# Date 2008-01-16 Time 00:46:00 PST -0800 (1200473160.42 s)
#phil __OFF__

Command line arguments: "../153.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11616
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 153

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 88.5498, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (68.845, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9067 1.96088
Completeness in resolution range: 0.940061
Completeness with d_max=infinity: 0.937228

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9067
                             d_min =   1.9609

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: (68.845, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9067 1.96088
Completeness in resolution range: 0.940061
Completeness with d_max=infinity: 0.937228

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9071 -  4.1961 [2192/2217]  1969   223  10.2%
  bin  2:  4.1961 -  3.3429 [2110/2129]  1900   210  10.0%
  bin  3:  3.3429 -  2.9240 [2081/2100]  1879   202   9.7%
  bin  4:  2.9240 -  2.6583 [2049/2079]  1832   217  10.6%
  bin  5:  2.6583 -  2.4687 [2035/2054]  1835   200   9.8%
  bin  6:  2.4687 -  2.3237 [2043/2068]  1841   202   9.9%
  bin  7:  2.3237 -  2.2077 [2011/2039]  1814   197   9.8%
  bin  8:  2.2077 -  2.1119 [2036/2072]  1831   205  10.1%
  bin  9:  2.1119 -  2.0308 [1961/2037]  1767   194   9.9%
  bin 10:  2.0308 -  1.9609 [1071/2043]   962   109  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_153/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.03 -     1.80: 9
        1.80 -     2.58: 83
        2.58 -     3.35: 4090
        3.35 -     4.13: 9495
        4.13 -     4.90: 14932
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.026 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.161 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.193 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  94 " - " NH1BARG A 145 "  1.657 3.120 -x+1,y+1/2,-z+1/2
  " NH1BARG A 145 " - " O   HOH Z  94 "  1.657 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28604 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_153/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_153/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.22605 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5150   r_free= 0.5074   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.307599                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9071 -  4.6803 0.99   1421  157 0.4260 0.4106      6.6455      6.6208|
|  2:  4.6803 -  3.7341 0.99   1370  153 0.4440 0.4771      6.8314      6.9014|
|  3:  3.7341 -  3.2678 0.99   1337  151 0.4994 0.4445      6.7338      6.7197|
|  4:  3.2678 -  2.9716 0.99   1332  144 0.5192 0.5204      6.5649      6.5276|
|  5:  2.9716 -  2.7600 0.99   1334  147 0.5388 0.5095       6.383      6.4429|
|  6:  2.7600 -  2.5982 0.99   1321  149 0.5511 0.5385      6.3033      6.2172|
|  7:  2.5982 -  2.4687 0.99   1300  151 0.5446 0.5239      6.2503      6.1616|
|  8:  2.4687 -  2.3617 0.98   1324  146 0.5592 0.5548       6.195      6.2134|
|  9:  2.3617 -  2.2711 0.98   1290  140 0.5421 0.5609      6.1208      6.2202|
| 10:  2.2711 -  2.1929 0.99   1332  142 0.5584 0.5552      6.1115      6.1043|
| 11:  2.1929 -  2.1246 0.98   1257  146 0.5496 0.5243      6.0251      6.0304|
| 12:  2.1246 -  2.0640 0.97   1302  140 0.5442 0.5320      5.9773      6.0152|
| 13:  2.0640 -  2.0098 0.90   1169  128 0.5490 0.5114      5.8964      5.8081|
| 14:  2.0098 -  1.9609 0.41    541   65 0.5511 0.5545      5.9128       5.837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9071 -  4.6803  1421   157  0.65  38.86   0.78     0.71      90807.64|
|  2:  4.6803 -  3.7341  1370   153  0.63  41.37   0.85     0.71     138276.75|
|  3:  3.7341 -  3.2678  1337   151  0.49  52.64   0.81     0.63     147168.02|
|  4:  3.2678 -  2.9716  1332   144  0.37  61.62   0.76     0.48     132812.36|
|  5:  2.9716 -  2.7600  1334   147  0.26  70.21   0.71     0.33     102300.21|
|  6:  2.7600 -  2.5982  1321   149  0.21  74.61   0.69     0.25      89018.12|
|  7:  2.5982 -  2.4687  1300   151  0.16  77.81   0.72     0.19      79453.62|
|  8:  2.4687 -  2.3617  1324   146  0.17  77.04   0.71     0.21      71300.23|
|  9:  2.3617 -  2.2711  1290   140  0.18  76.46   0.71     0.22      65115.00|
| 10:  2.2711 -  2.1929  1332   142  0.19  75.80   0.72     0.23      56771.78|
| 11:  2.1929 -  2.1246  1257   146  0.14  79.76   0.73     0.19      57783.80|
| 12:  2.1246 -  2.0640  1302   140  0.14  79.85   0.74     0.18      51799.65|
| 13:  2.0640 -  2.0098  1169   128  0.18  76.71   0.72     0.24      43829.34|
| 14:  2.0098 -  1.9609   541    65  0.34  64.65   0.73     0.37      30094.83|
|alpha:            min =        0.18 max =            0.71 mean =         0.36|
|beta:             min =    30094.83 max =       147168.02 mean =     85712.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.30|
|phase err.(work): min =        0.00 max =           90.00 mean =        67.40|
|phase err.(test): min =        0.00 max =           89.93 mean =        67.72|
|-----------------------------------------------------------------------------|

============================== 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 = 25.135850             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.132   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.635958              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.049   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.099 -  1.479:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.479 -  1.860:       18 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.860 -  2.240:      151 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.240 -  2.620:      617 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.620 -  3.000:     1411 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.000 -  3.380:     2566 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.380 -  3.760:     3995 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.760 -  4.140:     5177 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.140 -  4.520:     6736 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.520 -  4.900:     7952 |
|-----------------------------------------------------------------------------|
|-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 |       53.329 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.099 |       2.699 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    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 = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5193   r_free= 0.5108   ksol= 0.00   Bsol= 0.00   scale= 0.742    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.307932                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5064   r_free= 0.4963   ksol= 0.37   Bsol= 20.00   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.72,8.18,10.92,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.301854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.680835             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 86.028   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.224912              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.901   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5064      final r-factor (work) = 0.4505          |
| start r-factor (free) = 0.4963      final r-factor (free) = 0.4707          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 115.3519 = 19.68 * 0.50 * 6.3029 + 1.00 * 53.3285                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.7631 = 19.68 * 0.50 * 6.2610 + 1.00 * 0.1524                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4505      final r-factor (work) = 0.4102          |
| start r-factor (free) = 0.4707      final r-factor (free) = 0.4724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.9446 = 2.22 * 1.00 * 6.2610 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8434 = 2.22 * 1.00 * 6.2106 + 1.00 * 0.0254                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.85   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    90.85   17.74    None  None   None       |
|    Sol.    : 438    0      0.00    90.85   25.76    None  None   None       |
|    Mac.    : 2385   0      0.00    86.68   16.26    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:     0.000 -   9.085:  926   |   5:    45.427 -  54.513:   75        |
|      1:     9.085 -  18.171:  754   |   6:    54.513 -  63.598:   46        |
|      2:    18.171 -  27.256:  525   |   7:    63.598 -  72.683:   19        |
|      3:    27.256 -  36.342:  331   |   8:    72.683 -  81.769:    4        |
