# Date 2008-01-16 Time 01:16:05 PST -0800 (1200474965.06 s)
#phil __OFF__

Command line arguments: "../355.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18100
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 355

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 48.1033, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0137 1.97064
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941915

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0137
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0137 1.97064
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941915

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0141 -  4.2172 [2180/2209]  1960   220  10.1%
  bin  2:  4.2172 -  3.3597 [2089/2112]  1881   208  10.0%
  bin  3:  3.3597 -  2.9386 [2063/2088]  1855   208  10.1%
  bin  4:  2.9386 -  2.6716 [2030/2047]  1834   196   9.7%
  bin  5:  2.6716 -  2.4810 [2032/2075]  1820   212  10.4%
  bin  6:  2.4810 -  2.3353 [2026/2054]  1834   192   9.5%
  bin  7:  2.3353 -  2.2187 [2008/2044]  1802   206  10.3%
  bin  8:  2.2187 -  2.1224 [1991/2033]  1800   191   9.6%
  bin  9:  2.1224 -  2.0409 [1983/2039]  1779   204  10.3%
  bin 10:  2.0409 -  1.9706 [1187/2033]  1065   122  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_355/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:
        1.48 -     2.17: 19
        2.17 -     2.85: 1116
        2.85 -     3.53: 4430
        3.53 -     4.22: 9272
        4.22 -     4.90: 13527
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.484 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.531 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.766 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.804 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28359 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_355/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_355/model_refine_001.geo

CPU time processing inputs: 9.88


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 48.10325 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5077   r_free= 0.4919   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.305855                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.7039 0.99   1414  159 0.4250 0.4351      6.6457      6.6928|
|  2:  4.7039 -  3.7528 0.99   1360  151 0.4523 0.4473      6.8678      6.8772|
|  3:  3.7528 -  3.2841 0.99   1332  147 0.4827 0.4565       6.725      6.7158|
|  4:  3.2841 -  2.9864 0.99   1326  139 0.4967 0.4284      6.5557      6.4853|
|  5:  2.9864 -  2.7738 0.99   1316  151 0.5468 0.5475      6.3921      6.4104|
|  6:  2.7738 -  2.6111 0.99   1305  148 0.5324 0.4950      6.2886      6.1789|
|  7:  2.6111 -  2.4810 0.98   1297  149 0.5309 0.5027      6.2733      6.2067|
|  8:  2.4810 -  2.3734 0.98   1319  136 0.5330 0.5218      6.1816      6.2059|
|  9:  2.3734 -  2.2824 0.99   1288  144 0.5494 0.5523      6.1338      6.1494|
| 10:  2.2824 -  2.2039 0.98   1300  145 0.5495 0.5677      6.1215      6.1416|
| 11:  2.2039 -  2.1352 0.97   1268  145 0.5427 0.5397      6.0318      6.0362|
| 12:  2.1352 -  2.0743 0.98   1281  147 0.5388 0.4876      5.9668      5.9979|
| 13:  2.0743 -  2.0198 0.93   1225  129 0.5355 0.5468      5.8922      5.8806|
| 14:  2.0198 -  1.9706 0.46    599   69 0.5735 0.5065      5.8559      5.6943|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.7039  1414   159  0.61  42.34   0.78     0.63     100032.31|
|  2:  4.7039 -  3.7528  1360   151  0.63  41.54   0.85     0.69     132729.65|
|  3:  3.7528 -  3.2841  1332   147  0.53  49.28   0.81     0.66     134094.67|
|  4:  3.2841 -  2.9864  1326   139  0.47  54.11   0.78     0.57     108442.66|
|  5:  2.9864 -  2.7738  1316   151  0.35  63.59   0.71     0.43      91204.56|
|  6:  2.7738 -  2.6111  1305   148  0.31  66.68   0.70     0.35      78199.10|
|  7:  2.6111 -  2.4810  1297   149  0.28  69.26   0.72     0.32      73062.60|
|  8:  2.4810 -  2.3734  1319   136  0.29  68.22   0.72     0.34      63885.82|
|  9:  2.3734 -  2.2824  1288   144  0.28  68.83   0.71     0.35      59773.60|
| 10:  2.2824 -  2.2039  1300   145  0.28  69.11   0.74     0.33      53332.61|
| 11:  2.2039 -  2.1352  1268   145  0.26  70.87   0.74     0.33      51432.39|
| 12:  2.1352 -  2.0743  1281   147  0.25  71.03   0.73     0.34      47311.69|
| 13:  2.0743 -  2.0198  1225   129  0.26  70.90   0.74     0.33      40542.50|
| 14:  2.0198 -  1.9706   599    69  0.28  69.35   0.70     0.31      30714.56|
|alpha:            min =        0.31 max =            0.69 mean =         0.44|
|beta:             min =    30714.56 max =       134094.67 mean =     78597.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.97 mean =        61.94|
|phase err.(test): min =        0.00 max =           89.97 mean =        61.86|
|-----------------------------------------------------------------------------|

