# Date 2008-01-16 Time 01:03:47 PST -0800 (1200474227.54 s)
#phil __OFF__

Command line arguments: "../267.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28327
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 267

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.2261, 85.5261, 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: 3.32, 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: (69.1963, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.97009
Completeness in resolution range: 0.981314
Completeness with d_max=infinity: 0.978178

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7893
                             d_min =   1.9701

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.97009
Completeness in resolution range: 0.981314
Completeness with d_max=infinity: 0.978178

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7897 -  4.2147 [2096/2119]  1886   210  10.0%
  bin  2:  4.2147 -  3.3582 [2024/2044]  1822   202  10.0%
  bin  3:  3.3582 -  2.9375 [1989/2008]  1791   198  10.0%
  bin  4:  2.9375 -  2.6707 [1954/1984]  1758   196  10.0%
  bin  5:  2.6707 -  2.4802 [1970/1989]  1773   197  10.0%
  bin  6:  2.4802 -  2.3346 [1950/1975]  1753   197  10.1%
  bin  7:  2.3346 -  2.2181 [1929/1957]  1737   192  10.0%
  bin  8:  2.2181 -  2.1218 [1931/1967]  1737   194  10.0%
  bin  9:  2.1218 -  2.0403 [1922/1964]  1732   190   9.9%
  bin 10:  2.0403 -  1.9701 [1824/1955]  1641   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_267/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 14
        2.12 -     2.81: 861
        2.81 -     3.51: 4585
        3.51 -     4.20: 9517
        4.20 -     4.90: 13933
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.420 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.621 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.858 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.864 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28905 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_267/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_267/model_refine_001.geo

CPU time processing inputs: 9.35


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.22605 85.5261 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: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4794   r_free= 0.4696   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.277891                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.7005 0.99   1371  152 0.3966 0.4003      6.5787      6.6088|
|  2:  4.7005 -  3.7510 0.99   1299  146 0.4032 0.3806      6.7792      6.7506|
|  3:  3.7510 -  3.2828 0.99   1286  141 0.4391 0.4152      6.6812       6.724|
|  4:  3.2828 -  2.9853 0.99   1283  142 0.4549 0.4231      6.5348      6.4696|
|  5:  2.9853 -  2.7728 0.99   1258  141 0.5080 0.5125      6.3802       6.374|
|  6:  2.7728 -  2.6103 0.99   1268  141 0.5126 0.5552      6.2955      6.2694|
|  7:  2.6103 -  2.4802 0.99   1265  140 0.5033 0.4617      6.2514      6.1933|
|  8:  2.4802 -  2.3727 0.98   1248  137 0.5279 0.5139      6.2066      6.2136|
|  9:  2.3727 -  2.2817 0.98   1242  141 0.5164 0.5561      6.1219      6.1442|
| 10:  2.2817 -  2.2032 1.00   1242  139 0.5259 0.5215      6.1265      6.1165|
| 11:  2.2032 -  2.1345 0.97   1251  138 0.5183 0.4992      6.0409      6.0776|
| 12:  2.1345 -  2.0737 0.98   1239  138 0.5153 0.5225      6.0044      6.0555|
| 13:  2.0737 -  2.0192 0.99   1248  137 0.5496 0.4976      5.9157      5.8724|
| 14:  2.0192 -  1.9701 0.91   1130  126 0.5391 0.5016      5.8608       5.768|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.7005  1371   152  0.65  38.30   0.80     0.70      84701.10|
|  2:  4.7005 -  3.7510  1299   146  0.69  35.89   0.89     0.78     109774.36|
|  3:  3.7510 -  3.2828  1286   141  0.61  43.21   0.87     0.74     112470.16|
|  4:  3.2828 -  2.9853  1283   142  0.54  49.00   0.82     0.63      97895.29|
|  5:  2.9853 -  2.7728  1258   141  0.42  58.27   0.75     0.50      82388.25|
|  6:  2.7728 -  2.6103  1268   141  0.37  62.07   0.73     0.43      74859.03|
|  7:  2.6103 -  2.4802  1265   140  0.31  66.42   0.75     0.36      71490.30|
|  8:  2.4802 -  2.3727  1248   137  0.30  67.77   0.75     0.35      65229.41|
|  9:  2.3727 -  2.2817  1242   141  0.32  66.15   0.72     0.38      57675.78|
| 10:  2.2817 -  2.2032  1242   139  0.35  63.46   0.78     0.42      49474.06|
| 11:  2.2032 -  2.1345  1251   138  0.35  63.91   0.77     0.43      46433.87|
| 12:  2.1345 -  2.0737  1239   138  0.32  65.80   0.78     0.40      43916.70|
| 13:  2.0737 -  2.0192  1248   137  0.29  68.40   0.74     0.36      38732.44|
| 14:  2.0192 -  1.9701  1130   126  0.31  67.15   0.74     0.34      30580.13|
|alpha:            min =        0.34 max =            0.78 mean =         0.49|
|beta:             min =    30580.13 max =       112470.16 mean =     69644.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.96 mean =        57.96|
|phase err.(test): min =        0.00 max =           89.77 mean =        58.03|
|-----------------------------------------------------------------------------|

