# Date 2008-01-16 Time 03:15:12 PST -0800 (1200482112.39 s)
#phil __OFF__

Command line arguments: "../1164.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27664
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1164

-------------------------------------------------------------------------------
  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: (71.655, 47.1647, 88.1178, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (71.655, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.01261
Completeness in resolution range: 0.960952
Completeness with d_max=infinity: 0.957991

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   2.0126

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: (71.655, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.01261
Completeness in resolution range: 0.960952
Completeness with d_max=infinity: 0.957991

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.3068 [2145/2169]  1931   214  10.0%
  bin  2:  4.3068 -  3.4311 [2043/2063]  1838   205  10.0%
  bin  3:  3.4311 -  3.0011 [2039/2058]  1834   205  10.1%
  bin  4:  3.0011 -  2.7284 [2008/2038]  1810   198   9.9%
  bin  5:  2.7284 -  2.5338 [2006/2025]  1806   200  10.0%
  bin  6:  2.5338 -  2.3850 [1974/1999]  1774   200  10.1%
  bin  7:  2.3850 -  2.2660 [1987/2015]  1786   201  10.1%
  bin  8:  2.2660 -  2.1676 [1981/2017]  1787   194   9.8%
  bin  9:  2.1676 -  2.0844 [1948/1990]  1753   195  10.0%
  bin 10:  2.0844 -  2.0126 [1458/2011]  1311   147  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1164/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: 10
        2.42 -     3.04: 2160
        3.04 -     3.66: 4554
        3.66 -     4.28: 8824
        4.28 -     4.90: 12146
  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 "  1.839 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.367 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27689 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_1164/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1164/model_refine_001.geo

CPU time processing inputs: 9.08


============================ 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 = 71.655 47.16465 88.1178 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 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4804   r_free= 0.4740   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281064                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8037 0.99   1393  155 0.3928 0.3611      6.5994      6.5145|
|  2:  4.8037 -  3.8326 0.99   1337  150 0.3984 0.4267      6.7912       6.873|
|  3:  3.8326 -  3.3539 0.99   1314  141 0.4406 0.4077      6.6759      6.6624|
|  4:  3.3539 -  3.0499 0.99   1296  150 0.4692 0.4147      6.5377      6.4253|
|  5:  3.0499 -  2.8328 0.99   1298  146 0.5050 0.4995      6.3764      6.4223|
|  6:  2.8328 -  2.6667 0.99   1301  134 0.5032 0.5582      6.2801      6.1925|
|  7:  2.6667 -  2.5338 0.99   1280  146 0.5299 0.5144      6.2411      6.2422|
|  8:  2.5338 -  2.4240 0.98   1272  145 0.5376 0.4791      6.1909      6.1484|
|  9:  2.4240 -  2.3310 0.98   1265  140 0.5112 0.6042      6.1147      6.1736|
| 10:  2.3310 -  2.2508 1.00   1289  145 0.5275 0.4988      6.1214      6.1042|
| 11:  2.2508 -  2.1806 0.97   1265  137 0.5145 0.5253      6.0277      6.0815|
| 12:  2.1806 -  2.1185 0.98   1253  142 0.5204 0.5221       5.988      6.0138|
| 13:  2.1185 -  2.0628 0.99   1288  136 0.5378 0.4961        5.89      5.8176|
| 14:  2.0628 -  2.0126 0.61    779   92 0.5309 0.4990      5.8629      5.7657|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.8037  1393   155  0.72  32.78   0.79     0.74      66155.03|
|  2:  4.8037 -  3.8326  1337   150  0.72  33.52   0.87     0.77      98544.64|
|  3:  3.8326 -  3.3539  1314   141  0.63  41.59   0.81     0.71     105168.18|
|  4:  3.3539 -  3.0499  1296   150  0.53  49.51   0.79     0.61      96051.52|
|  5:  3.0499 -  2.8328  1298   146  0.43  57.42   0.72     0.50      80245.61|
|  6:  2.8328 -  2.6667  1301   134  0.39  60.98   0.72     0.43      73420.37|
|  7:  2.6667 -  2.5338  1280   146  0.34  64.39   0.71     0.39      67697.83|
|  8:  2.5338 -  2.4240  1272   145  0.32  66.12   0.70     0.37      62434.69|
|  9:  2.4240 -  2.3310  1265   140  0.32  66.39   0.71     0.36      57013.49|
| 10:  2.3310 -  2.2508  1289   145  0.33  65.69   0.72     0.37      50963.89|
| 11:  2.2508 -  2.1806  1265   137  0.34  64.58   0.74     0.41      46948.18|
| 12:  2.1806 -  2.1185  1253   142  0.36  62.91   0.73     0.43      42197.82|
| 13:  2.1185 -  2.0628  1288   136  0.35  64.18   0.69     0.42      35975.52|
| 14:  2.0628 -  2.0126   779    92  0.37  62.62   0.69     0.38      28791.93|
|alpha:            min =        0.36 max =            0.77 mean =         0.50|
|beta:             min =    28791.93 max =       105168.18 mean =     66430.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.17|
|phase err.(test): min =        0.00 max =           89.94 mean =        56.10|
|-----------------------------------------------------------------------------|