|      4:    36.342 -  45.427:  135   |   9:    81.769 -  90.854:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4102 r_free = 0.4724             target_work(ml) = 6.204         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4099 r_free = 0.4726             target_work(ml) = 6.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4099   r_free= 0.4726   ksol= 0.37   Bsol= 20.00   scale= 1.136   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.72,8.18,10.92,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.203221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4078   r_free= 0.4713   ksol= 0.36   Bsol= 50.00   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.49,4.42,7.15,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.205005                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.924070             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.385  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.797656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.775  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4078      final r-factor (work) = 0.3384          |
| start r-factor (free) = 0.4713      final r-factor (free) = 0.4075          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.5697 = 15.92 * 0.50 * 6.2066 + 1.00 * 0.1524                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.0111 = 15.92 * 0.50 * 6.1391 + 1.00 * 0.1315                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3384      final r-factor (work) = 0.3138          |
| start r-factor (free) = 0.4075      final r-factor (free) = 0.3837          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9221 = 0.80 * 1.00 * 6.1391 + 1.00 * 0.0253                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8283 = 0.80 * 1.00 * 6.0353 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.13   16.12    None  None   None       |
|    all(noH): 2823   0      0.00    97.13   16.12    None  None   None       |
|    Sol.    : 438    0      0.00    97.13   30.78    None  None   None       |
|    Mac.    : 2385   0      0.00    65.21   13.43    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 -   9.713: 1083   |   5:    48.565 -  58.277:   52        |
|      1:     9.713 -  19.426:  873   |   6:    58.277 -  67.990:   19        |
|      2:    19.426 -  29.139:  484   |   7:    67.990 -  77.703:    5        |
|      3:    29.139 -  38.852:  194   |   8:    77.703 -  87.416:    1        |
|      4:    38.852 -  48.565:  109   |   9:    87.416 -  97.129:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3138 r_free = 0.3837             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3134 r_free = 0.3843             target_work(ml) = 6.008         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3134   r_free= 0.3843   ksol= 0.36   Bsol= 50.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.49,4.42,7.15,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.008393                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3110   r_free= 0.3822   ksol= 0.34   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,1.95,4.36,0.00,0.00,0.00); trace/3= 2.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.006854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.205930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.007   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.425990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.831  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3110      final r-factor (work) = 0.2438          |
| start r-factor (free) = 0.3822      final r-factor (free) = 0.3110          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8771 = 7.21 * 0.50 * 6.0355 + 1.00 * 0.1314                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4143 = 7.21 * 0.50 * 5.9205 + 1.00 * 0.0829                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2438      final r-factor (work) = 0.2219          |
| start r-factor (free) = 0.3110      final r-factor (free) = 0.2902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5362 = 0.43 * 1.00 * 5.9205 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4711 = 0.43 * 1.00 * 5.7760 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.23   15.60    None  None   None       |
|    all(noH): 2823   0      0.00    89.23   15.60    None  None   None       |
|    Sol.    : 438    0      0.00    89.23   36.34    None  None   None       |
|    Mac.    : 2385   0      0.00    78.15   11.79    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 -   8.923: 1155   |   5:    44.616 -  53.539:   85        |
|      1:     8.923 -  17.847:  872   |   6:    53.539 -  62.463:   45        |
|      2:    17.847 -  26.770:  315   |   7:    62.463 -  71.386:   18        |
|      3:    26.770 -  35.693:  197   |   8:    71.386 -  80.309:    3        |
|      4:    35.693 -  44.616:  129   |   9:    80.309 -  89.232:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2219 r_free = 0.2902             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2214 r_free = 0.2894             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: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2214   r_free= 0.2894   ksol= 0.34   Bsol= 50.00   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,1.95,4.36,0.00,0.00,0.00); trace/3= 2.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.738814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2208   r_free= 0.2885   ksol= 0.33   Bsol= 53.99   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,0.67,2.90,0.00,0.00,0.00); trace/3= 1.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.738445                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.402461              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.605  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.067  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2208      final r-factor (work) = 0.1679          |
| start r-factor (free) = 0.2885      final r-factor (free) = 0.2243          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6920 = 5.40 * 0.50 * 5.7785 + 1.00 * 0.0829                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3046 = 5.40 * 0.50 * 5.6367 + 1.00 * 0.0787                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1679      final r-factor (work) = 0.1551          |
| start r-factor (free) = 0.2243      final r-factor (free) = 0.2135          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7366 = 0.48 * 1.00 * 5.6367 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6565 = 0.48 * 1.00 * 5.4571 + 1.00 * 1.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.02   15.35    None  None   None       |
|    all(noH): 2823   0      0.00    90.02   15.35    None  None   None       |
|    Sol.    : 438    0      2.22    89.07   38.09    None  None   None       |
|    Mac.    : 2385   0      0.00    90.02   11.17    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 -   9.002: 1252   |   5:    45.008 -  54.009:   99        |
|      1:     9.002 -  18.003:  845   |   6:    54.009 -  63.011:   46        |
|      2:    18.003 -  27.005:  249   |   7:    63.011 -  72.013:   17        |
|      3:    27.005 -  36.006:  168   |   8:    72.013 -  81.014:    4        |
|      4:    36.006 -  45.008:  138   |   9:    81.014 -  90.016:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1551 r_free = 0.2135             target_work(ml) = 5.428         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1547 r_free = 0.2129             target_work(ml) = 5.426         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1547   r_free= 0.2129   ksol= 0.33   Bsol= 53.99   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,0.67,2.90,0.00,0.00,0.00); trace/3= 1.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.425838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1547   r_free= 0.2128   ksol= 0.31   Bsol= 48.93   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.08,2.09,-0.00,0.00,0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.425974                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.268297              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.396  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 13.729085             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.173   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1547      final r-factor (work) = 0.1416          |
| start r-factor (free) = 0.2128      final r-factor (free) = 0.1959          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2711 = 2.27 * 0.50 * 5.4599 + 1.00 * 0.0787                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1753 = 2.27 * 0.50 * 5.3938 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1416      final r-factor (work) = 0.1346          |
