# Date 2008-01-16 Time 00:45:24 PST -0800 (1200473124.21 s)
#phil __OFF__

Command line arguments: "../134.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 = 18159
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 134

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 45.9914, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7143 1.96009
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 =  14.7143
                             d_min =   1.9601

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 45.9914, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7143 1.96009
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: 14.7147 -  4.1933 [2096/2119]  1886   210  10.0%
  bin  2:  4.1933 -  3.3412 [2024/2044]  1822   202  10.0%
  bin  3:  3.3412 -  2.9226 [1989/2008]  1791   198  10.0%
  bin  4:  2.9226 -  2.6571 [1954/1984]  1758   196  10.0%
  bin  5:  2.6571 -  2.4676 [1970/1989]  1773   197  10.0%
  bin  6:  2.4676 -  2.3227 [1951/1976]  1754   197  10.1%
  bin  7:  2.3227 -  2.2068 [1928/1956]  1736   192  10.0%
  bin  8:  2.2068 -  2.1110 [1932/1968]  1738   194  10.0%
  bin  9:  2.1110 -  2.0300 [1922/1964]  1732   190   9.9%
  bin 10:  2.0300 -  1.9601 [1823/1954]  1640   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_134/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:
        1.01 -     1.79: 7
        1.79 -     2.57: 108
        2.57 -     3.35: 4151
        3.35 -     4.12: 9690
        4.12 -     4.90: 15230
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.014 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.211 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.506 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.611 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.666 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29181 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_134/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_134/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 45.9914 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5104   r_free= 0.5091   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.303581                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7147 -  4.6767 0.99   1371  152 0.4292 0.4369      6.6361      6.6827|
|  2:  4.6767 -  3.7319 0.99   1299  146 0.4538 0.4261      6.8573      6.8374|
|  3:  3.7319 -  3.2661 0.99   1286  141 0.4892 0.4731      6.7453      6.8025|
|  4:  3.2661 -  2.9701 0.99   1283  142 0.4936 0.4568      6.5756      6.5062|
|  5:  2.9701 -  2.7588 0.99   1259  141 0.5384 0.5397      6.4055      6.4007|
|  6:  2.7588 -  2.5970 0.99   1267  141 0.5449 0.5753      6.3151       6.272|
|  7:  2.5970 -  2.4676 0.99   1265  140 0.5331 0.5052      6.2664      6.2082|
|  8:  2.4676 -  2.3606 0.98   1248  137 0.5562 0.5535      6.2167      6.2155|
|  9:  2.3606 -  2.2701 0.98   1242  141 0.5411 0.5889      6.1362      6.1548|
| 10:  2.2701 -  2.1920 1.00   1242  139 0.5469 0.5552      6.1322       6.156|
| 11:  2.1920 -  2.1237 0.97   1251  138 0.5390 0.5647      6.0499      6.0926|
| 12:  2.1237 -  2.0632 0.98   1240  138 0.5261 0.5504      6.0063      6.0626|
| 13:  2.0632 -  2.0090 0.99   1247  137 0.5584 0.5343      5.9161      5.8809|
| 14:  2.0090 -  1.9601 0.91   1130  126 0.5440 0.4924      5.8703      5.7617|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7147 -  4.6767  1371   152  0.59  43.43   0.78     0.65     104139.82|
|  2:  4.6767 -  3.7319  1299   146  0.62  41.82   0.86     0.71     141636.63|
|  3:  3.7319 -  3.2661  1286   141  0.52  50.54   0.84     0.66     144712.84|
|  4:  3.2661 -  2.9701  1283   142  0.44  56.46   0.80     0.55     121140.83|
|  5:  2.9701 -  2.7588  1259   141  0.33  65.15   0.73     0.41      96042.81|
|  6:  2.7588 -  2.5970  1267   141  0.27  69.72   0.71     0.32      83708.61|
|  7:  2.5970 -  2.4676  1265   140  0.18  76.32   0.73     0.21      79027.12|
|  8:  2.4676 -  2.3606  1248   137  0.16  78.32   0.74     0.19      72641.24|
|  9:  2.3606 -  2.2701  1242   141  0.15  78.77   0.71     0.18      66694.38|
| 10:  2.2701 -  2.1920  1242   139  0.18  76.38   0.77     0.22      58868.21|
| 11:  2.1920 -  2.1237  1251   138  0.15  78.90   0.77     0.19      56014.49|
| 12:  2.1237 -  2.0632  1240   138  0.16  77.83   0.78     0.21      50798.78|
| 13:  2.0632 -  2.0090  1247   137  0.20  75.42   0.75     0.25      42105.16|
| 14:  2.0090 -  1.9601  1130   126  0.33  65.07   0.74     0.38      29687.62|
|alpha:            min =        0.18 max =            0.71 mean =         0.37|
|beta:             min =    29687.62 max =       144712.84 mean =     82867.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.45|
|phase err.(test): min =        0.00 max =           89.95 mean =        66.74|
|-----------------------------------------------------------------------------|

============================== 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 = 28.848069             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.824   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.568739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.678   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.867 -  1.270:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.270 -  1.674:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.674 -  2.077:       75 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.077 -  2.480:      429 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.480 -  2.883:     1214 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.883 -  3.287:     2402 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.287 -  3.690:     4012 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.690 -  4.093:     5416 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.093 -  4.497:     7086 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.497 -  4.900:     8571 |
|-----------------------------------------------------------------------------|
|-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 |       52.508 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.867 |       3.200 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    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 = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5140   r_free= 0.5094   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| 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:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.303784                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5013   r_free= 0.4969   ksol= 0.38   Bsol= 0.00   scale= 0.976    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.97,9.34,7.92,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.296304                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.842542             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.503   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.252128              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.188   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5013      final r-factor (work) = 0.4431          |
