# Date 2008-01-16 Time 02:20:28 PST -0800 (1200478828.45 s)
#phil __OFF__

Command line arguments: "../789.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23442
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 789

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.93, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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: (70.6012, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.00203
Completeness in resolution range: 0.969417
Completeness with d_max=infinity: 0.966404

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   2.0020

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 2.00203
Completeness in resolution range: 0.969417
Completeness with d_max=infinity: 0.966404

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2836 [2127/2151]  1913   214  10.1%
  bin  2:  4.2836 -  3.4129 [2031/2051]  1829   202   9.9%
  bin  3:  3.4129 -  2.9852 [2017/2036]  1814   203  10.1%
  bin  4:  2.9852 -  2.7140 [1981/2011]  1783   198  10.0%
  bin  5:  2.7140 -  2.5204 [1991/2010]  1789   202  10.1%
  bin  6:  2.5204 -  2.3724 [1973/1998]  1778   195   9.9%
  bin  7:  2.3724 -  2.2540 [1946/1974]  1751   195  10.0%
  bin  8:  2.2540 -  2.1562 [1972/2008]  1780   192   9.7%
  bin  9:  2.1562 -  2.0734 [1928/1970]  1730   198  10.3%
  bin 10:  2.0734 -  2.0020 [1623/1998]  1463   160   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_789/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2172
        3.04 -     3.66: 4598
        3.66 -     4.28: 8922
        4.28 -     4.90: 12296
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.943 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.141 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.141 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.142 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27996 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_789/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_789/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 = 70.60125 46.93 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4363   r_free= 0.4201   ksol= 0.00   Bsol= 0.00   scale= 0.814    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.230075                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7775 0.99   1382  152 0.3641 0.3322      6.5423      6.4176|
|  2:  4.7775 -  3.8121 0.99   1318  151 0.3252 0.3403      6.6397      6.7359|
|  3:  3.8121 -  3.3361 0.99   1300  142 0.3822 0.3500      6.5755      6.5368|
|  4:  3.3361 -  3.0338 0.99   1300  142 0.4198 0.3737      6.4671      6.3521|
|  5:  3.0338 -  2.8179 0.99   1269  145 0.4502 0.4439        6.32      6.3311|
|  6:  2.8179 -  2.6527 0.99   1294  140 0.4586 0.5088      6.2329      6.1836|
|  7:  2.6527 -  2.5204 0.99   1265  147 0.4850 0.5000      6.2123      6.1831|
|  8:  2.5204 -  2.4112 0.98   1278  134 0.4879 0.4375      6.1486      6.1274|
|  9:  2.4112 -  2.3187 0.98   1257  142 0.4764 0.4954      6.0845      6.1191|
| 10:  2.3187 -  2.2390 1.00   1277  144 0.5011 0.4410      6.1077      6.0228|
| 11:  2.2390 -  2.1692 0.97   1241  138 0.4871 0.4818      6.0142      6.0381|
| 12:  2.1692 -  2.1073 0.98   1253  134 0.5077 0.4504      5.9759      5.9771|
| 13:  2.1073 -  2.0520 0.99   1253  140 0.4973 0.4819      5.8835      5.8414|
| 14:  2.0520 -  2.0020 0.74    943  108 0.4990 0.4498      5.8485      5.7156|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7775  1382   152  0.75  29.51   0.81     0.77      53848.24|
|  2:  4.7775 -  3.8121  1318   151  0.78  27.98   0.90     0.82      72117.85|
|  3:  3.8121 -  3.3361  1300   142  0.71  34.45   0.86     0.79      75650.47|
|  4:  3.3361 -  3.0338  1300   142  0.65  40.00   0.82     0.70      68833.50|
|  5:  3.0338 -  2.8179  1269   145  0.56  46.99   0.78     0.63      61149.19|
|  6:  2.8179 -  2.6527  1294   140  0.52  50.68   0.75     0.57      57517.97|
|  7:  2.6527 -  2.5204  1265   147  0.48  53.34   0.75     0.55      54394.34|
|  8:  2.5204 -  2.4112  1278   134  0.48  53.87   0.75     0.54      48689.87|
|  9:  2.4112 -  2.3187  1257   142  0.50  51.80   0.75     0.57      43130.59|
| 10:  2.3187 -  2.2390  1277   144  0.51  51.55   0.76     0.58      37662.52|
| 11:  2.2390 -  2.1692  1241   138  0.50  52.02   0.77     0.58      35396.58|
| 12:  2.1692 -  2.1073  1253   134  0.48  53.58   0.76     0.57      33219.51|
| 13:  2.1073 -  2.0520  1253   140  0.48  54.18   0.74     0.56      29208.82|
| 14:  2.0520 -  2.0020   943   108  0.52  50.69   0.74     0.55      22851.55|
|alpha:            min =        0.54 max =            0.82 mean =         0.63|
|beta:             min =    22851.55 max =        75650.47 mean =     50276.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.98 mean =        46.19|
|phase err.(test): min =        0.00 max =           89.97 mean =        46.24|
|-----------------------------------------------------------------------------|

============================== 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 = 7.641340              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.744   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.623856              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.513   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1474 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2587 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3879 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5046 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6488 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7655 |
|-----------------------------------------------------------------------------|
|-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 |       54.208 |
| 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 |       1.657 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    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 = 12.128)------------------------------------------|
|    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: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4440   r_free= 0.4230   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.236598                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4274   r_free= 0.4075   ksol= 0.34   Bsol= 20.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.29,7.65,10.85,0.00,0.00,0.00); trace/3= 8.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.223631                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.084571              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.311   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.618907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.899   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4274      final r-factor (work) = 0.3175          |
| start r-factor (free) = 0.4075      final r-factor (free) = 0.3357          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.3201 = 7.08 * 0.50 * 6.2425 + 1.00 * 54.2076                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.6077 = 7.08 * 0.50 * 6.0658 + 1.00 * 0.1208                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3175      final r-factor (work) = 0.2542          |
| start r-factor (free) = 0.3357      final r-factor (free) = 0.2881          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7690 = 0.62 * 1.00 * 6.0658 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6548 = 0.62 * 1.00 * 5.8858 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.17   10.83    None  None   None       |
|    all(noH): 2823   0      0.00    66.17   10.83    None  None   None       |
|    Sol.    : 438    0      0.00    66.17   27.82    None  None   None       |
|    Mac.    : 2385   0      0.00    56.66   7.71     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 -   6.617: 1336   |   5:    33.084 -  39.701:   87        |
|      1:     6.617 -  13.234:  754   |   6:    39.701 -  46.318:   53        |
|      2:    13.234 -  19.850:  276   |   7:    46.318 -  52.934:   28        |
|      3:    19.850 -  26.467:  145   |   8:    52.934 -  59.551:   12        |
