# Date 2008-01-16 Time 03:33:14 PST -0800 (1200483194.36 s)
#phil __OFF__

Command line arguments: "../1283.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 = 6756
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1283

-------------------------------------------------------------------------------
  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: (72.0062, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 2.01158
Completeness in resolution range: 0.964928
Completeness with d_max=infinity: 0.96199

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   2.0116

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: (72.0062, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 2.01158
Completeness in resolution range: 0.964928
Completeness with d_max=infinity: 0.96199

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.3047 [2124/2149]  1914   210   9.9%
  bin  2:  4.3047 -  3.4294 [2049/2069]  1843   206  10.1%
  bin  3:  3.4294 -  2.9996 [2030/2049]  1825   205  10.1%
  bin  4:  2.9996 -  2.7270 [2006/2036]  1810   196   9.8%
  bin  5:  2.7270 -  2.5325 [1999/2018]  1800   199  10.0%
  bin  6:  2.5325 -  2.3838 [1986/2011]  1781   205  10.3%
  bin  7:  2.3838 -  2.2648 [1943/1971]  1749   194  10.0%
  bin  8:  2.2648 -  2.1665 [1990/2026]  1790   200  10.1%
  bin  9:  2.1665 -  2.0833 [1955/1997]  1762   193   9.9%
  bin 10:  2.0833 -  2.0116 [1507/1975]  1356   151  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1283/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:
        1.58 -     2.24: 4
        2.24 -     2.91: 1380
        2.91 -     3.57: 4381
        3.57 -     4.24: 9019
        4.24 -     4.90: 13028
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.580 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.151 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27807 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_1283/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1283/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 72.00625 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4701   r_free= 0.4580   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.272112                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.8014 0.99   1390  155 0.3856 0.3574      6.5807      6.5033|
|  2:  4.8014 -  3.8307 0.99   1329  147 0.3802 0.4034      6.7687      6.7892|
|  3:  3.8307 -  3.3523 0.99   1306  142 0.4214 0.3910      6.6439      6.6664|
|  4:  3.3523 -  3.0484 0.99   1303  153 0.4509 0.4006      6.5188      6.4244|
|  5:  3.0484 -  2.8314 0.99   1293  142 0.4930 0.5016      6.3627      6.4004|
|  6:  2.8314 -  2.6654 0.99   1281  136 0.4953 0.5229      6.2736      6.2181|
|  7:  2.6654 -  2.5325 0.99   1290  141 0.5208 0.5043      6.2452      6.2621|
|  8:  2.5325 -  2.4227 0.98   1262  148 0.5332 0.4824       6.181      6.1448|
|  9:  2.4227 -  2.3298 0.98   1266  140 0.5025 0.5479      6.1169      6.1415|
| 10:  2.3298 -  2.2496 1.00   1277  140 0.5165 0.4744      6.1111      6.1162|
| 11:  2.2496 -  2.1795 0.97   1252  139 0.5186 0.5058      6.0415      6.0513|
| 12:  2.1795 -  2.1174 0.98   1256  140 0.5231 0.5476      5.9846      6.0363|
| 13:  2.1174 -  2.0618 1.00   1286  142 0.5288 0.4704      5.8972      5.8092|
| 14:  2.0618 -  2.0116 0.67    839   94 0.5282 0.4600      5.8772      5.7504|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.8014  1390   155  0.72  32.14   0.79     0.75      63678.12|
|  2:  4.8014 -  3.8307  1329   147  0.73  32.20   0.88     0.78      91208.91|
|  3:  3.8307 -  3.3523  1306   142  0.65  39.97   0.83     0.73      98741.73|
|  4:  3.3523 -  3.0484  1303   153  0.56  46.99   0.81     0.64      90544.97|
|  5:  3.0484 -  2.8314  1293   142  0.46  55.23   0.72     0.54      77194.45|
|  6:  2.8314 -  2.6654  1281   136  0.41  58.82   0.73     0.47      69248.75|
|  7:  2.6654 -  2.5325  1290   141  0.36  62.65   0.72     0.40      65615.23|
|  8:  2.5325 -  2.4227  1262   148  0.33  65.17   0.70     0.39      61341.13|
|  9:  2.4227 -  2.3298  1266   140  0.35  63.94   0.73     0.39      54905.20|
| 10:  2.3298 -  2.2496  1277   140  0.37  62.35   0.74     0.42      48390.44|
| 11:  2.2496 -  2.1795  1252   139  0.36  62.64   0.75     0.43      44677.80|
| 12:  2.1795 -  2.1174  1256   140  0.37  62.37   0.74     0.45      41679.87|
| 13:  2.1174 -  2.0618  1286   142  0.39  60.61   0.70     0.47      33967.60|
| 14:  2.0618 -  2.0116   839    94  0.50  52.03   0.70     0.53      22822.02|
|alpha:            min =        0.39 max =            0.78 mean =         0.53|
|beta:             min =    22822.02 max =        98741.73 mean =     62941.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.86|
|phase err.(test): min =        0.00 max =           89.97 mean =        53.51|
|-----------------------------------------------------------------------------|

============================== 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 = 12.537603             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.015   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.039596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.130   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      158 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1473 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2582 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3848 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4964 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6481 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7582 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.529 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.606 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4755   r_free= 0.4613   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.272878                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4623   r_free= 0.4462   ksol= 0.30   Bsol= 20.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.08,7.40,8.73,0.00,0.00,0.00); trace/3= 8.74                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.266335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.544036             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.199   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.967688              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.151   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4623      final r-factor (work) = 0.3645          |
| start r-factor (free) = 0.4462      final r-factor (free) = 0.3909          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.7424 = 11.54 * 0.50 * 6.2739 + 1.00 * 54.5291                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.6761 = 11.54 * 0.50 * 6.1558 + 1.00 * 0.1446                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3645      final r-factor (work) = 0.3193          |
| start r-factor (free) = 0.3909      final r-factor (free) = 0.3627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9714 = 0.97 * 1.00 * 6.1558 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8752 = 0.97 * 1.00 * 6.0564 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.67   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    91.67   11.65    None  None   None       |
|    Sol.    : 438    0      0.00    91.67   26.85    None  None   None       |
|    Mac.    : 2385   0      0.00    68.67   8.86     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 -   9.167: 1589   |   5:    45.833 -  54.999:   50        |
|      1:     9.167 -  18.333:  678   |   6:    54.999 -  64.166:   20        |
|      2:    18.333 -  27.500:  277   |   7:    64.166 -  73.332:    4        |
|      3:    27.500 -  36.666:  126   |   8:    73.332 -  82.499:    3        |
|      4:    36.666 -  45.833:   75   |   9:    82.499 -  91.665:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3193 r_free = 0.3627             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3186 r_free = 0.3634             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3186   r_free= 0.3634   ksol= 0.30   Bsol= 20.00   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.08,7.40,8.73,0.00,0.00,0.00); trace/3= 8.74                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.026149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3168   r_free= 0.3599   ksol= 0.32   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.92,4.75,5.95,0.00,0.00,0.00); trace/3= 5.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.026401                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.172852              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.224   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.546027              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.606  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3168      final r-factor (work) = 0.2279          |
