 273 " =    2.930
peak=    3.576 closest distance to " CD ALYS A 290 " =    1.039
peak=    3.569 closest distance to " CA  TYR A 116 " =    1.488
peak=    3.563 closest distance to " N   ASN A  39 " =    1.277
peak=    3.561 closest distance to " CA  VAL A 125 " =    1.262
peak=    3.547 closest distance to " CG  MET A 185 " =    1.044
peak=    3.544 closest distance to " CA  THR A 264 " =    0.764
peak=    3.538 closest distance to " CG2 ILE A 234 " =    0.858
peak=    3.534 closest distance to " O   HOH Z 299 " =    4.268
peak=    3.529 closest distance to " CG  PRO A 198 " =    1.291
peak=    3.529 closest distance to " CE  LYS A  76 " =    0.884
peak=    3.529 closest distance to " CB  SER A 212 " =    1.212
peak=    3.518 closest distance to " CB  GLN A  89 " =    1.189
peak=    3.515 closest distance to " NE2 GLN A  77 " =    3.371
peak=    3.514 closest distance to " CB  LEU A 143 " =    1.203
peak=    3.511 closest distance to " CD2 TRP A 179 " =    1.313
peak=    3.509 closest distance to " O   ASP A 124 " =    1.110
peak=    3.509 closest distance to " O   HOH Z  40 " =    1.788
peak=    3.506 closest distance to " CD1 LEU A   5 " =    1.314
peak=    3.495 closest distance to " CG2AVAL A  72 " =    1.806
peak=    3.493 closest distance to " CG2 THR A 221 " =    1.168
peak=    3.488 closest distance to " O   HOH Z   9 " =    1.254
peak=    3.485 closest distance to " CA  LYS A 117 " =    1.279
peak=    3.482 closest distance to " CG  GLN A  88 " =    1.060
peak=    3.477 closest distance to " CG1 VAL A 153 " =    0.960
peak=    3.473 closest distance to " CB  ASN A 110 " =    1.137
peak=    3.473 closest distance to " CA  MET A 105 " =    0.988
peak=    3.471 closest distance to " CG  LEU A 167 " =    1.193
peak=    3.466 closest distance to " CG1 ILE A 151 " =    1.096
peak=    3.462 closest distance to " CE1 TYR A 186 " =    1.273
peak=    3.459 closest distance to " N   ASP A 162 " =    1.207
peak=    3.444 closest distance to " CB  TRP A 179 " =    1.463
peak=    3.443 closest distance to " O   HOH Z 245 " =    1.325
peak=    3.441 closest distance to " O   HOH Z 365 " =    2.920
peak=    3.437 closest distance to " CB  LEU A 228 " =    1.199
peak=    3.436 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.434 closest distance to " N   VAL A 126 " =    1.426
peak=    3.434 closest distance to " O   HOH Z 145 " =    2.039
peak=    3.433 closest distance to " O   HOH Z  97 " =    2.052
peak=    3.432 closest distance to " O   HOH Z  48 " =    1.597
peak=    3.431 closest distance to " OG1 THR A 294 " =    2.468
peak=    3.430 closest distance to " O   HOH Z  10 " =    1.789
peak=    3.428 closest distance to " O   HOH Z   9 " =    2.027
peak=    3.423 closest distance to " O   HOH Z 148 " =    3.281
peak=    3.423 closest distance to " CB  SER A 245 " =    3.308
peak=    3.419 closest distance to " O   HOH Z 227 " =    1.817
peak=    3.419 closest distance to " CD  ARG A 269 " =    0.971
peak=    3.419 closest distance to " CA  ALA A  21 " =    1.149
peak=    3.418 closest distance to " O   HOH Z  97 " =    2.412
peak=    3.416 closest distance to " O   ALA A 158 " =    1.432
peak=    3.416 closest distance to " CA  ARG A  36 " =    1.118
peak=    3.414 closest distance to " O   HOH Z  88 " =    3.265
peak=    3.411 closest distance to " CA  ASN A 215 " =    1.208
peak=    3.409 closest distance to " OG  SER A  22 " =    2.816
peak=    3.409 closest distance to " CB  ARG A 139 " =    0.935
peak=    3.407 closest distance to " CB  ASP A 298 " =    1.212
peak=    3.406 closest distance to " O   HOH Z 203 " =    1.729
peak=    3.404 closest distance to " CB  ALA A 248 " =    1.111
peak=    3.404 closest distance to " CB  PRO A  54 " =    0.730
peak=    3.394 closest distance to " N   SER A 135 " =    1.406
peak=    3.393 closest distance to " CB  ALA A  34 " =    0.991
peak=    3.392 closest distance to " O   HOH Z 353 " =    2.616
peak=    3.390 closest distance to " CB  ASN A 187 " =    1.212
peak=    3.388 closest distance to " CB  ALA A 291 " =    1.310
peak=    3.385 closest distance to " O   ASN A 284 " =    1.815
peak=    3.384 closest distance to " CB  LYS A 117 " =    1.194
peak=    3.383 closest distance to " CB  MET A  40 " =    0.803
peak=    3.380 closest distance to " O   ALA A 165 " =    1.517
peak=    3.371 closest distance to " NZ  LYS A  48 " =    1.331
peak=    3.371 closest distance to " O   HOH Z 291 " =    1.604
peak=    3.371 closest distance to " CG BARG A 275 " =    1.413
peak=    3.370 closest distance to " O   HOH Z 329 " =    4.150
peak=    3.369 closest distance to " NZ  LYS A 117 " =    3.237
