# Date 2008-01-16 Time 01:50:48 PST -0800 (1200477048.37 s)
#phil __OFF__

Command line arguments: "../583.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19869
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 583

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.8686, 84.2302, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95155
Completeness in resolution range: 0.926632
Completeness with d_max=infinity: 0.923879

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9212
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95155
Completeness in resolution range: 0.926632
Completeness with d_max=infinity: 0.923879

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9216 -  4.1766 [2222/2251]  1999   223  10.0%
  bin  2:  4.1766 -  3.3272 [2122/2145]  1912   210   9.9%
  bin  3:  3.3272 -  2.9102 [2092/2117]  1882   210  10.0%
  bin  4:  2.9102 -  2.6457 [2083/2109]  1878   205   9.8%
  bin  5:  2.6457 -  2.4570 [2091/2125]  1881   210  10.0%
  bin  6:  2.4570 -  2.3127 [2043/2071]  1842   201   9.8%
  bin  7:  2.3127 -  2.1972 [2041/2077]  1834   207  10.1%
  bin  8:  2.1972 -  2.1019 [2042/2084]  1833   209  10.2%
  bin  9:  2.1019 -  2.0211 [1991/2073]  1793   198   9.9%
  bin 10:  2.0211 -  1.9516 [ 862/2088]   776    86  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_583/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 22
        2.09 -     2.80: 748
        2.80 -     3.50: 4477
        3.50 -     4.20: 9389
        4.20 -     4.90: 13901
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.393 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.539 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.539 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.626 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.654 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28532 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_583/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_583/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.8686 84.23025 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: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5056   r_free= 0.5069   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.305244                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1444  163 0.4220 0.4273      6.6513      6.6734|
|  2:  4.6588 -  3.7166 0.99   1382  148 0.4418 0.4487      6.8489       6.858|
|  3:  3.7166 -  3.2524 0.99   1360  152 0.4747 0.4529      6.7139      6.7489|
|  4:  3.2524 -  2.9575 0.98   1339  153 0.4877 0.4795      6.5371      6.5239|
|  5:  2.9575 -  2.7470 0.99   1355  149 0.5332 0.5589      6.3928      6.3696|
|  6:  2.7470 -  2.5859 0.99   1328  149 0.5283 0.5235      6.2816      6.2037|
|  7:  2.5859 -  2.4570 0.98   1344  144 0.5350 0.4927      6.2693      6.2066|
|  8:  2.4570 -  2.3504 0.98   1306  147 0.5466 0.5585      6.1518      6.1735|
|  9:  2.3504 -  2.2603 0.99   1325  140 0.5682 0.5567      6.1518       6.145|
| 10:  2.2603 -  2.1825 0.99   1316  153 0.5417 0.5758       6.101      6.1263|
| 11:  2.1825 -  2.1145 0.97   1296  140 0.5486 0.5366      6.0343      6.0302|
| 12:  2.1145 -  2.0542 0.98   1305  152 0.5362 0.5930       5.947      5.9811|
| 13:  2.0542 -  2.0002 0.87   1150  132 0.5642 0.5550      5.8844      5.8554|
| 14:  2.0002 -  1.9516 0.28    380   37 0.5773 0.5375      5.8298      5.6639|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1444   163  0.63  39.97   0.79     0.66      91525.18|
|  2:  4.6588 -  3.7166  1382   148  0.64  40.64   0.85     0.70     131744.50|
|  3:  3.7166 -  3.2524  1360   152  0.52  50.47   0.82     0.65     139867.70|
|  4:  3.2524 -  2.9575  1339   153  0.43  57.76   0.79     0.53     119373.23|
|  5:  2.9575 -  2.7470  1355   149  0.33  64.82   0.72     0.42      96262.58|
|  6:  2.7470 -  2.5859  1328   149  0.33  65.08   0.71     0.40      77768.23|
|  7:  2.5859 -  2.4570  1344   144  0.33  64.88   0.73     0.39      68404.94|
|  8:  2.4570 -  2.3504  1306   147  0.28  68.71   0.70     0.35      64499.24|
|  9:  2.3504 -  2.2603  1325   140  0.20  75.02   0.71     0.25      63110.85|
| 10:  2.2603 -  2.1825  1316   153  0.12  81.06   0.75     0.15      61143.03|
| 11:  2.1825 -  2.1145  1296   140  0.07  84.59   0.76     0.09      56696.37|
| 12:  2.1145 -  2.0542  1305   152  0.08  83.82   0.74     0.11      52365.38|
| 13:  2.0542 -  2.0002  1150   132  0.15  79.05   0.73     0.20      42381.64|
| 14:  2.0002 -  1.9516   380    37  0.29  68.55   0.68     0.35      31531.57|
|alpha:            min =        0.09 max =            0.70 mean =         0.38|
|beta:             min =    31531.57 max =       139867.70 mean =     81724.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           89.98 mean =        65.41|
|phase err.(test): min =        0.00 max =           89.97 mean =        65.80|
|-----------------------------------------------------------------------------|

============================== 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 = 21.670043             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.662   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.075583              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.000   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.765 -  1.178:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.178 -  1.592:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.592 -  2.005:       42 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.005 -  2.419:      322 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.419 -  2.832:     1050 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.832 -  3.246:     2294 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.246 -  3.659:     3819 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.659 -  4.073:     5351 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.073 -  4.486:     7059 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.486 -  4.900:     8591 |
|-----------------------------------------------------------------------------|
|-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 |       53.448 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.765 |       2.427 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    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 = 11.720)------------------------------------------|
|    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: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5100   r_free= 0.5114   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.305765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4989   r_free= 0.4976   ksol= 0.34   Bsol= 20.00   scale= 0.959   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.82,10.29,8.00,0.00,0.00,0.00); trace/3= 8.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.303233                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.008319             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.411   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.728780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.879   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4989      final r-factor (work) = 0.4437          |
| start r-factor (free) = 0.4976      final r-factor (free) = 0.4618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 110.1918 = 18.01 * 0.50 * 6.3019 + 1.00 * 53.4481                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.4319 = 18.01 * 0.50 * 6.2495 + 1.00 * 0.1607                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4437      final r-factor (work) = 0.4059          |
| start r-factor (free) = 0.4618      final r-factor (free) = 0.4576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8187 = 1.73 * 1.00 * 6.2495 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7535 = 1.73 * 1.00 * 6.2064 + 1.00 * 0.0241                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.24   16.84    None  None   None       |
|    all(noH): 2823   0      0.00    96.24   16.84    None  None   None       |
|    Sol.    : 438    0      0.00    96.24   25.69    None  None   None       |
|    Mac.    : 2385   0      0.00    90.56   15.22    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 -   9.624:  954   |   5:    48.119 -  57.743:   46        |
|      1:     9.624 -  19.248:  891   |   6:    57.743 -  67.367:   18        |
|      2:    19.248 -  28.872:  519   |   7:    67.367 -  76.991:   13        |
|      3:    28.872 -  38.495:  257   |   8:    76.991 -  86.614:    2        |