============================== 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 = 14.671683             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.669   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.318521              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.300   (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:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      673 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1471 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2562 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3841 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4951 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6459 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7554 |
|-----------------------------------------------------------------------------|
|-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 |       54.673 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.616 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    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 = 12.418)------------------------------------------|
|    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 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4852   r_free= 0.4769   ksol= 0.00   Bsol= 0.00   scale= 0.750    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.282199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4724   r_free= 0.4622   ksol= 0.32   Bsol= 50.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.30,6.69,10.48,0.00,0.00,0.00); trace/3= 8.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.276228                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.185224             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.513   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.163407              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.044   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4724      final r-factor (work) = 0.3822          |
| start r-factor (free) = 0.4622      final r-factor (free) = 0.4114          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.0763 = 13.19 * 0.50 * 6.2803 + 1.00 * 54.6728                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.8937 = 13.19 * 0.50 * 6.1794 + 1.00 * 0.1552                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3822      final r-factor (work) = 0.3374          |
| start r-factor (free) = 0.4114      final r-factor (free) = 0.3882          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2036 = 1.16 * 1.00 * 6.1794 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1020 = 1.16 * 1.00 * 6.0900 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.22   13.00    None  None   None       |
|    all(noH): 2823   0      0.00    92.22   13.00    None  None   None       |
|    Sol.    : 438    0      0.00    92.22   28.88    None  None   None       |
|    Mac.    : 2385   0      0.00    75.10   10.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.222: 1427   |   5:    46.110 -  55.332:   51        |
|      1:     9.222 -  18.444:  728   |   6:    55.332 -  64.554:   30        |
|      2:    18.444 -  27.666:  334   |   7:    64.554 -  73.775:    8        |
|      3:    27.666 -  36.888:  153   |   8:    73.775 -  82.997:    6        |
|      4:    36.888 -  46.110:   84   |   9:    82.997 -  92.219:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3374 r_free = 0.3882             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3371 r_free = 0.3891             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3371   r_free= 0.3891   ksol= 0.32   Bsol= 50.00   scale= 1.065   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.30,6.69,10.48,0.00,0.00,0.00); trace/3= 8.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.064600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3359   r_free= 0.3866   ksol= 0.34   Bsol= 76.44   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.35,4.33,7.41,0.00,0.00,0.00); trace/3= 5.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.066404                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.958428              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.412   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.581231              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.942  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3359      final r-factor (work) = 0.2492          |
| start r-factor (free) = 0.3866      final r-factor (free) = 0.3005          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2828 = 5.96 * 0.50 * 6.0847 + 1.00 * 0.1552                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8050 = 5.96 * 0.50 * 5.9494 + 1.00 * 0.0805                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2492      final r-factor (work) = 0.2260          |
| start r-factor (free) = 0.3005      final r-factor (free) = 0.2786          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5063 = 0.58 * 1.00 * 5.9494 + 1.00 * 0.0483                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5695 = 0.58 * 1.00 * 5.7712 + 1.00 * 0.2152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.67   12.99    None  None   None       |
|    all(noH): 2823   0      0.00    92.67   12.99    None  None   None       |
|    Sol.    : 438    0      0.00    92.67   33.40    None  None   None       |
|    Mac.    : 2385   0      0.00    75.65   9.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.267: 1552   |   5:    46.337 -  55.604:   64        |
|      1:     9.267 -  18.535:  641   |   6:    55.604 -  64.872:   29        |
|      2:    18.535 -  27.802:  235   |   7:    64.872 -  74.139:    9        |
|      3:    27.802 -  37.070:  187   |   8:    74.139 -  83.406:    5        |
|      4:    37.070 -  46.337:   99   |   9:    83.406 -  92.674:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2260 r_free = 0.2786             target_work(ml) = 5.740         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2258 r_free = 0.2786             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2258   r_free= 0.2786   ksol= 0.34   Bsol= 76.44   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.35,4.33,7.41,0.00,0.00,0.00); trace/3= 5.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.739225                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2244   r_free= 0.2780   ksol= 0.35   Bsol= 80.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.02,4.87,0.00,0.00,0.00); trace/3= 3.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.741309                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.804647              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.790   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.175076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.384   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2244      final r-factor (work) = 0.1639          |
| start r-factor (free) = 0.2780      final r-factor (free) = 0.2124          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8415 = 5.80 * 0.50 * 5.7749 + 1.00 * 0.0808                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3863 = 5.80 * 0.50 * 5.6162 + 1.00 * 0.0863                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1639      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.2124      final r-factor (free) = 0.1978          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 34.6997 = 6.18 * 1.00 * 5.6162 + 1.00 * 0.0192                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 33.3894 = 6.18 * 1.00 * 5.4041 + 1.00 * 0.0189                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.15  14.14    None  None   None       |
|    all(noH): 2823   0      0.00    106.15  14.14    None  None   None       |
|    Sol.    : 438    0      0.00    106.15  42.07    None  None   None       |
|    Mac.    : 2385   0      0.00    93.95   9.01     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 -  10.615: 1779   |   5:    53.077 -  63.692:   84        |
|      1:    10.615 -  21.231:  519   |   6:    63.692 -  74.307:   53        |
|      2:    21.231 -  31.846:  145   |   7:    74.307 -  84.923:   18        |
|      3:    31.846 -  42.461:  107   |   8:    84.923 -  95.538:    8        |
|      4:    42.461 -  53.077:  106   |   9:    95.538 - 106.153:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1978             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1449 r_free = 0.1977             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.1977   ksol= 0.35   Bsol= 80.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.02,4.87,0.00,0.00,0.00); trace/3= 3.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.374767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1976   ksol= 0.34   Bsol= 84.06   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,2.50,4.22,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.374836                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.764978              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.996  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.044  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1976      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2647 = 3.76 * 0.50 * 5.4069 + 1.00 * 0.0863                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1176 = 3.76 * 0.50 * 5.3288 + 1.00 * 0.0861                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1272          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2104 = 0.22 * 1.00 * 5.3288 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1961 = 0.22 * 1.00 * 5.2826 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.31  13.28    None  None   None       |
|    all(noH): 2823   0      0.00    102.31  13.28    None  None   None       |
|    Sol.    : 438    0      1.04    102.31  39.21    None  None   None       |
|    Mac.    : 2385   0      0.00    83.78   8.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.232: 1838   |   5:    51.157 -  61.389:   74        |
|      1:    10.232 -  20.463:  491   |   6:    61.389 -  71.620:   40        |
|      2:    20.463 -  30.695:  129   |   7:    71.620 -  81.852:   21        |
|      3:    30.695 -  40.926:  118   |   8:    81.852 -  92.083:    7        |
|      4:    40.926 -  51.157:  101   |   9:    92.083 - 102.315:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1272 r_free = 0.1746             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1271 r_free = 0.1746             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1746   ksol= 0.34   Bsol= 84.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,2.50,4.22,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.253132                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1745   ksol= 0.33   Bsol= 71.38   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.36,3.91,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.252646                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.671049              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.758  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.796956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.411   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5001 = 1.67 * 0.50 * 5.2815 + 1.00 * 0.0873                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4565 = 1.67 * 0.50 * 5.2563 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2027 = 0.80 * 1.00 * 5.2563 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1971 = 0.80 * 1.00 * 5.2432 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.88  13.20    None  None   None       |
|    all(noH): 2823   0      0.00    103.88  13.20    None  None   None       |
|    Sol.    : 438    0      1.04    103.88  38.97    None  None   None       |
|    Mac.    : 2385   0      0.00    86.98   8.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.388: 1842   |   5:    51.941 -  62.329:   81        |
|      1:    10.388 -  20.776:  479   |   6:    62.329 -  72.717:   38        |
|      2:    20.776 -  31.165:  142   |   7:    72.717 -  83.106:   16        |
|      3:    31.165 -  41.553:  131   |   8:    83.106 -  93.494:    9        |
|      4:    41.553 -  51.941:   82   |   9:    93.494 - 103.882:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1253 r_free = 0.1738             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1252 r_free = 0.1738             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1738   ksol= 0.33   Bsol= 71.38   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.43,2.36,3.91,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248372                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8037 0.99   1393  155 0.1046 0.1391      5.4322      5.5806|
|  2:  4.8037 -  3.8326 0.99   1337  150 0.0900 0.1194      5.4894      5.6884|
|  3:  3.8326 -  3.3539 0.99   1314  141 0.1151 0.1526      5.5471      5.8671|
|  4:  3.3539 -  3.0499 0.99   1296  150 0.1343 0.1834      5.5323      5.7126|
|  5:  3.0499 -  2.8328 0.99   1298  146 0.1553 0.1885       5.461       5.637|
|  6:  2.8328 -  2.6667 0.99   1301  134 0.1382 0.2353      5.3281      5.6167|
|  7:  2.6667 -  2.5338 0.99   1280  146 0.1459 0.1736      5.2852      5.4282|
|  8:  2.5338 -  2.4240 0.98   1272  145 0.1363 0.1860      5.1999      5.4242|
|  9:  2.4240 -  2.3310 0.98   1265  140 0.1349 0.2019      5.1586      5.4042|
| 10:  2.3310 -  2.2508 1.00   1289  145 0.1294 0.1847      5.0766      5.3054|
| 11:  2.2508 -  2.1806 0.97   1265  137 0.1324 0.1962      5.0573      5.3393|
| 12:  2.1806 -  2.1185 0.98   1253  142 0.1255 0.1925      4.9747       5.291|
| 13:  2.1185 -  2.0628 0.99   1288  136 0.1305 0.1952      4.9033      5.1367|
| 14:  2.0628 -  2.0126 0.61    779   92 0.1179 0.1817      4.8119      5.0288|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.8037  1393   155  0.94   9.53   0.96     0.94       7996.53|
|  2:  4.8037 -  3.8326  1337   150  0.95   8.54   0.99     0.98       9999.34|
|  3:  3.8326 -  3.3539  1314   141  0.93  12.28   1.01     1.01      11781.85|
|  4:  3.3539 -  3.0499  1296   150  0.91  14.93   1.00     0.98      11775.56|
|  5:  3.0499 -  2.8328  1298   146  0.88  18.07   0.99     0.97      10466.11|
|  6:  2.8328 -  2.6667  1301   134  0.88  18.09   0.97     0.94       8942.27|
|  7:  2.6667 -  2.5338  1280   146  0.89  17.86   0.98     0.95       7786.83|
|  8:  2.5338 -  2.4240  1272   145  0.89  17.65   0.98     0.95       6798.27|
|  9:  2.4240 -  2.3310  1265   140  0.89  17.43   0.99     0.94       6295.34|
| 10:  2.3310 -  2.2508  1289   145  0.89  17.72   0.99     0.94       5486.77|
| 11:  2.2508 -  2.1806  1265   137  0.89  17.89   0.98     0.91       5150.34|
| 12:  2.1806 -  2.1185  1253   142  0.90  16.71   0.99     0.98       4761.29|
| 13:  2.1185 -  2.0628  1288   136  0.88  18.71   0.97     0.94       4269.81|
| 14:  2.0628 -  2.0126   779    92  0.89  17.38   0.96     0.91       3519.44|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     3519.44 max =        11781.85 mean =      7648.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.80|
|phase err.(test): min =        0.00 max =           89.90 mean =        15.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1735   ksol= 0.33   Bsol= 74.28   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.54,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1735   ksol= 0.33   Bsol= 74.28   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.54,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247379                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8037 0.99   1393  155 0.1048 0.1324       5.421       5.554|
|  2:  4.8037 -  3.8326 0.99   1337  150 0.0903 0.1188      5.4863      5.6857|
|  3:  3.8326 -  3.3539 0.99   1314  141 0.1156 0.1530      5.5466      5.8693|
|  4:  3.3539 -  3.0499 0.99   1296  150 0.1341 0.1842      5.5331      5.7172|
|  5:  3.0499 -  2.8328 0.99   1298  146 0.1551 0.1885      5.4618      5.6379|
|  6:  2.8328 -  2.6667 0.99   1301  134 0.1381 0.2355      5.3286      5.6173|
|  7:  2.6667 -  2.5338 0.99   1280  146 0.1460 0.1737      5.2856      5.4287|
|  8:  2.5338 -  2.4240 0.98   1272  145 0.1363 0.1861      5.1999      5.4249|
|  9:  2.4240 -  2.3310 0.98   1265  140 0.1349 0.2020      5.1587      5.4037|
| 10:  2.3310 -  2.2508 1.00   1289  145 0.1293 0.1846      5.0766      5.3055|
| 11:  2.2508 -  2.1806 0.97   1265  137 0.1323 0.1963      5.0572      5.3393|
| 12:  2.1806 -  2.1185 0.98   1253  142 0.1255 0.1926      4.9747      5.2912|
| 13:  2.1185 -  2.0628 0.99   1288  136 0.1304 0.1952      4.9032      5.1366|
| 14:  2.0628 -  2.0126 0.61    779   92 0.1179 0.1818      4.8118      5.0287|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.8037  1393   155  0.94   9.51   0.96     0.93       7678.03|
|  2:  4.8037 -  3.8326  1337   150  0.95   8.39   0.99     0.98       9780.56|
|  3:  3.8326 -  3.3539  1314   141  0.93  12.24   1.01     1.01      11721.99|
|  4:  3.3539 -  3.0499  1296   150  0.91  14.98   1.00     0.98      11831.65|
|  5:  3.0499 -  2.8328  1298   146  0.88  18.12   0.99     0.97      10518.31|
|  6:  2.8328 -  2.6667  1301   134  0.88  18.11   0.97     0.94       8963.48|
|  7:  2.6667 -  2.5338  1280   146  0.89  17.87   0.98     0.95       7796.81|
|  8:  2.5338 -  2.4240  1272   145  0.89  17.66   0.98     0.95       6804.14|
|  9:  2.4240 -  2.3310  1265   140  0.89  17.43   0.99     0.94       6292.98|
| 10:  2.3310 -  2.2508  1289   145  0.89  17.72   0.99     0.94       5487.31|
| 11:  2.2508 -  2.1806  1265   137  0.89  17.89   0.98     0.91       5150.87|
| 12:  2.1806 -  2.1185  1253   142  0.90  16.71   0.99     0.98       4762.09|
| 13:  2.1185 -  2.0628  1288   136  0.88  18.71   0.97     0.94       4269.40|
| 14:  2.0628 -  2.0126   779    92  0.89  17.38   0.96     0.91       3519.60|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     3519.60 max =        11831.65 mean =      7612.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.80|
|phase err.(test): min =        0.00 max =           89.54 mean =        15.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.90    106.78  16.10    None  None   None       |
|    all(noH): 2823   0      2.90    106.78  16.10    None  None   None       |
|    Sol.    : 438    0      3.94    106.78  41.87    None  None   None       |
|    Mac.    : 2385   0      2.90    89.88   11.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.901 -  13.290: 1842   |   5:    54.842 -  65.231:   81        |
|      1:    13.290 -  23.678:  479   |   6:    65.231 -  75.619:   38        |
|      2:    23.678 -  34.066:  142   |   7:    75.619 -  86.007:   16        |
|      3:    34.066 -  44.454:  131   |   8:    86.007 -  96.395:    9        |
|      4:    44.454 -  54.842:   82   |   9:    96.395 - 106.783:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.402 - 4.845
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 343
   mapped sites are within: 0.701 - 4.845