============================== 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 = 14.335325             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.205   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.490412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.568   (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 |  1.119 -  1.497:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.497 -  1.875:       13 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.875 -  2.253:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.253 -  2.631:      633 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.631 -  3.009:     1463 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.009 -  3.387:     2602 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.387 -  3.766:     4061 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.766 -  4.144:     5218 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.144 -  4.522:     6779 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.522 -  4.900:     7978 |
|-----------------------------------------------------------------------------|
|-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 |       52.891 |
| 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  1.119 |       2.359 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    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 = 11.425)------------------------------------------|
|    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: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4846   r_free= 0.4739   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.279661                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4698   r_free= 0.4592   ksol= 0.38   Bsol= 6.19   scale= 1.008    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,9.80,7.94,0.00,0.00,0.00); trace/3= 8.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.269568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.961270             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.391   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.358016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.503   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4698      final r-factor (work) = 0.3913          |
| start r-factor (free) = 0.4592      final r-factor (free) = 0.4114          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.4423 = 11.96 * 0.50 * 6.2787 + 1.00 * 52.8914                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.1692 = 11.96 * 0.50 * 6.1917 + 1.00 * 0.1391                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3913      final r-factor (work) = 0.3457          |
| start r-factor (free) = 0.4114      final r-factor (free) = 0.3902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4227 = 1.36 * 1.00 * 6.1917 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3038 = 1.36 * 1.00 * 6.1003 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.29   13.18    None  None   None       |
|    all(noH): 2823   0      0.00    75.29   13.18    None  None   None       |
|    Sol.    : 438    0      0.00    67.16   25.53    None  None   None       |
|    Mac.    : 2385   0      0.00    75.29   10.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.529: 1071   |   5:    37.645 -  45.174:   68        |
|      1:     7.529 -  15.058:  794   |   6:    45.174 -  52.703:   40        |
|      2:    15.058 -  22.587:  465   |   7:    52.703 -  60.232:    7        |
|      3:    22.587 -  30.116:  244   |   8:    60.232 -  67.760:    8        |
|      4:    30.116 -  37.645:  125   |   9:    67.760 -  75.289:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3457 r_free = 0.3902             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3449 r_free = 0.3900             target_work(ml) = 6.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3449   r_free= 0.3900   ksol= 0.38   Bsol= 6.19   scale= 1.115    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,9.80,7.94,0.00,0.00,0.00); trace/3= 8.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.078367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3414   r_free= 0.3851   ksol= 0.35   Bsol= 27.82   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,5.31,4.79,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.076831                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.681699              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.014   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.515174              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.423  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3414      final r-factor (work) = 0.2513          |
| start r-factor (free) = 0.3851      final r-factor (free) = 0.3066          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4991 = 6.68 * 0.50 * 6.0942 + 1.00 * 0.1391                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.9609 = 6.68 * 0.50 * 5.9492 + 1.00 * 0.0856                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2513      final r-factor (work) = 0.2245          |
| start r-factor (free) = 0.3066      final r-factor (free) = 0.2784          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1131 = 0.52 * 1.00 * 5.9492 + 1.00 * 0.0482                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0577 = 0.52 * 1.00 * 5.7796 + 1.00 * 0.0802                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.09   12.80    None  None   None       |
|    all(noH): 2823   0      0.00    85.09   12.80    None  None   None       |
|    Sol.    : 438    0      1.18    79.29   31.88    None  None   None       |
|    Mac.    : 2385   0      0.00    85.09   9.29     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.509: 1441   |   5:    42.546 -  51.055:   72        |
|      1:     8.509 -  17.018:  729   |   6:    51.055 -  59.564:   30        |
|      2:    17.018 -  25.528:  238   |   7:    59.564 -  68.074:   12        |
|      3:    25.528 -  34.037:  166   |   8:    68.074 -  76.583:    1        |
|      4:    34.037 -  42.546:  132   |   9:    76.583 -  85.092:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2245 r_free = 0.2784             target_work(ml) = 5.737         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2239 r_free = 0.2782             target_work(ml) = 5.736         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2239   r_free= 0.2782   ksol= 0.35   Bsol= 27.82   scale= 1.060   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.90,5.31,4.79,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.736191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2226   r_free= 0.2777   ksol= 0.33   Bsol= 27.82   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.21,3.58,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.733794                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.523994              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.484   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.894538              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.119   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2226      final r-factor (work) = 0.1563          |
| start r-factor (free) = 0.2777      final r-factor (free) = 0.2038          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1620 = 4.52 * 0.50 * 5.7812 + 1.00 * 0.0850                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7190 = 4.52 * 0.50 * 5.5927 + 1.00 * 0.0684                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1563      final r-factor (work) = 0.1389          |
| start r-factor (free) = 0.2038      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.2179 = 2.89 * 1.00 * 5.5927 + 1.00 * 0.0296                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.5158 = 2.89 * 1.00 * 5.3553 + 1.00 * 0.0146                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.52   13.69    None  None   None       |
|    all(noH): 2823   0      0.00    96.52   13.69    None  None   None       |
|    Sol.    : 438    0      0.00    92.80   39.18    None  None   None       |
|    Mac.    : 2385   0      0.00    96.52   9.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.652: 1726   |   5:    48.259 -  57.910:   96        |
|      1:     9.652 -  19.304:  518   |   6:    57.910 -  67.562:   54        |
|      2:    19.304 -  28.955:  184   |   7:    67.562 -  77.214:   28        |
|      3:    28.955 -  38.607:  105   |   8:    77.214 -  86.866:    2        |
|      4:    38.607 -  48.259:  108   |   9:    86.866 -  96.517:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1389 r_free = 0.1919             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1388 r_free = 0.1917             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1388   r_free= 0.1917   ksol= 0.33   Bsol= 27.82   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.21,3.58,0.00,0.00,0.00); trace/3= 3.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324132                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1387   r_free= 0.1915   ksol= 0.31   Bsol= 32.31   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,2.26,3.16,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321234                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.543590              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.199  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.356673              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.645  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1915      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8843 = 2.54 * 0.50 * 5.3593 + 1.00 * 0.0684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7609 = 2.54 * 0.50 * 5.2697 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8940 = 0.36 * 1.00 * 5.2697 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8690 = 0.36 * 1.00 * 5.2073 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.62   13.25    None  None   None       |