| start r-factor (free) = 0.3599      final r-factor (free) = 0.2826          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8217 = 6.17 * 0.50 * 6.0514 + 1.00 * 0.1446                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2714 = 6.17 * 0.50 * 5.8940 + 1.00 * 0.0801                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2279      final r-factor (work) = 0.2147          |
| start r-factor (free) = 0.2826      final r-factor (free) = 0.2685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2919 = 0.55 * 1.00 * 5.8940 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6606 = 0.55 * 1.00 * 5.7204 + 1.00 * 0.5371                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.71   11.95    None  None   None       |
|    all(noH): 2823   0      0.00    91.71   11.95    None  None   None       |
|    Sol.    : 438    0      0.35    91.71   28.72    None  None   None       |
|    Mac.    : 2385   0      0.00    76.12   8.87     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 -   9.171: 1565   |   5:    45.857 -  55.029:   50        |
|      1:     9.171 -  18.343:  684   |   6:    55.029 -  64.200:   21        |
|      2:    18.343 -  27.514:  287   |   7:    64.200 -  73.371:    5        |
|      3:    27.514 -  36.686:  131   |   8:    73.371 -  82.543:    3        |
|      4:    36.686 -  45.857:   76   |   9:    82.543 -  91.714:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2147 r_free = 0.2685             target_work(ml) = 5.697         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2144 r_free = 0.2679             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2144   r_free= 0.2679   ksol= 0.32   Bsol= 50.00   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.92,4.75,5.95,0.00,0.00,0.00); trace/3= 5.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.695925                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2127   r_free= 0.2655   ksol= 0.33   Bsol= 50.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.29,3.38,4.47,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.695956                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.986115              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.483   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 16.382665             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.063   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2127      final r-factor (work) = 0.1613          |
| start r-factor (free) = 0.2655      final r-factor (free) = 0.2147          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2043 = 5.99 * 0.50 * 5.7213 + 1.00 * 0.0801                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7946 = 5.99 * 0.50 * 5.5796 + 1.00 * 0.0946                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1613      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.2147      final r-factor (free) = 0.1937          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 91.4229 = 16.38 * 1.00 * 5.5796 + 1.00 * 0.0144                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 88.2507 = 16.38 * 1.00 * 5.3857 + 1.00 * 0.0184                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.83   13.45    None  None   None       |
|    all(noH): 2823   0      0.00    90.83   13.45    None  None   None       |
|    Sol.    : 438    0      0.54    90.83   39.02    None  None   None       |
|    Mac.    : 2385   0      0.00    86.38   8.76     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 -   9.083: 1643   |   5:    45.415 -  54.498:   80        |
|      1:     9.083 -  18.166:  595   |   6:    54.498 -  63.581:   73        |
|      2:    18.166 -  27.249:  176   |   7:    63.581 -  72.664:   31        |
|      3:    27.249 -  36.332:   96   |   8:    72.664 -  81.746:   17        |
|      4:    36.332 -  45.415:  105   |   9:    81.746 -  90.829:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1380 r_free = 0.1937             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1379 r_free = 0.1936             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1379   r_free= 0.1936   ksol= 0.33   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.29,3.38,4.47,0.00,0.00,0.00); trace/3= 4.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.333461                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1929   ksol= 0.32   Bsol= 68.43   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,2.53,3.68,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.331656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.933018              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.956  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.151  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1377      final r-factor (work) = 0.1272          |
| start r-factor (free) = 0.1929      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0029 = 2.93 * 0.50 * 5.3926 + 1.00 * 0.0946                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8525 = 2.93 * 0.50 * 5.3027 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3333 = 0.25 * 1.00 * 5.3027 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3183 = 0.25 * 1.00 * 5.2713 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.55   12.76    None  None   None       |
|    all(noH): 2823   0      0.00    86.55   12.76    None  None   None       |
|    Sol.    : 438    0      1.38    86.55   36.69    None  None   None       |
|    Mac.    : 2385   0      0.00    84.21   8.37     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 -   8.655: 1671   |   5:    43.276 -  51.931:   78        |
|      1:     8.655 -  17.311:  583   |   6:    51.931 -  60.587:   65        |
|      2:    17.311 -  25.966:  168   |   7:    60.587 -  69.242:   27        |
|      3:    25.966 -  34.621:  117   |   8:    69.242 -  77.897:   15        |
|      4:    34.621 -  43.276:   91   |   9:    77.897 -  86.552:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1261 r_free = 0.1748             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1260 r_free = 0.1745             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1745   ksol= 0.32   Bsol= 68.43   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,2.53,3.68,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248088                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1744   ksol= 0.32   Bsol= 63.68   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,2.37,3.53,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247862                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.021242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.640  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.386  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1744      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4026 = 2.02 * 0.50 * 5.2707 + 1.00 * 0.0760                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3628 = 2.02 * 0.50 * 5.2386 + 1.00 * 0.0686                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0809 = 0.20 * 1.00 * 5.2386 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0774 = 0.20 * 1.00 * 5.2259 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.85   12.59    None  None   None       |
|    all(noH): 2823   0      0.00    86.85   12.59    None  None   None       |
|    Sol.    : 438    0      1.89    86.85   35.99    None  None   None       |
|    Mac.    : 2385   0      0.00    83.33   8.29     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 -   8.685: 1690   |   5:    43.424 -  52.109:   87        |
|      1:     8.685 -  17.370:  582   |   6:    52.109 -  60.794:   52        |
|      2:    17.370 -  26.055:  160   |   7:    60.794 -  69.479:   24        |
|      3:    26.055 -  34.739:  118   |   8:    69.479 -  78.164:   13        |