peak=   10.045 closest distance to " CB  VAL A 230 " =    1.483
peak=    5.693 closest distance to " CB  GLN A 223 " =    1.508
peak=    5.510 closest distance to " CG  LEU A   5 " =    1.193
peak=    5.358 closest distance to " CG2 VAL A 296 " =    1.003
peak=    5.237 closest distance to " CG  LEU A 228 " =    1.173
peak=    5.015 closest distance to " CZ  PHE A 218 " =    1.105
peak=    5.011 closest distance to " CD2 LEU A   5 " =    1.127
peak=    4.844 closest distance to " O   HOH Z 232 " =    2.213
peak=    4.813 closest distance to " O   HOH Z 102 " =    1.412
peak=    4.790 closest distance to " CG1 VAL A 296 " =    1.248
peak=    4.749 closest distance to " CD1AILE A 234 " =    1.049
peak=    4.726 closest distance to " CG  PRO A 198 " =    1.300
peak=    4.674 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.635 closest distance to " O   HOH Z 111 " =    2.032
peak=    4.532 closest distance to " NE2 GLN A  11 " =    1.059
peak=    4.529 closest distance to " CB  SER A  63 " =    1.335
peak=    4.512 closest distance to " CB  ASP A 124 " =    0.827
peak=    4.500 closest distance to " CB  VAL A 296 " =    1.124
peak=    4.473 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.405 closest distance to " O   HOH Z 425 " =    1.588
peak=    4.396 closest distance to " O   HOH Z 261 " =    1.893
peak=    4.370 closest distance to " CG  PRO A 243 " =    1.113
peak=    4.368 closest distance to " CA  VAL A 230 " =    1.188
peak=    4.360 closest distance to " O   HOH Z 265 " =    2.162
peak=    4.307 closest distance to " O   HOH Z 184 " =    1.615
peak=    4.305 closest distance to " CB  TRP A 266 " =    1.034
peak=    4.298 closest distance to " CG  PRO A 213 " =    1.244
peak=    4.295 closest distance to " O   HOH Z 411 " =    3.658
peak=    4.249 closest distance to " CD  ARG A 159 " =    0.778
peak=    4.248 closest distance to " O   HOH Z 368 " =    2.311
peak=    4.247 closest distance to " CB  ASN A 148 " =    1.329
peak=    4.224 closest distance to " O   HOH Z 287 " =    2.059
peak=    4.200 closest distance to " CA  TYR A  30 " =    1.014
peak=    4.194 closest distance to " O   HOH Z 427 " =    3.135
peak=    4.193 closest distance to " O   HOH Z 144 " =    1.828
peak=    4.169 closest distance to " O   HOH Z 303 " =    2.168
peak=    4.147 closest distance to " O   PRO A 198 " =    1.573
peak=    4.145 closest distance to " O   HOH Z 183 " =    1.372
peak=    4.140 closest distance to " O   HOH Z 214 " =    1.284
peak=    4.139 closest distance to " OE1 GLN A  55 " =    1.122
peak=    4.133 closest distance to " CG  ARG A 138 " =    1.223
peak=    4.118 closest distance to " CA  ARG A 195 " =    1.279
peak=    4.114 closest distance to " CB  GLU A 128 " =    1.035
peak=    4.110 closest distance to " CG  MET A 185 " =    1.359
peak=    4.087 closest distance to " CD  LYS A 166 " =    1.347
peak=    4.081 closest distance to " CB  ASN A 142 " =    1.026
peak=    4.065 closest distance to " CA  ALA A  51 " =    1.011
peak=    4.063 closest distance to " O   HOH Z 298 " =    2.106
peak=    4.061 closest distance to " O   HOH Z  49 " =    1.138
peak=    4.047 closest distance to " CG2 THR A 221 " =    1.079
peak=    4.028 closest distance to " O   HOH Z  43 " =    1.996
peak=    4.017 closest distance to " O   SER A  87 " =    2.385
peak=    4.013 closest distance to " CA  ALA A 295 " =    1.149
peak=    4.013 closest distance to " N   PHE A 130 " =    1.290
peak=    4.009 closest distance to " O   HOH Z 188 " =    3.087
peak=    3.992 closest distance to " CZ3 TRP A 266 " =    1.193
peak=    3.980 closest distance to " CB  ARG A 190 " =    1.684
peak=    3.946 closest distance to " CD2 LEU A 228 " =    1.226
peak=    3.942 closest distance to " CE  LYS A  76 " =    0.884
peak=    3.924 closest distance to " NE2 HIS A 207 " =    1.105
peak=    3.904 closest distance to " O   HOH Z 207 " =    1.250
peak=    3.901 closest distance to " O   HOH Z   9 " =    1.436
peak=    3.893 closest distance to " O   HOH Z 346 " =    1.606
peak=    3.893 closest distance to " O   HOH Z 247 " =    1.469
peak=    3.890 closest distance to " CD1 LEU A 300 " =    1.157
peak=    3.882 closest distance to " CB  ARG A  79 " =    1.516
peak=    3.874 closest distance to " NH1AARG A 145 " =    1.215
peak=    3.868 closest distance to " CD ALYS A 290 " =    1.033
peak=    3.856 closest distance to " CD  ARG A 269 " =    0.923
peak=    3.854 closest distance to " CB  ASP A 140 " =    0.838
peak=    3.848 closest distance to " CB AVAL A  41 " =    1.195
peak=    3.848 closest distance to " CB  ASN A  39 " =    0.906
peak=    3.846 closest distance to " CZ  PHE A 192 " =    1.012
peak=    3.837 closest distance to " CA  SER A  87 " =    0.920
peak=    3.834 closest distance to " O   HOH Z 193 " =    2.225
peak=    3.820 closest distance to " O   ASP A 124 " =    1.115
peak=    3.818 closest distance to " CB  SER A   3 " =    1.492
peak=    3.812 closest distance to " CB  VAL A 202 " =    1.616
peak=    3.803 closest distance to " CB  GLU A 277 " =    3.806
peak=    3.802 closest distance to " O   HOH Z 126 " =    1.612
peak=    3.798 closest distance to " ND2 ASN A 187 " =    1.528
peak=    3.795 closest distance to " O   HOH Z 316 " =    3.170
peak=    3.795 closest distance to " NH2AARG A 145 " =    1.187
peak=    3.786 closest distance to " CB  SER A 216 " =    0.935
peak=    3.782 closest distance to " O   HOH Z 290 " =    1.345
peak=    3.780 closest distance to " O   HOH Z 359 " =    1.602
peak=    3.779 closest distance to " CD1 LEU A   5 " =    1.360
peak=    3.758 closest distance to " CZ  PHE A  38 " =    1.230
peak=    3.746 closest distance to " O   HOH Z  78 " =    1.752
peak=    3.741 closest distance to " CG2 VAL A 257 " =    0.896
peak=    3.724 closest distance to " CB  LEU A  83 " =    0.784
peak=    3.724 closest distance to " CG  GLU A  37 " =    0.957
peak=    3.719 closest distance to " CG  LEU A 167 " =    1.190
peak=    3.707 closest distance to " CD  ARG A  66 " =    2.364
peak=    3.701 closest distance to " CB  PRO A  54 " =    0.846
peak=    3.700 closest distance to " O   HOH Z 272 " =    1.887
peak=    3.699 closest distance to " O   HOH Z 171 " =    3.967
peak=    3.695 closest distance to " O   ASP A 200 " =    1.684
peak=    3.691 closest distance to " O   HOH Z 158 " =    3.061
peak=    3.691 closest distance to " O   HOH Z 234 " =    3.844
peak=    3.691 closest distance to " CA  ALA A 184 " =    1.124
peak=    3.691 closest distance to " CD1 LEU A  96 " =    0.809
peak=    3.685 closest distance to " CA  ASN A 127 " =    1.115
peak=    3.680 closest distance to " CA  TYR A  30 " =    1.089
peak=    3.677 closest distance to " N   SER A 135 " =    1.440
peak=    3.673 closest distance to " O   HOH Z   4 " =    1.736
peak=    3.673 closest distance to " N   ASN A  39 " =    1.261
peak=    3.670 closest distance to " CA  GLY A 267 " =    0.758
peak=    3.663 closest distance to " O   HOH Z  80 " =    1.944
peak=    3.663 closest distance to " OG  SER A 276 " =    1.510
peak=    3.661 closest distance to " CG2 ILE A 234 " =    0.854