|    all(noH): 2823   0      0.00    96.62   13.25    None  None   None       |
|    Sol.    : 438    0      1.05    91.77   38.05    None  None   None       |
|    Mac.    : 2385   0      0.00    96.62   8.70     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 -   9.662: 1777   |   5:    48.311 -  57.973:   78        |
|      1:     9.662 -  19.324:  517   |   6:    57.973 -  67.635:   53        |
|      2:    19.324 -  28.987:  143   |   7:    67.635 -  77.297:   21        |
|      3:    28.987 -  38.649:  121   |   8:    77.297 -  86.959:    3        |
|      4:    38.649 -  48.311:  108   |   9:    86.959 -  96.622:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1648             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1647             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1647   ksol= 0.31   Bsol= 32.31   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,2.26,3.16,0.00,0.00,0.00); trace/3= 2.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182967                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1646   ksol= 0.32   Bsol= 37.02   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,2.05,3.12,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182650                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.363795              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.603  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.342064              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.341  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2129 = 2.36 * 0.50 * 5.2069 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1613 = 2.36 * 0.50 * 5.1617 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9390 = 1.34 * 1.00 * 5.1617 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9070 = 1.34 * 1.00 * 5.1372 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.65  13.09    None  None   None       |
|    all(noH): 2823   0      0.00    100.65  13.09    None  None   None       |
|    Sol.    : 438    0      1.86    93.15   37.66    None  None   None       |
|    Mac.    : 2385   0      0.00    100.65  8.58     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 -  10.065: 1830   |   5:    50.324 -  60.389:   76        |
|      1:    10.065 -  20.130:  490   |   6:    60.389 -  70.454:   33        |
|      2:    20.130 -  30.194:  135   |   7:    70.454 -  80.519:   18        |
|      3:    30.194 -  40.259:  126   |   8:    80.519 -  90.583:    1        |
|      4:    40.259 -  50.324:  110   |   9:    90.583 - 100.648:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1590             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1589             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1589   ksol= 0.32   Bsol= 37.02   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,2.05,3.12,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138382                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.7005 0.99   1371  152 0.1011 0.1241      5.3952       5.511|
|  2:  4.7005 -  3.7510 0.99   1299  146 0.0854 0.1164      5.4387      5.6454|
|  3:  3.7510 -  3.2828 0.99   1286  141 0.1076 0.1472      5.4931      5.8297|
|  4:  3.2828 -  2.9853 0.99   1283  142 0.1231 0.1688       5.464       5.657|
|  5:  2.9853 -  2.7728 0.99   1258  141 0.1278 0.1785      5.3215      5.5201|
|  6:  2.7728 -  2.6103 0.99   1268  141 0.1201 0.1750      5.2079      5.4534|
|  7:  2.6103 -  2.4802 0.99   1265  140 0.1238 0.1590      5.1607       5.368|
|  8:  2.4802 -  2.3727 0.98   1248  137 0.1158 0.1748      5.0799      5.3772|
|  9:  2.3727 -  2.2817 0.98   1242  141 0.1153 0.1628      5.0255      5.2321|
| 10:  2.2817 -  2.2032 1.00   1242  139 0.1101 0.1811       4.961      5.2556|
| 11:  2.2032 -  2.1345 0.97   1251  138 0.1119 0.1772      4.9475      5.2712|
| 12:  2.1345 -  2.0737 0.98   1239  138 0.1130 0.1717      4.8986      5.2469|
| 13:  2.0737 -  2.0192 0.99   1248  137 0.1111 0.1726      4.8028      5.0691|
| 14:  2.0192 -  1.9701 0.91   1130  126 0.0960 0.1731      4.6298       4.941|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.7005  1371   152  0.94   9.05   0.99     0.96       7043.21|
|  2:  4.7005 -  3.7510  1299   146  0.95   7.73   1.03     1.02       8957.30|
|  3:  3.7510 -  3.2828  1286   141  0.93  11.43   1.05     1.04      10607.07|
|  4:  3.2828 -  2.9853  1283   142  0.92  13.44   1.02     1.02      10303.89|
|  5:  2.9853 -  2.7728  1258   141  0.90  15.67   1.01     0.98       8325.30|
|  6:  2.7728 -  2.6103  1268   141  0.90  15.59   0.99     0.96       6928.58|
|  7:  2.6103 -  2.4802  1265   140  0.90  15.89   0.99     0.97       6218.42|
|  8:  2.4802 -  2.3727  1248   137  0.91  14.61   1.01     0.99       5247.08|
|  9:  2.3727 -  2.2817  1242   141  0.91  15.15   1.01     0.99       4976.39|
| 10:  2.2817 -  2.2032  1242   139  0.91  15.24   1.01     0.97       4363.19|
| 11:  2.2032 -  2.1345  1251   138  0.90  16.39   1.01     0.98       4608.18|
| 12:  2.1345 -  2.0737  1239   138  0.90  15.93   1.03     1.02       4144.33|
| 13:  2.0737 -  2.0192  1248   137  0.91  15.35   1.02     1.01       3384.23|
| 14:  2.0192 -  1.9701  1130   126  0.92  13.96   1.00     0.98       2455.41|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2455.41 max =        10607.07 mean =      6314.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.90|
|phase err.(test): min =        0.00 max =           89.05 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1594   ksol= 0.32   Bsol= 39.31   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.28,0.85,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138678                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1594   ksol= 0.32   Bsol= 39.31   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-0.28,0.85,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138678                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.7005 0.99   1371  152 0.1003 0.1273      5.3942      5.5267|
|  2:  4.7005 -  3.7510 0.99   1299  146 0.0866 0.1166      5.4507      5.6406|
|  3:  3.7510 -  3.2828 0.99   1286  141 0.1085 0.1463      5.4965      5.8237|
|  4:  3.2828 -  2.9853 0.99   1283  142 0.1236 0.1691      5.4632      5.6606|
|  5:  2.9853 -  2.7728 0.99   1258  141 0.1277 0.1771      5.3203      5.5136|
|  6:  2.7728 -  2.6103 0.99   1268  141 0.1197 0.1750      5.2057      5.4529|
|  7:  2.6103 -  2.4802 0.99   1265  140 0.1237 0.1602      5.1601      5.3698|
|  8:  2.4802 -  2.3727 0.98   1248  137 0.1159 0.1740      5.0785      5.3725|
|  9:  2.3727 -  2.2817 0.98   1242  141 0.1151 0.1635      5.0242      5.2352|
| 10:  2.2817 -  2.2032 1.00   1242  139 0.1100 0.1807      4.9604      5.2542|
| 11:  2.2032 -  2.1345 0.97   1251  138 0.1115 0.1769      4.9471      5.2711|
| 12:  2.1345 -  2.0737 0.98   1239  138 0.1126 0.1716      4.8975      5.2476|
| 13:  2.0737 -  2.0192 0.99   1248  137 0.1109 0.1726      4.8025       5.068|
| 14:  2.0192 -  1.9701 0.91   1130  126 0.0960 0.1727      4.6291      4.9401|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.7005  1371   152  0.94   9.18   0.98     0.96       7303.86|
|  2:  4.7005 -  3.7510  1299   146  0.95   7.88   1.03     1.02       9092.71|
|  3:  3.7510 -  3.2828  1286   141  0.93  11.40   1.05     1.04      10572.70|
|  4:  3.2828 -  2.9853  1283   142  0.92  13.41   1.02     1.02      10213.16|
|  5:  2.9853 -  2.7728  1258   141  0.90  15.66   1.01     0.98       8296.34|
|  6:  2.7728 -  2.6103  1268   141  0.90  15.56   0.99     0.96       6903.01|
|  7:  2.6103 -  2.4802  1265   140  0.90  15.86   1.00     0.97       6218.79|
|  8:  2.4802 -  2.3727  1248   137  0.91  14.61   1.01     0.99       5240.30|
|  9:  2.3727 -  2.2817  1242   141  0.91  15.13   1.01     0.99       4967.56|
| 10:  2.2817 -  2.2032  1242   139  0.91  15.24   1.01     0.97       4359.08|
| 11:  2.2032 -  2.1345  1251   138  0.90  16.39   1.01     0.98       4610.27|
| 12:  2.1345 -  2.0737  1239   138  0.90  15.93   1.03     1.02       4146.80|
| 13:  2.0737 -  2.0192  1248   137  0.91  15.35   1.02     1.01       3383.55|
| 14:  2.0192 -  1.9701  1130   126  0.92  13.95   1.00     0.98       2451.99|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2451.99 max =        10572.70 mean =      6330.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.91|
|phase err.(test): min =        0.00 max =           89.27 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.29    102.94  15.38    None  None   None       |
|    all(noH): 2823   0      2.29    102.94  15.38    None  None   None       |
|    Sol.    : 438    0      4.15    95.44   39.95    None  None   None       |
|    Mac.    : 2385   0      2.29    102.94  10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.290 -  12.355: 1830   |   5:    52.614 -  62.679:   76        |
|      1:    12.355 -  22.420:  490   |   6:    62.679 -  72.744:   33        |
|      2:    22.420 -  32.485:  135   |   7:    72.744 -  82.809:   18        |
|      3:    32.485 -  42.549:  126   |   8:    82.809 -  92.873:    1        |
|      4:    42.549 -  52.614:  110   |   9:    92.873 - 102.938:    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)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.385 - 5.569
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 297
   mapped sites are within: 0.763 - 5.569