|      4:    38.495 -  48.119:  118   |   9:    86.614 -  96.238:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4059 r_free = 0.4576             target_work(ml) = 6.199         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4054 r_free = 0.4573             target_work(ml) = 6.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4054   r_free= 0.4573   ksol= 0.34   Bsol= 20.00   scale= 1.117   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.82,10.29,8.00,0.00,0.00,0.00); trace/3= 8.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.198036                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4033   r_free= 0.4545   ksol= 0.32   Bsol= 32.76   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.45,6.22,4.85,0.00,0.00,0.00); trace/3= 4.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.199157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.928410             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.519  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.746373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.037  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4033      final r-factor (work) = 0.3457          |
| start r-factor (free) = 0.4545      final r-factor (free) = 0.4103          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.4581 = 14.93 * 0.50 * 6.2027 + 1.00 * 0.1598                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.9195 = 14.93 * 0.50 * 6.1365 + 1.00 * 0.1152                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3457      final r-factor (work) = 0.3266          |
| start r-factor (free) = 0.4103      final r-factor (free) = 0.3990          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6029 = 0.75 * 1.00 * 6.1365 + 1.00 * 0.0228                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5669 = 0.75 * 1.00 * 6.0711 + 1.00 * 0.0356                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.19   16.55    None  None   None       |
|    all(noH): 2823   0      0.00    92.19   16.55    None  None   None       |
|    Sol.    : 438    0      0.00    92.19   29.08    None  None   None       |
|    Mac.    : 2385   0      0.00    83.10   14.24    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 -   9.220:  984   |   5:    46.097 -  55.317:   47        |
|      1:     9.220 -  18.439:  841   |   6:    55.317 -  64.536:   19        |
|      2:    18.439 -  27.658:  508   |   7:    64.536 -  73.756:   15        |
|      3:    27.658 -  36.878:  292   |   8:    73.756 -  82.975:    3        |
|      4:    36.878 -  46.097:  109   |   9:    82.975 -  92.195:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3266 r_free = 0.3990             target_work(ml) = 6.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3264 r_free = 0.3984             target_work(ml) = 6.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3264   r_free= 0.3984   ksol= 0.32   Bsol= 32.76   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.45,6.22,4.85,0.00,0.00,0.00); trace/3= 4.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.055475                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3247   r_free= 0.3950   ksol= 0.33   Bsol= 50.87   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,3.32,2.28,0.00,0.00,0.00); trace/3= 2.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.053084                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.294580             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.261  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.542088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.323   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3247      final r-factor (work) = 0.2483          |
| start r-factor (free) = 0.3950      final r-factor (free) = 0.3149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4368 = 12.29 * 0.50 * 6.0712 + 1.00 * 0.1152                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.7638 = 12.29 * 0.50 * 5.9634 + 1.00 * 0.1053                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2483      final r-factor (work) = 0.2218          |
| start r-factor (free) = 0.3149      final r-factor (free) = 0.2832          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2516 = 0.54 * 1.00 * 5.9634 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1500 = 0.54 * 1.00 * 5.7905 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.97   16.10    None  None   None       |
|    all(noH): 2823   0      0.00    86.97   16.10    None  None   None       |
|    Sol.    : 438    0      3.23    86.97   35.89    None  None   None       |
|    Mac.    : 2385   0      0.00    73.07   12.47    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 -   8.697: 1052   |   5:    43.486 -  52.184:   91        |
|      1:     8.697 -  17.395:  888   |   6:    52.184 -  60.881:   53        |
|      2:    17.395 -  26.092:  358   |   7:    60.881 -  69.578:   16        |
|      3:    26.092 -  34.789:  201   |   8:    69.578 -  78.276:    6        |
|      4:    34.789 -  43.486:  154   |   9:    78.276 -  86.973:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2218 r_free = 0.2832             target_work(ml) = 5.740         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2216 r_free = 0.2826             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2216   r_free= 0.2826   ksol= 0.33   Bsol= 50.87   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,3.32,2.28,0.00,0.00,0.00); trace/3= 2.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.738523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2202   r_free= 0.2806   ksol= 0.33   Bsol= 47.40   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,1.49,0.64,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.736157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.135012              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.101  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.603750              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.397  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2202      final r-factor (work) = 0.1713          |
| start r-factor (free) = 0.2806      final r-factor (free) = 0.2244          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0852 = 4.14 * 0.50 * 5.7944 + 1.00 * 0.1053                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7357 = 4.14 * 0.50 * 5.6425 + 1.00 * 0.0699                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1713      final r-factor (work) = 0.1546          |
| start r-factor (free) = 0.2244      final r-factor (free) = 0.2106          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4176 = 0.60 * 1.00 * 5.6425 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3199 = 0.60 * 1.00 * 5.4716 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.92   16.28    None  None   None       |
|    all(noH): 2823   0      0.00    88.92   16.28    None  None   None       |
|    Sol.    : 438    0      4.92    88.92   41.67    None  None   None       |
|    Mac.    : 2385   0      0.00    88.64   11.62    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 -   8.892: 1170   |   5:    44.460 -  53.351:  101        |
|      1:     8.892 -  17.784:  930   |   6:    53.351 -  62.243:   66        |
|      2:    17.784 -  26.676:  246   |   7:    62.243 -  71.135:   47        |
|      3:    26.676 -  35.568:  122   |   8:    71.135 -  80.027:   20        |
|      4:    35.568 -  44.460:  112   |   9:    80.027 -  88.919:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1546 r_free = 0.2106             target_work(ml) = 5.434         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1544 r_free = 0.2104             target_work(ml) = 5.434         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1544   r_free= 0.2104   ksol= 0.33   Bsol= 47.40   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,1.49,0.64,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.433606                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1547   r_free= 0.2105   ksol= 0.32   Bsol= 49.13   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,0.70,0.07,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.434581                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.910476              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.396   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.255047              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.807   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1547      final r-factor (work) = 0.1340          |
| start r-factor (free) = 0.2105      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0364 = 2.91 * 0.50 * 5.4744 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8905 = 2.91 * 0.50 * 5.3770 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1340      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4131 = 0.26 * 1.00 * 5.3770 + 1.00 * 0.0417                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3602 = 0.26 * 1.00 * 5.2939 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    89.73   15.87    None  None   None       |
|    all(noH): 2823   0      0.48    89.73   15.87    None  None   None       |