peak=    3.655 closest distance to " CB  VAL A 296 " =    1.371
peak=    3.655 closest distance to " O   HOH Z 422 " =    2.660
peak=    3.655 closest distance to " O   HOH Z 213 " =    1.742
peak=    3.653 closest distance to " CB  GLU A  46 " =    0.932
peak=    3.649 closest distance to " NH1 ARG A  14 " =    1.035
peak=    3.645 closest distance to " CB  ARG A 275 " =    0.939
peak=    3.634 closest distance to " NH1 ARG A  56 " =    1.124
peak=    3.632 closest distance to " CG1 VAL A 153 " =    1.008
peak=    3.630 closest distance to " O  BHOH Z  74 " =    1.258
peak=    3.627 closest distance to " O   HOH Z  92 " =    2.479
peak=    3.626 closest distance to " CB  SER A 273 " =    0.972
peak=    3.614 closest distance to " CG AARG A 275 " =    1.272
peak=    3.613 closest distance to " CA  ARG A  36 " =    1.183
peak=    3.610 closest distance to " O   HOH Z 126 " =    2.077
peak=    3.608 closest distance to " N   ALA A 256 " =    1.179
peak=    3.605 closest distance to " CB  SER A 210 " =    0.923
peak=    3.604 closest distance to " O   HOH Z  88 " =    3.324
peak=    3.601 closest distance to " CB  VAL A 265 " =    1.266
peak=    3.601 closest distance to " CB  PRO A 243 " =    1.184
peak=    3.599 closest distance to " O   HOH Z 406 " =    1.537
peak=    3.596 closest distance to " ND2 ASN A 249 " =    0.939
peak=    3.591 closest distance to " O   HOH Z 124 " =    2.034
peak=    3.590 closest distance to " CA  ALA A 160 " =    1.043
peak=    3.589 closest distance to " CB  MET A  47 " =    1.016
peak=    3.579 closest distance to " CB  GLU A 152 " =    1.207
peak=    3.576 closest distance to " CB  GLN A  89 " =    1.204
peak=    3.572 closest distance to " CG  ARG A 269 " =    1.656
peak=    3.567 closest distance to " O   ALA A 165 " =    1.488
peak=    3.565 closest distance to " CB  ILE A 120 " =    1.335
peak=    3.563 closest distance to " CB  SER A  62 " =    0.939
peak=    3.553 closest distance to " O   HOH Z 227 " =    1.725
peak=    3.551 closest distance to " CE3 TRP A  85 " =    1.189
peak=    3.539 closest distance to " CB  THR A  82 " =    1.369
peak=    3.533 closest distance to " ND2 ASN A 249 " =    1.930
peak=    3.532 closest distance to " O   HOH Z 437 " =    1.395
peak=    3.532 closest distance to " CG1 ILE A  33 " =    1.308
peak=    3.521 closest distance to " CD2 TRP A 179 " =    1.328
peak=    3.517 closest distance to " CA  ALA A 291 " =    0.924
peak=    3.517 closest distance to " CB  SER A 212 " =    1.326
peak=    3.516 closest distance to " O   THR A 251 " =    1.221
peak=    3.508 closest distance to " CB  ALA A 291 " =    1.257
peak=    3.505 closest distance to " O   HOH Z 313 " =    1.823
peak=    3.501 closest distance to " ND2BASN A 224 " =    0.805
peak=    3.496 closest distance to " CA  VAL A 125 " =    1.306
peak=    3.495 closest distance to " NZ  LYS A 117 " =    3.148
peak=    3.479 closest distance to " CA  GLU A 152 " =    0.917
peak=    3.476 closest distance to " CA  ARG A 139 " =    1.214
peak=    3.468 closest distance to " O   HOH Z  76 " =    1.227
peak=    3.462 closest distance to " O   HOH Z  57 " =    1.478
peak=    3.460 closest distance to " CA  VAL A 112 " =    1.123
peak=    3.458 closest distance to " CB  ALA A 104 " =    0.827
peak=    3.447 closest distance to " O   HOH Z 394 " =    1.971
peak=    3.443 closest distance to " OG1 THR A 279 " =    1.494
peak=    3.441 closest distance to " OG  SER A 245 " =    1.698
peak=    3.440 closest distance to " CA  GLY A 211 " =    1.409
peak=    3.437 closest distance to " O   HOH Z 280 " =    2.944
peak=    3.436 closest distance to " CB  ALA A 137 " =    1.077
peak=    3.434 closest distance to " O   THR A 220 " =    1.208
peak=    3.431 closest distance to " O   HOH Z 193 " =    1.742
peak=    3.423 closest distance to " CB  LEU A 228 " =    1.227
peak=    3.422 closest distance to " CA  LEU A 282 " =    1.076
peak=    3.419 closest distance to " O   HOH Z  21 " =    1.791
peak=    3.408 closest distance to " O   ASN A  74 " =    1.462
peak=    3.407 closest distance to " CB  MET A  40 " =    0.773
peak=    3.406 closest distance to " O   HOH Z 258 " =    2.040
peak=    3.405 closest distance to " CZ3 TRP A 274 " =    4.845
peak=    3.405 closest distance to " CG1 ILE A  49 " =    1.606
peak=    3.403 closest distance to " O   MET A 105 " =    1.773
peak=    3.402 closest distance to " CA  TYR A 116 " =    1.441
peak=    3.401 closest distance to " CB  ALA A 242 " =    0.809
peak=    3.400 closest distance to " CB  ALA A 248 " =    1.118
peak=    3.395 closest distance to " CD  ARG A  66 " =    2.268
peak=    3.390 closest distance to " CB  ASN A 187 " =    1.105
peak=    3.388 closest distance to " O   HOH Z 156 " =    2.925
peak=    3.384 closest distance to " CB  ALA A 161 " =    1.010
peak=    3.384 closest distance to " OD1 ASN A  69 " =    2.616
peak=    3.382 closest distance to " O   HOH Z 215 " =    1.433
peak=    3.373 closest distance to " ND1 HIS A  81 " =    1.744
peak=    3.369 closest distance to " O   HOH Z 291 " =    1.664
peak=    3.368 closest distance to " O   HOH Z 353 " =    2.623
peak=    3.367 closest distance to " N   TYR A  15 " =    0.830
peak=    3.366 closest distance to " CH2 TRP A  70 " =    1.070
peak=    3.364 closest distance to " O  BHOH Z 338 " =    2.374
peak=    3.362 closest distance to " O   HOH Z 298 " =    2.350
peak=    3.359 closest distance to " CB  LYS A 117 " =    1.171
peak=    3.359 closest distance to " CB  ARG A 145 " =    0.858
peak=    3.358 closest distance to " O   HOH Z 410 " =    1.276
peak=    3.358 closest distance to " O   HOH Z 109 " =    2.778
peak=    3.357 closest distance to " O   HOH Z 112 " =    1.629
peak=    3.354 closest distance to " O   HOH Z 211 " =    1.298
peak=    3.353 closest distance to " O   HOH Z  63 " =    1.809
peak=    3.351 closest distance to " CB  LEU A 143 " =    1.317
peak=    3.348 closest distance to " CG BARG A 275 " =    1.522
peak=    3.348 closest distance to " CA  ASP A 124 " =    0.759
peak=    3.348 closest distance to " OD1 ASN A 217 " =    1.564
peak=    3.341 closest distance to " CA  ARG A 102 " =    1.219
peak=    3.340 closest distance to " O   HOH Z 134 " =    2.808
peak=    3.338 closest distance to " CB  TRP A 150 " =    1.393
peak=    3.333 closest distance to " CB  ALA A  10 " =    1.014
peak=    3.333 closest distance to " CA  GLN A  94 " =    0.834
peak=    3.332 closest distance to " CA  ALA A 154 " =    1.043
peak=    3.331 closest distance to " CA  ALA A  21 " =    1.221
peak=    3.329 closest distance to " C   ALA A 299 " =    0.940
peak=    3.324 closest distance to " CZ3 TRP A  85 " =    0.984
peak=    3.323 closest distance to " O   HOH Z 130 " =    1.040
peak=    3.323 closest distance to " CE2 TYR A 186 " =    0.902
peak=    3.322 closest distance to " OH  TYR A 247 " =    1.134
peak=    3.322 closest distance to " O   HOH Z 163 " =    1.501
peak=    3.321 closest distance to " O   HOH Z 423 " =    1.546
peak=    3.321 closest distance to " O   HOH Z 132 " =    2.670
peak=    3.321 closest distance to " O   HOH Z 368 " =    3.532
peak=    3.319 closest distance to " CD  ARG A 219 " =    1.116