peak=   11.057 closest distance to " CB  VAL A 296 " =    1.545
peak=   10.779 closest distance to " CB  VAL A 230 " =    1.418
peak=    7.429 closest distance to " O   HOH Z 130 " =    1.395
peak=    6.202 closest distance to " NE2 GLN A  11 " =    1.184
peak=    6.065 closest distance to " O   HOH Z 124 " =    1.612
peak=    6.052 closest distance to " CD2 LEU A   5 " =    1.198
peak=    6.001 closest distance to " O   HOH Z 142 " =    1.990
peak=    5.805 closest distance to " CG  LEU A   5 " =    1.171
peak=    5.759 closest distance to " NH2 ARG A  56 " =    2.052
peak=    5.543 closest distance to " O   HOH Z 193 " =    1.676
peak=    5.450 closest distance to " O   HOH Z   9 " =    1.487
peak=    5.413 closest distance to " O   HOH Z 236 " =    1.453
peak=    5.403 closest distance to " CG  PRO A  54 " =    1.268
peak=    5.138 closest distance to " CG  LEU A 228 " =    1.171
peak=    5.096 closest distance to " O   HOH Z 209 " =    2.277
peak=    5.037 closest distance to " O   HOH Z  65 " =    0.956
peak=    4.887 closest distance to " O   HOH Z 427 " =    2.514
peak=    4.871 closest distance to " CB  GLN A 183 " =    1.248
peak=    4.864 closest distance to " CB  ARG A 275 " =    0.939
peak=    4.861 closest distance to " O   HOH Z 232 " =    2.405
peak=    4.804 closest distance to " CB  VAL A 230 " =    1.138
peak=    4.746 closest distance to " O   HOH Z 126 " =    1.747
peak=    4.697 closest distance to " O   SER A  87 " =    2.269
peak=    4.689 closest distance to " CB  PRO A  54 " =    1.013
peak=    4.679 closest distance to " CG  PRO A 213 " =    1.220
peak=    4.622 closest distance to " CB  SER A   3 " =    1.318
peak=    4.620 closest distance to " CB  GLN A 223 " =    1.601
peak=    4.618 closest distance to " O   HOH Z 380 " =    1.780
peak=    4.595 closest distance to " O   HOH Z   7 " =    1.427
peak=    4.562 closest distance to " O   HOH Z  78 " =    1.625
peak=    4.552 closest distance to " O   HOH Z 423 " =    1.442
peak=    4.537 closest distance to " O   HOH Z  85 " =    1.342
peak=    4.468 closest distance to " O   HOH Z 263 " =    1.627
peak=    4.462 closest distance to " O   HOH Z 424 " =    1.159
peak=    4.453 closest distance to " O   HOH Z 272 " =    1.837
peak=    4.391 closest distance to " O   HOH Z 369 " =    2.241
peak=    4.373 closest distance to " O   HOH Z 403 " =    1.850
peak=    4.370 closest distance to " O   HOH Z 346 " =    1.606
peak=    4.332 closest distance to " O   HOH Z  68 " =    2.154
peak=    4.322 closest distance to " CB BVAL A  41 " =    1.221
peak=    4.318 closest distance to " CB  SER A  63 " =    1.189
peak=    4.248 closest distance to " C   PRO A 198 " =    1.455
peak=    4.183 closest distance to " O   HOH Z 316 " =    2.896
peak=    4.123 closest distance to " O   HOH Z  59 " =    1.640
peak=    4.120 closest distance to " CG  PRO A 198 " =    1.215
peak=    4.119 closest distance to " NZ  LYS A 117 " =    3.067
peak=    4.116 closest distance to " O   HOH Z 371 " =    2.844
peak=    4.102 closest distance to " O   HOH Z 203 " =    1.506
peak=    4.086 closest distance to " O   HOH Z 112 " =    1.171
peak=    4.073 closest distance to " O   HOH Z 130 " =    2.207
peak=    4.068 closest distance to " O   HOH Z 425 " =    1.407
peak=    4.062 closest distance to " CB  VAL A 202 " =    1.690
peak=    4.045 closest distance to " ND2 ASN A 187 " =    1.631
peak=    4.019 closest distance to " CA  TYR A  30 " =    1.025
peak=    4.015 closest distance to " CB  GLU A 152 " =    1.206
peak=    4.013 closest distance to " O   HOH Z  78 " =    1.869
peak=    4.008 closest distance to " O   HOH Z 366 " =    2.721
peak=    4.007 closest distance to " CB  ARG A  79 " =    1.417
peak=    4.007 closest distance to " CG  PRO A 243 " =    1.157
peak=    4.006 closest distance to " CB  ASN A 148 " =    1.308
peak=    3.991 closest distance to " O   HOH Z  44 " =    1.811
peak=    3.988 closest distance to " O   HOH Z 234 " =    3.426
peak=    3.986 closest distance to " OG BSER A 164 " =    2.114
peak=    3.983 closest distance to " O   HOH Z  93 " =    2.360
peak=    3.973 closest distance to " CA  PHE A 283 " =    1.332
peak=    3.944 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.933 closest distance to " CG  GLN A  11 " =    2.153
peak=    3.932 closest distance to " CD1AILE A 234 " =    0.923
peak=    3.926 closest distance to " CG1BVAL A  72 " =    1.291
peak=    3.922 closest distance to " O   HOH Z  61 " =    1.556
peak=    3.910 closest distance to " O   HOH Z 298 " =    1.728
peak=    3.906 closest distance to " O   HOH Z   2 " =    1.753
peak=    3.899 closest distance to " O   HOH Z 143 " =    1.170
peak=    3.894 closest distance to " O   HOH Z 422 " =    2.394
peak=    3.894 closest distance to " N   PHE A 130 " =    1.309
peak=    3.892 closest distance to " CG2 VAL A 257 " =    0.808
peak=    3.887 closest distance to " O   HOH Z 250 " =    1.376
peak=    3.885 closest distance to " O   HOH Z 423 " =    1.804
peak=    3.883 closest distance to " O   HOH Z 123 " =    1.183
peak=    3.877 closest distance to " O   HOH Z 405 " =    1.286
peak=    3.873 closest distance to " O   HOH Z 368 " =    2.195
peak=    3.869 closest distance to " O   HOH Z  61 " =    1.613
peak=    3.862 closest distance to " O   HOH Z  30 " =    1.408
peak=    3.841 closest distance to " O   HOH Z 411 " =    3.624
peak=    3.838 closest distance to " O   HOH Z 419 " =    2.049
peak=    3.830 closest distance to " CD2 LEU A 228 " =    1.210
peak=    3.829 closest distance to " O   HOH Z   9 " =    1.804
peak=    3.828 closest distance to " CB  SER A 216 " =    0.772
peak=    3.818 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.814 closest distance to " O   HOH Z 352 " =    1.377
peak=    3.814 closest distance to " O   HOH Z 189 " =    2.665
peak=    3.808 closest distance to " CB  ARG A 139 " =    1.030
peak=    3.808 closest distance to " O   HOH Z 144 " =    2.251
peak=    3.806 closest distance to " O   HOH Z  39 " =    1.256
peak=    3.794 closest distance to " O   HOH Z 357 " =    1.857
peak=    3.789 closest distance to " O   HOH Z 272 " =    2.097
peak=    3.784 closest distance to " CG AARG A 275 " =    1.015
peak=    3.782 closest distance to " CD  GLN A 194 " =    1.345
peak=    3.758 closest distance to " O   HOH Z 117 " =    2.002
peak=    3.744 closest distance to " NH2AARG A 190 " =    1.779
peak=    3.742 closest distance to " O   HOH Z  43 " =    1.864
peak=    3.731 closest distance to " O   HOH Z 196 " =    1.592
peak=    3.730 closest distance to " O   HOH Z 227 " =    1.934
peak=    3.728 closest distance to " O   HOH Z 108 " =    2.187
peak=    3.726 closest distance to " CB  TRP A 179 " =    1.259
peak=    3.724 closest distance to " O   HOH Z 118 " =    1.869
peak=    3.687 closest distance to " OD1 ASN A  69 " =    2.583
peak=    3.678 closest distance to " O   HOH Z 222 " =    2.362
peak=    3.651 closest distance to " CB  SER A  26 " =    1.656
peak=    3.647 closest distance to " O   HOH Z 287 " =    1.602
peak=    3.645 closest distance to " CB  TYR A 169 " =    0.763
peak=    3.636 closest distance to " CA  ASN A 215 " =    1.063
peak=    3.613 closest distance to " O   HOH Z 389 " =    1.273
peak=    3.613 closest distance to " O   HOH Z 290 " =    0.995
peak=    3.608 closest distance to " O   HOH Z 126 " =    1.494
peak=    3.603 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.603 closest distance to " O   HOH Z 145 " =    1.378
peak=    3.598 closest distance to " O   HOH Z  89 " =    2.196
peak=    3.596 closest distance to " CB  GLU A 277 " =    3.437
peak=    3.577 closest distance to " CG  TRP A 179 " =    2.283
peak=    3.577 closest distance to " CB  GLN A  88 " =    1.309
peak=    3.576 closest distance to " O   HOH Z 402 " =    1.393
peak=    3.566 closest distance to " OG  SER A  62 " =    2.912
peak=    3.561 closest distance to " O   HOH Z 303 " =    1.692
peak=    3.552 closest distance to " CG AARG A 275 " =    1.275
peak=    3.551 closest distance to " C   ALA A 299 " =    1.020
peak=    3.539 closest distance to " O   HOH Z 371 " =    1.633
peak=    3.537 closest distance to " CB  TRP A 266 " =    1.105
peak=    3.531 closest distance to " O   HOH Z  43 " =    2.711
peak=    3.529 closest distance to " O   HOH Z 345 " =    3.093
peak=    3.527 closest distance to " O   HOH Z 130 " =    1.797
peak=    3.521 closest distance to " CB  ASN A 148 " =    1.892
peak=    3.519 closest distance to " O   HOH Z 194 " =    2.008
peak=    3.511 closest distance to " O   HOH Z 368 " =    3.582
peak=    3.511 closest distance to " O   HOH Z 146 " =    1.624
peak=    3.504 closest distance to " CE1 TYR A 186 " =    1.325
peak=    3.496 closest distance to " NH1AARG A 145 " =    1.102
peak=    3.492 closest distance to " O   HOH Z 374 " =    2.398
peak=    3.492 closest distance to " CB  GLU A 128 " =    1.064
peak=    3.489 closest distance to " O   HOH Z 344 " =    2.814
peak=    3.489 closest distance to " O   HOH Z 383 " =    1.869
peak=    3.488 closest distance to " OE1 GLU A   2 " =    2.132
peak=    3.482 closest distance to " NH1BARG A 145 " =    1.422
peak=    3.477 closest distance to " CG  LEU A 167 " =    1.148
peak=    3.472 closest distance to " CA  LYS A 290 " =    1.264
peak=    3.470 closest distance to " NH1 ARG A  14 " =    1.120
peak=    3.465 closest distance to " CB  LEU A 255 " =    0.769