============================== 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 = 20.188170             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.436   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.754926              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.183   (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 |  0.960 -  1.354:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.354 -  1.748:       11 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.748 -  2.142:       74 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.142 -  2.536:      475 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.536 -  2.930:     1268 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.930 -  3.324:     2425 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.324 -  3.718:     3914 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.718 -  4.112:     5226 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.112 -  4.506:     6833 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.506 -  4.900:     8190 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.614 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.960 |       2.324 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5127   r_free= 0.4965   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.306192                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5010   r_free= 0.4854   ksol= 0.35   Bsol= 20.00   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.34,11.71,6.76,0.00,0.00,0.00); trace/3= 8.27                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.300337                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.423351             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.782   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.727481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.800   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5010      final r-factor (work) = 0.4398          |
| start r-factor (free) = 0.4854      final r-factor (free) = 0.4519          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 114.8334 = 19.42 * 0.50 * 6.3037 + 1.00 * 53.6142                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.8609 = 19.42 * 0.50 * 6.2506 + 1.00 * 0.1575                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4398      final r-factor (work) = 0.3989          |
| start r-factor (free) = 0.4519      final r-factor (free) = 0.4449          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8125 = 1.73 * 1.00 * 6.2506 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7357 = 1.73 * 1.00 * 6.2024 + 1.00 * 0.0211                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.28   15.32    None  None   None       |
|    all(noH): 2823   0      0.00    80.28   15.32    None  None   None       |
|    Sol.    : 438    0      0.00    80.28   24.44    None  None   None       |
|    Mac.    : 2385   0      0.00    61.29   13.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.028:  939   |   5:    40.140 -  48.168:   76        |
|      1:     8.028 -  16.056:  807   |   6:    48.168 -  56.196:   43        |
|      2:    16.056 -  24.084:  484   |   7:    56.196 -  64.224:   17        |
|      3:    24.084 -  32.112:  302   |   8:    64.224 -  72.252:    2        |
|      4:    32.112 -  40.140:  150   |   9:    72.252 -  80.280:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3989 r_free = 0.4449             target_work(ml) = 5.991         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3985 r_free = 0.4438             target_work(ml) = 5.990         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3985   r_free= 0.4438   ksol= 0.35   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.34,11.71,6.76,0.00,0.00,0.00); trace/3= 8.27                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 5.990489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3972   r_free= 0.4411   ksol= 0.29   Bsol= 20.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,7.04,4.02,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 5.992375                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.937066             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.414  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.671995              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.772  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3972      final r-factor (work) = 0.3356          |
| start r-factor (free) = 0.4411      final r-factor (free) = 0.3962          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.2517 = 12.94 * 0.50 * 6.1985 + 1.00 * 0.1566                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.4072 = 12.94 * 0.50 * 5.9200 + 1.00 * 0.1135                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3356      final r-factor (work) = 0.3219          |
| start r-factor (free) = 0.3962      final r-factor (free) = 0.3881          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0023 = 0.67 * 1.00 * 5.9200 + 1.00 * 0.0241                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1089 = 0.67 * 1.00 * 6.0612 + 1.00 * 0.0358                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.85  15.21    None  None   None       |
|    all(noH): 2823   0      0.00    106.85  15.21    None  None   None       |
|    Sol.    : 438    0      0.00    78.36   26.38    None  None   None       |
|    Mac.    : 2385   0      0.00    106.85  13.16    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 -  10.685: 1278   |   5:    53.424 -  64.109:   19        |
|      1:    10.685 -  21.370:  859   |   6:    64.109 -  74.794:    5        |
|      2:    21.370 -  32.055:  429   |   7:    74.794 -  85.479:    3        |
|      3:    32.055 -  42.739:  175   |   8:    85.479 -  96.164:    0        |
|      4:    42.739 -  53.424:   54   |   9:    96.164 - 106.849:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3219 r_free = 0.3881             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3216 r_free = 0.3877             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3216   r_free= 0.3877   ksol= 0.29   Bsol= 20.00   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,7.04,4.02,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.049762                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3206   r_free= 0.3875   ksol= 0.31   Bsol= 46.06   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,4.76,2.48,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.051144                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.212934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.647  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.842568              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.947   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3206      final r-factor (work) = 0.2632          |
| start r-factor (free) = 0.3875      final r-factor (free) = 0.3247          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0328 = 9.21 * 0.50 * 6.0609 + 1.00 * 0.1135                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6322 = 9.21 * 0.50 * 5.9774 + 1.00 * 0.0977                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2632      final r-factor (work) = 0.2363          |
| start r-factor (free) = 0.3247      final r-factor (free) = 0.3050          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0676 = 0.84 * 1.00 * 5.9774 + 1.00 * 0.0313                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9325 = 0.84 * 1.00 * 5.8360 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.32  15.85    None  None   None       |
|    all(noH): 2823   0      0.00    108.32  15.85    None  None   None       |
|    Sol.    : 438    0      1.78    108.32  35.45    None  None   None       |
|    Mac.    : 2385   0      0.00    89.70   12.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.832: 1433   |   5:    54.158 -  64.989:   68        |
|      1:    10.832 -  21.663:  718   |   6:    64.989 -  75.821:   16        |
|      2:    21.663 -  32.495:  303   |   7:    75.821 -  86.652:   11        |
|      3:    32.495 -  43.326:  163   |   8:    86.652 -  97.484:    4        |
|      4:    43.326 -  54.158:  106   |   9:    97.484 - 108.315:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2363 r_free = 0.3050             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2360 r_free = 0.3058             target_work(ml) = 5.810         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2360   r_free= 0.3058   ksol= 0.31   Bsol= 46.06   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,4.76,2.48,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.810266                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2358   r_free= 0.3062   ksol= 0.33   Bsol= 57.21   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.56,3.21,1.80,0.00,0.00,0.00); trace/3= 1.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.810693                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.784528              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.713  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.402233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.806  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2358      final r-factor (work) = 0.1839          |
| start r-factor (free) = 0.3062      final r-factor (free) = 0.2386          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9789 = 5.78 * 0.50 * 5.8367 + 1.00 * 0.0977                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6086 = 5.78 * 0.50 * 5.7149 + 1.00 * 0.0797                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1839      final r-factor (work) = 0.1683          |
