# Date 2008-01-16 Time 02:31:42 PST -0800 (1200479502.25 s)
#phil __OFF__

Command line arguments: "../864.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1757
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 864

-------------------------------------------------------------------------------
  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: (70.9525, 45.9914, 86.822, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.96355
Completeness in resolution range: 0.938575
Completeness with d_max=infinity: 0.935885

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   1.9636

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: (70.9525, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.96355
Completeness in resolution range: 0.938575
Completeness with d_max=infinity: 0.935885

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.2029 [2197/2224]  1976   221  10.1%
  bin  2:  4.2029 -  3.3479 [2109/2129]  1899   210  10.0%
  bin  3:  3.3479 -  2.9282 [2076/2095]  1870   206   9.9%
  bin  4:  2.9282 -  2.6620 [2058/2088]  1849   209  10.2%
  bin  5:  2.6620 -  2.4721 [2043/2062]  1847   196   9.6%
  bin  6:  2.4721 -  2.3269 [2044/2069]  1830   214  10.5%
  bin  7:  2.3269 -  2.2108 [2027/2055]  1821   206  10.2%
  bin  8:  2.2108 -  2.1148 [2006/2042]  1808   198   9.9%
  bin  9:  2.1148 -  2.0336 [2021/2063]  1825   196   9.7%
  bin 10:  2.0336 -  1.9636 [1008/2044]   905   103  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_864/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: 32
        2.42 -     3.04: 2205
        3.04 -     3.66: 4735
        3.66 -     4.28: 9049
        4.28 -     4.90: 12316
  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 201 " - " O   HOH Z 349 "  1.854 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28332 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_864/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_864/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 = 70.9525 45.9914 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4817   r_free= 0.4746   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.286950                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.6884 0.99   1421  158 0.4120 0.3950      6.6122      6.6217|
|  2:  4.6884 -  3.7398 0.99   1373  155 0.4001 0.3658      6.8118      6.7464|
|  3:  3.7398 -  3.2726 0.99   1342  142 0.4261 0.4037       6.661      6.6354|
|  4:  3.2726 -  2.9758 0.99   1331  155 0.4716 0.4537      6.5323      6.5108|
|  5:  2.9758 -  2.7639 0.99   1338  149 0.5182 0.5227      6.3755      6.3799|
|  6:  2.7639 -  2.6018 0.99   1327  146 0.5108 0.5223      6.2748      6.2214|
|  7:  2.6018 -  2.4721 0.99   1309  137 0.5295 0.4964      6.2462      6.1719|
|  8:  2.4721 -  2.3649 0.98   1299  152 0.5228 0.4834      6.1727      6.1846|
|  9:  2.3649 -  2.2742 0.98   1307  148 0.5216 0.5429      6.1232       6.183|
| 10:  2.2742 -  2.1960 1.00   1298  147 0.5279 0.5133      6.0974       6.068|
| 11:  2.1960 -  2.1275 0.98   1316  137 0.5039 0.5205       6.036      6.0346|
| 12:  2.1275 -  2.0668 0.98   1288  144 0.5268 0.5749      5.9453      5.9933|
| 13:  2.0668 -  2.0125 0.98   1265  142 0.5452 0.5584      5.8835      5.8073|
| 14:  2.0125 -  1.9636 0.31    416   47 0.5672 0.4856      5.8757      5.8412|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.6884  1421   158  0.67  37.12   0.79     0.73      82325.69|
|  2:  4.6884 -  3.7398  1373   155  0.72  33.85   0.86     0.79     103370.22|
|  3:  3.7398 -  3.2726  1342   142  0.61  42.86   0.86     0.74     109658.72|
|  4:  3.2726 -  2.9758  1331   155  0.52  50.34   0.79     0.62      99639.33|
|  5:  2.9758 -  2.7639  1338   149  0.40  59.42   0.73     0.50      85508.60|
|  6:  2.7639 -  2.6018  1327   146  0.38  61.18   0.71     0.45      73688.19|
|  7:  2.6018 -  2.4721  1309   137  0.33  65.05   0.74     0.39      68022.93|
|  8:  2.4721 -  2.3649  1299   152  0.31  66.57   0.72     0.37      61944.27|
|  9:  2.3649 -  2.2742  1307   148  0.31  66.62   0.73     0.37      56738.33|
| 10:  2.2742 -  2.1960  1298   147  0.33  65.59   0.74     0.39      50508.42|
| 11:  2.1960 -  2.1275  1316   137  0.30  67.70   0.79     0.37      50013.32|
| 12:  2.1275 -  2.0668  1288   144  0.26  70.98   0.74     0.34      46666.66|
| 13:  2.0668 -  2.0125  1265   142  0.24  71.80   0.71     0.33      40763.13|
| 14:  2.0125 -  1.9636   416    47  0.35  63.92   0.70     0.40      29363.55|
|alpha:            min =        0.33 max =            0.79 mean =         0.49|
|beta:             min =    29363.55 max =       109658.72 mean =     70891.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.98 mean =        58.21|
|phase err.(test): min =        0.00 max =           89.99 mean =        58.47|
|-----------------------------------------------------------------------------|

============================== 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 = 16.267225             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.741   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.363849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.753   (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:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1515 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2652 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3937 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5086 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6561 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7721 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.671 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.988 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4876   r_free= 0.4759   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.288642                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4738   r_free= 0.4605   ksol= 0.34   Bsol= 2.47   scale= 0.996    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,10.09,8.24,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.280343                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.760466             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.997   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.327861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.578   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4738      final r-factor (work) = 0.3947          |
| start r-factor (free) = 0.4605      final r-factor (free) = 0.4186          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.8957 = 13.76 * 0.50 * 6.2825 + 1.00 * 53.6708                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.8390 = 13.76 * 0.50 * 6.2056 + 1.00 * 0.1430                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3947      final r-factor (work) = 0.3518          |
| start r-factor (free) = 0.4186      final r-factor (free) = 0.4122          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2546 = 1.33 * 1.00 * 6.2056 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1614 = 1.33 * 1.00 * 6.1330 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.42   14.05    None  None   None       |
|    all(noH): 2823   0      0.00    77.42   14.05    None  None   None       |
|    Sol.    : 438    0      0.00    77.42   24.68    None  None   None       |
|    Mac.    : 2385   0      0.00    69.63   12.10    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 -   7.742: 1016   |   5:    38.709 -  46.451:   82        |
|      1:     7.742 -  15.484:  807   |   6:    46.451 -  54.193:   33        |
|      2:    15.484 -  23.226:  473   |   7:    54.193 -  61.935:   14        |
|      3:    23.226 -  30.968:  256   |   8:    61.935 -  69.677:   11        |
|      4:    30.968 -  38.709:  130   |   9:    69.677 -  77.419:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3518 r_free = 0.4122             target_work(ml) = 6.121         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3515 r_free = 0.4124             target_work(ml) = 6.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3515   r_free= 0.4124   ksol= 0.34   Bsol= 2.47   scale= 1.118    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,10.09,8.24,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.120570                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3480   r_free= 0.4061   ksol= 0.35   Bsol= 43.13   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.00,5.53,4.36,0.00,0.00,0.00); trace/3= 4.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.119787                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.959616              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.388  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.615291              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.294  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3480      final r-factor (work) = 0.2826          |