| start r-factor (free) = 0.4969      final r-factor (free) = 0.4675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 118.1700 = 20.84 * 0.50 * 6.3007 + 1.00 * 52.5083                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.2925 = 20.84 * 0.50 * 6.2494 + 1.00 * 0.1660                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4431      final r-factor (work) = 0.4033          |
| start r-factor (free) = 0.4675      final r-factor (free) = 0.4599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0888 = 2.25 * 1.00 * 6.2494 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.9939 = 2.25 * 1.00 * 6.2026 + 1.00 * 0.0249                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.55   15.76    None  None   None       |
|    all(noH): 2823   0      0.00    92.55   15.76    None  None   None       |
|    Sol.    : 438    0      0.00    92.55   23.92    None  None   None       |
|    Mac.    : 2385   0      0.00    89.21   14.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.255: 1077   |   5:    46.276 -  55.531:   61        |
|      1:     9.255 -  18.510:  783   |   6:    55.531 -  64.786:   24        |
|      2:    18.510 -  27.765:  498   |   7:    64.786 -  74.041:   12        |
|      3:    27.765 -  37.021:  256   |   8:    74.041 -  83.296:    2        |
|      4:    37.021 -  46.276:  107   |   9:    83.296 -  92.551:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4033 r_free = 0.4599             target_work(ml) = 6.192         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4029 r_free = 0.4599             target_work(ml) = 6.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4029   r_free= 0.4599   ksol= 0.38   Bsol= 0.00   scale= 1.105    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.97,9.34,7.92,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.190879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4019   r_free= 0.4554   ksol= 0.36   Bsol= 22.64   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.30,5.96,5.59,0.00,0.00,0.00); trace/3= 5.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.191266                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.642329             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.891  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.990084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.007  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4019      final r-factor (work) = 0.3216          |
| start r-factor (free) = 0.4554      final r-factor (free) = 0.3816          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.0478 = 19.64 * 0.50 * 6.1990 + 1.00 * 0.1660                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.2207 = 19.64 * 0.50 * 6.1182 + 1.00 * 0.1328                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3216      final r-factor (work) = 0.2911          |
| start r-factor (free) = 0.3816      final r-factor (free) = 0.3570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0833 = 0.99 * 1.00 * 6.1182 + 1.00 * 0.0257                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9475 = 0.99 * 1.00 * 5.9872 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.28  14.79    None  None   None       |
|    all(noH): 2823   0      0.00    101.28  14.79    None  None   None       |
|    Sol.    : 438    0      0.00    101.28  30.64    None  None   None       |
|    Mac.    : 2385   0      0.00    95.89   11.88    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 -  10.128: 1281   |   5:    50.639 -  60.766:   33        |
|      1:    10.128 -  20.256:  838   |   6:    60.766 -  70.894:   12        |
|      2:    20.256 -  30.383:  371   |   7:    70.894 -  81.022:    8        |
|      3:    30.383 -  40.511:  181   |   8:    81.022 -  91.150:    1        |
|      4:    40.511 -  50.639:   96   |   9:    91.150 - 101.277:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2911 r_free = 0.3570             target_work(ml) = 5.958         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2907 r_free = 0.3578             target_work(ml) = 5.958         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2907   r_free= 0.3578   ksol= 0.36   Bsol= 22.64   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.30,5.96,5.59,0.00,0.00,0.00); trace/3= 5.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.958040                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2878   r_free= 0.3566   ksol= 0.35   Bsol= 43.38   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,2.96,3.14,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.954457                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.149870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.110  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.331771              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.761   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2878      final r-factor (work) = 0.2366          |
| start r-factor (free) = 0.3566      final r-factor (free) = 0.3016          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5543 = 4.15 * 0.50 * 5.9865 + 1.00 * 0.1328                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2660 = 4.15 * 0.50 * 5.8800 + 1.00 * 0.0655                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2366      final r-factor (work) = 0.2209          |
| start r-factor (free) = 0.3016      final r-factor (free) = 0.2836          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9678 = 0.33 * 1.00 * 5.8800 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9227 = 0.33 * 1.00 * 5.7631 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.80   13.98    None  None   None       |
|    all(noH): 2823   0      0.00    96.80   13.98    None  None   None       |
|    Sol.    : 438    0      1.52    88.57   33.49    None  None   None       |
|    Mac.    : 2385   0      0.00    96.80   10.39    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 -   9.680: 1461   |   5:    48.399 -  58.079:   43        |
|      1:     9.680 -  19.360:  732   |   6:    58.079 -  67.759:   18        |
|      2:    19.360 -  29.039:  248   |   7:    67.759 -  77.438:    3        |
|      3:    29.039 -  38.719:  187   |   8:    77.438 -  87.118:    4        |
|      4:    38.719 -  48.399:  125   |   9:    87.118 -  96.798:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2209 r_free = 0.2836             target_work(ml) = 5.737         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2205 r_free = 0.2831             target_work(ml) = 5.735         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2205   r_free= 0.2831   ksol= 0.35   Bsol= 43.38   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,2.96,3.14,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.735069                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2203   r_free= 0.2818   ksol= 0.33   Bsol= 36.76   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.89,2.42,0.00,0.00,0.00); trace/3= 1.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.734100                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.660508              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.715  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267444              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.363  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2203      final r-factor (work) = 0.1721          |