peak=    3.365 closest distance to " CB  PRO A  90 " =    1.259
peak=    3.362 closest distance to " CB  SER A   3 " =    1.313
peak=    3.361 closest distance to " CA  TYR A  30 " =    1.050
peak=    3.359 closest distance to " CD1 LEU A 300 " =    1.179
peak=    3.355 closest distance to " CG1 ILE A  33 " =    1.270
peak=    3.349 closest distance to " O   HOH Z 368 " =    3.601
peak=    3.348 closest distance to " NE  ARG A  79 " =    1.208
peak=    3.345 closest distance to " NH2 ARG A 156 " =    1.123
peak=    3.345 closest distance to " O   HOH Z 325 " =    2.230
peak=    3.344 closest distance to " O   HOH Z 305 " =    3.616
peak=    3.334 closest distance to " O   HOH Z 184 " =    1.400
peak=    3.334 closest distance to " O   HOH Z 261 " =    1.619
peak=    3.334 closest distance to " CB  TRP A 150 " =    1.378
peak=    3.334 closest distance to " CZ  PHE A 192 " =    0.964
peak=    3.331 closest distance to " NE2 HIS A 207 " =    1.332
peak=    3.331 closest distance to " CB  LEU A  83 " =    0.797
peak=    3.330 closest distance to " CB  ARG A 138 " =    0.977
peak=    3.329 closest distance to " O   GLN A  88 " =    1.664
peak=    3.326 closest distance to " O   HOH Z 302 " =    1.990
peak=    3.325 closest distance to " CG2 ILE A  20 " =    1.361
peak=    3.322 closest distance to " O   HOH Z 166 " =    3.709
peak=    3.319 closest distance to " ND1 HIS A  81 " =    1.685
peak=    3.316 closest distance to " O   HOH Z 133 " =    2.412
peak=    3.315 closest distance to " O   HOH Z 172 " =    3.749
peak=    3.313 closest distance to " O   HOH Z 250 " =    1.333
peak=    3.307 closest distance to " O   HOH Z 112 " =    1.675
peak=    3.306 closest distance to " CG2 THR A 220 " =    0.881
peak=    3.305 closest distance to " O   HOH Z 417 " =    3.299
peak=    3.305 closest distance to " O   HOH Z 313 " =    1.605
peak=    3.303 closest distance to " CZ  PHE A  38 " =    1.158
peak=    3.299 closest distance to " O   HOH Z 128 " =    2.252
peak=    3.294 closest distance to " CB  THR A  52 " =    0.879
peak=    3.292 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.288 closest distance to " O   HOH Z  90 " =    2.327
peak=    3.281 closest distance to " CB  ALA A 100 " =    1.222
peak=    3.281 closest distance to " CA  ALA A 154 " =    1.006
peak=    3.280 closest distance to " OG  SER A 245 " =    1.602
peak=    3.279 closest distance to " CA  THR A 221 " =    0.949
peak=    3.278 closest distance to " CB  GLN A 205 " =    1.070
peak=    3.277 closest distance to " CB  ALA A 227 " =    0.990
peak=    3.276 closest distance to " CD1 LEU A 228 " =    2.063
peak=    3.274 closest distance to " O   HOH Z 294 " =    1.534
peak=    3.270 closest distance to " O   HOH Z 187 " =    2.311
peak=    3.270 closest distance to " CA  SER A  87 " =    0.992
peak=    3.267 closest distance to " CB  SER A 273 " =    0.836
peak=    3.263 closest distance to " O   HOH Z 141 " =    1.663
peak=    3.262 closest distance to " CA  LYS A 181 " =    1.088
peak=    3.260 closest distance to " CZ3 TRP A 274 " =    4.603
peak=    3.259 closest distance to " O   PRO A  90 " =    1.379
peak=    3.258 closest distance to " O   GLU A   2 " =    1.607
peak=    3.258 closest distance to " CA  LEU A 282 " =    1.046
peak=    3.248 closest distance to " CA  ASP A 162 " =    1.030
peak=    3.243 closest distance to " O   HOH Z 380 " =    1.893
peak=    3.240 closest distance to " O   HOH Z 193 " =    1.730
peak=    3.240 closest distance to " CG BARG A 102 " =    1.808
peak=    3.239 closest distance to " CB  GLN A  88 " =    1.226
peak=    3.234 closest distance to " CA  ALA A 233 " =    1.469
peak=    3.232 closest distance to " NH2AARG A 275 " =    3.411
peak=    3.227 closest distance to " CB  TYR A 116 " =    0.855
peak=    3.224 closest distance to " CG  PHE A 204 " =    0.893
peak=    3.224 closest distance to " O   HOH Z  68 " =    2.207
peak=    3.224 closest distance to " O   TRP A 274 " =    1.845
peak=    3.218 closest distance to " CB  GLN A 103 " =    1.034
peak=    3.215 closest distance to " O   HOH Z 174 " =    2.487
peak=    3.209 closest distance to " O   HOH Z 409 " =    3.233
peak=    3.203 closest distance to " CB  ILE A 120 " =    1.349
peak=    3.202 closest distance to " CB  ALA A 242 " =    0.852
peak=    3.202 closest distance to " O   HOH Z 290 " =    1.017
peak=    3.201 closest distance to " O   HOH Z  20 " =    1.562
peak=    3.198 closest distance to " CA  ARG A 159 " =    1.211
peak=    3.194 closest distance to " CA  ILE A 106 " =    0.763
peak=    3.194 closest distance to " CB  SER A  26 " =    1.844
