# Date 2008-01-16 Time 01:39:45 PST -0800 (1200476385.27 s)
#phil __OFF__

Command line arguments: "../510.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14926
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 510

-------------------------------------------------------------------------------
  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: (69.8988, 46.2261, 85.9581, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.97221
Completeness in resolution range: 0.969465
Completeness with d_max=infinity: 0.966451

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9722

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: (69.8988, 46.2261, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.97221
Completeness in resolution range: 0.969465
Completeness with d_max=infinity: 0.966451

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2200 [2118/2142]  1905   213  10.1%
  bin  2:  4.2200 -  3.3621 [2038/2058]  1835   203  10.0%
  bin  3:  3.3621 -  2.9408 [2013/2032]  1813   200   9.9%
  bin  4:  2.9408 -  2.6736 [2001/2031]  1801   200  10.0%
  bin  5:  2.6736 -  2.4829 [1985/2004]  1785   200  10.1%
  bin  6:  2.4829 -  2.3371 [1958/1983]  1760   198  10.1%
  bin  7:  2.3371 -  2.2205 [1958/1986]  1764   194   9.9%
  bin  8:  2.2205 -  2.1241 [1964/2000]  1770   194   9.9%
  bin  9:  2.1241 -  2.0425 [1947/1989]  1752   195  10.0%
  bin 10:  2.0425 -  1.9722 [1607/1981]  1445   162  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_510/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 32
        2.42 -     3.04: 2226
        3.04 -     3.66: 4756
        3.66 -     4.28: 9164
        4.28 -     4.90: 12445
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.007 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  2.007 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.062 3.040 -x+1,y+1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  ... (remaining 28618 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_510/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_510/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 = 69.89875 46.22605 85.95805 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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4563   r_free= 0.4454   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.257623                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7067 0.99   1381  153 0.3839 0.3808      6.5564      6.5663|
|  2:  4.7067 -  3.7554 0.99   1324  149 0.3692 0.3388      6.7316      6.6733|
|  3:  3.7554 -  3.2865 0.99   1298  142 0.3987 0.3760      6.6253      6.6511|
|  4:  3.2865 -  2.9887 0.99   1290  145 0.4370 0.4003      6.5057       6.426|
|  5:  2.9887 -  2.7759 0.99   1280  143 0.4851 0.4845      6.3482      6.3881|
|  6:  2.7759 -  2.6132 0.99   1299  140 0.4791 0.5353      6.2726      6.2093|
|  7:  2.6132 -  2.4829 0.99   1267  144 0.4916 0.4432      6.2278       6.201|
|  8:  2.4829 -  2.3753 0.98   1259  138 0.5109 0.4766      6.1842      6.1745|
|  9:  2.3753 -  2.2842 0.98   1263  143 0.4905 0.5247      6.0988      6.1286|
| 10:  2.2842 -  2.2056 1.00   1264  143 0.5086 0.5142      6.1173      6.0993|
| 11:  2.2056 -  2.1368 0.97   1263  135 0.5046 0.4508       6.036      6.0342|
| 12:  2.1368 -  2.0759 0.98   1238  140 0.4957 0.4924      5.9798      5.9778|
| 13:  2.0759 -  2.0214 0.99   1286  141 0.5220 0.5341      5.8943      5.8557|
| 14:  2.0214 -  1.9722 0.73    918  103 0.5411 0.5087      5.8506      5.7924|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7067  1381   153  0.69  34.91   0.81     0.74      73035.20|
|  2:  4.7067 -  3.7554  1324   149  0.74  31.66   0.90     0.82      89667.00|
|  3:  3.7554 -  3.2865  1298   142  0.66  38.46   0.88     0.78      92918.36|
|  4:  3.2865 -  2.9887  1290   145  0.59  44.79   0.82     0.68      84181.55|
|  5:  2.9887 -  2.7759  1280   143  0.47  54.21   0.77     0.56      73472.54|
|  6:  2.7759 -  2.6132  1299   140  0.44  56.63   0.75     0.49      66887.46|
|  7:  2.6132 -  2.4829  1267   144  0.40  60.14   0.76     0.46      63382.28|
|  8:  2.4829 -  2.3753  1259   138  0.39  60.87   0.75     0.45      58188.86|
|  9:  2.3753 -  2.2842  1263   143  0.42  58.55   0.74     0.48      50456.91|
| 10:  2.2842 -  2.2056  1264   143  0.44  56.98   0.78     0.51      42890.80|
| 11:  2.2056 -  2.1368  1263   135  0.44  57.29   0.78     0.53      40599.94|
| 12:  2.1368 -  2.0759  1238   140  0.38  61.21   0.80     0.47      39858.26|
| 13:  2.0759 -  2.0214  1286   141  0.33  65.75   0.74     0.40      36744.62|
| 14:  2.0214 -  1.9722   918   103  0.30  67.51   0.72     0.33      30296.04|
|alpha:            min =        0.33 max =            0.82 mean =         0.56|
|beta:             min =    30296.04 max =        92918.36 mean =     61083.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.97 mean =        52.99|
|phase err.(test): min =        0.00 max =           89.99 mean =        53.00|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.812753             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.353   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.055470              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.266   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       30 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      702 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1530 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2674 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3988 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5127 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6628 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7795 |
|-----------------------------------------------------------------------------|
|-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 |       53.251 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.924 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    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 = 11.608)------------------------------------------|
|    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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4640   r_free= 0.4499   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.261486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4475   r_free= 0.4333   ksol= 0.37   Bsol= 5.07   scale= 1.022    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,10.34,7.95,0.00,0.00,0.00); trace/3= 8.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.249776                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.435146              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.812   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.960540              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.114   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4475      final r-factor (work) = 0.3570          |
| start r-factor (free) = 0.4333      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.7882 = 9.44 * 0.50 * 6.2611 + 1.00 * 53.2509                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1150 = 9.44 * 0.50 * 6.1445 + 1.00 * 0.1279                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3570      final r-factor (work) = 0.3058          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.3484          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9167 = 0.96 * 1.00 * 6.1445 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8024 = 0.96 * 1.00 * 6.0255 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.58   11.94    None  None   None       |
|    all(noH): 2823   0      0.00    73.58   11.94    None  None   None       |
|    Sol.    : 438    0      0.00    73.58   25.96    None  None   None       |
|    Mac.    : 2385   0      0.00    73.48   9.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.358: 1224   |   5:    36.788 -  44.146:   65        |
|      1:     7.358 -  14.715:  777   |   6:    44.146 -  51.503:   29        |
|      2:    14.715 -  22.073:  372   |   7:    51.503 -  58.861:   16        |
|      3:    22.073 -  29.431:  211   |   8:    58.861 -  66.219:    1        |