peak=    3.465 closest distance to " CB  ALA A 248 " =    1.361
peak=    3.463 closest distance to " O   HOH Z 193 " =    1.930
peak=    3.461 closest distance to " O   HOH Z 141 " =    1.584
peak=    3.461 closest distance to " NE2 GLN A  58 " =    3.525
peak=    3.455 closest distance to " O   HOH Z 248 " =    1.671
peak=    3.453 closest distance to " CB  THR A 157 " =    1.032
peak=    3.450 closest distance to " CB  TYR A  30 " =    1.675
peak=    3.434 closest distance to " CE AMET A  47 " =    1.360
peak=    3.433 closest distance to " CD ALYS A 290 " =    1.169
peak=    3.430 closest distance to " CA  ASN A 127 " =    1.039
peak=    3.426 closest distance to " N   ASN A  39 " =    1.166
peak=    3.425 closest distance to " O   HOH Z 145 " =    1.950
peak=    3.422 closest distance to " N   ARG A 156 " =    1.278
peak=    3.417 closest distance to " CE  LYS A  76 " =    0.934
peak=    3.411 closest distance to " O   HOH Z 278 " =    0.838
peak=    3.410 closest distance to " ND2 ASN A 110 " =    1.665
peak=    3.408 closest distance to " O   HOH Z  63 " =    1.290
peak=    3.405 closest distance to " CG2 THR A 221 " =    1.329
peak=    3.404 closest distance to " CD2 TRP A 179 " =    1.412
peak=    3.401 closest distance to " CG  GLN A  88 " =    1.132
peak=    3.398 closest distance to " O   HOH Z 392 " =    3.049
peak=    3.392 closest distance to " O  BHOH Z 338 " =    2.468
peak=    3.391 closest distance to " O   HOH Z 432 " =    1.612
peak=    3.387 closest distance to " O   HOH Z 284 " =    2.776
peak=    3.384 closest distance to " CA  ALA A  51 " =    1.004
peak=    3.382 closest distance to " CB  ASN A 142 " =    1.066
peak=    3.381 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.381 closest distance to " O   HOH Z 407 " =    2.244
peak=    3.379 closest distance to " O   HOH Z 359 " =    1.119
peak=    3.378 closest distance to " CD2 LEU A 297 " =    1.013
peak=    3.378 closest distance to " CG1 ILE A  33 " =    1.257
peak=    3.374 closest distance to " O   HOH Z 344 " =    1.165
peak=    3.373 closest distance to " O   HOH Z 257 " =    2.279
peak=    3.371 closest distance to " CB  ARG A 138 " =    0.805
peak=    3.370 closest distance to " O   HOH Z 334 " =    1.493
peak=    3.369 closest distance to " OH  TYR A 116 " =    1.117
peak=    3.367 closest distance to " CD1 ILE A  33 " =    1.614
peak=    3.367 closest distance to " O   HOH Z  10 " =    1.755
peak=    3.364 closest distance to " O   HOH Z 148 " =    1.544
peak=    3.361 closest distance to " O   HOH Z 118 " =    1.512
peak=    3.360 closest distance to " O   HOH Z  80 " =    2.269
peak=    3.359 closest distance to " CG BARG A 102 " =    1.851
peak=    3.355 closest distance to " CD  ARG A 269 " =    1.070
peak=    3.346 closest distance to " CB  ASN A  39 " =    0.900
peak=    3.345 closest distance to " CB  ALA A   1 " =    1.059
peak=    3.344 closest distance to " O   HOH Z 329 " =    3.744
peak=    3.343 closest distance to " O   HOH Z  88 " =    2.481
peak=    3.341 closest distance to " CG2 ILE A  20 " =    1.646
peak=    3.340 closest distance to " O   HOH Z 435 " =    2.001
peak=    3.337 closest distance to " OD2 ASP A 286 " =    2.628
peak=    3.335 closest distance to " CA  ALA A  21 " =    1.199
peak=    3.328 closest distance to " NH2BARG A 190 " =    1.502
peak=    3.327 closest distance to " CB  ASN A 215 " =    1.043
peak=    3.326 closest distance to " O   HOH Z  47 " =    1.779
peak=    3.325 closest distance to " CB  SER A 276 " =    1.118
peak=    3.323 closest distance to " NH2BARG A 145 " =    1.994
peak=    3.320 closest distance to " CB  THR A  31 " =    1.686
peak=    3.319 closest distance to " O   HOH Z 251 " =    1.660
peak=    3.317 closest distance to " O   HOH Z 128 " =    1.980
peak=    3.315 closest distance to " O   HOH Z 116 " =    2.769
peak=    3.314 closest distance to " O   HOH Z 128 " =    2.589
peak=    3.313 closest distance to " CB  HIS A 108 " =    0.848
peak=    3.312 closest distance to " O   HOH Z 417 " =    1.895
peak=    3.305 closest distance to " CA  SER A 146 " =    1.876
peak=    3.304 closest distance to " O   HOH Z 255 " =    1.727
peak=    3.302 closest distance to " O   HOH Z 427 " =    1.403
peak=    3.299 closest distance to " CG  LYS A 119 " =    1.151
peak=    3.299 closest distance to " CG  MET A 185 " =    1.197
peak=    3.297 closest distance to " O   HOH Z 261 " =    1.560
peak=    3.295 closest distance to " O   HOH Z 234 " =    2.083
peak=    3.293 closest distance to " OG ASER A 134 " =    1.640
peak=    3.278 closest distance to " O   HOH Z 368 " =    2.515
peak=    3.276 closest distance to " CB  PRO A  90 " =    1.196
peak=    3.274 closest distance to " OE2 GLU A  53 " =    2.024
peak=    3.274 closest distance to " O   HOH Z 273 " =    2.857
peak=    3.272 closest distance to " CD  PRO A 243 " =    1.504
peak=    3.271 closest distance to " OG1 THR A 294 " =    2.360
peak=    3.269 closest distance to " O   HOH Z 424 " =    2.336
peak=    3.269 closest distance to " CB  SER A  62 " =    1.232
peak=    3.266 closest distance to " CG  LYS A  76 " =    1.758
peak=    3.266 closest distance to " NE  ARG A  56 " =    3.413
peak=    3.258 closest distance to " O   HOH Z  58 " =    1.637
peak=    3.254 closest distance to " N   TYR A  15 " =    1.061
peak=    3.252 closest distance to " O   HOH Z  59 " =    1.912
peak=    3.251 closest distance to " CB  SER A 273 " =    0.778
peak=    3.243 closest distance to " O   HOH Z   6 " =    1.924
peak=    3.243 closest distance to " CA  VAL A 126 " =    1.042
peak=    3.238 closest distance to " O   HOH Z  55 " =    2.093
peak=    3.237 closest distance to " CB  PHE A 204 " =    0.958
peak=    3.234 closest distance to " O   HOH Z 158 " =    3.059
peak=    3.230 closest distance to " O   HOH Z 353 " =    2.468
peak=    3.229 closest distance to " O   HOH Z 366 " =    2.174
peak=    3.228 closest distance to " O   HOH Z 109 " =    2.396
peak=    3.226 closest distance to " CA  ALA A 158 " =    1.268
peak=    3.223 closest distance to " CB  THR A  52 " =    1.119
peak=    3.223 closest distance to " CB  ARG A 190 " =    1.704
peak=    3.222 closest distance to " O   HOH Z 106 " =    2.569
peak=    3.221 closest distance to " O   HOH Z  95 " =    1.467
peak=    3.218 closest distance to " O   HOH Z  71 " =    1.165
peak=    3.216 closest distance to " O   HOH Z 132 " =    1.131
peak=    3.216 closest distance to " O   HOH Z 132 " =    2.183
peak=    3.214 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.214 closest distance to " O   HOH Z   1 " =    4.497
peak=    3.213 closest distance to " O   HOH Z   1 " =    1.750
peak=    3.213 closest distance to " O   HOH Z 406 " =    1.517
peak=    3.211 closest distance to " O   HOH Z 305 " =    3.292
peak=    3.210 closest distance to " CD2 HIS A  81 " =    1.056
peak=    3.205 closest distance to " CA  LEU A 101 " =    1.418
peak=    3.200 closest distance to " CG  GLN A  89 " =    1.423
peak=    3.197 closest distance to " O   HOH Z 365 " =    1.778
peak=    3.181 closest distance to " N   VAL A 257 " =    1.604
peak=    3.178 closest distance to " O   HOH Z 193 " =    1.869
peak=    3.175 closest distance to " O   HOH Z 435 " =    1.571
peak=    3.174 closest distance to " CB  ALA A 114 " =    1.547
peak=    3.171 closest distance to " O   HOH Z 213 " =    1.922
peak=    3.171 closest distance to " O   HOH Z  89 " =    1.685
peak=    3.167 closest distance to " O   HOH Z  48 " =    1.607
peak=    3.161 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.150 closest distance to " CA  GLN A 194 " =    1.175
peak=    3.149 closest distance to " O   HOH Z 110 " =    1.667
peak=    3.146 closest distance to " O   HOH Z 245 " =    1.336
peak=    3.146 closest distance to " CG  LEU A 281 " =    0.923
peak=    3.139 closest distance to " CD  LYS A 119 " =    1.645
peak=    3.137 closest distance to " CB  VAL A 268 " =    0.851
peak=    3.136 closest distance to " O   HOH Z 151 " =    1.530
peak=    3.134 closest distance to " OD1BASN A 224 " =    2.253
peak=    3.134 closest distance to " OE1 GLN A  58 " =    4.115
peak=    3.133 closest distance to " CG2 ILE A 120 " =    1.120
peak=    3.132 closest distance to " CB  LYS A 117 " =    1.192
peak=    3.126 closest distance to " CG1BVAL A 121 " =    0.940
peak=    3.125 closest distance to " CG1AVAL A 121 " =    0.818
peak=    3.123 closest distance to " O   HOH Z  48 " =    1.517
peak=    3.122 closest distance to " N   SER A 135 " =    1.342
peak=    3.121 closest distance to " O   HOH Z 326 " =    1.979
peak=    3.121 closest distance to " OE2 GLU A   2 " =    1.778
peak=    3.120 closest distance to " N   VAL A 126 " =    1.125
peak=    3.119 closest distance to " CA  MET A 105 " =    0.926
peak=    3.117 closest distance to " O   HOH Z 172 " =    5.569
peak=    3.116 closest distance to " CD1 LEU A   5 " =    1.780
peak=    3.107 closest distance to " CB  ASN A 110 " =    1.076
peak=    3.093 closest distance to " O   ASN A  74 " =    1.549
peak=    3.055 closest distance to " N   HIS A  86 " =    1.852
peak=    3.051 closest distance to " CD  LYS A 166 " =    1.368
peak=    3.048 closest distance to " O   HOH Z 213 " =    1.689
peak=    3.047 closest distance to " CB  GLN A 278 " =    0.923
peak=    3.046 closest distance to " O   HOH Z  51 " =    1.062
peak=    3.015 closest distance to " O   HOH Z 188 " =    2.546