peak=    3.319 closest distance to " CE1 TYR A 186 " =    1.226
peak=    3.316 closest distance to " CZ3 TRP A  92 " =    1.404
peak=    3.316 closest distance to " CA  MET A  40 " =    1.290
peak=    3.311 closest distance to " CG  MET A 185 " =    1.026
peak=    3.309 closest distance to " O   HOH Z 180 " =    2.068
peak=    3.307 closest distance to " O   HOH Z 116 " =    1.854
peak=    3.306 closest distance to " CG  GLN A  88 " =    1.139
peak=    3.303 closest distance to " O   HOH Z 293 " =    1.942
peak=    3.302 closest distance to " O   HOH Z 201 " =    2.777
peak=    3.297 closest distance to " CB  ALA A   9 " =    1.654
peak=    3.295 closest distance to " O   HOH Z  10 " =    1.832
peak=    3.288 closest distance to " CD1 ILE A 199 " =    0.946
peak=    3.287 closest distance to " O   ASN A 209 " =    1.327
peak=    3.283 closest distance to " CA  ILE A 234 " =    0.988
peak=    3.279 closest distance to " O   HOH Z 148 " =    2.086
peak=    3.277 closest distance to " O   HOH Z 172 " =    3.826
peak=    3.276 closest distance to " O   HOH Z 403 " =    1.622
peak=    3.276 closest distance to " CA  ASN A 215 " =    1.193
peak=    3.272 closest distance to " CG1 ILE A 120 " =    1.097
peak=    3.271 closest distance to " NH1 ARG A 138 " =    1.150
peak=    3.267 closest distance to " CB  ALA A 227 " =    1.092
peak=    3.266 closest distance to " CB  PHE A  61 " =    1.483
peak=    3.266 closest distance to " O   GLN A 278 " =    1.305
peak=    3.263 closest distance to " O   HOH Z 350 " =    1.614
peak=    3.261 closest distance to " O   HOH Z 248 " =    1.719
peak=    3.261 closest distance to " CG  PHE A 204 " =    0.945
peak=    3.258 closest distance to " O   HOH Z 133 " =    2.874
peak=    3.254 closest distance to " O   HOH Z 368 " =    4.105
peak=    3.254 closest distance to " O   HOH Z 222 " =    1.195
peak=    3.252 closest distance to " CA  THR A 264 " =    0.701
peak=    3.251 closest distance to " O   HOH Z 188 " =    1.975
peak=    3.248 closest distance to " OG BSER A 164 " =    2.211
peak=    3.248 closest distance to " CB  ASN A 173 " =    0.989
peak=    3.246 closest distance to " CA  ALA A 100 " =    1.019
peak=    3.242 closest distance to " O   HOH Z 332 " =    1.580
peak=    3.241 closest distance to " CD2 LEU A   5 " =    0.732
peak=    3.241 closest distance to " CB  SER A 288 " =    1.328
peak=    3.238 closest distance to " O   HOH Z 128 " =    2.266
peak=    3.237 closest distance to " O   HOH Z 261 " =    1.666
peak=    3.236 closest distance to " CG2 ILE A 263 " =    1.141
peak=    3.234 closest distance to " CB  ALA A 248 " =    1.293
peak=    3.233 closest distance to " O   HOH Z 285 " =    2.405
peak=    3.228 closest distance to " O   HOH Z 326 " =    2.317
peak=    3.228 closest distance to " CA  GLN A 223 " =    0.986
peak=    3.220 closest distance to " O   HOH Z 117 " =    2.194
peak=    3.218 closest distance to " O   TYR A 116 " =    1.274
peak=    3.218 closest distance to " N   ARG A 156 " =    1.445
peak=    3.217 closest distance to " CA  MET A 105 " =    0.956
peak=    3.214 closest distance to " O   HOH Z 200 " =    3.384
peak=    3.212 closest distance to " O   THR A 182 " =    1.377
peak=    3.212 closest distance to " O   HOH Z 199 " =    1.596
peak=    3.211 closest distance to " CB  TRP A 179 " =    1.303
peak=    3.211 closest distance to " CE1 HIS A 115 " =    1.053
peak=    3.210 closest distance to " CG1 ILE A 151 " =    1.153
peak=    3.210 closest distance to " O   HOH Z 357 " =    2.803
peak=    3.209 closest distance to " CD  GLU A 152 " =    0.903
peak=    3.206 closest distance to " O   HOH Z 167 " =    1.660
peak=    3.206 closest distance to " CA  ASN A 284 " =    0.925
peak=    3.203 closest distance to " NZ  LYS A  48 " =    1.427
peak=    3.201 closest distance to " CG  MET A 113 " =    1.783
peak=    3.201 closest distance to " O   HOH Z 155 " =    3.426
peak=    3.201 closest distance to " O   PHE A 192 " =    1.407
peak=    3.201 closest distance to " O   GLU A   2 " =    1.482
peak=    3.197 closest distance to " O   HOH Z 281 " =    2.566
peak=    3.193 closest distance to " CB  ASN A 187 " =    1.483
peak=    3.192 closest distance to " ND2 ASN A 127 " =    1.101
peak=    3.188 closest distance to " CD  GLU A 236 " =    1.028
peak=    3.188 closest distance to " CG BARG A 102 " =    1.888
peak=    3.185 closest distance to " CB  ALA A  43 " =    0.940
peak=    3.172 closest distance to " CG2 ILE A 106 " =    0.868
peak=    3.162 closest distance to " CA  LYS A 290 " =    1.248
peak=    3.159 closest distance to " O   HOH Z 391 " =    2.955
peak=    3.158 closest distance to " CB  VAL A 268 " =    0.826
peak=    3.158 closest distance to " O   HOH Z 371 " =    3.167
peak=    3.154 closest distance to " O   THR A 294 " =    1.231
peak=    3.144 closest distance to " O   HOH Z 145 " =    1.547
peak=    3.138 closest distance to " O   PRO A 213 " =    1.468
peak=    3.136 closest distance to " O   HOH Z 106 " =    4.216
peak=    3.134 closest distance to " N   GLU A  44 " =    1.057
peak=    3.133 closest distance to " OG  SER A  62 " =    3.084
peak=    3.128 closest distance to " OG  SER A  22 " =    2.925
peak=    3.128 closest distance to " CE3 TRP A 150 " =    1.093
peak=    3.127 closest distance to " O   HOH Z 166 " =    3.625
peak=    3.126 closest distance to " NE2 GLN A  58 " =    4.321
peak=    3.121 closest distance to " CG2 VAL A 268 " =    1.064
peak=    3.120 closest distance to " CD1 ILE A  33 " =    1.858
peak=    3.120 closest distance to " O   HOH Z  48 " =    1.696
peak=    3.113 closest distance to " O   CYS A 168 " =    1.209
peak=    3.112 closest distance to " CB  ASN A 285 " =    0.925
peak=    3.110 closest distance to " O   HOH Z 148 " =    3.437
peak=    3.109 closest distance to " N   ASN A 127 " =    1.271
peak=    3.107 closest distance to " CG  GLN A  89 " =    1.527
peak=    3.102 closest distance to " CA  GLN A  88 " =    1.530
peak=    3.100 closest distance to " CB  THR A  31 " =    1.471
peak=    3.097 closest distance to " CG2 ILE A  20 " =    1.487
peak=    3.097 closest distance to " N   VAL A 126 " =    1.554
peak=    3.092 closest distance to " O   HOH Z 302 " =    1.944
peak=    3.088 closest distance to " CB  PHE A 283 " =    0.888
peak=    3.085 closest distance to " O   ALA A 158 " =    1.466
peak=    3.083 closest distance to " N   GLY A 133 " =    3.784
peak=    3.082 closest distance to " CA  ALA A 158 " =    1.206
peak=    3.079 closest distance to " O   HOH Z 313 " =    1.620
peak=    3.078 closest distance to " O   HOH Z  59 " =    2.285
peak=    3.078 closest distance to " CB  ALA A 114 " =    0.724
peak=    3.076 closest distance to " O   HOH Z 272 " =    2.905
peak=    3.074 closest distance to " CA  GLY A 133 " =    3.795
peak=    3.072 closest distance to " O   PRO A 198 " =    1.316
peak=    3.065 closest distance to " CA  VAL A 153 " =    0.990
peak=    3.063 closest distance to " CA  ILE A  33 " =    1.741
peak=    3.060 closest distance to " CB  GLU A  37 " =    0.879
peak=    3.046 closest distance to " CD  ARG A 195 " =    0.970