|      4:    29.431 -  36.788:  125   |   9:    66.219 -  73.576:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3058 r_free = 0.3484             target_work(ml) = 5.993         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3053 r_free = 0.3476             target_work(ml) = 5.992         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3053   r_free= 0.3476   ksol= 0.37   Bsol= 5.07   scale= 1.109    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,10.34,7.95,0.00,0.00,0.00); trace/3= 8.52                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.991538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3005   r_free= 0.3406   ksol= 0.34   Bsol= 29.13   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,5.73,4.73,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.988994                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.181158              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.948   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.508085              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.259  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3005      final r-factor (work) = 0.2079          |
| start r-factor (free) = 0.3406      final r-factor (free) = 0.2571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7479 = 6.18 * 0.50 * 6.0250 + 1.00 * 0.1273                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0663 = 6.18 * 0.50 * 5.8204 + 1.00 * 0.0779                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2079      final r-factor (work) = 0.1833          |
| start r-factor (free) = 0.2571      final r-factor (free) = 0.2365          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9717 = 0.51 * 1.00 * 5.8204 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8738 = 0.51 * 1.00 * 5.6041 + 1.00 * 0.0265                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.71   11.92    None  None   None       |
|    all(noH): 2823   0      0.00    79.71   11.92    None  None   None       |
|    Sol.    : 438    0      0.61    77.33   31.22    None  None   None       |
|    Mac.    : 2385   0      0.00    79.71   8.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.971: 1524   |   5:    39.855 -  47.826:   91        |
|      1:     7.971 -  15.942:  638   |   6:    47.826 -  55.797:   34        |
|      2:    15.942 -  23.913:  213   |   7:    55.797 -  63.768:    3        |
|      3:    23.913 -  31.884:  165   |   8:    63.768 -  71.739:    1        |
|      4:    31.884 -  39.855:  151   |   9:    71.739 -  79.710:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1833 r_free = 0.2365             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1830 r_free = 0.2362             target_work(ml) = 5.563         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1830   r_free= 0.2362   ksol= 0.34   Bsol= 29.13   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,5.73,4.73,0.00,0.00,0.00); trace/3= 4.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.562579                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1818   r_free= 0.2339   ksol= 0.32   Bsol= 32.95   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.43,3.95,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.558694                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.445185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.512  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.722450              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.590   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1818      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.1889          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7398 = 3.45 * 0.50 * 5.6091 + 1.00 * 0.0776                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4410 = 3.45 * 0.50 * 5.4440 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1383      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1889      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9480 = 0.72 * 1.00 * 5.4440 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8355 = 0.72 * 1.00 * 5.2920 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.41   12.29    None  None   None       |
|    all(noH): 2823   0      0.00    83.41   12.29    None  None   None       |
|    Sol.    : 438    0      0.98    80.32   35.31    None  None   None       |
|    Mac.    : 2385   0      0.00    83.41   8.06     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 -   8.341: 1668   |   5:    41.704 -  50.044:  105        |
|      1:     8.341 -  16.682:  565   |   6:    50.044 -  58.385:   64        |
|      2:    16.682 -  25.022:  163   |   7:    58.385 -  66.726:   23        |
|      3:    25.022 -  33.363:  115   |   8:    66.726 -  75.066:    3        |
|      4:    33.363 -  41.704:  115   |   9:    75.066 -  83.407:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1775             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1772             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1772   ksol= 0.32   Bsol= 32.95   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.43,3.95,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.256372                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1770   ksol= 0.32   Bsol= 36.54   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.73,3.76,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.255716                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.130361              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.846  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.721718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.508  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7010 = 2.13 * 0.50 * 5.2929 + 1.00 * 0.0631                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6201 = 2.13 * 0.50 * 5.2238 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0067 = 1.72 * 1.00 * 5.2238 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9321 = 1.72 * 1.00 * 5.1802 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.11   12.33    None  None   None       |
|    all(noH): 2823   0      0.00    89.11   12.33    None  None   None       |
|    Sol.    : 438    0      1.31    83.40   36.16    None  None   None       |
|    Mac.    : 2385   0      0.00    89.11   7.96     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 -   8.911: 1754   |   5:    44.556 -  53.467:   91        |
|      1:     8.911 -  17.823:  520   |   6:    53.467 -  62.379:   53        |
|      2:    17.823 -  26.734:  145   |   7:    62.379 -  71.290:   23        |
|      3:    26.734 -  35.645:  121   |   8:    71.290 -  80.201:    5        |
|      4:    35.645 -  44.556:  109   |   9:    80.201 -  89.112:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1634             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1632             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1632   ksol= 0.32   Bsol= 36.54   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.73,3.76,0.00,0.00,0.00); trace/3= 2.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.173135                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1632   ksol= 0.32   Bsol= 36.54   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.54,2.70,3.89,0.00,0.00,0.00); trace/3= 3.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.173031                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.894951              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.634  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.425328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.590  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9640 = 1.89 * 0.50 * 5.1802 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9451 = 1.89 * 0.50 * 5.1614 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3701 = 1.43 * 1.00 * 5.1614 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3533 = 1.43 * 1.00 * 5.1490 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.37   12.17    None  None   None       |
|    all(noH): 2823   0      0.00    93.37   12.17    None  None   None       |
|    Sol.    : 438    0      1.37    84.63   35.84    None  None   None       |
|    Mac.    : 2385   0      0.00    93.37   7.82     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:     0.000 -   9.337: 1819   |   5:    46.686 -  56.023:   84        |
|      1:     9.337 -  18.674:  485   |   6:    56.023 -  65.360:   41        |