| start r-factor (free) = 0.2386      final r-factor (free) = 0.2162          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3141 = 0.40 * 1.00 * 5.7149 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2377 = 0.40 * 1.00 * 5.5346 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.81   15.43    None  None   None       |
|    all(noH): 2823   0      0.00    96.81   15.43    None  None   None       |
|    Sol.    : 438    0      3.09    96.81   38.86    None  None   None       |
|    Mac.    : 2385   0      0.00    91.55   11.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.681: 1405   |   5:    48.405 -  58.086:   96        |
|      1:     9.681 -  19.362:  764   |   6:    58.086 -  67.767:   37        |
|      2:    19.362 -  29.043:  223   |   7:    67.767 -  77.448:   19        |
|      3:    29.043 -  38.724:  143   |   8:    77.448 -  87.129:    8        |
|      4:    38.724 -  48.405:  122   |   9:    87.129 -  96.810:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1683 r_free = 0.2162             target_work(ml) = 5.487         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1681 r_free = 0.2163             target_work(ml) = 5.486         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2163   ksol= 0.33   Bsol= 57.21   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.56,3.21,1.80,0.00,0.00,0.00); trace/3= 1.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.486354                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2158   ksol= 0.33   Bsol= 56.38   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,1.92,1.22,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.488483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.597738              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.821521              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.166  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1681      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2158      final r-factor (free) = 0.1840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8136 = 4.60 * 0.50 * 5.5392 + 1.00 * 0.0797                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4923 = 4.60 * 0.50 * 5.3976 + 1.00 * 0.0839                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1840      final r-factor (free) = 0.1780          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4458 = 0.82 * 1.00 * 5.3976 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3476 = 0.82 * 1.00 * 5.2764 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.85   15.60    None  None   None       |
|    all(noH): 2823   0      0.00    98.85   15.60    None  None   None       |
|    Sol.    : 438    0      3.55    95.37   42.03    None  None   None       |
|    Mac.    : 2385   0      0.00    98.85   10.75    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 -   9.885: 1511   |   5:    49.424 -  59.309:   89        |
|      1:     9.885 -  19.770:  728   |   6:    59.309 -  69.193:   53        |
|      2:    19.770 -  29.654:  181   |   7:    69.193 -  79.078:   33        |
|      3:    29.654 -  39.539:  104   |   8:    79.078 -  88.963:   11        |
|      4:    39.539 -  49.424:  103   |   9:    88.963 -  98.847:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1780             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1779             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1779   ksol= 0.33   Bsol= 56.38   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,1.92,1.22,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.258027                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.7039 0.99   1414  159 0.1000 0.1368      5.4104      5.5864|
|  2:  4.7039 -  3.7528 0.99   1360  151 0.0906 0.1134      5.4983      5.7096|
|  3:  3.7528 -  3.2841 0.99   1332  147 0.1217 0.1825      5.5969       5.961|
|  4:  3.2841 -  2.9864 0.99   1326  139 0.1399 0.1837      5.5609      5.7707|
|  5:  2.9864 -  2.7738 0.99   1316  151 0.1559 0.1725      5.4456      5.5521|
|  6:  2.7738 -  2.6111 0.99   1305  148 0.1475 0.2317      5.3482        5.61|
|  7:  2.6111 -  2.4810 0.98   1297  149 0.1429 0.1827       5.284      5.4607|
|  8:  2.4810 -  2.3734 0.98   1319  136 0.1395 0.1858      5.1906      5.4208|
|  9:  2.3734 -  2.2824 0.99   1288  144 0.1360 0.2095      5.1276      5.4136|
| 10:  2.2824 -  2.2039 0.98   1300  145 0.1366 0.2051      5.1246      5.3798|
| 11:  2.2039 -  2.1352 0.97   1268  145 0.1321 0.2076       5.051      5.3535|
| 12:  2.1352 -  2.0743 0.98   1281  147 0.1305 0.1930      4.9879      5.2355|
| 13:  2.0743 -  2.0198 0.93   1225  129 0.1288 0.1961      4.8878      5.1391|
| 14:  2.0198 -  1.9706 0.46    599   69 0.1202 0.1877      4.7555       4.975|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0141 -  4.7039  1414   159  0.93   9.98   0.97     0.95       8037.93|
|  2:  4.7039 -  3.7528  1360   151  0.94   9.22   1.03     1.02      10771.05|
|  3:  3.7528 -  3.2841  1332   147  0.92  13.55   1.03     1.02      13256.40|
|  4:  3.2841 -  2.9864  1326   139  0.90  15.82   1.02     1.01      12606.84|
|  5:  2.9864 -  2.7738  1316   151  0.88  18.51   1.02     0.99      10593.24|
|  6:  2.7738 -  2.6111  1305   148  0.88  18.78   0.99     0.95       8998.45|
|  7:  2.6111 -  2.4810  1297   149  0.88  18.14   1.00     0.95       7818.47|
|  8:  2.4810 -  2.3734  1319   136  0.89  17.69   1.02     0.99       6845.78|
|  9:  2.3734 -  2.2824  1288   144  0.88  18.27   1.02     0.98       6105.68|
| 10:  2.2824 -  2.2039  1300   145  0.87  18.95   1.01     0.97       6170.14|
| 11:  2.2039 -  2.1352  1268   145  0.87  19.30   1.01     0.97       5708.80|
| 12:  2.1352 -  2.0743  1281   147  0.89  18.27   1.02     0.98       4963.67|
| 13:  2.0743 -  2.0198  1225   129  0.89  17.88   1.01     1.01       3993.72|
| 14:  2.0198 -  1.9706   599    69  0.89  16.85   0.99     0.95       3070.06|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     3070.06 max =        13256.40 mean =      8023.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.80 mean =        16.42|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.79|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1780   ksol= 0.33   Bsol= 55.04   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,0.73,0.38,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260089                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1780   ksol= 0.33   Bsol= 55.04   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,0.73,0.38,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.260089                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.7039 0.99   1414  159 0.1011 0.1370      5.4228      5.6019|
|  2:  4.7039 -  3.7528 0.99   1360  151 0.0916 0.1131      5.5078      5.7142|
|  3:  3.7528 -  3.2841 0.99   1332  147 0.1226 0.1817      5.6029      5.9589|
|  4:  3.2841 -  2.9864 0.99   1326  139 0.1405 0.1843      5.5629      5.7736|
|  5:  2.9864 -  2.7738 0.99   1316  151 0.1558 0.1727       5.446      5.5514|
|  6:  2.7738 -  2.6111 0.99   1305  148 0.1471 0.2321      5.3478      5.6126|
|  7:  2.6111 -  2.4810 0.98   1297  149 0.1426 0.1835      5.2841      5.4609|
|  8:  2.4810 -  2.3734 0.98   1319  136 0.1390 0.1856        5.19      5.4204|
|  9:  2.3734 -  2.2824 0.99   1288  144 0.1357 0.2104      5.1262      5.4146|
| 10:  2.2824 -  2.2039 0.98   1300  145 0.1362 0.2051       5.124      5.3798|
| 11:  2.2039 -  2.1352 0.97   1268  145 0.1318 0.2073        5.05      5.3528|
| 12:  2.1352 -  2.0743 0.98   1281  147 0.1305 0.1935      4.9882      5.2361|
| 13:  2.0743 -  2.0198 0.93   1225  129 0.1288 0.1954      4.8877      5.1377|
| 14:  2.0198 -  1.9706 0.46    599   69 0.1200 0.1875      4.7543      4.9731|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.7039  1414   159  0.93  10.09   0.97     0.95       8179.92|
|  2:  4.7039 -  3.7528  1360   151  0.94   9.35   1.02     1.01      10951.83|
|  3:  3.7528 -  3.2841  1332   147  0.92  13.60   1.03     1.02      13405.67|
|  4:  3.2841 -  2.9864  1326   139  0.90  15.80   1.02     1.01      12584.32|
|  5:  2.9864 -  2.7738  1316   151  0.88  18.52   1.01     0.98      10612.87|
|  6:  2.7738 -  2.6111  1305   148  0.88  18.81   0.98     0.94       9035.84|
|  7:  2.6111 -  2.4810  1297   149  0.88  18.17   0.99     0.94       7839.30|
|  8:  2.4810 -  2.3734  1319   136  0.89  17.69   1.01     0.98       6852.06|
|  9:  2.3734 -  2.2824  1288   144  0.88  18.25   1.00     0.97       6105.94|
| 10:  2.2824 -  2.2039  1300   145  0.87  18.95   1.00     0.96       6166.88|
| 11:  2.2039 -  2.1352  1268   145  0.87  19.29   1.00     0.96       5700.70|
| 12:  2.1352 -  2.0743  1281   147  0.89  18.26   1.00     0.97       4968.37|
| 13:  2.0743 -  2.0198  1225   129  0.89  17.86   1.00     0.99       3985.15|
| 14:  2.0198 -  1.9706   599    69  0.89  16.83   0.97     0.94       3054.36|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3054.36 max =        13405.67 mean =      8063.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.87 mean =        16.44|
|phase err.(test): min =        0.00 max =           89.92 mean =        15.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    99.57   16.33    None  None   None       |
|    all(noH): 2823   0      0.72    99.57   16.33    None  None   None       |
|    Sol.    : 438    0      4.27    96.10   42.76    None  None   None       |
|    Mac.    : 2385   0      0.72    99.57   11.47    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:     0.725 -  10.610: 1511   |   5:    50.149 -  60.033:   89        |
|      1:    10.610 -  20.494:  728   |   6:    60.033 -  69.918:   53        |
|      2:    20.494 -  30.379:  181   |   7:    69.918 -  79.803:   33        |
|      3:    30.379 -  40.264:  104   |   8:    79.803 -  89.688:   11        |
|      4:    40.264 -  50.149:  103   |   9:    89.688 -  99.572:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.674 - 5.998
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 324
   mapped sites are within: 0.778 - 5.998