|    Sol.    : 438    0      4.12    88.73   40.94    None  None   None       |
|    Mac.    : 2385   0      0.48    89.73   11.26    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:     0.480 -   9.404: 1308   |   5:    45.104 -  54.028:   96        |
|      1:     9.404 -  18.329:  878   |   6:    54.028 -  62.953:   66        |
|      2:    18.329 -  27.254:  194   |   7:    62.953 -  71.878:   41        |
|      3:    27.254 -  36.179:  106   |   8:    71.878 -  80.803:   15        |
|      4:    36.179 -  45.104:  113   |   9:    80.803 -  89.728:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1307 r_free = 0.1767             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1304 r_free = 0.1765             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1304   r_free= 0.1765   ksol= 0.32   Bsol= 49.13   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,0.70,0.07,0.00,0.00,0.00); trace/3= -0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.275275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1444  163 0.0997 0.1297      5.4078      5.5665|
|  2:  4.6588 -  3.7166 0.99   1382  148 0.0942 0.1234      5.5166       5.753|
|  3:  3.7166 -  3.2524 0.99   1360  152 0.1220 0.1769        5.59      5.9285|
|  4:  3.2524 -  2.9575 0.98   1339  153 0.1489 0.1779      5.5799      5.7339|
|  5:  2.9575 -  2.7470 0.99   1355  149 0.1545 0.1794      5.4473      5.5716|
|  6:  2.7470 -  2.5859 0.99   1328  149 0.1535 0.2330      5.3806      5.6363|
|  7:  2.5859 -  2.4570 0.98   1344  144 0.1470 0.1900      5.3138      5.4862|
|  8:  2.4570 -  2.3504 0.98   1306  147 0.1463 0.1928      5.2174      5.4111|
|  9:  2.3504 -  2.2603 0.99   1325  140 0.1388 0.1899      5.1434      5.3507|
| 10:  2.2603 -  2.1825 0.99   1316  153 0.1362 0.2027      5.1115      5.4126|
| 11:  2.1825 -  2.1145 0.97   1296  140 0.1357 0.1941      5.0517      5.2913|
| 12:  2.1145 -  2.0542 0.98   1305  152 0.1328 0.1953      4.9635      5.1947|
| 13:  2.0542 -  2.0002 0.87   1150  132 0.1348 0.1928      4.8879      5.1187|
| 14:  2.0002 -  1.9516 0.28    380   37 0.1282 0.2016      4.8074      5.0568|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1444   163  0.93   9.88   0.98     0.95       8057.97|
|  2:  4.6588 -  3.7166  1382   148  0.94   9.24   1.02     1.00      10637.01|
|  3:  3.7166 -  3.2524  1360   152  0.91  13.81   1.03     1.03      13355.01|
|  4:  3.2524 -  2.9575  1339   153  0.90  16.09   1.02     1.00      12448.73|
|  5:  2.9575 -  2.7470  1355   149  0.87  19.05   1.01     0.98      10769.30|
|  6:  2.7470 -  2.5859  1328   149  0.88  19.02   0.99     0.97       9642.64|
|  7:  2.5859 -  2.4570  1344   144  0.88  18.70   1.00     0.95       8395.65|
|  8:  2.4570 -  2.3504  1306   147  0.88  19.05   1.01     0.98       7351.50|
|  9:  2.3504 -  2.2603  1325   140  0.88  18.51   1.01     0.99       6347.33|
| 10:  2.2603 -  2.1825  1316   153  0.88  18.13   1.00     0.96       5919.94|
| 11:  2.1825 -  2.1145  1296   140  0.87  19.13   1.01     0.97       5483.14|
| 12:  2.1145 -  2.0542  1305   152  0.89  17.67   1.00     0.98       4616.63|
| 13:  2.0542 -  2.0002  1150   132  0.88  18.65   1.01     1.00       4029.19|
| 14:  2.0002 -  1.9516   380    37  0.87  18.91   0.99     0.96       3527.41|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3527.41 max =        13355.01 mean =      8210.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        16.64|
|phase err.(test): min =        0.00 max =           89.99 mean =        15.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1769   ksol= 0.32   Bsol= 48.02   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.40,-0.07,0.00,-0.00,-0.00); trace/3= -0.20                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.277531                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1769   ksol= 0.32   Bsol= 48.02   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.40,-0.07,0.00,-0.00,-0.00); trace/3= -0.20                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.277531                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1444  163 0.1010 0.1333      5.4218      5.5866|
|  2:  4.6588 -  3.7166 0.99   1382  148 0.0954 0.1246      5.5287      5.7642|
|  3:  3.7166 -  3.2524 0.99   1360  152 0.1228 0.1754      5.5965      5.9247|
|  4:  3.2524 -  2.9575 0.98   1339  153 0.1488 0.1773      5.5799      5.7341|
|  5:  2.9575 -  2.7470 0.99   1355  149 0.1549 0.1793      5.4485      5.5713|
|  6:  2.7470 -  2.5859 0.99   1328  149 0.1537 0.2321      5.3802      5.6357|
|  7:  2.5859 -  2.4570 0.98   1344  144 0.1470 0.1901      5.3126      5.4855|
|  8:  2.4570 -  2.3504 0.98   1306  147 0.1461 0.1926      5.2168        5.41|
|  9:  2.3504 -  2.2603 0.99   1325  140 0.1384 0.1902      5.1421      5.3519|
| 10:  2.2603 -  2.1825 0.99   1316  153 0.1360 0.2025       5.111       5.414|
| 11:  2.1825 -  2.1145 0.97   1296  140 0.1355 0.1940      5.0508      5.2892|
| 12:  2.1145 -  2.0542 0.98   1305  152 0.1330 0.1955      4.9635      5.1947|
| 13:  2.0542 -  2.0002 0.87   1150  132 0.1347 0.1927      4.8874      5.1167|
| 14:  2.0002 -  1.9516 0.28    380   37 0.1281 0.2005      4.8064      5.0545|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1444   163  0.93  10.18   0.97     0.95       8424.00|
|  2:  4.6588 -  3.7166  1382   148  0.94   9.40   1.02     1.00      10919.43|
|  3:  3.7166 -  3.2524  1360   152  0.91  13.90   1.03     1.03      13541.82|
|  4:  3.2524 -  2.9575  1339   153  0.90  16.08   1.01     0.99      12415.43|
|  5:  2.9575 -  2.7470  1355   149  0.87  19.01   1.00     0.97      10752.08|
|  6:  2.7470 -  2.5859  1328   149  0.88  19.02   0.98     0.96       9630.06|
|  7:  2.5859 -  2.4570  1344   144  0.88  18.66   0.99     0.94       8366.29|
|  8:  2.4570 -  2.3504  1306   147  0.88  19.05   1.01     0.97       7341.49|
|  9:  2.3504 -  2.2603  1325   140  0.88  18.50   1.01     0.98       6341.58|
| 10:  2.2603 -  2.1825  1316   153  0.88  18.12   0.99     0.95       5909.26|
| 11:  2.1825 -  2.1145  1296   140  0.87  19.11   1.00     0.96       5477.31|
| 12:  2.1145 -  2.0542  1305   152  0.89  17.66   0.99     0.97       4611.78|
| 13:  2.0542 -  2.0002  1150   132  0.88  18.63   1.00     0.99       4021.15|
| 14:  2.0002 -  1.9516   380    37  0.87  18.87   0.98     0.95       3513.36|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3513.36 max =        13541.82 mean =      8266.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.67|
|phase err.(test): min =        0.00 max =           89.88 mean =        15.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.46    89.71   15.85    None  None   None       |
|    all(noH): 2823   0      0.46    89.71   15.85    None  None   None       |
|    Sol.    : 438    0      4.10    88.72   40.92    None  None   None       |
|    Mac.    : 2385   0      0.46    89.71   11.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.465 -   9.389: 1308   |   5:    45.089 -  54.013:   96        |
|      1:     9.389 -  18.314:  878   |   6:    54.013 -  62.938:   66        |
|      2:    18.314 -  27.239:  194   |   7:    62.938 -  71.863:   41        |
|      3:    27.239 -  36.164:  106   |   8:    71.863 -  80.788:   15        |
|      4:    36.164 -  45.089:  113   |   9:    80.788 -  89.713:    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)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.688 - 5.944
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 351
   mapped sites are within: 0.715 - 5.944

peak=   10.230 closest distance to " O   HOH Z 138 " =    1.687
peak=    9.051 closest distance to " CG2 VAL A 230 " =    1.430
peak=    8.519 closest distance to " O   HOH Z 120 " =    2.332
peak=    7.322 closest distance to " CG2 VAL A 296 " =    1.202
peak=    6.474 closest distance to " CD1AILE A 234 " =    1.373
peak=    6.470 closest distance to " O   HOH Z 199 " =    1.561
peak=    6.235 closest distance to " O   HOH Z  37 " =    1.172
peak=    6.183 closest distance to " O   HOH Z 278 " =    1.787
peak=    6.098 closest distance to " CG  LEU A   5 " =    1.411
peak=    6.077 closest distance to " O   HOH Z 422 " =    1.143
peak=    5.990 closest distance to " O   HOH Z  46 " =    1.041
peak=    5.792 closest distance to " O   HOH Z 246 " =    1.727
peak=    5.659 closest distance to " NH2 ARG A  56 " =    2.223
peak=    5.634 closest distance to " O   HOH Z 279 " =    1.257
peak=    5.587 closest distance to " O   HOH Z 209 " =    1.339
peak=    5.560 closest distance to " CG  GLN A  77 " =    0.958
peak=    5.458 closest distance to " O   HOH Z  49 " =    1.485
peak=    5.451 closest distance to " O   HOH Z  48 " =    2.265
peak=    5.298 closest distance to " O   HOH Z  11 " =    1.293
peak=    5.276 closest distance to " O   HOH Z 277 " =    1.322
peak=    5.212 closest distance to " O   HOH Z 210 " =    1.600