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.787 - 5.966
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.787 - 5.966

peak=   -5.021 closest distance to " CD  ARG A 156 " =    2.000
peak=   -4.484 closest distance to " SG  CYS A 254 " =    3.232
peak=   -4.476 closest distance to " CD1 LEU A 255 " =    2.792
peak=   -4.454 closest distance to " CG2 VAL A 230 " =    0.787
peak=   -4.336 closest distance to " OG BSER A 134 " =    1.284
peak=   -4.314 closest distance to " C   HIS A 108 " =    1.147
peak=   -4.242 closest distance to " CA  VAL A  67 " =    2.882
peak=   -4.211 closest distance to " NH2 ARG A  79 " =    1.945
peak=   -4.159 closest distance to " O   VAL A  67 " =    2.640
peak=   -4.148 closest distance to " OD2 ASP A 191 " =    1.303
peak=   -4.098 closest distance to " CA  GLY A  23 " =    1.914
peak=   -4.076 closest distance to " CB  ALA A 248 " =    2.053
peak=   -4.043 closest distance to " O   ALA A 161 " =    1.653
peak=   -4.038 closest distance to " O   HOH Z 266 " =    4.649
peak=   -4.032 closest distance to " CG2 THR A   4 " =    1.892
peak=   -4.028 closest distance to " O   PRO A 198 " =    1.220
peak=   -3.943 closest distance to " CG  GLN A 223 " =    1.789
peak=   -3.928 closest distance to " CB  TYR A  15 " =    2.105
peak=   -3.912 closest distance to " O   HOH Z 231 " =    2.089
peak=   -3.904 closest distance to " CE1 PHE A  59 " =    2.087
peak=   -3.893 closest distance to " CE2 PHE A 218 " =    2.480
peak=   -3.874 closest distance to " CB  ASN A  39 " =    2.132
peak=   -3.859 closest distance to " O   HOH Z  65 " =    1.046
peak=   -3.853 closest distance to " N   GLN A  58 " =    1.845
peak=   -3.833 closest distance to " CD  LYS A 289 " =    2.432
peak=   -3.821 closest distance to " N   HIS A 115 " =    2.039
peak=   -3.795 closest distance to " CB  ALA A 244 " =    2.093
peak=   -3.794 closest distance to " O   HOH Z 313 " =    1.664
peak=   -3.783 closest distance to " O   ALA A 292 " =    2.128
peak=   -3.775 closest distance to " O   HOH Z 185 " =    2.049
peak=   -3.771 closest distance to " O   HOH Z 191 " =    5.353
peak=   -3.770 closest distance to " O   HOH Z 193 " =    1.736
peak=   -3.738 closest distance to " O   SER A 135 " =    1.519
peak=   -3.735 closest distance to " CB  ALA A   7 " =    2.039
peak=   -3.730 closest distance to " CA  GLY A 133 " =    1.911
peak=   -3.722 closest distance to " CA  GLY A  98 " =    1.833
peak=   -3.721 closest distance to " OD1 ASN A 187 " =    1.652
peak=   -3.718 closest distance to " O   HOH Z 130 " =    1.966
peak=   -3.718 closest distance to " O   PRO A 163 " =    1.920
peak=   -3.717 closest distance to " C   ASN A 285 " =    2.168
peak=   -3.710 closest distance to " CB  ALA A  43 " =    2.274
peak=   -3.690 closest distance to " O   HOH Z 351 " =    1.502
peak=   -3.690 closest distance to " O   HOH Z 385 " =    2.024
peak=   -3.686 closest distance to " C   ASN A 187 " =    1.851
peak=   -3.668 closest distance to " O   HOH Z 412 " =    5.966
peak=   -3.660 closest distance to " O   HOH Z 140 " =    1.449
peak=   -3.656 closest distance to " O   HOH Z 103 " =    1.670
peak=   -3.648 closest distance to " ND2 ASN A 187 " =    1.541
peak=   -3.631 closest distance to " O   HOH Z 427 " =    1.476
peak=   -3.629 closest distance to " CZ  PHE A  59 " =    1.391
peak=   -3.628 closest distance to " O   HOH Z 426 " =    1.673
peak=   -3.625 closest distance to " O   HOH Z 102 " =    1.548
peak=   -3.616 closest distance to " CD2 LEU A 237 " =    2.781
peak=   -3.612 closest distance to " N   ALA A 248 " =    1.593
peak=   -3.601 closest distance to " CG1 VAL A 112 " =    2.736
peak=   -3.601 closest distance to " O   HOH Z 290 " =    1.139
peak=   -3.584 closest distance to " O   ALA A  51 " =    1.204
peak=   -3.572 closest distance to " CG  PHE A 283 " =    2.573
peak=   -3.571 closest distance to " O   HOH Z 114 " =    3.055
peak=   -3.570 closest distance to " CG  GLN A  58 " =    1.142
peak=   -3.569 closest distance to " CD1 LEU A 228 " =    2.076
peak=   -3.563 closest distance to " O   HOH Z 211 " =    1.549
peak=   -3.552 closest distance to " O   HOH Z 131 " =    4.072
peak=   -3.543 closest distance to " O   HOH Z 250 " =    1.397
peak=   -3.542 closest distance to " O   HOH Z 165 " =    2.145
peak=   -3.539 closest distance to " CB  PHE A 192 " =    1.776
peak=   -3.537 closest distance to " CB  PRO A 243 " =    2.595
peak=   -3.520 closest distance to " CG2AVAL A  41 " =    2.931
peak=   -3.514 closest distance to " OG  SER A  87 " =    1.227
peak=   -3.506 closest distance to " O   HOH Z 407 " =    2.958
peak=   -3.504 closest distance to " CB  ALA A 161 " =    2.455
peak=   -3.500 closest distance to " O   HOH Z 137 " =    1.621
peak=   -3.494 closest distance to " O   SER A  22 " =    2.284
peak=   -3.492 closest distance to " CD  GLN A  88 " =    0.958
peak=   -3.491 closest distance to " CE2 TYR A  30 " =    2.789
peak=   -3.491 closest distance to " C   ILE A 239 " =    2.170
peak=   -3.487 closest distance to " CB  ASP A 132 " =    2.298
peak=   -3.480 closest distance to " OXT GLY A 302 " =    2.906
peak=   -3.467 closest distance to " O   HOH Z 423 " =    2.328
peak=   -3.463 closest distance to " O   ALA A   8 " =    1.824
peak=   -3.462 closest distance to " CZ2 TRP A 274 " =    0.866
peak=   -3.461 closest distance to " O   HOH Z 111 " =    4.404
peak=   -3.461 closest distance to " O   HOH Z 377 " =    1.018
peak=   -3.454 closest distance to " OE2 GLU A 152 " =    1.202
peak=   -3.452 closest distance to " O   HOH Z 388 " =    2.076
peak=   -3.451 closest distance to " O   HOH Z 389 " =    1.973
peak=   -3.448 closest distance to " N   ALA A 226 " =    1.921
peak=   -3.437 closest distance to " O   HOH Z 348 " =    1.723
peak=   -3.429 closest distance to " O   HOH Z  24 " =    1.245
peak=   -3.416 closest distance to " OD1 ASN A 301 " =    2.075
peak=   -3.410 closest distance to " O   HOH Z 426 " =    2.354
peak=   -3.408 closest distance to " C   MET A 188 " =    1.523
peak=   -3.401 closest distance to " N   THR A 157 " =    1.360
peak=   -3.400 closest distance to " C   GLN A 205 " =    1.946
peak=   -3.400 closest distance to " O   HOH Z 359 " =    3.316
peak=   -3.392 closest distance to " O   HOH Z 350 " =    1.918
peak=   -3.387 closest distance to " CG1 VAL A 197 " =    2.174
peak=   -3.382 closest distance to " O   HOH Z 234 " =    3.780
peak=   -3.377 closest distance to " O   ASN A 187 " =    1.487