| start r-factor (free) = 0.2818      final r-factor (free) = 0.2193          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7312 = 2.66 * 0.50 * 5.7627 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5430 = 2.66 * 0.50 * 5.6234 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1721      final r-factor (work) = 0.1602          |
| start r-factor (free) = 0.2193      final r-factor (free) = 0.2096          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5209 = 0.27 * 1.00 * 5.6234 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4695 = 0.27 * 1.00 * 5.4592 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.96   13.88    None  None   None       |
|    all(noH): 2823   0      0.00    94.96   13.88    None  None   None       |
|    Sol.    : 438    0      3.19    84.14   36.39    None  None   None       |
|    Mac.    : 2385   0      0.00    94.96   9.74     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 -   9.496: 1596   |   5:    47.479 -  56.975:   72        |
|      1:     9.496 -  18.992:  644   |   6:    56.975 -  66.471:   24        |
|      2:    18.992 -  28.488:  171   |   7:    66.471 -  75.967:    8        |
|      3:    28.488 -  37.983:  146   |   8:    75.967 -  85.463:    5        |
|      4:    37.983 -  47.479:  156   |   9:    85.463 -  94.959:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1602 r_free = 0.2096             target_work(ml) = 5.440         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1599 r_free = 0.2091             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1599   r_free= 0.2091   ksol= 0.33   Bsol= 36.76   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.26,1.89,2.42,0.00,0.00,0.00); trace/3= 1.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.437993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1601   r_free= 0.2090   ksol= 0.33   Bsol= 36.76   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,1.06,2.03,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.437407                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.103996              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.456  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.749990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.526  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1601      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.2090      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8074 = 2.10 * 0.50 * 5.4610 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7037 = 2.10 * 0.50 * 5.3648 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.1810      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0330 = 0.75 * 1.00 * 5.3648 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9653 = 0.75 * 1.00 * 5.2716 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.44   14.38    None  None   None       |
|    all(noH): 2823   0      0.00    98.44   14.38    None  None   None       |
|    Sol.    : 438    0      3.03    87.04   40.29    None  None   None       |
|    Mac.    : 2385   0      0.00    98.44   9.62     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.844: 1671   |   5:    49.218 -  59.062:   88        |
|      1:     9.844 -  19.687:  615   |   6:    59.062 -  68.905:   61        |
|      2:    19.687 -  29.531:  133   |   7:    68.905 -  78.749:   21        |
|      3:    29.531 -  39.375:  133   |   8:    78.749 -  88.593:    5        |
|      4:    39.375 -  49.218:   93   |   9:    88.593 -  98.436:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1295 r_free = 0.1767             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1768             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1768   ksol= 0.33   Bsol= 36.76   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,1.06,2.03,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.259392                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7147 -  4.6767 0.99   1371  152 0.1103 0.1367      5.4782      5.5922|
|  2:  4.6767 -  3.7319 0.99   1299  146 0.0976 0.1346      5.5532      5.7999|
|  3:  3.7319 -  3.2661 0.99   1286  141 0.1230 0.1442      5.6218      5.8499|
|  4:  3.2661 -  2.9701 0.99   1283  142 0.1419 0.2018      5.5917      5.8296|
|  5:  2.9701 -  2.7588 0.99   1259  141 0.1539 0.2033      5.4657      5.6331|
|  6:  2.7588 -  2.5970 0.99   1267  141 0.1427 0.1888      5.3411      5.5166|
|  7:  2.5970 -  2.4676 0.99   1265  140 0.1433 0.1857      5.2777      5.4846|
|  8:  2.4676 -  2.3606 0.98   1248  137 0.1439 0.2011      5.2311      5.4887|
|  9:  2.3606 -  2.2701 0.98   1242  141 0.1364 0.1847      5.1555      5.3227|
| 10:  2.2701 -  2.1920 1.00   1242  139 0.1308 0.2025      5.1035      5.3726|
| 11:  2.1920 -  2.1237 0.97   1251  138 0.1328 0.1990      5.0699      5.3769|
| 12:  2.1237 -  2.0632 0.98   1240  138 0.1300 0.1795       5.011      5.3205|
| 13:  2.0632 -  2.0090 0.99   1247  137 0.1274 0.1971      4.8955      5.1722|
| 14:  2.0090 -  1.9601 0.91   1130  126 0.1115 0.1823      4.7253      5.0166|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7147 -  4.6767  1371   152  0.93  10.38   0.99     0.96       8652.38|
|  2:  4.6767 -  3.7319  1299   146  0.94   9.24   1.04     1.02      10934.86|
|  3:  3.7319 -  3.2661  1286   141  0.92  13.40   1.06     1.05      13453.35|
|  4:  3.2661 -  2.9701  1283   142  0.90  15.66   1.03     1.01      13204.07|
|  5:  2.9701 -  2.7588  1259   141  0.88  18.06   1.01     0.97      10678.44|
|  6:  2.7588 -  2.5970  1267   141  0.88  18.17   0.99     0.94       8788.61|
|  7:  2.5970 -  2.4676  1265   140  0.88  18.43   1.00     0.97       7905.53|
|  8:  2.4676 -  2.3606  1248   137  0.89  17.29   1.01     1.00       6903.51|
|  9:  2.3606 -  2.2701  1242   141  0.89  17.63   1.01     0.99       6360.76|
| 10:  2.2701 -  2.1920  1242   139  0.89  17.77   1.02     0.96       5724.00|
| 11:  2.1920 -  2.1237  1251   138  0.88  18.65   1.02     0.96       5696.54|
| 12:  2.1237 -  2.0632  1240   138  0.88  18.40   1.03     1.01       5199.90|
| 13:  2.0632 -  2.0090  1247   137  0.89  17.20   1.02     1.01       4042.04|
| 14:  2.0090 -  1.9601  1130   126  0.91  15.44   1.01     0.98       2863.65|
|alpha:            min =        0.94 max =            1.05 mean =         0.99|
|beta:             min =     2863.65 max =        13453.35 mean =      7961.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        16.06|
|phase err.(test): min =        0.00 max =           88.31 mean =        15.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1764   ksol= 0.32   Bsol= 34.96   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.22,0.75,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.258020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.71 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1764   ksol= 0.32   Bsol= 34.96   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.22,0.75,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.258020                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7147 -  4.6767 0.99   1371  152 0.1096 0.1329      5.4616      5.5795|
|  2:  4.6767 -  3.7319 0.99   1299  146 0.0984 0.1338      5.5552      5.7976|
|  3:  3.7319 -  3.2661 0.99   1286  141 0.1232 0.1450       5.623      5.8501|