| start r-factor (free) = 0.1959      final r-factor (free) = 0.1900          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 74.0778 = 13.73 * 1.00 * 5.3938 + 1.00 * 0.0262                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 73.1827 = 13.73 * 1.00 * 5.3293 + 1.00 * 0.0163                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.02  16.38    None  None   None       |
|    all(noH): 2823   0      0.00    104.02  16.38    None  None   None       |
|    Sol.    : 438    0      3.18    104.02  45.03    None  None   None       |
|    Mac.    : 2385   0      0.00    101.99  11.12    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 -  10.402: 1521   |   5:    52.011 -  62.414:   85        |
|      1:    10.402 -  20.805:  706   |   6:    62.414 -  72.816:   66        |
|      2:    20.805 -  31.207:  184   |   7:    72.816 -  83.218:   34        |
|      3:    31.207 -  41.609:  106   |   8:    83.218 -  93.620:   14        |
|      4:    41.609 -  52.011:  103   |   9:    93.620 - 104.023:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1346 r_free = 0.1900             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1345 r_free = 0.1900             target_work(ml) = 5.311         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1345   r_free= 0.1900   ksol= 0.31   Bsol= 48.93   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.08,2.09,-0.00,0.00,0.00); trace/3= 0.41                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.311038                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9071 -  4.6803 0.99   1421  157 0.1043 0.1367      5.4434       5.614|
|  2:  4.6803 -  3.7341 0.99   1370  153 0.0962 0.1328      5.5567      5.7787|
|  3:  3.7341 -  3.2678 0.99   1337  151 0.1298 0.1793      5.6586      5.9855|
|  4:  3.2678 -  2.9716 0.99   1332  144 0.1522 0.2098      5.6311      5.8217|
|  5:  2.9716 -  2.7600 0.99   1334  147 0.1628 0.1855      5.5345      5.6773|
|  6:  2.7600 -  2.5982 0.99   1321  149 0.1521 0.2594       5.382      5.7202|
|  7:  2.5982 -  2.4687 0.99   1300  151 0.1543 0.2025      5.3553      5.4932|
|  8:  2.4687 -  2.3617 0.98   1324  146 0.1485 0.2159      5.2704      5.5466|
|  9:  2.3617 -  2.2711 0.98   1290  140 0.1476 0.2150      5.2115      5.4676|
| 10:  2.2711 -  2.1929 0.99   1332  142 0.1378 0.1854      5.1248      5.2703|
| 11:  2.1929 -  2.1246 0.98   1257  146 0.1372 0.2514      5.0861      5.5058|
| 12:  2.1246 -  2.0640 0.97   1302  140 0.1408 0.1908      5.0488      5.3337|
| 13:  2.0640 -  2.0098 0.90   1169  128 0.1190 0.1921      4.8814      5.0642|
| 14:  2.0098 -  1.9609 0.41    541   65 0.1092 0.1726      4.7413      4.9608|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9071 -  4.6803  1421   157  0.93  10.58   0.97     0.94       8640.11|
|  2:  4.6803 -  3.7341  1370   153  0.94   9.78   1.03     1.01      11730.72|
|  3:  3.7341 -  3.2678  1337   151  0.91  14.69   1.05     1.04      15137.65|
|  4:  3.2678 -  2.9716  1332   144  0.89  17.54   1.03     1.01      14871.50|
|  5:  2.9716 -  2.7600  1334   147  0.86  20.84   1.00     0.97      13717.98|
|  6:  2.7600 -  2.5982  1321   149  0.86  20.38   0.97     0.92      10029.62|
|  7:  2.5982 -  2.4687  1300   151  0.86  20.55   1.00     0.96       9672.95|
|  8:  2.4687 -  2.3617  1324   146  0.87  19.59   1.01     0.96       8080.64|
|  9:  2.3617 -  2.2711  1290   140  0.87  19.88   1.00     0.94       7276.05|
| 10:  2.2711 -  2.1929  1332   142  0.87  19.07   1.00     0.95       6132.84|
| 11:  2.1929 -  2.1246  1257   146  0.86  20.28   1.00     0.95       6281.19|
| 12:  2.1246 -  2.0640  1302   140  0.87  19.88   1.00     0.98       5689.28|
| 13:  2.0640 -  2.0098  1169   128  0.88  18.78   0.98     0.93       4230.71|
| 14:  2.0098 -  1.9609   541    65  0.92  14.67   0.98     0.94       2911.67|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     2911.67 max =        15137.65 mean =      9222.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.65|
|phase err.(test): min =        0.00 max =           89.87 mean =        17.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1900   ksol= 0.31   Bsol= 53.94   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.17,-0.50,1.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.311188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1900   ksol= 0.31   Bsol= 53.94   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.17,-0.50,1.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.311188                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9071 -  4.6803 0.99   1421  157 0.1042 0.1370      5.4443       5.617|
|  2:  4.6803 -  3.7341 0.99   1370  153 0.0963 0.1333      5.5589      5.7824|
|  3:  3.7341 -  3.2678 0.99   1337  151 0.1301 0.1796      5.6603      5.9871|
|  4:  3.2678 -  2.9716 0.99   1332  144 0.1521 0.2097       5.631      5.8216|
|  5:  2.9716 -  2.7600 0.99   1334  147 0.1627 0.1853      5.5339      5.6762|
|  6:  2.7600 -  2.5982 0.99   1321  149 0.1520 0.2592      5.3813      5.7195|
|  7:  2.5982 -  2.4687 0.99   1300  151 0.1542 0.2024      5.3547       5.493|
|  8:  2.4687 -  2.3617 0.98   1324  146 0.1484 0.2155      5.2701      5.5459|
|  9:  2.3617 -  2.2711 0.98   1290  140 0.1476 0.2150      5.2112      5.4677|
| 10:  2.2711 -  2.1929 0.99   1332  142 0.1377 0.1854      5.1245      5.2701|
| 11:  2.1929 -  2.1246 0.98   1257  146 0.1372 0.2512       5.086      5.5054|
| 12:  2.1246 -  2.0640 0.97   1302  140 0.1408 0.1909      5.0488      5.3341|
| 13:  2.0640 -  2.0098 0.90   1169  128 0.1189 0.1920      4.8814      5.0642|
| 14:  2.0098 -  1.9609 0.41    541   65 0.1092 0.1724      4.7409      4.9602|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9071 -  4.6803  1421   157  0.93  10.61   0.97     0.95       8680.12|
|  2:  4.6803 -  3.7341  1370   153  0.94   9.82   1.03     1.01      11796.59|
|  3:  3.7341 -  3.2678  1337   151  0.91  14.74   1.05     1.04      15216.21|
|  4:  3.2678 -  2.9716  1332   144  0.89  17.56   1.03     1.01      14892.22|
|  5:  2.9716 -  2.7600  1334   147  0.86  20.84   1.01     0.98      13701.69|
|  6:  2.7600 -  2.5982  1321   149  0.86  20.37   0.98     0.92      10011.69|
|  7:  2.5982 -  2.4687  1300   151  0.86  20.54   1.00     0.96       9661.18|
|  8:  2.4687 -  2.3617  1324   146  0.87  19.58   1.01     0.97       8074.96|
|  9:  2.3617 -  2.2711  1290   140  0.87  19.88   1.00     0.95       7269.12|
| 10:  2.2711 -  2.1929  1332   142  0.87  19.07   1.01     0.96       6130.73|
| 11:  2.1929 -  2.1246  1257   146  0.86  20.27   1.01     0.96       6276.43|
| 12:  2.1246 -  2.0640  1302   140  0.87  19.88   1.00     0.99       5692.55|
| 13:  2.0640 -  2.0098  1169   128  0.88  18.78   0.99     0.94       4228.89|
| 14:  2.0098 -  1.9609   541    65  0.92  14.66   0.99     0.95       2907.62|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     2907.62 max =        15216.21 mean =      9233.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.65|
|phase err.(test): min =        0.00 max =           89.92 mean =        17.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.605)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    104.56  16.92    None  None   None       |
|    all(noH): 2823   0      0.54    104.56  16.92    None  None   None       |
|    Sol.    : 438    0      3.72    104.56  45.58    None  None   None       |
|    Mac.    : 2385   0      0.54    102.53  11.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.542 -  10.944: 1521   |   5:    52.553 -  62.955:   85        |
|      1:    10.944 -  21.346:  706   |   6:    62.955 -  73.358:   66        |
|      2:    21.346 -  31.748:  184   |   7:    73.358 -  83.760:   34        |
|      3:    31.748 -  42.151:  106   |   8:    83.760 -  94.162:   14        |
|      4:    42.151 -  52.553:  103   |   9:    94.162 - 104.564:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 4.214
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 333
   mapped sites are within: 0.721 - 4.214

peak=    9.522 closest distance to " CB  VAL A 230 " =    1.438
peak=    8.242 closest distance to " CB  VAL A 296 " =    1.589
peak=    7.198 closest distance to " O   HOH Z 130 " =    1.992
peak=    6.963 closest distance to " O   ALA A 114 " =    0.917
peak=    6.932 closest distance to " O   HOH Z 103 " =    1.209
peak=    6.655 closest distance to " O  BHOH Z  74 " =    1.050
peak=    6.362 closest distance to " CD2 LEU A   5 " =    1.311
peak=    6.100 closest distance to " O   HOH Z 255 " =    1.020
peak=    5.529 closest distance to " O   HOH Z 258 " =    1.226