|      2:    18.674 -  28.012:  137   |   7:    65.360 -  74.697:   17        |
|      3:    28.012 -  37.349:  127   |   8:    74.697 -  84.035:    5        |
|      4:    37.349 -  46.686:  106   |   9:    84.035 -  93.372:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1594             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1593             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1593   ksol= 0.32   Bsol= 36.54   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.54,2.70,3.89,0.00,0.00,0.00); trace/3= 3.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146269                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7067 0.99   1381  153 0.0988 0.1255      5.3859      5.5327|
|  2:  4.7067 -  3.7554 0.99   1324  149 0.0850 0.1153      5.4368      5.6432|
|  3:  3.7554 -  3.2865 0.99   1298  142 0.1064 0.1447      5.4855        5.84|
|  4:  3.2865 -  2.9887 0.99   1290  145 0.1217 0.1677      5.4589      5.6103|
|  5:  2.9887 -  2.7759 0.99   1280  143 0.1297 0.1757      5.3277      5.5645|
|  6:  2.7759 -  2.6132 0.99   1299  140 0.1147 0.1838      5.1987      5.4509|
|  7:  2.6132 -  2.4829 0.99   1267  144 0.1288 0.1626      5.1782      5.3786|
|  8:  2.4829 -  2.3753 0.98   1259  138 0.1168 0.1753      5.0831      5.3656|
|  9:  2.3753 -  2.2842 0.98   1263  143 0.1171 0.1722      5.0447      5.2646|
| 10:  2.2842 -  2.2056 1.00   1264  143 0.1111 0.1764      4.9679      5.2583|
| 11:  2.2056 -  2.1368 0.97   1263  135 0.1130 0.1764       4.945      5.2771|
| 12:  2.1368 -  2.0759 0.98   1238  140 0.1119 0.1744      4.8878      5.2221|
| 13:  2.0759 -  2.0214 0.99   1286  141 0.1129 0.1810      4.7988      5.0908|
| 14:  2.0214 -  1.9722 0.73    918  103 0.1000 0.1629       4.661      4.8876|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7067  1381   153  0.94   9.15   0.98     0.96       7206.63|
|  2:  4.7067 -  3.7554  1324   149  0.95   7.88   1.03     1.01       9096.10|
|  3:  3.7554 -  3.2865  1298   142  0.93  11.31   1.04     1.03      10478.68|
|  4:  3.2865 -  2.9887  1290   145  0.92  13.66   1.02     1.00      10353.54|
|  5:  2.9887 -  2.7759  1280   143  0.90  15.79   1.00     0.97       8419.66|
|  6:  2.7759 -  2.6132  1299   140  0.90  15.73   0.99     0.96       7120.86|
|  7:  2.6132 -  2.4829  1267   144  0.90  16.18   0.99     0.96       6369.44|
|  8:  2.4829 -  2.3753  1259   138  0.91  15.23   1.00     0.98       5432.64|
|  9:  2.3753 -  2.2842  1263   143  0.91  15.43   1.01     0.97       5189.74|
| 10:  2.2842 -  2.2056  1264   143  0.90  15.59   1.00     0.96       4483.84|
| 11:  2.2056 -  2.1368  1263   135  0.90  16.69   1.00     0.97       4523.12|
| 12:  2.1368 -  2.0759  1238   140  0.91  15.32   1.02     1.01       4034.53|
| 13:  2.0759 -  2.0214  1286   141  0.90  16.05   1.01     0.99       3387.78|
| 14:  2.0214 -  1.9722   918   103  0.92  14.20   0.99     0.97       2610.42|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2610.42 max =        10478.68 mean =      6442.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.10|
|phase err.(test): min =        0.00 max =           88.66 mean =        13.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1593   ksol= 0.32   Bsol= 42.24   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.39,0.87,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146111                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1593   ksol= 0.32   Bsol= 42.24   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.48,-0.39,0.87,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146111                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7067 0.99   1381  153 0.0989 0.1258      5.3874      5.5347|
|  2:  4.7067 -  3.7554 0.99   1324  149 0.0852 0.1156      5.4386      5.6448|
|  3:  3.7554 -  3.2865 0.99   1298  142 0.1066 0.1448      5.4865      5.8412|
|  4:  3.2865 -  2.9887 0.99   1290  145 0.1216 0.1675      5.4586      5.6097|
|  5:  2.9887 -  2.7759 0.99   1280  143 0.1296 0.1755      5.3269      5.5629|
|  6:  2.7759 -  2.6132 0.99   1299  140 0.1145 0.1835      5.1977        5.45|
|  7:  2.6132 -  2.4829 0.99   1267  144 0.1287 0.1628      5.1773      5.3786|
|  8:  2.4829 -  2.3753 0.98   1259  138 0.1167 0.1749      5.0824      5.3636|
|  9:  2.3753 -  2.2842 0.98   1263  143 0.1171 0.1723      5.0443      5.2645|
| 10:  2.2842 -  2.2056 1.00   1264  143 0.1110 0.1764      4.9675      5.2587|
| 11:  2.2056 -  2.1368 0.97   1263  135 0.1129 0.1763      4.9447      5.2768|
| 12:  2.1368 -  2.0759 0.98   1238  140 0.1118 0.1743      4.8873      5.2219|
| 13:  2.0759 -  2.0214 0.99   1286  141 0.1129 0.1808      4.7982        5.09|
| 14:  2.0214 -  1.9722 0.73    918  103 0.1000 0.1626      4.6598      4.8861|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9194 -  4.7067  1381   153  0.94   9.18   0.98     0.96       7236.11|
|  2:  4.7067 -  3.7554  1324   149  0.95   7.90   1.03     1.02       9126.77|
|  3:  3.7554 -  3.2865  1298   142  0.93  11.33   1.04     1.03      10502.42|
|  4:  3.2865 -  2.9887  1290   145  0.92  13.65   1.02     1.00      10348.24|
|  5:  2.9887 -  2.7759  1280   143  0.90  15.77   1.01     0.98       8404.02|
|  6:  2.7759 -  2.6132  1299   140  0.90  15.71   0.99     0.96       7106.63|
|  7:  2.6132 -  2.4829  1267   144  0.90  16.17   1.00     0.96       6355.23|
|  8:  2.4829 -  2.3753  1259   138  0.91  15.22   1.00     0.98       5421.75|
|  9:  2.3753 -  2.2842  1263   143  0.91  15.43   1.01     0.98       5184.85|
| 10:  2.2842 -  2.2056  1264   143  0.90  15.59   1.01     0.97       4480.89|
| 11:  2.2056 -  2.1368  1263   135  0.90  16.69   1.01     0.97       4521.49|
| 12:  2.1368 -  2.0759  1238   140  0.91  15.32   1.02     1.02       4030.49|
| 13:  2.0759 -  2.0214  1286   141  0.90  16.04   1.01     0.99       3381.53|
| 14:  2.0214 -  1.9722   918   103  0.92  14.17   1.00     0.97       2602.27|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2602.27 max =        10502.42 mean =      6442.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.10|
|phase err.(test): min =        0.00 max =           88.76 mean =        13.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.608)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.15    96.52   15.32    None  None   None       |
|    all(noH): 2823   0      3.15    96.52   15.32    None  None   None       |
|    Sol.    : 438    0      4.51    87.77   38.99    None  None   None       |
|    Mac.    : 2385   0      3.15    96.52   10.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.145 -  12.482: 1819   |   5:    49.831 -  59.168:   84        |
|      1:    12.482 -  21.819:  485   |   6:    59.168 -  68.505:   41        |
|      2:    21.819 -  31.157:  137   |   7:    68.505 -  77.842:   17        |
|      3:    31.157 -  40.494:  127   |   8:    77.842 -  87.180:    5        |
|      4:    40.494 -  49.831:  106   |   9:    87.180 -  96.517:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.341 - 4.741
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 293
   mapped sites are within: 0.703 - 4.741

peak=   11.339 closest distance to " CB  VAL A 230 " =    1.457
peak=   10.193 closest distance to " CB  VAL A 296 " =    1.557
peak=    7.199 closest distance to " O   HOH Z 130 " =    1.315
peak=    6.257 closest distance to " NE2 GLN A  11 " =    1.209
peak=    6.189 closest distance to " CD2 LEU A   5 " =    1.233
peak=    6.050 closest distance to " CG  LEU A   5 " =    1.182
peak=    5.615 closest distance to " CG  PRO A  54 " =    1.341
peak=    5.402 closest distance to " O   HOH Z 144 " =    1.946
peak=    5.367 closest distance to " O   HOH Z 427 " =    2.461
peak=    5.215 closest distance to " O   HOH Z   9 " =    1.400
peak=    5.193 closest distance to " CG  LEU A 228 " =    1.065
peak=    5.184 closest distance to " NH2 ARG A  56 " =    2.040
peak=    4.885 closest distance to " CB  PRO A  54 " =    1.005
peak=    4.849 closest distance to " O   HOH Z 124 " =    1.454
peak=    4.842 closest distance to " CB  GLN A 183 " =    1.242
peak=    4.797 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.731 closest distance to " CB  GLN A 223 " =    1.520
peak=    4.729 closest distance to " O   HOH Z 232 " =    2.394
peak=    4.673 closest distance to " O   HOH Z 126 " =    2.015