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.537 - 5.444
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 220
   mapped sites are within: 0.728 - 5.444

peak=   -5.297 closest distance to " CG1 VAL A 296 " =    1.086
peak=   -4.816 closest distance to " CG2 VAL A 230 " =    0.825
peak=   -4.482 closest distance to " CG1 VAL A 112 " =    2.687
peak=   -4.311 closest distance to " CD  GLN A  58 " =    0.887
peak=   -4.238 closest distance to " CD  ARG A 156 " =    2.131
peak=   -4.156 closest distance to " CB  PRO A 243 " =    2.708
peak=   -4.152 closest distance to " CD  ARG A  14 " =    3.253
peak=   -4.147 closest distance to " O   HOH Z 231 " =    2.030
peak=   -4.048 closest distance to " OE1 GLN A 223 " =    2.376
peak=   -4.045 closest distance to " CG1 VAL A 250 " =    2.752
peak=   -4.020 closest distance to " O   HOH Z 196 " =    2.458
peak=   -4.018 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -4.010 closest distance to " C   GLY A  17 " =    1.304
peak=   -3.981 closest distance to " O   HOH Z 166 " =    1.771
peak=   -3.970 closest distance to " O   HOH Z 133 " =    1.105
peak=   -3.959 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.943 closest distance to " CG  ARG A 269 " =    2.309
peak=   -3.919 closest distance to " O   HOH Z 216 " =    1.043
peak=   -3.914 closest distance to " CE2 TYR A  30 " =    2.667
peak=   -3.897 closest distance to " CE3 TRP A  70 " =    1.802
peak=   -3.869 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.850 closest distance to " CG1 VAL A 112 " =    2.818
peak=   -3.846 closest distance to " CA  GLY A 241 " =    2.337
peak=   -3.840 closest distance to " O   HOH Z  73 " =    2.291
peak=   -3.830 closest distance to " C   ALA A 158 " =    1.302
peak=   -3.823 closest distance to " CG  MET A 105 " =    1.003
peak=   -3.786 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.775 closest distance to " CG  HIS A  86 " =    1.114
peak=   -3.771 closest distance to " O   ILE A 109 " =    2.689
peak=   -3.742 closest distance to " O   HOH Z 177 " =    1.801
peak=   -3.738 closest distance to " CZ2 TRP A  92 " =    2.887
peak=   -3.727 closest distance to " O   SER A 271 " =    2.232
peak=   -3.727 closest distance to " O   HOH Z 102 " =    1.299
peak=   -3.717 closest distance to " OG  SER A  97 " =    2.269
peak=   -3.716 closest distance to " O   VAL A 189 " =    2.564
peak=   -3.707 closest distance to " O   HOH Z 359 " =    3.058
peak=   -3.700 closest distance to " CG2BVAL A  41 " =    2.755
peak=   -3.697 closest distance to " O   HOH Z 231 " =    1.146
peak=   -3.692 closest distance to " O   HOH Z 351 " =    1.534
peak=   -3.685 closest distance to " CD  GLN A  55 " =    1.062
peak=   -3.644 closest distance to " O   HOH Z 251 " =    4.898
peak=   -3.640 closest distance to " CD2 TYR A 293 " =    1.914
peak=   -3.635 closest distance to " OD1 ASN A 148 " =    1.401
peak=   -3.625 closest distance to " O   HOH Z 411 " =    5.406
peak=   -3.625 closest distance to " O   GLY A 203 " =    2.396
peak=   -3.585 closest distance to " O   HOH Z 201 " =    2.033
peak=   -3.572 closest distance to " ND2 ASN A  45 " =    2.382
peak=   -3.571 closest distance to " CG  ASP A 231 " =    0.797
peak=   -3.571 closest distance to " CB  ALA A  43 " =    2.739
peak=   -3.570 closest distance to " CG  GLU A 277 " =    1.327
peak=   -3.559 closest distance to " O   HOH Z 118 " =    1.304
peak=   -3.555 closest distance to " CD1 LEU A 101 " =    2.818
peak=   -3.554 closest distance to " CD1 PHE A  59 " =    2.090
peak=   -3.544 closest distance to " OG1 THR A  82 " =    1.477
peak=   -3.541 closest distance to " CD2 LEU A 167 " =    1.819
peak=   -3.537 closest distance to " OG BSER A 134 " =    1.542
peak=   -3.532 closest distance to " O   HOH Z  19 " =    2.245
peak=   -3.531 closest distance to " OD2 ASP A  50 " =    2.352
peak=   -3.530 closest distance to " CG2 THR A 178 " =    2.333
peak=   -3.519 closest distance to " O   GLY A 211 " =    1.410
peak=   -3.518 closest distance to " CG  GLU A  53 " =    1.345
peak=   -3.517 closest distance to " O   PRO A 163 " =    2.202
peak=   -3.513 closest distance to " CD  GLN A  88 " =    0.873
peak=   -3.511 closest distance to " O   ASP A  27 " =    2.055
peak=   -3.508 closest distance to " O   HOH Z  10 " =    1.565
peak=   -3.507 closest distance to " O   HOH Z  38 " =    1.664
peak=   -3.507 closest distance to " O   HOH Z 407 " =    3.226
peak=   -3.506 closest distance to " CA  GLY A 203 " =    2.505
peak=   -3.505 closest distance to " N   ALA A  43 " =    2.573
peak=   -3.494 closest distance to " CB  VAL A 230 " =    1.118
peak=   -3.494 closest distance to " O   HOH Z 232 " =    1.899
peak=   -3.493 closest distance to " NE2 GLN A  55 " =    2.449
peak=   -3.492 closest distance to " CD1 LEU A 228 " =    2.450
peak=   -3.488 closest distance to " CG1 VAL A 265 " =    2.447
peak=   -3.486 closest distance to " O   HOH Z  52 " =    1.728
peak=   -3.477 closest distance to " CD1 LEU A   5 " =    2.534
peak=   -3.474 closest distance to " N   ALA A 226 " =    2.218
peak=   -3.466 closest distance to " CA  GLY A 241 " =    3.133
peak=   -3.464 closest distance to " CG1 VAL A 125 " =    1.879
peak=   -3.454 closest distance to " O   HOH Z 103 " =    1.910
peak=   -3.449 closest distance to " OE1 GLN A  88 " =    1.169
peak=   -3.433 closest distance to " O   HOH Z 128 " =    2.697
peak=   -3.431 closest distance to " C   ALA A 165 " =    1.985
peak=   -3.431 closest distance to " CG2 VAL A 296 " =    1.420
peak=   -3.431 closest distance to " CD2 PHE A  61 " =    2.071
peak=   -3.422 closest distance to " O   HOH Z   9 " =    1.583
peak=   -3.418 closest distance to " CZ3 TRP A 179 " =    1.147
peak=   -3.414 closest distance to " CA  GLY A 133 " =    2.305
peak=   -3.404 closest distance to " CB  ARG A  79 " =    2.659
peak=   -3.403 closest distance to " O   HOH Z  94 " =    1.963
peak=   -3.398 closest distance to " O   HOH Z  60 " =    2.283
peak=   -3.398 closest distance to " O   HOH Z 113 " =    2.431
peak=   -3.392 closest distance to " NH2 ARG A  66 " =    2.251
peak=   -3.390 closest distance to " O   HOH Z 259 " =    4.052
peak=   -3.390 closest distance to " CG  LEU A   5 " =    1.618
peak=   -3.389 closest distance to " O   HOH Z 255 " =    0.866
peak=   -3.388 closest distance to " CE3 TRP A 150 " =    2.321
peak=   -3.386 closest distance to " O   HOH Z 210 " =    0.917
peak=   -3.384 closest distance to " O   HOH Z  11 " =    1.832
peak=   -3.378 closest distance to " O   HOH Z 106 " =    1.995
peak=   -3.377 closest distance to " O   HOH Z 341 " =    1.117
peak=   -3.373 closest distance to " CD2 LEU A 237 " =    2.882
peak=   -3.364 closest distance to " O   HOH Z 357 " =    2.166
peak=   -3.364 closest distance to " O   HOH Z  44 " =    0.976
peak=   -3.364 closest distance to " C   HIS A 108 " =    1.142
peak=   -3.363 closest distance to " OG  SER A  87 " =    1.625
peak=   -3.361 closest distance to " CE2 TRP A  70 " =    2.349
peak=   -3.357 closest distance to " O   HOH Z 183 " =    1.111