peak=    5.492 closest distance to " O   HOH Z  70 " =    1.089
peak=    5.477 closest distance to " CB  VAL A 230 " =    1.268
peak=    5.412 closest distance to " CG  PRO A  54 " =    1.505
peak=    5.398 closest distance to " O   HOH Z 203 " =    0.914
peak=    5.146 closest distance to " O   HOH Z 236 " =    1.689
peak=    5.127 closest distance to " O   HOH Z 246 " =    1.272
peak=    5.097 closest distance to " O   HOH Z 425 " =    1.651
peak=    5.059 closest distance to " O   HOH Z 402 " =    1.583
peak=    4.989 closest distance to " CB  ARG A 275 " =    1.113
peak=    4.978 closest distance to " O   HOH Z 427 " =    2.706
peak=    4.972 closest distance to " NH1 ARG A 138 " =    0.953
peak=    4.954 closest distance to " CG  GLN A  58 " =    1.303
peak=    4.943 closest distance to " NE2 GLN A  11 " =    1.110
peak=    4.805 closest distance to " O   HOH Z 182 " =    1.232
peak=    4.787 closest distance to " CD1AILE A 234 " =    0.889
peak=    4.738 closest distance to " O   HOH Z 105 " =    1.095
peak=    4.674 closest distance to " O   HOH Z 375 " =    1.190
peak=    4.656 closest distance to " O   HOH Z  65 " =    1.445
peak=    4.632 closest distance to " CB  ALA A 114 " =    1.018
peak=    4.629 closest distance to " NH2AARG A 145 " =    1.219
peak=    4.629 closest distance to " O   HOH Z 124 " =    1.446
peak=    4.618 closest distance to " CB  GLN A 223 " =    1.524
peak=    4.598 closest distance to " O   HOH Z 142 " =    1.765
peak=    4.596 closest distance to " CB  ASN A 142 " =    1.070
peak=    4.581 closest distance to " O   HOH Z 199 " =    1.162
peak=    4.576 closest distance to " O   HOH Z 249 " =    1.382
peak=    4.548 closest distance to " O   HOH Z   9 " =    2.420
peak=    4.548 closest distance to " O   HOH Z 222 " =    1.338
peak=    4.531 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.500 closest distance to " CA  PHE A 283 " =    1.079
peak=    4.466 closest distance to " CG  PRO A 243 " =    1.071
peak=    4.426 closest distance to " O   HOH Z 117 " =    1.335
peak=    4.426 closest distance to " O   HOH Z  69 " =    1.445
peak=    4.425 closest distance to " O   HOH Z 112 " =    1.227
peak=    4.412 closest distance to " CG2 ILE A 234 " =    1.046
peak=    4.389 closest distance to " CG  LEU A 228 " =    1.112
peak=    4.387 closest distance to " O   PRO A 198 " =    1.446
peak=    4.371 closest distance to " O   HOH Z  49 " =    1.521
peak=    4.366 closest distance to " O   HOH Z   7 " =    1.496
peak=    4.361 closest distance to " CG2 VAL A 257 " =    0.962
peak=    4.350 closest distance to " NZ  LYS A 117 " =    2.996
peak=    4.341 closest distance to " O   HOH Z 178 " =    1.254
peak=    4.316 closest distance to " O   HOH Z 417 " =    1.806
peak=    4.314 closest distance to " CG  LYS A  76 " =    1.743
peak=    4.313 closest distance to " O   HOH Z  39 " =    1.523
peak=    4.301 closest distance to " O   HOH Z 369 " =    2.345
peak=    4.298 closest distance to " O   HOH Z 368 " =    2.961
peak=    4.274 closest distance to " O   HOH Z 123 " =    1.456
peak=    4.267 closest distance to " O   HOH Z 232 " =    2.334
peak=    4.244 closest distance to " O   HOH Z 143 " =    1.835
peak=    4.236 closest distance to " CG  GLN A  11 " =    2.234
peak=    4.225 closest distance to " O   HOH Z 263 " =    1.396
peak=    4.182 closest distance to " O   HOH Z 287 " =    1.725
peak=    4.176 closest distance to " O   HOH Z 406 " =    1.566
peak=    4.149 closest distance to " O   HOH Z 248 " =    1.099
peak=    4.146 closest distance to " OD1 ASN A  69 " =    0.905
peak=    4.121 closest distance to " C   GLN A  73 " =    1.075
peak=    4.113 closest distance to " O   HOH Z  78 " =    1.731
peak=    4.107 closest distance to " CB  ASN A 110 " =    1.127
peak=    4.104 closest distance to " O   HOH Z 188 " =    1.569
peak=    4.100 closest distance to " CB  PRO A  54 " =    1.013
peak=    4.089 closest distance to " CD2 TRP A 179 " =    1.365
peak=    4.080 closest distance to " O   HOH Z 211 " =    1.380
peak=    4.077 closest distance to " O   HOH Z 423 " =    1.740
peak=    4.053 closest distance to " N   TYR A  15 " =    1.298
peak=    4.036 closest distance to " O   HOH Z 365 " =    2.868
peak=    4.027 closest distance to " O   HOH Z  83 " =    1.061
peak=    4.023 closest distance to " O   HOH Z 126 " =    1.902
peak=    4.014 closest distance to " O   HOH Z 414 " =    1.317
peak=    4.011 closest distance to " O   HOH Z 147 " =    1.210
peak=    3.997 closest distance to " O   HOH Z 251 " =    1.700
peak=    3.969 closest distance to " O   HOH Z 342 " =    0.869
peak=    3.949 closest distance to " CH2 TRP A 266 " =    1.161
peak=    3.942 closest distance to " O   HOH Z  26 " =    1.742
peak=    3.940 closest distance to " O   HOH Z 425 " =    1.983
peak=    3.933 closest distance to " O   HOH Z 331 " =    1.054
peak=    3.932 closest distance to " O   HOH Z 238 " =    1.327
peak=    3.926 closest distance to " O   HOH Z 380 " =    2.033
peak=    3.926 closest distance to " O   HOH Z 272 " =    1.751
peak=    3.920 closest distance to " CG  PRO A  90 " =    1.207
peak=    3.899 closest distance to " O   HOH Z 403 " =    1.731
peak=    3.889 closest distance to " OG ASER A 258 " =    3.108
peak=    3.880 closest distance to " O   HOH Z  91 " =    2.536
peak=    3.872 closest distance to " CG AARG A 275 " =    1.261
peak=    3.865 closest distance to " CZ  PHE A  38 " =    1.104
peak=    3.861 closest distance to " CB  SER A 216 " =    1.106
peak=    3.856 closest distance to " O   HOH Z 313 " =    1.986
peak=    3.850 closest distance to " O   HOH Z 177 " =    1.206
peak=    3.838 closest distance to " CB  THR A  52 " =    0.869
peak=    3.827 closest distance to " NE2 GLN A 103 " =    1.042
peak=    3.825 closest distance to " O   HOH Z  40 " =    1.770
peak=    3.822 closest distance to " CA  ARG A 195 " =    1.338
peak=    3.821 closest distance to " CB  HIS A 108 " =    0.902
peak=    3.813 closest distance to " CG2 ILE A 120 " =    0.982
peak=    3.802 closest distance to " ND2BASN A 224 " =    0.847
peak=    3.794 closest distance to " O   HOH Z 346 " =    1.606
peak=    3.793 closest distance to " CA  ILE A 234 " =    1.127
peak=    3.771 closest distance to " O   HOH Z 213 " =    1.930
peak=    3.770 closest distance to " CB  LYS A 117 " =    1.199
peak=    3.761 closest distance to " CB  THR A  31 " =    1.618
peak=    3.759 closest distance to " CB  TYR A 169 " =    0.879
peak=    3.756 closest distance to " O  BHOH Z 338 " =    2.385
peak=    3.753 closest distance to " O   HOH Z  59 " =    1.663
peak=    3.750 closest distance to " NE1 TRP A 274 " =    0.908
peak=    3.748 closest distance to " O   HOH Z  66 " =    2.357
peak=    3.747 closest distance to " N   PHE A 130 " =    1.349
peak=    3.746 closest distance to " NH2 ARG A  56 " =    1.985
peak=    3.744 closest distance to " O   HOH Z 392 " =    0.974
peak=    3.739 closest distance to " CG  ARG A 138 " =    1.099
peak=    3.737 closest distance to " O   HOH Z 193 " =    1.958
peak=    3.723 closest distance to " O   HOH Z 116 " =    1.080
peak=    3.711 closest distance to " O   HOH Z 422 " =    2.379
peak=    3.707 closest distance to " CB  SER A  63 " =    1.271
peak=    3.697 closest distance to " NH1BARG A 102 " =    0.984
peak=    3.689 closest distance to " CA  TYR A  30 " =    1.044
peak=    3.687 closest distance to " N   ASP A 162 " =    1.141
peak=    3.683 closest distance to " CA  ALA A 129 " =    1.255
peak=    3.679 closest distance to " O   HOH Z  41 " =    2.378
peak=    3.675 closest distance to " CB  SER A 273 " =    0.948
peak=    3.671 closest distance to " O   HOH Z 298 " =    1.546
peak=    3.663 closest distance to " O   HOH Z 146 " =    1.528
peak=    3.653 closest distance to " CG  LEU A 167 " =    1.213
peak=    3.650 closest distance to " O   HOH Z  63 " =    1.634
peak=    3.648 closest distance to " CB  ARG A  79 " =    0.832
peak=    3.644 closest distance to " CB BVAL A  41 " =    1.088
peak=    3.644 closest distance to " O   HOH Z 234 " =    3.632
peak=    3.641 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.641 closest distance to " O   HOH Z 398 " =    1.425
peak=    3.632 closest distance to " O   HOH Z  80 " =    1.622
peak=    3.624 closest distance to " CG  LEU A 281 " =    1.015
peak=    3.610 closest distance to " O   HOH Z 324 " =    1.583
peak=    3.597 closest distance to " O   HOH Z 411 " =    3.793
peak=    3.594 closest distance to " O   HOH Z 261 " =    2.152
peak=    3.591 closest distance to " CB  ASN A  39 " =    0.929
peak=    3.585 closest distance to " O   HOH Z  24 " =    1.751
peak=    3.584 closest distance to " CE2 PHE A  16 " =    0.871
peak=    3.580 closest distance to " CZ  PHE A 218 " =    1.144