|      4:    34.739 -  43.424:   91   |   9:    78.164 -  86.849:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1229 r_free = 0.1694             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1693             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1693   ksol= 0.32   Bsol= 63.68   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.65,2.37,3.53,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222391                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.8014 0.99   1390  155 0.1058 0.1367      5.4298      5.5691|
|  2:  4.8014 -  3.8307 0.99   1329  147 0.0913 0.1201       5.492      5.6873|
|  3:  3.8307 -  3.3523 0.99   1306  142 0.1125 0.1554      5.5303      5.8684|
|  4:  3.3523 -  3.0484 0.99   1303  153 0.1306 0.1668      5.5146      5.6444|
|  5:  3.0484 -  2.8314 0.99   1293  142 0.1505 0.1944      5.4272      5.6542|
|  6:  2.8314 -  2.6654 0.99   1281  136 0.1361 0.2087       5.304      5.5556|
|  7:  2.6654 -  2.5325 0.99   1290  141 0.1421 0.1697      5.2616      5.4073|
|  8:  2.5325 -  2.4227 0.98   1262  148 0.1323 0.1824      5.1621      5.4133|
|  9:  2.4227 -  2.3298 0.98   1266  140 0.1301 0.1954      5.1283       5.361|
| 10:  2.3298 -  2.2496 1.00   1277  140 0.1297 0.1864      5.0564      5.3178|
| 11:  2.2496 -  2.1795 0.97   1252  139 0.1284 0.1850      5.0353      5.2875|
| 12:  2.1795 -  2.1174 0.98   1256  140 0.1231 0.1919      4.9535      5.2716|
| 13:  2.1174 -  2.0618 1.00   1286  142 0.1290 0.1882      4.8673      5.1274|
| 14:  2.0618 -  2.0116 0.67    839   94 0.1154 0.1666      4.7293      4.9218|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.8014  1390   155  0.94   9.43   0.97     0.94       7778.06|
|  2:  4.8014 -  3.8307  1329   147  0.95   8.50   0.99     0.97       9910.14|
|  3:  3.8307 -  3.3523  1306   142  0.93  12.20   1.01     1.01      11592.83|
|  4:  3.3523 -  3.0484  1303   153  0.91  14.44   0.99     0.97      11382.16|
|  5:  3.0484 -  2.8314  1293   142  0.89  17.46   0.99     0.97       9751.37|
|  6:  2.8314 -  2.6654  1281   136  0.89  17.40   0.98     0.95       8383.94|
|  7:  2.6654 -  2.5325  1290   141  0.89  16.84   0.98     0.96       7125.71|
|  8:  2.5325 -  2.4227  1262   148  0.90  16.74   0.98     0.96       6264.34|
|  9:  2.4227 -  2.3298  1266   140  0.89  16.97   0.99     0.95       5949.74|
| 10:  2.3298 -  2.2496  1277   140  0.89  16.67   0.99     0.95       5038.36|
| 11:  2.2496 -  2.1795  1252   139  0.89  17.20   0.99     0.93       4912.99|
| 12:  2.1795 -  2.1174  1256   140  0.90  16.09   1.00     1.00       4513.19|
| 13:  2.1174 -  2.0618  1286   142  0.89  17.56   0.98     0.96       3817.74|
| 14:  2.0618 -  2.0116   839    94  0.91  15.29   0.96     0.93       2771.35|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2771.35 max =        11592.83 mean =      7227.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.13|
|phase err.(test): min =        0.00 max =           89.00 mean =        14.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1693   ksol= 0.32   Bsol= 65.53   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.45,0.72,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1693   ksol= 0.32   Bsol= 65.53   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.45,0.72,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222399                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.8014 0.99   1390  155 0.1057 0.1365      5.4287      5.5683|
|  2:  4.8014 -  3.8307 0.99   1329  147 0.0912 0.1200      5.4914      5.6867|
|  3:  3.8307 -  3.3523 0.99   1306  142 0.1124 0.1553      5.5299      5.8678|
|  4:  3.3523 -  3.0484 0.99   1303  153 0.1305 0.1667      5.5146      5.6444|
|  5:  3.0484 -  2.8314 0.99   1293  142 0.1506 0.1947      5.4276      5.6551|
|  6:  2.8314 -  2.6654 0.99   1281  136 0.1362 0.2086      5.3044      5.5552|
|  7:  2.6654 -  2.5325 0.99   1290  141 0.1421 0.1696      5.2615       5.407|
|  8:  2.5325 -  2.4227 0.98   1262  148 0.1322 0.1825      5.1621      5.4137|
|  9:  2.4227 -  2.3298 0.98   1266  140 0.1302 0.1954      5.1286       5.361|
| 10:  2.3298 -  2.2496 1.00   1277  140 0.1297 0.1864      5.0565      5.3181|
| 11:  2.2496 -  2.1795 0.97   1252  139 0.1284 0.1851      5.0356      5.2882|
| 12:  2.1795 -  2.1174 0.98   1256  140 0.1231 0.1920       4.954       5.272|
| 13:  2.1174 -  2.0618 1.00   1286  142 0.1290 0.1882      4.8675       5.128|
| 14:  2.0618 -  2.0116 0.67    839   94 0.1154 0.1667      4.7295      4.9221|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.8014  1390   155  0.94   9.42   0.96     0.94       7762.88|
|  2:  4.8014 -  3.8307  1329   147  0.95   8.49   0.99     0.97       9895.12|
|  3:  3.8307 -  3.3523  1306   142  0.93  12.19   1.01     1.00      11578.31|
|  4:  3.3523 -  3.0484  1303   153  0.91  14.44   0.99     0.97      11384.70|
|  5:  3.0484 -  2.8314  1293   142  0.89  17.46   0.98     0.96       9754.73|
|  6:  2.8314 -  2.6654  1281   136  0.89  17.40   0.97     0.95       8390.15|
|  7:  2.6654 -  2.5325  1290   141  0.89  16.84   0.98     0.95       7125.84|
|  8:  2.5325 -  2.4227  1262   148  0.90  16.73   0.98     0.96       6265.09|
|  9:  2.4227 -  2.3298  1266   140  0.89  16.97   0.99     0.95       5949.10|
| 10:  2.3298 -  2.2496  1277   140  0.89  16.68   0.98     0.95       5042.10|
| 11:  2.2496 -  2.1795  1252   139  0.89  17.21   0.98     0.93       4916.41|
| 12:  2.1795 -  2.1174  1256   140  0.90  16.10   1.00     0.99       4519.34|
| 13:  2.1174 -  2.0618  1286   142  0.89  17.57   0.98     0.96       3820.86|
| 14:  2.0618 -  2.0116   839    94  0.91  15.30   0.96     0.92       2773.55|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2773.55 max =        11578.31 mean =      7226.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.13|
|phase err.(test): min =        0.00 max =           89.00 mean =        14.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.377)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.78    89.63   15.36    None  None   None       |
|    all(noH): 2823   0      2.78    89.63   15.36    None  None   None       |
|    Sol.    : 438    0      4.67    89.63   38.77    None  None   None       |
|    Mac.    : 2385   0      2.78    86.11   11.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.777 -  11.462: 1690   |   5:    46.201 -  54.886:   87        |
|      1:    11.462 -  20.147:  582   |   6:    54.886 -  63.571:   52        |
|      2:    20.147 -  28.832:  160   |   7:    63.571 -  72.256:   24        |
|      3:    28.832 -  37.517:  118   |   8:    72.256 -  80.941:   13        |
|      4:    37.517 -  46.201:   91   |   9:    80.941 -  89.626:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.391 - 4.861
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 331
   mapped sites are within: 0.725 - 4.861

peak=   10.028 closest distance to " CG2 VAL A 230 " =    1.449
peak=    7.857 closest distance to " CG2 VAL A 296 " =    1.255
peak=    6.031 closest distance to " CG  LEU A   5 " =    1.268
peak=    5.619 closest distance to " CB  GLN A 223 " =    1.431
peak=    5.500 closest distance to " O   HOH Z 111 " =    1.967
peak=    5.487 closest distance to " CD2 LEU A   5 " =    1.201
peak=    5.219 closest distance to " CG  LEU A 228 " =    1.224
peak=    5.077 closest distance to " O   HOH Z 232 " =    2.207
peak=    5.011 closest distance to " NH1 ARG A 138 " =    1.052
peak=    4.858 closest distance to " CB  SER A  63 " =    1.300
peak=    4.848 closest distance to " CG  PRO A 198 " =    1.342
peak=    4.803 closest distance to " CA  VAL A 230 " =    1.321
peak=    4.646 closest distance to " CG  PRO A 243 " =    1.146
peak=    4.629 closest distance to " CZ  PHE A 218 " =    1.109
peak=    4.566 closest distance to " NH1AARG A 145 " =    1.241
peak=    4.545 closest distance to " CB  TRP A 266 " =    0.961
peak=    4.532 closest distance to " CB  GLN A 183 " =    1.206
peak=    4.516 closest distance to " O   HOH Z 425 " =    1.613
peak=    4.497 closest distance to " O   HOH Z 369 " =    2.069
peak=    4.489 closest distance to " O   HOH Z 265 " =    2.252
peak=    4.487 closest distance to " CB  ASP A 124 " =    0.750
peak=    4.483 closest distance to " CG  PRO A 213 " =    1.283
peak=    4.439 closest distance to " O   HOH Z 298 " =    2.060
peak=    4.382 closest distance to " CB  ASN A 148 " =    1.301
peak=    4.307 closest distance to " O   HOH Z 236 " =    1.995