| start r-factor (free) = 0.4061      final r-factor (free) = 0.3432          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5338 = 7.96 * 0.50 * 6.1286 + 1.00 * 0.1430                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1069 = 7.96 * 0.50 * 6.0357 + 1.00 * 0.0859                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2826      final r-factor (work) = 0.2615          |
| start r-factor (free) = 0.3432      final r-factor (free) = 0.3283          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7314 = 0.62 * 1.00 * 6.0357 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6523 = 0.62 * 1.00 * 5.9150 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.63   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    80.63   13.93    None  None   None       |
|    Sol.    : 438    0      0.00    80.63   30.79    None  None   None       |
|    Mac.    : 2385   0      0.00    64.94   10.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.063: 1148   |   5:    40.314 -  48.377:   76        |
|      1:     8.063 -  16.126:  813   |   6:    48.377 -  56.440:   28        |
|      2:    16.126 -  24.189:  377   |   7:    56.440 -  64.503:   17        |
|      3:    24.189 -  32.252:  207   |   8:    64.503 -  72.566:    6        |
|      4:    32.252 -  40.314:  148   |   9:    72.566 -  80.629:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2615 r_free = 0.3283             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2614 r_free = 0.3286             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2614   r_free= 0.3286   ksol= 0.35   Bsol= 43.13   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.00,5.53,4.36,0.00,0.00,0.00); trace/3= 4.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.894398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2604   r_free= 0.3260   ksol= 0.33   Bsol= 43.13   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,2.95,3.28,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.894289                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.391379              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.604  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.529513              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.265  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2604      final r-factor (work) = 0.1974          |
| start r-factor (free) = 0.3260      final r-factor (free) = 0.2556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0736 = 4.39 * 0.50 * 5.9151 + 1.00 * 0.0859                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7636 = 4.39 * 0.50 * 5.7803 + 1.00 * 0.0717                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1974      final r-factor (work) = 0.1781          |
| start r-factor (free) = 0.2556      final r-factor (free) = 0.2360          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0736 = 0.53 * 1.00 * 5.7803 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9722 = 0.53 * 1.00 * 5.5905 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.71   14.12    None  None   None       |
|    all(noH): 2823   0      0.00    83.71   14.12    None  None   None       |
|    Sol.    : 438    0      2.95    83.71   36.15    None  None   None       |
|    Mac.    : 2385   0      0.00    75.21   10.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.371: 1310   |   5:    41.857 -  50.228:  117        |
|      1:     8.371 -  16.743:  793   |   6:    50.228 -  58.599:   52        |
|      2:    16.743 -  25.114:  250   |   7:    58.599 -  66.971:   19        |
|      3:    25.114 -  33.485:  132   |   8:    66.971 -  75.342:    5        |
|      4:    33.485 -  41.857:  142   |   9:    75.342 -  83.713:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1781 r_free = 0.2360             target_work(ml) = 5.548         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1780 r_free = 0.2358             target_work(ml) = 5.547         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1780   r_free= 0.2358   ksol= 0.33   Bsol= 43.13   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,2.95,3.28,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.547005                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1775   r_free= 0.2349   ksol= 0.31   Bsol= 46.05   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.34,2.54,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.544968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.282238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.583  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.117834              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.357  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1775      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2349      final r-factor (free) = 0.1936          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0523 = 4.28 * 0.50 * 5.5954 + 1.00 * 0.0717                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7289 = 4.28 * 0.50 * 5.4449 + 1.00 * 0.0706                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1936      final r-factor (free) = 0.1836          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0982 = 1.12 * 1.00 * 5.4449 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9597 = 1.12 * 1.00 * 5.3201 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.45   14.31    None  None   None       |
|    all(noH): 2823   0      0.00    85.45   14.31    None  None   None       |
|    Sol.    : 438    0      3.13    85.45   39.60    None  None   None       |
|    Mac.    : 2385   0      0.00    84.96   9.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.545: 1445   |   5:    42.724 -  51.269:   91        |
|      1:     8.545 -  17.090:  722   |   6:    51.269 -  59.814:   80        |
|      2:    17.090 -  25.635:  194   |   7:    59.814 -  68.359:   47        |
|      3:    25.635 -  34.180:  122   |   8:    68.359 -  76.904:   10        |
|      4:    34.180 -  42.724:  104   |   9:    76.904 -  85.449:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1836             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1302 r_free = 0.1831             target_work(ml) = 5.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1831   ksol= 0.31   Bsol= 46.05   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.34,2.54,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.289175                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1822   ksol= 0.32   Bsol= 49.99   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.31,1.00,2.49,0.00,0.00,0.00); trace/3= 1.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.287646                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.808683              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.368  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.074841              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.636  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1822      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5425 = 2.81 * 0.50 * 5.3206 + 1.00 * 0.0706                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4533 = 2.81 * 0.50 * 5.2615 + 1.00 * 0.0643                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9295 = 2.07 * 1.00 * 5.2615 + 1.00 * 0.0127                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8424 = 2.07 * 1.00 * 5.2191 + 1.00 * 0.0137                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.02   14.22    None  None   None       |
|    all(noH): 2823   0      0.00    95.02   14.22    None  None   None       |
|    Sol.    : 438    0      2.67    95.02   40.10    None  None   None       |
|    Mac.    : 2385   0      0.00    93.83   9.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.503: 1629   |   5:    47.512 -  57.015:   91        |
|      1:     9.503 -  19.005:  611   |   6:    57.015 -  66.517:   66        |
|      2:    19.005 -  28.507:  180   |   7:    66.517 -  76.020:   26        |
|      3:    28.507 -  38.010:  116   |   8:    76.020 -  85.522:    9        |