|  4:  3.2661 -  2.9701 0.99   1283  142 0.1420 0.2015      5.5918        5.83|
|  5:  2.9701 -  2.7588 0.99   1259  141 0.1538 0.2014      5.4645      5.6283|
|  6:  2.7588 -  2.5970 0.99   1267  141 0.1430 0.1894      5.3405      5.5165|
|  7:  2.5970 -  2.4676 0.99   1265  140 0.1431 0.1857      5.2762      5.4816|
|  8:  2.4676 -  2.3606 0.98   1248  137 0.1438 0.2002      5.2299      5.4853|
|  9:  2.3606 -  2.2701 0.98   1242  141 0.1364 0.1847      5.1555      5.3238|
| 10:  2.2701 -  2.1920 1.00   1242  139 0.1309 0.2029      5.1042      5.3747|
| 11:  2.1920 -  2.1237 0.97   1251  138 0.1327 0.1988      5.0702      5.3761|
| 12:  2.1237 -  2.0632 0.98   1240  138 0.1299 0.1800      5.0104      5.3214|
| 13:  2.0632 -  2.0090 0.99   1247  137 0.1274 0.1974      4.8951      5.1724|
| 14:  2.0090 -  1.9601 0.91   1130  126 0.1116 0.1818      4.7248      5.0151|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7147 -  4.6767  1371   152  0.93  10.20   0.99     0.96       8310.46|
|  2:  4.6767 -  3.7319  1299   146  0.94   9.20   1.04     1.02      10803.50|
|  3:  3.7319 -  3.2661  1286   141  0.92  13.41   1.06     1.04      13476.33|
|  4:  3.2661 -  2.9701  1283   142  0.90  15.63   1.03     1.01      13189.07|
|  5:  2.9701 -  2.7588  1259   141  0.88  17.97   1.01     0.97      10587.71|
|  6:  2.7588 -  2.5970  1267   141  0.88  18.12   0.99     0.94       8746.13|
|  7:  2.5970 -  2.4676  1265   140  0.88  18.37   1.00     0.97       7865.64|
|  8:  2.4676 -  2.3606  1248   137  0.89  17.27   1.01     0.99       6884.77|
|  9:  2.3606 -  2.2701  1242   141  0.89  17.62   1.01     0.99       6358.81|
| 10:  2.2701 -  2.1920  1242   139  0.89  17.78   1.02     0.96       5727.23|
| 11:  2.1920 -  2.1237  1251   138  0.88  18.69   1.02     0.97       5715.09|
| 12:  2.1237 -  2.0632  1240   138  0.88  18.42   1.03     1.01       5202.96|
| 13:  2.0632 -  2.0090  1247   137  0.89  17.21   1.02     1.01       4040.06|
| 14:  2.0090 -  1.9601  1130   126  0.91  15.41   1.01     0.98       2857.74|
|alpha:            min =        0.94 max =            1.04 mean =         0.99|
|beta:             min =     2857.74 max =        13476.33 mean =      7913.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.91 mean =        16.03|
|phase err.(test): min =        0.00 max =           88.92 mean =        15.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.229)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.28    99.72   15.66    None  None   None       |
|    all(noH): 2823   0      1.28    99.72   15.66    None  None   None       |
|    Sol.    : 438    0      4.31    88.32   41.57    None  None   None       |
|    Mac.    : 2385   0      1.28    99.72   10.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.282 -  11.126: 1671   |   5:    50.500 -  60.344:   88        |
|      1:    11.126 -  20.969:  615   |   6:    60.344 -  70.187:   61        |
|      2:    20.969 -  30.813:  133   |   7:    70.187 -  80.031:   21        |
|      3:    30.813 -  40.657:  133   |   8:    80.031 -  89.875:    5        |
|      4:    40.657 -  50.500:   93   |   9:    89.875 -  99.718:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.626 - 5.673
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 336
   mapped sites are within: 0.741 - 5.673

peak=   10.309 closest distance to " CB  VAL A 296 " =    1.501
peak=    9.718 closest distance to " CB  VAL A 230 " =    1.432
peak=    8.442 closest distance to " O   HOH Z 390 " =    1.264
peak=    7.270 closest distance to " O   HOH Z 381 " =    1.315
peak=    7.007 closest distance to " O   HOH Z 130 " =    1.574
peak=    6.967 closest distance to " CG  ARG A 138 " =    1.248
peak=    6.776 closest distance to " CD1AILE A 234 " =    1.012
peak=    6.522 closest distance to " CD2 LEU A   5 " =    1.349
peak=    6.406 closest distance to " O   HOH Z  65 " =    1.743
peak=    6.399 closest distance to " O   HOH Z 385 " =    1.364
peak=    6.081 closest distance to " O   HOH Z 375 " =    1.413
peak=    6.002 closest distance to " O   HOH Z  28 " =    1.762
peak=    5.782 closest distance to " O   HOH Z 124 " =    1.732
peak=    5.527 closest distance to " O   HOH Z   9 " =    1.497
peak=    5.399 closest distance to " O   HOH Z  69 " =    1.826
peak=    5.393 closest distance to " O   HOH Z 193 " =    1.794
peak=    5.392 closest distance to " O   HOH Z 236 " =    1.596
peak=    5.349 closest distance to " O   HOH Z 142 " =    1.968
peak=    5.343 closest distance to " O   HOH Z 278 " =    1.335
peak=    5.264 closest distance to " O   HOH Z 126 " =    1.832
peak=    5.256 closest distance to " O   HOH Z 424 " =    1.682
peak=    5.139 closest distance to " CB  VAL A 230 " =    1.128
peak=    5.026 closest distance to " CB  ARG A 275 " =    1.121
peak=    5.017 closest distance to " O   PRO A 198 " =    1.348
peak=    5.007 closest distance to " O   HOH Z  78 " =    1.796
peak=    4.966 closest distance to " NH1 ARG A 138 " =    0.975
peak=    4.936 closest distance to " O   HOH Z 415 " =    1.218
peak=    4.925 closest distance to " O   HOH Z 410 " =    1.505
peak=    4.924 closest distance to " O   HOH Z 132 " =    1.310
peak=    4.890 closest distance to " O   HOH Z 112 " =    1.475
peak=    4.878 closest distance to " O   HOH Z  92 " =    1.394
peak=    4.828 closest distance to " O   HOH Z   7 " =    1.754
peak=    4.789 closest distance to " O   HOH Z 423 " =    1.924
peak=    4.756 closest distance to " O   HOH Z 427 " =    1.162
peak=    4.724 closest distance to " O   HOH Z  51 " =    2.240
peak=    4.723 closest distance to " CG  LEU A   5 " =    1.260
peak=    4.717 closest distance to " O   HOH Z 120 " =    1.030
peak=    4.670 closest distance to " NE2 GLN A  11 " =    1.064
peak=    4.632 closest distance to " O   HOH Z 358 " =    1.376
peak=    4.631 closest distance to " CG  PRO A 213 " =    1.231
peak=    4.606 closest distance to " OD1 ASP A  27 " =    0.891
peak=    4.596 closest distance to " O   HOH Z 369 " =    2.349
peak=    4.561 closest distance to " O   HOH Z 422 " =    0.980
peak=    4.529 closest distance to " O   HOH Z 414 " =    1.549
peak=    4.510 closest distance to " O   HOH Z 199 " =    1.103
peak=    4.499 closest distance to " CG  PRO A  54 " =    1.270
peak=    4.469 closest distance to " O   HOH Z 291 " =    1.501
peak=    4.469 closest distance to " CG2 ILE A 234 " =    0.967
peak=    4.460 closest distance to " NH2BARG A 145 " =    1.522
peak=    4.428 closest distance to " O   HOH Z 388 " =    1.181
peak=    4.426 closest distance to " NH2 ARG A  56 " =    1.930
peak=    4.399 closest distance to " NE1 TRP A 274 " =    1.065
peak=    4.395 closest distance to " CD2 LEU A 228 " =    1.149
peak=    4.370 closest distance to " CB  SER A   3 " =    1.180
peak=    4.369 closest distance to " O   HOH Z 123 " =    1.362
peak=    4.368 closest distance to " CE AMET A  47 " =    1.283
peak=    4.351 closest distance to " O   HOH Z 427 " =    2.195
peak=    4.345 closest distance to " O   HOH Z 156 " =    2.683
peak=    4.303 closest distance to " O   HOH Z 403 " =    2.063
peak=    4.286 closest distance to " O   HOH Z 344 " =    1.400
peak=    4.252 closest distance to " O   HOH Z 214 " =    1.328
peak=    4.228 closest distance to " O   HOH Z 316 " =    2.648