peak=    3.186 closest distance to " O   HOH Z 171 " =    2.230
peak=    3.184 closest distance to " OE2 GLU A  53 " =    2.013
peak=    3.184 closest distance to " O   HOH Z 128 " =    2.221
peak=    3.178 closest distance to " O   HOH Z  85 " =    2.302
peak=    3.175 closest distance to " O   LEU A 228 " =    1.959
peak=    3.173 closest distance to " CE  MET A 113 " =    1.739
peak=    3.173 closest distance to " O   ARG A  56 " =    2.907
peak=    3.172 closest distance to " O   HOH Z 327 " =    1.788
peak=    3.172 closest distance to " O   PHE A  61 " =    1.393
peak=    3.172 closest distance to " O   HOH Z 263 " =    1.690
peak=    3.171 closest distance to " O   HOH Z  88 " =    3.401
peak=    3.168 closest distance to " CB  THR A 157 " =    1.168
peak=    3.164 closest distance to " OG  SER A  62 " =    2.941
peak=    3.161 closest distance to " CB  VAL A 268 " =    0.843
peak=    3.160 closest distance to " O   HOH Z 188 " =    1.927
peak=    3.158 closest distance to " CD1 ILE A  33 " =    1.746
peak=    3.157 closest distance to " O   HOH Z 250 " =    1.279
peak=    3.155 closest distance to " CB  ASN A 224 " =    0.999
peak=    3.155 closest distance to " CA  ARG A 139 " =    1.064
peak=    3.153 closest distance to " CZ3 TRP A  85 " =    0.989
peak=    3.150 closest distance to " O   HOH Z 215 " =    3.016
peak=    3.148 closest distance to " O   HOH Z 383 " =    2.200
peak=    3.147 closest distance to " CB  PHE A 204 " =    0.966
peak=    3.147 closest distance to " CZ3 TRP A 266 " =    1.125
peak=    3.138 closest distance to " CB  ALA A  43 " =    0.789
peak=    3.134 closest distance to " N   ASN A 127 " =    1.243
peak=    3.133 closest distance to " O   GLN A 278 " =    1.530
peak=    3.133 closest distance to " OG BSER A  99 " =    2.231
peak=    3.129 closest distance to " CB  SER A 216 " =    0.820
peak=    3.126 closest distance to " N   SER A  12 " =    1.619
peak=    3.119 closest distance to " CE2 TYR A  30 " =    0.886
peak=    3.118 closest distance to " CB  ASN A 215 " =    1.214
peak=    3.114 closest distance to " CB  LEU A 261 " =    0.783
peak=    3.113 closest distance to " CD  ARG A  79 " =    2.046
peak=    3.112 closest distance to " CA  GLY A 211 " =    1.362
peak=    3.111 closest distance to " CD1 ILE A 106 " =    0.983
peak=    3.106 closest distance to " O   HOH Z 426 " =    1.548
peak=    3.098 closest distance to " CG  ARG A 159 " =    0.959
peak=    3.090 closest distance to " CB  ALA A 114 " =    1.270
peak=    3.086 closest distance to " CB  ALA A   1 " =    4.874
peak=    3.077 closest distance to " O   HOH Z 185 " =    1.959
peak=    3.075 closest distance to " CB  LEU A  96 " =    1.302
peak=    3.070 closest distance to " OD1 ASN A 217 " =    1.664
peak=    3.065 closest distance to " O   HOH Z 359 " =    4.188
peak=    3.064 closest distance to " CG  MET A 113 " =    1.691
peak=    3.058 closest distance to " CA  VAL A  41 " =    0.877
peak=    3.058 closest distance to " OH  TYR A 214 " =    1.249
peak=    3.056 closest distance to " CB  PRO A 243 " =    1.619
peak=    3.050 closest distance to " CB  ASN A 173 " =    1.086
peak=    3.043 closest distance to " O   HOH Z 271 " =    2.359
peak=    3.032 closest distance to " O   HOH Z 201 " =    3.034
peak=    3.025 closest distance to " N   ALA A  51 " =    1.156
peak=    3.005 closest distance to " O   HOH Z 134 " =    2.684

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.688 - 5.436
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.765 - 5.436

peak=   -5.218 closest distance to " CG2 VAL A 230 " =    0.784
peak=   -4.551 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -4.459 closest distance to " CD  ARG A 156 " =    2.071
peak=   -4.411 closest distance to " CD  GLN A  58 " =    0.983
peak=   -4.378 closest distance to " CD  ARG A  14 " =    3.324
peak=   -4.321 closest distance to " CB  PRO A 243 " =    2.657
peak=   -4.217 closest distance to " O   HOH Z 266 " =    5.436
peak=   -4.166 closest distance to " OE1 GLN A 223 " =    2.203
peak=   -4.162 closest distance to " CG2BVAL A  41 " =    2.740
peak=   -4.131 closest distance to " O   HOH Z  73 " =    2.272
peak=   -4.115 closest distance to " O   HOH Z 196 " =    2.221
peak=   -4.011 closest distance to " O   HOH Z 211 " =    1.413
peak=   -4.008 closest distance to " OG  SER A  97 " =    2.331
peak=   -3.993 closest distance to " CZ3 TRP A 179 " =    1.172
peak=   -3.963 closest distance to " N   ALA A  43 " =    2.593
peak=   -3.960 closest distance to " CB  ALA A 161 " =    2.592