|      4:    38.010 -  47.512:   89   |   9:    85.522 -  95.025:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1708             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1707             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1707   ksol= 0.32   Bsol= 49.99   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.31,1.00,2.49,0.00,0.00,0.00); trace/3= 1.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215129                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.6884 0.99   1421  158 0.0990 0.1311      5.3804      5.5783|
|  2:  4.6884 -  3.7398 0.99   1373  155 0.0870 0.1163      5.4562      5.6711|
|  3:  3.7398 -  3.2726 0.99   1342  142 0.1095 0.1570      5.5086      5.8496|
|  4:  3.2726 -  2.9758 0.99   1331  155 0.1313 0.1848      5.5049      5.6845|
|  5:  2.9758 -  2.7639 0.99   1338  149 0.1408 0.1820       5.385      5.6058|
|  6:  2.7639 -  2.6018 0.99   1327  146 0.1307 0.2031      5.2653      5.5503|
|  7:  2.6018 -  2.4721 0.99   1309  137 0.1343 0.1742       5.239      5.3842|
|  8:  2.4721 -  2.3649 0.98   1299  152 0.1282 0.1879      5.1498      5.4262|
|  9:  2.3649 -  2.2742 0.98   1307  148 0.1306 0.2061      5.1315      5.4271|
| 10:  2.2742 -  2.1960 1.00   1298  147 0.1212 0.1767      5.0307      5.2376|
| 11:  2.1960 -  2.1275 0.98   1316  137 0.1195 0.2166      5.0299       5.455|
| 12:  2.1275 -  2.0668 0.98   1288  144 0.1244 0.1817      4.9568      5.1993|
| 13:  2.0668 -  2.0125 0.98   1265  142 0.1182 0.1853      4.8552      5.0874|
| 14:  2.0125 -  1.9636 0.31    416   47 0.1076 0.1525       4.722      4.8953|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.6884  1421   158  0.94   9.33   0.97     0.95       7260.92|
|  2:  4.6884 -  3.7398  1373   155  0.95   8.30   1.02     1.00       9622.02|
|  3:  3.7398 -  3.2726  1342   142  0.93  12.09   1.04     1.03      11405.88|
|  4:  3.2726 -  2.9758  1331   155  0.91  15.23   1.02     1.00      11602.10|
|  5:  2.9758 -  2.7639  1338   149  0.89  17.33   1.00     0.98       9587.31|
|  6:  2.7639 -  2.6018  1327   146  0.89  17.70   0.98     0.95       8154.82|
|  7:  2.6018 -  2.4721  1309   137  0.89  17.03   0.99     0.96       7349.61|
|  8:  2.4721 -  2.3649  1299   152  0.89  17.44   0.98     0.95       6433.34|
|  9:  2.3649 -  2.2742  1307   148  0.89  17.91   0.99     0.94       6285.08|
| 10:  2.2742 -  2.1960  1298   147  0.89  17.80   0.99     0.95       5306.50|
| 11:  2.1960 -  2.1275  1316   137  0.89  17.85   0.99     0.94       5357.05|
| 12:  2.1275 -  2.0668  1288   144  0.88  18.30   1.00     1.00       4875.36|
| 13:  2.0668 -  2.0125  1265   142  0.88  18.56   0.99     0.96       4062.67|
| 14:  2.0125 -  1.9636   416    47  0.90  15.94   0.98     0.95       3054.17|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3054.17 max =        11602.10 mean =      7416.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.84 mean =        15.68|
|phase err.(test): min =        0.00 max =           89.66 mean =        15.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1706   ksol= 0.32   Bsol= 50.80   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.67,0.93,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1706   ksol= 0.32   Bsol= 50.80   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.67,0.93,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.215188                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.6884 0.99   1421  158 0.0990 0.1312      5.3809      5.5796|
|  2:  4.6884 -  3.7398 0.99   1373  155 0.0870 0.1163      5.4565      5.6706|
|  3:  3.7398 -  3.2726 0.99   1342  142 0.1094 0.1570      5.5084      5.8495|
|  4:  3.2726 -  2.9758 0.99   1331  155 0.1313 0.1848      5.5049      5.6843|
|  5:  2.9758 -  2.7639 0.99   1338  149 0.1408 0.1820      5.3849      5.6054|
|  6:  2.7639 -  2.6018 0.99   1327  146 0.1307 0.2030      5.2652        5.55|
|  7:  2.6018 -  2.4721 0.99   1309  137 0.1343 0.1744      5.2392      5.3846|
|  8:  2.4721 -  2.3649 0.98   1299  152 0.1283 0.1878        5.15      5.4263|
|  9:  2.3649 -  2.2742 0.98   1307  148 0.1306 0.2057      5.1317      5.4262|
| 10:  2.2742 -  2.1960 1.00   1298  147 0.1212 0.1768      5.0311      5.2392|
| 11:  2.1960 -  2.1275 0.98   1316  137 0.1193 0.2166      5.0302      5.4555|
| 12:  2.1275 -  2.0668 0.98   1288  144 0.1244 0.1818      4.9567      5.1994|
| 13:  2.0668 -  2.0125 0.98   1265  142 0.1182 0.1850      4.8547      5.0863|
| 14:  2.0125 -  1.9636 0.31    416   47 0.1075 0.1522      4.7212      4.8938|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1239 -  4.6884  1421   158  0.94   9.34   0.97     0.95       7272.19|
|  2:  4.6884 -  3.7398  1373   155  0.95   8.30   1.02     1.01       9628.60|
|  3:  3.7398 -  3.2726  1342   142  0.93  12.09   1.04     1.04      11403.56|
|  4:  3.2726 -  2.9758  1331   155  0.91  15.22   1.02     1.00      11596.54|
|  5:  2.9758 -  2.7639  1338   149  0.89  17.32   1.01     0.98       9582.02|
|  6:  2.7639 -  2.6018  1327   146  0.89  17.70   0.99     0.96       8153.09|
|  7:  2.6018 -  2.4721  1309   137  0.89  17.03   1.00     0.96       7351.54|
|  8:  2.4721 -  2.3649  1299   152  0.89  17.45   0.99     0.96       6433.69|
|  9:  2.3649 -  2.2742  1307   148  0.89  17.92   1.00     0.95       6286.29|
| 10:  2.2742 -  2.1960  1298   147  0.89  17.81   1.00     0.95       5313.34|
| 11:  2.1960 -  2.1275  1316   137  0.89  17.86   1.00     0.95       5365.11|
| 12:  2.1275 -  2.0668  1288   144  0.88  18.31   1.01     1.01       4877.37|
| 13:  2.0668 -  2.0125  1265   142  0.88  18.56   1.00     0.97       4059.56|
| 14:  2.0125 -  1.9636   416    47  0.90  15.92   0.99     0.96       3048.44|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3048.44 max =        11596.54 mean =      7417.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        15.68|
|phase err.(test): min =        0.00 max =           89.63 mean =        15.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.76    96.79   15.98    None  None   None       |
|    all(noH): 2823   0      1.76    96.79   15.98    None  None   None       |
|    Sol.    : 438    0      4.43    96.79   41.86    None  None   None       |
|    Mac.    : 2385   0      1.76    95.60   11.23    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:     1.762 -  11.265: 1629   |   5:    49.275 -  58.777:   91        |
|      1:    11.265 -  20.767:  611   |   6:    58.777 -  68.279:   66        |
|      2:    20.767 -  30.270:  180   |   7:    68.279 -  77.782:   26        |
|      3:    30.270 -  39.772:  116   |   8:    77.782 -  87.284:    9        |
|      4:    39.772 -  49.275:   89   |   9:    87.284 -  96.787:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.302 - 4.710
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 334
   mapped sites are within: 0.739 - 4.710

peak=   10.023 closest distance to " CB  VAL A 230 " =    1.451
peak=    8.163 closest distance to " O   HOH Z 130 " =    1.672
peak=    7.650 closest distance to " CG2 VAL A 296 " =    1.187
peak=    6.876 closest distance to " CG  ARG A 138 " =    1.118
peak=    6.703 closest distance to " CD2 LEU A   5 " =    1.271
peak=    5.992 closest distance to " NE2 GLN A  11 " =    1.167
peak=    5.910 closest distance to " O   HOH Z  65 " =    1.366
peak=    5.546 closest distance to " CD1AILE A 234 " =    1.065
peak=    5.399 closest distance to " O   HOH Z   9 " =    1.776
peak=    5.361 closest distance to " CG  LEU A   5 " =    1.169
peak=    5.251 closest distance to " O   HOH Z 142 " =    2.028
peak=    5.251 closest distance to " NH2 ARG A  56 " =    2.101
peak=    5.236 closest distance to " CG  PRO A  54 " =    1.358
peak=    5.232 closest distance to " CG  LEU A 228 " =    1.182
peak=    5.189 closest distance to " O   HOH Z 222 " =    1.339
peak=    5.138 closest distance to " O   HOH Z 427 " =    2.379
peak=    5.064 closest distance to " O   HOH Z   7 " =    1.650
peak=    4.954 closest distance to " O   HOH Z 232 " =    2.190
peak=    4.889 closest distance to " NH1 ARG A 138 " =    0.997
peak=    4.881 closest distance to " CB  GLN A 183 " =    1.265
peak=    4.802 closest distance to " O   HOH Z 425 " =    1.692
peak=    4.737 closest distance to " CB  VAL A 230 " =    1.186
peak=    4.698 closest distance to " O   HOH Z 126 " =    2.095
peak=    4.687 closest distance to " CB  PRO A  54 " =    1.039
peak=    4.630 closest distance to " O   HOH Z  63 " =    1.579
peak=    4.611 closest distance to " O   HOH Z 139 " =    1.361
peak=    4.579 closest distance to " CB  GLN A 223 " =    1.514
peak=    4.559 closest distance to " O   HOH Z 417 " =    1.532
peak=    4.548 closest distance to " O   HOH Z 369 " =    2.055
peak=    4.535 closest distance to " CB  VAL A 296 " =    1.157