peak=    4.205 closest distance to " O   HOH Z 417 " =    1.283
peak=    4.169 closest distance to " O   HOH Z  63 " =    1.534
peak=    4.162 closest distance to " CB  PRO A  54 " =    1.122
peak=    4.153 closest distance to " O   SER A  87 " =    2.397
peak=    4.142 closest distance to " O   HOH Z 143 " =    1.436
peak=    4.136 closest distance to " O   HOH Z 192 " =    1.398
peak=    4.131 closest distance to " O   HOH Z 130 " =    1.951
peak=    4.107 closest distance to " O   HOH Z 263 " =    1.653
peak=    4.103 closest distance to " O   HOH Z 232 " =    2.251
peak=    4.099 closest distance to " O   HOH Z 426 " =    1.148
peak=    4.098 closest distance to " CB  VAL A 265 " =    1.237
peak=    4.094 closest distance to " CD  ARG A 138 " =    0.818
peak=    4.093 closest distance to " O   HOH Z  59 " =    1.525
peak=    4.092 closest distance to " O   HOH Z 289 " =    1.231
peak=    4.089 closest distance to " O   HOH Z 227 " =    2.012
peak=    4.079 closest distance to " O   HOH Z 347 " =    1.020
peak=    4.065 closest distance to " O   HOH Z 406 " =    1.176
peak=    4.060 closest distance to " O   HOH Z   1 " =    1.621
peak=    4.049 closest distance to " O   HOH Z   4 " =    1.320
peak=    4.033 closest distance to " O   HOH Z 425 " =    1.476
peak=    4.031 closest distance to " O   HOH Z 276 " =    1.436
peak=    4.030 closest distance to " O   HOH Z   2 " =    1.854
peak=    4.027 closest distance to " O   HOH Z 108 " =    1.894
peak=    4.027 closest distance to " NE2 GLN A  73 " =    1.651
peak=    4.021 closest distance to " O   HOH Z 249 " =    1.238
peak=    4.013 closest distance to " O   HOH Z 334 " =    1.573
peak=    4.012 closest distance to " CB  VAL A 202 " =    1.685
peak=    4.008 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.003 closest distance to " O   HOH Z 366 " =    2.525
peak=    4.002 closest distance to " O   HOH Z 222 " =    1.272
peak=    3.999 closest distance to " O   HOH Z 209 " =    1.172
peak=    3.984 closest distance to " CB  GLN A 223 " =    1.665
peak=    3.968 closest distance to " O   HOH Z 145 " =    1.795
peak=    3.963 closest distance to " CB  VAL A 121 " =    1.054
peak=    3.956 closest distance to " O   HOH Z  18 " =    1.965
peak=    3.936 closest distance to " O   HOH Z  97 " =    2.059
peak=    3.926 closest distance to " O   HOH Z 380 " =    1.764
peak=    3.925 closest distance to " O   HOH Z  39 " =    1.515
peak=    3.910 closest distance to " CA  PHE A 283 " =    1.262
peak=    3.900 closest distance to " OD2 ASP A 286 " =    2.383
peak=    3.899 closest distance to " O   HOH Z  71 " =    1.527
peak=    3.896 closest distance to " CG  GLN A  11 " =    2.071
peak=    3.896 closest distance to " CG2 VAL A 257 " =    0.958
peak=    3.893 closest distance to " O   HOH Z 130 " =    1.683
peak=    3.883 closest distance to " O   HOH Z 423 " =    1.827
peak=    3.881 closest distance to " O   HOH Z 352 " =    1.367
peak=    3.880 closest distance to " CB  SER A 216 " =    0.911
peak=    3.870 closest distance to " OG BSER A 212 " =    2.742
peak=    3.864 closest distance to " O   HOH Z 202 " =    1.266
peak=    3.863 closest distance to " CA  ILE A 234 " =    0.963
peak=    3.857 closest distance to " O   HOH Z 244 " =    1.599
peak=    3.857 closest distance to " O   HOH Z  27 " =    1.055
peak=    3.856 closest distance to " CB  SER A 276 " =    1.301
peak=    3.848 closest distance to " O   HOH Z  47 " =    1.432
peak=    3.832 closest distance to " O   HOH Z 305 " =    3.027
peak=    3.832 closest distance to " NE2 GLN A  55 " =    1.234
peak=    3.828 closest distance to " CE  MET A  40 " =    0.908
peak=    3.828 closest distance to " O   HOH Z 419 " =    1.981
peak=    3.793 closest distance to " CB  ASN A 148 " =    1.131
peak=    3.780 closest distance to " OG ASER A 134 " =    1.575
peak=    3.780 closest distance to " NH1 ARG A  14 " =    0.955
peak=    3.761 closest distance to " O   HOH Z 148 " =    1.683
peak=    3.740 closest distance to " O   HOH Z 262 " =    2.355
peak=    3.736 closest distance to " O   HOH Z 137 " =    1.641
peak=    3.725 closest distance to " CG  LEU A 228 " =    1.158
peak=    3.724 closest distance to " O   HOH Z 392 " =    1.224
peak=    3.722 closest distance to " CG  LYS A 166 " =    1.289
peak=    3.713 closest distance to " CB  TRP A 179 " =    1.199
peak=    3.698 closest distance to " CA  TYR A  30 " =    1.054
peak=    3.694 closest distance to " O   HOH Z 384 " =    1.462
peak=    3.687 closest distance to " O   HOH Z 425 " =    2.081
peak=    3.684 closest distance to " CE  MET A  93 " =    1.424
peak=    3.684 closest distance to " O  BHOH Z  74 " =    1.232
peak=    3.680 closest distance to " CB  ASN A 215 " =    1.069
peak=    3.666 closest distance to " O   HOH Z 147 " =    1.505
peak=    3.663 closest distance to " CG  PRO A 198 " =    1.332
peak=    3.657 closest distance to " O   HOH Z  30 " =    1.702
peak=    3.656 closest distance to " O   HOH Z 259 " =    1.923
peak=    3.654 closest distance to " O   HOH Z 233 " =    1.475
peak=    3.652 closest distance to " N   TYR A  15 " =    1.151
peak=    3.652 closest distance to " O   HOH Z 423 " =    1.984
peak=    3.647 closest distance to " OG  SER A  62 " =    3.018
peak=    3.640 closest distance to " NZ  LYS A 117 " =    3.241
peak=    3.640 closest distance to " O   HOH Z  65 " =    1.501
peak=    3.634 closest distance to " O   HOH Z  28 " =    1.917
peak=    3.631 closest distance to " O   HOH Z 287 " =    1.516
peak=    3.625 closest distance to " O   HOH Z 114 " =    1.814
peak=    3.617 closest distance to " O   HOH Z 371 " =    1.860
peak=    3.614 closest distance to " CD  GLN A 194 " =    1.362
peak=    3.612 closest distance to " O   HOH Z 245 " =    1.392
peak=    3.612 closest distance to " NE2 GLN A  58 " =    5.622
peak=    3.602 closest distance to " O   HOH Z  44 " =    1.961
peak=    3.597 closest distance to " CA  ALA A  21 " =    1.072
peak=    3.591 closest distance to " O   HOH Z 153 " =    3.199
peak=    3.581 closest distance to " CA  LEU A 282 " =    1.104
peak=    3.577 closest distance to " O   HOH Z 176 " =    1.833
peak=    3.575 closest distance to " O   HOH Z 179 " =    1.156
peak=    3.566 closest distance to " O   HOH Z 260 " =    1.216
peak=    3.565 closest distance to " O   HOH Z 108 " =    1.248
peak=    3.565 closest distance to " CA  ASN A 127 " =    1.083
peak=    3.561 closest distance to " CG  LEU A 281 " =    1.003
peak=    3.560 closest distance to " O   HOH Z 247 " =    1.256
peak=    3.550 closest distance to " CB  PRO A  90 " =    1.276
peak=    3.550 closest distance to " CB  SER A  62 " =    1.148
peak=    3.549 closest distance to " CA  ASN A 284 " =    0.991
peak=    3.536 closest distance to " CG AARG A 275 " =    1.217
peak=    3.535 closest distance to " O   HOH Z 422 " =    2.191
peak=    3.533 closest distance to " O   HOH Z 193 " =    1.862
peak=    3.532 closest distance to " O   HOH Z 326 " =    1.895
peak=    3.530 closest distance to " NE BARG A 275 " =    1.177
peak=    3.518 closest distance to " O   HOH Z 418 " =    0.972
peak=    3.515 closest distance to " O   HOH Z  50 " =    1.495
peak=    3.503 closest distance to " O   HOH Z 298 " =    1.740
peak=    3.502 closest distance to " O   HOH Z 158 " =    3.019
peak=    3.499 closest distance to " OD1 ASN A  45 " =    1.141