|      4:    26.467 -  33.084:  129   |   9:    59.551 -  66.168:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2542 r_free = 0.2881             target_work(ml) = 5.826         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2535 r_free = 0.2886             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2535   r_free= 0.2886   ksol= 0.34   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.29,7.65,10.85,0.00,0.00,0.00); trace/3= 8.60                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.824252                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2483   r_free= 0.2838   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,4.04,7.03,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.822552                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.172296              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.346904              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.650  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2483      final r-factor (work) = 0.1653          |
| start r-factor (free) = 0.2838      final r-factor (free) = 0.2077          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4180 = 4.17 * 0.50 * 5.8948 + 1.00 * 0.1206                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8354 = 4.17 * 0.50 * 5.6387 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1653      final r-factor (work) = 0.1483          |
| start r-factor (free) = 0.2077      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9681 = 0.35 * 1.00 * 5.6387 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8852 = 0.35 * 1.00 * 5.4031 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.69   11.14    None  None   None       |
|    all(noH): 2823   0      0.00    65.69   11.14    None  None   None       |
|    Sol.    : 438    0      0.00    65.69   31.74    None  None   None       |
|    Mac.    : 2385   0      0.00    56.80   7.36     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 -   6.569: 1455   |   5:    32.846 -  39.416:  114        |
|      1:     6.569 -  13.139:  672   |   6:    39.416 -  45.985:   95        |
|      2:    13.139 -  19.708:  202   |   7:    45.985 -  52.554:   37        |
|      3:    19.708 -  26.277:  117   |   8:    52.554 -  59.124:   16        |
|      4:    26.277 -  32.846:  108   |   9:    59.124 -  65.693:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1483 r_free = 0.1911             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1482 r_free = 0.1911             target_work(ml) = 5.364         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1482   r_free= 0.1911   ksol= 0.33   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,4.04,7.03,0.00,0.00,0.00); trace/3= 4.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.364315                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.1906   ksol= 0.33   Bsol= 52.69   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.34,5.14,0.00,0.00,0.00); trace/3= 3.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.364216                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.660572              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.585  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.619232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.355  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1474      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1906      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9750 = 3.66 * 0.50 * 5.4105 + 1.00 * 0.0721                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7432 = 3.66 * 0.50 * 5.2814 + 1.00 * 0.0768                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5625 = 1.62 * 1.00 * 5.2814 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4190 = 1.62 * 1.00 * 5.1906 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.34   11.82    None  None   None       |
|    all(noH): 2823   0      0.00    74.34   11.82    None  None   None       |
|    Sol.    : 438    0      0.00    74.34   35.35    None  None   None       |
|    Mac.    : 2385   0      0.00    74.03   7.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.434: 1609   |   5:    37.172 -  44.606:   73        |
|      1:     7.434 -  14.869:  589   |   6:    44.606 -  52.041:   85        |
|      2:    14.869 -  22.303:  170   |   7:    52.041 -  59.475:   63        |
|      3:    22.303 -  29.738:  106   |   8:    59.475 -  66.910:   19        |
|      4:    29.738 -  37.172:   98   |   9:    66.910 -  74.344:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1637             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1167 r_free = 0.1636             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1636   ksol= 0.33   Bsol= 52.69   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.34,5.14,0.00,0.00,0.00); trace/3= 3.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.184640                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1637   ksol= 0.33   Bsol= 52.69   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.30,4.87,0.00,0.00,0.00); trace/3= 3.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.184524                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.897699              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.098  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.315504              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.161  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5966 = 2.90 * 0.50 * 5.1902 + 1.00 * 0.0768                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5716 = 2.90 * 0.50 * 5.1729 + 1.00 * 0.0768                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6461 = 0.32 * 1.00 * 5.1729 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6428 = 0.32 * 1.00 * 5.1690 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.74   11.48    None  None   None       |
|    all(noH): 2823   0      0.00    74.74   11.48    None  None   None       |
|    Sol.    : 438    0      0.65    73.35   34.07    None  None   None       |
|    Mac.    : 2385   0      0.00    74.74   7.34     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.474: 1648   |   5:    37.369 -  44.843:   81        |
|      1:     7.474 -  14.948:  575   |   6:    44.843 -  52.317:   75        |
|      2:    14.948 -  22.422:  163   |   7:    52.317 -  59.791:   46        |
|      3:    22.422 -  29.896:  105   |   8:    59.791 -  67.265:   18        |
|      4:    29.896 -  37.369:  103   |   9:    67.265 -  74.739:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1605             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1605   ksol= 0.33   Bsol= 52.69   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.30,4.87,0.00,0.00,0.00); trace/3= 3.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.162962                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1599   ksol= 0.33   Bsol= 52.69   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.30,4.87,0.00,0.00,0.00); trace/3= 3.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161752                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.098880              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.175  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5011 = 2.10 * 0.50 * 5.1687 + 1.00 * 0.0768                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4859 = 2.10 * 0.50 * 5.1642 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6729 = 0.32 * 1.00 * 5.1642 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6728 = 0.32 * 1.00 * 5.1647 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.92   11.39    None  None   None       |
|    all(noH): 2823   0      0.00    74.92   11.39    None  None   None       |
|    Sol.    : 438    0      0.62    73.00   33.84    None  None   None       |
|    Mac.    : 2385   0      0.00    74.92   7.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.492: 1663   |   5:    37.461 -  44.953:   82        |
|      1:     7.492 -  14.984:  566   |   6:    44.953 -  52.445:   75        |
|      2:    14.984 -  22.477:  159   |   7:    52.445 -  59.938:   41        |
|      3:    22.477 -  29.969:  105   |   8:    59.938 -  67.430:   19        |