peak=    4.531 closest distance to " CG  LEU A 167 " =    1.283
peak=    4.476 closest distance to " O   HOH Z 225 " =    1.528
peak=    4.443 closest distance to " O   HOH Z   2 " =    1.897
peak=    4.420 closest distance to " O   HOH Z 361 " =    1.416
peak=    4.419 closest distance to " CG  PRO A 198 " =    1.251
peak=    4.385 closest distance to " O   HOH Z 287 " =    1.870
peak=    4.383 closest distance to " O   HOH Z 298 " =    1.918
peak=    4.372 closest distance to " O   HOH Z 424 " =    1.140
peak=    4.368 closest distance to " CB  ASN A 148 " =    1.399
peak=    4.356 closest distance to " CB  SER A   3 " =    1.475
peak=    4.338 closest distance to " O   HOH Z 127 " =    1.116
peak=    4.312 closest distance to " O   HOH Z  78 " =    1.609
peak=    4.294 closest distance to " CB  SER A  63 " =    1.299
peak=    4.277 closest distance to " CD2 LEU A 228 " =    1.231
peak=    4.241 closest distance to " O   HOH Z 375 " =    0.966
peak=    4.233 closest distance to " O   HOH Z 380 " =    1.933
peak=    4.204 closest distance to " CB  SER A 216 " =    0.999
peak=    4.203 closest distance to " O   HOH Z 392 " =    1.293
peak=    4.203 closest distance to " CB  ASP A 124 " =    0.834
peak=    4.194 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.178 closest distance to " O   HOH Z 193 " =    1.716
peak=    4.152 closest distance to " O   HOH Z 410 " =    1.451
peak=    4.146 closest distance to " O   PRO A 198 " =    1.248
peak=    4.135 closest distance to " CB  VAL A 202 " =    1.646
peak=    4.130 closest distance to " O   HOH Z 414 " =    1.329
peak=    4.087 closest distance to " O   HOH Z 316 " =    3.034
peak=    4.055 closest distance to " CB  ARG A 275 " =    0.992
peak=    4.053 closest distance to " O   HOH Z 418 " =    1.000
peak=    4.050 closest distance to " O   HOH Z 158 " =    2.889
peak=    4.034 closest distance to " O   HOH Z 209 " =    2.386
peak=    4.031 closest distance to " CB  ASN A  39 " =    0.981
peak=    4.023 closest distance to " O   HOH Z 133 " =    1.559
peak=    4.006 closest distance to " O   SER A  87 " =    2.420
peak=    4.006 closest distance to " NH1AARG A 145 " =    1.077
peak=    3.989 closest distance to " O   HOH Z 371 " =    2.633
peak=    3.974 closest distance to " O   HOH Z  59 " =    1.655
peak=    3.973 closest distance to " O   HOH Z 423 " =    1.622
peak=    3.970 closest distance to " CD  GLN A 240 " =    1.615
peak=    3.959 closest distance to " O   HOH Z 427 " =    1.164
peak=    3.953 closest distance to " CD  ARG A  66 " =    2.422
peak=    3.952 closest distance to " O   HOH Z 214 " =    2.086
peak=    3.948 closest distance to " O   HOH Z  24 " =    1.989
peak=    3.940 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.885 closest distance to " O   HOH Z 195 " =    1.510
peak=    3.880 closest distance to " O   HOH Z   1 " =    1.961
peak=    3.879 closest distance to " CB  GLU A 128 " =    1.122
peak=    3.877 closest distance to " CD  ARG A 138 " =    1.190
peak=    3.866 closest distance to " CG  LYS A  76 " =    1.725
peak=    3.862 closest distance to " O   HOH Z 234 " =    3.814
peak=    3.847 closest distance to " CA  ASN A 127 " =    1.142
peak=    3.836 closest distance to " O   HOH Z 411 " =    3.357
peak=    3.828 closest distance to " O   HOH Z 352 " =    1.604
peak=    3.813 closest distance to " CB  LEU A 228 " =    1.323
peak=    3.812 closest distance to " O   HOH Z  55 " =    1.849
peak=    3.807 closest distance to " O   HOH Z 167 " =    1.848
peak=    3.801 closest distance to " CD2 TRP A 179 " =    2.261
peak=    3.789 closest distance to " CG  PRO A 243 " =    1.125
peak=    3.782 closest distance to " O   HOH Z  59 " =    2.080
peak=    3.779 closest distance to " O   HOH Z 425 " =    1.985
peak=    3.777 closest distance to " CB  GLU A 277 " =    3.588
peak=    3.773 closest distance to " O   HOH Z 422 " =    2.666
peak=    3.768 closest distance to " O   HOH Z 419 " =    1.974
peak=    3.756 closest distance to " OG  SER A  62 " =    2.787
peak=    3.749 closest distance to " N   SER A 271 " =    0.967
peak=    3.743 closest distance to " CB  LEU A 237 " =    0.857
peak=    3.742 closest distance to " CB AVAL A  41 " =    1.252
peak=    3.726 closest distance to " O   HOH Z 389 " =    1.331
peak=    3.715 closest distance to " CA  GLY A 267 " =    1.200
peak=    3.712 closest distance to " CG1 ILE A 151 " =    1.102
peak=    3.712 closest distance to " CB  ASN A 142 " =    0.946
peak=    3.710 closest distance to " O   HOH Z 133 " =    2.529
peak=    3.708 closest distance to " O   ASN A 209 " =    1.595
peak=    3.698 closest distance to " O   HOH Z 236 " =    1.637
peak=    3.691 closest distance to " CD  ARG A 159 " =    0.765
peak=    3.683 closest distance to " O   HOH Z 346 " =    1.683
peak=    3.683 closest distance to " O   HOH Z 217 " =    3.020
peak=    3.673 closest distance to " CG  GLN A  11 " =    2.225
peak=    3.669 closest distance to " CB  VAL A 265 " =    1.275
peak=    3.665 closest distance to " O   HOH Z 373 " =    1.523
peak=    3.663 closest distance to " N   GLN A 278 " =    1.284
peak=    3.660 closest distance to " CA  ALA A  51 " =    1.080
peak=    3.657 closest distance to " CB  GLN A  88 " =    1.362
peak=    3.652 closest distance to " O   HOH Z 193 " =    1.705
peak=    3.648 closest distance to " CB  TRP A 266 " =    1.111
peak=    3.645 closest distance to " O   HOH Z 425 " =    2.114
peak=    3.644 closest distance to " CB  MET A  40 " =    0.853
peak=    3.641 closest distance to " CE3 TRP A 274 " =    2.419
peak=    3.638 closest distance to " CH2 TRP A 266 " =    1.074
peak=    3.637 closest distance to " CG2 THR A 221 " =    1.166
peak=    3.629 closest distance to " N   TYR A  15 " =    1.014
peak=    3.625 closest distance to " O   HOH Z 368 " =    1.992
peak=    3.623 closest distance to " O   HOH Z 181 " =    2.283
peak=    3.622 closest distance to " O   HOH Z 133 " =    2.430
peak=    3.621 closest distance to " O   HOH Z 365 " =    3.049
peak=    3.620 closest distance to " O   HOH Z 305 " =    3.553
peak=    3.613 closest distance to " O   HOH Z 403 " =    1.503
peak=    3.612 closest distance to " CA  ALA A 160 " =    0.938
peak=    3.611 closest distance to " O   HOH Z 175 " =    2.073
peak=    3.608 closest distance to " O   HOH Z  88 " =    3.426
peak=    3.602 closest distance to " O   HOH Z 258 " =    2.062
peak=    3.594 closest distance to " CB  SER A 276 " =    1.108
peak=    3.590 closest distance to " CG  GLN A  88 " =    1.206
peak=    3.589 closest distance to " O   MET A 105 " =    1.719
peak=    3.588 closest distance to " O   HOH Z  51 " =    1.420
peak=    3.587 closest distance to " O   HOH Z 438 " =    2.065
peak=    3.579 closest distance to " O   HOH Z 362 " =    2.089
peak=    3.574 closest distance to " O   HOH Z 184 " =    1.472
peak=    3.571 closest distance to " O   HOH Z 405 " =    1.495
peak=    3.560 closest distance to " CA  LYS A 117 " =    1.146
peak=    3.557 closest distance to " OG  SER A  62 " =    3.100
peak=    3.557 closest distance to " O   HOH Z 327 " =    1.532
peak=    3.550 closest distance to " CB  ARG A 190 " =    1.765
peak=    3.544 closest distance to " CG BARG A 102 " =    1.963
peak=    3.540 closest distance to " O   HOH Z 222 " =    1.982
peak=    3.539 closest distance to " CG2 ILE A 234 " =    0.851
peak=    3.539 closest distance to " CA  ASN A 215 " =    1.204
peak=    3.538 closest distance to " NE AARG A 275 " =    1.404
peak=    3.528 closest distance to " CB  THR A 157 " =    1.130
peak=    3.528 closest distance to " O   HOH Z 146 " =    1.592
peak=    3.524 closest distance to " CB  LEU A 143 " =    1.049
peak=    3.521 closest distance to " CE1 TYR A 186 " =    1.306
peak=    3.517 closest distance to " CB  ILE A 234 " =    1.131
peak=    3.514 closest distance to " O   HOH Z  56 " =    2.000
peak=    3.513 closest distance to " O   HOH Z 272 " =    1.817
peak=    3.511 closest distance to " O   HOH Z  68 " =    2.039
peak=    3.509 closest distance to " N   PHE A 130 " =    1.249
peak=    3.507 closest distance to " OG BSER A  99 " =    2.157
peak=    3.499 closest distance to " O   HOH Z 109 " =    2.280
peak=    3.494 closest distance to " N   ALA A 256 " =    0.996
peak=    3.494 closest distance to " CA  TYR A  30 " =    0.955
peak=    3.493 closest distance to " CA  ILE A 234 " =    1.026
peak=    3.493 closest distance to " CB  TRP A 179 " =    1.433
peak=    3.489 closest distance to " OD2 ASP A 286 " =    2.721
peak=    3.488 closest distance to " CB  LYS A 117 " =    1.217
peak=    3.484 closest distance to " O   HOH Z 193 " =    1.929