peak=    7.949 closest distance to " O   HOH Z 120 " =    1.721
peak=    7.621 closest distance to " CG2 VAL A 230 " =    1.224
peak=    7.110 closest distance to " O   HOH Z  46 " =    1.452
peak=    6.922 closest distance to " CG1 ILE A 234 " =    1.411
peak=    6.680 closest distance to " O   HOH Z  57 " =    1.051
peak=    6.338 closest distance to " O   HOH Z 210 " =    1.583
peak=    6.025 closest distance to " CG2 VAL A 296 " =    1.137
peak=    5.927 closest distance to " O   HOH Z 247 " =    1.700
peak=    5.751 closest distance to " CG  LEU A   5 " =    1.331
peak=    5.317 closest distance to " O   HOH Z 128 " =    1.703
peak=    5.243 closest distance to " NH2 ARG A  56 " =    2.358
peak=    5.223 closest distance to " CB  VAL A 230 " =    1.245
peak=    5.185 closest distance to " O   HOH Z 404 " =    1.278
peak=    5.063 closest distance to " O   HOH Z 126 " =    1.626
peak=    5.014 closest distance to " O   HOH Z 422 " =    1.000
peak=    4.995 closest distance to " O   HOH Z  48 " =    1.782
peak=    4.975 closest distance to " O   HOH Z 116 " =    1.372
peak=    4.973 closest distance to " O   HOH Z 193 " =    1.533
peak=    4.824 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.783 closest distance to " O   HOH Z 403 " =    1.960
peak=    4.771 closest distance to " CB  VAL A 296 " =    1.039
peak=    4.759 closest distance to " O   HOH Z 146 " =    1.625
peak=    4.746 closest distance to " O   HOH Z  80 " =    2.384
peak=    4.735 closest distance to " O   HOH Z  49 " =    1.437
peak=    4.717 closest distance to " O   HOH Z 395 " =    1.512
peak=    4.716 closest distance to " O   HOH Z 124 " =    1.757
peak=    4.652 closest distance to " O   HOH Z 154 " =    1.750
peak=    4.613 closest distance to " O   HOH Z 412 " =    3.328
peak=    4.608 closest distance to " O   HOH Z 389 " =    2.073
peak=    4.601 closest distance to " O   HOH Z 209 " =    2.302
peak=    4.591 closest distance to " CB  SER A  63 " =    1.225
peak=    4.557 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.556 closest distance to " O   HOH Z 402 " =    1.578
peak=    4.550 closest distance to " CG AARG A 275 " =    1.341
peak=    4.539 closest distance to " O   HOH Z 278 " =    1.148
peak=    4.534 closest distance to " O   HOH Z 102 " =    1.526
peak=    4.530 closest distance to " O   HOH Z 433 " =    1.851
peak=    4.528 closest distance to " O   HOH Z 142 " =    1.759
peak=    4.523 closest distance to " O   HOH Z 425 " =    1.580
peak=    4.490 closest distance to " NE2 GLN A  11 " =    1.046
peak=    4.458 closest distance to " O   HOH Z 144 " =    1.862
peak=    4.445 closest distance to " O   HOH Z 126 " =    2.290
peak=    4.370 closest distance to " O   HOH Z 134 " =    2.543
peak=    4.349 closest distance to " O   HOH Z 234 " =    3.421
peak=    4.345 closest distance to " CG  GLN A  77 " =    0.836
peak=    4.317 closest distance to " O   HOH Z 357 " =    2.019
peak=    4.312 closest distance to " NH2 ARG A 156 " =    1.179
peak=    4.251 closest distance to " O   HOH Z 403 " =    1.505
peak=    4.232 closest distance to " O   HOH Z 414 " =    2.472
peak=    4.228 closest distance to " O   HOH Z 272 " =    2.051
peak=    4.223 closest distance to " O   HOH Z 261 " =    2.264
peak=    4.207 closest distance to " O   HOH Z  40 " =    1.919
peak=    4.179 closest distance to " OE1 GLU A   2 " =    1.592
peak=    4.148 closest distance to " O   HOH Z 236 " =    1.480
peak=    4.128 closest distance to " O   HOH Z 245 " =    1.355
peak=    4.122 closest distance to " CG  ARG A  66 " =    1.090
peak=    4.121 closest distance to " O   HOH Z  15 " =    2.024
peak=    4.104 closest distance to " CE1 HIS A 108 " =    1.168
peak=    4.093 closest distance to " CB  GLN A 223 " =    1.412
peak=    4.089 closest distance to " CD2 TRP A 179 " =    1.325
peak=    4.081 closest distance to " CG2 VAL A 296 " =    1.751
peak=    4.069 closest distance to " OD1 ASN A 301 " =    1.152
peak=    4.050 closest distance to " CG  LEU A 228 " =    1.290
peak=    4.040 closest distance to " CB  ASN A 285 " =    0.989
peak=    4.033 closest distance to " OE1 GLN A  11 " =    1.945
peak=    4.031 closest distance to " O   HOH Z 196 " =    1.449
peak=    4.019 closest distance to " O   SER A  87 " =    2.400
peak=    4.013 closest distance to " O   HOH Z 155 " =    1.619
peak=    4.008 closest distance to " CD  LYS A 166 " =    1.528
peak=    4.004 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.001 closest distance to " CG1 ILE A  33 " =    1.301
peak=    3.996 closest distance to " CE  LYS A 119 " =    1.156
peak=    3.996 closest distance to " CA  VAL A  41 " =    0.899
peak=    3.976 closest distance to " CG2 THR A 220 " =    0.907
peak=    3.954 closest distance to " CG  PRO A 213 " =    1.224
peak=    3.936 closest distance to " O   PRO A 198 " =    1.548
peak=    3.930 closest distance to " O   GLY A  23 " =    2.401
peak=    3.925 closest distance to " O   HOH Z  44 " =    1.968
peak=    3.922 closest distance to " O   HOH Z 130 " =    2.563
peak=    3.915 closest distance to " O   HOH Z  61 " =    1.494
peak=    3.909 closest distance to " NZ  LYS A  76 " =    0.991
peak=    3.904 closest distance to " O   HOH Z  43 " =    1.944
peak=    3.892 closest distance to " O   HOH Z 303 " =    2.468
peak=    3.891 closest distance to " CA  ARG A 195 " =    1.216
peak=    3.882 closest distance to " CD  GLN A  73 " =    1.113
peak=    3.880 closest distance to " O   HOH Z 418 " =    1.627
peak=    3.878 closest distance to " O   HOH Z 132 " =    2.483
peak=    3.871 closest distance to " O   HOH Z  68 " =    2.013
peak=    3.870 closest distance to " OG  SER A  62 " =    3.020
peak=    3.867 closest distance to " CB  TRP A 179 " =    1.192
peak=    3.836 closest distance to " CA  THR A 294 " =    1.823
peak=    3.832 closest distance to " O   HOH Z 431 " =    1.721
peak=    3.815 closest distance to " O   GLN A  11 " =    0.951
peak=    3.806 closest distance to " O   HOH Z  88 " =    3.598
peak=    3.796 closest distance to " O   HOH Z  54 " =    1.194
peak=    3.792 closest distance to " OG BSER A 210 " =    0.985
peak=    3.790 closest distance to " O   HOH Z 265 " =    1.928
peak=    3.787 closest distance to " CB  ALA A 100 " =    1.289
peak=    3.785 closest distance to " CA  SER A  12 " =    1.356
peak=    3.776 closest distance to " O   HOH Z 406 " =    1.570
peak=    3.763 closest distance to " CB BVAL A  41 " =    1.105
peak=    3.759 closest distance to " O   HOH Z  85 " =    1.701
peak=    3.752 closest distance to " CB  PRO A 198 " =    1.146
peak=    3.752 closest distance to " CB  GLU A 175 " =    1.258
peak=    3.750 closest distance to " CB  SER A 141 " =    1.026
peak=    3.747 closest distance to " CD2 LEU A 228 " =    1.221
peak=    3.742 closest distance to " O   HOH Z 156 " =    3.072
peak=    3.740 closest distance to " CG2 ILE A  20 " =    1.275
peak=    3.738 closest distance to " O   HOH Z 136 " =    1.213
peak=    3.734 closest distance to " CG  PRO A 243 " =    1.273
peak=    3.725 closest distance to " CA  GLY A 196 " =    0.895
peak=    3.721 closest distance to " O   HOH Z  48 " =    2.041
peak=    3.717 closest distance to " CG  PRO A 280 " =    0.786
peak=    3.711 closest distance to " N   SER A 164 " =    1.050
peak=    3.703 closest distance to " O   HOH Z 316 " =    2.290
peak=    3.701 closest distance to " CG  PRO A 198 " =    1.218
peak=    3.697 closest distance to " O   HOH Z 130 " =    1.160
peak=    3.688 closest distance to " O   HOH Z  95 " =    1.579
peak=    3.683 closest distance to " O   HOH Z 361 " =    2.514
peak=    3.679 closest distance to " O   HOH Z  39 " =    1.624
peak=    3.678 closest distance to " O   HOH Z  57 " =    2.373
peak=    3.671 closest distance to " O   HOH Z  78 " =    1.642
peak=    3.667 closest distance to " O   HOH Z 249 " =    1.059
peak=    3.659 closest distance to " CB  GLN A  58 " =    1.140
peak=    3.658 closest distance to " O   ASP A 124 " =    1.788
peak=    3.658 closest distance to " N   ASN A  39 " =    1.287
peak=    3.658 closest distance to " O   HOH Z 409 " =    3.216
peak=    3.652 closest distance to " O   HOH Z 116 " =    2.581
peak=    3.651 closest distance to " O   HOH Z 394 " =    1.712
peak=    3.651 closest distance to " CD  ARG A  36 " =    1.204
peak=    3.650 closest distance to " O   HOH Z 427 " =    2.801
peak=    3.637 closest distance to " O   HOH Z  59 " =    2.290
peak=    3.636 closest distance to " O   HOH Z 189 " =    2.796
peak=    3.633 closest distance to " O   HOH Z 339 " =    1.536
peak=    3.628 closest distance to " CB  THR A  31 " =    1.453
peak=    3.621 closest distance to " OG  SER A 245 " =    1.320
peak=    3.618 closest distance to " O   HOH Z   4 " =    1.473
peak=    3.616 closest distance to " CB  ASN A 148 " =    1.278
peak=    3.612 closest distance to " CB  VAL A 202 " =    1.457
peak=    3.609 closest distance to " ND1 HIS A  81 " =    1.427
peak=    3.604 closest distance to " O   HOH Z 298 " =    5.164
peak=    3.601 closest distance to " O   HOH Z 369 " =    1.447
peak=    3.599 closest distance to " O   ALA A 165 " =    1.210
peak=    3.598 closest distance to " OD1 ASN A  60 " =    1.026
peak=    3.597 closest distance to " O   HOH Z 408 " =    1.761
peak=    3.594 closest distance to " CG2 THR A 221 " =    1.238
peak=    3.594 closest distance to " O   HOH Z 272 " =    1.162
peak=    3.591 closest distance to " NZ  LYS A 117 " =    2.880
peak=    3.581 closest distance to " O   HOH Z 166 " =    1.881
peak=    3.581 closest distance to " O   HOH Z 253 " =    1.761
peak=    3.573 closest distance to " O   HOH Z 263 " =    1.650
peak=    3.570 closest distance to " NE  ARG A  14 " =    1.362
peak=    3.568 closest distance to " O   HOH Z   9 " =    2.465
peak=    3.566 closest distance to " O   HOH Z 332 " =    1.663
peak=    3.557 closest distance to " O   HOH Z 435 " =    1.869
peak=    3.551 closest distance to " CB  SER A  62 " =    1.051
peak=    3.544 closest distance to " O   HOH Z  66 " =    2.049
peak=    3.541 closest distance to " O   HOH Z 359 " =    1.783
peak=    3.540 closest distance to " O   HOH Z 109 " =    1.514
peak=    3.529 closest distance to " O   HOH Z 284 " =    1.465
peak=    3.526 closest distance to " CB  GLU A 152 " =    1.058