peak=    4.267 closest distance to " O   HOH Z 303 " =    2.176
peak=    4.246 closest distance to " CB  ASP A 140 " =    0.787
peak=    4.243 closest distance to " NE2 GLN A  11 " =    1.105
peak=    4.230 closest distance to " O   PRO A 198 " =    1.598
peak=    4.216 closest distance to " O   HOH Z 427 " =    3.274
peak=    4.147 closest distance to " O   HOH Z 234 " =    3.826
peak=    4.144 closest distance to " O   HOH Z 368 " =    2.299
peak=    4.140 closest distance to " CZ  PHE A 192 " =    1.005
peak=    4.118 closest distance to " ND2 ASN A 187 " =    1.524
peak=    4.108 closest distance to " O   HOH Z 102 " =    1.364
peak=    4.103 closest distance to " CD  LYS A 166 " =    1.274
peak=    4.097 closest distance to " CB  GLU A 152 " =    1.190
peak=    4.085 closest distance to " O   HOH Z 272 " =    1.955
peak=    4.069 closest distance to " CD1 LEU A 300 " =    1.216
peak=    4.056 closest distance to " O   HOH Z 261 " =    1.854
peak=    4.027 closest distance to " CD  ARG A 159 " =    0.788
peak=    4.025 closest distance to " CB  GLU A 128 " =    1.041
peak=    4.013 closest distance to " NH1 ARG A  56 " =    0.984
peak=    4.011 closest distance to " CA  ALA A  51 " =    1.005
peak=    4.008 closest distance to " CB  ALA A 104 " =    0.843
peak=    4.003 closest distance to " CB  ASN A  39 " =    0.857
peak=    4.001 closest distance to " O   HOH Z 411 " =    3.607
peak=    4.000 closest distance to " CB  ARG A 275 " =    0.921
peak=    3.999 closest distance to " O   HOH Z 410 " =    1.275
peak=    3.998 closest distance to " CB  LEU A 228 " =    1.161
peak=    3.993 closest distance to " CD1 LEU A   5 " =    1.288
peak=    3.992 closest distance to " CG2 THR A 221 " =    0.997
peak=    3.984 closest distance to " CB  SER A 216 " =    0.863
peak=    3.967 closest distance to " O   HOH Z 183 " =    1.257
peak=    3.959 closest distance to " O   HOH Z 184 " =    1.638
peak=    3.943 closest distance to " CB  ASN A 142 " =    0.938
peak=    3.924 closest distance to " CB  LEU A 143 " =    1.185
peak=    3.921 closest distance to " CD2 LEU A 228 " =    1.185
peak=    3.920 closest distance to " CG BARG A 275 " =    1.533
peak=    3.906 closest distance to " CB  VAL A 202 " =    1.584
peak=    3.875 closest distance to " CB  VAL A 265 " =    1.324
peak=    3.868 closest distance to " CA  ALA A 295 " =    1.144
peak=    3.865 closest distance to " CB  ALA A 242 " =    0.773
peak=    3.864 closest distance to " N   SER A 135 " =    1.363
peak=    3.863 closest distance to " CB  ARG A  79 " =    1.477
peak=    3.862 closest distance to " CB  GLU A  46 " =    0.980
peak=    3.849 closest distance to " CB  ARG A 190 " =    1.623
peak=    3.841 closest distance to " CG  MET A 185 " =    1.317
peak=    3.828 closest distance to " CG1 ILE A  33 " =    1.324
peak=    3.827 closest distance to " CB  ILE A 120 " =    1.279
peak=    3.827 closest distance to " CD  ARG A 269 " =    0.959
peak=    3.820 closest distance to " O   HOH Z 193 " =    2.213
peak=    3.818 closest distance to " O   HOH Z 171 " =    3.956
peak=    3.795 closest distance to " CD ALYS A 290 " =    1.035
peak=    3.792 closest distance to " O   HOH Z  88 " =    3.401
peak=    3.789 closest distance to " O   SER A  87 " =    2.382
peak=    3.787 closest distance to " O   HOH Z 188 " =    3.079
peak=    3.765 closest distance to " CA  SER A  87 " =    0.915
peak=    3.764 closest distance to " O   HOH Z 132 " =    2.584
peak=    3.759 closest distance to " O   HOH Z 437 " =    1.742
peak=    3.759 closest distance to " O   HOH Z 201 " =    3.047
peak=    3.755 closest distance to " O   HOH Z 112 " =    1.643
peak=    3.747 closest distance to " CB  SER A   3 " =    1.422
peak=    3.744 closest distance to " CD1 LEU A  96 " =    0.769
peak=    3.742 closest distance to " O   HOH Z 247 " =    1.507
peak=    3.740 closest distance to " O   HOH Z 158 " =    3.052
peak=    3.740 closest distance to " CA  TYR A  30 " =    0.966
peak=    3.738 closest distance to " CB  ALA A 291 " =    1.402
peak=    3.738 closest distance to " O   HOH Z 126 " =    1.628
peak=    3.737 closest distance to " O   HOH Z 316 " =    3.153
peak=    3.732 closest distance to " CA  ALA A  21 " =    1.209
peak=    3.723 closest distance to " O   HOH Z 403 " =    1.732
peak=    3.720 closest distance to " CB  SER A 210 " =    0.908
peak=    3.715 closest distance to " ND2 ASN A 249 " =    1.960
peak=    3.714 closest distance to " NH2 ARG A 156 " =    1.100
peak=    3.703 closest distance to " CA  MET A  40 " =    1.183
peak=    3.700 closest distance to " O   HOH Z 346 " =    1.541
peak=    3.698 closest distance to " CA  ARG A 195 " =    1.210
peak=    3.697 closest distance to " NE2 HIS A 207 " =    1.166
peak=    3.696 closest distance to " O   HOH Z 290 " =    1.386
peak=    3.689 closest distance to " ND1 HIS A  81 " =    1.696
peak=    3.688 closest distance to " N   PHE A 130 " =    1.235
peak=    3.686 closest distance to " CB  ALA A   9 " =    1.632
peak=    3.684 closest distance to " CE2 TYR A 186 " =    0.989
peak=    3.682 closest distance to " CB  ALA A  34 " =    0.891
peak=    3.680 closest distance to " O   MET A 105 " =    1.808
peak=    3.676 closest distance to " CB  GLU A 277 " =    3.740
peak=    3.676 closest distance to " O   HOH Z 126 " =    2.051
peak=    3.670 closest distance to " CB  PRO A  54 " =    0.848
peak=    3.666 closest distance to " O   HOH Z 213 " =    1.992
peak=    3.652 closest distance to " CD  ARG A  66 " =    2.347
peak=    3.649 closest distance to " O   HOH Z  78 " =    2.214
peak=    3.642 closest distance to " O   HOH Z  57 " =    1.491
peak=    3.632 closest distance to " CG  LEU A 167 " =    1.228
peak=    3.624 closest distance to " CG1 VAL A 153 " =    0.983
peak=    3.620 closest distance to " CB  SER A 212 " =    1.225
peak=    3.618 closest distance to " CA  ALA A 158 " =    1.097
peak=    3.612 closest distance to " O   HOH Z  80 " =    1.911
peak=    3.610 closest distance to " CA  VAL A 112 " =    1.099
peak=    3.608 closest distance to " CB  GLN A  88 " =    1.263
peak=    3.599 closest distance to " O   HOH Z  98 " =    2.004
peak=    3.594 closest distance to " CB  LEU A  83 " =    0.825
peak=    3.581 closest distance to " O   HOH Z 250 " =    1.345
peak=    3.575 closest distance to " O   HOH Z  78 " =    1.813
peak=    3.574 closest distance to " O   HOH Z  15 " =    1.980
peak=    3.566 closest distance to " O   HOH Z  68 " =    1.690
peak=    3.564 closest distance to " CB  VAL A 296 " =    1.097
peak=    3.554 closest distance to " O   HOH Z  10 " =    1.835
peak=    3.553 closest distance to " O   HOH Z 423 " =    1.682
peak=    3.551 closest distance to " CA  ASP A 124 " =    0.725
peak=    3.542 closest distance to " CG1 ILE A  49 " =    1.615
peak=    3.536 closest distance to " CG BARG A 102 " =    1.828
peak=    3.533 closest distance to " CB  THR A  82 " =    1.367
peak=    3.531 closest distance to " O   HOH Z  21 " =    1.728
peak=    3.528 closest distance to " O   HOH Z 350 " =    1.711
peak=    3.528 closest distance to " N   ASN A  39 " =    1.204
peak=    3.525 closest distance to " CA  ASP A 191 " =    0.754
peak=    3.520 closest distance to " N   VAL A 126 " =    1.473
peak=    3.519 closest distance to " CB  ALA A 161 " =    0.943
peak=    3.518 closest distance to " CG  GLU A  37 " =    0.869
peak=    3.517 closest distance to " CD2 LEU A 255 " =    1.564
peak=    3.515 closest distance to " O   HOH Z   4 " =    1.827
peak=    3.507 closest distance to " CG1 ILE A 151 " =    1.244
peak=    3.507 closest distance to " CG AARG A 275 " =    1.344
peak=    3.507 closest distance to " CA  LEU A 282 " =    0.966
peak=    3.500 closest distance to " CG2 VAL A 257 " =    0.894
peak=    3.496 closest distance to " CB  ASN A 187 " =    1.045
peak=    3.495 closest distance to " O   HOH Z  61 " =    1.697
peak=    3.494 closest distance to " O  BHOH Z 338 " =    2.477
peak=    3.491 closest distance to " OD1 ASN A  69 " =    2.591
peak=    3.491 closest distance to " CA  ILE A 106 " =    0.828
peak=    3.488 closest distance to " CG  GLN A  88 " =    1.071
peak=    3.485 closest distance to " CA  ALA A 184 " =    1.041
peak=    3.484 closest distance to " O   GLN A 278 " =    1.264
peak=    3.482 closest distance to " O   HOH Z 163 " =    1.787
peak=    3.476 closest distance to " CB  GLN A 103 " =    1.097