peak=    5.097 closest distance to " O   HOH Z 389 " =    1.932
peak=    4.952 closest distance to " O   HOH Z 126 " =    1.719
peak=    4.875 closest distance to " O   HOH Z 193 " =    1.772
peak=    4.830 closest distance to " O   HOH Z 124 " =    1.730
peak=    4.807 closest distance to " O   HOH Z 412 " =    3.332
peak=    4.779 closest distance to " O   HOH Z  43 " =    1.815
peak=    4.766 closest distance to " O   HOH Z 156 " =    3.238
peak=    4.756 closest distance to " O   HOH Z 135 " =    2.193
peak=    4.756 closest distance to " O   HOH Z 402 " =    1.573
peak=    4.735 closest distance to " O   HOH Z 221 " =    1.323
peak=    4.692 closest distance to " C   PRO A 198 " =    1.569
peak=    4.678 closest distance to " CG  PRO A  54 " =    1.180
peak=    4.642 closest distance to " O   HOH Z 155 " =    1.864
peak=    4.638 closest distance to " CG  PRO A 198 " =    1.205
peak=    4.621 closest distance to " O   HOH Z  39 " =    2.123
peak=    4.590 closest distance to " CD2 LEU A 228 " =    1.179
peak=    4.542 closest distance to " CD2 LEU A   5 " =    1.187
peak=    4.505 closest distance to " O   HOH Z 316 " =    2.200
peak=    4.501 closest distance to " O  BHOH Z 338 " =    1.302
peak=    4.473 closest distance to " CB  ALA A 100 " =    1.425
peak=    4.450 closest distance to " O   HOH Z 316 " =    1.087
peak=    4.425 closest distance to " O   HOH Z 202 " =    1.644
peak=    4.413 closest distance to " CA  VAL A  41 " =    0.872
peak=    4.387 closest distance to " CB  GLN A  58 " =    0.911
peak=    4.386 closest distance to " O   HOH Z 130 " =    1.220
peak=    4.377 closest distance to " CB  ARG A 275 " =    0.963
peak=    4.368 closest distance to " O   HOH Z 326 " =    1.547
peak=    4.313 closest distance to " O   HOH Z 137 " =    2.024
peak=    4.296 closest distance to " O   HOH Z 236 " =    1.401
peak=    4.293 closest distance to " O   HOH Z 406 " =    1.542
peak=    4.285 closest distance to " CA  ALA A  21 " =    1.295
peak=    4.283 closest distance to " O   HOH Z  30 " =    1.903
peak=    4.280 closest distance to " O   HOH Z 196 " =    1.515
peak=    4.276 closest distance to " CA  TYR A  30 " =    1.007
peak=    4.264 closest distance to " O   HOH Z  68 " =    2.053
peak=    4.251 closest distance to " CB  VAL A 230 " =    1.267
peak=    4.230 closest distance to " CB  ARG A 275 " =    1.241
peak=    4.227 closest distance to " O   GLY A  91 " =    1.341
peak=    4.225 closest distance to " CB  PRO A  54 " =    0.750
peak=    4.210 closest distance to " O   HOH Z 208 " =    1.605
peak=    4.210 closest distance to " O   HOH Z 192 " =    1.593
peak=    4.202 closest distance to " O   HOH Z 272 " =    2.054
peak=    4.178 closest distance to " O   HOH Z 234 " =    3.831
peak=    4.176 closest distance to " O   HOH Z 133 " =    2.111
peak=    4.146 closest distance to " CB  GLN A  73 " =    1.037
peak=    4.143 closest distance to " CE  LYS A 119 " =    1.357
peak=    4.136 closest distance to " CB  GLN A 223 " =    1.464
peak=    4.126 closest distance to " CB  SER A  63 " =    1.278
peak=    4.125 closest distance to " O   HOH Z 433 " =    1.557
peak=    4.115 closest distance to " O   HOH Z 272 " =    1.009
peak=    4.113 closest distance to " OE1 GLN A  11 " =    1.952
peak=    4.112 closest distance to " CG  ARG A  66 " =    1.106
peak=    4.105 closest distance to " O   HOH Z 431 " =    1.408
peak=    4.099 closest distance to " OG ASER A 164 " =    0.715
peak=    4.098 closest distance to " O   HOH Z 132 " =    1.468
peak=    4.049 closest distance to " CB  SER A  62 " =    0.960
peak=    4.047 closest distance to " CD  PRO A  54 " =    1.038
peak=    4.018 closest distance to " OD1 ASN A  60 " =    1.195
peak=    3.996 closest distance to " O   HOH Z  80 " =    2.197
peak=    3.985 closest distance to " O   HOH Z 133 " =    1.746
peak=    3.971 closest distance to " O   HOH Z 331 " =    1.447
peak=    3.954 closest distance to " CG  PRO A 213 " =    1.335
peak=    3.953 closest distance to " O   HOH Z 128 " =    1.457
peak=    3.950 closest distance to " CD  LYS A 119 " =    1.297
peak=    3.947 closest distance to " CB  TRP A 179 " =    1.270
peak=    3.941 closest distance to " O   HOH Z  97 " =    1.635
peak=    3.939 closest distance to " O   HOH Z 315 " =    2.097
peak=    3.936 closest distance to " O   HOH Z 108 " =    1.361
peak=    3.931 closest distance to " O   HOH Z 232 " =    2.197
peak=    3.929 closest distance to " CB  PRO A 198 " =    1.090
peak=    3.919 closest distance to " O   HOH Z 403 " =    1.890
peak=    3.914 closest distance to " CB BVAL A  41 " =    1.210
peak=    3.913 closest distance to " NH1 ARG A  14 " =    1.084
peak=    3.908 closest distance to " O   HOH Z 154 " =    1.534
peak=    3.896 closest distance to " O   HOH Z 128 " =    2.012
peak=    3.886 closest distance to " O   HOH Z 163 " =    1.692
peak=    3.876 closest distance to " CB  ALA A 256 " =    1.069
peak=    3.871 closest distance to " O   HOH Z 136 " =    1.377
peak=    3.854 closest distance to " O   HOH Z 352 " =    1.304
peak=    3.836 closest distance to " CG  PRO A 243 " =    1.237
peak=    3.830 closest distance to " O   SER A  87 " =    2.242
peak=    3.829 closest distance to " CB  VAL A 296 " =    1.160
peak=    3.824 closest distance to " CB  VAL A 265 " =    1.263
peak=    3.817 closest distance to " O   HOH Z 263 " =    1.586
peak=    3.805 closest distance to " O   HOH Z 421 " =    1.702
peak=    3.802 closest distance to " O   HOH Z  15 " =    2.267
peak=    3.788 closest distance to " O   HOH Z  44 " =    2.491
peak=    3.787 closest distance to " CD  ARG A 269 " =    1.107
peak=    3.776 closest distance to " CB  GLU A 277 " =    1.113
peak=    3.758 closest distance to " OD2 ASP A 286 " =    2.785
peak=    3.750 closest distance to " CB  GLN A 194 " =    0.839
peak=    3.749 closest distance to " O   HOH Z 414 " =    1.788
peak=    3.743 closest distance to " O   HOH Z 346 " =    1.600
peak=    3.736 closest distance to " O   HOH Z 273 " =    2.597
peak=    3.735 closest distance to " O   HOH Z 394 " =    1.656
peak=    3.735 closest distance to " CD2 LEU A 255 " =    1.254
peak=    3.723 closest distance to " O   HOH Z  47 " =    1.787
peak=    3.720 closest distance to " O   HOH Z   4 " =    1.211
peak=    3.717 closest distance to " O   HOH Z 112 " =    1.589
peak=    3.716 closest distance to " O   HOH Z 427 " =    1.027
peak=    3.705 closest distance to " CA  LEU A 282 " =    1.196
peak=    3.699 closest distance to " O   HOH Z 174 " =    2.213
peak=    3.697 closest distance to " OG  SER A  97 " =    2.852
peak=    3.692 closest distance to " CB  VAL A 202 " =    1.495
peak=    3.690 closest distance to " O   HOH Z 358 " =    1.363
peak=    3.681 closest distance to " O   HOH Z  97 " =    2.298
peak=    3.679 closest distance to " CD  LYS A 166 " =    1.534
peak=    3.678 closest distance to " O   HOH Z 368 " =    1.199
peak=    3.672 closest distance to " O   HOH Z 395 " =    1.351
peak=    3.668 closest distance to " O   HOH Z 118 " =    1.582
peak=    3.662 closest distance to " O   HOH Z  61 " =    1.438
peak=    3.656 closest distance to " CG  LYS A 166 " =    1.532
peak=    3.647 closest distance to " OE1 GLN A  58 " =    5.872
peak=    3.627 closest distance to " CB  GLU A 152 " =    1.051
peak=    3.620 closest distance to " CA  ALA A 295 " =    1.037
peak=    3.617 closest distance to " O   HOH Z  14 " =    2.260
peak=    3.616 closest distance to " O   HOH Z 130 " =    2.494
peak=    3.612 closest distance to " O   HOH Z 369 " =    2.015
peak=    3.609 closest distance to " OE1 GLU A   2 " =    2.040
peak=    3.608 closest distance to " O   HOH Z 426 " =    1.433
peak=    3.602 closest distance to " OG1 THR A 294 " =    2.204
peak=    3.601 closest distance to " O   HOH Z  39 " =    1.607
peak=    3.596 closest distance to " O   HOH Z 284 " =    2.763
peak=    3.592 closest distance to " O   HOH Z 374 " =    1.078
peak=    3.590 closest distance to " O   HOH Z 211 " =    1.121
peak=    3.585 closest distance to " O   ALA A 165 " =    1.139
peak=    3.583 closest distance to " O   HOH Z  54 " =    1.591
peak=    3.583 closest distance to " OH  TYR A  30 " =    1.275
peak=    3.579 closest distance to " CB  TYR A 169 " =    0.718
peak=    3.574 closest distance to " NE2 HIS A 115 " =    0.780
peak=    3.571 closest distance to " O   HOH Z 146 " =    1.320
peak=    3.556 closest distance to " N   HIS A 108 " =    1.839
peak=    3.555 closest distance to " O   HOH Z 225 " =    1.968
peak=    3.554 closest distance to " O   HOH Z 423 " =    1.970
peak=    3.553 closest distance to " O   HOH Z 301 " =    1.524
peak=    3.550 closest distance to " NZ  LYS A 117 " =    2.975
peak=    3.549 closest distance to " CB  GLN A 183 " =    1.253
peak=    3.543 closest distance to " CB  ASN A 148 " =    1.167
peak=    3.542 closest distance to " CB  THR A  31 " =    1.471