peak=    3.522 closest distance to " CA  ALA A  51 " =    1.091
peak=    3.521 closest distance to " CA  ALA A  21 " =    1.397
peak=    3.520 closest distance to " O   HOH Z 438 " =    2.531
peak=    3.520 closest distance to " O   HOH Z 112 " =    1.657
peak=    3.517 closest distance to " CD  ARG A 159 " =    0.830
peak=    3.510 closest distance to " NH1 ARG A  14 " =    1.283
peak=    3.503 closest distance to " CD  ARG A 195 " =    1.255
peak=    3.503 closest distance to " OG1 THR A 294 " =    2.342
peak=    3.493 closest distance to " O   HOH Z 289 " =    1.616
peak=    3.490 closest distance to " O   HOH Z 142 " =    1.976
peak=    3.487 closest distance to " CB  VAL A 265 " =    1.389
peak=    3.485 closest distance to " O   ASP A 200 " =    1.619
peak=    3.483 closest distance to " O   HOH Z 291 " =    1.440
peak=    3.482 closest distance to " O   GLY A  91 " =    1.242
peak=    3.481 closest distance to " O   HOH Z   7 " =    1.043
peak=    3.478 closest distance to " CD1 LEU A 228 " =    1.729
peak=    3.477 closest distance to " CB  TRP A 266 " =    1.171
peak=    3.465 closest distance to " CD2 LEU A   5 " =    1.188
peak=    3.460 closest distance to " CB  GLN A  73 " =    1.281
peak=    3.460 closest distance to " O   HOH Z  85 " =    1.820
peak=    3.459 closest distance to " O   HOH Z 172 " =    5.998
peak=    3.454 closest distance to " NE2 GLN A  58 " =    4.060
peak=    3.453 closest distance to " O   HOH Z 418 " =    3.029
peak=    3.451 closest distance to " O   HOH Z 423 " =    1.912
peak=    3.441 closest distance to " O   HOH Z 250 " =    1.787
peak=    3.436 closest distance to " O   HOH Z 232 " =    2.328
peak=    3.434 closest distance to " CB  GLU A 128 " =    1.275
peak=    3.434 closest distance to " O   HOH Z 406 " =    1.209
peak=    3.433 closest distance to " O   HOH Z 203 " =    1.607
peak=    3.429 closest distance to " O   HOH Z 155 " =    2.635
peak=    3.422 closest distance to " O   HOH Z 273 " =    2.805
peak=    3.419 closest distance to " O   HOH Z 301 " =    1.928
peak=    3.415 closest distance to " CA  TYR A 214 " =    1.159
peak=    3.408 closest distance to " CD  PRO A  54 " =    0.853
peak=    3.403 closest distance to " O   HOH Z 271 " =    1.382
peak=    3.402 closest distance to " O   HOH Z 345 " =    2.601
peak=    3.401 closest distance to " O   HOH Z 388 " =    2.210
peak=    3.399 closest distance to " O   HOH Z 417 " =    1.207
peak=    3.395 closest distance to " CD  ARG A 269 " =    1.102
peak=    3.388 closest distance to " CB  ALA A  71 " =    1.212
peak=    3.388 closest distance to " O   HOH Z 214 " =    1.380
peak=    3.382 closest distance to " NE2 HIS A 115 " =    0.954
peak=    3.381 closest distance to " CB  TRP A 179 " =    1.890
peak=    3.374 closest distance to " CG AARG A 275 " =    1.092
peak=    3.370 closest distance to " O   HOH Z 130 " =    2.520
peak=    3.370 closest distance to " O   HOH Z  32 " =    1.704
peak=    3.367 closest distance to " CB  MET A  40 " =    0.778
peak=    3.366 closest distance to " O   HOH Z 327 " =    1.597
peak=    3.365 closest distance to " O   HOH Z 344 " =    2.915
peak=    3.359 closest distance to " CB  ARG A  79 " =    0.911
peak=    3.357 closest distance to " O   HOH Z 113 " =    2.018
peak=    3.356 closest distance to " O   HOH Z 248 " =    1.751
peak=    3.354 closest distance to " CB  PHE A  16 " =    1.162
peak=    3.352 closest distance to " O   HOH Z 329 " =    3.671
peak=    3.345 closest distance to " O   HOH Z 279 " =    1.146
peak=    3.344 closest distance to " CB  SER A  26 " =    1.691
peak=    3.341 closest distance to " CA  LEU A  83 " =    1.305
peak=    3.340 closest distance to " NH2BARG A 145 " =    1.957
peak=    3.337 closest distance to " O   HOH Z 380 " =    1.854
peak=    3.336 closest distance to " CB  ARG A 190 " =    1.821
peak=    3.334 closest distance to " CA  ALA A 100 " =    1.238
peak=    3.334 closest distance to " NE1 TRP A  92 " =    1.258
peak=    3.325 closest distance to " CG2 THR A 251 " =    1.243
peak=    3.325 closest distance to " CA  THR A 246 " =    1.009
peak=    3.322 closest distance to " CG  MET A  40 " =    2.447
peak=    3.315 closest distance to " CD1 TRP A 274 " =    1.138
peak=    3.315 closest distance to " CA  ARG A 195 " =    1.467
peak=    3.314 closest distance to " N   THR A  42 " =    1.425
peak=    3.310 closest distance to " O   ASN A 301 " =    2.535
peak=    3.307 closest distance to " NH1AARG A 145 " =    1.048
peak=    3.304 closest distance to " O   HOH Z 128 " =    1.736
peak=    3.302 closest distance to " O   HOH Z 163 " =    1.586
peak=    3.299 closest distance to " CG2 VAL A 112 " =    1.661
peak=    3.299 closest distance to " NH1 ARG A  36 " =    1.181
peak=    3.294 closest distance to " CG  MET A 185 " =    1.279
peak=    3.293 closest distance to " O   PHE A  61 " =    1.426
peak=    3.289 closest distance to " O   HOH Z 194 " =    1.828
peak=    3.286 closest distance to " NH2 ARG A  36 " =    1.795
peak=    3.282 closest distance to " CB  GLU A 277 " =    0.956
peak=    3.282 closest distance to " O   HOH Z 334 " =    1.645
peak=    3.280 closest distance to " O   HOH Z 428 " =    1.213
peak=    3.280 closest distance to " O   HOH Z 313 " =    1.983
peak=    3.278 closest distance to " OG BSER A 164 " =    2.010
peak=    3.276 closest distance to " CE1 TYR A 186 " =    1.439
peak=    3.272 closest distance to " CB  ASN A 187 " =    1.196
peak=    3.271 closest distance to " CZ3 TRP A  92 " =    1.013
peak=    3.270 closest distance to " O   HOH Z 255 " =    1.605
peak=    3.270 closest distance to " O  BHOH Z 338 " =    2.343
peak=    3.266 closest distance to " O   HOH Z 123 " =    1.990
peak=    3.261 closest distance to " O   HOH Z  52 " =    1.496
peak=    3.260 closest distance to " CA  ALA A 248 " =    1.161
peak=    3.259 closest distance to " O   HOH Z 367 " =    2.960
peak=    3.257 closest distance to " O   HOH Z 227 " =    1.763
peak=    3.256 closest distance to " O   THR A 264 " =    1.459
peak=    3.255 closest distance to " O   VAL A  72 " =    1.088
peak=    3.251 closest distance to " O   HOH Z 132 " =    2.558
peak=    3.250 closest distance to " CA  ASN A 176 " =    1.686
peak=    3.241 closest distance to " CG  PRO A  54 " =    1.429
peak=    3.237 closest distance to " O   ASN A 285 " =    0.922
peak=    3.236 closest distance to " O   HOH Z 340 " =    1.408
peak=    3.235 closest distance to " O   HOH Z 284 " =    3.042
peak=    3.234 closest distance to " CZ3 TRP A  85 " =    0.993
peak=    3.232 closest distance to " O   HOH Z 250 " =    1.406
peak=    3.226 closest distance to " O   HOH Z 367 " =    1.485
peak=    3.222 closest distance to " O   HOH Z 183 " =    1.613
peak=    3.219 closest distance to " CZ  PHE A 218 " =    1.270
peak=    3.217 closest distance to " O   HOH Z 185 " =    1.707
peak=    3.216 closest distance to " O   HOH Z 421 " =    1.917
peak=    3.215 closest distance to " CB  TYR A  30 " =    0.972
peak=    3.209 closest distance to " O   HOH Z  63 " =    1.970
peak=    3.206 closest distance to " O   GLU A   2 " =    1.626
peak=    3.203 closest distance to " O   HOH Z 412 " =    3.904
peak=    3.201 closest distance to " CA  ARG A  66 " =    1.100
peak=    3.200 closest distance to " O   HOH Z 271 " =    1.973
peak=    3.199 closest distance to " CA  LYS A 166 " =    1.176
peak=    3.193 closest distance to " N   GLU A  44 " =    1.252
peak=    3.190 closest distance to " O   ALA A 158 " =    1.178
peak=    3.189 closest distance to " O   HOH Z 173 " =    2.281
peak=    3.187 closest distance to " N   GLY A  75 " =    1.029
peak=    3.186 closest distance to " O   HOH Z 365 " =    2.667
peak=    3.182 closest distance to " O   HOH Z  66 " =    1.687
peak=    3.180 closest distance to " CB  SER A 273 " =    0.984
peak=    3.178 closest distance to " OG1 THR A 294 " =    4.080
peak=    3.175 closest distance to " O   HOH Z 423 " =    3.127
peak=    3.175 closest distance to " O   HOH Z 154 " =    2.809
peak=    3.173 closest distance to " O   HOH Z 125 " =    2.142
peak=    3.171 closest distance to " CG2 ILE A  33 " =    1.329
peak=    3.169 closest distance to " CG2 VAL A 197 " =    1.175
peak=    3.167 closest distance to " O   HOH Z 368 " =    2.189
peak=    3.167 closest distance to " CA  GLY A 133 " =    3.834
peak=    3.160 closest distance to " CG2 ILE A 120 " =    1.549
peak=    3.159 closest distance to " OG BSER A 258 " =    2.593
peak=    3.158 closest distance to " O   HOH Z 124 " =    1.927
peak=    3.156 closest distance to " CG2 VAL A  78 " =    0.931
peak=    3.154 closest distance to " O   HOH Z 356 " =    1.658
peak=    3.150 closest distance to " O   HOH Z 158 " =    3.401
peak=    3.149 closest distance to " CA  VAL A 126 " =    0.929
peak=    3.146 closest distance to " O   HOH Z  90 " =    3.726
peak=    3.140 closest distance to " N   ASP A 286 " =    0.935
peak=    3.129 closest distance to " O   HOH Z 370 " =    1.081
peak=    3.124 closest distance to " O   HOH Z  11 " =    1.266
peak=    3.122 closest distance to " O   HOH Z 358 " =    2.283
peak=    3.120 closest distance to " O   HOH Z 296 " =    1.681
peak=    3.119 closest distance to " O   HOH Z 151 " =    1.862
peak=    3.106 closest distance to " O   HOH Z  29 " =    1.369
peak=    3.101 closest distance to " CD  GLN A  73 " =    1.444
peak=    3.100 closest distance to " CD2 TYR A  68 " =    0.876
peak=    3.099 closest distance to " CD  ARG A  24 " =    1.343
peak=    3.097 closest distance to " CE BMET A  47 " =    1.066
peak=    3.097 closest distance to " CD  GLN A 194 " =    1.624
peak=    3.095 closest distance to " O   HOH Z 193 " =    1.880
peak=    3.092 closest distance to " O   HOH Z 277 " =    2.616
peak=    3.090 closest distance to " N   TYR A  15 " =    0.875
peak=    3.078 closest distance to " CB  THR A 235 " =    1.162
peak=    3.074 closest distance to " O   HOH Z 352 " =    1.226
peak=    3.069 closest distance to " O   HOH Z 280 " =    3.622
peak=    3.062 closest distance to " CA  GLN A  11 " =    1.106
peak=    3.060 closest distance to " O   HOH Z 426 " =    1.372
peak=    3.054 closest distance to " CA  ARG A 139 " =    1.536
peak=    3.043 closest distance to " O   HOH Z 162 " =    2.186
peak=    3.038 closest distance to " CD  LYS A 119 " =    1.847