peak=   -3.357 closest distance to " O   HOH Z 411 " =    1.718
peak=   -3.353 closest distance to " C   LEU A 143 " =    1.108
peak=   -3.351 closest distance to " O   HOH Z 243 " =    1.719
peak=   -3.348 closest distance to " O   HOH Z  70 " =    2.171
peak=   -3.344 closest distance to " CA  ARG A  36 " =    1.245
peak=   -3.340 closest distance to " O   HOH Z 350 " =    1.910
peak=   -3.337 closest distance to " O   HOH Z 185 " =    2.429
peak=   -3.333 closest distance to " CG2 VAL A 189 " =    2.089
peak=   -3.330 closest distance to " O   HOH Z 275 " =    1.640
peak=   -3.330 closest distance to " CD2 HIS A 207 " =    2.180
peak=   -3.329 closest distance to " N   PHE A  59 " =    2.054
peak=   -3.325 closest distance to " C   MET A 188 " =    1.355
peak=   -3.320 closest distance to " CB  ALA A 248 " =    2.117
peak=   -3.319 closest distance to " O   HOH Z 377 " =    1.709
peak=   -3.314 closest distance to " CD1 TRP A 274 " =    1.017
peak=   -3.314 closest distance to " OD2 ASP A 171 " =    1.884
peak=   -3.309 closest distance to " O   HOH Z 111 " =    1.921
peak=   -3.308 closest distance to " O   HOH Z  17 " =    1.440
peak=   -3.302 closest distance to " O   GLY A 262 " =    2.473
peak=   -3.299 closest distance to " CG2 VAL A 230 " =    2.788
peak=   -3.297 closest distance to " O   HOH Z  30 " =    1.760
peak=   -3.294 closest distance to " O   HOH Z 113 " =    2.512
peak=   -3.291 closest distance to " CE  LYS A  76 " =    2.624
peak=   -3.290 closest distance to " O   HOH Z 290 " =    1.449
peak=   -3.289 closest distance to " OH  TYR A 247 " =    1.815
peak=   -3.289 closest distance to " CG  LEU A 101 " =    2.487
peak=   -3.289 closest distance to " SD BMET A  47 " =    1.150
peak=   -3.285 closest distance to " N   ILE A 120 " =    1.082
peak=   -3.282 closest distance to " CD  GLN A 223 " =    1.324
peak=   -3.281 closest distance to " O   HOH Z 265 " =    1.809
peak=   -3.275 closest distance to " O   HOH Z 426 " =    1.700
peak=   -3.269 closest distance to " NE2 GLN A 240 " =    1.664
peak=   -3.268 closest distance to " CG  TRP A 266 " =    1.902
peak=   -3.265 closest distance to " CG  PRO A 163 " =    2.356
peak=   -3.264 closest distance to " CB  HIS A  81 " =    1.036
peak=   -3.262 closest distance to " CA  VAL A  67 " =    2.726
peak=   -3.261 closest distance to " O   HOH Z 177 " =    1.531
peak=   -3.260 closest distance to " CD1 ILE A  33 " =    2.599
peak=   -3.259 closest distance to " CB  ALA A   9 " =    2.624
peak=   -3.257 closest distance to " N   ASP A 191 " =    1.180
peak=   -3.257 closest distance to " O   HOH Z 285 " =    1.869
peak=   -3.250 closest distance to " O   HOH Z 252 " =    3.667
peak=   -3.250 closest distance to " C   LEU A 222 " =    1.125
peak=   -3.249 closest distance to " CA  GLY A  98 " =    2.182
peak=   -3.241 closest distance to " O   HOH Z 236 " =    1.457
peak=   -3.241 closest distance to " N   THR A  52 " =    1.654
peak=   -3.240 closest distance to " O   HOH Z 110 " =    1.298
peak=   -3.236 closest distance to " NH2AARG A 275 " =    5.444
peak=   -3.235 closest distance to " O   TYR A  30 " =    2.407
peak=   -3.227 closest distance to " C   GLY A 133 " =    1.166
peak=   -3.225 closest distance to " N   SER A 212 " =    1.846
peak=   -3.222 closest distance to " C   ASN A 187 " =    1.776
peak=   -3.214 closest distance to " O   HOH Z 174 " =    2.617
peak=   -3.213 closest distance to " O   HOH Z 134 " =    2.893
peak=   -3.212 closest distance to " CD  LYS A 289 " =    2.402
peak=   -3.212 closest distance to " CE2 PHE A  61 " =    2.647
peak=   -3.210 closest distance to " CZ2 TRP A 274 " =    0.976
peak=   -3.210 closest distance to " O   HOH Z 431 " =    1.878
peak=   -3.208 closest distance to " N   TYR A  68 " =    2.887
peak=   -3.205 closest distance to " O   ARG A  56 " =    1.710
peak=   -3.202 closest distance to " O   HOH Z 353 " =    2.132
peak=   -3.199 closest distance to " CB  PRO A 163 " =    2.512
peak=   -3.198 closest distance to " O   GLY A  80 " =    2.567
peak=   -3.196 closest distance to " ND2 ASN A  45 " =    1.153
peak=   -3.194 closest distance to " O   TRP A  70 " =    1.489
peak=   -3.188 closest distance to " CB  ALA A  10 " =    2.258
peak=   -3.187 closest distance to " CB  TRP A  85 " =    2.657
peak=   -3.187 closest distance to " NH2 ARG A  79 " =    1.545
peak=   -3.181 closest distance to " CB  PHE A 130 " =    1.329
peak=   -3.179 closest distance to " CB  GLN A  55 " =    1.448
peak=   -3.177 closest distance to " CB  ALA A 129 " =    2.432
peak=   -3.177 closest distance to " CA  SER A 135 " =    1.267
peak=   -3.177 closest distance to " CD  GLU A 236 " =    1.114
peak=   -3.176 closest distance to " NE2 GLN A 194 " =    1.924
peak=   -3.176 closest distance to " CA  ASN A 127 " =    1.096
peak=   -3.173 closest distance to " CB  ALA A 291 " =    2.355
peak=   -3.170 closest distance to " OG  SER A  62 " =    4.564
peak=   -3.167 closest distance to " CG  LEU A   5 " =    0.954
peak=   -3.164 closest distance to " CB  ASN A  69 " =    1.462
peak=   -3.160 closest distance to " CZ  PHE A 218 " =    1.182
peak=   -3.160 closest distance to " OD1 ASP A 171 " =    1.575
peak=   -3.142 closest distance to " O   GLY A 196 " =    1.320
peak=   -3.140 closest distance to " O   HOH Z   6 " =    1.635
peak=   -3.138 closest distance to " C   GLY A  13 " =    0.906
peak=   -3.135 closest distance to " CG  LEU A 281 " =    1.912
peak=   -3.135 closest distance to " O   HOH Z  13 " =    1.720
peak=   -3.133 closest distance to " CG2AVAL A  41 " =    2.693
peak=   -3.132 closest distance to " OD1 ASN A 173 " =    1.222
peak=   -3.130 closest distance to " O   TYR A 186 " =    1.833
peak=   -3.125 closest distance to " CB  TYR A  15 " =    2.226
peak=   -3.125 closest distance to " O   HOH Z  43 " =    1.690
peak=   -3.124 closest distance to " CD  GLN A 223 " =    0.728
peak=   -3.118 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.117 closest distance to " CD1 TYR A 247 " =    2.340
peak=   -3.115 closest distance to " CG  GLN A  11 " =    1.428
peak=   -3.110 closest distance to " O   HOH Z 438 " =    3.180
peak=   -3.099 closest distance to " OG  SER A  63 " =    1.092
peak=   -3.096 closest distance to " O   HOH Z 219 " =    4.807
peak=   -3.094 closest distance to " O   HOH Z 114 " =    1.625
peak=   -3.094 closest distance to " CG1 VAL A  78 " =    2.549
peak=   -3.093 closest distance to " O   HOH Z 390 " =    2.138
peak=   -3.092 closest distance to " O   HOH Z 325 " =    1.692
peak=   -3.091 closest distance to " O   HOH Z  60 " =    2.319
peak=   -3.091 closest distance to " O   HOH Z 368 " =    1.600
peak=   -3.088 closest distance to " C   PHE A  59 " =    1.200
peak=   -3.082 closest distance to " O   HOH Z 136 " =    0.845
peak=   -3.078 closest distance to " N   SER A 276 " =    1.400
peak=   -3.069 closest distance to " O   GLU A  44 " =    1.552
peak=   -3.038 closest distance to " O   HOH Z 109 " =    1.234
peak=   -3.020 closest distance to " C   ASP A 270 " =    1.181