peak=    3.576 closest distance to " O   HOH Z  10 " =    1.761
peak=    3.574 closest distance to " CB  ASN A 215 " =    1.179
peak=    3.568 closest distance to " O   HIS A 115 " =    1.000
peak=    3.564 closest distance to " CB  SER A  26 " =    1.737
peak=    3.556 closest distance to " CE  LYS A 119 " =    1.187
peak=    3.554 closest distance to " O   HOH Z   1 " =    1.870
peak=    3.552 closest distance to " CA  ASN A 127 " =    1.093
peak=    3.551 closest distance to " CB  VAL A 265 " =    1.413
peak=    3.550 closest distance to " CB  ASP A 107 " =    1.198
peak=    3.541 closest distance to " O   HOH Z 389 " =    1.688
peak=    3.539 closest distance to " CG  LEU A   5 " =    1.155
peak=    3.531 closest distance to " O   VAL A 153 " =    1.194
peak=    3.527 closest distance to " O   HOH Z 218 " =    2.110
peak=    3.524 closest distance to " N   GLN A 278 " =    1.541
peak=    3.522 closest distance to " CA  ALA A 100 " =    0.795
peak=    3.516 closest distance to " O   HOH Z 357 " =    2.018
peak=    3.515 closest distance to " O   HOH Z 284 " =    1.449
peak=    3.511 closest distance to " O   HOH Z 303 " =    2.042
peak=    3.510 closest distance to " O   HOH Z 295 " =    1.538
peak=    3.508 closest distance to " CA  GLN A  58 " =    0.920
peak=    3.501 closest distance to " O   HOH Z 359 " =    1.594
peak=    3.496 closest distance to " O   HOH Z 385 " =    1.143
peak=    3.496 closest distance to " O   HOH Z  85 " =    1.234
peak=    3.492 closest distance to " CG  LYS A 119 " =    1.034
peak=    3.489 closest distance to " O   HOH Z 207 " =    1.043
peak=    3.488 closest distance to " CB  GLN A 183 " =    1.213
peak=    3.487 closest distance to " O   HOH Z 368 " =    0.909
peak=    3.483 closest distance to " CG1 VAL A 257 " =    1.368
peak=    3.483 closest distance to " O   HOH Z 172 " =    3.057
peak=    3.482 closest distance to " NH1 ARG A  14 " =    1.197
peak=    3.475 closest distance to " CB  SER A 276 " =    1.140
peak=    3.474 closest distance to " O   HOH Z 128 " =    1.933
peak=    3.471 closest distance to " CD  ARG A 159 " =    0.721
peak=    3.469 closest distance to " CB  ALA A 292 " =    0.907
peak=    3.468 closest distance to " O   HOH Z  30 " =    1.475
peak=    3.464 closest distance to " O   HOH Z 130 " =    2.248
peak=    3.459 closest distance to " CB  GLN A  88 " =    1.313
peak=    3.455 closest distance to " CE AMET A  47 " =    1.358
peak=    3.451 closest distance to " CB  LEU A 300 " =    0.996
peak=    3.445 closest distance to " CB  ARG A 102 " =    0.812
peak=    3.442 closest distance to " CB  PHE A 204 " =    0.750
peak=    3.439 closest distance to " CE3 TRP A 274 " =    1.195
peak=    3.436 closest distance to " O   HOH Z 330 " =    1.030
peak=    3.432 closest distance to " O   HOH Z 150 " =    1.367
peak=    3.429 closest distance to " CB  ALA A  43 " =    1.060
peak=    3.425 closest distance to " CB  SER A  62 " =    1.059
peak=    3.417 closest distance to " O   HOH Z 153 " =    3.632
peak=    3.416 closest distance to " CB  ALA A 233 " =    1.068
peak=    3.414 closest distance to " O   HOH Z   4 " =    1.986
peak=    3.412 closest distance to " ND2 ASN A 249 " =    0.898
peak=    3.408 closest distance to " NE AARG A 145 " =    1.033
peak=    3.406 closest distance to " O   THR A 182 " =    1.544
peak=    3.403 closest distance to " O   HOH Z 162 " =    1.484
peak=    3.403 closest distance to " CD2 LEU A 228 " =    1.169
peak=    3.401 closest distance to " CD1 ILE A 199 " =    1.540
peak=    3.399 closest distance to " O   HOH Z 158 " =    2.849
peak=    3.398 closest distance to " O   HOH Z 132 " =    2.493
peak=    3.396 closest distance to " CA  CYS A 260 " =    1.418
peak=    3.396 closest distance to " CB  VAL A 202 " =    1.628
peak=    3.394 closest distance to " O   HOH Z 216 " =    3.461
peak=    3.394 closest distance to " O   HOH Z 305 " =    3.442
peak=    3.390 closest distance to " CE3 TRP A 150 " =    1.180
peak=    3.389 closest distance to " O   HOH Z 191 " =    3.145
peak=    3.388 closest distance to " CB  GLN A  55 " =    1.035
peak=    3.386 closest distance to " O   HOH Z 371 " =    2.075
peak=    3.385 closest distance to " CB  GLU A 128 " =    0.955
peak=    3.384 closest distance to " CG  GLN A  11 " =    1.786
peak=    3.383 closest distance to " O   HOH Z 362 " =    2.264
peak=    3.382 closest distance to " OG  SER A 146 " =    0.823
peak=    3.377 closest distance to " O   HOH Z  51 " =    1.561
peak=    3.377 closest distance to " CB  TYR A  30 " =    1.678
peak=    3.371 closest distance to " O   HOH Z 132 " =    2.656
peak=    3.365 closest distance to " CB  ALA A 248 " =    1.459
peak=    3.362 closest distance to " CE  LYS A  48 " =    1.184
peak=    3.359 closest distance to " CB  TRP A 179 " =    1.293
peak=    3.358 closest distance to " N   ARG A 156 " =    1.382
peak=    3.355 closest distance to " CA  ARG A  36 " =    0.977
peak=    3.355 closest distance to " O   THR A 157 " =    1.417
peak=    3.354 closest distance to " O   PRO A 198 " =    1.570
peak=    3.351 closest distance to " CA  GLY A  57 " =    1.016
peak=    3.350 closest distance to " CB  LEU A 237 " =    0.864
peak=    3.349 closest distance to " O   HOH Z 180 " =    2.224
peak=    3.345 closest distance to " O   HOH Z 434 " =    3.307
peak=    3.344 closest distance to " O   HOH Z 281 " =    2.203
peak=    3.343 closest distance to " CB  GLU A 277 " =    3.554
peak=    3.341 closest distance to " O   HOH Z 253 " =    2.438
peak=    3.333 closest distance to " O   HOH Z 422 " =    1.000
peak=    3.328 closest distance to " OG  SER A  62 " =    2.856
peak=    3.325 closest distance to " O   HOH Z 423 " =    2.177
peak=    3.325 closest distance to " CG  PRO A 213 " =    1.243
peak=    3.321 closest distance to " N   ALA A 131 " =    0.975
peak=    3.320 closest distance to " O   HOH Z 344 " =    1.355
peak=    3.317 closest distance to " CD2 TYR A 186 " =    1.032
peak=    3.315 closest distance to " CB  ASP A 272 " =    1.041
peak=    3.314 closest distance to " O   HOH Z  55 " =    2.014
peak=    3.307 closest distance to " O   HOH Z 427 " =    1.310
peak=    3.298 closest distance to " CA  TYR A 214 " =    1.152
peak=    3.297 closest distance to " CA  VAL A 125 " =    1.039
peak=    3.297 closest distance to " CB  ASP A 124 " =    0.958
peak=    3.296 closest distance to " CA  SER A 210 " =    1.425
peak=    3.294 closest distance to " O   HOH Z  85 " =    2.238
peak=    3.292 closest distance to " O   HOH Z 407 " =    1.421
peak=    3.291 closest distance to " CZ3 TRP A  92 " =    1.165
peak=    3.291 closest distance to " O   HOH Z 423 " =    1.527
peak=    3.286 closest distance to " N   ASP A 231 " =    1.128
peak=    3.284 closest distance to " OG BSER A 164 " =    2.100
peak=    3.284 closest distance to " O   HOH Z   6 " =    1.438
peak=    3.283 closest distance to " O   HOH Z 127 " =    1.034
peak=    3.275 closest distance to " CB  SER A   3 " =    1.205
peak=    3.273 closest distance to " OG ASER A 212 " =    1.508
peak=    3.273 closest distance to " O   HOH Z 389 " =    2.742
peak=    3.272 closest distance to " O   HOH Z 437 " =    1.710
peak=    3.272 closest distance to " O   HOH Z 418 " =    0.980
peak=    3.271 closest distance to " NH1AARG A 145 " =    1.041
peak=    3.268 closest distance to " CB  THR A 264 " =    1.482
peak=    3.268 closest distance to " O   HOH Z 148 " =    1.340
peak=    3.265 closest distance to " CD2 LEU A 297 " =    1.149
peak=    3.264 closest distance to " CG2 ILE A 106 " =    0.925
peak=    3.263 closest distance to " CE  MET A  93 " =    1.456
peak=    3.258 closest distance to " O   HOH Z  61 " =    1.787
peak=    3.253 closest distance to " NH2AARG A 190 " =    1.776
peak=    3.253 closest distance to " CG1 VAL A 296 " =    1.215
peak=    3.252 closest distance to " O   HOH Z 173 " =    2.138
peak=    3.251 closest distance to " CA  ALA A 160 " =    1.014
peak=    3.249 closest distance to " CG2 ILE A  20 " =    1.643
peak=    3.240 closest distance to " O   HOH Z 392 " =    1.282
peak=    3.238 closest distance to " O   ASP A 124 " =    1.337
peak=    3.234 closest distance to " O   HOH Z 104 " =    1.889
peak=    3.229 closest distance to " O   HOH Z 403 " =    1.447
peak=    3.223 closest distance to " O   HOH Z 323 " =    1.453
peak=    3.219 closest distance to " O   HOH Z 329 " =    4.214
peak=    3.210 closest distance to " CB  ASP A 191 " =    1.380
peak=    3.201 closest distance to " O   HOH Z  97 " =    1.332
peak=    3.199 closest distance to " OE1 GLU A   2 " =    1.288
peak=    3.193 closest distance to " O   HOH Z 145 " =    1.789
peak=    3.191 closest distance to " CG1 VAL A 153 " =    0.889
peak=    3.189 closest distance to " O   HOH Z 343 " =    2.625