peak=    3.478 closest distance to " CB  HIS A 108 " =    0.818
peak=    3.474 closest distance to " CA  ALA A 299 " =    0.964
peak=    3.474 closest distance to " O   HOH Z  88 " =    2.895
peak=    3.473 closest distance to " O   HOH Z  20 " =    1.679
peak=    3.471 closest distance to " CE3 TRP A 150 " =    1.040
peak=    3.465 closest distance to " CZ  PHE A 218 " =    1.098
peak=    3.462 closest distance to " CD1 LEU A 300 " =    1.232
peak=    3.461 closest distance to " O   PRO A 198 " =    1.503
peak=    3.461 closest distance to " O   HOH Z 126 " =    1.449
peak=    3.453 closest distance to " O   HOH Z 154 " =    1.900
peak=    3.449 closest distance to " CB  ASN A 110 " =    1.082
peak=    3.448 closest distance to " O   HOH Z 124 " =    1.278
peak=    3.446 closest distance to " O   HOH Z 290 " =    0.953
peak=    3.444 closest distance to " NH2AARG A 190 " =    1.710
peak=    3.442 closest distance to " CD  ARG A 269 " =    1.058
peak=    3.437 closest distance to " O   HOH Z 368 " =    3.640
peak=    3.434 closest distance to " NH1 ARG A  14 " =    1.033
peak=    3.432 closest distance to " O   HOH Z  10 " =    1.797
peak=    3.429 closest distance to " OE2 GLU A  53 " =    1.840
peak=    3.428 closest distance to " O   HOH Z 313 " =    1.505
peak=    3.424 closest distance to " O   HOH Z 261 " =    2.393
peak=    3.424 closest distance to " CA  SER A  87 " =    0.991
peak=    3.421 closest distance to " CA  THR A 221 " =    0.940
peak=    3.413 closest distance to " CB  SER A 210 " =    1.017
peak=    3.412 closest distance to " O   HOH Z 334 " =    1.475
peak=    3.406 closest distance to " O   HOH Z 213 " =    2.156
peak=    3.399 closest distance to " O   HOH Z 424 " =    2.528
peak=    3.395 closest distance to " O   HOH Z 329 " =    3.934
peak=    3.388 closest distance to " OE2 GLU A   2 " =    1.921
peak=    3.383 closest distance to " N   ASN A 127 " =    1.394
peak=    3.381 closest distance to " ND1 HIS A  81 " =    1.843
peak=    3.371 closest distance to " ND2 ASN A 249 " =    0.759
peak=    3.369 closest distance to " CB  ALA A 114 " =    1.494
peak=    3.368 closest distance to " NE2 GLN A  58 " =    3.801
peak=    3.366 closest distance to " CG  LEU A 281 " =    1.088
peak=    3.365 closest distance to " CA  LEU A 101 " =    1.479
peak=    3.364 closest distance to " NE1 TRP A 274 " =    0.940
peak=    3.362 closest distance to " OG BSER A 210 " =    1.255
peak=    3.361 closest distance to " CD BLYS A 290 " =    1.036
peak=    3.360 closest distance to " CB  SER A 212 " =    1.339
peak=    3.360 closest distance to " CG  GLN A  89 " =    1.446
peak=    3.354 closest distance to " CE3 TRP A  85 " =    1.157
peak=    3.350 closest distance to " O   HOH Z 211 " =    1.075
peak=    3.348 closest distance to " CE3 TRP A 274 " =    1.209
peak=    3.345 closest distance to " O   HOH Z 207 " =    2.353
peak=    3.342 closest distance to " O   HOH Z 189 " =    2.864
peak=    3.341 closest distance to " O   HOH Z  32 " =    2.208
peak=    3.340 closest distance to " CB  LEU A 300 " =    0.863
peak=    3.340 closest distance to " NZ BLYS A 290 " =    0.981
peak=    3.339 closest distance to " O   HOH Z 359 " =    1.173
peak=    3.336 closest distance to " CG BARG A 190 " =    1.276
peak=    3.335 closest distance to " O   HOH Z 128 " =    1.910
peak=    3.331 closest distance to " O   HOH Z 389 " =    1.616
peak=    3.322 closest distance to " O   HOH Z 145 " =    1.814
peak=    3.322 closest distance to " O   HOH Z 222 " =    2.190
peak=    3.320 closest distance to " OE1 GLU A   2 " =    2.020
peak=    3.319 closest distance to " O   HOH Z 385 " =    3.745
peak=    3.316 closest distance to " O   HOH Z 128 " =    2.144
peak=    3.316 closest distance to " CA  PHE A 283 " =    1.374
peak=    3.315 closest distance to " O   GLY A 302 " =    2.206
peak=    3.312 closest distance to " O   HOH Z 250 " =    1.303
peak=    3.312 closest distance to " O   HOH Z 130 " =    2.777
peak=    3.312 closest distance to " OG BSER A 212 " =    2.876
peak=    3.311 closest distance to " O   HOH Z 384 " =    1.343
peak=    3.309 closest distance to " CA  ALA A 180 " =    1.330
peak=    3.307 closest distance to " CB  ARG A 139 " =    1.066
peak=    3.307 closest distance to " O   HOH Z 409 " =    2.273
peak=    3.306 closest distance to " CB  GLU A 152 " =    1.371
peak=    3.305 closest distance to " O   HOH Z  90 " =    2.029
peak=    3.304 closest distance to " CD1 ILE A  33 " =    1.727
peak=    3.303 closest distance to " O   HOH Z 371 " =    1.895
peak=    3.300 closest distance to " CE  MET A  93 " =    1.478
peak=    3.297 closest distance to " CG1 ILE A  33 " =    1.310
peak=    3.295 closest distance to " O   HOH Z  44 " =    2.564
peak=    3.292 closest distance to " CG1BVAL A  72 " =    0.757
peak=    3.291 closest distance to " N   SER A  97 " =    0.835
peak=    3.289 closest distance to " CB  ASN A 187 " =    1.087
peak=    3.288 closest distance to " OG1 THR A 221 " =    1.355
peak=    3.282 closest distance to " O   HOH Z  97 " =    1.972
peak=    3.281 closest distance to " OG BSER A 164 " =    2.228
peak=    3.281 closest distance to " O   HOH Z 153 " =    3.728
peak=    3.281 closest distance to " O   THR A 294 " =    0.946
peak=    3.277 closest distance to " O   HOH Z 233 " =    1.626
peak=    3.272 closest distance to " O   HOH Z 323 " =    1.651
peak=    3.272 closest distance to " O   HOH Z 345 " =    3.317
peak=    3.270 closest distance to " O   HOH Z  39 " =    1.162
peak=    3.269 closest distance to " ND2 ASN A 187 " =    1.673
peak=    3.269 closest distance to " O   HOH Z 209 " =    2.472
peak=    3.268 closest distance to " ND2 ASN A 110 " =    1.789
peak=    3.268 closest distance to " O   HOH Z 303 " =    2.745
peak=    3.265 closest distance to " N   ARG A 156 " =    1.270
peak=    3.260 closest distance to " CZ3 TRP A  92 " =    1.181
peak=    3.260 closest distance to " CA  MET A 105 " =    0.908
peak=    3.257 closest distance to " O   HOH Z 402 " =    1.359
peak=    3.254 closest distance to " CG  ARG A 159 " =    0.960
peak=    3.253 closest distance to " CB  GLU A 236 " =    1.158
peak=    3.250 closest distance to " NH2BARG A 145 " =    2.054
peak=    3.249 closest distance to " CD  LYS A 166 " =    1.443
peak=    3.248 closest distance to " O   HOH Z 145 " =    2.079
peak=    3.247 closest distance to " O   HOH Z 180 " =    2.152
peak=    3.246 closest distance to " O   HOH Z 273 " =    2.779
peak=    3.245 closest distance to " O   HOH Z 148 " =    2.332
peak=    3.238 closest distance to " O   HOH Z 115 " =    1.397
peak=    3.237 closest distance to " CB  ARG A 138 " =    1.241
peak=    3.235 closest distance to " O   HOH Z 356 " =    1.394
peak=    3.234 closest distance to " CA  ARG A 102 " =    1.098
peak=    3.233 closest distance to " CA  ARG A 156 " =    1.038
peak=    3.231 closest distance to " CH2 TRP A 150 " =    0.956
peak=    3.229 closest distance to " CB  ALA A   1 " =    4.710
peak=    3.227 closest distance to " O   HOH Z  80 " =    1.484
peak=    3.227 closest distance to " CB  TRP A 150 " =    0.992
peak=    3.224 closest distance to " CB  ARG A  79 " =    1.294
peak=    3.222 closest distance to " NE  ARG A  56 " =    3.521
peak=    3.218 closest distance to " O   HOH Z 414 " =    3.064
peak=    3.211 closest distance to " O   HOH Z 132 " =    1.203
peak=    3.210 closest distance to " O   HOH Z 189 " =    3.182
peak=    3.206 closest distance to " O   HOH Z 357 " =    2.127
peak=    3.204 closest distance to " O   HOH Z  76 " =    1.022
peak=    3.202 closest distance to " O   HOH Z  55 " =    1.573
peak=    3.201 closest distance to " CA  THR A 264 " =    0.739
peak=    3.198 closest distance to " O   HOH Z 119 " =    1.559
peak=    3.194 closest distance to " O   HOH Z   1 " =    1.774
peak=    3.193 closest distance to " O   HOH Z 392 " =    2.089
peak=    3.192 closest distance to " NZ  LYS A 117 " =    1.229
peak=    3.192 closest distance to " CG2 VAL A 257 " =    0.752
peak=    3.192 closest distance to " O   HOH Z  61 " =    1.552
peak=    3.191 closest distance to " CZ  PHE A 192 " =    0.854
peak=    3.191 closest distance to " O   HOH Z  40 " =    2.012
peak=    3.190 closest distance to " O   HOH Z  88 " =    3.451
peak=    3.189 closest distance to " CA  ARG A 195 " =    1.292
peak=    3.189 closest distance to " N   SER A 135 " =    1.220
peak=    3.187 closest distance to " O   HOH Z  44 " =    1.942
peak=    3.187 closest distance to " CA  ALA A 158 " =    1.162
peak=    3.184 closest distance to " ND2BASN A 224 " =    0.850
peak=    3.183 closest distance to " CB  LEU A 143 " =    1.026