peak=    3.497 closest distance to " OD1 ASP A 286 " =    1.293
peak=    3.493 closest distance to " O   HOH Z 356 " =    1.305
peak=    3.484 closest distance to " O   HOH Z  89 " =    2.201
peak=    3.483 closest distance to " CB  GLN A 183 " =    1.096
peak=    3.481 closest distance to " NH2 ARG A 156 " =    1.115
peak=    3.481 closest distance to " N   PHE A 130 " =    1.302
peak=    3.477 closest distance to " OG1 THR A 294 " =    2.443
peak=    3.475 closest distance to " O   HOH Z 394 " =    1.544
peak=    3.474 closest distance to " OD2 ASP A  50 " =    0.916
peak=    3.473 closest distance to " OG BSER A 210 " =    1.420
peak=    3.467 closest distance to " O   HOH Z 393 " =    1.444
peak=    3.464 closest distance to " O   HOH Z  93 " =    2.029
peak=    3.460 closest distance to " O   HOH Z 411 " =    3.486
peak=    3.456 closest distance to " O   HOH Z 389 " =    1.328
peak=    3.456 closest distance to " CB  GLN A 278 " =    0.789
peak=    3.452 closest distance to " O   HOH Z 406 " =    1.417
peak=    3.451 closest distance to " O   HOH Z 129 " =    0.864
peak=    3.441 closest distance to " O   HOH Z 106 " =    2.557
peak=    3.438 closest distance to " O   HOH Z 134 " =    1.385
peak=    3.433 closest distance to " O   HOH Z  58 " =    1.808
peak=    3.430 closest distance to " NH2BARG A 190 " =    1.446
peak=    3.429 closest distance to " CA  ARG A 195 " =    1.401
peak=    3.425 closest distance to " O   HOH Z  46 " =    1.014
peak=    3.425 closest distance to " CA  ALA A  51 " =    1.069
peak=    3.417 closest distance to " N   ALA A   1 " =    3.049
peak=    3.416 closest distance to " O   HOH Z 185 " =    1.319
peak=    3.415 closest distance to " CB  TYR A  30 " =    1.744
peak=    3.413 closest distance to " CB  LEU A 255 " =    0.952
peak=    3.413 closest distance to " NZ  LYS A 119 " =    2.416
peak=    3.407 closest distance to " O   HOH Z 400 " =    0.779
peak=    3.403 closest distance to " NZ BLYS A 290 " =    1.088
peak=    3.403 closest distance to " N   GLN A 278 " =    1.024
peak=    3.402 closest distance to " O   HOH Z 234 " =    1.967
peak=    3.402 closest distance to " O   HOH Z 405 " =    1.527
peak=    3.399 closest distance to " CB  ALA A   1 " =    1.020
peak=    3.396 closest distance to " CG1 ILE A 120 " =    1.360
peak=    3.396 closest distance to " CB  ALA A 291 " =    1.292
peak=    3.396 closest distance to " O   HOH Z 119 " =    1.453
peak=    3.387 closest distance to " CG  GLN A  88 " =    1.115
peak=    3.387 closest distance to " CB  ASN A  60 " =    0.955
peak=    3.386 closest distance to " CG  LYS A  76 " =    1.627
peak=    3.380 closest distance to " CB BVAL A  41 " =    1.115
peak=    3.379 closest distance to " CB  ASP A 200 " =    0.920
peak=    3.378 closest distance to " CG2 ILE A  20 " =    1.740
peak=    3.378 closest distance to " O   HOH Z  59 " =    2.135
peak=    3.377 closest distance to " CB  ASN A 127 " =    0.872
peak=    3.376 closest distance to " CD  LYS A 119 " =    1.747
peak=    3.370 closest distance to " O   HOH Z 261 " =    1.693
peak=    3.362 closest distance to " CB  PHE A 130 " =    1.044
peak=    3.359 closest distance to " O   HOH Z 364 " =    1.762
peak=    3.358 closest distance to " CB  GLU A 128 " =    1.042
peak=    3.357 closest distance to " O   HOH Z 412 " =    1.992
peak=    3.354 closest distance to " CA  ASN A 176 " =    1.151
peak=    3.354 closest distance to " CA  ASN A 215 " =    0.915
peak=    3.352 closest distance to " O   HOH Z 212 " =    1.600
peak=    3.344 closest distance to " O   HOH Z 251 " =    1.878
peak=    3.343 closest distance to " ND1 HIS A  81 " =    1.080
peak=    3.342 closest distance to " CA  ARG A  36 " =    1.036
peak=    3.342 closest distance to " CG  ARG A 156 " =    1.019
peak=    3.336 closest distance to " O   HOH Z 329 " =    3.250
peak=    3.333 closest distance to " O   HOH Z 303 " =    1.753
peak=    3.330 closest distance to " CD  ARG A 269 " =    1.057
peak=    3.327 closest distance to " O   HOH Z 290 " =    1.071
peak=    3.325 closest distance to " CZ  PHE A  38 " =    1.143
peak=    3.324 closest distance to " CB  ALA A 248 " =    1.390
peak=    3.321 closest distance to " NH2AARG A 145 " =    0.982
peak=    3.319 closest distance to " CB  SER A  26 " =    1.614
peak=    3.315 closest distance to " CB  ALA A 131 " =    1.708
peak=    3.315 closest distance to " O   HOH Z  85 " =    1.231
peak=    3.312 closest distance to " O   HOH Z 203 " =    1.724
peak=    3.312 closest distance to " CG2 ILE A  20 " =    1.124
peak=    3.309 closest distance to " CD1 ILE A  33 " =    1.715
peak=    3.305 closest distance to " O   HOH Z  55 " =    1.990
peak=    3.304 closest distance to " O   HOH Z 367 " =    3.828
peak=    3.299 closest distance to " CA  ALA A 158 " =    1.256
peak=    3.297 closest distance to " O   HOH Z 118 " =    2.090
peak=    3.295 closest distance to " CG  LYS A 119 " =    1.099
peak=    3.294 closest distance to " CG1 VAL A 153 " =    0.857
peak=    3.288 closest distance to " O   HOH Z 428 " =    1.029
peak=    3.285 closest distance to " N   GLU A   2 " =    1.185
peak=    3.285 closest distance to " O   HOH Z 257 " =    2.140
peak=    3.284 closest distance to " O   HOH Z 211 " =    1.065
peak=    3.283 closest distance to " CB  ARG A  79 " =    1.447
peak=    3.282 closest distance to " O   HOH Z 194 " =    1.799
peak=    3.281 closest distance to " O   HOH Z 402 " =    1.439
peak=    3.280 closest distance to " CG1 VAL A 126 " =    0.995
peak=    3.279 closest distance to " O   HOH Z 366 " =    1.963
peak=    3.278 closest distance to " CB  ASN A 187 " =    1.058
peak=    3.276 closest distance to " CD2 LEU A 297 " =    1.005
peak=    3.273 closest distance to " O   HOH Z 314 " =    1.628
peak=    3.270 closest distance to " CB  GLU A 277 " =    3.490
peak=    3.268 closest distance to " O   HOH Z 413 " =    1.360
peak=    3.266 closest distance to " CB  LYS A 117 " =    1.169
peak=    3.263 closest distance to " CB  PRO A 198 " =    1.139
peak=    3.259 closest distance to " O   HOH Z  78 " =    2.177
peak=    3.251 closest distance to " O   HOH Z 344 " =    2.836
peak=    3.248 closest distance to " CG  PRO A 243 " =    1.248
peak=    3.248 closest distance to " O   HOH Z 272 " =    2.022
peak=    3.246 closest distance to " O   HOH Z 128 " =    2.181
peak=    3.243 closest distance to " O   HOH Z 365 " =    5.603
peak=    3.243 closest distance to " O   HOH Z 222 " =    1.956
peak=    3.243 closest distance to " O   HOH Z 126 " =    1.361
peak=    3.241 closest distance to " CB  ARG A 138 " =    0.899
peak=    3.240 closest distance to " CB  MET A  40 " =    0.907
peak=    3.238 closest distance to " O   HOH Z 116 " =    5.673
peak=    3.237 closest distance to " CA  VAL A 265 " =    1.364
peak=    3.236 closest distance to " O   HOH Z 303 " =    2.282
peak=    3.235 closest distance to " N   ASN A 148 " =    1.043
peak=    3.234 closest distance to " O   HOH Z 134 " =    1.907
peak=    3.230 closest distance to " NZ  LYS A 117 " =    0.973
peak=    3.222 closest distance to " O   HOH Z 410 " =    3.162
peak=    3.218 closest distance to " CD2 LEU A 167 " =    1.168
peak=    3.215 closest distance to " O   HOH Z 213 " =    1.746
peak=    3.206 closest distance to " OG BSER A 216 " =    1.868