|      4:    29.969 -  37.461:  105   |   9:    67.430 -  74.922:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1598             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1597             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1597   ksol= 0.33   Bsol= 52.69   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,3.30,4.87,0.00,0.00,0.00); trace/3= 3.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7775 0.99   1382  152 0.1021 0.1320      5.4014      5.5169|
|  2:  4.7775 -  3.8121 0.99   1318  151 0.0869 0.1129       5.452      5.6613|
|  3:  3.8121 -  3.3361 0.99   1300  142 0.1060 0.1481      5.4884      5.8252|
|  4:  3.3361 -  3.0338 0.99   1300  142 0.1207 0.1649      5.4564       5.616|
|  5:  3.0338 -  2.8179 0.99   1269  145 0.1344 0.1683      5.3483      5.5488|
|  6:  2.8179 -  2.6527 0.99   1294  140 0.1214 0.2105      5.2173      5.5425|
|  7:  2.6527 -  2.5204 0.99   1265  147 0.1307 0.1638      5.1949      5.3567|
|  8:  2.5204 -  2.4112 0.98   1278  134 0.1214 0.1707      5.1095      5.3658|
|  9:  2.4112 -  2.3187 0.98   1257  142 0.1206 0.1853      5.0749      5.3242|
| 10:  2.3187 -  2.2390 1.00   1277  144 0.1193 0.1650      5.0027      5.2343|
| 11:  2.2390 -  2.1692 0.97   1241  138 0.1167 0.1762      4.9691      5.2282|
| 12:  2.1692 -  2.1073 0.98   1253  134 0.1155 0.1788      4.8996       5.284|
| 13:  2.1073 -  2.0520 0.99   1253  140 0.1146 0.1713      4.8073      5.0334|
| 14:  2.0520 -  2.0020 0.74    943  108 0.1061 0.1740      4.6957      4.9578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7775  1382   152  0.94   9.21   0.97     0.95       7282.62|
|  2:  4.7775 -  3.8121  1318   151  0.95   8.02   1.01     0.99       9153.67|
|  3:  3.8121 -  3.3361  1300   142  0.93  11.24   1.02     1.01      10608.46|
|  4:  3.3361 -  3.0338  1300   142  0.92  13.40   1.00     0.98      10290.31|
|  5:  3.0338 -  2.8179  1269   145  0.90  15.70   0.99     0.97       8502.54|
|  6:  2.8179 -  2.6527  1294   140  0.90  16.19   0.98     0.95       7192.20|
|  7:  2.6527 -  2.5204  1265   147  0.90  16.02   0.98     0.95       6434.20|
|  8:  2.5204 -  2.4112  1278   134  0.91  15.48   0.99     0.97       5665.44|
|  9:  2.4112 -  2.3187  1257   142  0.90  16.07   1.00     0.97       5460.21|
| 10:  2.3187 -  2.2390  1277   144  0.90  16.26   1.00     0.96       4705.46|
| 11:  2.2390 -  2.1692  1241   138  0.90  16.59   0.99     0.95       4635.43|
| 12:  2.1692 -  2.1073  1253   134  0.91  15.72   1.01     0.99       4066.15|
| 13:  2.1073 -  2.0520  1253   140  0.90  16.12   0.99     0.97       3436.30|
| 14:  2.0520 -  2.0020   943   108  0.92  14.52   0.98     0.94       2700.08|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2700.08 max =        10608.46 mean =      6542.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.26|
|phase err.(test): min =        0.00 max =           89.78 mean =        13.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1597   ksol= 0.33   Bsol= 56.44   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.45,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164129                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1597   ksol= 0.33   Bsol= 56.44   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.45,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7775 0.99   1382  152 0.1021 0.1320      5.4014      5.5169|
|  2:  4.7775 -  3.8121 0.99   1318  151 0.0869 0.1129       5.452      5.6613|
|  3:  3.8121 -  3.3361 0.99   1300  142 0.1060 0.1481      5.4884      5.8252|
|  4:  3.3361 -  3.0338 0.99   1300  142 0.1207 0.1649      5.4564       5.616|
|  5:  3.0338 -  2.8179 0.99   1269  145 0.1344 0.1683      5.3483      5.5488|
|  6:  2.8179 -  2.6527 0.99   1294  140 0.1214 0.2105      5.2173      5.5425|
|  7:  2.6527 -  2.5204 0.99   1265  147 0.1307 0.1638      5.1949      5.3567|
|  8:  2.5204 -  2.4112 0.98   1278  134 0.1214 0.1707      5.1095      5.3658|
|  9:  2.4112 -  2.3187 0.98   1257  142 0.1206 0.1853      5.0749      5.3242|
| 10:  2.3187 -  2.2390 1.00   1277  144 0.1193 0.1650      5.0027      5.2343|
| 11:  2.2390 -  2.1692 0.97   1241  138 0.1167 0.1762      4.9691      5.2282|
| 12:  2.1692 -  2.1073 0.98   1253  134 0.1155 0.1788      4.8996       5.284|
| 13:  2.1073 -  2.0520 0.99   1253  140 0.1146 0.1713      4.8073      5.0334|
| 14:  2.0520 -  2.0020 0.74    943  108 0.1061 0.1740      4.6957      4.9578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7775  1382   152  0.94   9.21   0.97     0.95       7282.62|
|  2:  4.7775 -  3.8121  1318   151  0.95   8.02   1.01     0.99       9153.67|
|  3:  3.8121 -  3.3361  1300   142  0.93  11.24   1.02     1.01      10608.46|
|  4:  3.3361 -  3.0338  1300   142  0.92  13.40   1.00     0.98      10290.31|
|  5:  3.0338 -  2.8179  1269   145  0.90  15.70   0.99     0.97       8502.54|
|  6:  2.8179 -  2.6527  1294   140  0.90  16.19   0.98     0.95       7192.20|
|  7:  2.6527 -  2.5204  1265   147  0.90  16.02   0.98     0.95       6434.20|
|  8:  2.5204 -  2.4112  1278   134  0.91  15.48   0.99     0.97       5665.44|
|  9:  2.4112 -  2.3187  1257   142  0.90  16.07   1.00     0.97       5460.21|
| 10:  2.3187 -  2.2390  1277   144  0.90  16.26   1.00     0.96       4705.46|
| 11:  2.2390 -  2.1692  1241   138  0.90  16.59   0.99     0.95       4635.43|
| 12:  2.1692 -  2.1073  1253   134  0.91  15.72   1.01     0.99       4066.15|
| 13:  2.1073 -  2.0520  1253   140  0.90  16.12   0.99     0.97       3436.30|
| 14:  2.0520 -  2.0020   943   108  0.92  14.52   0.98     0.94       2700.08|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2700.08 max =        10608.46 mean =      6542.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.26|
|phase err.(test): min =        0.00 max =           89.78 mean =        13.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.128)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.74    78.66   15.13    None  None   None       |
|    all(noH): 2823   0      3.74    78.66   15.13    None  None   None       |
|    Sol.    : 438    0      4.36    76.75   37.58    None  None   None       |
|    Mac.    : 2385   0      3.74    78.66   11.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.742 -  11.235: 1663   |   5:    41.203 -  48.696:   82        |
|      1:    11.235 -  18.727:  566   |   6:    48.696 -  56.188:   75        |
|      2:    18.727 -  26.219:  159   |   7:    56.188 -  63.680:   41        |
|      3:    26.219 -  33.711:  105   |   8:    63.680 -  71.172:   19        |
|      4:    33.711 -  41.203:  105   |   9:    71.172 -  78.664:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.288 - 4.636
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 321
   mapped sites are within: 0.703 - 4.636

peak=   11.100 closest distance to " CB  VAL A 230 " =    1.497
peak=    7.144 closest distance to " CG2 VAL A 296 " =    1.153
peak=    6.374 closest distance to " CG  LEU A   5 " =    1.250
peak=    6.253 closest distance to " NH2 ARG A  56 " =    2.212
peak=    5.621 closest distance to " CB  GLN A 223 " =    1.444
peak=    5.600 closest distance to " CG  LEU A 228 " =    1.212
peak=    5.409 closest distance to " CD2 LEU A   5 " =    1.182
peak=    5.309 closest distance to " NE2 GLN A  11 " =    1.154
peak=    5.082 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.936 closest distance to " O   HOH Z 142 " =    1.795
peak=    4.741 closest distance to " CZ  PHE A 218 " =    1.139
peak=    4.685 closest distance to " CB  ARG A 275 " =    0.906
peak=    4.662 closest distance to " CG  PRO A 243 " =    1.135
peak=    4.655 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.635 closest distance to " O   HOH Z 232 " =    2.311
peak=    4.623 closest distance to " CB  VAL A 296 " =    1.043
peak=    4.608 closest distance to " O   HOH Z 126 " =    1.923
peak=    4.559 closest distance to " CB  SER A  63 " =    1.236
peak=    4.558 closest distance to " CG  PRO A 198 " =    1.271
peak=    4.524 closest distance to " ND2 ASN A 187 " =    1.526
peak=    4.445 closest distance to " O   SER A  87 " =    2.332
peak=    4.416 closest distance to " CB  ARG A  79 " =    1.451
peak=    4.414 closest distance to " O   HOH Z 427 " =    3.095