peak=   -3.933 closest distance to " C   HIS A 108 " =    1.148
peak=   -3.925 closest distance to " CG1 VAL A 250 " =    2.780
peak=   -3.924 closest distance to " OG BSER A 134 " =    1.324
peak=   -3.911 closest distance to " CA  ASP A 298 " =    1.044
peak=   -3.883 closest distance to " CB  PHE A 192 " =    1.968
peak=   -3.871 closest distance to " O   VAL A  67 " =    2.829
peak=   -3.833 closest distance to " NE2 GLN A 194 " =    1.851
peak=   -3.824 closest distance to " O   HOH Z 231 " =    2.171
peak=   -3.821 closest distance to " OD1 ASN A 148 " =    1.478
peak=   -3.802 closest distance to " CG2 ILE A  49 " =    2.760
peak=   -3.796 closest distance to " CG1 VAL A 296 " =    1.276
peak=   -3.767 closest distance to " OXT GLY A 302 " =    2.984
peak=   -3.764 closest distance to " O   HOH Z 351 " =    1.574
peak=   -3.762 closest distance to " NH2AARG A 275 " =    5.285
peak=   -3.749 closest distance to " CA  GLY A 241 " =    3.172
peak=   -3.731 closest distance to " O   HOH Z 394 " =    1.582
peak=   -3.708 closest distance to " O   HOH Z 290 " =    1.338
peak=   -3.707 closest distance to " CG1 VAL A 112 " =    2.763
peak=   -3.703 closest distance to " O   VAL A 189 " =    2.629
peak=   -3.697 closest distance to " CG  ARG A 269 " =    2.450
peak=   -3.683 closest distance to " O   HOH Z 166 " =    1.916
peak=   -3.673 closest distance to " O   HOH Z 216 " =    1.323
peak=   -3.657 closest distance to " O   HOH Z 185 " =    2.409
peak=   -3.652 closest distance to " CE3 TRP A 150 " =    2.254
peak=   -3.647 closest distance to " O   HOH Z  37 " =    1.882
peak=   -3.641 closest distance to " CE2 TYR A  30 " =    2.737
peak=   -3.639 closest distance to " CA  GLY A 241 " =    2.329
peak=   -3.636 closest distance to " CG  HIS A  86 " =    1.088
peak=   -3.636 closest distance to " CB  ALA A 248 " =    2.364
peak=   -3.613 closest distance to " O   HOH Z 435 " =    2.758
peak=   -3.612 closest distance to " O   PRO A 163 " =    2.218
peak=   -3.603 closest distance to " CD2 PHE A  61 " =    2.567
peak=   -3.597 closest distance to " CB  ALA A 248 " =    2.194
peak=   -3.583 closest distance to " CD2 TYR A 293 " =    2.029
peak=   -3.573 closest distance to " C   ALA A 158 " =    1.304
peak=   -3.565 closest distance to " NE2 GLN A  88 " =    2.091
peak=   -3.553 closest distance to " O   HOH Z  38 " =    1.546
peak=   -3.541 closest distance to " O   HOH Z  10 " =    1.484
peak=   -3.534 closest distance to " CB  ALA A  43 " =    2.562
peak=   -3.524 closest distance to " CG2BVAL A  41 " =    1.780
peak=   -3.521 closest distance to " OG  SER A  87 " =    1.462
peak=   -3.521 closest distance to " C   MET A 188 " =    1.388
peak=   -3.518 closest distance to " O   HOH Z 114 " =    3.052
peak=   -3.516 closest distance to " ND2 ASN A  45 " =    1.517
peak=   -3.514 closest distance to " CB  PRO A 163 " =    2.530
peak=   -3.512 closest distance to " O   HOH Z  44 " =    2.206
peak=   -3.503 closest distance to " CG  GLU A 277 " =    1.180
peak=   -3.498 closest distance to " O   HOH Z 407 " =    3.190
peak=   -3.496 closest distance to " CD1 LEU A 101 " =    2.434
peak=   -3.489 closest distance to " CD1 PHE A  59 " =    2.025
peak=   -3.488 closest distance to " N   ALA A 226 " =    2.143
peak=   -3.488 closest distance to " O   HOH Z 359 " =    2.954
peak=   -3.487 closest distance to " O   HOH Z 426 " =    1.619
peak=   -3.487 closest distance to " CG  TRP A 266 " =    1.821
peak=   -3.484 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.481 closest distance to " CD1 ILE A 199 " =    2.588
peak=   -3.477 closest distance to " O   HOH Z 241 " =    1.237
peak=   -3.474 closest distance to " O   HOH Z  52 " =    1.598
peak=   -3.469 closest distance to " O   HOH Z 113 " =    2.455
peak=   -3.463 closest distance to " CE BMET A  47 " =    1.830
peak=   -3.458 closest distance to " CD1 LEU A 228 " =    2.310
peak=   -3.455 closest distance to " O   HOH Z 377 " =    2.148
peak=   -3.454 closest distance to " O   SER A 271 " =    2.156
peak=   -3.447 closest distance to " N   THR A 157 " =    1.546
peak=   -3.446 closest distance to " O   HOH Z 166 " =    1.579
peak=   -3.445 closest distance to " O   HOH Z  11 " =    1.858
peak=   -3.443 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.425 closest distance to " O   HOH Z  60 " =    1.936
peak=   -3.424 closest distance to " O   GLY A  80 " =    2.603
peak=   -3.419 closest distance to " ND2 ASN A  45 " =    1.308
peak=   -3.417 closest distance to " O   GLY A 196 " =    1.272
peak=   -3.416 closest distance to " CG2 ILE A 263 " =    2.419