peak=    4.647 closest distance to " O   HOH Z 209 " =    2.249
peak=    4.626 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.603 closest distance to " CB  SER A   3 " =    1.365
peak=    4.564 closest distance to " O   HOH Z  78 " =    1.653
peak=    4.537 closest distance to " ND2 ASN A 187 " =    1.594
peak=    4.532 closest distance to " CG  PRO A 198 " =    1.192
peak=    4.469 closest distance to " CB BVAL A  41 " =    1.187
peak=    4.469 closest distance to " CB  VAL A 230 " =    1.073
peak=    4.443 closest distance to " O   HOH Z 193 " =    1.641
peak=    4.407 closest distance to " CB  SER A  63 " =    1.277
peak=    4.366 closest distance to " O   HOH Z 425 " =    1.431
peak=    4.364 closest distance to " CB  ASN A 148 " =    1.340
peak=    4.325 closest distance to " O   SER A  87 " =    2.360
peak=    4.273 closest distance to " O   HOH Z 287 " =    1.994
peak=    4.270 closest distance to " CD2 LEU A 228 " =    1.186
peak=    4.248 closest distance to " CB  GLU A 128 " =    1.117
peak=    4.224 closest distance to " O   HOH Z 203 " =    1.742
peak=    4.204 closest distance to " O   HOH Z 316 " =    3.004
peak=    4.171 closest distance to " O   HOH Z 369 " =    2.223
peak=    4.166 closest distance to " O   HOH Z 272 " =    1.781
peak=    4.165 closest distance to " O   HOH Z 298 " =    1.731
peak=    4.159 closest distance to " N   PHE A 130 " =    1.308
peak=    4.159 closest distance to " O   HOH Z   7 " =    1.326
peak=    4.152 closest distance to " O   PRO A 198 " =    1.555
peak=    4.134 closest distance to " CB  SER A 216 " =    0.818
peak=    4.132 closest distance to " O   HOH Z   9 " =    1.817
peak=    4.131 closest distance to " O   HOH Z 422 " =    2.546
peak=    4.130 closest distance to " CB  TRP A 179 " =    1.315
peak=    4.066 closest distance to " O   HOH Z 234 " =    3.486
peak=    4.061 closest distance to " CB  TRP A 266 " =    1.028
peak=    4.048 closest distance to " O   HOH Z 380 " =    1.698
peak=    4.042 closest distance to " CG  PRO A 243 " =    1.164
peak=    4.042 closest distance to " O   HOH Z 346 " =    1.596
peak=    4.016 closest distance to " O   HOH Z  78 " =    2.110
peak=    4.011 closest distance to " NZ  LYS A 117 " =    3.066
peak=    3.999 closest distance to " OD1 ASN A  69 " =    2.514
peak=    3.990 closest distance to " OG BSER A 164 " =    2.123
peak=    3.990 closest distance to " O   HOH Z   2 " =    1.592
peak=    3.979 closest distance to " CB  TYR A 169 " =    0.720
peak=    3.979 closest distance to " O   HOH Z 371 " =    2.803
peak=    3.979 closest distance to " CG1BVAL A  72 " =    1.443
peak=    3.976 closest distance to " CG2 VAL A 257 " =    0.835
peak=    3.959 closest distance to " O   HOH Z 303 " =    2.214
peak=    3.938 closest distance to " O   HOH Z 222 " =    2.338
peak=    3.933 closest distance to " O   HOH Z 423 " =    1.404
peak=    3.930 closest distance to " CB  VAL A 265 " =    1.314
peak=    3.924 closest distance to " O   HOH Z 189 " =    2.639
peak=    3.914 closest distance to " CB  VAL A 202 " =    1.712
peak=    3.912 closest distance to " O   HOH Z 405 " =    1.337
peak=    3.893 closest distance to " O   HOH Z 263 " =    1.621
peak=    3.884 closest distance to " CB  GLU A 152 " =    1.230
peak=    3.882 closest distance to " O   HOH Z  55 " =    2.188
peak=    3.876 closest distance to " O   HOH Z 130 " =    2.355
peak=    3.870 closest distance to " O   HOH Z 144 " =    2.343
peak=    3.862 closest distance to " CA  TYR A  30 " =    0.976
peak=    3.860 closest distance to " O   HOH Z 425 " =    2.134
peak=    3.855 closest distance to " O   HOH Z 411 " =    3.659
peak=    3.844 closest distance to " CB  ARG A  79 " =    1.314
peak=    3.839 closest distance to " CA  ASN A 215 " =    1.148
peak=    3.824 closest distance to " CA  PHE A 283 " =    1.371
peak=    3.823 closest distance to " O   HOH Z 193 " =    1.677
peak=    3.819 closest distance to " O   HOH Z 175 " =    2.266
peak=    3.818 closest distance to " O   HOH Z  43 " =    1.945
peak=    3.816 closest distance to " O   HOH Z  44 " =    1.727
peak=    3.802 closest distance to " O   HOH Z 419 " =    1.994
peak=    3.797 closest distance to " O   HOH Z  61 " =    1.537
peak=    3.795 closest distance to " O   HOH Z 389 " =    1.782
peak=    3.792 closest distance to " O   HOH Z  65 " =    0.908
peak=    3.782 closest distance to " CB  GLU A 277 " =    3.503
peak=    3.775 closest distance to " CB  ARG A 139 " =    0.949
peak=    3.774 closest distance to " O   HOH Z  68 " =    2.115
peak=    3.761 closest distance to " O   HOH Z 403 " =    1.618
peak=    3.761 closest distance to " CG  LEU A 167 " =    1.188
peak=    3.755 closest distance to " C   ALA A 299 " =    0.963
peak=    3.750 closest distance to " O   HOH Z  30 " =    1.583
peak=    3.745 closest distance to " CG2 THR A 221 " =    1.288
peak=    3.740 closest distance to " CB  SER A  26 " =    1.663
peak=    3.737 closest distance to " CB  THR A 157 " =    1.071
peak=    3.737 closest distance to " O   HOH Z  97 " =    1.991
peak=    3.730 closest distance to " O   HOH Z 368 " =    1.966
peak=    3.729 closest distance to " CB  ASN A 142 " =    1.075
peak=    3.729 closest distance to " O   HOH Z   1 " =    1.749
peak=    3.728 closest distance to " O   HOH Z  10 " =    1.771
peak=    3.709 closest distance to " CG  GLN A  88 " =    1.149
peak=    3.708 closest distance to " OD2 ASP A 286 " =    2.658
peak=    3.703 closest distance to " CB  LYS A 117 " =    1.202
peak=    3.703 closest distance to " O   HOH Z  61 " =    1.565
peak=    3.698 closest distance to " O   HOH Z 146 " =    1.575
peak=    3.695 closest distance to " O   HOH Z 371 " =    1.704
peak=    3.693 closest distance to " O   HOH Z 128 " =    2.106
peak=    3.681 closest distance to " O   HOH Z 227 " =    1.780
peak=    3.676 closest distance to " O   HOH Z  63 " =    1.247
peak=    3.674 closest distance to " O   HOH Z  59 " =    1.655
peak=    3.671 closest distance to " CG  MET A 185 " =    1.205
peak=    3.658 closest distance to " CA  LYS A 117 " =    1.216
peak=    3.654 closest distance to " O   HOH Z 193 " =    1.886
peak=    3.649 closest distance to " O   HOH Z   3 " =    2.019
peak=    3.646 closest distance to " O   HOH Z 290 " =    0.989
peak=    3.641 closest distance to " NH2AARG A 190 " =    1.824
peak=    3.631 closest distance to " O   HOH Z 250 " =    1.403
peak=    3.625 closest distance to " N   ASN A 127 " =    1.394
peak=    3.622 closest distance to " CG1 ILE A  33 " =    1.307
peak=    3.610 closest distance to " OG  SER A  62 " =    2.937
peak=    3.610 closest distance to " OG BSER A  99 " =    2.151
peak=    3.606 closest distance to " CB  ASN A  39 " =    0.956
peak=    3.592 closest distance to " O   HOH Z 368 " =    3.616
peak=    3.588 closest distance to " O   HOH Z  40 " =    2.035
peak=    3.587 closest distance to " O   HOH Z 366 " =    2.813
peak=    3.579 closest distance to " O   HOH Z 180 " =    2.136
peak=    3.577 closest distance to " O   HOH Z 145 " =    3.427
peak=    3.577 closest distance to " CA  ALA A 158 " =    1.228
peak=    3.569 closest distance to " CB  ASN A 187 " =    1.238
peak=    3.560 closest distance to " NH1AARG A 145 " =    1.130
peak=    3.558 closest distance to " O   HOH Z 214 " =    2.212
peak=    3.557 closest distance to " O   HOH Z  93 " =    2.396
peak=    3.551 closest distance to " CG AARG A 275 " =    1.059
peak=    3.537 closest distance to " O   HOH Z 213 " =    2.118
peak=    3.537 closest distance to " O   HOH Z 344 " =    2.846
peak=    3.529 closest distance to " O   HOH Z 273 " =    2.793
peak=    3.528 closest distance to " O   HOH Z 359 " =    1.271
peak=    3.525 closest distance to " O   HOH Z 126 " =    1.472
peak=    3.511 closest distance to " CB  VAL A 296 " =    1.079
peak=    3.496 closest distance to " O   HOH Z 435 " =    2.066
peak=    3.490 closest distance to " CB  ARG A 190 " =    1.653
peak=    3.488 closest distance to " CE AMET A  47 " =    1.436
peak=    3.487 closest distance to " O   HOH Z 353 " =    2.452
peak=    3.482 closest distance to " O   HOH Z 145 " =    1.908
peak=    3.480 closest distance to " O   HOH Z 424 " =    2.355
peak=    3.480 closest distance to " CD1 ILE A  33 " =    1.662
peak=    3.473 closest distance to " CB  ARG A  79 " =    0.856