                           ----------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: 0.642 - 5.967
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 220
   mapped sites are within: 0.715 - 5.967

peak=   -5.139 closest distance to " O   HOH Z 155 " =    1.656
peak=   -4.815 closest distance to " CG2 VAL A 230 " =    0.889
peak=   -4.527 closest distance to " CG2BVAL A  41 " =    2.422
peak=   -4.516 closest distance to " CA  SER A 164 " =    1.930
peak=   -4.513 closest distance to " O   HOH Z 137 " =    1.341
peak=   -4.408 closest distance to " CD  ARG A  14 " =    3.120
peak=   -4.256 closest distance to " CG  PRO A 243 " =    1.784
peak=   -4.241 closest distance to " NH2 ARG A  36 " =    1.112
peak=   -4.225 closest distance to " O   HOH Z 196 " =    2.071
peak=   -4.205 closest distance to " O   HOH Z 266 " =    4.761
peak=   -4.172 closest distance to " CD1 PHE A  59 " =    1.919
peak=   -4.161 closest distance to " O   HOH Z 210 " =    0.722
peak=   -4.134 closest distance to " CA  SER A 276 " =    1.395
peak=   -4.099 closest distance to " CA  TYR A  68 " =    2.713
peak=   -4.094 closest distance to " OXT GLY A 302 " =    2.756
peak=   -4.057 closest distance to " CD  GLN A  58 " =    1.280
peak=   -4.053 closest distance to " O   HOH Z 109 " =    3.158
peak=   -4.044 closest distance to " O   HOH Z 400 " =    0.715
peak=   -4.024 closest distance to " OG  SER A  97 " =    2.223
peak=   -3.968 closest distance to " O   HOH Z 166 " =    1.906
peak=   -3.947 closest distance to " ND2 ASN A  39 " =    1.166
peak=   -3.944 closest distance to " CG2 ILE A  49 " =    2.525
peak=   -3.932 closest distance to " CA  ASP A 298 " =    1.108
peak=   -3.930 closest distance to " CG2 THR A 182 " =    2.262
peak=   -3.924 closest distance to " O   HOH Z  52 " =    2.198
peak=   -3.921 closest distance to " CB  LEU A 167 " =    2.070
peak=   -3.887 closest distance to " O   HOH Z 151 " =    0.848
peak=   -3.862 closest distance to " O   VAL A  67 " =    2.820
peak=   -3.854 closest distance to " O   HOH Z 401 " =    1.574
peak=   -3.835 closest distance to " O   HOH Z 423 " =    2.383
peak=   -3.788 closest distance to " O   TYR A  15 " =    1.708
peak=   -3.787 closest distance to " O   HOH Z 407 " =    1.141
peak=   -3.784 closest distance to " O   HOH Z 384 " =    1.908
peak=   -3.777 closest distance to " CB  ALA A 161 " =    2.518
peak=   -3.757 closest distance to " CD2 PHE A  59 " =    2.401
peak=   -3.752 closest distance to " CD  ARG A 156 " =    2.044
peak=   -3.748 closest distance to " NH2 ARG A  66 " =    1.208
peak=   -3.744 closest distance to " O   HOH Z  56 " =    1.553
peak=   -3.733 closest distance to " O   HOH Z 119 " =    1.907
peak=   -3.729 closest distance to " CD2 LEU A 237 " =    2.362
peak=   -3.727 closest distance to " O   HOH Z 124 " =    1.360
peak=   -3.724 closest distance to " O   HOH Z 109 " =    5.967
peak=   -3.720 closest distance to " OD1 ASN A 301 " =    0.863
peak=   -3.719 closest distance to " CG2 THR A  18 " =    2.736
peak=   -3.718 closest distance to " CA  GLY A 203 " =    2.308
peak=   -3.715 closest distance to " O   SER A 273 " =    1.119
peak=   -3.705 closest distance to " C   THR A 279 " =    1.121
peak=   -3.682 closest distance to " O   PRO A 198 " =    1.364
peak=   -3.658 closest distance to " O   HOH Z 265 " =    1.489
peak=   -3.653 closest distance to " CG1 VAL A 112 " =    2.368
peak=   -3.644 closest distance to " O   ALA A  34 " =    2.252
peak=   -3.628 closest distance to " O   HOH Z 174 " =    1.855
peak=   -3.612 closest distance to " N   ALA A 226 " =    2.035
peak=   -3.606 closest distance to " O   HOH Z 120 " =    1.410
peak=   -3.605 closest distance to " O   HOH Z   6 " =    2.139
peak=   -3.604 closest distance to " CG  GLN A 223 " =    1.787
peak=   -3.600 closest distance to " OD1 ASP A 298 " =    2.076
peak=   -3.597 closest distance to " CD1 LEU A  96 " =    2.207
peak=   -3.594 closest distance to " O   HOH Z 176 " =    1.559
peak=   -3.588 closest distance to " O   ASP A 191 " =    1.935
peak=   -3.588 closest distance to " CG1 VAL A  78 " =    2.774
peak=   -3.586 closest distance to " CG  ARG A 219 " =    2.305
peak=   -3.569 closest distance to " O   HOH Z 120 " =    0.954
peak=   -3.563 closest distance to " OG BSER A 210 " =    1.158
peak=   -3.562 closest distance to " O   HOH Z 412 " =    5.160
peak=   -3.560 closest distance to " O   HOH Z 422 " =    1.411
peak=   -3.559 closest distance to " O   HOH Z 221 " =    1.269
peak=   -3.528 closest distance to " O   GLN A  11 " =    1.074
peak=   -3.525 closest distance to " O   HOH Z 234 " =    3.962
peak=   -3.518 closest distance to " O   HOH Z  16 " =    2.487
peak=   -3.514 closest distance to " OG BSER A 134 " =    1.437
peak=   -3.512 closest distance to " CB  ALA A 248 " =    2.073
peak=   -3.510 closest distance to " OG  SER A   3 " =    1.656
peak=   -3.507 closest distance to " O   HOH Z  15 " =    1.529
peak=   -3.505 closest distance to " CB  ALA A 100 " =    1.725
peak=   -3.504 closest distance to " C   ASN A 285 " =    2.348
peak=   -3.503 closest distance to " O   ASN A 187 " =    1.504
peak=   -3.501 closest distance to " O   HOH Z 290 " =    1.083
peak=   -3.496 closest distance to " O   HOH Z 252 " =    1.287
peak=   -3.486 closest distance to " O   HOH Z  29 " =    1.663
peak=   -3.482 closest distance to " CD1 TRP A 179 " =    1.196
peak=   -3.467 closest distance to " O   HOH Z  60 " =    1.608
peak=   -3.464 closest distance to " N   THR A 235 " =    1.280
peak=   -3.460 closest distance to " O   SER A  95 " =    1.705
peak=   -3.460 closest distance to " O   VAL A 174 " =    2.204
peak=   -3.460 closest distance to " CG2 VAL A 296 " =    1.088
peak=   -3.451 closest distance to " CD  GLN A  73 " =    0.746
peak=   -3.450 closest distance to " CD2 TYR A  30 " =    2.590
peak=   -3.437 closest distance to " CB  PHE A  59 " =    2.268
peak=   -3.431 closest distance to " O   HOH Z 426 " =    1.685
peak=   -3.430 closest distance to " ND2 ASN A  60 " =    1.328
peak=   -3.424 closest distance to " O   HOH Z 126 " =    1.943
peak=   -3.423 closest distance to " O   THR A  18 " =    1.446
peak=   -3.422 closest distance to " CA  SER A 210 " =    1.207
peak=   -3.414 closest distance to " CG  ASP A 231 " =    0.853
peak=   -3.413 closest distance to " OH  TYR A 169 " =    0.864
peak=   -3.410 closest distance to " C   HIS A 108 " =    1.228
peak=   -3.409 closest distance to " O   HOH Z 136 " =    2.340
peak=   -3.409 closest distance to " O   HOH Z   7 " =    1.025
peak=   -3.405 closest distance to " O   HOH Z  20 " =    1.128
peak=   -3.404 closest distance to " CA  GLY A 133 " =    2.034
peak=   -3.402 closest distance to " OXT GLY A 302 " =    3.477
peak=   -3.401 closest distance to " N   GLN A  58 " =    1.660
peak=   -3.390 closest distance to " O   HOH Z 369 " =    2.400
peak=   -3.387 closest distance to " CD1 TYR A 247 " =    2.293
peak=   -3.380 closest distance to " O   HOH Z  37 " =    1.421
peak=   -3.379 closest distance to " C   GLY A 133 " =    1.229
peak=   -3.378 closest distance to " O   HOH Z 135 " =    1.970