peak=   -3.413 closest distance to " CE  MET A 105 " =    2.413
peak=   -3.409 closest distance to " CD2 LEU A 300 " =    2.811
peak=   -3.408 closest distance to " C   LEU A 143 " =    1.022
peak=   -3.405 closest distance to " CD  PRO A 213 " =    2.212
peak=   -3.398 closest distance to " O   HOH Z 177 " =    1.831
peak=   -3.383 closest distance to " CB  ALA A 291 " =    2.356
peak=   -3.380 closest distance to " O   HOH Z 389 " =    2.038
peak=   -3.379 closest distance to " CA  GLY A 203 " =    2.425
peak=   -3.374 closest distance to " O   HOH Z   6 " =    1.619
peak=   -3.366 closest distance to " CD1 ILE A 151 " =    2.409
peak=   -3.364 closest distance to " CB  ASP A 132 " =    2.322
peak=   -3.361 closest distance to " N   THR A  52 " =    1.699
peak=   -3.359 closest distance to " O   HOH Z 102 " =    1.584
peak=   -3.354 closest distance to " O   HOH Z 234 " =    4.357
peak=   -3.349 closest distance to " CG2 VAL A 296 " =    1.194
peak=   -3.340 closest distance to " CD2 LEU A 167 " =    1.848
peak=   -3.334 closest distance to " OD2 ASP A  50 " =    2.218
peak=   -3.324 closest distance to " O   ARG A  24 " =    2.136
peak=   -3.323 closest distance to " N   ALA A 248 " =    2.431
peak=   -3.322 closest distance to " N   ALA A 248 " =    1.899
peak=   -3.311 closest distance to " CB  VAL A 230 " =    1.044
peak=   -3.311 closest distance to " CG1 VAL A  67 " =    2.821
peak=   -3.307 closest distance to " O   HOH Z 123 " =    2.467
peak=   -3.303 closest distance to " NE2 GLN A  88 " =    1.067
peak=   -3.301 closest distance to " C   GLY A  17 " =    1.279
peak=   -3.300 closest distance to " O   HOH Z 198 " =    2.489
peak=   -3.296 closest distance to " N   SER A 276 " =    1.455
peak=   -3.293 closest distance to " CD1 LEU A   5 " =    2.574
peak=   -3.292 closest distance to " O   HOH Z 134 " =    2.914
peak=   -3.291 closest distance to " N   ASP A 171 " =    2.274
peak=   -3.289 closest distance to " O   HOH Z 353 " =    2.070
peak=   -3.287 closest distance to " CG  PRO A 163 " =    2.564
peak=   -3.286 closest distance to " O   HOH Z 252 " =    3.919
peak=   -3.285 closest distance to " OD1 ASN A 187 " =    1.573
peak=   -3.285 closest distance to " O   HOH Z 128 " =    2.670
peak=   -3.282 closest distance to " O   HOH Z 350 " =    2.064
peak=   -3.280 closest distance to " O   HOH Z 275 " =    1.508
peak=   -3.279 closest distance to " O   HOH Z 136 " =    2.379
peak=   -3.271 closest distance to " NE2 GLN A 278 " =    1.885
peak=   -3.268 closest distance to " OG  SER A  62 " =    4.553
peak=   -3.266 closest distance to " O   HOH Z 174 " =    2.514
peak=   -3.262 closest distance to " O   HOH Z 232 " =    1.745
peak=   -3.258 closest distance to " CD1 ILE A 239 " =    2.157
peak=   -3.253 closest distance to " CE3 TRP A  70 " =    1.793
peak=   -3.250 closest distance to " CG2 VAL A 189 " =    2.048
peak=   -3.244 closest distance to " O   HOH Z 262 " =    2.843
peak=   -3.243 closest distance to " CG2 THR A 178 " =    2.268
peak=   -3.241 closest distance to " CG1 VAL A 197 " =    2.243
peak=   -3.238 closest distance to " O   HOH Z 111 " =    1.450
peak=   -3.235 closest distance to " O   HOH Z 396 " =    2.095
peak=   -3.235 closest distance to " CG  ASN A 252 " =    1.555
peak=   -3.234 closest distance to " CA  GLY A  98 " =    1.973
peak=   -3.233 closest distance to " O   HOH Z  13 " =    1.545
peak=   -3.233 closest distance to " O   HOH Z 106 " =    1.801
peak=   -3.230 closest distance to " N   SER A   3 " =    2.070
peak=   -3.229 closest distance to " CG2 ILE A  20 " =    2.902
peak=   -3.229 closest distance to " NH2 ARG A  79 " =    2.078
peak=   -3.228 closest distance to " O   HOH Z 434 " =    1.742
peak=   -3.224 closest distance to " N   ASN A  60 " =    1.315
peak=   -3.221 closest distance to " OD1 ASN A 249 " =    2.355
peak=   -3.220 closest distance to " O   HOH Z 431 " =    1.936
peak=   -3.220 closest distance to " N   GLN A  77 " =    1.710
peak=   -3.219 closest distance to " CB  ALA A 291 " =    2.223
peak=   -3.218 closest distance to " NE2 GLN A 103 " =    1.759
peak=   -3.214 closest distance to " OE1 GLN A 223 " =    2.196
peak=   -3.213 closest distance to " O   HOH Z  71 " =    1.811
peak=   -3.213 closest distance to " O   HOH Z 139 " =    3.063
peak=   -3.212 closest distance to " O   HOH Z 380 " =    1.445
peak=   -3.210 closest distance to " OG BSER A 134 " =    1.847
peak=   -3.208 closest distance to " CG1 VAL A 230 " =    1.969
peak=   -3.208 closest distance to " CZ  TYR A 169 " =    1.757
peak=   -3.207 closest distance to " O   HOH Z 326 " =    5.081