peak=    3.182 closest distance to " O   ALA A 158 " =    1.384
peak=    3.174 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.173 closest distance to " O   HOH Z 302 " =    1.516
peak=    3.171 closest distance to " CA  LEU A 282 " =    1.002
peak=    3.168 closest distance to " CB  ALA A 291 " =    1.405
peak=    3.161 closest distance to " O   HOH Z 172 " =    2.578
peak=    3.157 closest distance to " CB  SER A  26 " =    1.622
peak=    3.154 closest distance to " NH2BARG A 190 " =    1.436
peak=    3.150 closest distance to " CB  MET A  47 " =    1.130
peak=    3.149 closest distance to " O   HOH Z   9 " =    1.631
peak=    3.149 closest distance to " OG BSER A 258 " =    0.849
peak=    3.148 closest distance to " O   HOH Z 183 " =    1.344
peak=    3.147 closest distance to " O   HOH Z 285 " =    2.590
peak=    3.143 closest distance to " N   ALA A   1 " =    2.451
peak=    3.142 closest distance to " OH  TYR A 116 " =    1.048
peak=    3.142 closest distance to " N   GLU A   2 " =    1.417
peak=    3.141 closest distance to " OD1 ASN A 217 " =    1.648
peak=    3.140 closest distance to " O   HOH Z 209 " =    2.300
peak=    3.128 closest distance to " CZ  PHE A  38 " =    1.264
peak=    3.122 closest distance to " CB  THR A 235 " =    1.025
peak=    3.117 closest distance to " O   HOH Z 272 " =    2.228
peak=    3.114 closest distance to " CA  ALA A 291 " =    0.895
peak=    3.111 closest distance to " O   HOH Z 345 " =    1.804
peak=    3.110 closest distance to " NH2AARG A 145 " =    1.119
peak=    3.099 closest distance to " O   HOH Z 217 " =    1.590
peak=    3.097 closest distance to " O   CYS A 168 " =    1.386
peak=    3.083 closest distance to " CG1 ILE A 263 " =    1.254
peak=    3.077 closest distance to " CZ3 TRP A  92 " =    1.037
peak=    3.072 closest distance to " O   HOH Z 260 " =    1.378
peak=    3.057 closest distance to " O   HOH Z 438 " =    1.956

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.600 - 5.962
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 208
   mapped sites are within: 0.811 - 5.962

peak=   -4.544 closest distance to " OG BSER A 134 " =    1.541
peak=   -4.401 closest distance to " CG2 VAL A 230 " =    0.811
peak=   -4.321 closest distance to " O   HOH Z 266 " =    4.992
peak=   -4.303 closest distance to " CD  ARG A  14 " =    3.025
peak=   -4.198 closest distance to " CG  ARG A 138 " =    1.006
peak=   -4.150 closest distance to " CE2 PHE A 218 " =    2.495
peak=   -4.084 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.037 closest distance to " O   HOH Z 131 " =    4.003
peak=   -4.030 closest distance to " CB  ALA A  43 " =    2.468
peak=   -4.003 closest distance to " CB  PRO A 243 " =    2.613
peak=   -3.979 closest distance to " CD1 LEU A 255 " =    2.984
peak=   -3.956 closest distance to " N   THR A 157 " =    1.467
peak=   -3.949 closest distance to " O   SER A 135 " =    1.462
peak=   -3.941 closest distance to " CB  VAL A 230 " =    1.012
peak=   -3.932 closest distance to " OG  SER A  87 " =    1.367
peak=   -3.923 closest distance to " CD  ARG A 138 " =    1.340
peak=   -3.901 closest distance to " O   PRO A 198 " =    1.208
peak=   -3.864 closest distance to " O   HOH Z 198 " =    2.361
peak=   -3.856 closest distance to " CD  LYS A 289 " =    2.393
peak=   -3.841 closest distance to " O   HOH Z  43 " =    1.778
peak=   -3.836 closest distance to " CG  ARG A 219 " =    2.504
peak=   -3.832 closest distance to " O   HOH Z  52 " =    1.451
peak=   -3.819 closest distance to " CB  ASP A 132 " =    2.412
peak=   -3.810 closest distance to " O   HOH Z 409 " =    5.962
peak=   -3.783 closest distance to " O   SER A  22 " =    2.564
peak=   -3.782 closest distance to " OE1 GLU A 277 " =    2.271
peak=   -3.780 closest distance to " O   HOH Z 185 " =    2.098
peak=   -3.778 closest distance to " CA  GLY A  98 " =    1.888
peak=   -3.764 closest distance to " CE2 TYR A  30 " =    2.668
peak=   -3.761 closest distance to " O   HOH Z 216 " =    1.664
peak=   -3.752 closest distance to " CZ2 TRP A 274 " =    0.877
peak=   -3.746 closest distance to " O   HOH Z 350 " =    1.810
peak=   -3.726 closest distance to " O   HOH Z 407 " =    3.182
peak=   -3.723 closest distance to " CA  ASP A  27 " =    2.393
peak=   -3.710 closest distance to " CA  GLY A 241 " =    2.181
peak=   -3.707 closest distance to " O   PRO A 243 " =    2.406
peak=   -3.703 closest distance to " O   ALA A  84 " =    1.738
peak=   -3.683 closest distance to " O   HOH Z 389 " =    1.413
peak=   -3.672 closest distance to " O   HOH Z 389 " =    2.088
peak=   -3.670 closest distance to " CD2 TYR A 293 " =    1.884
peak=   -3.670 closest distance to " N   ALA A  43 " =    2.615
peak=   -3.669 closest distance to " CB  PHE A 130 " =    1.282
peak=   -3.661 closest distance to " O   MET A  40 " =    2.852
peak=   -3.659 closest distance to " O   HOH Z 238 " =    0.930
peak=   -3.656 closest distance to " O   HOH Z 377 " =    1.754
peak=   -3.650 closest distance to " O   HOH Z 359 " =    1.630
peak=   -3.647 closest distance to " CB  ALA A 248 " =    2.054
peak=   -3.636 closest distance to " O   HOH Z  11 " =    1.855
peak=   -3.635 closest distance to " CB  ALA A 227 " =    2.416
peak=   -3.627 closest distance to " C   ARG A 269 " =    1.381
peak=   -3.626 closest distance to " NH2 ARG A  79 " =    2.036
peak=   -3.623 closest distance to " CB  ALA A   9 " =    2.382
peak=   -3.605 closest distance to " CG2 VAL A 296 " =    1.576
peak=   -3.593 closest distance to " O   HOH Z 292 " =    1.657
peak=   -3.576 closest distance to " CG1 VAL A 296 " =    1.369
peak=   -3.571 closest distance to " CB  TRP A  85 " =    2.583
peak=   -3.563 closest distance to " O   HOH Z  39 " =    1.137
peak=   -3.562 closest distance to " CD1 LEU A 101 " =    2.243
peak=   -3.557 closest distance to " O   HOH Z 348 " =    1.773
peak=   -3.550 closest distance to " O   PRO A 163 " =    1.908
peak=   -3.549 closest distance to " CE2 TYR A 116 " =    3.121
peak=   -3.543 closest distance to " O   HOH Z 111 " =    1.947
peak=   -3.536 closest distance to " O   HOH Z 231 " =    1.862
peak=   -3.533 closest distance to " CB  ASN A  39 " =    2.162
peak=   -3.516 closest distance to " CD2 LEU A   5 " =    0.986
peak=   -3.515 closest distance to " CA  ASN A 127 " =    1.024
peak=   -3.514 closest distance to " CA  GLY A 203 " =    2.313
peak=   -3.509 closest distance to " CB  PRO A  54 " =    2.428
peak=   -3.504 closest distance to " N   PRO A 163 " =    1.552
peak=   -3.491 closest distance to " CD  LYS A 166 " =    2.380
peak=   -3.487 closest distance to " OG ASER A 134 " =    1.173
peak=   -3.481 closest distance to " N   VAL A  72 " =    1.600
peak=   -3.480 closest distance to " O   HOH Z 298 " =    2.805
peak=   -3.477 closest distance to " O   HOH Z 435 " =    2.285
peak=   -3.472 closest distance to " O   VAL A 197 " =    1.765
peak=   -3.466 closest distance to " O   HOH Z  60 " =    2.380
peak=   -3.461 closest distance to " ND2 ASN A 249 " =    2.386
peak=   -3.460 closest distance to " O   GLY A 211 " =    1.179
peak=   -3.459 closest distance to " C   LEU A 143 " =    1.385
peak=   -3.450 closest distance to " O   HOH Z 352 " =    1.998
peak=   -3.446 closest distance to " OG  SER A  97 " =    2.225
peak=   -3.446 closest distance to " CA  GLY A 133 " =    2.019
peak=   -3.444 closest distance to " O   HOH Z 352 " =    1.571
peak=   -3.442 closest distance to " OG  SER A  62 " =    4.418
peak=   -3.442 closest distance to " O   HOH Z 211 " =    1.379
peak=   -3.439 closest distance to " ND2 ASN A 285 " =    2.021
peak=   -3.427 closest distance to " CG  PRO A 163 " =    2.546
peak=   -3.421 closest distance to " O   GLY A 203 " =    2.513
peak=   -3.420 closest distance to " O   TYR A  30 " =    2.560
peak=   -3.419 closest distance to " O   HOH Z 427 " =    1.733
peak=   -3.419 closest distance to " CB  TYR A  15 " =    2.100
peak=   -3.413 closest distance to " O   HOH Z 359 " =    3.431
peak=   -3.411 closest distance to " OG  SER A 245 " =    1.361
peak=   -3.408 closest distance to " O   GLY A  80 " =    2.470
peak=   -3.406 closest distance to " OD1 ASP A 191 " =    1.975
peak=   -3.406 closest distance to " O   HOH Z 134 " =    3.035
peak=   -3.405 closest distance to " NH2 ARG A 219 " =    1.762
peak=   -3.393 closest distance to " O   ARG A 145 " =    1.393
peak=   -3.387 closest distance to " O   HOH Z  60 " =    1.893
peak=   -3.386 closest distance to " NH2AARG A 275 " =    5.411
peak=   -3.386 closest distance to " O   VAL A  67 " =    2.391
peak=   -3.386 closest distance to " CD2 TYR A 116 " =    2.315