peak=    3.189 closest distance to " OD2 ASP A 286 " =    2.114
peak=    3.188 closest distance to " O   HOH Z  11 " =    1.352
peak=    3.188 closest distance to " NZ  LYS A 117 " =    1.101
peak=    3.186 closest distance to " CZ3 TRP A 177 " =    1.017
peak=    3.186 closest distance to " CA  ASN A 215 " =    1.024
peak=    3.184 closest distance to " O   HOH Z 408 " =    2.783
peak=    3.184 closest distance to " CA  TRP A 150 " =    0.979
peak=    3.181 closest distance to " O   HOH Z  47 " =    1.739
peak=    3.181 closest distance to " NH2AARG A 145 " =    2.293
peak=    3.181 closest distance to " CE  LYS A  76 " =    0.932
peak=    3.180 closest distance to " O   HOH Z   1 " =    1.619
peak=    3.178 closest distance to " OG BSER A 210 " =    1.542
peak=    3.176 closest distance to " O   HOH Z 287 " =    1.959
peak=    3.171 closest distance to " O   HOH Z 238 " =    1.843
peak=    3.166 closest distance to " CB  PHE A 130 " =    0.856
peak=    3.163 closest distance to " CD1 LEU A  96 " =    0.729
peak=    3.161 closest distance to " CB  ARG A 219 " =    1.036
peak=    3.152 closest distance to " O   HOH Z  44 " =    2.000
peak=    3.147 closest distance to " NE BARG A 275 " =    1.262
peak=    3.145 closest distance to " O   HOH Z 286 " =    2.390
peak=    3.142 closest distance to " CD  ARG A  79 " =    1.088
peak=    3.142 closest distance to " O   HOH Z 270 " =    1.410
peak=    3.137 closest distance to " CA  THR A 221 " =    0.924
peak=    3.134 closest distance to " CB  ARG A 156 " =    1.179
peak=    3.133 closest distance to " CB  ARG A  79 " =    1.192
peak=    3.127 closest distance to " O   HOH Z  43 " =    1.125
peak=    3.125 closest distance to " O   THR A 220 " =    1.259
peak=    3.123 closest distance to " CE2 PHE A 192 " =    1.455
peak=    3.121 closest distance to " CG BARG A 102 " =    1.982
peak=    3.120 closest distance to " CD2 TYR A  15 " =    1.023
peak=    3.116 closest distance to " NE2 GLN A  73 " =    1.537
peak=    3.114 closest distance to " O   HOH Z 372 " =    0.974
peak=    3.109 closest distance to " O   HOH Z  94 " =    1.394
peak=    3.107 closest distance to " O   HOH Z 365 " =    2.452
peak=    3.097 closest distance to " O   THR A 294 " =    1.092
peak=    3.091 closest distance to " O   HOH Z 290 " =    1.550
peak=    3.084 closest distance to " O   HOH Z  88 " =    3.695
peak=    3.083 closest distance to " CB  GLU A 277 " =    1.013
peak=    3.078 closest distance to " CB  GLN A  89 " =    1.206
peak=    3.068 closest distance to " CA  ASP A 162 " =    0.990
peak=    3.063 closest distance to " O   HOH Z 438 " =    2.292
peak=    3.037 closest distance to " CG1 ILE A 151 " =    1.143
peak=    3.028 closest distance to " O   HOH Z 184 " =    1.587
peak=    3.025 closest distance to " O   HOH Z 410 " =    1.597

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.607 - 5.779
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 199
   mapped sites are within: 0.737 - 5.779

peak=   -4.782 closest distance to " O   HOH Z 203 " =    1.126
peak=   -4.613 closest distance to " CB  GLN A  55 " =    1.150
peak=   -4.585 closest distance to " O   PRO A 198 " =    1.195
peak=   -4.585 closest distance to " CB  VAL A 230 " =    1.004
peak=   -4.571 closest distance to " O   HOH Z  69 " =    1.506
peak=   -4.454 closest distance to " O   ALA A 114 " =    0.832
peak=   -4.336 closest distance to " CD2 HIS A 207 " =    1.998
peak=   -4.157 closest distance to " O  BHOH Z  74 " =    0.765
peak=   -4.112 closest distance to " O   HOH Z 276 " =    1.191
peak=   -4.070 closest distance to " O   HOH Z 131 " =    4.208
peak=   -4.046 closest distance to " CA  GLN A  58 " =    1.205
peak=   -4.034 closest distance to " CG2 ILE A  20 " =    2.797
peak=   -4.027 closest distance to " CD1 LEU A 255 " =    2.880
peak=   -3.996 closest distance to " O   ARG A 219 " =    1.830
peak=   -3.939 closest distance to " C   HIS A 108 " =    1.247
peak=   -3.926 closest distance to " CD  ARG A  14 " =    3.149
peak=   -3.902 closest distance to " O   HOH Z 242 " =    1.638
peak=   -3.875 closest distance to " OE1 GLN A  88 " =    1.136
peak=   -3.867 closest distance to " O   HOH Z 134 " =    4.176
peak=   -3.866 closest distance to " O   HOH Z  64 " =    1.233
peak=   -3.846 closest distance to " CD2 TYR A 293 " =    1.880
peak=   -3.830 closest distance to " CB  ALA A  43 " =    2.508
peak=   -3.822 closest distance to " O   HOH Z 147 " =    2.022
peak=   -3.817 closest distance to " OE1 GLN A 223 " =    2.294
peak=   -3.811 closest distance to " CB  ASP A 132 " =    2.612
peak=   -3.780 closest distance to " O   HOH Z 177 " =    1.084
peak=   -3.776 closest distance to " OG  SER A  87 " =    1.537
peak=   -3.768 closest distance to " CG  GLN A  58 " =    1.035
peak=   -3.712 closest distance to " NE  ARG A 156 " =    5.657
peak=   -3.707 closest distance to " O   VAL A  67 " =    2.567
peak=   -3.680 closest distance to " CG  TYR A 169 " =    2.196
peak=   -3.678 closest distance to " OG  SER A  97 " =    2.196
peak=   -3.676 closest distance to " CE2 TYR A  30 " =    2.654
peak=   -3.672 closest distance to " O   HOH Z 147 " =    1.222
peak=   -3.666 closest distance to " O   HOH Z  70 " =    0.942
peak=   -3.665 closest distance to " CZ2 TRP A  92 " =    2.758
peak=   -3.663 closest distance to " O   HOH Z  68 " =    1.465
peak=   -3.656 closest distance to " O   HOH Z  39 " =    1.282
peak=   -3.652 closest distance to " O   HOH Z 105 " =    1.734
peak=   -3.649 closest distance to " C   SER A 276 " =    1.620
peak=   -3.645 closest distance to " CB  SER A 210 " =    1.005
peak=   -3.638 closest distance to " O   HOH Z 281 " =    2.833
peak=   -3.637 closest distance to " O   HOH Z 286 " =    1.629
peak=   -3.628 closest distance to " NE2 GLN A  11 " =    1.746
peak=   -3.627 closest distance to " O   HOH Z 211 " =    1.179
peak=   -3.624 closest distance to " O   HOH Z 394 " =    1.716
peak=   -3.619 closest distance to " NE2 GLN A  55 " =    1.081
peak=   -3.618 closest distance to " O   HOH Z  40 " =    1.460
peak=   -3.599 closest distance to " O   HOH Z 329 " =    0.944
peak=   -3.590 closest distance to " O   HOH Z 128 " =    2.532
peak=   -3.588 closest distance to " CD  PRO A 213 " =    2.166
peak=   -3.587 closest distance to " O   HOH Z 164 " =    5.779
peak=   -3.576 closest distance to " O   HOH Z  67 " =    1.588
peak=   -3.572 closest distance to " CZ  PHE A  38 " =    2.349
peak=   -3.571 closest distance to " O   HOH Z 185 " =    1.605
peak=   -3.563 closest distance to " CB  TYR A  68 " =    1.182
peak=   -3.558 closest distance to " CG  ARG A 138 " =    1.049
peak=   -3.546 closest distance to " O   HOH Z 149 " =    1.988
peak=   -3.537 closest distance to " O   HOH Z 236 " =    1.504
peak=   -3.537 closest distance to " O   ILE A 234 " =    1.393
peak=   -3.532 closest distance to " OD1 ASP A 107 " =    1.036
peak=   -3.525 closest distance to " O   HOH Z 165 " =    2.286
peak=   -3.524 closest distance to " O   HOH Z 116 " =    1.423
peak=   -3.522 closest distance to " OG BSER A 134 " =    1.527
peak=   -3.515 closest distance to " O   HOH Z 275 " =    1.710
peak=   -3.512 closest distance to " SG BCYS A 201 " =    2.284
peak=   -3.507 closest distance to " O   HOH Z 231 " =    2.113
peak=   -3.493 closest distance to " CD1 LEU A 101 " =    2.198
peak=   -3.493 closest distance to " O   VAL A 125 " =    2.285
peak=   -3.493 closest distance to " O   HOH Z 105 " =    1.516
peak=   -3.483 closest distance to " CG2 VAL A 296 " =    2.071
peak=   -3.478 closest distance to " CG  LEU A 281 " =    2.066
peak=   -3.474 closest distance to " O   HOH Z 385 " =    1.623
peak=   -3.472 closest distance to " CZ2 TRP A 274 " =    0.949
peak=   -3.468 closest distance to " CG2 VAL A 230 " =    0.765
peak=   -3.465 closest distance to " O   HOH Z 295 " =    1.745
peak=   -3.450 closest distance to " O   LEU A 297 " =    0.737
peak=   -3.435 closest distance to " O   SER A 245 " =    1.289
peak=   -3.435 closest distance to " CD  PRO A 243 " =    1.975
peak=   -3.434 closest distance to " O   HOH Z 231 " =    1.151
peak=   -3.429 closest distance to " O   HOH Z 368 " =    1.212
peak=   -3.428 closest distance to " O   HOH Z 359 " =    3.093
peak=   -3.411 closest distance to " OG  SER A  63 " =    1.106
peak=   -3.404 closest distance to " O   ALA A 227 " =    1.431
peak=   -3.403 closest distance to " CG2 VAL A 189 " =    1.937
peak=   -3.380 closest distance to " O   HOH Z 166 " =    1.721
peak=   -3.379 closest distance to " O   HOH Z 107 " =    0.792
peak=   -3.377 closest distance to " O   HOH Z  65 " =    1.612
peak=   -3.370 closest distance to " ND2 ASN A 249 " =    2.397
peak=   -3.364 closest distance to " CG2 VAL A 202 " =    2.658