peak=   -3.205 closest distance to " CD1 LEU A 101 " =    2.746
peak=   -3.202 closest distance to " N   MET A 188 " =    1.863
peak=   -3.197 closest distance to " O   SER A 276 " =    1.685
peak=   -3.196 closest distance to " CG1 VAL A 112 " =    2.835
peak=   -3.194 closest distance to " O   HOH Z  43 " =    1.726
peak=   -3.194 closest distance to " ND2 ASN A 187 " =    1.565
peak=   -3.189 closest distance to " CA  GLY A 133 " =    2.325
peak=   -3.186 closest distance to " CD2 TYR A 247 " =    2.265
peak=   -3.174 closest distance to " O   HOH Z 313 " =    1.145
peak=   -3.174 closest distance to " O   ARG A 145 " =    1.670
peak=   -3.170 closest distance to " CD  ARG A 139 " =    1.643
peak=   -3.169 closest distance to " C   ASN A 285 " =    2.335
peak=   -3.169 closest distance to " NH2 ARG A  79 " =    1.608
peak=   -3.168 closest distance to " OH  TYR A 214 " =    1.239
peak=   -3.167 closest distance to " O   TYR A  30 " =    2.553
peak=   -3.160 closest distance to " CA  SER A 135 " =    1.377
peak=   -3.159 closest distance to " O   HOH Z 191 " =    3.283
peak=   -3.158 closest distance to " O   HOH Z 145 " =    1.420
peak=   -3.155 closest distance to " O   PHE A 218 " =    1.675
peak=   -3.146 closest distance to " ND2 ASN A  60 " =    1.307
peak=   -3.142 closest distance to " OG  SER A 206 " =    1.795
peak=   -3.142 closest distance to " O   HOH Z 200 " =    4.533
peak=   -3.140 closest distance to " O   HOH Z 409 " =    4.782
peak=   -3.140 closest distance to " OG  SER A  62 " =    1.814
peak=   -3.136 closest distance to " C   LEU A 222 " =    0.855
peak=   -3.134 closest distance to " O   GLY A  80 " =    2.344
peak=   -3.132 closest distance to " OG BSER A 210 " =    1.526
peak=   -3.132 closest distance to " CG  ARG A 269 " =    2.065
peak=   -3.125 closest distance to " CG  PHE A 283 " =    2.699
peak=   -3.120 closest distance to " CG  GLU A 152 " =    1.516
peak=   -3.116 closest distance to " O   HOH Z 222 " =    1.558
peak=   -3.116 closest distance to " CG1 VAL A 125 " =    1.978
peak=   -3.111 closest distance to " O   HOH Z  40 " =    2.291
peak=   -3.108 closest distance to " CB  ASP A 171 " =    2.294
peak=   -3.108 closest distance to " O   MET A  40 " =    2.827
peak=   -3.108 closest distance to " O   HOH Z 193 " =    1.764
peak=   -3.106 closest distance to " O   HOH Z 176 " =    0.785
peak=   -3.105 closest distance to " O   HOH Z 265 " =    1.865
peak=   -3.104 closest distance to " O   LYS A 289 " =    2.985
peak=   -3.102 closest distance to " CD  PRO A 243 " =    2.159
peak=   -3.100 closest distance to " O   HOH Z   9 " =    1.601
peak=   -3.099 closest distance to " CD1 TYR A 247 " =    2.313
peak=   -3.097 closest distance to " OH  TYR A 247 " =    1.933
peak=   -3.096 closest distance to " C   SER A 206 " =    1.442
peak=   -3.091 closest distance to " CB  GLN A  11 " =    1.831
peak=   -3.091 closest distance to " OD1 ASN A 173 " =    1.420
peak=   -3.081 closest distance to " OD1 ASP A 171 " =    1.647
peak=   -3.079 closest distance to " C   ASP A 270 " =    1.213
peak=   -3.062 closest distance to " O   HOH Z 251 " =    5.137
peak=   -2.925 closest distance to " CB  SER A  97 " =    2.389

================= 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    :  0.4488 0.4361   6.245611e+00   6.218856e+00
   1_bss:  0.4400 0.4203   6.239807e+00   6.206635e+00
   1_xyz:  0.3328 0.3562   6.049241e+00   6.089500e+00
   1_adp:  0.2772 0.3141   5.895711e+00   5.997506e+00
   1_occ:  0.2766 0.3151   5.894460e+00   5.999126e+00
   2_bss:  0.2730 0.3108   5.895386e+00   5.996831e+00
   2_xyz:  0.1886 0.2300   5.571916e+00   5.732630e+00
   2_adp:  0.1714 0.2153   5.495211e+00   5.673729e+00
   2_occ:  0.1713 0.2157   5.495329e+00   5.675141e+00
   3_bss:  0.1704 0.2159   5.496581e+00   5.677025e+00
   3_xyz:  0.1359 0.1767   5.291212e+00   5.498806e+00
   3_adp:  0.1274 0.1720   5.248141e+00   5.473753e+00
   3_occ:  0.1274 0.1721   5.247997e+00   5.473731e+00
   4_bss:  0.1274 0.1721   5.247785e+00   5.472403e+00
   4_xyz:  0.1185 0.1654   5.196548e+00   5.435719e+00
   4_adp:  0.1190 0.1632   5.192084e+00   5.421699e+00
   4_occ:  0.1190 0.1632   5.191958e+00   5.421978e+00
   5_bss:  0.1189 0.1632   5.191979e+00   5.421981e+00
   5_xyz:  0.1125 0.1611   5.158148e+00   5.407545e+00
   5_adp:  0.1112 0.1614   5.155148e+00   5.410471e+00
   5_occ:  0.1112 0.1615   5.155171e+00   5.410667e+00
   5_bss:  0.1112 0.1614   5.155002e+00   5.410607e+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:  0.352  50.000   7.452   7.705  10.433   0.000   0.000   0.000