peak=    3.538 closest distance to " O   HOH Z 284 " =    1.422
peak=    3.533 closest distance to " OD1 ASN A  69 " =    2.057
peak=    3.533 closest distance to " CG2 THR A 220 " =    0.858
peak=    3.529 closest distance to " CG  LEU A 228 " =    1.454
peak=    3.529 closest distance to " O   HOH Z 203 " =    1.618
peak=    3.527 closest distance to " NE2 GLN A  11 " =    1.049
peak=    3.511 closest distance to " CG2 THR A 251 " =    1.195
peak=    3.510 closest distance to " CD2 TRP A 179 " =    1.288
peak=    3.509 closest distance to " CB  SER A  26 " =    0.985
peak=    3.508 closest distance to " O   HOH Z 117 " =    1.087
peak=    3.508 closest distance to " CB  LEU A 228 " =    1.344
peak=    3.508 closest distance to " O   HOH Z 180 " =    2.131
peak=    3.506 closest distance to " O   HOH Z 359 " =    1.978
peak=    3.506 closest distance to " O   HOH Z 102 " =    1.309
peak=    3.505 closest distance to " O   HOH Z 217 " =    1.725
peak=    3.502 closest distance to " CG1 ILE A  33 " =    1.279
peak=    3.501 closest distance to " O   HOH Z 386 " =    2.085
peak=    3.499 closest distance to " O   HOH Z 154 " =    2.379
peak=    3.498 closest distance to " CB  SER A 141 " =    1.044
peak=    3.486 closest distance to " OG  SER A 276 " =    1.528
peak=    3.482 closest distance to " CA  ALA A 248 " =    1.265
peak=    3.480 closest distance to " O   HOH Z 261 " =    1.975
peak=    3.477 closest distance to " O   HOH Z  44 " =    2.006
peak=    3.477 closest distance to " OD1 ASP A 238 " =    0.842
peak=    3.471 closest distance to " CA  ILE A 263 " =    1.000
peak=    3.468 closest distance to " N   ASN A  39 " =    1.231
peak=    3.460 closest distance to " O   HOH Z 166 " =    1.613
peak=    3.459 closest distance to " CA  SER A  12 " =    1.388
peak=    3.458 closest distance to " CB  ALA A  71 " =    1.244
peak=    3.456 closest distance to " CE BMET A  47 " =    1.367
peak=    3.454 closest distance to " O   GLY A  23 " =    2.298
peak=    3.453 closest distance to " O   HOH Z 138 " =    1.481
peak=    3.452 closest distance to " O   HOH Z  54 " =    2.384
peak=    3.452 closest distance to " O   HOH Z 427 " =    3.427
peak=    3.444 closest distance to " O   HOH Z 344 " =    2.700
peak=    3.443 closest distance to " O   HOH Z 363 " =    1.113
peak=    3.437 closest distance to " O   HOH Z 331 " =    1.474
peak=    3.435 closest distance to " ND1 HIS A  81 " =    1.245
peak=    3.431 closest distance to " CA  VAL A 126 " =    1.031
peak=    3.431 closest distance to " O   ASP A 124 " =    1.603
peak=    3.427 closest distance to " CG1BVAL A 121 " =    1.255
peak=    3.426 closest distance to " CZ3 TRP A  92 " =    1.139
peak=    3.423 closest distance to " CA  LEU A 101 " =    1.541
peak=    3.415 closest distance to " CD BLYS A 290 " =    1.017
peak=    3.414 closest distance to " O   HOH Z 412 " =    4.101
peak=    3.411 closest distance to " O   HOH Z 364 " =    2.099
peak=    3.406 closest distance to " NH2BARG A 102 " =    0.882
peak=    3.403 closest distance to " O   GLY A 211 " =    1.292
peak=    3.403 closest distance to " CG1 VAL A 153 " =    1.085
peak=    3.402 closest distance to " CG1BVAL A  72 " =    1.640
peak=    3.395 closest distance to " O   HOH Z 189 " =    2.877
peak=    3.388 closest distance to " O   HOH Z 109 " =    2.226
peak=    3.384 closest distance to " O   HOH Z 227 " =    1.580
peak=    3.384 closest distance to " O   HOH Z  88 " =    3.184
peak=    3.377 closest distance to " O   HOH Z 236 " =    1.909
peak=    3.371 closest distance to " O   HOH Z  99 " =    1.661
peak=    3.370 closest distance to " O   HOH Z 368 " =    2.771
peak=    3.369 closest distance to " O   HOH Z 215 " =    1.520
peak=    3.359 closest distance to " O   HOH Z 214 " =    0.954
peak=    3.358 closest distance to " NE1 TRP A 274 " =    0.867
peak=    3.358 closest distance to " O   HOH Z 194 " =    1.789
peak=    3.356 closest distance to " O   HOH Z 357 " =    2.380
peak=    3.349 closest distance to " NZ  LYS A 117 " =    3.699
peak=    3.348 closest distance to " CA  ASP A 191 " =    1.031
peak=    3.348 closest distance to " CE1 HIS A 108 " =    1.129
peak=    3.347 closest distance to " NH1AARG A 145 " =    0.929
peak=    3.345 closest distance to " O   ASN A 301 " =    2.537
peak=    3.338 closest distance to " O   HOH Z 260 " =    1.389
peak=    3.338 closest distance to " CB  ASN A 285 " =    0.878
peak=    3.338 closest distance to " O   HOH Z 344 " =    1.728
peak=    3.337 closest distance to " CA  TYR A 116 " =    1.423
peak=    3.337 closest distance to " CD2 LEU A 297 " =    0.972
peak=    3.336 closest distance to " CB  ASN A 187 " =    1.081
peak=    3.335 closest distance to " NH2BARG A 145 " =    1.953
peak=    3.333 closest distance to " O   HOH Z  85 " =    1.987
peak=    3.331 closest distance to " O   HOH Z  63 " =    1.943
peak=    3.331 closest distance to " O   HOH Z 255 " =    1.397
peak=    3.328 closest distance to " CD  ARG A 159 " =    0.801
peak=    3.328 closest distance to " NE  ARG A  14 " =    1.508
peak=    3.320 closest distance to " CA  ARG A 195 " =    1.175
peak=    3.318 closest distance to " CB  ARG A 102 " =    0.849
peak=    3.317 closest distance to " O   HOH Z 136 " =    1.764
peak=    3.316 closest distance to " O   HOH Z 409 " =    3.653
peak=    3.308 closest distance to " N   ASP A 162 " =    1.550
peak=    3.306 closest distance to " O   HOH Z 172 " =    5.944
peak=    3.306 closest distance to " O   HOH Z  33 " =    1.562
peak=    3.303 closest distance to " CB  SER A  26 " =    1.763
peak=    3.303 closest distance to " O   HOH Z 258 " =    2.964
peak=    3.301 closest distance to " CB  GLN A  88 " =    1.207
peak=    3.296 closest distance to " O   HOH Z 171 " =    3.293
peak=    3.291 closest distance to " OG1 THR A 220 " =    1.801
peak=    3.288 closest distance to " O   HOH Z 342 " =    0.891
peak=    3.285 closest distance to " NH2 ARG A  36 " =    1.727
peak=    3.280 closest distance to " CA  MET A  40 " =    0.982
peak=    3.280 closest distance to " OG ASER A 134 " =    1.411
peak=    3.280 closest distance to " O   HOH Z 402 " =    2.656
peak=    3.280 closest distance to " O   HOH Z 292 " =    1.475
peak=    3.279 closest distance to " O   HOH Z 313 " =    1.939
peak=    3.278 closest distance to " O   HOH Z 327 " =    1.648
peak=    3.276 closest distance to " CB  ALA A  34 " =    1.170
peak=    3.270 closest distance to " OG  SER A  62 " =    3.383
peak=    3.267 closest distance to " O   SER A 164 " =    1.146
peak=    3.266 closest distance to " CB  SER A   3 " =    1.496
peak=    3.265 closest distance to " O   HOH Z  69 " =    1.137
peak=    3.262 closest distance to " O   HOH Z 114 " =    1.427
peak=    3.262 closest distance to " NZ  LYS A  76 " =    0.924
peak=    3.259 closest distance to " CD2 HIS A  81 " =    1.402
peak=    3.257 closest distance to " O   HOH Z  20 " =    1.938
peak=    3.250 closest distance to " O   HOH Z 197 " =    2.193
peak=    3.244 closest distance to " O   HOH Z 272 " =    1.075
peak=    3.242 closest distance to " O   HOH Z 368 " =    3.722
peak=    3.241 closest distance to " O   HOH Z  62 " =    1.754
peak=    3.239 closest distance to " ND2 ASN A 187 " =    1.475
peak=    3.235 closest distance to " O   HOH Z  85 " =    1.496
peak=    3.229 closest distance to " N   LYS A 166 " =    0.893
peak=    3.229 closest distance to " CA  ASN A 284 " =    1.143
peak=    3.227 closest distance to " O   HOH Z 277 " =    1.928
peak=    3.222 closest distance to " O   HOH Z 417 " =    3.381
peak=    3.222 closest distance to " CB  GLN A  89 " =    1.115
peak=    3.220 closest distance to " O   HOH Z 173 " =    2.002
peak=    3.217 closest distance to " CB  GLU A 277 " =    0.933
peak=    3.216 closest distance to " CB  SER A  28 " =    1.004
peak=    3.215 closest distance to " O   HOH Z  59 " =    2.184
peak=    3.214 closest distance to " O   HOH Z 398 " =    1.265
peak=    3.210 closest distance to " O   HOH Z 248 " =    1.783
peak=    3.210 closest distance to " O   HOH Z 155 " =    2.360
peak=    3.210 closest distance to " O   HOH Z 152 " =    1.662
peak=    3.205 closest distance to " O   HOH Z 250 " =    1.467
peak=    3.203 closest distance to " CG2 ILE A 120 " =    1.361
peak=    3.203 closest distance to " O   HOH Z 204 " =    1.337
peak=    3.202 closest distance to " O   HOH Z 217 " =    2.251
peak=    3.201 closest distance to " O   HOH Z 280 " =    1.741
peak=    3.196 closest distance to " NZ  LYS A 117 " =    0.744
peak=    3.196 closest distance to " CB  ASN A 217 " =    1.071
peak=    3.193 closest distance to " O   HOH Z 183 " =    1.580
peak=    3.186 closest distance to " CB  MET A 105 " =    1.111
peak=    3.185 closest distance to " CG  GLN A  11 " =    1.343
peak=    3.182 closest distance to " O   HOH Z 162 " =    1.640
peak=    3.178 closest distance to " O   HOH Z 126 " =    2.248
peak=    3.177 closest distance to " CB  ARG A 190 " =    1.701