peak=    3.472 closest distance to " CA  THR A 264 " =    0.708
peak=    3.461 closest distance to " NH2BARG A 145 " =    2.105
peak=    3.460 closest distance to " CA  ALA A  21 " =    1.206
peak=    3.457 closest distance to " CB  LEU A 255 " =    0.740
peak=    3.452 closest distance to " CB  ASN A 148 " =    1.917
peak=    3.446 closest distance to " CA  ALA A  51 " =    0.951
peak=    3.440 closest distance to " O   HOH Z 392 " =    1.265
peak=    3.439 closest distance to " O   HOH Z 329 " =    3.847
peak=    3.438 closest distance to " CA  ALA A 248 " =    1.259
peak=    3.438 closest distance to " CA  LYS A 290 " =    1.234
peak=    3.437 closest distance to " CD BLYS A 290 " =    1.148
peak=    3.437 closest distance to " OE2 GLU A  53 " =    1.927
peak=    3.425 closest distance to " CG  LYS A  76 " =    1.747
peak=    3.417 closest distance to " N   ARG A 156 " =    1.295
peak=    3.415 closest distance to " N   SER A 146 " =    1.773
peak=    3.407 closest distance to " O   HOH Z 248 " =    1.604
peak=    3.406 closest distance to " O   HOH Z 128 " =    1.959
peak=    3.406 closest distance to " O   HOH Z 423 " =    1.627
peak=    3.405 closest distance to " OG  SER A  62 " =    2.783
peak=    3.404 closest distance to " O   HOH Z 334 " =    1.572
peak=    3.400 closest distance to " O   HOH Z 345 " =    3.315
peak=    3.394 closest distance to " CZ  PHE A 218 " =    1.097
peak=    3.391 closest distance to " CH2 TRP A 266 " =    1.094
peak=    3.377 closest distance to " O   HOH Z  88 " =    2.710
peak=    3.376 closest distance to " ND1 HIS A  86 " =    1.888
peak=    3.376 closest distance to " O   HOH Z 437 " =    2.182
peak=    3.373 closest distance to " NH1 ARG A 138 " =    1.106
peak=    3.371 closest distance to " CB  MET A  40 " =    0.838
peak=    3.370 closest distance to " CG  GLN A  89 " =    1.416
peak=    3.370 closest distance to " O   HOH Z 305 " =    3.384
peak=    3.368 closest distance to " NE AARG A 275 " =    1.290
peak=    3.368 closest distance to " CB  ALA A  34 " =    1.144
peak=    3.368 closest distance to " CB  HIS A 108 " =    0.829
peak=    3.368 closest distance to " CB  LEU A 143 " =    1.088
peak=    3.366 closest distance to " CG BARG A 102 " =    1.836
peak=    3.361 closest distance to " O   HOH Z 158 " =    3.119
peak=    3.358 closest distance to " O   HOH Z 368 " =    2.756
peak=    3.356 closest distance to " CG1 ILE A 151 " =    1.069
peak=    3.356 closest distance to " CD1 ILE A 106 " =    1.052
peak=    3.353 closest distance to " CB  GLN A  88 " =    1.286
peak=    3.353 closest distance to " O   HOH Z 284 " =    2.970
peak=    3.351 closest distance to " O   HOH Z   6 " =    1.979
peak=    3.339 closest distance to " N   ASN A  39 " =    1.181
peak=    3.337 closest distance to " NE2 GLN A  58 " =    3.585
peak=    3.324 closest distance to " CB  SER A  62 " =    1.136
peak=    3.323 closest distance to " O   HOH Z   1 " =    1.680
peak=    3.319 closest distance to " OE1 GLU A   2 " =    2.092
peak=    3.318 closest distance to " O   HOH Z 197 " =    3.171
peak=    3.307 closest distance to " CA  ARG A  36 " =    1.033
peak=    3.307 closest distance to " O   PRO A 198 " =    1.221
peak=    3.304 closest distance to " CB  ALA A 291 " =    1.429
peak=    3.302 closest distance to " CA  GLY A 267 " =    0.844
peak=    3.301 closest distance to " N   GLN A 278 " =    1.104
peak=    3.293 closest distance to " CB  PHE A 204 " =    1.035
peak=    3.293 closest distance to " ND2 ASN A 249 " =    0.794
peak=    3.289 closest distance to " O   HOH Z 245 " =    1.349
peak=    3.289 closest distance to " O   HOH Z 119 " =    1.613
peak=    3.288 closest distance to " O   HOH Z  47 " =    1.699
peak=    3.277 closest distance to " OG1 THR A 294 " =    2.419
peak=    3.277 closest distance to " O   HOH Z 424 " =    0.902
peak=    3.277 closest distance to " O   HOH Z 303 " =    1.746
peak=    3.276 closest distance to " O   HOH Z 383 " =    1.966
peak=    3.270 closest distance to " CB  THR A  52 " =    1.059
peak=    3.269 closest distance to " CA  LEU A 101 " =    1.548
peak=    3.264 closest distance to " CD  ARG A 159 " =    0.703
peak=    3.263 closest distance to " CD  ARG A 269 " =    1.053
peak=    3.261 closest distance to " O   HOH Z 357 " =    1.934
peak=    3.259 closest distance to " O   HOH Z 130 " =    1.905
peak=    3.254 closest distance to " CA  ASN A 127 " =    0.977
peak=    3.252 closest distance to " ND2 ASN A 110 " =    1.700
peak=    3.252 closest distance to " O   HOH Z  59 " =    2.083
peak=    3.249 closest distance to " CD2 TRP A 179 " =    1.396
peak=    3.247 closest distance to " CG  ARG A 269 " =    1.507
peak=    3.245 closest distance to " CD1 LEU A 300 " =    1.277
peak=    3.243 closest distance to " CE1 TYR A 186 " =    1.278
peak=    3.243 closest distance to " O   HOH Z 258 " =    2.258
peak=    3.241 closest distance to " O   HOH Z 109 " =    2.383
peak=    3.241 closest distance to " O   HOH Z 132 " =    2.312
peak=    3.241 closest distance to " O   HOH Z  78 " =    2.324
peak=    3.239 closest distance to " O   HOH Z 132 " =    1.300
peak=    3.239 closest distance to " O  BHOH Z 338 " =    2.496
peak=    3.238 closest distance to " O   HOH Z 426 " =    1.794
peak=    3.237 closest distance to " CA  ALA A 233 " =    0.957
peak=    3.226 closest distance to " CG1 ILE A  49 " =    1.339
peak=    3.226 closest distance to " O   HOH Z 272 " =    2.137
peak=    3.224 closest distance to " O   HOH Z 427 " =    1.435
peak=    3.223 closest distance to " CD2 LEU A 297 " =    0.957
peak=    3.222 closest distance to " NH1BARG A 145 " =    1.345
peak=    3.221 closest distance to " CB  TYR A  30 " =    1.698
peak=    3.221 closest distance to " O   HOH Z 133 " =    1.465
peak=    3.219 closest distance to " CB  GLN A  89 " =    1.263
peak=    3.214 closest distance to " CB  TRP A 150 " =    1.390
peak=    3.212 closest distance to " O   HOH Z 135 " =    1.888
peak=    3.211 closest distance to " CB  VAL A 250 " =    1.050
peak=    3.210 closest distance to " CG  GLN A  77 " =    2.451
peak=    3.209 closest distance to " CA  ARG A 102 " =    1.095
peak=    3.206 closest distance to " O   HOH Z 438 " =    2.042
peak=    3.206 closest distance to " O   HOH Z 423 " =    2.292
peak=    3.206 closest distance to " CB  ASP A 140 " =    0.843
peak=    3.205 closest distance to " N   SER A 135 " =    1.260
peak=    3.203 closest distance to " CD  LYS A 166 " =    1.391
peak=    3.202 closest distance to " CA  VAL A  41 " =    0.742
peak=    3.199 closest distance to " CB  ASN A 110 " =    1.030
peak=    3.192 closest distance to " O   HOH Z 145 " =    1.341
peak=    3.192 closest distance to " CG1 ILE A 263 " =    1.307
peak=    3.182 closest distance to " O   HOH Z 327 " =    1.536
peak=    3.181 closest distance to " O   HOH Z 280 " =    2.549
peak=    3.179 closest distance to " NZ  LYS A  76 " =    1.532
peak=    3.176 closest distance to " CG1BVAL A  72 " =    1.098
peak=    3.172 closest distance to " CG2 ILE A  20 " =    1.636
peak=    3.171 closest distance to " CD  ARG A  14 " =    1.519
peak=    3.169 closest distance to " O   HOH Z 251 " =    1.707
peak=    3.165 closest distance to " OG ASER A  99 " =    1.518
peak=    3.162 closest distance to " OG1 THR A 221 " =    1.286
peak=    3.162 closest distance to " N   VAL A 126 " =    1.199
peak=    3.161 closest distance to " CD2 HIS A  81 " =    0.962
peak=    3.161 closest distance to " O   HOH Z  85 " =    1.347
peak=    3.159 closest distance to " CG2 ILE A 120 " =    1.126
peak=    3.155 closest distance to " CA  SER A  87 " =    1.001
peak=    3.148 closest distance to " O   HOH Z 110 " =    1.471
peak=    3.144 closest distance to " NZ  LYS A  48 " =    2.106
peak=    3.141 closest distance to " O   HOH Z   4 " =    1.560
peak=    3.139 closest distance to " O   HOH Z   1 " =    4.556
peak=    3.138 closest distance to " CG  GLN A 278 " =    1.294
peak=    3.133 closest distance to " O   HOH Z  89 " =    2.163
peak=    3.131 closest distance to " CD2 LEU A 255 " =    1.436
peak=    3.120 closest distance to " N   ALA A 233 " =    0.957
peak=    3.118 closest distance to " CG  LEU A 281 " =    0.982
peak=    3.116 closest distance to " O   HOH Z 153 " =    3.618
peak=    3.116 closest distance to " CB  GLN A 278 " =    0.975
peak=    3.116 closest distance to " CB  ASN A 215 " =    1.107