   1_xyz:  0.352  50.000   7.452   7.705  10.433   0.000   0.000   0.000
   1_adp:  0.352  50.000   7.452   7.705  10.433   0.000   0.000   0.000
   1_occ:  0.352  50.000   7.452   7.705  10.433   0.000   0.000   0.000
   2_bss:  0.323  50.000   4.236   4.532   6.766   0.000   0.000   0.000
   2_xyz:  0.323  50.000   4.236   4.532   6.766   0.000   0.000   0.000
   2_adp:  0.323  50.000   4.236   4.532   6.766   0.000   0.000   0.000
   2_occ:  0.323  50.000   4.236   4.532   6.766   0.000   0.000   0.000
   3_bss:  0.323  64.495   3.232   3.565   5.008   0.000   0.000   0.000
   3_xyz:  0.323  64.495   3.232   3.565   5.008   0.000   0.000   0.000
   3_adp:  0.323  64.495   3.232   3.565   5.008   0.000   0.000   0.000
   3_occ:  0.323  64.495   3.232   3.565   5.008   0.000   0.000   0.000
   4_bss:  0.332  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   4_xyz:  0.332  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   4_adp:  0.332  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   4_occ:  0.332  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   5_bss:  0.333  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   5_xyz:  0.333  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   5_adp:  0.333  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   5_occ:  0.333  64.495   2.964   3.215   4.585   0.000   0.000   0.000
   5_bss:  0.322  61.965  -0.603  -0.381   0.984   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.672 0.5384  0.5954    54103.120
   1_bss:  47.709 0.5496  0.7890    52073.415
   1_xyz:  38.781 0.6565  0.9094    34746.238
   1_adp:  32.508 0.7303  0.9996    26283.774
   1_occ:  32.560 0.7297  0.9984    26381.679
   2_bss:  32.418 0.7311  0.8865    26161.460
   2_xyz:  22.533 0.8366  0.9843    13464.799
   2_adp:  20.520 0.8573  0.9961    11805.191
   2_occ:  20.574 0.8567  0.9954    11831.515
   3_bss:  20.605 0.8566  0.9513    11915.081
   3_xyz:  16.249 0.8964  0.9750     8025.158
   3_adp:  15.671 0.9015  0.9739     7591.447
   3_occ:  15.669 0.9015  0.9739     7592.224
   4_bss:  15.645 0.9017  0.9619     7570.960
   4_xyz:  14.868 0.9083  0.9650     6960.706
   4_adp:  14.527 0.9112  0.9634     6796.578
   4_occ:  14.535 0.9111  0.9633     6798.290
   5_bss:  14.535 0.9111  0.9633     6798.582
   5_xyz:  14.244 0.9134  0.9653     6638.297
   5_adp:  14.313 0.9130  0.9609     6654.095
   5_occ:  14.317 0.9129  0.9609     6656.150
   5_bss:  14.318 0.9129  0.9655     6651.394
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4392e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4392e+01
   1_xyz:   1.614  0.013  0.106 18.017  0.006  4.113   1.3081e-01
   1_adp:   1.614  0.013  0.106 18.017  0.006  4.113   1.3081e-01
   1_occ:   1.614  0.013  0.106 18.017  0.006  4.113   1.3081e-01
   2_bss:   1.614  0.013  0.106 18.017  0.006  4.113   1.3081e-01
   2_xyz:   1.043  0.008  0.073 16.508  0.004  4.131   6.7797e-02
   2_adp:   1.043  0.008  0.073 16.508  0.004  4.131   6.7797e-02
   2_occ:   1.043  0.008  0.073 16.508  0.004  4.131   6.7797e-02
   3_bss:   1.043  0.008  0.073 16.508  0.004  4.131   6.7797e-02
   3_xyz:   1.052  0.008  0.082 16.230  0.004  4.134   6.7274e-02
   3_adp:   1.052  0.008  0.082 16.230  0.004  4.134   6.7274e-02
   3_occ:   1.052  0.008  0.082 16.230  0.004  4.134   6.7274e-02
   4_bss:   1.052  0.008  0.082 16.230  0.004  4.134   6.7274e-02
   4_xyz:   1.069  0.009  0.086 15.850  0.004  4.116   7.0896e-02
   4_adp:   1.069  0.009  0.086 15.850  0.004  4.116   7.0896e-02
   4_occ:   1.069  0.009  0.086 15.850  0.004  4.116   7.0896e-02
   5_bss:   1.069  0.009  0.086 15.850  0.004  4.116   7.0896e-02
   5_xyz:   1.207  0.013  0.099 15.958  0.004  4.120   9.2511e-02
   5_adp:   1.207  0.013  0.099 15.958  0.004  4.120   9.2511e-02
   5_occ:   1.207  0.013  0.099 15.958  0.004  4.120   9.2511e-02
   5_bss:   1.207  0.013  0.099 15.958  0.004  4.120   9.2511e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0527e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0527e+00
   1_xyz:  14.073  0.152  0.431 85.172  0.037  2.248   9.9156e-02
   1_adp:  14.073  0.152  0.431 85.172  0.037  2.248   9.9156e-02
   1_occ:  14.073  0.152  0.431 85.172  0.037  2.248   9.9156e-02
   2_bss:  14.073  0.152  0.431 85.172  0.037  2.248   9.9156e-02
   2_xyz:   6.280  0.079  0.228 88.011  0.032  2.357   5.5457e-02
   2_adp:   6.280  0.079  0.228 88.011  0.032  2.357   5.5457e-02
   2_occ:   6.280  0.079  0.228 88.011  0.032  2.357   5.5457e-02
   3_bss:   6.280  0.079  0.228 88.011  0.032  2.357   5.5457e-02
   3_xyz:   8.788  0.052  0.385 82.034  0.040  2.401   3.6949e-02