peak=    3.206 closest distance to " O   HOH Z 337 " =    1.659
peak=    3.200 closest distance to " O   HOH Z   9 " =    1.895
peak=    3.199 closest distance to " O   HOH Z 215 " =    1.497
peak=    3.197 closest distance to " CG2 THR A 221 " =    1.221
peak=    3.185 closest distance to " O   HOH Z 327 " =    1.818
peak=    3.184 closest distance to " O   HOH Z 326 " =    1.251
peak=    3.182 closest distance to " O   HOH Z 261 " =    1.554
peak=    3.181 closest distance to " CG1BVAL A 121 " =    2.258
peak=    3.176 closest distance to " CB  ALA A 114 " =    1.203
peak=    3.172 closest distance to " O   HOH Z 392 " =    1.574
peak=    3.171 closest distance to " OD1 ASP A 171 " =    1.309
peak=    3.165 closest distance to " O   ASP A 124 " =    1.142
peak=    3.163 closest distance to " CD1 TYR A  15 " =    1.068
peak=    3.162 closest distance to " N   ASP A 286 " =    1.027
peak=    3.160 closest distance to " O   HOH Z 250 " =    1.395
peak=    3.160 closest distance to " CG2 VAL A 232 " =    1.214
peak=    3.160 closest distance to " OG BSER A 164 " =    2.401
peak=    3.157 closest distance to " O   HOH Z  22 " =    1.993
peak=    3.157 closest distance to " O   HOH Z 128 " =    1.923
peak=    3.156 closest distance to " C   LYS A 290 " =    1.319
peak=    3.156 closest distance to " O   HOH Z 128 " =    2.247
peak=    3.153 closest distance to " CB  TYR A 247 " =    0.894
peak=    3.149 closest distance to " CB  ASN A 142 " =    1.141
peak=    3.147 closest distance to " CD1 LEU A   5 " =    1.771
peak=    3.143 closest distance to " O   HOH Z 293 " =    1.574
peak=    3.137 closest distance to " O   HOH Z  89 " =    1.596
peak=    3.136 closest distance to " OE2 GLU A  53 " =    2.058
peak=    3.134 closest distance to " O   HOH Z 433 " =    2.117
peak=    3.134 closest distance to " NE2 GLN A  58 " =    3.367
peak=    3.134 closest distance to " O   HOH Z 345 " =    3.031
peak=    3.130 closest distance to " O   HOH Z 145 " =    2.259
peak=    3.125 closest distance to " O   HOH Z 324 " =    1.379
peak=    3.113 closest distance to " NE2 GLN A 278 " =    3.722
peak=    3.108 closest distance to " O   HOH Z 384 " =    1.542
peak=    3.105 closest distance to " O   HOH Z 368 " =    1.992
peak=    3.085 closest distance to " O   HOH Z  61 " =    1.436
peak=    3.073 closest distance to " CB  SER A 273 " =    0.741
peak=    3.071 closest distance to " O   HOH Z 207 " =    1.964
peak=    3.065 closest distance to " O   HOH Z 164 " =    4.503
peak=    3.049 closest distance to " NH2AARG A 145 " =    2.296
peak=    3.040 closest distance to " CE BMET A  47 " =    1.403
peak=    3.035 closest distance to " O   HOH Z 189 " =    2.545
peak=    3.001 closest distance to " O   HOH Z  89 " =    2.054
peak=    2.991 closest distance to " CD  LYS A 119 " =    1.955

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.799 - 4.996
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.799 - 4.996

peak=   -4.900 closest distance to " CD  ARG A 138 " =    1.233
peak=   -4.759 closest distance to " O   HOH Z 385 " =    1.010
peak=   -4.394 closest distance to " O   HOH Z  69 " =    1.311
peak=   -4.346 closest distance to " O   PRO A 198 " =    1.062
peak=   -4.339 closest distance to " CG2 VAL A 230 " =    0.873
peak=   -4.213 closest distance to " CE2 PHE A 218 " =    2.517
peak=   -4.153 closest distance to " NH2 ARG A  79 " =    1.948
peak=   -4.116 closest distance to " CD  ARG A 156 " =    1.948
peak=   -4.113 closest distance to " OD2 ASP A  50 " =    1.019
peak=   -4.097 closest distance to " O   HOH Z 412 " =    4.996
peak=   -4.097 closest distance to " OG ASER A 134 " =    1.108
peak=   -4.097 closest distance to " O   HOH Z 195 " =    1.659
peak=   -4.039 closest distance to " O   HOH Z 103 " =    1.477
peak=   -3.962 closest distance to " C   HIS A 108 " =    1.195
peak=   -3.956 closest distance to " O   SER A 135 " =    1.642
peak=   -3.920 closest distance to " O   ILE A  49 " =    1.687
peak=   -3.911 closest distance to " O   HOH Z  88 " =    1.829
peak=   -3.903 closest distance to " CG2 THR A  52 " =    3.008
peak=   -3.886 closest distance to " O   HOH Z 131 " =    3.915
peak=   -3.875 closest distance to " NH1 ARG A  56 " =    2.507
peak=   -3.856 closest distance to " O   HOH Z  56 " =    1.784
peak=   -3.852 closest distance to " O   VAL A  67 " =    2.901
peak=   -3.847 closest distance to " OG BSER A 134 " =    1.287
peak=   -3.846 closest distance to " OD1 ASN A  39 " =    2.079
peak=   -3.817 closest distance to " O   SER A 245 " =    1.293
peak=   -3.812 closest distance to " O   HOH Z  65 " =    0.836
peak=   -3.800 closest distance to " CA  GLY A 133 " =    1.880
peak=   -3.784 closest distance to " CG  ARG A 138 " =    0.843
peak=   -3.768 closest distance to " O   HOH Z 385 " =    1.320
peak=   -3.721 closest distance to " O   HOH Z 347 " =    0.881
peak=   -3.716 closest distance to " O   HOH Z 359 " =    1.805
peak=   -3.705 closest distance to " N   GLN A  58 " =    1.118
peak=   -3.704 closest distance to " CB  SER A 245 " =    1.734
peak=   -3.690 closest distance to " N   ALA A   1 " =    1.280
peak=   -3.689 closest distance to " CD1 ILE A 239 " =    2.514
peak=   -3.658 closest distance to " O   HOH Z 125 " =    3.332
peak=   -3.653 closest distance to " O   HOH Z 357 " =    1.749
peak=   -3.651 closest distance to " CA  GLY A  98 " =    1.832
peak=   -3.644 closest distance to " CB  ALA A 248 " =    1.882
peak=   -3.643 closest distance to " OG  SER A   3 " =    1.188
peak=   -3.640 closest distance to " CA  GLY A  23 " =    1.923
peak=   -3.640 closest distance to " C   ASN A 285 " =    2.111
peak=   -3.632 closest distance to " O   HOH Z 388 " =    1.812
peak=   -3.629 closest distance to " O   HOH Z 372 " =    1.327
peak=   -3.625 closest distance to " O   SER A  22 " =    2.427
peak=   -3.625 closest distance to " O   HOH Z 235 " =    0.998
peak=   -3.624 closest distance to " O   HOH Z 368 " =    2.543
peak=   -3.613 closest distance to " O   SER A 271 " =    1.898
peak=   -3.611 closest distance to " CB  ILE A  33 " =    2.907
peak=   -3.604 closest distance to " O   HOH Z 404 " =    1.413
peak=   -3.595 closest distance to " SG  CYS A 254 " =    3.142
peak=   -3.581 closest distance to " O   GLY A  80 " =    2.358
peak=   -3.566 closest distance to " CE  LYS A 166 " =    1.038
peak=   -3.565 closest distance to " O   PRO A 198 " =    1.325
peak=   -3.563 closest distance to " N   MET A 188 " =    1.875
peak=   -3.553 closest distance to " O   HOH Z 134 " =    2.624
peak=   -3.551 closest distance to " OE2 GLU A 152 " =    0.995
peak=   -3.549 closest distance to " OE1 GLU A 277 " =    2.055
peak=   -3.535 closest distance to " N   THR A 157 " =    1.464
peak=   -3.534 closest distance to " O   PRO A 163 " =    1.843
peak=   -3.532 closest distance to " O   HOH Z 397 " =    1.418
peak=   -3.525 closest distance to " O   HOH Z 415 " =    1.017
peak=   -3.524 closest distance to " CE2 TYR A  30 " =    2.883
peak=   -3.516 closest distance to " CD1 TRP A 179 " =    1.073
peak=   -3.509 closest distance to " O   HOH Z 414 " =    2.502
peak=   -3.508 closest distance to " ND2 ASN A 173 " =    1.489
peak=   -3.498 closest distance to " O   HOH Z 407 " =    2.673
peak=   -3.486 closest distance to " CD2 LEU A   5 " =    1.064