peak=    3.091 closest distance to " CB  ALA A   1 " =    4.741
peak=    3.082 closest distance to " CB  ALA A 180 " =    1.267
peak=    3.078 closest distance to " CA  MET A 105 " =    0.929
peak=    3.077 closest distance to " O   TYR A 116 " =    1.256
peak=    3.072 closest distance to " CB  LEU A 300 " =    0.870
peak=    3.068 closest distance to " CG  MET A 113 " =    1.018
peak=    3.052 closest distance to " CG BARG A 190 " =    1.169
peak=    3.046 closest distance to " CB  ILE A  20 " =    1.442
peak=    3.040 closest distance to " O   HOH Z 172 " =    3.226
peak=    3.027 closest distance to " CB  LYS A 290 " =    1.167

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.783 - 5.388
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 215
   mapped sites are within: 0.783 - 5.388

peak=   -4.732 closest distance to " CG2 VAL A 230 " =    0.785
peak=   -4.670 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.580 closest distance to " CD1 LEU A 255 " =    2.783
peak=   -4.550 closest distance to " OG BSER A 134 " =    1.261
peak=   -4.419 closest distance to " CD  ARG A  14 " =    3.226
peak=   -4.250 closest distance to " C   HIS A 108 " =    1.175
peak=   -4.250 closest distance to " O   HOH Z 266 " =    4.777
peak=   -4.214 closest distance to " CB  PRO A 243 " =    2.664
peak=   -4.166 closest distance to " O   HOH Z  43 " =    1.961
peak=   -4.029 closest distance to " O   HOH Z  65 " =    1.174
peak=   -4.024 closest distance to " O   HOH Z 185 " =    2.148
peak=   -4.002 closest distance to " O   VAL A  67 " =    2.554
peak=   -3.960 closest distance to " CE2 PHE A 218 " =    2.476
peak=   -3.954 closest distance to " O   HOH Z 191 " =    5.388
peak=   -3.949 closest distance to " NH2 ARG A  79 " =    1.875
peak=   -3.873 closest distance to " CB  ALA A 248 " =    2.055
peak=   -3.871 closest distance to " CG2 VAL A 296 " =    1.942
peak=   -3.866 closest distance to " O   HOH Z  11 " =    1.863
peak=   -3.864 closest distance to " O   PRO A 198 " =    1.231
peak=   -3.851 closest distance to " CG  GLN A 223 " =    2.008
peak=   -3.850 closest distance to " O   HOH Z 231 " =    1.935
peak=   -3.845 closest distance to " OG  SER A   3 " =    1.637
peak=   -3.837 closest distance to " O   HOH Z 290 " =    1.127
peak=   -3.828 closest distance to " O   HOH Z 351 " =    1.523
peak=   -3.825 closest distance to " N   GLN A  58 " =    1.813
peak=   -3.790 closest distance to " O   VAL A  67 " =    2.846
peak=   -3.782 closest distance to " O   HOH Z  52 " =    1.378
peak=   -3.763 closest distance to " CB  ASN A  39 " =    2.234
peak=   -3.762 closest distance to " O   HOH Z  60 " =    2.309
peak=   -3.761 closest distance to " O   HOH Z 114 " =    2.892
peak=   -3.725 closest distance to " N   THR A 157 " =    1.381
peak=   -3.707 closest distance to " CZ  PHE A  59 " =    1.456
peak=   -3.706 closest distance to " O   HOH Z 359 " =    1.662
peak=   -3.700 closest distance to " O   HOH Z 140 " =    1.483
peak=   -3.691 closest distance to " O   HOH Z 389 " =    1.906
peak=   -3.686 closest distance to " N   ALA A  43 " =    2.594
peak=   -3.675 closest distance to " CE2 TYR A  30 " =    2.781
peak=   -3.673 closest distance to " O   ALA A 161 " =    1.669
peak=   -3.669 closest distance to " CB  TYR A  15 " =    2.127
peak=   -3.666 closest distance to " O   SER A  22 " =    2.315
peak=   -3.637 closest distance to " O   SER A 135 " =    1.465
peak=   -3.628 closest distance to " O   PRO A 163 " =    2.015
peak=   -3.625 closest distance to " CB  ALA A   7 " =    2.065
peak=   -3.616 closest distance to " CB  PHE A 192 " =    1.784
peak=   -3.609 closest distance to " CZ2 TRP A 274 " =    0.879
peak=   -3.604 closest distance to " CD2 LEU A   5 " =    1.107
peak=   -3.595 closest distance to " CD1 LEU A 228 " =    2.099
peak=   -3.592 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.592 closest distance to " O   HOH Z 427 " =    1.502
peak=   -3.578 closest distance to " O   HOH Z 377 " =    2.137
peak=   -3.577 closest distance to " ND2 ASN A 187 " =    1.479
peak=   -3.574 closest distance to " O   HOH Z 111 " =    4.257
peak=   -3.574 closest distance to " CE  MET A 105 " =    2.395
peak=   -3.572 closest distance to " CB  ALA A 244 " =    2.075
peak=   -3.570 closest distance to " CA  GLY A 133 " =    1.973
peak=   -3.568 closest distance to " CA  GLY A  98 " =    1.842
peak=   -3.558 closest distance to " O   HOH Z  13 " =    1.736
peak=   -3.556 closest distance to " O   HOH Z 389 " =    1.477
peak=   -3.554 closest distance to " C   MET A 188 " =    1.477
peak=   -3.549 closest distance to " O   HOH Z 407 " =    3.062
peak=   -3.547 closest distance to " CA  GLY A 203 " =    2.292
peak=   -3.546 closest distance to " N   ALA A 248 " =    1.586
peak=   -3.546 closest distance to " ND2 ASN A 249 " =    2.447
peak=   -3.543 closest distance to " CB  ALA A 161 " =    2.514
peak=   -3.538 closest distance to " O   HOH Z 377 " =    1.061
peak=   -3.533 closest distance to " OG  SER A  87 " =    1.241
peak=   -3.531 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.529 closest distance to " CG  GLN A  58 " =    1.111
peak=   -3.526 closest distance to " O   HOH Z 211 " =    1.495
peak=   -3.517 closest distance to " OD2 ASP A 191 " =    1.281
peak=   -3.510 closest distance to " CE1 PHE A  59 " =    1.973
peak=   -3.501 closest distance to " N   ALA A 226 " =    2.078
peak=   -3.494 closest distance to " O   HOH Z 423 " =    2.320
peak=   -3.492 closest distance to " ND2 ASN A 252 " =    1.789
peak=   -3.491 closest distance to " CB  ASP A 132 " =    2.325
peak=   -3.483 closest distance to " CD2 LEU A 237 " =    2.659
peak=   -3.482 closest distance to " OG  SER A   3 " =    1.185
peak=   -3.476 closest distance to " CA  ASN A 127 " =    1.342
peak=   -3.473 closest distance to " O   HOH Z 166 " =    1.641
peak=   -3.473 closest distance to " CZ  TYR A 169 " =    1.706
peak=   -3.470 closest distance to " CB  PRO A  90 " =    1.575
peak=   -3.464 closest distance to " O   HOH Z 103 " =    1.758
peak=   -3.463 closest distance to " O   HOH Z 394 " =    1.461
peak=   -3.457 closest distance to " O   HOH Z 198 " =    2.137
peak=   -3.456 closest distance to " ND2 ASN A  45 " =    1.084
peak=   -3.455 closest distance to " CG1 VAL A 112 " =    2.972
peak=   -3.453 closest distance to " N   SER A 276 " =    1.220
peak=   -3.435 closest distance to " CE BMET A  47 " =    1.348
peak=   -3.435 closest distance to " C   ASN A 285 " =    2.165
peak=   -3.432 closest distance to " O   HOH Z 359 " =    3.408
peak=   -3.416 closest distance to " OG  SER A 206 " =    1.687
peak=   -3.414 closest distance to " O   HOH Z 134 " =    3.271
peak=   -3.412 closest distance to " C   LEU A 222 " =    0.783
peak=   -3.410 closest distance to " O   HOH Z  47 " =    1.579
peak=   -3.402 closest distance to " CG  TRP A 266 " =    1.953
peak=   -3.400 closest distance to " N   VAL A  72 " =    1.596
peak=   -3.390 closest distance to " CG  PHE A 283 " =    2.610
peak=   -3.389 closest distance to " CG2 VAL A 202 " =    2.588
peak=   -3.385 closest distance to " CZ3 TRP A 179 " =    1.257
peak=   -3.378 closest distance to " CD2 TYR A 293 " =    1.901
peak=   -3.376 closest distance to " N   HIS A 115 " =    2.172
peak=   -3.375 closest distance to " O   GLY A  80 " =    2.441
peak=   -3.374 closest distance to " O   HOH Z 131 " =    4.017
peak=   -3.372 closest distance to " CB  CYS A 201 " =    2.449
peak=   -3.372 closest distance to " CD1 LEU A 101 " =    2.820
peak=   -3.371 closest distance to " CG1 VAL A 230 " =    1.831
peak=   -3.368 closest distance to " CB  ALA A  43 " =    2.401
peak=   -3.364 closest distance to " OG  SER A  63 " =    1.157
peak=   -3.363 closest distance to " O   HOH Z 350 " =    1.950
peak=   -3.362 closest distance to " O   PHE A 218 " =    1.499
peak=   -3.361 closest distance to " CG  GLN A 278 " =    2.099
peak=   -3.356 closest distance to " O   HOH Z 348 " =    1.785
peak=   -3.355 closest distance to " CG1 VAL A 250 " =    2.670
peak=   -3.351 closest distance to " CB  PRO A 163 " =    2.455
peak=   -3.349 closest distance to " O   HOH Z 417 " =    2.494
peak=   -3.344 closest distance to " O   HOH Z 388 " =    2.202
peak=   -3.344 closest distance to " OG  SER A  62 " =    4.431
peak=   -3.343 closest distance to " O   HOH Z   9 " =    1.503