peak=   -3.353 closest distance to " CE1 TYR A 247 " =    2.573
peak=   -3.345 closest distance to " CG  GLN A  77 " =    1.032
peak=   -3.345 closest distance to " OE1 GLU A 277 " =    2.154
peak=   -3.341 closest distance to " CD  LYS A 289 " =    2.313
peak=   -3.340 closest distance to " O   HOH Z 388 " =    2.122
peak=   -3.338 closest distance to " OG BSER A  99 " =    0.965
peak=   -3.335 closest distance to " O   HOH Z 155 " =    1.082
peak=   -3.326 closest distance to " O   HOH Z  91 " =    1.516
peak=   -3.326 closest distance to " O   PRO A 163 " =    1.817
peak=   -3.321 closest distance to " CG1BVAL A  72 " =    2.701
peak=   -3.319 closest distance to " CB  ALA A  51 " =    1.702
peak=   -3.319 closest distance to " O   GLY A 241 " =    2.298
peak=   -3.309 closest distance to " NE2 GLN A 240 " =    1.791
peak=   -3.305 closest distance to " O   HOH Z 215 " =    1.652
peak=   -3.303 closest distance to " CB  CYS A 254 " =    2.195
peak=   -3.302 closest distance to " CD2 LEU A 237 " =    2.731
peak=   -3.296 closest distance to " O   HOH Z  89 " =    2.784
peak=   -3.288 closest distance to " O   ILE A  49 " =    1.686
peak=   -3.288 closest distance to " CB  ASN A  45 " =    2.025
peak=   -3.284 closest distance to " O   HOH Z 421 " =    2.901
peak=   -3.283 closest distance to " O   HOH Z 100 " =    0.879
peak=   -3.277 closest distance to " OG BSER A 210 " =    1.838
peak=   -3.277 closest distance to " O   HOH Z 260 " =    1.940
peak=   -3.276 closest distance to " O   HOH Z 111 " =    1.747
peak=   -3.271 closest distance to " OE2 GLU A 152 " =    1.411
peak=   -3.268 closest distance to " OD2 ASP A 191 " =    1.410
peak=   -3.261 closest distance to " CB  ALA A 248 " =    2.054
peak=   -3.255 closest distance to " O   HOH Z  35 " =    2.481
peak=   -3.253 closest distance to " CE1 TYR A 186 " =    2.193
peak=   -3.251 closest distance to " OE1 GLU A  44 " =    1.135
peak=   -3.249 closest distance to " CG1 VAL A 112 " =    3.119
peak=   -3.249 closest distance to " NZ  LYS A 166 " =    1.566
peak=   -3.249 closest distance to " O   ASP A 298 " =    1.992
peak=   -3.244 closest distance to " O   HOH Z 244 " =    1.577
peak=   -3.242 closest distance to " CD2 PHE A 225 " =    1.073
peak=   -3.242 closest distance to " NE2 GLN A  94 " =    1.758
peak=   -3.242 closest distance to " CA  ALA A 114 " =    1.223
peak=   -3.239 closest distance to " O   GLN A 144 " =    1.324
peak=   -3.232 closest distance to " O   HOH Z 293 " =    1.630
peak=   -3.228 closest distance to " O   ASN A 252 " =    1.371
peak=   -3.228 closest distance to " ND2 ASN A 285 " =    1.981
peak=   -3.224 closest distance to " O   HOH Z 352 " =    1.558
peak=   -3.221 closest distance to " NE  ARG A 138 " =    1.718
peak=   -3.219 closest distance to " O   HOH Z 426 " =    1.688
peak=   -3.219 closest distance to " N   GLN A  58 " =    1.204
peak=   -3.215 closest distance to " O   HOH Z  66 " =    1.001
peak=   -3.214 closest distance to " ND2 ASN A  69 " =    1.565
peak=   -3.213 closest distance to " CD1 TRP A  85 " =    1.059
peak=   -3.212 closest distance to " O   HOH Z 257 " =    1.081
peak=   -3.210 closest distance to " C   ASN A 285 " =    2.057
peak=   -3.205 closest distance to " O   GLU A 152 " =    1.493
peak=   -3.204 closest distance to " O   HOH Z 429 " =    1.545
peak=   -3.203 closest distance to " OD2 ASP A  50 " =    1.497
peak=   -3.203 closest distance to " CG2 THR A  18 " =    2.836
peak=   -3.199 closest distance to " CG2 THR A 178 " =    2.268
peak=   -3.196 closest distance to " CD2 TYR A 116 " =    2.223
peak=   -3.195 closest distance to " O   HOH Z 216 " =    1.530
peak=   -3.192 closest distance to " N   ALA A 244 " =    1.209
peak=   -3.185 closest distance to " N   MET A 188 " =    1.935
peak=   -3.182 closest distance to " CG1 VAL A 125 " =    2.257
peak=   -3.181 closest distance to " O   HOH Z 235 " =    1.150
peak=   -3.180 closest distance to " O   HOH Z 427 " =    2.023
peak=   -3.180 closest distance to " O   HOH Z  44 " =    1.358
peak=   -3.178 closest distance to " O   ALA A  84 " =    1.556
peak=   -3.176 closest distance to " O   SER A  22 " =    2.354
peak=   -3.175 closest distance to " O   HOH Z  60 " =    1.884
peak=   -3.174 closest distance to " CA  ASP A 298 " =    1.012
peak=   -3.169 closest distance to " O   HOH Z 105 " =    0.941
peak=   -3.167 closest distance to " O   HOH Z 149 " =    1.823
peak=   -3.166 closest distance to " CB  ASP A 132 " =    2.465
peak=   -3.164 closest distance to " O   VAL A 189 " =    2.443
peak=   -3.163 closest distance to " O   HOH Z 414 " =    2.392
peak=   -3.162 closest distance to " CD2 LEU A   5 " =    1.036
peak=   -3.161 closest distance to " O   HOH Z 135 " =    2.134
peak=   -3.159 closest distance to " CG  TRP A 266 " =    1.788
peak=   -3.158 closest distance to " CA  ASP A  27 " =    2.353
peak=   -3.153 closest distance to " CA  HIS A 207 " =    1.220
peak=   -3.148 closest distance to " C   GLU A   2 " =    1.971
peak=   -3.148 closest distance to " OG ASER A 134 " =    1.471
peak=   -3.147 closest distance to " CG  ARG A 259 " =    2.276
peak=   -3.145 closest distance to " O   HOH Z  52 " =    1.626
peak=   -3.143 closest distance to " CD  GLN A 223 " =    1.250
peak=   -3.143 closest distance to " O   ALA A 137 " =    0.861
peak=   -3.143 closest distance to " CG  LEU A  83 " =    2.249
peak=   -3.142 closest distance to " O   HOH Z 353 " =    2.090
peak=   -3.140 closest distance to " O   HOH Z 292 " =    1.551
peak=   -3.138 closest distance to " O   TRP A  70 " =    1.358
peak=   -3.138 closest distance to " NE2 GLN A 194 " =    2.077
peak=   -3.136 closest distance to " O   ASN A 187 " =    1.449
peak=   -3.136 closest distance to " OG ASER A 134 " =    1.351
peak=   -3.135 closest distance to " O   HOH Z 165 " =    1.471
peak=   -3.129 closest distance to " CB  ALA A  10 " =    2.304
peak=   -3.124 closest distance to " C   MET A 188 " =    1.434
peak=   -3.124 closest distance to " N   THR A 157 " =    1.408
peak=   -3.120 closest distance to " O   HOH Z 387 " =    2.006
peak=   -3.120 closest distance to " N   ALA A  43 " =    2.451
peak=   -3.103 closest distance to " O   HOH Z  20 " =    1.529
peak=   -3.098 closest distance to " OE1 GLU A   2 " =    1.801
peak=   -3.097 closest distance to " O   HIS A  81 " =    1.168
peak=   -3.097 closest distance to " CD  ARG A 269 " =    1.439
peak=   -3.094 closest distance to " CB  HIS A  86 " =    1.087
peak=   -3.081 closest distance to " O   HOH Z 144 " =    1.116
peak=   -3.075 closest distance to " OD1 ASN A  69 " =    0.876
peak=   -3.062 closest distance to " C   LEU A 222 " =    1.478
peak=   -3.050 closest distance to " C   ILE A 239 " =    2.100
peak=   -3.047 closest distance to " CB  PHE A  16 " =    2.318
peak=   -3.038 closest distance to " N   ALA A 248 " =    1.499
peak=   -3.027 closest distance to " OG  SER A 245 " =    1.628

================= 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    :  0.5150 0.5074   6.307599e+00   6.301225e+00
   1_bss:  0.5064 0.4963   6.301854e+00   6.293874e+00
   1_xyz:  0.4505 0.4707   6.245792e+00   6.266803e+00
   1_adp:  0.4102 0.4724   6.204356e+00   6.266153e+00
   1_occ:  0.4099 0.4726   6.203221e+00   6.266711e+00
   2_bss:  0.4078 0.4713   6.205005e+00   6.268372e+00
   2_xyz:  0.3384 0.4075   6.062106e+00   6.189944e+00
   2_adp:  0.3138 0.3837   6.007727e+00   6.141894e+00
   2_occ:  0.3134 0.3843   6.008393e+00   6.142028e+00
   3_bss:  0.3110 0.3822   6.006854e+00   6.140596e+00
   3_xyz:  0.2438 0.3110   5.813598e+00   5.993115e+00
   3_adp:  0.2219 0.2902   5.740967e+00   5.931537e+00
   3_occ:  0.2214 0.2894   5.738814e+00   5.929834e+00
   4_bss:  0.2208 0.2885   5.738445e+00   5.929444e+00
   4_xyz:  0.1679 0.2243   5.493773e+00   5.707658e+00
   4_adp:  0.1551 0.2135   5.427890e+00   5.653381e+00
   4_occ:  0.1547 0.2129   5.425838e+00   5.651271e+00
   5_bss:  0.1547 0.2128   5.425974e+00   5.651178e+00
   5_xyz:  0.1416 0.1959   5.352823e+00   5.582640e+00
   5_adp:  0.1346 0.1900   5.311514e+00   5.548499e+00
   5_occ:  0.1345 0.1900   5.311038e+00   5.548198e+00
   5_bss:  0.1344 0.1900   5.311188e+00   5.548599e+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:  0.372  20.000   6.725   8.184  10.920   0.000   0.000   0.000
   1_xyz:  0.372  20.000   6.725   8.184  10.920   0.000   0.000   0.000
   1_adp:  0.372  20.000   6.725   8.184  10.920   0.000   0.000   0.000
   1_occ:  0.372  20.000   6.725   8.184  10.920   0.000   0.000   0.000
   2_bss:  0.360  50.000   3.492   4.416   7.148   0.000   0.000   0.000
   2_xyz:  0.360  50.000   3.492   4.416   7.148   0.000   0.000   0.000
   2_adp:  0.360  50.000   3.492   4.416   7.148   0.000   0.000   0.000