peak=    3.474 closest distance to " O   HOH Z 280 " =    2.985
peak=    3.473 closest distance to " NH1 ARG A  14 " =    0.901
peak=    3.468 closest distance to " CB  ASP A 140 " =    0.732
peak=    3.460 closest distance to " CB  ALA A 248 " =    1.151
peak=    3.459 closest distance to " CA  ARG A  36 " =    1.201
peak=    3.457 closest distance to " CA  ALA A 154 " =    1.046
peak=    3.456 closest distance to " O   HOH Z 214 " =    2.179
peak=    3.456 closest distance to " O   ASP A 124 " =    1.183
peak=    3.453 closest distance to " CB  ALA A 248 " =    1.298
peak=    3.445 closest distance to " C   GLN A  88 " =    1.711
peak=    3.444 closest distance to " CA  GLY A 267 " =    0.833
peak=    3.441 closest distance to " OG  SER A  22 " =    2.916
peak=    3.438 closest distance to " O   HOH Z  48 " =    1.787
peak=    3.437 closest distance to " O   HOH Z 313 " =    1.777
peak=    3.436 closest distance to " CB  TRP A 150 " =    1.471
peak=    3.434 closest distance to " CA  LYS A 181 " =    1.081
peak=    3.423 closest distance to " O   HOH Z 193 " =    1.738
peak=    3.419 closest distance to " CD  ARG A 138 " =    1.108
peak=    3.415 closest distance to " O   HOH Z 185 " =    2.305
peak=    3.413 closest distance to " CB AVAL A  41 " =    1.257
peak=    3.407 closest distance to " O   HOH Z 435 " =    2.099
peak=    3.398 closest distance to " OH  TYR A 247 " =    1.060
peak=    3.396 closest distance to " O   TYR A 116 " =    1.200
peak=    3.396 closest distance to " CB  GLU A 236 " =    1.067
peak=    3.391 closest distance to " CZ3 TRP A  92 " =    1.408
peak=    3.390 closest distance to " CB  ALA A 100 " =    1.355
peak=    3.384 closest distance to " O   HOH Z 215 " =    3.020
peak=    3.383 closest distance to " N   TYR A  15 " =    0.732
peak=    3.377 closest distance to " CA  ALA A 291 " =    0.911
peak=    3.374 closest distance to " CA  ASN A 215 " =    1.161
peak=    3.373 closest distance to " CA  GLN A 223 " =    0.917
peak=    3.371 closest distance to " CA  GLU A 152 " =    0.911
peak=    3.362 closest distance to " CG1BVAL A  72 " =    1.763
peak=    3.361 closest distance to " CB  PRO A 198 " =    1.023
peak=    3.361 closest distance to " CE1 TYR A 186 " =    1.288
peak=    3.360 closest distance to " O   HOH Z 294 " =    1.600
peak=    3.359 closest distance to " OG  SER A  28 " =    1.551
peak=    3.355 closest distance to " O   HOH Z 332 " =    1.551
peak=    3.353 closest distance to " OD2 ASP A 286 " =    2.961
peak=    3.352 closest distance to " O   HOH Z 197 " =    2.779
peak=    3.352 closest distance to " O   HOH Z  35 " =    4.861
peak=    3.347 closest distance to " CB  LYS A 117 " =    1.174
peak=    3.347 closest distance to " O   HOH Z 353 " =    2.691
peak=    3.343 closest distance to " N   ASN A 127 " =    1.252
peak=    3.342 closest distance to " O   HOH Z 285 " =    2.729
peak=    3.339 closest distance to " CB  MET A  40 " =    0.751
peak=    3.327 closest distance to " CD1 ILE A 106 " =    0.897
peak=    3.324 closest distance to " CD1 TRP A 266 " =    1.068
peak=    3.323 closest distance to " CA  THR A 221 " =    0.870
peak=    3.323 closest distance to " CD2 LEU A 237 " =    0.998
peak=    3.317 closest distance to " O   HOH Z 302 " =    1.903
peak=    3.316 closest distance to " CB  ALA A 114 " =    1.102
peak=    3.315 closest distance to " O   HOH Z 116 " =    1.902
peak=    3.310 closest distance to " CB  PRO A 243 " =    1.268
peak=    3.310 closest distance to " O   HOH Z  63 " =    1.928
peak=    3.310 closest distance to " O   HOH Z 128 " =    2.231
peak=    3.309 closest distance to " O   HOH Z 133 " =    2.417
peak=    3.309 closest distance to " CZ3 TRP A  85 " =    0.978
peak=    3.308 closest distance to " CB  VAL A 268 " =    0.830
peak=    3.307 closest distance to " O   HOH Z  49 " =    3.312
peak=    3.306 closest distance to " CA  ASN A 284 " =    0.905
peak=    3.306 closest distance to " CG2 THR A  42 " =    0.823
peak=    3.301 closest distance to " O   ALA A 158 " =    1.377
peak=    3.292 closest distance to " O   ASP A 200 " =    1.500
peak=    3.291 closest distance to " O   HOH Z 227 " =    1.718
peak=    3.289 closest distance to " O   HOH Z 368 " =    3.592
peak=    3.286 closest distance to " CA  ILE A  33 " =    1.665
peak=    3.285 closest distance to " CG  ARG A 159 " =    1.039
peak=    3.285 closest distance to " O   HOH Z 185 " =    2.015
peak=    3.283 closest distance to " O   HOH Z 406 " =    1.566
peak=    3.283 closest distance to " O   HOH Z 359 " =    4.231
peak=    3.282 closest distance to " CB  MET A  47 " =    1.013
peak=    3.280 closest distance to " O   HOH Z 359 " =    1.480
peak=    3.277 closest distance to " O   HOH Z  30 " =    1.266
peak=    3.273 closest distance to " O   TRP A 274 " =    1.790
peak=    3.272 closest distance to " CA  ASN A 127 " =    0.988
peak=    3.272 closest distance to " CA  ALA A 299 " =    0.969
peak=    3.270 closest distance to " CG  ARG A 269 " =    1.769
peak=    3.270 closest distance to " NE AARG A 275 " =    1.359
peak=    3.264 closest distance to " CB  THR A  31 " =    1.581
peak=    3.261 closest distance to " O   HOH Z 128 " =    2.310
peak=    3.258 closest distance to " O   HOH Z 156 " =    2.894
peak=    3.254 closest distance to " OD1 ASN A 217 " =    1.564
peak=    3.253 closest distance to " O   HOH Z  53 " =    2.551
peak=    3.252 closest distance to " CG2 ILE A 106 " =    0.826
peak=    3.246 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.242 closest distance to " O   HOH Z 134 " =    2.578
peak=    3.242 closest distance to " O   HOH Z 326 " =    2.221
peak=    3.241 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.241 closest distance to " O   HOH Z 383 " =    2.151
peak=    3.240 closest distance to " CB  ALA A 137 " =    1.090
peak=    3.239 closest distance to " CB  PHE A 204 " =    0.943
peak=    3.237 closest distance to " OG BSER A 164 " =    2.293
peak=    3.236 closest distance to " O   HOH Z 271 " =    2.783
peak=    3.236 closest distance to " CA  TYR A 116 " =    1.543
peak=    3.236 closest distance to " CG  ASP A 231 " =    1.152
peak=    3.235 closest distance to " CB  ALA A 227 " =    1.046
peak=    3.233 closest distance to " OH  TYR A 186 " =    1.033
peak=    3.232 closest distance to " O   HOH Z 109 " =    2.702
peak=    3.232 closest distance to " O   HOH Z 175 " =    3.612
peak=    3.231 closest distance to " OG BSER A 212 " =    2.508
peak=    3.226 closest distance to " O   HOH Z 197 " =    1.809
peak=    3.225 closest distance to " OG1 THR A 279 " =    1.548
peak=    3.224 closest distance to " O   HOH Z  89 " =    1.917
peak=    3.223 closest distance to " CB  ALA A   1 " =    4.802
peak=    3.214 closest distance to " OG  SER A 135 " =    1.283
peak=    3.212 closest distance to " O   HOH Z 215 " =    1.413
peak=    3.212 closest distance to " CA  GLY A 211 " =    1.320
peak=    3.211 closest distance to " CA  LYS A 290 " =    1.252
peak=    3.209 closest distance to " O   HOH Z  43 " =    1.796
peak=    3.209 closest distance to " OG  SER A  62 " =    3.021
peak=    3.209 closest distance to " CE3 TRP A  85 " =    1.171
peak=    3.207 closest distance to " CZ  PHE A  38 " =    1.225
peak=    3.200 closest distance to " CB  ASN A 110 " =    1.163
peak=    3.198 closest distance to " OG  SER A 206 " =    1.164
peak=    3.197 closest distance to " O   HOH Z  88 " =    3.358
peak=    3.193 closest distance to " CE2 TYR A  30 " =    0.871
peak=    3.192 closest distance to " CG2 ILE A 234 " =    1.029
peak=    3.191 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.190 closest distance to " O   HOH Z 135 " =    1.978
peak=    3.190 closest distance to " CG1 VAL A 174 " =    1.117
peak=    3.186 closest distance to " O   HOH Z 313 " =    1.780
peak=    3.186 closest distance to " CA  GLU A  46 " =    0.743
peak=    3.184 closest distance to " O   HOH Z 172 " =    3.803
peak=    3.181 closest distance to " O   HOH Z 422 " =    2.626
peak=    3.178 closest distance to " CA  ALA A 160 " =    1.043
peak=    3.178 closest distance to " CA  VAL A 125 " =    1.166
peak=    3.178 closest distance to " CA  ASN A 217 " =    1.464
peak=    3.177 closest distance to " CD2 TRP A 179 " =    1.272
peak=    3.177 closest distance to " N   GLY A  98 " =    1.133
peak=    3.176 closest distance to " O   HOH Z  56 " =    1.643
peak=    3.175 closest distance to " CE  MET A 113 " =    1.774