peak=    4.413 closest distance to " O   HOH Z  61 " =    1.735
peak=    4.362 closest distance to " C   PRO A 198 " =    1.543
peak=    4.337 closest distance to " CB  TRP A 266 " =    1.012
peak=    4.316 closest distance to " CB  VAL A 230 " =    1.178
peak=    4.300 closest distance to " O   HOH Z 369 " =    2.121
peak=    4.262 closest distance to " O   HOH Z 265 " =    2.254
peak=    4.235 closest distance to " O   HOH Z 346 " =    1.616
peak=    4.232 closest distance to " O   HOH Z 298 " =    1.784
peak=    4.232 closest distance to " CB  ASN A 148 " =    1.357
peak=    4.227 closest distance to " O   HOH Z 303 " =    2.104
peak=    4.212 closest distance to " CB  ASP A 124 " =    0.722
peak=    4.189 closest distance to " CB  ASN A 142 " =    1.087
peak=    4.182 closest distance to " O   HOH Z 368 " =    2.192
peak=    4.181 closest distance to " CA  TYR A  30 " =    0.998
peak=    4.110 closest distance to " CD2 LEU A 228 " =    1.102
peak=    4.096 closest distance to " O   HOH Z 248 " =    1.610
peak=    4.094 closest distance to " O   HOH Z  78 " =    1.720
peak=    4.080 closest distance to " CB  GLU A 128 " =    0.993
peak=    4.076 closest distance to " CB  ARG A 190 " =    1.545
peak=    4.070 closest distance to " O   HOH Z  43 " =    2.001
peak=    4.067 closest distance to " OG  SER A  97 " =    2.969
peak=    4.063 closest distance to " O   HOH Z 236 " =    2.089
peak=    4.059 closest distance to " O   HOH Z 158 " =    3.268
peak=    4.034 closest distance to " O   HOH Z 272 " =    1.855
peak=    4.026 closest distance to " CB  VAL A 202 " =    1.585
peak=    4.019 closest distance to " CB  VAL A 265 " =    1.325
peak=    3.996 closest distance to " CB  GLU A 152 " =    1.162
peak=    3.979 closest distance to " CB  ASP A 140 " =    0.918
peak=    3.973 closest distance to " N   ASN A  39 " =    1.149
peak=    3.955 closest distance to " CB  ASN A  39 " =    0.909
peak=    3.951 closest distance to " O   HOH Z 234 " =    3.725
peak=    3.942 closest distance to " O   HOH Z   9 " =    1.307
peak=    3.942 closest distance to " CG  MET A 185 " =    1.182
peak=    3.931 closest distance to " O   HOH Z 423 " =    1.789
peak=    3.930 closest distance to " O   HOH Z  92 " =    2.412
peak=    3.919 closest distance to " O   HOH Z 214 " =    2.146
peak=    3.901 closest distance to " O   HOH Z  21 " =    1.781
peak=    3.891 closest distance to " CB  ALA A   9 " =    1.606
peak=    3.888 closest distance to " N   PHE A 130 " =    1.223
peak=    3.878 closest distance to " O   HOH Z 261 " =    1.874
peak=    3.858 closest distance to " O   HOH Z 411 " =    3.884
peak=    3.856 closest distance to " O   HOH Z 209 " =    2.306
peak=    3.854 closest distance to " OG ASER A 258 " =    3.115
peak=    3.851 closest distance to " O  BHOH Z 338 " =    2.373
peak=    3.849 closest distance to " CA  ALA A  51 " =    0.949
peak=    3.849 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.837 closest distance to " O   HOH Z 313 " =    1.825
peak=    3.824 closest distance to " CB  PRO A  54 " =    0.848
peak=    3.823 closest distance to " OD1 ASN A  69 " =    2.608
peak=    3.816 closest distance to " O   HOH Z 126 " =    1.948
peak=    3.811 closest distance to " CD  LYS A 166 " =    1.274
peak=    3.811 closest distance to " CB  GLU A 277 " =    3.645
peak=    3.802 closest distance to " O   HOH Z 251 " =    1.505
peak=    3.800 closest distance to " CB  ASN A 187 " =    1.190
peak=    3.798 closest distance to " CB  SER A   3 " =    1.298
peak=    3.794 closest distance to " CG1 ILE A  49 " =    1.469
peak=    3.791 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.786 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.783 closest distance to " NH1AARG A 145 " =    1.189
peak=    3.783 closest distance to " O   HOH Z 126 " =    1.597
peak=    3.782 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.768 closest distance to " CB  LEU A  83 " =    0.703
peak=    3.763 closest distance to " CG1 VAL A 153 " =    0.973
peak=    3.760 closest distance to " CD1 LEU A  96 " =    0.779
peak=    3.750 closest distance to " CB BVAL A  41 " =    1.173
peak=    3.749 closest distance to " CB  ARG A  79 " =    0.923
peak=    3.748 closest distance to " CA  SER A  87 " =    0.988
peak=    3.743 closest distance to " O   HOH Z 126 " =    1.602
peak=    3.742 closest distance to " O   HOH Z  66 " =    2.220
peak=    3.739 closest distance to " O   HOH Z 425 " =    1.371
peak=    3.733 closest distance to " ND2 ASN A 249 " =    1.899
peak=    3.702 closest distance to " CB  ALA A 104 " =    0.742
peak=    3.700 closest distance to " CA  THR A 264 " =    0.814
peak=    3.694 closest distance to " CA  ARG A  36 " =    1.093
peak=    3.693 closest distance to " O   HOH Z 193 " =    1.958
peak=    3.684 closest distance to " O   HOH Z 353 " =    2.564
peak=    3.676 closest distance to " CD  ARG A  66 " =    2.480
peak=    3.675 closest distance to " CD  ARG A 269 " =    0.988
peak=    3.674 closest distance to " O   HOH Z  78 " =    2.434
peak=    3.672 closest distance to " CB  SER A 212 " =    1.306
peak=    3.660 closest distance to " CG2AVAL A  72 " =    1.757
peak=    3.653 closest distance to " CB  ALA A 291 " =    1.261
peak=    3.648 closest distance to " CZ  PHE A  38 " =    1.151
peak=    3.636 closest distance to " CA  ASN A 215 " =    1.037
peak=    3.630 closest distance to " ND2 ASN A 249 " =    0.882
peak=    3.627 closest distance to " O   HOH Z  59 " =    2.051
peak=    3.627 closest distance to " OG BSER A 164 " =    2.272
peak=    3.619 closest distance to " O   HOH Z 371 " =    2.905
peak=    3.617 closest distance to " CA  TYR A 116 " =    1.440
peak=    3.603 closest distance to " CA  LEU A 282 " =    1.136
peak=    3.598 closest distance to " CB  LYS A 117 " =    1.248
peak=    3.582 closest distance to " O   HOH Z  40 " =    1.696
peak=    3.580 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.578 closest distance to " O   HOH Z 273 " =    2.841
peak=    3.573 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.567 closest distance to " O   HOH Z 128 " =    2.186
peak=    3.564 closest distance to " O   HOH Z 402 " =    1.436
peak=    3.562 closest distance to " CA  ALA A  21 " =    1.093
peak=    3.557 closest distance to " CB  TRP A 179 " =    1.448
peak=    3.553 closest distance to " CD  ARG A 159 " =    0.714
peak=    3.552 closest distance to " O   HOH Z 285 " =    2.494
peak=    3.541 closest distance to " CB  LEU A 228 " =    1.206
peak=    3.540 closest distance to " CZ  PHE A 192 " =    0.972
peak=    3.536 closest distance to " O   HOH Z 145 " =    3.969
peak=    3.528 closest distance to " CD  ARG A  66 " =    2.347
peak=    3.526 closest distance to " CG1 VAL A 296 " =    1.199
peak=    3.524 closest distance to " CA  ALA A 291 " =    0.875
peak=    3.523 closest distance to " CB  THR A  31 " =    1.590
peak=    3.516 closest distance to " O   HOH Z  10 " =    1.795
peak=    3.514 closest distance to " O   HOH Z   3 " =    1.866
peak=    3.512 closest distance to " O   HOH Z 180 " =    2.149
peak=    3.509 closest distance to " NZ  LYS A  48 " =    1.279
peak=    3.500 closest distance to " CB  PRO A  90 " =    1.185
peak=    3.498 closest distance to " CD BLYS A 290 " =    1.060
peak=    3.497 closest distance to " O   HOH Z 187 " =    2.325
peak=    3.494 closest distance to " O   HOH Z 203 " =    1.693
peak=    3.488 closest distance to " CA  TYR A  30 " =    1.081
peak=    3.480 closest distance to " CZ3 TRP A 266 " =    1.099
peak=    3.479 closest distance to " O   HOH Z 403 " =    1.575
peak=    3.474 closest distance to " CB  LEU A 143 " =    1.200
peak=    3.471 closest distance to " CB  MET A  40 " =    0.796
peak=    3.471 closest distance to " O   HOH Z 280 " =    3.038
peak=    3.467 closest distance to " CA  ASP A 162 " =    0.960
peak=    3.463 closest distance to " O   HOH Z 359 " =    1.444
peak=    3.462 closest distance to " CD1 ILE A  33 " =    1.792
peak=    3.451 closest distance to " O   HOH Z 141 " =    1.713
peak=    3.450 closest distance to " CE1 TYR A 186 " =    1.287
peak=    3.447 closest distance to " CG  MET A 185 " =    1.027
peak=    3.447 closest distance to " CA  ALA A 295 " =    1.090