peak=   -3.341 closest distance to " O   HOH Z  90 " =    2.757
peak=   -3.340 closest distance to " CA  GLY A 241 " =    2.193
peak=   -3.337 closest distance to " OE1 GLN A  88 " =    1.135
peak=   -3.334 closest distance to " CG  GLU A 152 " =    1.810
peak=   -3.328 closest distance to " CE  LYS A 166 " =    1.274
peak=   -3.327 closest distance to " CG2 THR A 178 " =    2.088
peak=   -3.327 closest distance to " NH1 ARG A  56 " =    2.466
peak=   -3.326 closest distance to " CD1 LEU A 101 " =    2.272
peak=   -3.325 closest distance to " O   HOH Z 369 " =    2.101
peak=   -3.323 closest distance to " OE1 GLU A 277 " =    2.253
peak=   -3.322 closest distance to " O   PRO A 243 " =    2.465
peak=   -3.318 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.315 closest distance to " O   VAL A 189 " =    2.591
peak=   -3.315 closest distance to " O   HOH Z 102 " =    1.657
peak=   -3.313 closest distance to " OG ASER A 134 " =    1.081
peak=   -3.311 closest distance to " N   MET A 188 " =    1.817
peak=   -3.306 closest distance to " CD1 TYR A 247 " =    2.681
peak=   -3.305 closest distance to " OD1 ASN A 148 " =    1.550
peak=   -3.302 closest distance to " O   HOH Z 134 " =    3.535
peak=   -3.294 closest distance to " CB  ALA A 291 " =    2.400
peak=   -3.291 closest distance to " O   SER A 271 " =    1.991
peak=   -3.281 closest distance to " O   HOH Z 313 " =    1.709
peak=   -3.278 closest distance to " CA  GLY A  35 " =    1.991
peak=   -3.277 closest distance to " OE2 GLU A 152 " =    1.159
peak=   -3.277 closest distance to " N   PHE A  59 " =    2.184
peak=   -3.274 closest distance to " CE1 PHE A  59 " =    2.032
peak=   -3.271 closest distance to " CE  LYS A  76 " =    2.801
peak=   -3.270 closest distance to " CA  ASP A  27 " =    2.453
peak=   -3.264 closest distance to " O   HOH Z 165 " =    2.212
peak=   -3.262 closest distance to " CZ  TYR A 172 " =    1.847
peak=   -3.255 closest distance to " O   HOH Z 295 " =    1.653
peak=   -3.254 closest distance to " CB  ALA A 248 " =    2.365
peak=   -3.253 closest distance to " CG2 THR A  42 " =    1.717
peak=   -3.250 closest distance to " O   HOH Z 281 " =    2.916
peak=   -3.246 closest distance to " OD1 ASP A 191 " =    1.755
peak=   -3.239 closest distance to " NE2 GLN A 278 " =    1.941
peak=   -3.234 closest distance to " ND2 ASN A  45 " =    1.451
peak=   -3.233 closest distance to " O   HOH Z 385 " =    2.047
peak=   -3.228 closest distance to " OXT GLY A 302 " =    2.992
peak=   -3.227 closest distance to " C   ALA A 158 " =    1.272
peak=   -3.226 closest distance to " CG1 VAL A 197 " =    2.275
peak=   -3.221 closest distance to " OG1 THR A 178 " =    1.154
peak=   -3.217 closest distance to " O   HOH Z 207 " =    2.095
peak=   -3.217 closest distance to " O   GLY A 211 " =    1.216
peak=   -3.217 closest distance to " CG1 VAL A 268 " =    2.746
peak=   -3.212 closest distance to " O   HOH Z  71 " =    1.283
peak=   -3.211 closest distance to " OD2 ASP A 171 " =    2.099
peak=   -3.205 closest distance to " O   HOH Z 426 " =    1.753
peak=   -3.204 closest distance to " O   SER A 210 " =    1.950
peak=   -3.203 closest distance to " OG  SER A 245 " =    1.239
peak=   -3.200 closest distance to " CB  ALA A 291 " =    2.152
peak=   -3.200 closest distance to " OG  SER A  97 " =    2.198
peak=   -3.198 closest distance to " O   SER A  95 " =    1.453
peak=   -3.194 closest distance to " ND2 ASN A  39 " =    1.400
peak=   -3.192 closest distance to " CA  GLY A  57 " =    2.154
peak=   -3.191 closest distance to " SD BMET A  47 " =    2.961
peak=   -3.185 closest distance to " CB  ALA A   1 " =    2.830
peak=   -3.171 closest distance to " O   HOH Z 210 " =    1.074
peak=   -3.167 closest distance to " ND2 ASN A  69 " =    1.747
peak=   -3.166 closest distance to " O   HOH Z  97 " =    1.536
peak=   -3.165 closest distance to " OD1 ASN A 301 " =    2.085
peak=   -3.163 closest distance to " CB  SER A 210 " =    1.207
peak=   -3.160 closest distance to " CB  ASN A  69 " =    1.196
peak=   -3.159 closest distance to " OG  SER A  62 " =    1.549
peak=   -3.157 closest distance to " OH  TYR A 214 " =    1.151
peak=   -3.152 closest distance to " C   VAL A 265 " =    0.872
peak=   -3.150 closest distance to " O   HOH Z 166 " =    1.887
peak=   -3.147 closest distance to " O   GLU A  44 " =    1.689
peak=   -3.145 closest distance to " CD2 PHE A  61 " =    1.911
peak=   -3.138 closest distance to " NH1AARG A 275 " =    1.911
peak=   -3.134 closest distance to " O   HOH Z 139 " =    2.996
peak=   -3.132 closest distance to " ND2 ASN A  60 " =    1.642
peak=   -3.131 closest distance to " O   HOH Z 393 " =    3.412
peak=   -3.129 closest distance to " O   HOH Z 435 " =    2.032
peak=   -3.122 closest distance to " NH2AARG A 275 " =    5.206
peak=   -3.121 closest distance to " O   GLN A 240 " =    1.659
peak=   -3.115 closest distance to " CH2 TRP A 179 " =    1.948
peak=   -3.101 closest distance to " NH1BARG A 145 " =    3.577
peak=   -3.100 closest distance to " CG  PRO A 163 " =    2.577
peak=   -3.097 closest distance to " O   HOH Z 364 " =    2.114
peak=   -3.095 closest distance to " O   HOH Z  93 " =    2.006
peak=   -3.086 closest distance to " O   HOH Z 250 " =    1.424
peak=   -3.083 closest distance to " CB  ASP A 132 " =    2.304
peak=   -3.081 closest distance to " CD1 PHE A  61 " =    2.670
peak=   -3.078 closest distance to " O   HOH Z 216 " =    1.929
peak=   -3.073 closest distance to " O   HOH Z 189 " =    1.920
peak=   -3.073 closest distance to " N   GLN A  77 " =    1.585
peak=   -3.071 closest distance to " O   HOH Z 137 " =    1.543
peak=   -3.069 closest distance to " O   ALA A  51 " =    1.324
peak=   -3.067 closest distance to " O   HOH Z 313 " =    1.065
peak=   -3.059 closest distance to " CE  MET A  93 " =    1.156
peak=   -3.058 closest distance to " CB  GLN A  11 " =    1.894
peak=   -3.055 closest distance to " CB  TYR A 172 " =    2.392
peak=   -3.053 closest distance to " CA  ASP A  27 " =    2.447
peak=   -3.047 closest distance to " O   VAL A 125 " =    2.245
peak=   -3.044 closest distance to " O   HOH Z  28 " =    2.170

================= 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    :  0.4563 0.4454   6.257623e+00   6.240629e+00
   1_bss:  0.4475 0.4333   6.249776e+00   6.226490e+00
   1_xyz:  0.3570 0.3794   6.105476e+00   6.137482e+00
   1_adp:  0.3058 0.3484   5.992685e+00   6.083922e+00
   1_occ:  0.3053 0.3476   5.991538e+00   6.084509e+00
   2_bss:  0.3005 0.3406   5.988994e+00   6.076589e+00
   2_xyz:  0.2079 0.2571   5.669255e+00   5.832593e+00
   2_adp:  0.1833 0.2365   5.563791e+00   5.758590e+00
   2_occ:  0.1830 0.2362   5.562579e+00   5.757502e+00
   3_bss:  0.1818 0.2339   5.558694e+00   5.752493e+00
   3_xyz:  0.1383 0.1889   5.325816e+00   5.558281e+00
   3_adp:  0.1278 0.1775   5.256866e+00   5.494817e+00
   3_occ:  0.1276 0.1772   5.256372e+00   5.494105e+00
   4_bss:  0.1279 0.1770   5.255716e+00   5.492558e+00
   4_xyz:  0.1181 0.1651   5.187955e+00   5.432703e+00
   4_adp:  0.1158 0.1634   5.173741e+00   5.419857e+00
   4_occ:  0.1157 0.1632   5.173135e+00   5.418872e+00
   5_bss:  0.1157 0.1632   5.173031e+00   5.418794e+00
   5_xyz:  0.1122 0.1607   5.152303e+00   5.403294e+00
   5_adp:  0.1114 0.1594   5.146623e+00   5.397926e+00
   5_occ:  0.1113 0.1593   5.146269e+00   5.397360e+00
   5_bss:  0.1113 0.1593   5.146111e+00   5.397216e+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:  0.370   5.073   7.258  10.345   7.953   0.000   0.000   0.000
   1_xyz:  0.370   5.073   7.258  10.345   7.953   0.000   0.000   0.000
   1_adp:  0.370   5.073   7.258  10.345   7.953   0.000   0.000   0.000
   1_occ:  0.370   5.073   7.258  10.345   7.953   0.000   0.000   0.000
   2_bss:  0.343  29.129   3.733   5.732   4.728   0.000   0.000   0.000
   2_xyz:  0.343  29.129   3.733   5.732   4.728   0.000   0.000   0.000
   2_adp:  0.343  29.129   3.733   5.732   4.728   0.000   0.000   0.000
   2_occ:  0.343  29.129   3.733   5.732   4.728   0.000   0.000   0.000
   3_bss:  0.318  32.949   2.631   3.433   3.950   0.000   0.000   0.000
   3_xyz:  0.318  32.949   2.631   3.433   3.950   0.000   0.000   0.000
   3_adp:  0.318  32.949   2.631   3.433   3.950   0.000   0.000   0.000
   3_occ:  0.318  32.949   2.631   3.433   3.950   0.000   0.000   0.000