peak=    3.174 closest distance to " CA  ARG A 139 " =    1.165
peak=    3.172 closest distance to " CA  TRP A  92 " =    0.925
peak=    3.170 closest distance to " O   HOH Z 193 " =    2.069
peak=    3.170 closest distance to " O   HOH Z 125 " =    3.876
peak=    3.163 closest distance to " O   HOH Z 155 " =    3.381
peak=    3.163 closest distance to " O   HOH Z 273 " =    2.740
peak=    3.159 closest distance to " O   HOH Z 133 " =    1.758
peak=    3.158 closest distance to " O   HOH Z 148 " =    3.292
peak=    3.155 closest distance to " O   HOH Z 344 " =    3.061
peak=    3.155 closest distance to " O   HOH Z 352 " =    1.872
peak=    3.155 closest distance to " CD  ARG A 219 " =    1.077
peak=    3.152 closest distance to " OE1 GLU A 152 " =    0.911
peak=    3.151 closest distance to " O   HOH Z   1 " =    2.131
peak=    3.147 closest distance to " CB  ASN A 173 " =    1.022
peak=    3.147 closest distance to " ND1 HIS A  86 " =    1.699
peak=    3.146 closest distance to " O   HOH Z 188 " =    1.985
peak=    3.144 closest distance to " N   GLN A 278 " =    0.925
peak=    3.139 closest distance to " O   HOH Z 180 " =    2.045
peak=    3.136 closest distance to " CB  SER A  62 " =    1.101
peak=    3.133 closest distance to " CB  GLN A  89 " =    1.157
peak=    3.120 closest distance to " CZ3 TRP A 266 " =    1.126
peak=    3.114 closest distance to " CG2 THR A  29 " =    1.444
peak=    3.108 closest distance to " O   HOH Z 355 " =    1.808
peak=    3.107 closest distance to " CB  TYR A  30 " =    1.095
peak=    3.105 closest distance to " N   ARG A 156 " =    1.453
peak=    3.091 closest distance to " CG2 THR A 178 " =    1.300
peak=    3.086 closest distance to " O   HOH Z 391 " =    2.991
peak=    3.077 closest distance to " O   HOH Z  44 " =    2.146
peak=    3.065 closest distance to " CA  MET A 105 " =    0.949
peak=    3.058 closest distance to " O   HOH Z 263 " =    1.556
peak=    3.047 closest distance to " O   HOH Z 148 " =    2.018
peak=    3.040 closest distance to " O   HOH Z 213 " =    2.769
peak=    3.026 closest distance to " O   HOH Z 173 " =    1.631
peak=    3.018 closest distance to " O   HOH Z 295 " =    1.509

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.647 - 5.575
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 193
   mapped sites are within: 0.747 - 5.575

peak=   -5.512 closest distance to " CG2 VAL A 230 " =    0.788
peak=   -4.618 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -4.417 closest distance to " O   HOH Z 211 " =    1.166
peak=   -4.062 closest distance to " O   HOH Z  52 " =    1.611
peak=   -4.038 closest distance to " O   HOH Z 231 " =    1.815
peak=   -4.005 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.973 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.958 closest distance to " O   HOH Z 179 " =    2.240
peak=   -3.955 closest distance to " CA  GLY A 241 " =    2.354
peak=   -3.954 closest distance to " O   HOH Z 231 " =    1.080
peak=   -3.929 closest distance to " OE1 GLN A 223 " =    2.147
peak=   -3.927 closest distance to " CG1 VAL A 296 " =    1.389
peak=   -3.923 closest distance to " CG  ASP A 231 " =    0.747
peak=   -3.916 closest distance to " NH2AARG A 275 " =    5.575
peak=   -3.911 closest distance to " CD  ARG A 156 " =    2.120
peak=   -3.894 closest distance to " OE1 GLN A  88 " =    1.137
peak=   -3.866 closest distance to " CD1 LEU A   5 " =    2.637
peak=   -3.865 closest distance to " O   HOH Z  73 " =    2.078
peak=   -3.863 closest distance to " O   VAL A 189 " =    2.590
peak=   -3.862 closest distance to " O   HOH Z 394 " =    1.562
peak=   -3.857 closest distance to " O   HOH Z 103 " =    2.159
peak=   -3.849 closest distance to " C   ALA A 158 " =    1.328
peak=   -3.846 closest distance to " CG2BVAL A  41 " =    2.591
peak=   -3.834 closest distance to " CD2 LEU A 237 " =    2.769
peak=   -3.821 closest distance to " O   ILE A 109 " =    2.638
peak=   -3.798 closest distance to " O   HOH Z 166 " =    1.979
peak=   -3.789 closest distance to " O   HOH Z  19 " =    2.426
peak=   -3.773 closest distance to " CD  GLN A  58 " =    0.948
peak=   -3.765 closest distance to " O   HOH Z 196 " =    2.347
peak=   -3.756 closest distance to " OG  SER A  87 " =    1.657
peak=   -3.754 closest distance to " CG  LEU A 101 " =    2.486
peak=   -3.735 closest distance to " CD2 LEU A 167 " =    1.843
peak=   -3.733 closest distance to " CD  ARG A  14 " =    3.227
peak=   -3.733 closest distance to " CG2 VAL A 296 " =    0.873
peak=   -3.730 closest distance to " O   HOH Z 177 " =    1.730
peak=   -3.728 closest distance to " O   HOH Z  92 " =    1.747
peak=   -3.726 closest distance to " O   HOH Z 377 " =    1.683
peak=   -3.708 closest distance to " O   HOH Z 435 " =    2.720
peak=   -3.705 closest distance to " SD BMET A  47 " =    0.975
peak=   -3.705 closest distance to " OG  SER A  97 " =    2.250
peak=   -3.694 closest distance to " CD1 TYR A 247 " =    2.841
peak=   -3.692 closest distance to " CD1 PHE A  59 " =    1.961
peak=   -3.690 closest distance to " N   THR A  18 " =    1.330
peak=   -3.686 closest distance to " CZ3 TRP A 179 " =    1.120
peak=   -3.685 closest distance to " O   HOH Z  10 " =    1.556
peak=   -3.684 closest distance to " CG  HIS A  86 " =    1.104
peak=   -3.683 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.681 closest distance to " O   GLY A  80 " =    2.568
peak=   -3.679 closest distance to " CB  PRO A 243 " =    2.712
peak=   -3.674 closest distance to " O   HOH Z  38 " =    1.188
peak=   -3.667 closest distance to " CG  TRP A 266 " =    1.864
peak=   -3.666 closest distance to " O   GLY A 211 " =    1.410
peak=   -3.664 closest distance to " O   HOH Z 290 " =    1.468
peak=   -3.654 closest distance to " N   THR A 157 " =    1.586
peak=   -3.654 closest distance to " CD2 TYR A 293 " =    1.914
peak=   -3.648 closest distance to " O   HOH Z 111 " =    2.060
peak=   -3.642 closest distance to " CA  GLY A 241 " =    3.106
peak=   -3.624 closest distance to " CZ2 TRP A  92 " =    2.860
peak=   -3.624 closest distance to " CG2 VAL A 296 " =    1.378
peak=   -3.624 closest distance to " ND2 ASN A  60 " =    1.538
peak=   -3.622 closest distance to " OG  SER A 206 " =    1.818
peak=   -3.615 closest distance to " O   HOH Z 411 " =    5.295
peak=   -3.591 closest distance to " CE2 TYR A  30 " =    2.808
peak=   -3.580 closest distance to " CG1 VAL A 112 " =    2.850
peak=   -3.578 closest distance to " O   PRO A 163 " =    2.130
peak=   -3.578 closest distance to " O   GLY A 203 " =    2.346
peak=   -3.576 closest distance to " OD2 ASP A  50 " =    2.241
peak=   -3.575 closest distance to " CG  ARG A 269 " =    2.308
peak=   -3.564 closest distance to " ND2 ASN A  45 " =    2.162
peak=   -3.560 closest distance to " O   HOH Z 275 " =    1.571
peak=   -3.560 closest distance to " CG1 VAL A 265 " =    2.490
peak=   -3.558 closest distance to " N   ALA A 226 " =    2.242
peak=   -3.554 closest distance to " C   ASN A 285 " =    2.572
peak=   -3.554 closest distance to " O   HOH Z 113 " =    1.835
peak=   -3.542 closest distance to " CE3 TRP A  70 " =    1.804
peak=   -3.537 closest distance to " O   HOH Z 351 " =    1.485
peak=   -3.524 closest distance to " O   HOH Z 389 " =    1.967
peak=   -3.499 closest distance to " N   ALA A  43 " =    2.547
peak=   -3.493 closest distance to " CD1 LEU A 228 " =    2.497
peak=   -3.493 closest distance to " C   ALA A 165 " =    2.026
peak=   -3.492 closest distance to " CG2 VAL A 112 " =    2.659
peak=   -3.492 closest distance to " NH2 ARG A  79 " =    2.011
peak=   -3.489 closest distance to " ND2 ASN A  60 " =    1.764
peak=   -3.484 closest distance to " C   GLY A  13 " =    0.904
peak=   -3.477 closest distance to " O   HOH Z  17 " =    1.422
peak=   -3.470 closest distance to " CB  TRP A  85 " =    2.629
peak=   -3.466 closest distance to " O   HOH Z 216 " =    1.422
peak=   -3.443 closest distance to " O   HOH Z 166 " =    1.799
peak=   -3.443 closest distance to " CE3 TRP A 150 " =    2.233
peak=   -3.431 closest distance to " NH2 ARG A  66 " =    2.040
peak=   -3.416 closest distance to " OG BSER A 134 " =    1.336
peak=   -3.416 closest distance to " CE BMET A  47 " =    1.867
peak=   -3.412 closest distance to " NE2 GLN A  88 " =    0.897
peak=   -3.395 closest distance to " O   HOH Z  43 " =    1.653
peak=   -3.395 closest distance to " N   SER A 212 " =    1.741