peak=   -3.373 closest distance to " O   HOH Z 389 " =    1.490
peak=   -3.371 closest distance to " CD1 TYR A 247 " =    2.517
peak=   -3.361 closest distance to " CG  GLN A 278 " =    2.049
peak=   -3.361 closest distance to " O   HOH Z  47 " =    1.525
peak=   -3.359 closest distance to " O   HOH Z 392 " =    0.870
peak=   -3.356 closest distance to " N   VAL A  72 " =    1.643
peak=   -3.351 closest distance to " O   HOH Z 134 " =    2.911
peak=   -3.349 closest distance to " CD1 LEU A 101 " =    2.225
peak=   -3.347 closest distance to " O   HOH Z 198 " =    2.005
peak=   -3.345 closest distance to " CZ  TYR A 169 " =    1.742
peak=   -3.343 closest distance to " O   HOH Z 406 " =    1.201
peak=   -3.337 closest distance to " NH1 ARG A  56 " =    2.520
peak=   -3.329 closest distance to " CA  GLY A 241 " =    2.163
peak=   -3.327 closest distance to " N   SER A 276 " =    1.214
peak=   -3.325 closest distance to " CG  PRO A 243 " =    1.405
peak=   -3.313 closest distance to " CG2 THR A 178 " =    1.997
peak=   -3.312 closest distance to " O   HOH Z  56 " =    2.279
peak=   -3.310 closest distance to " CD1 ILE A 239 " =    2.542
peak=   -3.303 closest distance to " OG ASER A 134 " =    1.082
peak=   -3.302 closest distance to " CG  ASP A 231 " =    0.800
peak=   -3.300 closest distance to " CE3 TRP A 274 " =    2.236
peak=   -3.288 closest distance to " O   HOH Z  13 " =    1.529
peak=   -3.286 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.280 closest distance to " CG  GLU A 152 " =    1.377
peak=   -3.278 closest distance to " CB  ALA A 248 " =    2.333
peak=   -3.276 closest distance to " CG1 VAL A 230 " =    1.853
peak=   -3.274 closest distance to " CA  GLY A 203 " =    2.200
peak=   -3.274 closest distance to " O   SER A  95 " =    1.448
peak=   -3.274 closest distance to " O   HOH Z 393 " =    3.441
peak=   -3.270 closest distance to " O   HOH Z  90 " =    2.627
peak=   -3.268 closest distance to " ND2 ASN A  45 " =    1.130
peak=   -3.267 closest distance to " O   PRO A 198 " =    1.156
peak=   -3.267 closest distance to " O   GLY A  80 " =    2.484
peak=   -3.265 closest distance to " O   TRP A 179 " =    1.618
peak=   -3.257 closest distance to " O   HOH Z 166 " =    1.644
peak=   -3.257 closest distance to " O   ALA A   1 " =    1.675
peak=   -3.256 closest distance to " O   HOH Z 417 " =    2.399
peak=   -3.253 closest distance to " C   LEU A 143 " =    0.945
peak=   -3.253 closest distance to " O   HOH Z 158 " =    2.016
peak=   -3.249 closest distance to " O   MET A  40 " =    2.675
peak=   -3.247 closest distance to " OG  SER A 206 " =    1.631
peak=   -3.245 closest distance to " O   HOH Z 357 " =    1.976
peak=   -3.240 closest distance to " O   HOH Z 210 " =    1.903
peak=   -3.239 closest distance to " O   HOH Z 385 " =    1.895
peak=   -3.235 closest distance to " ND2 ASN A  60 " =    1.615
peak=   -3.235 closest distance to " OG  SER A   3 " =    1.212
peak=   -3.222 closest distance to " O   HOH Z 110 " =    1.832
peak=   -3.218 closest distance to " O   ALA A  10 " =    1.865
peak=   -3.217 closest distance to " CD2 LEU A   5 " =    1.149
peak=   -3.214 closest distance to " O   HOH Z 256 " =    1.118
peak=   -3.211 closest distance to " O   HOH Z 359 " =    1.693
peak=   -3.209 closest distance to " O   HOH Z 298 " =    1.291
peak=   -3.206 closest distance to " CG  TRP A 266 " =    1.957
peak=   -3.203 closest distance to " O   HOH Z 166 " =    1.676
peak=   -3.203 closest distance to " CA  GLY A  57 " =    2.109
peak=   -3.201 closest distance to " O   HOH Z 251 " =    1.454
peak=   -3.199 closest distance to " ND2 ASN A 209 " =    1.921
peak=   -3.198 closest distance to " O   HOH Z  68 " =    1.937
peak=   -3.191 closest distance to " CB  ALA A  64 " =    2.551
peak=   -3.190 closest distance to " O   HOH Z 143 " =    1.270
peak=   -3.188 closest distance to " O   HOH Z 368 " =    2.325
peak=   -3.188 closest distance to " CA  ASP A  27 " =    2.350
peak=   -3.182 closest distance to " ND2 ASN A  45 " =    1.755
peak=   -3.174 closest distance to " O   HOH Z  51 " =    1.133
peak=   -3.171 closest distance to " CB  ALA A  51 " =    1.805
peak=   -3.167 closest distance to " CD2 TRP A 150 " =    0.835
peak=   -3.167 closest distance to " O   HOH Z 137 " =    1.471
peak=   -3.165 closest distance to " OE1 GLN A  88 " =    1.168
peak=   -3.157 closest distance to " O   ALA A 256 " =    2.531
peak=   -3.156 closest distance to " N   ALA A  43 " =    2.658
peak=   -3.152 closest distance to " O   LEU A 261 " =    1.636
peak=   -3.147 closest distance to " O   HOH Z 397 " =    1.197
peak=   -3.145 closest distance to " OE1 GLU A 277 " =    2.231
peak=   -3.140 closest distance to " O   HOH Z  97 " =    1.513
peak=   -3.133 closest distance to " O   PHE A 218 " =    1.509
peak=   -3.133 closest distance to " CG  GLU A   2 " =    2.057
peak=   -3.131 closest distance to " O   HOH Z 184 " =    1.207
peak=   -3.131 closest distance to " CG2 VAL A 189 " =    1.933
peak=   -3.131 closest distance to " O   HOH Z 235 " =    1.162
peak=   -3.128 closest distance to " CB  ALA A 291 " =    2.150
peak=   -3.125 closest distance to " O   HOH Z 208 " =    1.964
peak=   -3.125 closest distance to " O   HOH Z 346 " =    1.735
peak=   -3.123 closest distance to " O   SER A 210 " =    1.850
peak=   -3.123 closest distance to " CG  LYS A 193 " =    2.439
peak=   -3.113 closest distance to " CG  PRO A  90 " =    1.582
peak=   -3.106 closest distance to " O   GLN A 240 " =    1.896
peak=   -3.103 closest distance to " CB  ASP A 132 " =    2.221
peak=   -3.102 closest distance to " NH1BARG A 145 " =    3.538
peak=   -3.100 closest distance to " CB  PRO A 163 " =    2.427
peak=   -3.094 closest distance to " CE  MET A 105 " =    1.939
peak=   -3.090 closest distance to " CE BMET A  47 " =    1.202
peak=   -3.087 closest distance to " O   HOH Z 414 " =    1.850
peak=   -3.077 closest distance to " O   HOH Z 263 " =    2.566
peak=   -3.072 closest distance to " O   HOH Z 414 " =    2.148
peak=   -3.071 closest distance to " O   HOH Z 152 " =    4.651
peak=   -3.069 closest distance to " O   HOH Z 265 " =    1.872
peak=   -3.068 closest distance to " C   ALA A 158 " =    1.250
peak=   -3.067 closest distance to " OG  SER A  87 " =    1.584
peak=   -3.051 closest distance to " O   GLU A 152 " =    1.481
peak=   -3.023 closest distance to " O   HOH Z 134 " =    3.606
peak=   -3.014 closest distance to " O   ASN A 127 " =    1.423