peak=    3.444 closest distance to " O   ASP A 124 " =    1.063
peak=    3.441 closest distance to " CD2 TRP A 179 " =    1.294
peak=    3.440 closest distance to " CA  VAL A 125 " =    1.122
peak=    3.439 closest distance to " CG  GLN A  88 " =    1.077
peak=    3.437 closest distance to " O   HOH Z 290 " =    1.088
peak=    3.435 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.429 closest distance to " CA  ALA A 154 " =    1.027
peak=    3.427 closest distance to " O   HOH Z 291 " =    1.604
peak=    3.426 closest distance to " O   HOH Z  97 " =    2.436
peak=    3.423 closest distance to " O   HOH Z 365 " =    2.958
peak=    3.423 closest distance to " O   HOH Z 147 " =    1.773
peak=    3.423 closest distance to " O   HOH Z 368 " =    3.553
peak=    3.417 closest distance to " CB  THR A  82 " =    1.434
peak=    3.414 closest distance to " O   HOH Z 422 " =    2.686
peak=    3.402 closest distance to " NH2 ARG A 156 " =    1.073
peak=    3.398 closest distance to " N   SER A 135 " =    1.373
peak=    3.396 closest distance to " CA  ALA A 233 " =    1.393
peak=    3.396 closest distance to " CB  GLN A  88 " =    1.185
peak=    3.396 closest distance to " CB  ALA A 114 " =    1.203
peak=    3.390 closest distance to " NE2 HIS A 207 " =    1.214
peak=    3.388 closest distance to " O   HOH Z 171 " =    3.962
peak=    3.382 closest distance to " CB  GLN A  89 " =    1.228
peak=    3.382 closest distance to " O   HOH Z  48 " =    1.586
peak=    3.380 closest distance to " O   HOH Z 250 " =    1.331
peak=    3.377 closest distance to " CB  ASN A 110 " =    1.070
peak=    3.375 closest distance to " O   HOH Z 261 " =    1.627
peak=    3.374 closest distance to " CA  LYS A 117 " =    1.188
peak=    3.373 closest distance to " O   HOH Z 145 " =    2.063
peak=    3.369 closest distance to " CA  ASN A 127 " =    1.024
peak=    3.367 closest distance to " CA  GLY A 267 " =    0.801
peak=    3.366 closest distance to " NE2 GLN A  77 " =    3.393
peak=    3.359 closest distance to " C   ALA A 299 " =    0.921
peak=    3.359 closest distance to " CB  ALA A 248 " =    1.383
peak=    3.358 closest distance to " CD1 LEU A 300 " =    1.176
peak=    3.356 closest distance to " O   HOH Z 258 " =    2.210
peak=    3.352 closest distance to " O   HOH Z   9 " =    1.901
peak=    3.347 closest distance to " CB  SER A 216 " =    0.830
peak=    3.347 closest distance to " CB  ALA A  34 " =    0.983
peak=    3.346 closest distance to " CB  SER A 273 " =    0.922
peak=    3.340 closest distance to " O   HOH Z 350 " =    1.684
peak=    3.339 closest distance to " O   HOH Z 406 " =    1.576
peak=    3.333 closest distance to " CG BARG A 102 " =    1.786
peak=    3.331 closest distance to " O   TRP A 274 " =    1.844
peak=    3.330 closest distance to " O   ASN A  74 " =    1.520
peak=    3.330 closest distance to " O   HOH Z 403 " =    1.490
peak=    3.328 closest distance to " CB  GLN A 103 " =    1.006
peak=    3.318 closest distance to " CG BARG A 275 " =    1.380
peak=    3.318 closest distance to " O   HOH Z  88 " =    3.053
peak=    3.317 closest distance to " O   HOH Z 263 " =    1.703
peak=    3.314 closest distance to " O   HOH Z 421 " =    3.003
peak=    3.312 closest distance to " O   HOH Z 384 " =    3.284
peak=    3.311 closest distance to " CA  MET A 105 " =    0.967
peak=    3.307 closest distance to " CB  ALA A 242 " =    0.793
peak=    3.304 closest distance to " O   HOH Z 172 " =    3.530
peak=    3.301 closest distance to " O   MET A 105 " =    1.817
peak=    3.300 closest distance to " CG2 ILE A  20 " =    1.510
peak=    3.297 closest distance to " NZ  LYS A 117 " =    3.286
peak=    3.290 closest distance to " OG  SER A 245 " =    1.662
peak=    3.288 closest distance to " CA  ILE A 234 " =    0.935
peak=    3.287 closest distance to " O   HOH Z 435 " =    2.012
peak=    3.286 closest distance to " O   HOH Z 197 " =    3.118
peak=    3.286 closest distance to " CG  ARG A 269 " =    1.835
peak=    3.282 closest distance to " O   HOH Z 234 " =    1.804
peak=    3.282 closest distance to " O   HOH Z 148 " =    3.382
peak=    3.282 closest distance to " O   SER A 164 " =    1.291
peak=    3.282 closest distance to " O   ALA A 165 " =    1.554
peak=    3.281 closest distance to " O   HOH Z 299 " =    4.219
peak=    3.281 closest distance to " CA  VAL A  41 " =    0.781
peak=    3.280 closest distance to " N   ASP A 162 " =    1.235
peak=    3.277 closest distance to " CB  SER A 210 " =    0.814
peak=    3.275 closest distance to " O   HOH Z 417 " =    3.158
peak=    3.273 closest distance to " O   HOH Z 329 " =    4.091
peak=    3.273 closest distance to " CG1 ILE A 151 " =    1.117
peak=    3.273 closest distance to " O   HOH Z 294 " =    1.550
peak=    3.272 closest distance to " CA  PHE A 283 " =    1.119
peak=    3.271 closest distance to " CA  ASN A 217 " =    1.281
peak=    3.270 closest distance to " O   HOH Z 185 " =    1.905
peak=    3.265 closest distance to " CD1 ILE A 199 " =    0.970
peak=    3.265 closest distance to " CB  ALA A 248 " =    1.118
peak=    3.265 closest distance to " CD1 LEU A 261 " =    1.258
peak=    3.263 closest distance to " CA  ILE A 106 " =    0.742
peak=    3.262 closest distance to " O   HOH Z 213 " =    1.827
peak=    3.262 closest distance to " CB  ASN A 173 " =    1.044
peak=    3.259 closest distance to " O   HOH Z 305 " =    3.621
peak=    3.251 closest distance to " O   HOH Z 171 " =    2.248
peak=    3.251 closest distance to " O   HOH Z  88 " =    2.699
peak=    3.249 closest distance to " CB  TRP A 150 " =    1.418
peak=    3.249 closest distance to " CA  GLY A 211 " =    1.342
peak=    3.248 closest distance to " N   GLN A 278 " =    1.262
peak=    3.246 closest distance to " O   HOH Z 409 " =    3.161
peak=    3.243 closest distance to " CB  GLN A 205 " =    1.083
peak=    3.243 closest distance to " CB  GLN A 278 " =    0.859
peak=    3.241 closest distance to " O   HOH Z 193 " =    1.701
peak=    3.240 closest distance to " CA  ALA A 158 " =    1.257
peak=    3.238 closest distance to " CD1 ILE A 106 " =    0.991
peak=    3.238 closest distance to " CB  HIS A 108 " =    0.795
peak=    3.234 closest distance to " CB  THR A 157 " =    1.149
peak=    3.232 closest distance to " CB  ILE A 120 " =    1.292
peak=    3.231 closest distance to " CB  LEU A 300 " =    0.859
peak=    3.230 closest distance to " O   HOH Z 128 " =    2.182
peak=    3.225 closest distance to " CB  PHE A 204 " =    0.821
peak=    3.224 closest distance to " CB  ASN A 215 " =    1.187
peak=    3.222 closest distance to " CB  SER A  26 " =    1.765
peak=    3.221 closest distance to " CB  PRO A 243 " =    1.474
peak=    3.217 closest distance to " O   HOH Z 313 " =    1.596
peak=    3.215 closest distance to " CE3 TRP A 150 " =    1.009
peak=    3.214 closest distance to " OG  SER A  22 " =    2.783
peak=    3.208 closest distance to " CZ3 TRP A  85 " =    0.983
peak=    3.203 closest distance to " OG BSER A 134 " =    2.871
peak=    3.203 closest distance to " CB  ALA A  43 " =    0.859
peak=    3.202 closest distance to " O   HOH Z 293 " =    1.760
peak=    3.198 closest distance to " N   ARG A 156 " =    1.380
peak=    3.193 closest distance to " O   GLN A 278 " =    1.530
peak=    3.192 closest distance to " CA  LYS A 290 " =    1.214
peak=    3.188 closest distance to " CB  LYS A 290 " =    0.894
peak=    3.184 closest distance to " O   HOH Z 337 " =    3.516
peak=    3.180 closest distance to " O   HOH Z 302 " =    1.946
peak=    3.178 closest distance to " CA  ASP A 191 " =    1.013
peak=    3.174 closest distance to " CB  ALA A 227 " =    1.032
peak=    3.172 closest distance to " O   TYR A 116 " =    1.340
peak=    3.165 closest distance to " O   HOH Z 148 " =    2.077
peak=    3.164 closest distance to " CA  THR A 221 " =    0.970
peak=    3.161 closest distance to " CZ3 TRP A 274 " =    4.636
peak=    3.161 closest distance to " O   HOH Z  80 " =    1.634
peak=    3.157 closest distance to " CB  TYR A 116 " =    0.850
peak=    3.157 closest distance to " O   HOH Z 437 " =    1.633
peak=    3.156 closest distance to " CB  ASN A 224 " =    1.016
peak=    3.155 closest distance to " O   THR A 220 " =    1.238
peak=    3.155 closest distance to " CD1 ILE A 263 " =    1.189