peak=   -3.376 closest distance to " O   HOH Z 422 " =    0.932
peak=   -3.376 closest distance to " O   HOH Z 378 " =    1.428
peak=   -3.375 closest distance to " O   HOH Z 227 " =    0.902
peak=   -3.368 closest distance to " O   HOH Z 388 " =    1.797
peak=   -3.367 closest distance to " O   HOH Z 132 " =    1.570
peak=   -3.364 closest distance to " CG2 VAL A 189 " =    1.936
peak=   -3.364 closest distance to " O   HOH Z 377 " =    2.280
peak=   -3.362 closest distance to " O   HOH Z  35 " =    0.948
peak=   -3.360 closest distance to " OG1 THR A  18 " =    1.939
peak=   -3.358 closest distance to " O   HOH Z 424 " =    2.992
peak=   -3.353 closest distance to " O   HOH Z  57 " =    0.865
peak=   -3.352 closest distance to " O   HOH Z 126 " =    1.804
peak=   -3.345 closest distance to " O   HOH Z  71 " =    1.630
peak=   -3.344 closest distance to " CB  PRO A 163 " =    2.783
peak=   -3.343 closest distance to " OD2 ASP A 298 " =    0.965
peak=   -3.339 closest distance to " O   HOH Z 193 " =    1.625
peak=   -3.329 closest distance to " O   HOH Z 109 " =    3.140
peak=   -3.329 closest distance to " C   GLY A 147 " =    1.622
peak=   -3.328 closest distance to " ND2 ASN A  60 " =    1.617
peak=   -3.327 closest distance to " O   ALA A 161 " =    1.429
peak=   -3.323 closest distance to " OG  SER A  22 " =    1.191
peak=   -3.318 closest distance to " CG  GLN A  73 " =    0.827
peak=   -3.310 closest distance to " OG1 THR A  82 " =    1.446
peak=   -3.307 closest distance to " O   HOH Z  92 " =    1.382
peak=   -3.304 closest distance to " O   HOH Z 152 " =    1.645
peak=   -3.304 closest distance to " N   GLY A  17 " =    1.634
peak=   -3.300 closest distance to " NZ  LYS A  76 " =    2.015
peak=   -3.300 closest distance to " ND2 ASN A  69 " =    1.481
peak=   -3.297 closest distance to " CG  MET A 105 " =    0.910
peak=   -3.292 closest distance to " CG  GLU A   2 " =    1.656
peak=   -3.289 closest distance to " O  BHOH Z 338 " =    1.468
peak=   -3.286 closest distance to " C   VAL A 265 " =    1.007
peak=   -3.281 closest distance to " O   HOH Z 166 " =    1.712
peak=   -3.281 closest distance to " C   ASN A 148 " =    1.554
peak=   -3.278 closest distance to " CD1 ILE A 109 " =    2.232
peak=   -3.277 closest distance to " O   GLY A 118 " =    1.201
peak=   -3.270 closest distance to " OD1 ASN A  39 " =    2.278
peak=   -3.268 closest distance to " O   ILE A 234 " =    1.374
peak=   -3.267 closest distance to " CD1 LEU A 228 " =    2.204
peak=   -3.264 closest distance to " C   TRP A 274 " =    1.237
peak=   -3.256 closest distance to " OE1 GLN A  88 " =    1.019
peak=   -3.253 closest distance to " CD2 LEU A 237 " =    2.199
peak=   -3.249 closest distance to " ND2 ASN A  45 " =    1.300
peak=   -3.244 closest distance to " O   HOH Z 368 " =    1.791
peak=   -3.237 closest distance to " O   HOH Z 109 " =    3.362
peak=   -3.236 closest distance to " SG BCYS A 201 " =    0.922
peak=   -3.235 closest distance to " CG  ASP A 231 " =    0.976
peak=   -3.232 closest distance to " O   HOH Z 392 " =    1.531
peak=   -3.231 closest distance to " CB  ALA A 131 " =    2.363
peak=   -3.230 closest distance to " O   HOH Z 200 " =    1.440
peak=   -3.229 closest distance to " OG  SER A 141 " =    2.482
peak=   -3.228 closest distance to " CE3 TRP A  70 " =    1.778
peak=   -3.226 closest distance to " CA  ALA A 137 " =    2.551
peak=   -3.226 closest distance to " CB  ALA A 291 " =    2.470
peak=   -3.216 closest distance to " O   HOH Z 198 " =    1.360
peak=   -3.209 closest distance to " CD2 PHE A 192 " =    2.074
peak=   -3.206 closest distance to " O   HOH Z 185 " =    2.076
peak=   -3.204 closest distance to " O   ASP A 171 " =    1.916
peak=   -3.203 closest distance to " OD1 ASN A 148 " =    1.589
peak=   -3.200 closest distance to " O   GLN A 144 " =    0.874
peak=   -3.198 closest distance to " O   HOH Z   1 " =    4.962
peak=   -3.195 closest distance to " O   HOH Z 249 " =    1.197
peak=   -3.193 closest distance to " O   HOH Z 191 " =    5.690
peak=   -3.193 closest distance to " N   ALA A 248 " =    1.834
peak=   -3.193 closest distance to " O   HOH Z 196 " =    2.946
peak=   -3.190 closest distance to " NE2 GLN A 223 " =    1.604
peak=   -3.190 closest distance to " O   HOH Z 145 " =    2.253
peak=   -3.187 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.186 closest distance to " CD1 LEU A   5 " =    2.080
peak=   -3.183 closest distance to " OD1 ASN A  69 " =    1.849
peak=   -3.183 closest distance to " O   HOH Z  94 " =    2.322
peak=   -3.181 closest distance to " O   HOH Z 351 " =    1.581
peak=   -3.178 closest distance to " O   HOH Z 208 " =    1.683
peak=   -3.178 closest distance to " O   HOH Z 171 " =    2.484
peak=   -3.177 closest distance to " O   HOH Z 377 " =    1.198
peak=   -3.177 closest distance to " NH2 ARG A  79 " =    1.905
peak=   -3.173 closest distance to " OG  SER A  87 " =    1.569
peak=   -3.171 closest distance to " OD1 ASP A 200 " =    1.377
peak=   -3.171 closest distance to " O   HOH Z 391 " =    1.188
peak=   -3.169 closest distance to " N   VAL A  72 " =    1.262
peak=   -3.165 closest distance to " CE  MET A 105 " =    2.002
peak=   -3.165 closest distance to " O   HOH Z 244 " =    1.272
peak=   -3.161 closest distance to " CD  GLU A 236 " =    0.929
peak=   -3.157 closest distance to " CD  GLN A 223 " =    0.843
peak=   -3.156 closest distance to " O   HOH Z 110 " =    1.277
peak=   -3.155 closest distance to " CB  ALA A  84 " =    2.383
peak=   -3.154 closest distance to " O   ALA A   8 " =    1.851
peak=   -3.146 closest distance to " CD  ARG A 195 " =    4.985
peak=   -3.144 closest distance to " O   HOH Z  39 " =    1.519
peak=   -3.142 closest distance to " NE2 GLN A  88 " =    0.994
peak=   -3.137 closest distance to " CG2 THR A 178 " =    2.561
peak=   -3.126 closest distance to " CD2 TYR A 293 " =    1.817
peak=   -3.118 closest distance to " O   ALA A 165 " =    2.286
peak=   -3.116 closest distance to " O   VAL A 197 " =    1.435
peak=   -3.109 closest distance to " CZ  TYR A 169 " =    1.752
peak=   -3.109 closest distance to " N   VAL A 230 " =    1.040
peak=   -3.102 closest distance to " O   ASP A 200 " =    1.130
peak=   -3.100 closest distance to " O   HOH Z 417 " =    1.029
peak=   -3.100 closest distance to " CA  ASN A 127 " =    1.053
peak=   -3.098 closest distance to " O   HOH Z 435 " =    1.643
peak=   -3.093 closest distance to " SG  CYS A 260 " =    2.572
peak=   -3.076 closest distance to " O   HOH Z 366 " =    1.333
peak=   -3.075 closest distance to " O   HOH Z 139 " =    3.522
peak=   -3.069 closest distance to " SG  CYS A 254 " =    2.521
peak=   -3.063 closest distance to " N   ASP A 286 " =    1.268
peak=   -3.054 closest distance to " OG1 THR A  31 " =    1.408
peak=   -3.054 closest distance to " O   HOH Z 156 " =    2.133
peak=   -3.045 closest distance to " O   ALA A 256 " =    1.539
peak=   -3.042 closest distance to " O   HOH Z 353 " =    1.517
peak=   -3.016 closest distance to " O   HOH Z 231 " =    1.476
peak=   -3.006 closest distance to " O   HOH Z 340 " =    1.422