peak=   -3.383 closest distance to " C   HIS A 108 " =    1.232
peak=   -3.382 closest distance to " OG  SER A  63 " =    1.247
peak=   -3.382 closest distance to " O   HOH Z 103 " =    1.452
peak=   -3.372 closest distance to " O   HOH Z 368 " =    2.367
peak=   -3.371 closest distance to " O   HOH Z 313 " =    1.378
peak=   -3.339 closest distance to " CE2 TRP A  70 " =    2.393
peak=   -3.336 closest distance to " N   ARG A 138 " =    1.517
peak=   -3.335 closest distance to " O   SER A 141 " =    1.795
peak=   -3.335 closest distance to " CG2 ILE A  49 " =    2.828
peak=   -3.331 closest distance to " O   HOH Z  90 " =    2.938
peak=   -3.330 closest distance to " OE2 GLU A 152 " =    1.113
peak=   -3.329 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.328 closest distance to " C   MET A 188 " =    1.548
peak=   -3.326 closest distance to " N   ALA A 248 " =    1.496
peak=   -3.323 closest distance to " C   ALA A 158 " =    1.314
peak=   -3.322 closest distance to " CD2 LEU A 237 " =    2.672
peak=   -3.320 closest distance to " O   HOH Z 290 " =    1.236
peak=   -3.318 closest distance to " CB  ALA A 161 " =    2.531
peak=   -3.317 closest distance to " CB  PRO A  90 " =    1.653
peak=   -3.314 closest distance to " CB  ALA A 248 " =    2.433
peak=   -3.313 closest distance to " O   HOH Z 377 " =    1.105
peak=   -3.309 closest distance to " CE  MET A 105 " =    2.368
peak=   -3.308 closest distance to " O   HOH Z 298 " =    1.017
peak=   -3.307 closest distance to " O   VAL A 189 " =    2.551
peak=   -3.305 closest distance to " O   HOH Z 166 " =    1.768
peak=   -3.302 closest distance to " OG  SER A 206 " =    1.776
peak=   -3.301 closest distance to " CG2 VAL A 202 " =    2.688
peak=   -3.299 closest distance to " ND2 ASN A 187 " =    1.524
peak=   -3.298 closest distance to " O   ALA A   1 " =    1.304
peak=   -3.294 closest distance to " O   HOH Z 351 " =    1.582
peak=   -3.293 closest distance to " O   HOH Z 155 " =    1.242
peak=   -3.291 closest distance to " O   HOH Z 415 " =    1.169
peak=   -3.288 closest distance to " O   HOH Z 286 " =    1.794
peak=   -3.285 closest distance to " CG  GLN A  58 " =    1.101
peak=   -3.284 closest distance to " O   HOH Z 420 " =    3.274
peak=   -3.284 closest distance to " O   HOH Z 426 " =    2.119
peak=   -3.280 closest distance to " O   HOH Z 191 " =    5.469
peak=   -3.280 closest distance to " O   HOH Z 134 " =    3.706
peak=   -3.279 closest distance to " CD2 HIS A 207 " =    2.461
peak=   -3.270 closest distance to " O   HOH Z 122 " =    2.069
peak=   -3.270 closest distance to " O   HOH Z 394 " =    1.545
peak=   -3.269 closest distance to " O   HOH Z 353 " =    1.463
peak=   -3.265 closest distance to " O   HOH Z 243 " =    1.917
peak=   -3.251 closest distance to " CG2 ILE A 151 " =    2.527
peak=   -3.241 closest distance to " OH  TYR A 172 " =    1.811
peak=   -3.238 closest distance to " ND2 ASN A  45 " =    1.164
peak=   -3.233 closest distance to " CG2 THR A 178 " =    2.214
peak=   -3.229 closest distance to " O   HOH Z  53 " =    1.708
peak=   -3.229 closest distance to " C   LYS A  76 " =    1.325
peak=   -3.227 closest distance to " ND2 ASN A 252 " =    2.045
peak=   -3.227 closest distance to " O   HOH Z  67 " =    3.066
peak=   -3.225 closest distance to " CB  GLN A  55 " =    1.175
peak=   -3.221 closest distance to " O   GLN A 240 " =    2.479
peak=   -3.218 closest distance to " CZ  TYR A 169 " =    1.595
peak=   -3.213 closest distance to " CD2 LEU A 237 " =    2.760
peak=   -3.212 closest distance to " CZ  PHE A  59 " =    1.542
peak=   -3.209 closest distance to " OG  SER A  28 " =    2.000
peak=   -3.209 closest distance to " O   HOH Z  51 " =    0.812
peak=   -3.206 closest distance to " CD1 ILE A  33 " =    2.308
peak=   -3.206 closest distance to " CB  ALA A 114 " =    2.393
peak=   -3.205 closest distance to " OD2 ASP A 171 " =    1.678
peak=   -3.205 closest distance to " CB  CYS A 201 " =    2.085
peak=   -3.204 closest distance to " O   ASP A 162 " =    2.238
peak=   -3.201 closest distance to " CD2 LEU A   5 " =    2.739
peak=   -3.192 closest distance to " CG  PHE A 283 " =    2.635
peak=   -3.190 closest distance to " O   HOH Z 207 " =    2.015
peak=   -3.184 closest distance to " CD1 LEU A 228 " =    2.341
peak=   -3.180 closest distance to " C   GLU A 236 " =    0.890
peak=   -3.179 closest distance to " O   HOH Z 200 " =    3.344
peak=   -3.179 closest distance to " CE3 TRP A 123 " =    1.355
peak=   -3.178 closest distance to " C   LEU A 222 " =    0.936
peak=   -3.169 closest distance to " O   HOH Z 111 " =    4.691
peak=   -3.168 closest distance to " OE1 GLN A  88 " =    1.107
peak=   -3.167 closest distance to " OG  SER A  26 " =    1.107
peak=   -3.166 closest distance to " CG  TRP A 266 " =    1.739
peak=   -3.165 closest distance to " O   ALA A  10 " =    1.816
peak=   -3.145 closest distance to " CB  PHE A 192 " =    1.620
peak=   -3.144 closest distance to " O   HOH Z 368 " =    1.440
peak=   -3.144 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.143 closest distance to " CB  PRO A 163 " =    2.382
peak=   -3.142 closest distance to " CG  GLN A 278 " =    2.262
peak=   -3.140 closest distance to " N   ALA A   1 " =    1.623
peak=   -3.138 closest distance to " O   SER A 271 " =    2.091
peak=   -3.138 closest distance to " O   HOH Z 429 " =    1.820
peak=   -3.138 closest distance to " CG1 VAL A 197 " =    2.384
peak=   -3.136 closest distance to " CG2 ILE A  20 " =    2.989
peak=   -3.134 closest distance to " O   HOH Z 166 " =    1.414
peak=   -3.128 closest distance to " O   HOH Z 114 " =    1.744
peak=   -3.125 closest distance to " CD2 PHE A  61 " =    2.077
peak=   -3.125 closest distance to " CB  CYS A 254 " =    1.882
peak=   -3.124 closest distance to " CE  LYS A  76 " =    2.768
peak=   -3.105 closest distance to " O   ILE A  49 " =    1.722
peak=   -3.103 closest distance to " CD1 LEU A   5 " =    2.466
peak=   -3.097 closest distance to " CB  PRO A 213 " =    2.145
peak=   -3.096 closest distance to " CG  LEU A 281 " =    1.748
peak=   -3.092 closest distance to " O   GLU A  44 " =    1.707
peak=   -3.089 closest distance to " O   HOH Z 174 " =    2.943
peak=   -3.083 closest distance to " O   HOH Z  65 " =    1.271
peak=   -3.082 closest distance to " CG  ASN A 301 " =    1.905
peak=   -3.076 closest distance to " CD  GLN A  77 " =    1.434
peak=   -3.073 closest distance to " CZ BARG A 275 " =    1.595
peak=   -3.071 closest distance to " CG1 VAL A 112 " =    2.568
peak=   -3.070 closest distance to " CG  GLN A 240 " =    2.295
peak=   -3.054 closest distance to " CB  ASP A 132 " =    2.387

================= 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    :  0.4817 0.4746   6.286950e+00   6.270484e+00
   1_bss:  0.4738 0.4605   6.280343e+00   6.261961e+00
   1_xyz:  0.3947 0.4186   6.182113e+00   6.212858e+00
   1_adp:  0.3518 0.4122   6.120729e+00   6.204279e+00
   1_occ:  0.3515 0.4124   6.120570e+00   6.204779e+00
   2_bss:  0.3480 0.4061   6.119787e+00   6.202888e+00
   2_xyz:  0.2826 0.3432   5.944310e+00   6.074746e+00
   2_adp:  0.2615 0.3283   5.894343e+00   6.040685e+00
   2_occ:  0.2614 0.3286   5.894398e+00   6.041161e+00
   3_bss:  0.2604 0.3260   5.894289e+00   6.039009e+00
   3_xyz:  0.1974 0.2556   5.640518e+00   5.826601e+00
   3_adp:  0.1781 0.2360   5.548091e+00   5.752584e+00
   3_occ:  0.1780 0.2358   5.547005e+00   5.751614e+00
   4_bss:  0.1775 0.2349   5.544968e+00   5.748377e+00
   4_xyz:  0.1399 0.1936   5.348826e+00   5.584941e+00
   4_adp:  0.1303 0.1836   5.290132e+00   5.528578e+00
   4_occ:  0.1302 0.1831   5.289175e+00   5.527352e+00
   5_bss:  0.1305 0.1822   5.287646e+00   5.524100e+00
   5_xyz:  0.1217 0.1719   5.227683e+00   5.470308e+00
   5_adp:  0.1188 0.1708   5.215640e+00   5.463574e+00
   5_occ:  0.1187 0.1707   5.215129e+00   5.462893e+00
   5_bss:  0.1187 0.1706   5.215188e+00   5.462911e+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:  0.343   2.471   7.753  10.088   8.240   0.000   0.000   0.000
   1_xyz:  0.343   2.471   7.753  10.088   8.240   0.000   0.000   0.000
   1_adp:  0.343   2.471   7.753  10.088   8.240   0.000   0.000   0.000
   1_occ:  0.343   2.471   7.753  10.088   8.240   0.000   0.000   0.000
   2_bss:  0.354  43.132   4.003   5.533   4.361   0.000   0.000   0.000
   2_xyz:  0.354  43.132   4.003   5.533   4.361   0.000   0.000   0.000
   2_adp:  0.354  43.132   4.003   5.533   4.361   0.000   0.000   0.000
   2_occ:  0.354  43.132   4.003   5.533   4.361   0.000   0.000   0.000
   3_bss:  0.331  43.132   2.463   2.950   3.275   0.000   0.000   0.000