peak=   -3.391 closest distance to " CD  GLN A  88 " =    0.820
peak=   -3.377 closest distance to " CB  VAL A 230 " =    1.031
peak=   -3.375 closest distance to " O   HOH Z 128 " =    2.671
peak=   -3.366 closest distance to " O   LEU A 101 " =    2.837
peak=   -3.361 closest distance to " O   HOH Z 183 " =    1.207
peak=   -3.358 closest distance to " CD1 ILE A  33 " =    2.462
peak=   -3.356 closest distance to " CA  ASN A 127 " =    1.153
peak=   -3.355 closest distance to " O   HOH Z  13 " =    1.448
peak=   -3.354 closest distance to " CD2 PHE A  61 " =    1.909
peak=   -3.350 closest distance to " O   HOH Z 407 " =    3.399
peak=   -3.349 closest distance to " O   HOH Z 184 " =    1.443
peak=   -3.348 closest distance to " O   HOH Z  11 " =    1.870
peak=   -3.345 closest distance to " CG  PHE A 283 " =    2.824
peak=   -3.336 closest distance to " CB  ALA A 114 " =    2.510
peak=   -3.332 closest distance to " OG ASER A 134 " =    1.464
peak=   -3.324 closest distance to " O   HOH Z 295 " =    1.484
peak=   -3.323 closest distance to " O   HOH Z 377 " =    1.260
peak=   -3.319 closest distance to " OD1 ASN A 148 " =    1.367
peak=   -3.314 closest distance to " CA  GLY A 203 " =    2.470
peak=   -3.313 closest distance to " CZ  PHE A 218 " =    1.242
peak=   -3.308 closest distance to " O   HOH Z  60 " =    2.250
peak=   -3.304 closest distance to " N   SER A   3 " =    2.165
peak=   -3.303 closest distance to " C   PHE A  59 " =    1.218
peak=   -3.302 closest distance to " O   HOH Z 426 " =    1.651
peak=   -3.301 closest distance to " NH2 ARG A  79 " =    1.579
peak=   -3.300 closest distance to " OD1 ASN A 173 " =    1.192
peak=   -3.298 closest distance to " O   HOH Z  44 " =    2.221
peak=   -3.296 closest distance to " OXT GLY A 302 " =    3.162
peak=   -3.292 closest distance to " O   HOH Z 113 " =    2.310
peak=   -3.291 closest distance to " CG  TYR A 186 " =    2.347
peak=   -3.287 closest distance to " O   ASP A  27 " =    1.979
peak=   -3.277 closest distance to " CB  ASN A  69 " =    1.357
peak=   -3.276 closest distance to " O   HOH Z 357 " =    2.113
peak=   -3.276 closest distance to " O   ALA A   7 " =    1.436
peak=   -3.266 closest distance to " CD  LYS A 289 " =    2.521
peak=   -3.265 closest distance to " N   SER A 276 " =    1.447
peak=   -3.265 closest distance to " NE2 GLN A 194 " =    1.976
peak=   -3.264 closest distance to " CA  GLY A 133 " =    2.271
peak=   -3.263 closest distance to " O   LEU A 167 " =    1.519
peak=   -3.262 closest distance to " CG  LEU A 228 " =    0.968
peak=   -3.262 closest distance to " CB  PRO A 163 " =    2.540
peak=   -3.249 closest distance to " O   HOH Z 396 " =    2.056
peak=   -3.247 closest distance to " N   ALA A 248 " =    2.380
peak=   -3.245 closest distance to " CD1 LEU A 101 " =    2.668
peak=   -3.241 closest distance to " O   HOH Z 390 " =    2.181
peak=   -3.239 closest distance to " O   HOH Z 136 " =    0.966
peak=   -3.233 closest distance to " O   HOH Z 198 " =    1.480
peak=   -3.230 closest distance to " O   HOH Z 236 " =    1.278
peak=   -3.227 closest distance to " CE  LYS A  76 " =    2.614
peak=   -3.227 closest distance to " O   HOH Z 185 " =    2.436
peak=   -3.226 closest distance to " CE1 TYR A 169 " =    2.521
peak=   -3.224 closest distance to " O   HOH Z 292 " =    4.703
peak=   -3.222 closest distance to " N   PHE A  59 " =    2.087
peak=   -3.220 closest distance to " N   TYR A  68 " =    2.854
peak=   -3.217 closest distance to " CG1 VAL A 197 " =    2.358
peak=   -3.214 closest distance to " OD2 ASP A 171 " =    1.902
peak=   -3.206 closest distance to " CG  PRO A 163 " =    2.449
peak=   -3.202 closest distance to " CA  GLY A  98 " =    2.200
peak=   -3.199 closest distance to " O   HOH Z 114 " =    1.670
peak=   -3.196 closest distance to " O   VAL A  67 " =    2.569
peak=   -3.195 closest distance to " O   ASP A 270 " =    1.615
peak=   -3.193 closest distance to " CB  ALA A  43 " =    2.692
peak=   -3.182 closest distance to " O   HOH Z 371 " =    1.433
peak=   -3.178 closest distance to " NE2 GLN A 103 " =    1.827
peak=   -3.176 closest distance to " CG  GLU A 277 " =    1.446
peak=   -3.176 closest distance to " OG BSER A 134 " =    1.971
peak=   -3.176 closest distance to " C   ASN A 187 " =    1.758
peak=   -3.174 closest distance to " N   THR A  52 " =    1.670
peak=   -3.166 closest distance to " O   VAL A 121 " =    1.152
peak=   -3.164 closest distance to " O   HOH Z 325 " =    1.680
peak=   -3.164 closest distance to " C   MET A 188 " =    1.505
peak=   -3.163 closest distance to " O   HOH Z  51 " =    1.495
peak=   -3.162 closest distance to " CD2 TRP A 274 " =    2.440
peak=   -3.160 closest distance to " O   HOH Z 198 " =    1.177
peak=   -3.159 closest distance to " O   HOH Z 353 " =    2.187
peak=   -3.149 closest distance to " NH2 ARG A  36 " =    2.361
peak=   -3.146 closest distance to " O   HOH Z 251 " =    4.911
peak=   -3.144 closest distance to " NE2 GLN A 240 " =    1.607
peak=   -3.144 closest distance to " CD  PRO A 213 " =    2.182
peak=   -3.143 closest distance to " O   HOH Z 176 " =    0.821
peak=   -3.143 closest distance to " O   HOH Z 290 " =    0.824
peak=   -3.136 closest distance to " C   ASP A 270 " =    1.260
peak=   -3.126 closest distance to " CB  ALA A   9 " =    2.670
peak=   -3.124 closest distance to " OG1 THR A  82 " =    1.931
peak=   -3.110 closest distance to " O   GLY A 196 " =    1.345
peak=   -3.104 closest distance to " CD1 TYR A 247 " =    2.183
peak=   -3.097 closest distance to " CD1 TRP A 179 " =    0.954
peak=   -3.085 closest distance to " CB  LEU A  83 " =    2.353
peak=   -3.085 closest distance to " CB  PHE A 130 " =    1.320
peak=   -3.083 closest distance to " O   HOH Z  60 " =    2.038
peak=   -3.076 closest distance to " OG BSER A 210 " =    1.622
peak=   -3.051 closest distance to " O   TRP A  70 " =    1.481
peak=   -3.050 closest distance to " NH2 ARG A  66 " =    1.697
peak=   -3.043 closest distance to " O   HOH Z 177 " =    1.809
peak=   -3.020 closest distance to " O   HOH Z 106 " =    1.980
peak=   -3.011 closest distance to " CG2 THR A 235 " =    1.927
peak=   -3.000 closest distance to " CG1 VAL A 296 " =    1.323

================= 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    :  0.4701 0.4580   6.272112e+00   6.253301e+00
   1_bss:  0.4623 0.4462   6.266335e+00   6.245456e+00
   1_xyz:  0.3645 0.3909   6.122609e+00   6.165644e+00
   1_adp:  0.3193 0.3627   6.026961e+00   6.120609e+00
   1_occ:  0.3186 0.3634   6.026149e+00   6.121774e+00
   2_bss:  0.3168 0.3599   6.026401e+00   6.119871e+00
   2_xyz:  0.2279 0.2826   5.750121e+00   5.909532e+00
   2_adp:  0.2147 0.2685   5.697050e+00   5.867476e+00
   2_occ:  0.2144 0.2679   5.695925e+00   5.865774e+00
   3_bss:  0.2127 0.2655   5.695956e+00   5.864419e+00
   3_xyz:  0.1613 0.2147   5.454050e+00   5.663696e+00
   3_adp:  0.1380 0.1937   5.334071e+00   5.575520e+00
   3_occ:  0.1379 0.1936   5.333461e+00   5.575081e+00
   4_bss:  0.1377 0.1929   5.331656e+00   5.572775e+00
   4_xyz:  0.1272 0.1821   5.270222e+00   5.519068e+00
   4_adp:  0.1261 0.1748   5.249119e+00   5.480982e+00
   4_occ:  0.1260 0.1745   5.248088e+00   5.480035e+00
   5_bss:  0.1259 0.1744   5.247862e+00   5.479696e+00
   5_xyz:  0.1230 0.1701   5.225513e+00   5.454982e+00
   5_adp:  0.1229 0.1694   5.222864e+00   5.450579e+00
   5_occ:  0.1229 0.1693   5.222391e+00   5.450215e+00
   5_bss:  0.1229 0.1693   5.222399e+00   5.450257e+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:  0.295  20.000  10.084   7.398   8.728   0.000   0.000   0.000
   1_xyz:  0.295  20.000  10.084   7.398   8.728   0.000   0.000   0.000
   1_adp:  0.295  20.000  10.084   7.398   8.728   0.000   0.000   0.000
   1_occ:  0.295  20.000  10.084   7.398   8.728   0.000   0.000   0.000
   2_bss:  0.322  50.000   6.923   4.754   5.954   0.000   0.000   0.000
   2_xyz:  0.322  50.000   6.923   4.754   5.954   0.000   0.000   0.000
   2_adp:  0.322  50.000   6.923   4.754   5.954   0.000   0.000   0.000
   2_occ:  0.322  50.000   6.923   4.754   5.954   0.000   0.000   0.000
   3_bss:  0.330  50.000   4.288   3.380   4.466   0.000   0.000   0.000
   3_xyz:  0.330  50.000   4.288   3.380   4.466   0.000   0.000   0.000
   3_adp:  0.330  50.000   4.288   3.380   4.466   0.000   0.000   0.000
   3_occ:  0.330  50.000   4.288   3.380   4.466   0.000   0.000   0.000
   4_bss:  0.321  68.432   3.063   2.533   3.684   0.000   0.000   0.000