peak=    3.152 closest distance to " CB  ARG A 145 " =    0.837
peak=    3.152 closest distance to " O   HOH Z 327 " =    1.968
peak=    3.151 closest distance to " CD1 LEU A 228 " =    2.082
peak=    3.149 closest distance to " O   GLN A  88 " =    1.683
peak=    3.147 closest distance to " O   HOH Z  89 " =    1.701
peak=    3.145 closest distance to " CE1 HIS A 108 " =    1.140
peak=    3.144 closest distance to " O   PHE A 192 " =    1.421
peak=    3.142 closest distance to " O   HOH Z  90 " =    2.309
peak=    3.142 closest distance to " CD2 LEU A 297 " =    0.926
peak=    3.141 closest distance to " CB  ARG A 138 " =    0.959
peak=    3.139 closest distance to " ND1 HIS A  81 " =    1.732
peak=    3.136 closest distance to " N   ALA A 256 " =    1.105
peak=    3.134 closest distance to " O   HOH Z 245 " =    1.383
peak=    3.130 closest distance to " OE1 GLU A   2 " =    1.986
peak=    3.130 closest distance to " O   HOH Z 128 " =    1.854
peak=    3.123 closest distance to " CG  GLU A  37 " =    0.848
peak=    3.120 closest distance to " O   HOH Z 329 " =    2.924
peak=    3.120 closest distance to " O   HOH Z  97 " =    2.059
peak=    3.119 closest distance to " CB  MET A  47 " =    1.006
peak=    3.119 closest distance to " CG1 ILE A  33 " =    1.303
peak=    3.118 closest distance to " O   ALA A 158 " =    1.408
peak=    3.107 closest distance to " N   GLY A 133 " =    3.747
peak=    3.098 closest distance to " CB  TYR A 247 " =    0.966
peak=    3.097 closest distance to " O   HOH Z 383 " =    2.107
peak=    3.082 closest distance to " CB  ARG A 139 " =    0.920
peak=    3.082 closest distance to " O   THR A 182 " =    1.388
peak=    3.081 closest distance to " CA  ARG A 139 " =    0.999
peak=    3.073 closest distance to " O   PHE A  61 " =    1.398
peak=    3.072 closest distance to " O   HOH Z 162 " =    3.987
peak=    3.065 closest distance to " O   HOH Z 344 " =    3.001
peak=    3.060 closest distance to " CD  LYS A 119 " =    1.859
peak=    3.043 closest distance to " OG  SER A  62 " =    2.909
peak=    3.042 closest distance to " O   HOH Z 260 " =    1.570
peak=    3.026 closest distance to " CA  ASP A 149 " =    1.099
peak=    3.012 closest distance to " O   HOH Z 132 " =    3.222

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 5.533
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 185
   mapped sites are within: 0.724 - 5.533

peak=   -5.541 closest distance to " CG2 VAL A 230 " =    0.724
peak=   -4.516 closest distance to " CD  ARG A  14 " =    3.300
peak=   -4.509 closest distance to " CD  GLN A  58 " =    0.987
peak=   -4.494 closest distance to " CD  ARG A 156 " =    2.022
peak=   -4.309 closest distance to " O   HOH Z 162 " =    2.656
peak=   -4.240 closest distance to " CG1 VAL A 112 " =    2.642
peak=   -4.164 closest distance to " OG BSER A 134 " =    1.256
peak=   -4.121 closest distance to " CG  GLN A 223 " =    2.148
peak=   -4.120 closest distance to " O   VAL A  67 " =    2.656
peak=   -4.107 closest distance to " CG2 ILE A  49 " =    2.843
peak=   -4.069 closest distance to " O   HOH Z 196 " =    2.161
peak=   -4.052 closest distance to " O   HOH Z 266 " =    5.458
peak=   -4.037 closest distance to " CB  PHE A 192 " =    1.977
peak=   -3.912 closest distance to " O   HOH Z 351 " =    1.529
peak=   -3.910 closest distance to " C   HIS A 108 " =    1.172
peak=   -3.899 closest distance to " CB  ALA A 248 " =    2.371
peak=   -3.894 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -3.878 closest distance to " O   HOH Z 290 " =    1.287
peak=   -3.877 closest distance to " CZ3 TRP A 179 " =    1.186
peak=   -3.874 closest distance to " O   ILE A 109 " =    2.583
peak=   -3.856 closest distance to " CG2 VAL A 296 " =    1.154
peak=   -3.855 closest distance to " O   HOH Z 231 " =    2.103
peak=   -3.838 closest distance to " O   HOH Z 185 " =    2.402
peak=   -3.812 closest distance to " O   VAL A 189 " =    2.635
peak=   -3.803 closest distance to " O   HOH Z 211 " =    1.473
peak=   -3.793 closest distance to " O   VAL A  67 " =    2.835
peak=   -3.786 closest distance to " CG1 VAL A 112 " =    2.827
peak=   -3.749 closest distance to " OG  SER A  97 " =    2.322
peak=   -3.731 closest distance to " CD1 LEU A 255 " =    2.845
peak=   -3.730 closest distance to " O   HOH Z  73 " =    2.249
peak=   -3.729 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.713 closest distance to " CE3 TRP A 150 " =    2.087
peak=   -3.708 closest distance to " CA  GLY A 241 " =    3.159
peak=   -3.705 closest distance to " C   MET A 188 " =    1.367
peak=   -3.679 closest distance to " OD1 ASN A 148 " =    1.422
peak=   -3.663 closest distance to " O   HOH Z 166 " =    2.052
peak=   -3.662 closest distance to " ND2 ASN A  45 " =    1.217
peak=   -3.657 closest distance to " O   HOH Z 394 " =    1.547
peak=   -3.656 closest distance to " CB  ALA A  43 " =    2.576
peak=   -3.639 closest distance to " CA  GLY A 241 " =    2.394
peak=   -3.635 closest distance to " ND2 ASN A  45 " =    1.939
peak=   -3.635 closest distance to " O   PRO A 198 " =    1.187
peak=   -3.608 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.606 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.598 closest distance to " CG1 VAL A 265 " =    2.412
peak=   -3.598 closest distance to " CG  ASP A 231 " =    0.778
peak=   -3.596 closest distance to " OXT GLY A 302 " =    2.955
peak=   -3.591 closest distance to " O   PRO A 163 " =    2.174
peak=   -3.589 closest distance to " O   HOH Z 114 " =    3.024
peak=   -3.572 closest distance to " CE BMET A  47 " =    1.690
peak=   -3.571 closest distance to " NH2AARG A 275 " =    5.255
peak=   -3.568 closest distance to " O   HOH Z  37 " =    1.860
peak=   -3.559 closest distance to " O   HOH Z  44 " =    2.320
peak=   -3.532 closest distance to " CG1 VAL A 250 " =    2.789
peak=   -3.530 closest distance to " O   HOH Z  60 " =    2.148
peak=   -3.520 closest distance to " CG  HIS A  86 " =    1.159
peak=   -3.513 closest distance to " CD2 TYR A 293 " =    2.067
peak=   -3.511 closest distance to " N   ASP A 171 " =    2.344
peak=   -3.502 closest distance to " O   HOH Z 407 " =    3.095
peak=   -3.500 closest distance to " CD2 PHE A  61 " =    2.597
peak=   -3.494 closest distance to " NH2 ARG A  79 " =    1.562
peak=   -3.473 closest distance to " N   THR A 157 " =    1.478
peak=   -3.471 closest distance to " CG  TRP A 266 " =    1.902
peak=   -3.466 closest distance to " O   HOH Z 216 " =    1.386
peak=   -3.462 closest distance to " OG  SER A  87 " =    1.442
peak=   -3.461 closest distance to " O   HOH Z 198 " =    2.272
peak=   -3.457 closest distance to " CE  MET A 105 " =    2.398
peak=   -3.457 closest distance to " N   ALA A  43 " =    2.508
peak=   -3.447 closest distance to " O   HOH Z  52 " =    1.542
peak=   -3.433 closest distance to " O   TYR A 247 " =    2.901
peak=   -3.432 closest distance to " NH2 ARG A 159 " =    2.370
peak=   -3.432 closest distance to " C   LEU A 222 " =    0.852
peak=   -3.418 closest distance to " O   HOH Z 265 " =    1.763
peak=   -3.413 closest distance to " O   MET A  40 " =    2.795
peak=   -3.408 closest distance to " O   GLY A  17 " =    1.314
peak=   -3.406 closest distance to " NE2 GLN A 194 " =    1.841
peak=   -3.405 closest distance to " NE2 GLN A  88 " =    1.001
peak=   -3.397 closest distance to " O   HOH Z 389 " =    2.093
peak=   -3.396 closest distance to " CG  ARG A 269 " =    2.383
peak=   -3.392 closest distance to " CZ  PHE A 155 " =    1.108
peak=   -3.391 closest distance to " NH2 ARG A  79 " =    2.044
peak=   -3.385 closest distance to " O   HOH Z 179 " =    2.252
peak=   -3.383 closest distance to " C   LEU A 143 " =    1.055
peak=   -3.382 closest distance to " O   GLY A 196 " =    1.266
peak=   -3.380 closest distance to " N   ALA A 248 " =    1.852
peak=   -3.379 closest distance to " N   ALA A 226 " =    2.150
peak=   -3.378 closest distance to " O   HOH Z 377 " =    2.099
peak=   -3.376 closest distance to " C   ALA A 158 " =    1.382
peak=   -3.375 closest distance to " O   GLY A  80 " =    2.571
peak=   -3.374 closest distance to " CG1 VAL A 296 " =    1.358
peak=   -3.372 closest distance to " O   HOH Z 262 " =    2.866