   4_bss:  0.317  36.540   2.412   2.728   3.757   0.000   0.000   0.000
   4_xyz:  0.317  36.540   2.412   2.728   3.757   0.000   0.000   0.000
   4_adp:  0.317  36.540   2.412   2.728   3.757   0.000   0.000   0.000
   4_occ:  0.317  36.540   2.412   2.728   3.757   0.000   0.000   0.000
   5_bss:  0.318  36.540   2.542   2.701   3.885   0.000   0.000   0.000
   5_xyz:  0.318  36.540   2.542   2.701   3.885   0.000   0.000   0.000
   5_adp:  0.318  36.540   2.542   2.701   3.885   0.000   0.000   0.000
   5_occ:  0.318  36.540   2.542   2.701   3.885   0.000   0.000   0.000
   5_bss:  0.321  42.244  -0.480  -0.389   0.869   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.993 0.4837  0.5563    61084.443
   1_bss:  52.867 0.4831  0.7085    58106.236
   1_xyz:  42.470 0.6120  0.8837    41136.521
   1_adp:  36.751 0.6817  1.0027    33944.558
   1_occ:  36.808 0.6810  1.0006    33931.983
   2_bss:  36.146 0.6885  0.8844    32953.909
   2_xyz:  25.658 0.8042  0.9950    16928.447
   2_adp:  22.873 0.8336  1.0140    14265.996
   2_occ:  22.825 0.8341  1.0140    14213.120
   3_bss:  22.615 0.8360  0.9657    13985.592
   3_xyz:  17.788 0.8820  0.9927     8967.145
   3_adp:  16.327 0.8952  0.9944     7904.276
   3_occ:  16.321 0.8953  0.9941     7883.346
   4_bss:  16.280 0.8956  0.9805     7860.780
   4_xyz:  14.888 0.9075  0.9861     6889.446
   4_adp:  14.583 0.9102  0.9828     6732.886
   4_occ:  14.564 0.9104  0.9827     6715.853
   5_bss:  14.561 0.9104  0.9856     6715.456
   5_xyz:  14.211 0.9134  0.9856     6522.633
   5_adp:  14.064 0.9148  0.9815     6453.632
   5_occ:  14.053 0.9149  0.9814     6442.033
   5_bss:  14.048 0.9149  0.9853     6442.179
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3251e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3251e+01
   1_xyz:   1.602  0.012  0.102 18.022  0.006  4.117   1.2790e-01
   1_adp:   1.602  0.012  0.102 18.022  0.006  4.117   1.2790e-01
   1_occ:   1.602  0.012  0.102 18.022  0.006  4.117   1.2790e-01
   2_bss:   1.602  0.012  0.102 18.022  0.006  4.117   1.2790e-01
   2_xyz:   1.122  0.008  0.083 15.992  0.005  4.117   7.7948e-02
   2_adp:   1.122  0.008  0.083 15.992  0.005  4.117   7.7948e-02
   2_occ:   1.122  0.008  0.083 15.992  0.005  4.117   7.7948e-02
   3_bss:   1.122  0.008  0.083 15.992  0.005  4.117   7.7948e-02
   3_xyz:   1.022  0.006  0.076 15.913  0.003  4.115   6.3219e-02
   3_adp:   1.022  0.006  0.076 15.913  0.003  4.115   6.3219e-02
   3_occ:   1.022  0.006  0.076 15.913  0.003  4.115   6.3219e-02
   4_bss:   1.022  0.006  0.076 15.913  0.003  4.115   6.3219e-02
   4_xyz:   0.932  0.005  0.073 15.531  0.003  4.111   5.5833e-02
   4_adp:   0.932  0.005  0.073 15.531  0.003  4.111   5.5833e-02
   4_occ:   0.932  0.005  0.073 15.531  0.003  4.111   5.5833e-02
   5_bss:   0.932  0.005  0.073 15.531  0.003  4.111   5.5833e-02
   5_xyz:   0.935  0.005  0.072 15.314  0.003  4.115   5.4729e-02
   5_adp:   0.935  0.005  0.072 15.314  0.003  4.115   5.4729e-02
   5_occ:   0.935  0.005  0.072 15.314  0.003  4.115   5.4729e-02
   5_bss:   0.935  0.005  0.072 15.314  0.003  4.115   5.4729e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9027e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9027e+00
   1_xyz:  12.734  0.159  0.409 88.499  0.033  2.229   9.1875e-02
   1_adp:  12.734  0.159  0.409 88.499  0.033  2.229   9.1875e-02
   1_occ:  12.734  0.159  0.409 88.499  0.033  2.229   9.1875e-02
   2_bss:  12.734  0.159  0.409 88.499  0.033  2.229   9.1875e-02
   2_xyz:   8.025  0.098  0.332 87.820  0.034  2.243   6.5326e-02
   2_adp:   8.025  0.098  0.332 87.820  0.034  2.243   6.5326e-02
   2_occ:   8.025  0.098  0.332 87.820  0.034  2.243   6.5326e-02
   3_bss:   8.025  0.098  0.332 87.820  0.034  2.243   6.5326e-02
   3_xyz:   8.140  0.046  0.342 82.239  0.030  2.287   6.2564e-02
   3_adp:   8.140  0.046  0.342 82.239  0.030  2.287   6.2564e-02
   3_occ:   8.140  0.046  0.342 82.239  0.030  2.287   6.2564e-02
   4_bss:   8.140  0.046  0.342 82.239  0.030  2.287   6.2564e-02
   4_xyz:   6.440  0.037  0.341 83.672  0.034  2.332   4.9399e-02
   4_adp:   6.440  0.037  0.341 83.672  0.034  2.332   4.9399e-02
   4_occ:   6.440  0.037  0.341 83.672  0.034  2.332   4.9399e-02
   5_bss:   6.440  0.037  0.341 83.672  0.034  2.332   4.9399e-02
   5_xyz:   6.341  0.044  0.331 84.156  0.036  2.324   3.4182e-02
   5_adp:   6.341  0.044  0.331 84.156  0.036  2.324   3.4182e-02
   5_occ:   6.341  0.044  0.331 84.156  0.036  2.324   3.4182e-02
   5_bss:   6.341  0.044  0.331 84.156  0.036  2.324   3.4182e-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:  73.58   0.00  11.94  73.48   0.00   9.37  73.58   0.00  25.96
   1_occ:  73.58   0.00  11.94  73.48   0.00   9.37  73.58   0.00  25.96
   2_bss:  73.58   0.00  11.94  73.48   0.00   9.37  73.58   0.00  25.96
   2_xyz:  73.58   0.00  11.94  73.48   0.00   9.37  73.58   0.00  25.96
   2_adp:  79.71   0.00  11.92  79.71   0.00   8.38  77.33   0.61  31.22
   2_occ:  79.71   0.00  11.92  79.71   0.00   8.38  77.33   0.61  31.22
   3_bss:  79.71   0.00  11.92  79.71   0.00   8.38  77.33   0.61  31.22
   3_xyz:  79.71   0.00  11.92  79.71   0.00   8.38  77.33   0.61  31.22
   3_adp:  83.41   0.00  12.29  83.41   0.00   8.06  80.32   0.98  35.31
   3_occ:  83.41   0.00  12.29  83.41   0.00   8.06  80.32   0.98  35.31
   4_bss:  83.41   0.00  12.29  83.41   0.00   8.06  80.32   0.98  35.31
   4_xyz:  83.41   0.00  12.29  83.41   0.00   8.06  80.32   0.98  35.31
   4_adp:  89.11   0.00  12.33  89.11   0.00   7.96  83.40   1.31  36.16
   4_occ:  89.11   0.00  12.33  89.11   0.00   7.96  83.40   1.31  36.16
   5_bss:  89.11   0.00  12.33  89.11   0.00   7.96  83.40   1.31  36.16
   5_xyz:  89.11   0.00  12.33  89.11   0.00   7.96  83.40   1.31  36.16
   5_adp:  93.37   0.00  12.17  93.37   0.00   7.82  84.63   1.37  35.84
   5_occ:  93.37   0.00  12.17  93.37   0.00   7.82  84.63   1.37  35.84
   5_bss:  96.52   3.15  15.32  96.52   3.15  10.97  87.77   4.51  38.99
------------------------------------------------------------------------
 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:    1.217    0.014    0.405
   1_adp:    1.217    0.014    0.405
   1_occ:    1.217    0.014    0.405
   2_bss:    1.217    0.014    0.405
   2_xyz:    1.383    0.032    0.570
   2_adp:    1.383    0.032    0.570
   2_occ:    1.383    0.032    0.570
   3_bss:    1.383    0.032    0.570
   3_xyz:    1.573    0.036    0.620
   3_adp:    1.573    0.036    0.620
   3_occ:    1.573    0.036    0.620
   4_bss:    1.573    0.036    0.620
   4_xyz:    1.689    0.036    0.642
   4_adp:    1.689    0.036    0.642
   4_occ:    1.689    0.036    0.642
   5_bss:    1.689    0.036    0.642
   5_xyz:    1.709    0.073    0.657
   5_adp:    1.709    0.073    0.657
   5_occ:    1.709    0.073    0.657
   5_bss:    1.709    0.073    0.657
------------------------------------------------------------------------

CPU time actual refinement: 350.85


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_510/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_510/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_510/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_510/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_510/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.70 
  Macro-tasks:
    bulk solvent and scale       = 42.03  
    individual site refinement   = 147.46 
    weights calculation          = 34.52  
    collect and process          = 6.72   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 230.88 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 107.99 
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.66 
    fmodel                         = 7.71   
    r_factors                      = 0.25   
    phase_errors                   = 10.82  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 258.98 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.817 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    682 calls, 107.60 s
gradients_fft:          627 calls, 106.07 s

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

# Date 2008-01-16 Time 01:45:49 PST -0800 (1200476749.24 s)
Start R-work = 0.4563, R-free = 0.4454 (no bulk solvent and anisotropic scale)
Final R-work = 0.1287, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.4475, R-free = 0.4333
Final R-work = 0.1113, R-free = 0.1593