   4_xyz:  0.321  68.432   3.063   2.533   3.684   0.000   0.000   0.000
   4_adp:  0.321  68.432   3.063   2.533   3.684   0.000   0.000   0.000
   4_occ:  0.321  68.432   3.063   2.533   3.684   0.000   0.000   0.000
   5_bss:  0.321  63.680   2.653   2.373   3.532   0.000   0.000   0.000
   5_xyz:  0.321  63.680   2.653   2.373   3.532   0.000   0.000   0.000
   5_adp:  0.321  63.680   2.653   2.373   3.532   0.000   0.000   0.000
   5_occ:  0.321  63.680   2.653   2.373   3.532   0.000   0.000   0.000
   5_bss:  0.319  65.529  -0.267  -0.453   0.720   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.829 0.4728  0.5301    62943.540
   1_bss:  53.355 0.4778  0.6935    61139.916
   1_xyz:  45.518 0.5741  0.8079    44896.802
   1_adp:  40.459 0.6366  0.9028    38137.063
   1_occ:  40.536 0.6356  0.9003    38229.442
   2_bss:  40.407 0.6371  0.8184    38023.148
   2_xyz:  28.876 0.7695  0.9646    21005.299
   2_adp:  26.743 0.7933  1.0065    18859.008
   2_occ:  26.687 0.7939  1.0065    18783.225
   3_bss:  26.628 0.7946  0.9432    18735.700
   3_xyz:  20.346 0.8583  0.9905    11614.540
   3_adp:  18.248 0.8780  0.9960     9481.930
   3_occ:  18.231 0.8781  0.9959     9470.069
   4_bss:  18.170 0.8786  0.9625     9395.821
   4_xyz:  16.774 0.8916  0.9669     8311.798
   4_adp:  15.831 0.9002  0.9679     7757.734
   4_occ:  15.809 0.9004  0.9679     7740.039
   5_bss:  15.805 0.9004  0.9598     7728.811
   5_xyz:  15.228 0.9054  0.9622     7291.191
   5_adp:  15.079 0.9068  0.9615     7231.101
   5_occ:  15.072 0.9068  0.9615     7227.661
   5_bss:  15.072 0.9068  0.9589     7226.444
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4529e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4529e+01
   1_xyz:   1.708  0.014  0.111 18.213  0.006  4.113   1.4463e-01
   1_adp:   1.708  0.014  0.111 18.213  0.006  4.113   1.4463e-01
   1_occ:   1.708  0.014  0.111 18.213  0.006  4.113   1.4463e-01
   2_bss:   1.708  0.014  0.111 18.213  0.006  4.113   1.4463e-01
   2_xyz:   1.112  0.009  0.079 16.699  0.005  4.136   8.0094e-02
   2_adp:   1.112  0.009  0.079 16.699  0.005  4.136   8.0094e-02
   2_occ:   1.112  0.009  0.079 16.699  0.005  4.136   8.0094e-02
   3_bss:   1.112  0.009  0.079 16.699  0.005  4.136   8.0094e-02
   3_xyz:   1.230  0.011  0.091 16.485  0.005  4.119   9.4554e-02
   3_adp:   1.230  0.011  0.091 16.485  0.005  4.119   9.4554e-02
   3_occ:   1.230  0.011  0.091 16.485  0.005  4.119   9.4554e-02
   4_bss:   1.230  0.011  0.091 16.485  0.005  4.119   9.4554e-02
   4_xyz:   1.111  0.010  0.085 16.104  0.004  4.127   7.5955e-02
   4_adp:   1.111  0.010  0.085 16.104  0.004  4.127   7.5955e-02
   4_occ:   1.111  0.010  0.085 16.104  0.004  4.127   7.5955e-02
   5_bss:   1.111  0.010  0.085 16.104  0.004  4.127   7.5955e-02
   5_xyz:   1.054  0.009  0.081 15.589  0.004  4.132   6.8559e-02
   5_adp:   1.054  0.009  0.081 15.589  0.004  4.132   6.8559e-02
   5_occ:   1.054  0.009  0.081 15.589  0.004  4.132   6.8559e-02
   5_bss:   1.054  0.009  0.081 15.589  0.004  4.132   6.8559e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0707e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0707e+00
   1_xyz:  14.116  0.164  0.450 85.655  0.041  2.183   1.0856e-01
   1_adp:  14.116  0.164  0.450 85.655  0.041  2.183   1.0856e-01
   1_occ:  14.116  0.164  0.450 85.655  0.041  2.183   1.0856e-01
   2_bss:  14.116  0.164  0.450 85.655  0.041  2.183   1.0856e-01
   2_xyz:   6.987  0.072  0.269 83.027  0.037  2.254   9.8476e-02
   2_adp:   6.987  0.072  0.269 83.027  0.037  2.254   9.8476e-02
   2_occ:   6.987  0.072  0.269 83.027  0.037  2.254   9.8476e-02
   3_bss:   6.987  0.072  0.269 83.027  0.037  2.254   9.8476e-02
   3_xyz:   9.048  0.082  0.441 85.452  0.047  2.265   1.3947e-01
   3_adp:   9.048  0.082  0.441 85.452  0.047  2.265   1.3947e-01
   3_occ:   9.048  0.082  0.441 85.452  0.047  2.265   1.3947e-01
   4_bss:   9.048  0.082  0.441 85.452  0.047  2.265   1.3947e-01
   4_xyz:   9.011  0.064  0.457 82.971  0.042  2.364   4.5508e-02
   4_adp:   9.011  0.064  0.457 82.971  0.042  2.364   4.5508e-02
   4_occ:   9.011  0.064  0.457 82.971  0.042  2.364   4.5508e-02
   5_bss:   9.011  0.064  0.457 82.971  0.042  2.364   4.5508e-02
   5_xyz:   8.642  0.047  0.442 82.716  0.040  2.387   4.9046e-02
   5_adp:   8.642  0.047  0.442 82.716  0.040  2.387   4.9046e-02
   5_occ:   8.642  0.047  0.442 82.716  0.040  2.387   4.9046e-02
   5_bss:   8.642  0.047  0.442 82.716  0.040  2.387   4.9046e-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:  91.67   0.00  11.65  68.67   0.00   8.86  91.67   0.00  26.85
   1_occ:  91.67   0.00  11.65  68.67   0.00   8.86  91.67   0.00  26.85
   2_bss:  91.67   0.00  11.65  68.67   0.00   8.86  91.67   0.00  26.85
   2_xyz:  91.67   0.00  11.65  68.67   0.00   8.86  91.67   0.00  26.85
   2_adp:  91.71   0.00  11.95  76.12   0.00   8.87  91.71   0.35  28.72
   2_occ:  91.71   0.00  11.95  76.12   0.00   8.87  91.71   0.35  28.72
   3_bss:  91.71   0.00  11.95  76.12   0.00   8.87  91.71   0.35  28.72
   3_xyz:  91.71   0.00  11.95  76.12   0.00   8.87  91.71   0.35  28.72
   3_adp:  90.83   0.00  13.45  86.38   0.00   8.76  90.83   0.54  39.02
   3_occ:  90.83   0.00  13.45  86.38   0.00   8.76  90.83   0.54  39.02
   4_bss:  90.83   0.00  13.45  86.38   0.00   8.76  90.83   0.54  39.02
   4_xyz:  90.83   0.00  13.45  86.38   0.00   8.76  90.83   0.54  39.02
   4_adp:  86.55   0.00  12.76  84.21   0.00   8.37  86.55   1.38  36.69
   4_occ:  86.55   0.00  12.76  84.21   0.00   8.37  86.55   1.38  36.69
   5_bss:  86.55   0.00  12.76  84.21   0.00   8.37  86.55   1.38  36.69
   5_xyz:  86.55   0.00  12.76  84.21   0.00   8.37  86.55   1.38  36.69
   5_adp:  86.85   0.00  12.59  83.33   0.00   8.29  86.85   1.89  35.99
   5_occ:  86.85   0.00  12.59  83.33   0.00   8.29  86.85   1.89  35.99
   5_bss:  89.63   2.78  15.36  86.11   2.78  11.07  89.63   4.67  38.77
------------------------------------------------------------------------
 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:    1.246    0.022    0.415
   1_adp:    1.246    0.022    0.415
   1_occ:    1.246    0.022    0.415
   2_bss:    1.246    0.022    0.415
   2_xyz:    1.585    0.020    0.570
   2_adp:    1.585    0.020    0.570
   2_occ:    1.585    0.020    0.570
   3_bss:    1.585    0.020    0.570
   3_xyz:    1.566    0.078    0.650
   3_adp:    1.566    0.078    0.650
   3_occ:    1.566    0.078    0.650
   4_bss:    1.566    0.078    0.650
   4_xyz:    1.592    0.069    0.674
   4_adp:    1.592    0.069    0.674
   4_occ:    1.592    0.069    0.674
   5_bss:    1.592    0.069    0.674
   5_xyz:    1.627    0.023    0.687
   5_adp:    1.627    0.023    0.687
   5_occ:    1.627    0.023    0.687
   5_bss:    1.627    0.023    0.687
------------------------------------------------------------------------

CPU time actual refinement: 313.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1283/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_1283/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1283/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1283/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1283/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 313.38 
  Macro-tasks:
    bulk solvent and scale       = 39.74  
    individual site refinement   = 125.15 
    weights calculation          = 31.29  
    collect and process          = 6.57   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 202.89 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 94.18  
    alpha_beta                      = 8.31   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 103.91 
    fmodel                         = 7.09   
    r_factors                      = 0.20   
    phase_errors                   = 10.84  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 227.68 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.493 micro seconds
Total CPU time: 5.45 minutes
from_scatterers_fft:    623 calls, 93.81 s
gradients_fft:          569 calls, 91.22 s

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

# Date 2008-01-16 Time 03:38:40 PST -0800 (1200483520.37 s)
Start R-work = 0.4701, R-free = 0.4580 (no bulk solvent and anisotropic scale)
Final R-work = 0.1388, R-free = 0.1845 (no bulk solvent and anisotropic scale)

Start R-work = 0.4623, R-free = 0.4462
Final R-work = 0.1229, R-free = 0.1693