   3_xyz:  0.331  43.132   2.463   2.950   3.275   0.000   0.000   0.000
   3_adp:  0.331  43.132   2.463   2.950   3.275   0.000   0.000   0.000
   3_occ:  0.331  43.132   2.463   2.950   3.275   0.000   0.000   0.000
   4_bss:  0.315  46.051   1.367   1.338   2.539   0.000   0.000   0.000
   4_xyz:  0.315  46.051   1.367   1.338   2.539   0.000   0.000   0.000
   4_adp:  0.315  46.051   1.367   1.338   2.539   0.000   0.000   0.000
   4_occ:  0.315  46.051   1.367   1.338   2.539   0.000   0.000   0.000
   5_bss:  0.317  49.994   1.305   1.002   2.488   0.000   0.000   0.000
   5_xyz:  0.317  49.994   1.305   1.002   2.488   0.000   0.000   0.000
   5_adp:  0.317  49.994   1.305   1.002   2.488   0.000   0.000   0.000
   5_occ:  0.317  49.994   1.305   1.002   2.488   0.000   0.000   0.000
   5_bss:  0.315  50.801  -0.253  -0.675   0.928  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.235 0.4162  0.4929    70889.777
   1_bss:  57.792 0.4209  0.6386    68922.420
   1_xyz:  50.565 0.5116  0.7566    54559.584
   1_adp:  48.343 0.5397  0.8561    52243.103
   1_occ:  48.437 0.5386  0.8538    52425.139
   2_bss:  47.905 0.5451  0.7561    51613.905
   2_xyz:  37.603 0.6696  0.9069    33425.223
   2_adp:  34.821 0.7030  0.9453    30168.944
   2_occ:  34.871 0.7024  0.9444    30219.913
   3_bss:  34.661 0.7048  0.8907    29988.313
   3_xyz:  25.489 0.8055  0.9853    16920.077
   3_adp:  22.801 0.8338  1.0016    14112.161
   3_occ:  22.774 0.8340  1.0014    14060.360
   4_bss:  22.648 0.8351  0.9617    13891.977
   4_xyz:  18.662 0.8738  0.9799     9693.167
   4_adp:  17.301 0.8867  0.9763     8702.085
   4_occ:  17.272 0.8870  0.9762     8675.112
   5_bss:  17.205 0.8874  0.9711     8581.858
   5_xyz:  15.887 0.8990  0.9766     7541.204
   5_adp:  15.631 0.9016  0.9695     7431.097
   5_occ:  15.621 0.9017  0.9694     7416.072
   5_bss:  15.625 0.9016  0.9751     7417.512
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3671e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3671e+01
   1_xyz:   1.689  0.013  0.107 18.395  0.007  4.107   1.4296e-01
   1_adp:   1.689  0.013  0.107 18.395  0.007  4.107   1.4296e-01
   1_occ:   1.689  0.013  0.107 18.395  0.007  4.107   1.4296e-01
   2_bss:   1.689  0.013  0.107 18.395  0.007  4.107   1.4296e-01
   2_xyz:   1.171  0.008  0.084 16.540  0.005  4.106   8.5936e-02
   2_adp:   1.171  0.008  0.084 16.540  0.005  4.106   8.5936e-02
   2_occ:   1.171  0.008  0.084 16.540  0.005  4.106   8.5936e-02
   3_bss:   1.171  0.008  0.084 16.540  0.005  4.106   8.5936e-02
   3_xyz:   1.110  0.008  0.079 15.732  0.004  4.121   7.1740e-02
   3_adp:   1.110  0.008  0.079 15.732  0.004  4.121   7.1740e-02
   3_occ:   1.110  0.008  0.079 15.732  0.004  4.121   7.1740e-02
   4_bss:   1.110  0.008  0.079 15.732  0.004  4.121   7.1740e-02
   4_xyz:   1.077  0.008  0.082 15.820  0.004  4.108   7.0627e-02
   4_adp:   1.077  0.008  0.082 15.820  0.004  4.108   7.0627e-02
   4_occ:   1.077  0.008  0.082 15.820  0.004  4.108   7.0627e-02
   5_bss:   1.077  0.008  0.082 15.820  0.004  4.108   7.0627e-02
   5_xyz:   1.021  0.007  0.079 15.732  0.004  4.113   6.4349e-02
   5_adp:   1.021  0.007  0.079 15.732  0.004  4.113   6.4349e-02
   5_occ:   1.021  0.007  0.079 15.732  0.004  4.113   6.4349e-02
   5_bss:   1.021  0.007  0.079 15.732  0.004  4.113   6.4349e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9566e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9566e+00
   1_xyz:  13.179  0.188  0.417 88.785  0.038  2.169   1.0046e-01
   1_adp:  13.179  0.188  0.417 88.785  0.038  2.169   1.0046e-01
   1_occ:  13.179  0.188  0.417 88.785  0.038  2.169   1.0046e-01
   2_bss:  13.179  0.188  0.417 88.785  0.038  2.169   1.0046e-01
   2_xyz:   7.134  0.096  0.320 89.406  0.052  2.132   5.6867e-02
   2_adp:   7.134  0.096  0.320 89.406  0.052  2.132   5.6867e-02
   2_occ:   7.134  0.096  0.320 89.406  0.052  2.132   5.6867e-02
   3_bss:   7.134  0.096  0.320 89.406  0.052  2.132   5.6867e-02
   3_xyz:   7.660  0.049  0.367 82.589  0.028  2.288   6.0838e-02
   3_adp:   7.660  0.049  0.367 82.589  0.028  2.288   6.0838e-02
   3_occ:   7.660  0.049  0.367 82.589  0.028  2.288   6.0838e-02
   4_bss:   7.660  0.049  0.367 82.589  0.028  2.288   6.0838e-02
   4_xyz:   7.978  0.067  0.428 81.117  0.037  2.278   5.6419e-02
   4_adp:   7.978  0.067  0.428 81.117  0.037  2.278   5.6419e-02
   4_occ:   7.978  0.067  0.428 81.117  0.037  2.278   5.6419e-02
   5_bss:   7.978  0.067  0.428 81.117  0.037  2.278   5.6419e-02
   5_xyz:   8.574  0.054  0.461 82.203  0.041  2.317   4.2486e-02
   5_adp:   8.574  0.054  0.461 82.203  0.041  2.317   4.2486e-02
   5_occ:   8.574  0.054  0.461 82.203  0.041  2.317   4.2486e-02
   5_bss:   8.574  0.054  0.461 82.203  0.041  2.317   4.2486e-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:  77.42   0.00  14.05  69.63   0.00  12.10  77.42   0.00  24.68
   1_occ:  77.42   0.00  14.05  69.63   0.00  12.10  77.42   0.00  24.68
   2_bss:  77.42   0.00  14.05  69.63   0.00  12.10  77.42   0.00  24.68
   2_xyz:  77.42   0.00  14.05  69.63   0.00  12.10  77.42   0.00  24.68
   2_adp:  80.63   0.00  13.93  64.94   0.00  10.83  80.63   0.00  30.79
   2_occ:  80.63   0.00  13.93  64.94   0.00  10.83  80.63   0.00  30.79
   3_bss:  80.63   0.00  13.93  64.94   0.00  10.83  80.63   0.00  30.79
   3_xyz:  80.63   0.00  13.93  64.94   0.00  10.83  80.63   0.00  30.79
   3_adp:  83.71   0.00  14.12  75.21   0.00  10.08  83.71   2.95  36.15
   3_occ:  83.71   0.00  14.12  75.21   0.00  10.08  83.71   2.95  36.15
   4_bss:  83.71   0.00  14.12  75.21   0.00  10.08  83.71   2.95  36.15
   4_xyz:  83.71   0.00  14.12  75.21   0.00  10.08  83.71   2.95  36.15
   4_adp:  85.45   0.00  14.31  84.96   0.00   9.66  85.45   3.13  39.60
   4_occ:  85.45   0.00  14.31  84.96   0.00   9.66  85.45   3.13  39.60
   5_bss:  85.45   0.00  14.31  84.96   0.00   9.66  85.45   3.13  39.60
   5_xyz:  85.45   0.00  14.31  84.96   0.00   9.66  85.45   3.13  39.60
   5_adp:  95.02   0.00  14.22  93.83   0.00   9.47  95.02   2.67  40.10
   5_occ:  95.02   0.00  14.22  93.83   0.00   9.47  95.02   2.67  40.10
   5_bss:  96.79   1.76  15.98  95.60   1.76  11.23  96.79   4.43  41.86
------------------------------------------------------------------------
 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:    1.245    0.016    0.411
   1_adp:    1.245    0.016    0.411
   1_occ:    1.245    0.016    0.411
   2_bss:    1.245    0.016    0.411
   2_xyz:    1.469    0.034    0.570
   2_adp:    1.469    0.034    0.570
   2_occ:    1.469    0.034    0.570
   3_bss:    1.469    0.034    0.570
   3_xyz:    1.749    0.032    0.672
   3_adp:    1.749    0.032    0.672
   3_occ:    1.749    0.032    0.672
   4_bss:    1.749    0.032    0.672
   4_xyz:    1.929    0.039    0.748
   4_adp:    1.929    0.039    0.748
   4_occ:    1.929    0.039    0.748
   5_bss:    1.929    0.039    0.748
   5_xyz:    1.984    0.025    0.766
   5_adp:    1.984    0.025    0.766
   5_occ:    1.984    0.025    0.766
   5_bss:    1.984    0.025    0.766
------------------------------------------------------------------------

CPU time actual refinement: 345.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_864/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_864/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_864/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_864/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_864/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.27 
  Macro-tasks:
    bulk solvent and scale       = 41.89  
    individual site refinement   = 141.40 
    weights calculation          = 32.67  
    collect and process          = 6.48   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 222.57 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 108.97 
    alpha_beta                      = 8.16   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.59 
    fmodel                         = 7.08   
    r_factors                      = 0.32   
    phase_errors                   = 10.39  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 256.38 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.901 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    635 calls, 108.71 s
gradients_fft:          579 calls, 104.62 s

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

# Date 2008-01-16 Time 02:37:40 PST -0800 (1200479860.62 s)
Start R-work = 0.4817, R-free = 0.4746 (no bulk solvent and anisotropic scale)
Final R-work = 0.1349, R-free = 0.1856 (no bulk solvent and anisotropic scale)

Start R-work = 0.4738, R-free = 0.4605
Final R-work = 0.1187, R-free = 0.1706