   3_adp:   8.788  0.052  0.385 82.034  0.040  2.401   3.6949e-02
   3_occ:   8.788  0.052  0.385 82.034  0.040  2.401   3.6949e-02
   4_bss:   8.788  0.052  0.385 82.034  0.040  2.401   3.6949e-02
   4_xyz:   7.302  0.046  0.459 82.370  0.039  2.366   4.5087e-02
   4_adp:   7.302  0.046  0.459 82.370  0.039  2.366   4.5087e-02
   4_occ:   7.302  0.046  0.459 82.370  0.039  2.366   4.5087e-02
   5_bss:   7.302  0.046  0.459 82.370  0.039  2.366   4.5087e-02
   5_xyz:   7.893  0.061  0.608 82.293  0.040  2.259   6.9878e-02
   5_adp:   7.893  0.061  0.608 82.293  0.040  2.259   6.9878e-02
   5_occ:   7.893  0.061  0.608 82.293  0.040  2.259   6.9878e-02
   5_bss:   7.893  0.061  0.608 82.293  0.040  2.259   6.9878e-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:  86.60   0.00  11.18  64.70   0.00   8.01  86.60   0.00  28.44
   1_occ:  86.60   0.00  11.18  64.70   0.00   8.01  86.60   0.00  28.44
   2_bss:  86.60   0.00  11.18  64.70   0.00   8.01  86.60   0.00  28.44
   2_xyz:  86.60   0.00  11.18  64.70   0.00   8.01  86.60   0.00  28.44
   2_adp:  85.45   0.00  11.27  64.70   0.00   7.55  85.45   0.00  31.57
   2_occ:  85.45   0.00  11.27  64.70   0.00   7.55  85.45   0.00  31.57
   3_bss:  85.45   0.00  11.27  64.70   0.00   7.55  85.45   0.00  31.57
   3_xyz:  85.45   0.00  11.27  64.70   0.00   7.55  85.45   0.00  31.57
   3_adp:  79.38   0.00  12.11  72.05   0.00   7.67  79.38   0.00  36.26
   3_occ:  79.38   0.00  12.11  72.05   0.00   7.67  79.38   0.00  36.26
   4_bss:  79.38   0.00  12.11  72.05   0.00   7.67  79.38   0.00  36.26
   4_xyz:  79.38   0.00  12.11  72.05   0.00   7.67  79.38   0.00  36.26
   4_adp:  75.70   0.00  11.52  72.54   0.00   7.41  75.70   0.77  33.90
   4_occ:  75.70   0.00  11.52  72.54   0.00   7.41  75.70   0.77  33.90
   5_bss:  75.70   0.00  11.52  72.54   0.00   7.41  75.70   0.77  33.90
   5_xyz:  75.70   0.00  11.52  72.54   0.00   7.41  75.70   0.77  33.90
   5_adp:  76.06   0.00  11.59  74.34   0.00   7.38  76.06   0.76  34.50
   5_occ:  76.06   0.00  11.59  74.34   0.00   7.38  76.06   0.76  34.50
   5_bss:  79.79   3.73  15.32  78.07   3.73  11.11  79.79   4.49  38.23
------------------------------------------------------------------------
 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:    1.243    0.023    0.410
   1_adp:    1.243    0.023    0.410
   1_occ:    1.243    0.023    0.410
   2_bss:    1.243    0.023    0.410
   2_xyz:    1.661    0.022    0.529
   2_adp:    1.661    0.022    0.529
   2_occ:    1.661    0.022    0.529
   3_bss:    1.661    0.022    0.529
   3_xyz:    1.629    0.076    0.570
   3_adp:    1.629    0.076    0.570
   3_occ:    1.629    0.076    0.570
   4_bss:    1.629    0.076    0.570
   4_xyz:    1.727    0.034    0.592
   4_adp:    1.727    0.034    0.592
   4_occ:    1.727    0.034    0.592
   5_bss:    1.727    0.034    0.592
   5_xyz:    1.634    0.020    0.605
   5_adp:    1.634    0.020    0.605
   5_occ:    1.634    0.020    0.605
   5_bss:    1.634    0.020    0.605
------------------------------------------------------------------------

CPU time actual refinement: 326.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_921/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_921/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_921/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_921/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_921/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.81 
  Macro-tasks:
    bulk solvent and scale       = 37.52  
    individual site refinement   = 134.56 
    weights calculation          = 31.92  
    collect and process          = 6.74   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 210.88 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 101.22 
    alpha_beta                      = 8.38   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 111.49 
    fmodel                         = 6.62   
    r_factors                      = 0.18   
    phase_errors                   = 11.00  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 242.15 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.619 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    650 calls, 100.82 s
gradients_fft:          594 calls,  98.25 s

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

# Date 2008-01-16 Time 02:44:57 PST -0800 (1200480297.68 s)
Start R-work = 0.4488, R-free = 0.4361 (no bulk solvent and anisotropic scale)
Final R-work = 0.1283, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.4400, R-free = 0.4203
Final R-work = 0.1112, R-free = 0.1614