================= 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    :  0.5077 0.4919   6.305855e+00   6.292498e+00
   1_bss:  0.5010 0.4854   6.300337e+00   6.288772e+00
   1_xyz:  0.4398 0.4519   6.240399e+00   6.256385e+00
   1_adp:  0.3989 0.4449   5.991406e+00   6.043833e+00
   1_occ:  0.3985 0.4438   5.990489e+00   6.043774e+00
   2_bss:  0.3972 0.4411   5.992375e+00   6.043812e+00
   2_xyz:  0.3356 0.3962   6.073459e+00   6.178080e+00
   2_adp:  0.3219 0.3881   6.050141e+00   6.163820e+00
   2_occ:  0.3216 0.3877   6.049762e+00   6.163281e+00
   3_bss:  0.3206 0.3875   6.051144e+00   6.164311e+00
   3_xyz:  0.2632 0.3247   5.880150e+00   6.033771e+00
   3_adp:  0.2363 0.3050   5.810508e+00   5.986776e+00
   3_occ:  0.2360 0.3058   5.810266e+00   5.987305e+00
   4_bss:  0.2358 0.3062   5.810693e+00   5.986825e+00
   4_xyz:  0.1839 0.2386   5.572821e+00   5.776063e+00
   4_adp:  0.1683 0.2162   5.486694e+00   5.683357e+00
   4_occ:  0.1681 0.2163   5.486354e+00   5.683338e+00
   5_bss:  0.1681 0.2158   5.488483e+00   5.683280e+00
   5_xyz:  0.1366 0.1840   5.305429e+00   5.527267e+00
   5_adp:  0.1278 0.1780   5.258056e+00   5.492203e+00
   5_occ:  0.1277 0.1779   5.258027e+00   5.492603e+00
   5_bss:  0.1280 0.1780   5.260089e+00   5.494314e+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:  0.346  20.000   6.341  11.707   6.760   0.000   0.000   0.000
   1_xyz:  0.346  20.000   6.341  11.707   6.760   0.000   0.000   0.000
   1_adp:  0.346  20.000   6.341  11.707   6.760   0.000   0.000   0.000
   1_occ:  0.346  20.000   6.341  11.707   6.760   0.000   0.000   0.000
   2_bss:  0.287  20.002   2.963   7.036   4.018   0.000   0.000   0.000
   2_xyz:  0.287  20.002   2.963   7.036   4.018   0.000   0.000   0.000
   2_adp:  0.287  20.002   2.963   7.036   4.018   0.000   0.000   0.000
   2_occ:  0.287  20.002   2.963   7.036   4.018   0.000   0.000   0.000
   3_bss:  0.310  46.056   1.475   4.761   2.483   0.000   0.000   0.000
   3_xyz:  0.310  46.056   1.475   4.761   2.483   0.000   0.000   0.000
   3_adp:  0.310  46.056   1.475   4.761   2.483   0.000   0.000   0.000
   3_occ:  0.310  46.056   1.475   4.761   2.483   0.000   0.000   0.000
   4_bss:  0.326  57.214   0.564   3.205   1.800   0.000   0.000   0.000
   4_xyz:  0.326  57.214   0.564   3.205   1.800   0.000   0.000   0.000
   4_adp:  0.326  57.214   0.564   3.205   1.800   0.000   0.000   0.000
   4_occ:  0.326  57.214   0.564   3.205   1.800   0.000   0.000   0.000
   5_bss:  0.328  56.383  -0.221   1.924   1.220   0.000   0.000   0.000
   5_xyz:  0.328  56.383  -0.221   1.924   1.220   0.000   0.000   0.000
   5_adp:  0.328  56.383  -0.221   1.924   1.220   0.000   0.000   0.000
   5_occ:  0.328  56.383  -0.221   1.924   1.220   0.000   0.000   0.000
   5_bss:  0.326  55.041  -1.108   0.731   0.377   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.932 0.3697  0.4355    78586.501
   1_bss:  62.788 0.3570  0.5314    77693.095
   1_xyz:  56.272 0.4400  0.6426    65005.818
   1_adp:  53.471 0.4755  0.7655    60558.078
   1_occ:  53.381 0.4765  0.7656    60305.250
   2_bss:  53.175 0.4791  0.6838    59948.817
   2_xyz:  46.227 0.5656  0.8042    47025.236
   2_adp:  44.181 0.5913  0.8480    44485.352
   2_occ:  44.127 0.5920  0.8481    44432.144
   3_bss:  43.974 0.5940  0.8028    44433.919
   3_xyz:  34.696 0.7038  0.9251    29013.637
   3_adp:  32.148 0.7334  0.9389    25606.591
   3_occ:  32.158 0.7333  0.9386    25630.196
   4_bss:  32.112 0.7339  0.9053    25600.729
   4_xyz:  23.852 0.8227  0.9820    14757.692
   4_adp:  20.914 0.8529  0.9977    12007.301
   4_occ:  20.906 0.8530  0.9979    12016.861
   5_bss:  20.893 0.8532  0.9670    12021.016
   5_xyz:  17.196 0.8873  0.9852     8487.878
   5_adp:  16.351 0.8952  0.9834     8012.751
   5_occ:  16.355 0.8951  0.9832     8022.219
   5_bss:  16.375 0.8950  0.9744     8061.807
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3614e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3614e+01
   1_xyz:   1.774  0.014  0.110 18.574  0.007  4.118   1.5748e-01
   1_adp:   1.774  0.014  0.110 18.574  0.007  4.118   1.5748e-01
   1_occ:   1.774  0.014  0.110 18.574  0.007  4.118   1.5748e-01
   2_bss:   1.774  0.014  0.110 18.574  0.007  4.118   1.5748e-01
   2_xyz:   1.350  0.010  0.087 17.298  0.006  4.105   1.1353e-01
   2_adp:   1.350  0.010  0.087 17.298  0.006  4.105   1.1353e-01
   2_occ:   1.350  0.010  0.087 17.298  0.006  4.105   1.1353e-01
   3_bss:   1.350  0.010  0.087 17.298  0.006  4.105   1.1353e-01
   3_xyz:   1.291  0.010  0.092 16.534  0.006  4.107   9.7741e-02
   3_adp:   1.291  0.010  0.092 16.534  0.006  4.107   9.7741e-02
   3_occ:   1.291  0.010  0.092 16.534  0.006  4.107   9.7741e-02
   4_bss:   1.291  0.010  0.092 16.534  0.006  4.107   9.7741e-02
   4_xyz:   1.134  0.008  0.076 15.865  0.004  4.122   7.9745e-02
   4_adp:   1.134  0.008  0.076 15.865  0.004  4.122   7.9745e-02
   4_occ:   1.134  0.008  0.076 15.865  0.004  4.122   7.9745e-02
   5_bss:   1.134  0.008  0.076 15.865  0.004  4.122   7.9745e-02
   5_xyz:   1.206  0.009  0.091 15.912  0.004  4.120   8.3889e-02
   5_adp:   1.206  0.009  0.091 15.912  0.004  4.120   8.3889e-02
   5_occ:   1.206  0.009  0.091 15.912  0.004  4.120   8.3889e-02
   5_bss:   1.206  0.009  0.091 15.912  0.004  4.120   8.3889e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.960   6.9468e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.960   6.9468e+00
   1_xyz:  15.893  0.126  0.551 89.271  0.041  2.134   1.0617e-01
   1_adp:  15.893  0.126  0.551 89.271  0.041  2.134   1.0617e-01
   1_occ:  15.893  0.126  0.551 89.271  0.041  2.134   1.0617e-01
   2_bss:  15.893  0.126  0.551 89.271  0.041  2.134   1.0617e-01
   2_xyz:   7.696  0.094  0.331 81.062  0.044  1.965   9.9154e-02
   2_adp:   7.696  0.094  0.331 81.062  0.044  1.965   9.9154e-02
   2_occ:   7.696  0.094  0.331 81.062  0.044  1.965   9.9154e-02
   3_bss:   7.696  0.094  0.331 81.062  0.044  1.965   9.9154e-02
   3_xyz:   8.052  0.067  0.321 83.883  0.040  2.189   7.8006e-02
   3_adp:   8.052  0.067  0.321 83.883  0.040  2.189   7.8006e-02
   3_occ:   8.052  0.067  0.321 83.883  0.040  2.189   7.8006e-02
   4_bss:   8.052  0.067  0.321 83.883  0.040  2.189   7.8006e-02
   4_xyz:   7.263  0.063  0.299 88.607  0.024  2.195   1.0226e-01
   4_adp:   7.263  0.063  0.299 88.607  0.024  2.195   1.0226e-01
   4_occ:   7.263  0.063  0.299 88.607  0.024  2.195   1.0226e-01
   5_bss:   7.263  0.063  0.299 88.607  0.024  2.195   1.0226e-01
   5_xyz:   7.996  0.061  0.681 83.160  0.033  2.159   6.1976e-02
   5_adp:   7.996  0.061  0.681 83.160  0.033  2.159   6.1976e-02
   5_occ:   7.996  0.061  0.681 83.160  0.033  2.159   6.1976e-02
   5_bss:   7.996  0.061  0.681 83.160  0.033  2.159   6.1976e-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:  80.28   0.00  15.32  61.29   0.00  13.64  80.28   0.00  24.44
   1_occ:  80.28   0.00  15.32  61.29   0.00  13.64  80.28   0.00  24.44
   2_bss:  80.28   0.00  15.32  61.29   0.00  13.64  80.28   0.00  24.44
   2_xyz:  80.28   0.00  15.32  61.29   0.00  13.64  80.28   0.00  24.44
   2_adp: 106.85   0.00  15.21 106.85   0.00  13.16  78.36   0.00  26.38
   2_occ: 106.85   0.00  15.21 106.85   0.00  13.16  78.36   0.00  26.38
   3_bss: 106.85   0.00  15.21 106.85   0.00  13.16  78.36   0.00  26.38
   3_xyz: 106.85   0.00  15.21 106.85   0.00  13.16  78.36   0.00  26.38
   3_adp: 108.32   0.00  15.85  89.70   0.00  12.25 108.32   1.78  35.45
   3_occ: 108.32   0.00  15.85  89.70   0.00  12.25 108.32   1.78  35.45
   4_bss: 108.32   0.00  15.85  89.70   0.00  12.25 108.32   1.78  35.45
   4_xyz: 108.32   0.00  15.85  89.70   0.00  12.25 108.32   1.78  35.45
   4_adp:  96.81   0.00  15.43  91.55   0.00  11.13  96.81   3.09  38.86
   4_occ:  96.81   0.00  15.43  91.55   0.00  11.13  96.81   3.09  38.86
   5_bss:  96.81   0.00  15.43  91.55   0.00  11.13  96.81   3.09  38.86
   5_xyz:  96.81   0.00  15.43  91.55   0.00  11.13  96.81   3.09  38.86
   5_adp:  98.85   0.00  15.60  98.85   0.00  10.75  95.37   3.55  42.03
   5_occ:  98.85   0.00  15.60  98.85   0.00  10.75  95.37   3.55  42.03
   5_bss:  99.57   0.72  16.33  99.57   0.72  11.47  96.10   4.27  42.76
------------------------------------------------------------------------
 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:    1.093    0.016    0.414
   1_adp:    1.093    0.016    0.414
   1_occ:    1.093    0.016    0.414
   2_bss:    1.093    0.016    0.414
   2_xyz:    1.837    0.033    0.599
   2_adp:    1.837    0.033    0.599
   2_occ:    1.837    0.033    0.599
   3_bss:    1.837    0.033    0.599
   3_xyz:    1.716    0.042    0.735
   3_adp:    1.716    0.042    0.735
   3_occ:    1.716    0.042    0.735
   4_bss:    1.716    0.042    0.735
   4_xyz:    1.991    0.055    0.854
   4_adp:    1.991    0.055    0.854
   4_occ:    1.991    0.055    0.854
   5_bss:    1.991    0.055    0.854
   5_xyz:    2.059    0.073    0.923
   5_adp:    2.059    0.073    0.923
   5_occ:    2.059    0.073    0.923
   5_bss:    2.059    0.073    0.923
------------------------------------------------------------------------

CPU time actual refinement: 360.27


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_355/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_355/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_355/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_355/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_355/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 360.12 
  Macro-tasks:
    bulk solvent and scale       = 47.58  
    individual site refinement   = 151.97 
    weights calculation          = 33.62  
    collect and process          = 6.42   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 239.74 
  Micro-tasks:
    mask                            = 3.07   
    f_calc                          = 110.88 
    alpha_beta                      = 8.39   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 122.83 
    fmodel                         = 8.25   
    r_factors                      = 0.35   
    phase_errors                   = 9.80   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 264.97 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.027 micro seconds
Total CPU time: 6.24 minutes
from_scatterers_fft:    644 calls, 110.53 s
gradients_fft:          589 calls, 109.36 s

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

# Date 2008-01-16 Time 01:22:19 PST -0800 (1200475339.12 s)
Start R-work = 0.5077, R-free = 0.4919 (no bulk solvent and anisotropic scale)
Final R-work = 0.1450, R-free = 0.1939 (no bulk solvent and anisotropic scale)

Start R-work = 0.5010, R-free = 0.4854
Final R-work = 0.1280, R-free = 0.1780