peak=    3.177 closest distance to " CA  ASN A 176 " =    1.732
peak=    3.176 closest distance to " CD1 LEU A 300 " =    1.122
peak=    3.175 closest distance to " CA  ALA A 160 " =    0.942
peak=    3.175 closest distance to " O   HOH Z 322 " =    1.821
peak=    3.175 closest distance to " O   HOH Z 145 " =    2.000
peak=    3.175 closest distance to " NH2 ARG A 156 " =    1.129
peak=    3.174 closest distance to " O   HOH Z 425 " =    1.344
peak=    3.167 closest distance to " O   HOH Z 408 " =    1.367
peak=    3.166 closest distance to " NH1 ARG A 269 " =    0.844
peak=    3.164 closest distance to " CG2 THR A 221 " =    1.226
peak=    3.162 closest distance to " CA  ALA A 158 " =    1.210
peak=    3.161 closest distance to " O   HOH Z  63 " =    1.651
peak=    3.155 closest distance to " O   HOH Z 409 " =    2.370
peak=    3.153 closest distance to " OD1 ASN A  45 " =    1.275
peak=    3.152 closest distance to " O   HOH Z  26 " =    1.901
peak=    3.152 closest distance to " O   HOH Z 170 " =    1.872
peak=    3.151 closest distance to " O   HOH Z 279 " =    2.165
peak=    3.151 closest distance to " CA  SER A  87 " =    0.912
peak=    3.149 closest distance to " CG2 VAL A 265 " =    1.197
peak=    3.139 closest distance to " CA  LEU A  83 " =    1.442
peak=    3.137 closest distance to " CD  LYS A  76 " =    1.884
peak=    3.136 closest distance to " CA  GLY A 196 " =    1.064
peak=    3.135 closest distance to " C   SER A  32 " =    1.146
peak=    3.133 closest distance to " O   HOH Z 214 " =    2.056
peak=    3.131 closest distance to " O   HOH Z  94 " =    1.868
peak=    3.129 closest distance to " CA  GLU A 152 " =    0.954
peak=    3.129 closest distance to " OG  SER A  22 " =    2.763
peak=    3.127 closest distance to " CG2 VAL A 112 " =    1.612
peak=    3.126 closest distance to " CB  PHE A  16 " =    1.319
peak=    3.123 closest distance to " O   HOH Z 241 " =    1.980
peak=    3.123 closest distance to " O   HOH Z 156 " =    2.329
peak=    3.122 closest distance to " O   HOH Z 303 " =    2.155
peak=    3.117 closest distance to " O   HOH Z  38 " =    1.618
peak=    3.117 closest distance to " OG BSER A 210 " =    1.196
peak=    3.116 closest distance to " CA  TRP A 150 " =    0.806
peak=    3.114 closest distance to " CG2 VAL A  78 " =    0.987
peak=    3.112 closest distance to " NZ  LYS A 166 " =    3.118
peak=    3.110 closest distance to " CG  MET A 185 " =    1.249
peak=    3.108 closest distance to " O   HOH Z 433 " =    3.658
peak=    3.101 closest distance to " N   ARG A 156 " =    1.415
peak=    3.096 closest distance to " O   HOH Z 386 " =    2.488
peak=    3.092 closest distance to " NE2 GLN A  89 " =    1.275
peak=    3.086 closest distance to " O   HOH Z 345 " =    2.886
peak=    3.071 closest distance to " CB  ALA A   1 " =    1.299
peak=    3.062 closest distance to " O   HOH Z 374 " =    2.436
peak=    3.056 closest distance to " CB  ILE A 199 " =    1.256
peak=    3.053 closest distance to " CB  TRP A 266 " =    1.078
peak=    3.046 closest distance to " CA  THR A 221 " =    0.946
peak=    3.040 closest distance to " O   HOH Z 189 " =    2.653
peak=    3.015 closest distance to " CB  TRP A 179 " =    1.903

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.564 - 4.923
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 201
   mapped sites are within: 0.723 - 4.923

peak=   -4.978 closest distance to " CG2 VAL A 230 " =    0.840
peak=   -4.958 closest distance to " CA  SER A 164 " =    1.807
peak=   -4.646 closest distance to " O   HOH Z  13 " =    1.140
peak=   -4.577 closest distance to " O   HOH Z 221 " =    1.113
peak=   -4.569 closest distance to " O   HOH Z 166 " =    1.625
peak=   -4.370 closest distance to " O   HOH Z 208 " =    0.723
peak=   -4.232 closest distance to " O   HOH Z 423 " =    2.338
peak=   -4.206 closest distance to " O  BHOH Z 338 " =    1.333
peak=   -4.184 closest distance to " CG  ASP A 231 " =    0.808
peak=   -4.112 closest distance to " O   HOH Z 196 " =    2.217
peak=   -4.058 closest distance to " C   ASN A 285 " =    2.464
peak=   -4.043 closest distance to " OG ASER A 134 " =    1.171
peak=   -4.003 closest distance to " O   HOH Z 120 " =    1.012
peak=   -3.955 closest distance to " CG2 THR A 221 " =    2.321
peak=   -3.942 closest distance to " CA  TYR A  68 " =    2.801
peak=   -3.942 closest distance to " O   HOH Z 155 " =    1.377
peak=   -3.932 closest distance to " NH2 ARG A  66 " =    1.281
peak=   -3.930 closest distance to " OXT GLY A 302 " =    2.700
peak=   -3.926 closest distance to " CD1 PHE A  59 " =    1.787
peak=   -3.925 closest distance to " CB  ALA A 161 " =    2.550
peak=   -3.887 closest distance to " N   ALA A 226 " =    1.999
peak=   -3.828 closest distance to " C   GLY A  91 " =    1.454
peak=   -3.825 closest distance to " O   HOH Z  52 " =    2.235
peak=   -3.818 closest distance to " CB  ALA A 100 " =    1.825
peak=   -3.810 closest distance to " O   VAL A  67 " =    2.629
peak=   -3.798 closest distance to " SG  CYS A 254 " =    3.174
peak=   -3.760 closest distance to " N   GLN A  58 " =    1.764
peak=   -3.756 closest distance to " O   HOH Z 427 " =    1.428
peak=   -3.753 closest distance to " O   ALA A  34 " =    2.029
peak=   -3.733 closest distance to " O   HOH Z  71 " =    1.135
peak=   -3.725 closest distance to " O   HOH Z  92 " =    1.219
peak=   -3.724 closest distance to " OG  SER A  97 " =    2.176
peak=   -3.716 closest distance to " O   HOH Z  37 " =    1.181
peak=   -3.691 closest distance to " CD2 PHE A  59 " =    2.510
peak=   -3.683 closest distance to " O   HOH Z 266 " =    4.275
peak=   -3.671 closest distance to " O   HOH Z 414 " =    1.668
peak=   -3.665 closest distance to " CD2 LEU A 300 " =    2.563
peak=   -3.663 closest distance to " O   HOH Z 100 " =    0.805
peak=   -3.655 closest distance to " O   HOH Z 109 " =    3.380
peak=   -3.632 closest distance to " O   HOH Z 266 " =    4.525
peak=   -3.632 closest distance to " OE2 GLU A   2 " =    1.607
peak=   -3.627 closest distance to " C   GLY A 133 " =    1.240
peak=   -3.611 closest distance to " O   ALA A 161 " =    1.241
peak=   -3.611 closest distance to " CD1 LEU A 255 " =    2.587
peak=   -3.600 closest distance to " NH2 ARG A  79 " =    1.905
peak=   -3.587 closest distance to " O   HOH Z 193 " =    1.428
peak=   -3.585 closest distance to " CG  GLN A  88 " =    0.848
peak=   -3.582 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.574 closest distance to " CA  LEU A 222 " =    2.527
peak=   -3.551 closest distance to " OG1 THR A   4 " =    1.800
peak=   -3.548 closest distance to " C   ASN A 187 " =    1.886
peak=   -3.544 closest distance to " OG  SER A  32 " =    1.149
peak=   -3.544 closest distance to " O   HOH Z 290 " =    0.905
peak=   -3.538 closest distance to " O   HOH Z  11 " =    1.488
peak=   -3.536 closest distance to " ND2 ASN A 252 " =    1.610
peak=   -3.531 closest distance to " O   HOH Z  48 " =    1.264
peak=   -3.529 closest distance to " OG BSER A 134 " =    1.513
peak=   -3.526 closest distance to " O   ASN A 187 " =    1.484
peak=   -3.521 closest distance to " O   HOH Z 130 " =    2.216
peak=   -3.487 closest distance to " C   THR A 279 " =    1.094
peak=   -3.485 closest distance to " CZ2 TRP A 179 " =    1.194
peak=   -3.482 closest distance to " O   HOH Z  39 " =    1.357
peak=   -3.473 closest distance to " CD2 LEU A 237 " =    2.409
peak=   -3.470 closest distance to " O   HOH Z 151 " =    1.392
peak=   -3.463 closest distance to " CD2 TYR A 293 " =    2.124
peak=   -3.457 closest distance to " O   MET A  40 " =    2.740
peak=   -3.456 closest distance to " CG  ARG A 269 " =    2.285
peak=   -3.446 closest distance to " O   LEU A 228 " =    2.371
peak=   -3.437 closest distance to " CD1 TRP A 179 " =    1.098
peak=   -3.425 closest distance to " O   HOH Z 275 " =    1.440
peak=   -3.420 closest distance to " NH1BARG A 190 " =    2.002
peak=   -3.418 closest distance to " CG  ARG A 219 " =    2.386
peak=   -3.414 closest distance to " O   HOH Z 435 " =    2.115
peak=   -3.412 closest distance to " O   THR A  18 " =    1.527
peak=   -3.411 closest distance to " OG ASER A 164 " =    0.895
peak=   -3.407 closest distance to " CA  SER A 276 " =    1.426
peak=   -3.404 closest distance to " CB  ALA A 248 " =    2.306
peak=   -3.402 closest distance to " O   SER A 273 " =    1.421
peak=   -3.398 closest distance to " O   HOH Z  29 " =    1.129
peak=   -3.395 closest distance to " O   GLN A  11 " =    1.215
peak=   -3.391 closest distance to " CA  VAL A 197 " =    0.915
peak=   -3.382 closest distance to " O   HOH Z 426 " =    2.323
peak=   -3.381 closest distance to " OD2 ASP A 171 " =    1.819
peak=   -3.381 closest distance to " CD2 HIS A 115 " =    0.977
peak=   -3.379 closest distance to " CB  CYS A 254 " =    2.541
peak=   -3.378 closest distance to " O   HOH Z 210 " =    2.119