================= 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    :  0.4794 0.4696   6.277891e+00   6.268573e+00
   1_bss:  0.4698 0.4592   6.269568e+00   6.255640e+00
   1_xyz:  0.3913 0.4114   6.162088e+00   6.188518e+00
   1_adp:  0.3457 0.3902   6.079284e+00   6.162025e+00
   1_occ:  0.3449 0.3900   6.078367e+00   6.162745e+00
   2_bss:  0.3414 0.3851   6.076831e+00   6.158610e+00
   2_xyz:  0.2513 0.3066   5.831075e+00   5.982472e+00
   2_adp:  0.2245 0.2784   5.737040e+00   5.903784e+00
   2_occ:  0.2239 0.2782   5.736191e+00   5.903463e+00
   3_bss:  0.2226 0.2777   5.733794e+00   5.901330e+00
   3_xyz:  0.1563 0.2038   5.411653e+00   5.619760e+00
   3_adp:  0.1389 0.1919   5.324650e+00   5.559889e+00
   3_occ:  0.1388 0.1917   5.324132e+00   5.559082e+00
   4_bss:  0.1387 0.1915   5.321234e+00   5.554875e+00
   4_xyz:  0.1219 0.1708   5.215594e+00   5.462190e+00
   4_adp:  0.1191 0.1648   5.183684e+00   5.422836e+00
   4_occ:  0.1190 0.1647   5.182967e+00   5.421704e+00
   5_bss:  0.1189 0.1646   5.182650e+00   5.421462e+00
   5_xyz:  0.1131 0.1596   5.143368e+00   5.390999e+00
   5_adp:  0.1116 0.1590   5.138646e+00   5.390692e+00
   5_occ:  0.1115 0.1589   5.138382e+00   5.390213e+00
   5_bss:  0.1116 0.1594   5.138678e+00   5.390247e+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:  0.376   6.194   7.451   9.803   7.935   0.000   0.000   0.000
   1_xyz:  0.376   6.194   7.451   9.803   7.935   0.000   0.000   0.000
   1_adp:  0.376   6.194   7.451   9.803   7.935   0.000   0.000   0.000
   1_occ:  0.376   6.194   7.451   9.803   7.935   0.000   0.000   0.000
   2_bss:  0.348  27.824   3.902   5.313   4.788   0.000   0.000   0.000
   2_xyz:  0.348  27.824   3.902   5.313   4.788   0.000   0.000   0.000
   2_adp:  0.348  27.824   3.902   5.313   4.788   0.000   0.000   0.000
   2_occ:  0.348  27.824   3.902   5.313   4.788   0.000   0.000   0.000
   3_bss:  0.332  27.824   2.455   3.214   3.576   0.000   0.000   0.000
   3_xyz:  0.332  27.824   2.455   3.214   3.576   0.000   0.000   0.000
   3_adp:  0.332  27.824   2.455   3.214   3.576   0.000   0.000   0.000
   3_occ:  0.332  27.824   2.455   3.214   3.576   0.000   0.000   0.000
   4_bss:  0.308  32.312   1.850   2.260   3.158   0.000   0.000   0.000
   4_xyz:  0.308  32.312   1.850   2.260   3.158   0.000   0.000   0.000
   4_adp:  0.308  32.312   1.850   2.260   3.158   0.000   0.000   0.000
   4_occ:  0.308  32.312   1.850   2.260   3.158   0.000   0.000   0.000
   5_bss:  0.321  37.020   1.703   2.048   3.118   0.000   0.000   0.000
   5_xyz:  0.321  37.020   1.703   2.048   3.118   0.000   0.000   0.000
   5_adp:  0.321  37.020   1.703   2.048   3.118   0.000   0.000   0.000
   5_occ:  0.321  37.020   1.703   2.048   3.118   0.000   0.000   0.000
   5_bss:  0.321  39.310  -0.575  -0.275   0.850   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.969 0.4203  0.4915    69643.977
   1_bss:  58.183 0.4153  0.6142    66477.453
   1_xyz:  46.976 0.5572  0.8158    49098.569
   1_adp:  42.842 0.6091  0.9370    44408.432
   1_occ:  42.899 0.6084  0.9341    44409.269
   2_bss:  42.344 0.6150  0.8272    43579.008
   2_xyz:  31.781 0.7376  0.9685    25055.206
   2_adp:  27.798 0.7825  1.0058    20331.910
   2_occ:  27.758 0.7830  1.0057    20297.326
   3_bss:  27.627 0.7842  0.9505    20132.542
   3_xyz:  19.192 0.8691  1.0102    10287.043
   3_adp:  17.714 0.8831  1.0113     9177.554
   3_occ:  17.699 0.8832  1.0112     9157.326
   4_bss:  17.594 0.8840  0.9870     9034.162
   4_xyz:  15.483 0.9026  0.9956     7321.020
   4_adp:  14.586 0.9102  0.9967     6828.203
   4_occ:  14.571 0.9103  0.9966     6802.587
   5_bss:  14.563 0.9104  0.9920     6803.811
   5_xyz:  13.897 0.9158  0.9942     6343.681
   5_adp:  13.864 0.9163  0.9903     6325.299
   5_occ:  13.860 0.9163  0.9903     6314.236
   5_bss:  13.873 0.9162  0.9901     6330.167
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2891e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2891e+01
   1_xyz:   1.682  0.013  0.105 18.110  0.006  4.105   1.3911e-01
   1_adp:   1.682  0.013  0.105 18.110  0.006  4.105   1.3911e-01
   1_occ:   1.682  0.013  0.105 18.110  0.006  4.105   1.3911e-01
   2_bss:   1.682  0.013  0.105 18.110  0.006  4.105   1.3911e-01
   2_xyz:   1.180  0.009  0.082 15.871  0.005  4.115   8.5596e-02
   2_adp:   1.180  0.009  0.082 15.871  0.005  4.115   8.5596e-02
   2_occ:   1.180  0.009  0.082 15.871  0.005  4.115   8.5596e-02
   3_bss:   1.180  0.009  0.082 15.871  0.005  4.115   8.5596e-02
   3_xyz:   1.064  0.007  0.076 15.846  0.004  4.115   6.8365e-02
   3_adp:   1.064  0.007  0.076 15.846  0.004  4.115   6.8365e-02
   3_occ:   1.064  0.007  0.076 15.846  0.004  4.115   6.8365e-02
   4_bss:   1.064  0.007  0.076 15.846  0.004  4.115   6.8365e-02
   4_xyz:   0.978  0.006  0.071 15.552  0.004  4.107   5.8900e-02
   4_adp:   0.978  0.006  0.071 15.552  0.004  4.107   5.8900e-02
   4_occ:   0.978  0.006  0.071 15.552  0.004  4.107   5.8900e-02
   5_bss:   0.978  0.006  0.071 15.552  0.004  4.107   5.8900e-02
   5_xyz:   1.001  0.006  0.074 15.532  0.004  4.108   6.0731e-02
   5_adp:   1.001  0.006  0.074 15.532  0.004  4.108   6.0731e-02
   5_occ:   1.001  0.006  0.074 15.532  0.004  4.108   6.0731e-02
   5_bss:   1.001  0.006  0.074 15.532  0.004  4.108   6.0731e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.119   6.8527e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.119   6.8527e+00
   1_xyz:  14.530  0.162  0.466 88.099  0.037  2.188   9.6711e-02
   1_adp:  14.530  0.162  0.466 88.099  0.037  2.188   9.6711e-02
   1_occ:  14.530  0.162  0.466 88.099  0.037  2.188   9.6711e-02
   2_bss:  14.530  0.162  0.466 88.099  0.037  2.188   9.6711e-02
   2_xyz:   7.795  0.125  0.352 83.198  0.051  2.215   8.7193e-02
   2_adp:   7.795  0.125  0.352 83.198  0.051  2.215   8.7193e-02
   2_occ:   7.795  0.125  0.352 83.198  0.051  2.215   8.7193e-02
   3_bss:   7.795  0.125  0.352 83.198  0.051  2.215   8.7193e-02
   3_xyz:   7.080  0.052  0.296 82.744  0.030  2.300   8.4607e-02
   3_adp:   7.080  0.052  0.296 82.744  0.030  2.300   8.4607e-02
   3_occ:   7.080  0.052  0.296 82.744  0.030  2.300   8.4607e-02
   4_bss:   7.080  0.052  0.296 82.744  0.030  2.300   8.4607e-02
   4_xyz:   6.480  0.044  0.225 83.745  0.030  2.336   4.6704e-02
   4_adp:   6.480  0.044  0.225 83.745  0.030  2.336   4.6704e-02
   4_occ:   6.480  0.044  0.225 83.745  0.030  2.336   4.6704e-02
   5_bss:   6.480  0.044  0.225 83.745  0.030  2.336   4.6704e-02
   5_xyz:   6.705  0.044  0.256 84.309  0.037  2.274   4.3292e-02
   5_adp:   6.705  0.044  0.256 84.309  0.037  2.274   4.3292e-02
   5_occ:   6.705  0.044  0.256 84.309  0.037  2.274   4.3292e-02
   5_bss:   6.705  0.044  0.256 84.309  0.037  2.274   4.3292e-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:  75.29   0.00  13.18  75.29   0.00  10.91  67.16   0.00  25.53
   1_occ:  75.29   0.00  13.18  75.29   0.00  10.91  67.16   0.00  25.53
   2_bss:  75.29   0.00  13.18  75.29   0.00  10.91  67.16   0.00  25.53
   2_xyz:  75.29   0.00  13.18  75.29   0.00  10.91  67.16   0.00  25.53
   2_adp:  85.09   0.00  12.80  85.09   0.00   9.29  79.29   1.18  31.88
   2_occ:  85.09   0.00  12.80  85.09   0.00   9.29  79.29   1.18  31.88
   3_bss:  85.09   0.00  12.80  85.09   0.00   9.29  79.29   1.18  31.88
   3_xyz:  85.09   0.00  12.80  85.09   0.00   9.29  79.29   1.18  31.88
   3_adp:  96.52   0.00  13.69  96.52   0.00   9.01  92.80   0.00  39.18
   3_occ:  96.52   0.00  13.69  96.52   0.00   9.01  92.80   0.00  39.18
   4_bss:  96.52   0.00  13.69  96.52   0.00   9.01  92.80   0.00  39.18
   4_xyz:  96.52   0.00  13.69  96.52   0.00   9.01  92.80   0.00  39.18
   4_adp:  96.62   0.00  13.25  96.62   0.00   8.70  91.77   1.05  38.05
   4_occ:  96.62   0.00  13.25  96.62   0.00   8.70  91.77   1.05  38.05
   5_bss:  96.62   0.00  13.25  96.62   0.00   8.70  91.77   1.05  38.05
   5_xyz:  96.62   0.00  13.25  96.62   0.00   8.70  91.77   1.05  38.05
   5_adp: 100.65   0.00  13.09 100.65   0.00   8.58  93.15   1.86  37.66
   5_occ: 100.65   0.00  13.09 100.65   0.00   8.58  93.15   1.86  37.66
   5_bss: 102.94   2.29  15.38 102.94   2.29  10.87  95.44   4.15  39.95
------------------------------------------------------------------------
 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:    1.242    0.006    0.410
   1_adp:    1.242    0.006    0.410
   1_occ:    1.242    0.006    0.410
   2_bss:    1.242    0.006    0.410
   2_xyz:    1.475    0.055    0.583
   2_adp:    1.475    0.055    0.583
   2_occ:    1.475    0.055    0.583
   3_bss:    1.475    0.055    0.583
   3_xyz:    1.536    0.055    0.672
   3_adp:    1.536    0.055    0.672
   3_occ:    1.536    0.055    0.672
   4_bss:    1.536    0.055    0.672
   4_xyz:    1.669    0.044    0.707
   4_adp:    1.669    0.044    0.707
   4_occ:    1.669    0.044    0.707
   5_bss:    1.669    0.044    0.707
   5_xyz:    1.666    0.050    0.722
   5_adp:    1.666    0.050    0.722
   5_occ:    1.666    0.050    0.722
   5_bss:    1.666    0.050    0.722
------------------------------------------------------------------------

CPU time actual refinement: 331.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_267/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_267/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_267/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_267/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_267/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.47 
  Macro-tasks:
    bulk solvent and scale       = 42.16  
    individual site refinement   = 137.86 
    weights calculation          = 32.34  
    collect and process          = 6.65   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.13 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 100.69 
    alpha_beta                      = 8.28   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.25 
    fmodel                         = 7.22   
    r_factors                      = 0.29   
    phase_errors                   = 10.67  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 242.09 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.685 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    626 calls, 100.28 s
gradients_fft:          572 calls,  98.10 s

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

# Date 2008-01-16 Time 01:09:33 PST -0800 (1200474573.34 s)
Start R-work = 0.4794, R-free = 0.4696 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.4698, R-free = 0.4592
Final R-work = 0.1116, R-free = 0.1594