peak=   -3.371 closest distance to " CG2 VAL A 202 " =    2.734
peak=   -3.367 closest distance to " CB  ALA A 291 " =    2.275
peak=   -3.364 closest distance to " ND2 ASN A 249 " =    2.428
peak=   -3.364 closest distance to " N   THR A  52 " =    1.677
peak=   -3.357 closest distance to " O   HOH Z 359 " =    3.058
peak=   -3.355 closest distance to " N   SER A 212 " =    1.930
peak=   -3.342 closest distance to " O   HOH Z 285 " =    1.896
peak=   -3.339 closest distance to " O   HOH Z 243 " =    1.839
peak=   -3.335 closest distance to " OD2 ASP A  50 " =    2.407
peak=   -3.334 closest distance to " CB  PRO A 163 " =    2.532
peak=   -3.328 closest distance to " CG1 VAL A  67 " =    2.869
peak=   -3.328 closest distance to " CG1 VAL A 125 " =    1.936
peak=   -3.326 closest distance to " N   ALA A 248 " =    2.402
peak=   -3.324 closest distance to " O   HOH Z 426 " =    1.668
peak=   -3.314 closest distance to " CD1 LEU A 228 " =    2.299
peak=   -3.314 closest distance to " O   HOH Z  10 " =    1.460
peak=   -3.312 closest distance to " O   HOH Z  13 " =    1.736
peak=   -3.310 closest distance to " CG  ASP A 132 " =    2.304
peak=   -3.306 closest distance to " CB  ASN A  69 " =    1.263
peak=   -3.294 closest distance to " CG2 THR A 178 " =    2.197
peak=   -3.293 closest distance to " CD1 LEU A 101 " =    2.386
peak=   -3.287 closest distance to " O   HOH Z 353 " =    2.060
peak=   -3.284 closest distance to " O   HOH Z 275 " =    1.856
peak=   -3.283 closest distance to " O   HOH Z  38 " =    1.593
peak=   -3.271 closest distance to " CG  GLU A 277 " =    1.256
peak=   -3.270 closest distance to " NE2 GLN A  88 " =    2.021
peak=   -3.266 closest distance to " O   HOH Z 134 " =    3.108
peak=   -3.265 closest distance to " O   HOH Z 295 " =    1.573
peak=   -3.262 closest distance to " CD  PRO A 213 " =    2.098
peak=   -3.260 closest distance to " CB  GLN A  11 " =    1.791
peak=   -3.259 closest distance to " CD  ARG A 139 " =    1.643
peak=   -3.253 closest distance to " O   HOH Z 275 " =    1.523
peak=   -3.252 closest distance to " OE1 GLN A  88 " =    1.039
peak=   -3.251 closest distance to " O   HOH Z 191 " =    5.533
peak=   -3.248 closest distance to " CG1 VAL A 197 " =    2.276
peak=   -3.246 closest distance to " OG  SER A 206 " =    1.768
peak=   -3.246 closest distance to " O   HOH Z 174 " =    2.521
peak=   -3.234 closest distance to " CA  GLY A  98 " =    1.885
peak=   -3.230 closest distance to " O   HOH Z 177 " =    1.745
peak=   -3.225 closest distance to " NE2 GLN A 278 " =    1.887
peak=   -3.225 closest distance to " CB  ALA A 291 " =    2.205
peak=   -3.220 closest distance to " SD BMET A  47 " =    1.115
peak=   -3.216 closest distance to " O   HOH Z 326 " =    5.112
peak=   -3.216 closest distance to " ND2 ASN A  60 " =    1.389
peak=   -3.207 closest distance to " O   ARG A 145 " =    1.634
peak=   -3.205 closest distance to " C   PHE A  59 " =    1.285
peak=   -3.204 closest distance to " OG BSER A 134 " =    1.880
peak=   -3.200 closest distance to " OD1 ASN A 187 " =    1.689
peak=   -3.197 closest distance to " O   HOH Z 102 " =    1.638
peak=   -3.196 closest distance to " O   HOH Z 256 " =    1.333
peak=   -3.194 closest distance to " CD1 TRP A 274 " =    1.040
peak=   -3.192 closest distance to " CD1 ILE A 239 " =    2.176
peak=   -3.192 closest distance to " CA  GLY A 203 " =    2.498
peak=   -3.191 closest distance to " O   HOH Z 313 " =    1.151
peak=   -3.189 closest distance to " CG2 VAL A 189 " =    1.978
peak=   -3.185 closest distance to " N   SER A   3 " =    2.024
peak=   -3.185 closest distance to " ND2 ASN A 187 " =    1.491
peak=   -3.182 closest distance to " O   HOH Z 241 " =    1.280
peak=   -3.181 closest distance to " O   PRO A 198 " =    1.349
peak=   -3.180 closest distance to " CA  GLY A 133 " =    2.342
peak=   -3.175 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.175 closest distance to " O   LEU A 101 " =    2.833
peak=   -3.172 closest distance to " O   HOH Z 176 " =    0.799
peak=   -3.171 closest distance to " CD1 LEU A   5 " =    2.543
peak=   -3.166 closest distance to " O   GLY A  80 " =    2.309
peak=   -3.160 closest distance to " O   ASP A  27 " =    2.069
peak=   -3.152 closest distance to " O   HOH Z 313 " =    1.682
peak=   -3.150 closest distance to " O   ALA A 161 " =    1.770
peak=   -3.145 closest distance to " CA  SER A 135 " =    1.315
peak=   -3.143 closest distance to " CD2 PHE A 225 " =    1.080
peak=   -3.143 closest distance to " O   HOH Z 252 " =    3.915
peak=   -3.139 closest distance to " CG2 VAL A 296 " =    1.814
peak=   -3.130 closest distance to " CG  PHE A 283 " =    2.664
peak=   -3.127 closest distance to " CB  ASP A 171 " =    2.314
peak=   -3.124 closest distance to " O   HOH Z 359 " =    1.564
peak=   -3.120 closest distance to " O   ALA A  51 " =    1.426
peak=   -3.115 closest distance to " CD1 ILE A 151 " =    2.465
peak=   -3.112 closest distance to " O   SER A  22 " =    2.336
peak=   -3.111 closest distance to " CD1 ILE A 199 " =    2.514
peak=   -3.110 closest distance to " O   HOH Z 123 " =    2.414
peak=   -3.109 closest distance to " CB  TRP A 177 " =    2.337
peak=   -3.104 closest distance to " O   HOH Z 350 " =    1.896
peak=   -3.100 closest distance to " O   HOH Z 166 " =    1.671
peak=   -3.088 closest distance to " O   HOH Z  89 " =    3.049
peak=   -3.079 closest distance to " OG  SER A  63 " =    1.156
peak=   -3.071 closest distance to " CD  PRO A 243 " =    2.091
peak=   -3.071 closest distance to " O   HOH Z 390 " =    2.315
peak=   -3.066 closest distance to " N   SER A 276 " =    1.357
peak=   -3.062 closest distance to " O   HOH Z  96 " =    1.482
peak=   -3.055 closest distance to " O   HOH Z 140 " =    1.443
peak=   -3.053 closest distance to " C   ASP A 270 " =    1.323
peak=   -3.052 closest distance to " OD1 ASP A 171 " =    1.653
peak=   -3.035 closest distance to " C   GLN A  58 " =    2.001
peak=   -3.032 closest distance to " CD2 TYR A 247 " =    2.342

================= 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    :  0.4363 0.4201   6.230075e+00   6.198055e+00
   1_bss:  0.4274 0.4075   6.223631e+00   6.184582e+00
   1_xyz:  0.3175 0.3357   6.013046e+00   6.048599e+00
   1_adp:  0.2542 0.2881   5.825748e+00   5.933528e+00
   1_occ:  0.2535 0.2886   5.824252e+00   5.935391e+00
   2_bss:  0.2483 0.2838   5.822552e+00   5.931262e+00
   2_xyz:  0.1653 0.2077   5.457891e+00   5.637258e+00
   2_adp:  0.1483 0.1911   5.364820e+00   5.562180e+00
   2_occ:  0.1482 0.1911   5.364315e+00   5.561984e+00
   3_bss:  0.1474 0.1906   5.364216e+00   5.562067e+00
   3_xyz:  0.1220 0.1660   5.210727e+00   5.439729e+00
   3_adp:  0.1168 0.1637   5.184961e+00   5.426116e+00
   3_occ:  0.1167 0.1636   5.184640e+00   5.425907e+00
   4_bss:  0.1167 0.1637   5.184524e+00   5.425964e+00
   4_xyz:  0.1131 0.1618   5.167072e+00   5.416188e+00
   4_adp:  0.1134 0.1605   5.163188e+00   5.406797e+00
   4_occ:  0.1134 0.1605   5.162962e+00   5.406819e+00
   5_bss:  0.1134 0.1599   5.161752e+00   5.403610e+00
   5_xyz:  0.1140 0.1601   5.165112e+00   5.404650e+00
   5_adp:  0.1139 0.1598   5.164229e+00   5.402974e+00
   5_occ:  0.1139 0.1597   5.164129e+00   5.403008e+00
   5_bss:  0.1139 0.1597   5.164129e+00   5.403008e+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:  0.340  20.001   7.287   7.645  10.852   0.000   0.000   0.000
   1_xyz:  0.340  20.001   7.287   7.645  10.852   0.000   0.000   0.000
   1_adp:  0.340  20.001   7.287   7.645  10.852   0.000   0.000   0.000
   1_occ:  0.340  20.001   7.287   7.645  10.852   0.000   0.000   0.000
   2_bss:  0.326  50.000   3.896   4.043   7.030   0.000   0.000   0.000
   2_xyz:  0.326  50.000   3.896   4.043   7.030   0.000   0.000   0.000
   2_adp:  0.326  50.000   3.896   4.043   7.030   0.000   0.000   0.000
   2_occ:  0.326  50.000   3.896   4.043   7.030   0.000   0.000   0.000
   3_bss:  0.327  52.695   3.071   3.342   5.142   0.000   0.000   0.000
   3_xyz:  0.327  52.695   3.071   3.342   5.142   0.000   0.000   0.000
   3_adp:  0.327  52.695   3.071   3.342   5.142   0.000   0.000   0.000
   3_occ:  0.327  52.695   3.071   3.342   5.142   0.000   0.000   0.000