peak=   -3.376 closest distance to " C   ALA A 158 " =    1.167
peak=   -3.368 closest distance to " CE BMET A  47 " =    1.368
peak=   -3.368 closest distance to " CD1 PHE A  59 " =    1.639
peak=   -3.367 closest distance to " O   HOH Z 134 " =    2.158
peak=   -3.360 closest distance to " NH2AARG A 275 " =    4.923
peak=   -3.357 closest distance to " O   HOH Z 377 " =    2.258
peak=   -3.354 closest distance to " CA  ASP A  27 " =    2.432
peak=   -3.351 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -3.341 closest distance to " O   HOH Z 396 " =    1.527
peak=   -3.339 closest distance to " CG  GLU A   2 " =    1.509
peak=   -3.334 closest distance to " CB  PHE A 208 " =    2.303
peak=   -3.334 closest distance to " O   HOH Z 171 " =    2.360
peak=   -3.330 closest distance to " CB  ALA A 227 " =    2.424
peak=   -3.330 closest distance to " O   HOH Z 313 " =    1.379
peak=   -3.329 closest distance to " CD  ARG A 156 " =    1.979
peak=   -3.328 closest distance to " O   HOH Z 103 " =    1.910
peak=   -3.319 closest distance to " O   HOH Z 292 " =    2.840
peak=   -3.319 closest distance to " O   ALA A   1 " =    1.938
peak=   -3.317 closest distance to " O   HOH Z 124 " =    1.471
peak=   -3.317 closest distance to " CD1 TRP A  85 " =    1.113
peak=   -3.312 closest distance to " OG BSER A 134 " =    1.791
peak=   -3.308 closest distance to " O   HOH Z  62 " =    1.287
peak=   -3.302 closest distance to " O   HOH Z  38 " =    1.577
peak=   -3.291 closest distance to " O   CYS A 260 " =    0.899
peak=   -3.289 closest distance to " O   HOH Z 198 " =    2.430
peak=   -3.287 closest distance to " O   HOH Z 418 " =    1.471
peak=   -3.284 closest distance to " O   HOH Z 377 " =    1.121
peak=   -3.282 closest distance to " CA  GLY A 203 " =    2.177
peak=   -3.279 closest distance to " CG2 VAL A 189 " =    1.889
peak=   -3.277 closest distance to " CG  TYR A 169 " =    2.099
peak=   -3.274 closest distance to " O   HOH Z 340 " =    1.057
peak=   -3.273 closest distance to " O   HOH Z 109 " =    0.928
peak=   -3.273 closest distance to " N   THR A 235 " =    1.253
peak=   -3.272 closest distance to " CD1 LEU A 101 " =    2.558
peak=   -3.272 closest distance to " O   HOH Z 281 " =    2.908
peak=   -3.264 closest distance to " O   HOH Z  17 " =    1.295
peak=   -3.263 closest distance to " O   HOH Z 117 " =    1.687
peak=   -3.263 closest distance to " CD1 LEU A 228 " =    2.428
peak=   -3.261 closest distance to " O   HOH Z 150 " =    1.039
peak=   -3.261 closest distance to " O   HOH Z 138 " =    0.987
peak=   -3.259 closest distance to " CA  ARG A  66 " =    1.872
peak=   -3.256 closest distance to " OG  SER A  26 " =    1.225
peak=   -3.253 closest distance to " OG  SER A 206 " =    1.809
peak=   -3.236 closest distance to " CD  GLN A  77 " =    1.248
peak=   -3.235 closest distance to " O   GLY A 211 " =    1.370
peak=   -3.235 closest distance to " O   HOH Z 385 " =    3.760
peak=   -3.233 closest distance to " CG2 VAL A 296 " =    0.896
peak=   -3.229 closest distance to " O   LEU A 143 " =    1.399
peak=   -3.229 closest distance to " O   PHE A 218 " =    1.250
peak=   -3.228 closest distance to " OD1 ASP A 200 " =    1.209
peak=   -3.221 closest distance to " O   HOH Z 222 " =    1.215
peak=   -3.220 closest distance to " OG  SER A  62 " =    1.390
peak=   -3.217 closest distance to " CB  GLN A 223 " =    1.910
peak=   -3.214 closest distance to " ND2 ASN A 173 " =    1.728
peak=   -3.214 closest distance to " C   VAL A 265 " =    0.899
peak=   -3.203 closest distance to " CD  ARG A 139 " =    1.565
peak=   -3.202 closest distance to " O   HOH Z 407 " =    1.087
peak=   -3.194 closest distance to " CG1AVAL A  72 " =    2.003
peak=   -3.190 closest distance to " O   HOH Z 189 " =    1.313
peak=   -3.184 closest distance to " CD2 PHE A  61 " =    1.888
peak=   -3.183 closest distance to " O   MET A  47 " =    2.506
peak=   -3.179 closest distance to " CG  ASP A  50 " =    2.002
peak=   -3.178 closest distance to " O   GLY A 196 " =    0.974
peak=   -3.177 closest distance to " O   HOH Z 233 " =    2.288
peak=   -3.176 closest distance to " CE  MET A 105 " =    2.188
peak=   -3.174 closest distance to " O   HOH Z 246 " =    1.312
peak=   -3.173 closest distance to " C   HIS A 108 " =    1.131
peak=   -3.172 closest distance to " NH2BARG A 145 " =    2.118
peak=   -3.167 closest distance to " CD  GLU A 236 " =    0.957
peak=   -3.166 closest distance to " O   HOH Z 219 " =    3.042
peak=   -3.165 closest distance to " CD2 LEU A 167 " =    1.694
peak=   -3.162 closest distance to " O   HOH Z 132 " =    0.765
peak=   -3.162 closest distance to " O   HOH Z  49 " =    0.917
peak=   -3.156 closest distance to " O   HOH Z 136 " =    1.745
peak=   -3.156 closest distance to " CA  GLY A  98 " =    2.159
peak=   -3.156 closest distance to " O   HOH Z 145 " =    1.554
peak=   -3.147 closest distance to " CD  GLN A  73 " =    1.045
peak=   -3.137 closest distance to " ND2 ASN A 187 " =    1.664
peak=   -3.135 closest distance to " C   TRP A 274 " =    1.506
peak=   -3.135 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.134 closest distance to " O   ASP A 107 " =    1.305
peak=   -3.134 closest distance to " CD2 LEU A 237 " =    2.911
peak=   -3.129 closest distance to " CG  GLN A  58 " =    1.536
peak=   -3.129 closest distance to " OG  SER A 273 " =    2.122
peak=   -3.127 closest distance to " ND2 ASN A  39 " =    1.161
peak=   -3.126 closest distance to " O   HOH Z  55 " =    2.520
peak=   -3.125 closest distance to " CB  GLN A  73 " =    1.045
peak=   -3.123 closest distance to " O   HOH Z 389 " =    1.234
peak=   -3.121 closest distance to " CB  ALA A 248 " =    1.971
peak=   -3.120 closest distance to " O   HOH Z 198 " =    1.008
peak=   -3.117 closest distance to " CD1 ILE A 151 " =    2.254
peak=   -3.114 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.114 closest distance to " O   HOH Z 310 " =    1.651
peak=   -3.114 closest distance to " O   HOH Z 269 " =    4.313
peak=   -3.112 closest distance to " C   LEU A 101 " =    0.901
peak=   -3.111 closest distance to " O   HOH Z 138 " =    1.499
peak=   -3.110 closest distance to " CD  ARG A 259 " =    1.814
peak=   -3.101 closest distance to " OG1 THR A  82 " =    1.592
peak=   -3.097 closest distance to " O   GLY A 118 " =    2.004
peak=   -3.095 closest distance to " N   ALA A 248 " =    1.774
peak=   -3.085 closest distance to " CE  MET A 105 " =    2.192
peak=   -3.084 closest distance to " CD  GLN A  11 " =    1.039
peak=   -3.079 closest distance to " CB  ALA A 291 " =    2.333
peak=   -3.077 closest distance to " CE2 PHE A 218 " =    2.231
peak=   -3.073 closest distance to " N   ALA A  43 " =    2.636
peak=   -3.072 closest distance to " OH  TYR A 169 " =    0.928
peak=   -3.070 closest distance to " O   HOH Z 139 " =    3.460
peak=   -3.042 closest distance to " NE2 GLN A  88 " =    0.966
peak=   -3.039 closest distance to " O   HOH Z 410 " =    2.209
peak=   -3.031 closest distance to " O   HOH Z 252 " =    1.008
peak=   -3.031 closest distance to " CE3 TRP A  70 " =    1.833
peak=   -3.025 closest distance to " NE2 GLN A  77 " =    1.549

================= 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    :  0.5056 0.5069   6.305244e+00   6.296507e+00
   1_bss:  0.4989 0.4976   6.303233e+00   6.290127e+00
   1_xyz:  0.4437 0.4618   6.240482e+00   6.261358e+00
   1_adp:  0.4059 0.4576   6.198806e+00   6.255145e+00
   1_occ:  0.4054 0.4573   6.198036e+00   6.254936e+00
   2_bss:  0.4033 0.4545   6.199157e+00   6.253992e+00
   2_xyz:  0.3457 0.4103   6.089491e+00   6.197873e+00
   2_adp:  0.3266 0.3990   6.056190e+00   6.177055e+00
   2_occ:  0.3264 0.3984   6.055475e+00   6.176684e+00
   3_bss:  0.3247 0.3950   6.053084e+00   6.175316e+00
   3_xyz:  0.2483 0.3149   5.836364e+00   6.007200e+00
   3_adp:  0.2218 0.2832   5.739529e+00   5.922354e+00
   3_occ:  0.2216 0.2826   5.738523e+00   5.921046e+00
   4_bss:  0.2202 0.2806   5.736157e+00   5.917625e+00
   4_xyz:  0.1713 0.2244   5.514337e+00   5.722007e+00
   4_adp:  0.1546 0.2106   5.434322e+00   5.652220e+00
   4_occ:  0.1544 0.2104   5.433606e+00   5.651771e+00
   5_bss:  0.1547 0.2105   5.434581e+00   5.652827e+00
   5_xyz:  0.1340 0.1830   5.303325e+00   5.527078e+00
   5_adp:  0.1307 0.1767   5.276354e+00   5.494799e+00
   5_occ:  0.1304 0.1765   5.275275e+00   5.494136e+00
   5_bss:  0.1309 0.1769   5.277531e+00   5.496014e+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:  0.338  20.001   5.818  10.286   8.000   0.000   0.000   0.000
   1_xyz:  0.338  20.001   5.818  10.286   8.000   0.000   0.000   0.000
   1_adp:  0.338  20.001   5.818  10.286   8.000   0.000   0.000   0.000
   1_occ:  0.338  20.001   5.818  10.286   8.000   0.000   0.000   0.000
   2_bss:  0.322  32.760   2.448   6.216   4.849   0.000   0.000   0.000
   2_xyz:  0.322  32.760   2.448   6.216   4.849   0.000   0.000   0.000