================= 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    :  0.4804 0.4740   6.281064e+00   6.264618e+00
   1_bss:  0.4724 0.4622   6.276228e+00   6.256630e+00
   1_xyz:  0.3822 0.4114   6.151736e+00   6.186254e+00
   1_adp:  0.3374 0.3882   6.065443e+00   6.148638e+00
   1_occ:  0.3371 0.3891   6.064600e+00   6.149553e+00
   2_bss:  0.3359 0.3866   6.066404e+00   6.148779e+00
   2_xyz:  0.2492 0.3005   5.817154e+00   5.958741e+00
   2_adp:  0.2260 0.2786   5.739799e+00   5.899385e+00
   2_occ:  0.2258 0.2786   5.739225e+00   5.899305e+00
   3_bss:  0.2244 0.2780   5.741309e+00   5.900455e+00
   3_xyz:  0.1639 0.2124   5.459544e+00   5.662227e+00
   3_adp:  0.1449 0.1978   5.374712e+00   5.605164e+00
   3_occ:  0.1449 0.1977   5.374767e+00   5.605725e+00
   4_bss:  0.1450 0.1976   5.374836e+00   5.604425e+00
   4_xyz:  0.1283 0.1830   5.281994e+00   5.526348e+00
   4_adp:  0.1272 0.1746   5.253519e+00   5.477402e+00
   4_occ:  0.1271 0.1746   5.253132e+00   5.477323e+00
   5_bss:  0.1270 0.1745   5.252646e+00   5.477031e+00
   5_xyz:  0.1274 0.1727   5.253094e+00   5.469363e+00
   5_adp:  0.1253 0.1738   5.248513e+00   5.475881e+00
   5_occ:  0.1252 0.1738   5.248372e+00   5.475748e+00
   5_bss:  0.1254 0.1735   5.247379e+00   5.474122e+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:  0.320  50.000   8.298   6.694  10.475   0.000   0.000   0.000
   1_xyz:  0.320  50.000   8.298   6.694  10.475   0.000   0.000   0.000
   1_adp:  0.320  50.000   8.298   6.694  10.475   0.000   0.000   0.000
   1_occ:  0.320  50.000   8.298   6.694  10.475   0.000   0.000   0.000
   2_bss:  0.341  76.440   5.354   4.335   7.406   0.000   0.000   0.000
   2_xyz:  0.341  76.440   5.354   4.335   7.406   0.000   0.000   0.000
   2_adp:  0.341  76.440   5.354   4.335   7.406   0.000   0.000   0.000
   2_occ:  0.341  76.440   5.354   4.335   7.406   0.000   0.000   0.000
   3_bss:  0.346  80.000   3.322   3.024   4.868   0.000   0.000   0.000
   3_xyz:  0.346  80.000   3.322   3.024   4.868   0.000   0.000   0.000
   3_adp:  0.346  80.000   3.322   3.024   4.868   0.000   0.000   0.000
   3_occ:  0.346  80.000   3.322   3.024   4.868   0.000   0.000   0.000
   4_bss:  0.342  84.056   2.685   2.502   4.218   0.000   0.000   0.000
   4_xyz:  0.342  84.056   2.685   2.502   4.218   0.000   0.000   0.000
   4_adp:  0.342  84.056   2.685   2.502   4.218   0.000   0.000   0.000
   4_occ:  0.342  84.056   2.685   2.502   4.218   0.000   0.000   0.000
   5_bss:  0.326  71.378   2.429   2.364   3.911   0.000   0.000   0.000
   5_xyz:  0.326  71.378   2.429   2.364   3.911   0.000   0.000   0.000
   5_adp:  0.326  71.378   2.429   2.364   3.911   0.000   0.000   0.000
   5_occ:  0.326  71.378   2.429   2.364   3.911   0.000   0.000   0.000
   5_bss:  0.326  74.279  -0.472  -0.537   1.009   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.164 0.4428  0.4994    66428.834
   1_bss:  55.102 0.4559  0.6627    64668.523
   1_xyz:  47.537 0.5495  0.7727    48401.470
   1_adp:  43.439 0.6006  0.8675    42725.498
   1_occ:  43.465 0.6002  0.8662    42779.979
   2_bss:  43.373 0.6013  0.7887    42663.339
   2_xyz:  31.261 0.7432  0.9528    24229.359
   2_adp:  28.175 0.7782  0.9859    20583.284
   2_occ:  28.204 0.7777  0.9848    20569.090
   3_bss:  28.231 0.7776  0.9188    20684.402
   3_xyz:  20.398 0.8577  0.9793    11516.405
   3_adp:  18.955 0.8715  0.9791    10081.854
   3_occ:  18.965 0.8714  0.9788    10082.012
   4_bss:  18.933 0.8716  0.9580    10045.149
   4_xyz:  17.055 0.8889  0.9670     8472.573
   4_adp:  15.821 0.9003  0.9678     7725.300
   4_occ:  15.826 0.9002  0.9676     7719.331
   5_bss:  15.821 0.9002  0.9596     7709.981
   5_xyz:  15.557 0.9029  0.9605     7541.104
   5_adp:  15.742 0.9013  0.9547     7649.169
   5_occ:  15.742 0.9012  0.9546     7648.245
   5_bss:  15.736 0.9012  0.9543     7612.659
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4673e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4673e+01
   1_xyz:   1.780  0.015  0.113 18.312  0.007  4.112   1.5519e-01
   1_adp:   1.780  0.015  0.113 18.312  0.007  4.112   1.5519e-01
   1_occ:   1.780  0.015  0.113 18.312  0.007  4.112   1.5519e-01
   2_bss:   1.780  0.015  0.113 18.312  0.007  4.112   1.5519e-01
   2_xyz:   1.151  0.009  0.080 16.688  0.005  4.134   8.0489e-02
   2_adp:   1.151  0.009  0.080 16.688  0.005  4.134   8.0489e-02
   2_occ:   1.151  0.009  0.080 16.688  0.005  4.134   8.0489e-02
   3_bss:   1.151  0.009  0.080 16.688  0.005  4.134   8.0489e-02
   3_xyz:   1.220  0.011  0.090 16.566  0.004  4.141   8.6264e-02
   3_adp:   1.220  0.011  0.090 16.566  0.004  4.141   8.6264e-02
   3_occ:   1.220  0.011  0.090 16.566  0.004  4.141   8.6264e-02
   4_bss:   1.220  0.011  0.090 16.566  0.004  4.141   8.6264e-02
   4_xyz:   1.192  0.011  0.091 16.213  0.004  4.153   8.6107e-02
   4_adp:   1.192  0.011  0.091 16.213  0.004  4.153   8.6107e-02
   4_occ:   1.192  0.011  0.091 16.213  0.004  4.153   8.6107e-02
   5_bss:   1.192  0.011  0.091 16.213  0.004  4.153   8.6107e-02
   5_xyz:   1.015  0.008  0.079 15.658  0.003  4.127   6.4735e-02
   5_adp:   1.015  0.008  0.079 15.658  0.003  4.127   6.4735e-02
   5_occ:   1.015  0.008  0.079 15.658  0.003  4.127   6.4735e-02
   5_bss:   1.015  0.008  0.079 15.658  0.003  4.127   6.4735e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0893e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0893e+00
   1_xyz:  15.119  0.172  0.475 85.902  0.040  2.224   1.1541e-01
   1_adp:  15.119  0.172  0.475 85.902  0.040  2.224   1.1541e-01
   1_occ:  15.119  0.172  0.475 85.902  0.040  2.224   1.1541e-01
   2_bss:  15.119  0.172  0.475 85.902  0.040  2.224   1.1541e-01
   2_xyz:   7.060  0.075  0.293 82.128  0.039  2.072   7.4311e-02
   2_adp:   7.060  0.075  0.293 82.128  0.039  2.072   7.4311e-02
   2_occ:   7.060  0.075  0.293 82.128  0.039  2.072   7.4311e-02
   3_bss:   7.060  0.075  0.293 82.128  0.039  2.072   7.4311e-02
   3_xyz:   9.425  0.072  0.385 88.465  0.044  2.282   5.8628e-02
   3_adp:   9.425  0.072  0.385 88.465  0.044  2.282   5.8628e-02
   3_occ:   9.425  0.072  0.385 88.465  0.044  2.282   5.8628e-02
   4_bss:   9.425  0.072  0.385 88.465  0.044  2.282   5.8628e-02
   4_xyz:   9.896  0.065  0.444 83.313  0.041  2.307   5.7746e-02
   4_adp:   9.896  0.065  0.444 83.313  0.041  2.307   5.7746e-02
   4_occ:   9.896  0.065  0.444 83.313  0.041  2.307   5.7746e-02
   5_bss:   9.896  0.065  0.444 83.313  0.041  2.307   5.7746e-02
   5_xyz:   8.244  0.044  0.353 81.764  0.040  2.413   4.1607e-02
   5_adp:   8.244  0.044  0.353 81.764  0.040  2.413   4.1607e-02
   5_occ:   8.244  0.044  0.353 81.764  0.040  2.413   4.1607e-02
   5_bss:   8.244  0.044  0.353 81.764  0.040  2.413   4.1607e-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:  92.22   0.00  13.00  75.10   0.00  10.08  92.22   0.00  28.88
   1_occ:  92.22   0.00  13.00  75.10   0.00  10.08  92.22   0.00  28.88
   2_bss:  92.22   0.00  13.00  75.10   0.00  10.08  92.22   0.00  28.88
   2_xyz:  92.22   0.00  13.00  75.10   0.00  10.08  92.22   0.00  28.88
   2_adp:  92.67   0.00  12.99  75.65   0.00   9.24  92.67   0.00  33.40
   2_occ:  92.67   0.00  12.99  75.65   0.00   9.24  92.67   0.00  33.40
   3_bss:  92.67   0.00  12.99  75.65   0.00   9.24  92.67   0.00  33.40
   3_xyz:  92.67   0.00  12.99  75.65   0.00   9.24  92.67   0.00  33.40
   3_adp: 106.15   0.00  14.14  93.95   0.00   9.01 106.15   0.00  42.07
   3_occ: 106.15   0.00  14.14  93.95   0.00   9.01 106.15   0.00  42.07
   4_bss: 106.15   0.00  14.14  93.95   0.00   9.01 106.15   0.00  42.07
   4_xyz: 106.15   0.00  14.14  93.95   0.00   9.01 106.15   0.00  42.07
   4_adp: 102.31   0.00  13.28  83.78   0.00   8.52 102.31   1.04  39.21
   4_occ: 102.31   0.00  13.28  83.78   0.00   8.52 102.31   1.04  39.21
   5_bss: 102.31   0.00  13.28  83.78   0.00   8.52 102.31   1.04  39.21
   5_xyz: 102.31   0.00  13.28  83.78   0.00   8.52 102.31   1.04  39.21
   5_adp: 103.88   0.00  13.20  86.98   0.00   8.47 103.88   1.04  38.97
   5_occ: 103.88   0.00  13.20  86.98   0.00   8.47 103.88   1.04  38.97
   5_bss: 106.78   2.90  16.10  89.88   2.90  11.37 106.78   3.94  41.87
------------------------------------------------------------------------
 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:    1.284    0.017    0.420
   1_adp:    1.284    0.017    0.420
   1_occ:    1.284    0.017    0.420
   2_bss:    1.284    0.017    0.420
   2_xyz:    1.745    0.058    0.584
   2_adp:    1.745    0.058    0.584
   2_occ:    1.745    0.058    0.584
   3_bss:    1.745    0.058    0.584
   3_xyz:    1.646    0.035    0.668
   3_adp:    1.646    0.035    0.668
   3_occ:    1.646    0.035    0.668
   4_bss:    1.646    0.035    0.668
   4_xyz:    1.732    0.034    0.703
   4_adp:    1.732    0.034    0.703
   4_occ:    1.732    0.034    0.703
   5_bss:    1.732    0.034    0.703
   5_xyz:    1.799    0.049    0.711
   5_adp:    1.799    0.049    0.711
   5_occ:    1.799    0.049    0.711
   5_bss:    1.799    0.049    0.711
------------------------------------------------------------------------

CPU time actual refinement: 334.31


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1164/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_1164/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1164/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1164/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1164/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.16 
  Macro-tasks:
    bulk solvent and scale       = 51.55  
    individual site refinement   = 129.60 
    weights calculation          = 32.34  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.24 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 97.94  
    alpha_beta                      = 8.67   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 108.08 
    fmodel                         = 8.68   
    r_factors                      = 0.25   
    phase_errors                   = 10.63  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 238.09 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.735 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    628 calls, 97.63 s
gradients_fft:          574 calls, 95.11 s

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

# Date 2008-01-16 Time 03:20:59 PST -0800 (1200482459.63 s)
Start R-work = 0.4804, R-free = 0.4740 (no bulk solvent and anisotropic scale)
Final R-work = 0.1411, R-free = 0.1889 (no bulk solvent and anisotropic scale)

Start R-work = 0.4724, R-free = 0.4622
Final R-work = 0.1254, R-free = 0.1735