   4_bss:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   4_xyz:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   4_adp:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   4_occ:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   5_bss:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   5_xyz:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   5_adp:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   5_occ:  0.327  52.695   3.058   3.297   4.872   0.000   0.000   0.000
   5_bss:  0.327  56.437  -0.684  -0.445   1.129   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.194 0.5694  0.6310    50275.216
   1_bss:  45.741 0.5737  0.8245    48115.355
   1_xyz:  35.914 0.6903  0.9542    30400.653
   1_adp:  29.212 0.7673  1.0352    21817.946
   1_occ:  29.261 0.7667  1.0339    21887.645
   2_bss:  28.971 0.7698  0.9123    21541.890
   2_xyz:  19.777 0.8636  0.9956    10684.049
   2_adp:  17.728 0.8832  1.0088     9146.979
   2_occ:  17.721 0.8833  1.0088     9134.554
   3_bss:  17.699 0.8836  0.9680     9170.960
   3_xyz:  15.049 0.9064  0.9778     7068.017
   3_adp:  14.763 0.9090  0.9756     6879.200
   3_occ:  14.756 0.9090  0.9756     6875.392
   4_bss:  14.754 0.9090  0.9719     6877.263
   4_xyz:  14.461 0.9118  0.9727     6751.190
   4_adp:  14.249 0.9135  0.9710     6636.133
   4_occ:  14.249 0.9135  0.9710     6634.524
   5_bss:  14.213 0.9137  0.9706     6572.252
   5_xyz:  14.238 0.9135  0.9703     6564.158
   5_adp:  14.206 0.9138  0.9681     6542.489
   5_occ:  14.207 0.9138  0.9680     6542.296
   5_bss:  14.207 0.9138  0.9680     6542.296
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4208e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4208e+01
   1_xyz:   1.537  0.012  0.103 18.033  0.006  4.125   1.2079e-01
   1_adp:   1.537  0.012  0.103 18.033  0.006  4.125   1.2079e-01
   1_occ:   1.537  0.012  0.103 18.033  0.006  4.125   1.2079e-01
   2_bss:   1.537  0.012  0.103 18.033  0.006  4.125   1.2079e-01
   2_xyz:   1.074  0.009  0.079 16.624  0.004  4.128   7.2143e-02
   2_adp:   1.074  0.009  0.079 16.624  0.004  4.128   7.2143e-02
   2_occ:   1.074  0.009  0.079 16.624  0.004  4.128   7.2143e-02
   3_bss:   1.074  0.009  0.079 16.624  0.004  4.128   7.2143e-02
   3_xyz:   1.119  0.010  0.090 16.198  0.004  4.141   7.6832e-02
   3_adp:   1.119  0.010  0.090 16.198  0.004  4.141   7.6832e-02
   3_occ:   1.119  0.010  0.090 16.198  0.004  4.141   7.6832e-02
   4_bss:   1.119  0.010  0.090 16.198  0.004  4.141   7.6832e-02
   4_xyz:   1.101  0.010  0.090 15.964  0.004  4.113   7.6814e-02
   4_adp:   1.101  0.010  0.090 15.964  0.004  4.113   7.6814e-02
   4_occ:   1.101  0.010  0.090 15.964  0.004  4.113   7.6814e-02
   5_bss:   1.101  0.010  0.090 15.964  0.004  4.113   7.6814e-02
   5_xyz:   1.025  0.008  0.083 15.671  0.004  4.114   6.6396e-02
   5_adp:   1.025  0.008  0.083 15.671  0.004  4.114   6.6396e-02
   5_occ:   1.025  0.008  0.083 15.671  0.004  4.114   6.6396e-02
   5_bss:   1.025  0.008  0.083 15.671  0.004  4.114   6.6396e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0286e+00
   1_xyz:  13.021  0.139  0.394 86.557  0.034  2.191   9.0442e-02
   1_adp:  13.021  0.139  0.394 86.557  0.034  2.191   9.0442e-02
   1_occ:  13.021  0.139  0.394 86.557  0.034  2.191   9.0442e-02
   2_bss:  13.021  0.139  0.394 86.557  0.034  2.191   9.0442e-02
   2_xyz:   7.940  0.089  0.344 88.773  0.033  2.322   7.4322e-02
   2_adp:   7.940  0.089  0.344 88.773  0.033  2.322   7.4322e-02
   2_occ:   7.940  0.089  0.344 88.773  0.033  2.322   7.4322e-02
   3_bss:   7.940  0.089  0.344 88.773  0.033  2.322   7.4322e-02
   3_xyz:   7.178  0.046  0.622 83.320  0.041  2.313   5.4457e-02
   3_adp:   7.178  0.046  0.622 83.320  0.041  2.313   5.4457e-02
   3_occ:   7.178  0.046  0.622 83.320  0.041  2.313   5.4457e-02
   4_bss:   7.178  0.046  0.622 83.320  0.041  2.313   5.4457e-02
   4_xyz:   7.132  0.056  0.612 82.880  0.040  2.348   5.4179e-02
   4_adp:   7.132  0.056  0.612 82.880  0.040  2.348   5.4179e-02
   4_occ:   7.132  0.056  0.612 82.880  0.040  2.348   5.4179e-02
   5_bss:   7.132  0.056  0.612 82.880  0.040  2.348   5.4179e-02
   5_xyz:   6.884  0.048  0.520 82.504  0.039  2.356   4.2153e-02
   5_adp:   6.884  0.048  0.520 82.504  0.039  2.356   4.2153e-02
   5_occ:   6.884  0.048  0.520 82.504  0.039  2.356   4.2153e-02
   5_bss:   6.884  0.048  0.520 82.504  0.039  2.356   4.2153e-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:  66.17   0.00  10.83  56.66   0.00   7.71  66.17   0.00  27.82
   1_occ:  66.17   0.00  10.83  56.66   0.00   7.71  66.17   0.00  27.82
   2_bss:  66.17   0.00  10.83  56.66   0.00   7.71  66.17   0.00  27.82
   2_xyz:  66.17   0.00  10.83  56.66   0.00   7.71  66.17   0.00  27.82
   2_adp:  65.69   0.00  11.14  56.80   0.00   7.36  65.69   0.00  31.74
   2_occ:  65.69   0.00  11.14  56.80   0.00   7.36  65.69   0.00  31.74
   3_bss:  65.69   0.00  11.14  56.80   0.00   7.36  65.69   0.00  31.74
   3_xyz:  65.69   0.00  11.14  56.80   0.00   7.36  65.69   0.00  31.74
   3_adp:  74.34   0.00  11.82  74.03   0.00   7.50  74.34   0.00  35.35
   3_occ:  74.34   0.00  11.82  74.03   0.00   7.50  74.34   0.00  35.35
   4_bss:  74.34   0.00  11.82  74.03   0.00   7.50  74.34   0.00  35.35
   4_xyz:  74.34   0.00  11.82  74.03   0.00   7.50  74.34   0.00  35.35
   4_adp:  74.74   0.00  11.48  74.74   0.00   7.34  73.35   0.65  34.07
   4_occ:  74.74   0.00  11.48  74.74   0.00   7.34  73.35   0.65  34.07
   5_bss:  74.74   0.00  11.48  74.74   0.00   7.34  73.35   0.65  34.07
   5_xyz:  74.74   0.00  11.48  74.74   0.00   7.34  73.35   0.65  34.07
   5_adp:  74.92   0.00  11.39  74.92   0.00   7.27  73.00   0.62  33.84
   5_occ:  74.92   0.00  11.39  74.92   0.00   7.27  73.00   0.62  33.84
   5_bss:  78.66   3.74  15.13  78.66   3.74  11.01  76.75   4.36  37.58
------------------------------------------------------------------------
 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:    1.226    0.011    0.403
   1_adp:    1.226    0.011    0.403
   1_occ:    1.226    0.011    0.403
   2_bss:    1.226    0.011    0.403
   2_xyz:    1.562    0.038    0.513
   2_adp:    1.562    0.038    0.513
   2_occ:    1.562    0.038    0.513
   3_bss:    1.562    0.038    0.513
   3_xyz:    1.561    0.047    0.545
   3_adp:    1.561    0.047    0.545
   3_occ:    1.561    0.047    0.545
   4_bss:    1.561    0.047    0.545
   4_xyz:    1.645    0.041    0.554
   4_adp:    1.645    0.041    0.554
   4_occ:    1.645    0.041    0.554
   5_bss:    1.645    0.041    0.554
   5_xyz:    1.693    0.039    0.566
   5_adp:    1.693    0.039    0.566
   5_occ:    1.693    0.039    0.566
   5_bss:    1.693    0.039    0.566
------------------------------------------------------------------------

CPU time actual refinement: 316.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_789/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_789/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_789/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_789/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_789/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.38 
  Macro-tasks:
    bulk solvent and scale       = 40.15  
    individual site refinement   = 126.97 
    weights calculation          = 31.69  
    collect and process          = 6.62   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 205.54 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 94.61  
    alpha_beta                      = 8.27   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 105.62 
    fmodel                         = 7.14   
    r_factors                      = 0.22   
    phase_errors                   = 11.01  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 230.03 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.474 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    641 calls, 94.20 s
gradients_fft:          587 calls, 92.22 s

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

# Date 2008-01-16 Time 02:25:57 PST -0800 (1200479157.71 s)
Start R-work = 0.4363, R-free = 0.4201 (no bulk solvent and anisotropic scale)
Final R-work = 0.1314, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.4274, R-free = 0.4075
Final R-work = 0.1139, R-free = 0.1597