   2_occ:  0.360  50.000   3.492   4.416   7.148   0.000   0.000   0.000
   3_bss:  0.342  50.000   1.143   1.953   4.355   0.000   0.000   0.000
   3_xyz:  0.342  50.000   1.143   1.953   4.355   0.000   0.000   0.000
   3_adp:  0.342  50.000   1.143   1.953   4.355   0.000   0.000   0.000
   3_occ:  0.342  50.000   1.143   1.953   4.355   0.000   0.000   0.000
   4_bss:  0.333  53.995  -0.146   0.671   2.902   0.000   0.000   0.000
   4_xyz:  0.333  53.995  -0.146   0.671   2.902   0.000   0.000   0.000
   4_adp:  0.333  53.995  -0.146   0.671   2.902   0.000   0.000   0.000
   4_occ:  0.333  53.995  -0.146   0.671   2.902   0.000   0.000   0.000
   5_bss:  0.313  48.925  -0.777  -0.084   2.090  -0.000   0.000   0.000
   5_xyz:  0.313  48.925  -0.777  -0.084   2.090  -0.000   0.000   0.000
   5_adp:  0.313  48.925  -0.777  -0.084   2.090  -0.000   0.000   0.000
   5_occ:  0.313  48.925  -0.777  -0.084   2.090  -0.000   0.000   0.000
   5_bss:  0.315  53.943  -1.174  -0.495   1.669   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  67.430 0.2964  0.3578    85712.120
   1_bss:  66.988 0.3014  0.4611    84064.944
   1_xyz:  58.009 0.4179  0.6373    70202.078
   1_adp:  56.832 0.4331  0.7434    70062.288
   1_occ:  56.818 0.4332  0.7417    70056.020
   2_bss:  56.746 0.4341  0.6589    70001.853
   2_xyz:  45.689 0.5728  0.8622    48225.381
   2_adp:  41.783 0.6207  0.9215    41407.121
   2_occ:  41.899 0.6193  0.9190    41551.495
   3_bss:  41.686 0.6216  0.8429    41092.067
   3_xyz:  32.504 0.7287  0.9600    25954.565
   3_adp:  29.237 0.7663  0.9820    22256.879
   3_occ:  29.162 0.7671  0.9821    22110.516
   4_bss:  29.108 0.7676  0.9360    22061.654
   4_xyz:  21.888 0.8429  0.9892    13041.205
   4_adp:  20.342 0.8584  0.9904    11739.875
   4_occ:  20.291 0.8589  0.9905    11673.657
   5_bss:  20.260 0.8592  0.9648    11656.204
   5_xyz:  18.429 0.8767  0.9733     9939.228
   5_adp:  17.607 0.8842  0.9674     9230.998
   5_occ:  17.595 0.8843  0.9675     9222.610
   5_bss:  17.601 0.8843  0.9721     9233.597
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3329e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3329e+01
   1_xyz:   1.761  0.014  0.106 18.433  0.006  4.103   1.5240e-01
   1_adp:   1.761  0.014  0.106 18.433  0.006  4.103   1.5240e-01
   1_occ:   1.761  0.014  0.106 18.433  0.006  4.103   1.5240e-01
   2_bss:   1.761  0.014  0.106 18.433  0.006  4.103   1.5240e-01
   2_xyz:   1.424  0.011  0.091 17.030  0.006  4.103   1.3153e-01
   2_adp:   1.424  0.011  0.091 17.030  0.006  4.103   1.3153e-01
   2_occ:   1.424  0.011  0.091 17.030  0.006  4.103   1.3153e-01
   3_bss:   1.424  0.011  0.091 17.030  0.006  4.103   1.3153e-01
   3_xyz:   1.173  0.008  0.083 16.125  0.005  4.121   8.2858e-02
   3_adp:   1.173  0.008  0.083 16.125  0.005  4.121   8.2858e-02
   3_occ:   1.173  0.008  0.083 16.125  0.005  4.121   8.2858e-02
   4_bss:   1.173  0.008  0.083 16.125  0.005  4.121   8.2858e-02
   4_xyz:   1.156  0.008  0.079 16.038  0.005  4.111   7.8661e-02
   4_adp:   1.156  0.008  0.079 16.038  0.005  4.111   7.8661e-02
   4_occ:   1.156  0.008  0.079 16.038  0.005  4.111   7.8661e-02
   5_bss:   1.156  0.008  0.079 16.038  0.005  4.111   7.8661e-02
   5_xyz:   0.946  0.006  0.068 15.438  0.004  4.120   5.7986e-02
   5_adp:   0.946  0.006  0.068 15.438  0.004  4.120   5.7986e-02
   5_occ:   0.946  0.006  0.068 15.438  0.004  4.120   5.7986e-02
   5_bss:   0.946  0.006  0.068 15.438  0.004  4.120   5.7986e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.099   6.9065e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.099   6.9065e+00
   1_xyz:  13.964  0.176  0.419 84.623  0.035  2.094   1.0075e-01
   1_adp:  13.964  0.176  0.419 84.623  0.035  2.094   1.0075e-01
   1_occ:  13.964  0.176  0.419 84.623  0.035  2.094   1.0075e-01
   2_bss:  13.964  0.176  0.419 84.623  0.035  2.094   1.0075e-01
   2_xyz:   8.532  0.134  0.328 83.789  0.040  1.987   2.0299e-01
   2_adp:   8.532  0.134  0.328 83.789  0.040  1.987   2.0299e-01
   2_occ:   8.532  0.134  0.328 83.789  0.040  1.987   2.0299e-01
   3_bss:   8.532  0.134  0.328 83.789  0.040  1.987   2.0299e-01
   3_xyz:   7.500  0.056  0.290 89.237  0.034  2.124   7.1501e-02
   3_adp:   7.500  0.056  0.290 89.237  0.034  2.124   7.1501e-02
   3_occ:   7.500  0.056  0.290 89.237  0.034  2.124   7.1501e-02
   4_bss:   7.500  0.056  0.290 89.237  0.034  2.124   7.1501e-02
   4_xyz:   8.950  0.047  0.285 86.937  0.040  2.103   6.1831e-02
   4_adp:   8.950  0.047  0.285 86.937  0.040  2.103   6.1831e-02
   4_occ:   8.950  0.047  0.285 86.937  0.040  2.103   6.1831e-02
   5_bss:   8.950  0.047  0.285 86.937  0.040  2.103   6.1831e-02
   5_xyz:   7.022  0.048  0.198 83.263  0.040  2.270   5.1732e-02
   5_adp:   7.022  0.048  0.198 83.263  0.040  2.270   5.1732e-02
   5_occ:   7.022  0.048  0.198 83.263  0.040  2.270   5.1732e-02
   5_bss:   7.022  0.048  0.198 83.263  0.040  2.270   5.1732e-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:  90.85   0.00  17.74  86.68   0.00  16.26  90.85   0.00  25.76
   1_occ:  90.85   0.00  17.74  86.68   0.00  16.26  90.85   0.00  25.76
   2_bss:  90.85   0.00  17.74  86.68   0.00  16.26  90.85   0.00  25.76
   2_xyz:  90.85   0.00  17.74  86.68   0.00  16.26  90.85   0.00  25.76
   2_adp:  97.13   0.00  16.12  65.21   0.00  13.43  97.13   0.00  30.78
   2_occ:  97.13   0.00  16.12  65.21   0.00  13.43  97.13   0.00  30.78
   3_bss:  97.13   0.00  16.12  65.21   0.00  13.43  97.13   0.00  30.78
   3_xyz:  97.13   0.00  16.12  65.21   0.00  13.43  97.13   0.00  30.78
   3_adp:  89.23   0.00  15.60  78.15   0.00  11.79  89.23   0.00  36.34
   3_occ:  89.23   0.00  15.60  78.15   0.00  11.79  89.23   0.00  36.34
   4_bss:  89.23   0.00  15.60  78.15   0.00  11.79  89.23   0.00  36.34
   4_xyz:  89.23   0.00  15.60  78.15   0.00  11.79  89.23   0.00  36.34
   4_adp:  90.02   0.00  15.35  90.02   0.00  11.17  89.07   2.22  38.09
   4_occ:  90.02   0.00  15.35  90.02   0.00  11.17  89.07   2.22  38.09
   5_bss:  90.02   0.00  15.35  90.02   0.00  11.17  89.07   2.22  38.09
   5_xyz:  90.02   0.00  15.35  90.02   0.00  11.17  89.07   2.22  38.09
   5_adp: 104.02   0.00  16.38 101.99   0.00  11.12 104.02   3.18  45.03
   5_occ: 104.02   0.00  16.38 101.99   0.00  11.12 104.02   3.18  45.03
   5_bss: 104.56   0.54  16.92 102.53   0.54  11.66 104.56   3.72  45.58
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.287    0.023    0.411
   1_adp:    1.287    0.023    0.411
   1_occ:    1.287    0.023    0.411
   2_bss:    1.287    0.023    0.411
   2_xyz:    1.845    0.015    0.618
   2_adp:    1.845    0.015    0.618
   2_occ:    1.845    0.015    0.618
   3_bss:    1.845    0.015    0.618
   3_xyz:    1.711    0.061    0.736
   3_adp:    1.711    0.061    0.736
   3_occ:    1.711    0.061    0.736
   4_bss:    1.711    0.061    0.736
   4_xyz:    1.805    0.060    0.843
   4_adp:    1.805    0.060    0.843
   4_occ:    1.805    0.060    0.843
   5_bss:    1.805    0.060    0.843
   5_xyz:    1.844    0.056    0.859
   5_adp:    1.844    0.056    0.859
   5_occ:    1.844    0.056    0.859
   5_bss:    1.844    0.056    0.859
------------------------------------------------------------------------

CPU time actual refinement: 342.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_153/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_153/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_153/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_153/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_153/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.65 
  Macro-tasks:
    bulk solvent and scale       = 42.89  
    individual site refinement   = 139.45 
    weights calculation          = 33.00  
    collect and process          = 6.44   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.89 
  Micro-tasks:
    mask                            = 2.24   
    f_calc                          = 109.04 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 112.47 
    fmodel                         = 7.45   
    r_factors                      = 0.28   
    phase_errors                   = 10.76  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 252.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.900 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    632 calls, 108.64 s
gradients_fft:          578 calls, 101.70 s

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

# Date 2008-01-16 Time 00:51:56 PST -0800 (1200473516.66 s)
Start R-work = 0.5150, R-free = 0.5074 (no bulk solvent and anisotropic scale)
Final R-work = 0.1514, R-free = 0.2049 (no bulk solvent and anisotropic scale)

Start R-work = 0.5064, R-free = 0.4963
Final R-work = 0.1344, R-free = 0.1900