   2_adp:  0.322  32.760   2.448   6.216   4.849   0.000   0.000   0.000
   2_occ:  0.322  32.760   2.448   6.216   4.849   0.000   0.000   0.000
   3_bss:  0.328  50.875   0.791   3.322   2.277   0.000   0.000   0.000
   3_xyz:  0.328  50.875   0.791   3.322   2.277   0.000   0.000   0.000
   3_adp:  0.328  50.875   0.791   3.322   2.277   0.000   0.000   0.000
   3_occ:  0.328  50.875   0.791   3.322   2.277   0.000   0.000   0.000
   4_bss:  0.325  47.402  -0.421   1.487   0.644   0.000   0.000   0.000
   4_xyz:  0.325  47.402  -0.421   1.487   0.644   0.000   0.000   0.000
   4_adp:  0.325  47.402  -0.421   1.487   0.644   0.000   0.000   0.000
   4_occ:  0.325  47.402  -0.421   1.487   0.644   0.000   0.000   0.000
   5_bss:  0.323  49.127  -0.878   0.698   0.066   0.000   0.000   0.000
   5_xyz:  0.323  49.127  -0.878   0.698   0.066   0.000   0.000   0.000
   5_adp:  0.323  49.127  -0.878   0.698   0.066   0.000   0.000   0.000
   5_occ:  0.323  49.127  -0.878   0.698   0.066   0.000   0.000   0.000
   5_bss:  0.324  48.019  -0.935   0.403  -0.070   0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.445 0.3224  0.3832    81721.998
   1_bss:  65.193 0.3238  0.4749    78868.244
   1_xyz:  60.177 0.3876  0.5590    67704.661
   1_adp:  58.615 0.4079  0.6631    65642.972
   1_occ:  58.511 0.4092  0.6645    65499.084
   2_bss:  58.297 0.4118  0.6010    65123.195
   2_xyz:  47.831 0.5461  0.8166    50750.587
   2_adp:  45.212 0.5788  0.8742    46844.645
   2_occ:  45.223 0.5786  0.8729    46763.597
   3_bss:  44.864 0.5827  0.8093    46003.907
   3_xyz:  33.719 0.7149  0.9570    27361.782
   3_adp:  29.292 0.7655  0.9853    21951.787
   3_occ:  29.271 0.7657  0.9851    21881.184
   4_bss:  29.098 0.7674  0.9327    21621.380
   4_xyz:  22.358 0.8378  0.9819    13295.419
   4_adp:  20.333 0.8583  0.9845    11460.143
   4_occ:  20.324 0.8584  0.9844    11445.083
   5_bss:  20.312 0.8585  0.9637    11461.719
   5_xyz:  17.399 0.8856  0.9791     8737.312
   5_adp:  16.587 0.8933  0.9802     8220.539
   5_occ:  16.568 0.8934  0.9802     8210.503
   5_bss:  16.597 0.8933  0.9740     8266.383
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3448e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3448e+01
   1_xyz:   1.807  0.014  0.110 18.432  0.007  4.119   1.6067e-01
   1_adp:   1.807  0.014  0.110 18.432  0.007  4.119   1.6067e-01
   1_occ:   1.807  0.014  0.110 18.432  0.007  4.119   1.6067e-01
   2_bss:   1.807  0.014  0.110 18.432  0.007  4.119   1.6067e-01
   2_xyz:   1.347  0.010  0.087 17.413  0.006  4.108   1.1525e-01
   2_adp:   1.347  0.010  0.087 17.413  0.006  4.108   1.1525e-01
   2_occ:   1.347  0.010  0.087 17.413  0.006  4.108   1.1525e-01
   3_bss:   1.347  0.010  0.087 17.413  0.006  4.108   1.1525e-01
   3_xyz:   1.359  0.011  0.100 16.499  0.005  4.112   1.0532e-01
   3_adp:   1.359  0.011  0.100 16.499  0.005  4.112   1.0532e-01
   3_occ:   1.359  0.011  0.100 16.499  0.005  4.112   1.0532e-01
   4_bss:   1.359  0.011  0.100 16.499  0.005  4.112   1.0532e-01
   4_xyz:   1.053  0.008  0.075 15.428  0.004  4.111   6.9855e-02
   4_adp:   1.053  0.008  0.075 15.428  0.004  4.111   6.9855e-02
   4_occ:   1.053  0.008  0.075 15.428  0.004  4.111   6.9855e-02
   5_bss:   1.053  0.008  0.075 15.428  0.004  4.111   6.9855e-02
   5_xyz:   1.056  0.007  0.080 15.363  0.004  4.118   6.5744e-02
   5_adp:   1.056  0.007  0.080 15.363  0.004  4.118   6.5744e-02
   5_occ:   1.056  0.007  0.080 15.363  0.004  4.118   6.5744e-02
   5_bss:   1.056  0.007  0.080 15.363  0.004  4.118   6.5744e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.765   6.9241e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.765   6.9241e+00
   1_xyz:  15.567  0.174  0.519 87.775  0.055  2.123   1.0613e-01
   1_adp:  15.567  0.174  0.519 87.775  0.055  2.123   1.0613e-01
   1_occ:  15.567  0.174  0.519 87.775  0.055  2.123   1.0613e-01
   2_bss:  15.567  0.174  0.519 87.775  0.055  2.123   1.0613e-01
   2_xyz:  11.100  0.096  0.270 85.813  0.050  2.001   9.2870e-02
   2_adp:  11.100  0.096  0.270 85.813  0.050  2.001   9.2870e-02
   2_occ:  11.100  0.096  0.270 85.813  0.050  2.001   9.2870e-02
   3_bss:  11.100  0.096  0.270 85.813  0.050  2.001   9.2870e-02
   3_xyz:   9.226  0.073  0.328 79.709  0.050  2.151   8.3903e-02
   3_adp:   9.226  0.073  0.328 79.709  0.050  2.151   8.3903e-02
   3_occ:   9.226  0.073  0.328 79.709  0.050  2.151   8.3903e-02
   4_bss:   9.226  0.073  0.328 79.709  0.050  2.151   8.3903e-02
   4_xyz:   8.030  0.042  0.379 82.878  0.041  2.282   1.1495e-01
   4_adp:   8.030  0.042  0.379 82.878  0.041  2.282   1.1495e-01
   4_occ:   8.030  0.042  0.379 82.878  0.041  2.282   1.1495e-01
   5_bss:   8.030  0.042  0.379 82.878  0.041  2.282   1.1495e-01
   5_xyz:   6.862  0.050  0.529 81.258  0.026  2.301   4.1931e-02
   5_adp:   6.862  0.050  0.529 81.258  0.026  2.301   4.1931e-02
   5_occ:   6.862  0.050  0.529 81.258  0.026  2.301   4.1931e-02
   5_bss:   6.862  0.050  0.529 81.258  0.026  2.301   4.1931e-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:  96.24   0.00  16.84  90.56   0.00  15.22  96.24   0.00  25.69
   1_occ:  96.24   0.00  16.84  90.56   0.00  15.22  96.24   0.00  25.69
   2_bss:  96.24   0.00  16.84  90.56   0.00  15.22  96.24   0.00  25.69
   2_xyz:  96.24   0.00  16.84  90.56   0.00  15.22  96.24   0.00  25.69
   2_adp:  92.19   0.00  16.55  83.10   0.00  14.24  92.19   0.00  29.08
   2_occ:  92.19   0.00  16.55  83.10   0.00  14.24  92.19   0.00  29.08
   3_bss:  92.19   0.00  16.55  83.10   0.00  14.24  92.19   0.00  29.08
   3_xyz:  92.19   0.00  16.55  83.10   0.00  14.24  92.19   0.00  29.08
   3_adp:  86.97   0.00  16.10  73.07   0.00  12.47  86.97   3.23  35.89
   3_occ:  86.97   0.00  16.10  73.07   0.00  12.47  86.97   3.23  35.89
   4_bss:  86.97   0.00  16.10  73.07   0.00  12.47  86.97   3.23  35.89
   4_xyz:  86.97   0.00  16.10  73.07   0.00  12.47  86.97   3.23  35.89
   4_adp:  88.92   0.00  16.28  88.64   0.00  11.62  88.92   4.92  41.67
   4_occ:  88.92   0.00  16.28  88.64   0.00  11.62  88.92   4.92  41.67
   5_bss:  88.92   0.00  16.28  88.64   0.00  11.62  88.92   4.92  41.67
   5_xyz:  88.92   0.00  16.28  88.64   0.00  11.62  88.92   4.92  41.67
   5_adp:  89.73   0.48  15.87  89.73   0.48  11.26  88.73   4.12  40.94
   5_occ:  89.73   0.48  15.87  89.73   0.48  11.26  88.73   4.12  40.94
   5_bss:  89.71   0.46  15.85  89.71   0.46  11.25  88.72   4.10  40.92
------------------------------------------------------------------------
 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:    1.165    0.010    0.417
   1_adp:    1.165    0.010    0.417
   1_occ:    1.165    0.010    0.417
   2_bss:    1.165    0.010    0.417
   2_xyz:    2.152    0.021    0.610
   2_adp:    2.152    0.021    0.610
   2_occ:    2.152    0.021    0.610
   3_bss:    2.152    0.021    0.610
   3_xyz:    1.779    0.052    0.765
   3_adp:    1.779    0.052    0.765
   3_occ:    1.779    0.052    0.765
   4_bss:    1.779    0.052    0.765
   4_xyz:    1.898    0.009    0.868
   4_adp:    1.898    0.009    0.868
   4_occ:    1.898    0.009    0.868
   5_bss:    1.898    0.009    0.868
   5_xyz:    1.949    0.096    0.905
   5_adp:    1.949    0.096    0.905
   5_occ:    1.949    0.096    0.905
   5_bss:    1.949    0.096    0.905
------------------------------------------------------------------------

CPU time actual refinement: 339.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_583/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_583/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_583/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_583/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_583/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.75 
  Macro-tasks:
    bulk solvent and scale       = 41.37  
    individual site refinement   = 138.33 
    weights calculation          = 31.58  
    collect and process          = 6.18   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.59 
  Micro-tasks:
    mask                            = 2.96   
    f_calc                          = 107.48 
    alpha_beta                      = 8.04   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 116.19 
    fmodel                         = 7.10   
    r_factors                      = 0.22   
    phase_errors                   = 9.85   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 253.24 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.824 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    644 calls, 107.16 s
gradients_fft:          588 calls, 103.46 s

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

# Date 2008-01-16 Time 01:56:40 PST -0800 (1200477400.63 s)
Start R-work = 0.5056, R-free = 0.5069 (no bulk solvent and anisotropic scale)
Final R-work = 0.1474, R-free = 0.1939 (no bulk solvent and anisotropic scale)

Start R-work = 0.4989, R-free = 0.4976
Final R-work = 0.1309, R-free = 0.1769