peak=   -3.485 closest distance to " N   ALA A 226 " =    2.010
peak=   -3.484 closest distance to " CD  LYS A 289 " =    2.440
peak=   -3.467 closest distance to " O   HOH Z  52 " =    0.987
peak=   -3.451 closest distance to " CG  GLU A 152 " =    2.361
peak=   -3.449 closest distance to " C   LEU A 143 " =    1.003
peak=   -3.449 closest distance to " O   HOH Z 429 " =    2.016
peak=   -3.445 closest distance to " O   HOH Z 393 " =    3.133
peak=   -3.440 closest distance to " CD  GLU A 277 " =    1.098
peak=   -3.436 closest distance to " O   HOH Z  11 " =    1.940
peak=   -3.430 closest distance to " CG  GLN A  58 " =    0.999
peak=   -3.429 closest distance to " O   HOH Z 365 " =    1.417
peak=   -3.427 closest distance to " O   HOH Z 290 " =    0.971
peak=   -3.425 closest distance to " CD1 LEU A 228 " =    1.900
peak=   -3.419 closest distance to " O   HOH Z  54 " =    0.884
peak=   -3.417 closest distance to " O   HOH Z 210 " =    2.028
peak=   -3.413 closest distance to " O   HOH Z  24 " =    1.056
peak=   -3.410 closest distance to " CG  PHE A 283 " =    2.444
peak=   -3.404 closest distance to " CD1 LEU A 255 " =    2.730
peak=   -3.402 closest distance to " O   HOH Z 137 " =    1.465
peak=   -3.396 closest distance to " OG ASER A 134 " =    0.836
peak=   -3.396 closest distance to " CG  ARG A 219 " =    2.166
peak=   -3.388 closest distance to " OD2 ASP A  50 " =    1.382
peak=   -3.381 closest distance to " O   HOH Z 424 " =    1.654
peak=   -3.378 closest distance to " CG1 ILE A 263 " =    2.026
peak=   -3.377 closest distance to " O   ARG A  24 " =    1.819
peak=   -3.374 closest distance to " O   HOH Z 231 " =    1.858
peak=   -3.374 closest distance to " C   GLN A 205 " =    1.874
peak=   -3.358 closest distance to " CG  PRO A 163 " =    2.606
peak=   -3.355 closest distance to " O   PRO A 198 " =    1.029
peak=   -3.340 closest distance to " OG1 THR A 178 " =    1.030
peak=   -3.338 closest distance to " O   THR A 220 " =    1.537
peak=   -3.336 closest distance to " CD1 LEU A 101 " =    2.207
peak=   -3.335 closest distance to " O   GLU A  44 " =    1.795
peak=   -3.335 closest distance to " O   HOH Z 130 " =    1.989
peak=   -3.334 closest distance to " O   HOH Z 184 " =    0.924
peak=   -3.332 closest distance to " CG1BVAL A  72 " =    1.954
peak=   -3.330 closest distance to " ND2 ASN A 209 " =    1.630
peak=   -3.325 closest distance to " OD2 ASP A  50 " =    0.877
peak=   -3.323 closest distance to " O   HOH Z 211 " =    1.286
peak=   -3.317 closest distance to " O   HOH Z 416 " =    0.859
peak=   -3.316 closest distance to " OG  SER A 206 " =    1.332
peak=   -3.316 closest distance to " O   LYS A 289 " =    1.917
peak=   -3.310 closest distance to " CG  PRO A 243 " =    1.238
peak=   -3.304 closest distance to " O   HOH Z 102 " =    1.536
peak=   -3.301 closest distance to " O   HOH Z 377 " =    1.071
peak=   -3.293 closest distance to " CE1 TYR A 247 " =    2.472
peak=   -3.290 closest distance to " O   HOH Z 308 " =    1.625
peak=   -3.287 closest distance to " CB  ALA A   7 " =    1.934
peak=   -3.285 closest distance to " CB  GLN A  55 " =    1.239
peak=   -3.284 closest distance to " N   GLN A  58 " =    2.186
peak=   -3.284 closest distance to " N   VAL A  72 " =    1.901
peak=   -3.280 closest distance to " CG  PRO A 163 " =    1.400
peak=   -3.276 closest distance to " N   HIS A 115 " =    2.019
peak=   -3.273 closest distance to " O   HOH Z 298 " =    1.118
peak=   -3.270 closest distance to " O   HOH Z 431 " =    1.288
peak=   -3.268 closest distance to " CG  ASP A 231 " =    0.826
peak=   -3.267 closest distance to " ND2 ASN A 252 " =    1.946
peak=   -3.263 closest distance to " O   HOH Z 351 " =    1.450
peak=   -3.262 closest distance to " O   HOH Z 423 " =    2.550
peak=   -3.261 closest distance to " OD2 ASP A 270 " =    1.244
peak=   -3.259 closest distance to " CE BMET A  47 " =    1.377
peak=   -3.259 closest distance to " O   HOH Z 313 " =    1.580
peak=   -3.255 closest distance to " O   HOH Z 100 " =    1.308
peak=   -3.250 closest distance to " CB  ALA A 291 " =    2.372
peak=   -3.247 closest distance to " CG  GLN A  11 " =    1.983
peak=   -3.246 closest distance to " OXT GLY A 302 " =    2.840
peak=   -3.244 closest distance to " O   ILE A 106 " =    2.064
peak=   -3.239 closest distance to " CG  GLN A  88 " =    0.991
peak=   -3.235 closest distance to " O   VAL A 197 " =    1.325
peak=   -3.232 closest distance to " CD2 LEU A 282 " =    2.227
peak=   -3.231 closest distance to " CA  GLY A  35 " =    1.951
peak=   -3.228 closest distance to " CG  ARG A 219 " =    2.632
peak=   -3.225 closest distance to " O   HOH Z  52 " =    1.422
peak=   -3.223 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.223 closest distance to " O   HOH Z  92 " =    1.220
peak=   -3.223 closest distance to " O   HOH Z  13 " =    1.410
peak=   -3.220 closest distance to " O   HOH Z 313 " =    1.730
peak=   -3.219 closest distance to " O   ASN A 301 " =    1.611
peak=   -3.218 closest distance to " O   ALA A 161 " =    1.785
peak=   -3.216 closest distance to " CB  ASN A  39 " =    2.240
peak=   -3.215 closest distance to " OG BSER A 212 " =    1.854
peak=   -3.214 closest distance to " O   HOH Z 437 " =    1.992
peak=   -3.210 closest distance to " O   HOH Z  53 " =    1.645
peak=   -3.204 closest distance to " CE3 TRP A 274 " =    2.488
peak=   -3.202 closest distance to " O   HOH Z 203 " =    1.679
peak=   -3.192 closest distance to " CG  LEU A 228 " =    1.143
peak=   -3.183 closest distance to " CB  PHE A  59 " =    2.055
peak=   -3.183 closest distance to " O   HOH Z 438 " =    0.799
peak=   -3.182 closest distance to " CZ2 TRP A 179 " =    2.507
peak=   -3.180 closest distance to " CD1 ILE A 151 " =    2.370
peak=   -3.174 closest distance to " CD2 TRP A 150 " =    0.973
peak=   -3.170 closest distance to " O   HOH Z 266 " =    4.482
peak=   -3.167 closest distance to " O   HOH Z 166 " =    1.692
peak=   -3.163 closest distance to " CD2 LEU A 237 " =    2.491
peak=   -3.157 closest distance to " OG  SER A  97 " =    2.020
peak=   -3.156 closest distance to " O   GLY A 111 " =    1.833
peak=   -3.155 closest distance to " OG ASER A 216 " =    1.332
peak=   -3.153 closest distance to " O   HOH Z 359 " =    3.491
peak=   -3.138 closest distance to " CB  ALA A  43 " =    2.045
peak=   -3.136 closest distance to " O   HOH Z 185 " =    1.828
peak=   -3.133 closest distance to " C   ASN A 285 " =    1.367
peak=   -3.129 closest distance to " C   ARG A 269 " =    1.164
peak=   -3.126 closest distance to " O   HOH Z  60 " =    1.739
peak=   -3.122 closest distance to " O   HOH Z 234 " =    3.739
peak=   -3.118 closest distance to " O   HOH Z 137 " =    1.466
peak=   -3.118 closest distance to " O   PHE A 218 " =    1.599
peak=   -3.113 closest distance to " O   PRO A 163 " =    1.316
peak=   -3.111 closest distance to " O   LYS A 117 " =    1.508
peak=   -3.109 closest distance to " CG  ARG A 259 " =    2.835
peak=   -3.108 closest distance to " O   VAL A 125 " =    1.950
peak=   -3.107 closest distance to " O   HOH Z 387 " =    1.077
peak=   -3.095 closest distance to " NE2 GLN A  94 " =    1.621
peak=   -3.095 closest distance to " N   SER A 276 " =    1.078
peak=   -3.094 closest distance to " CG1 VAL A 197 " =    1.766
peak=   -3.094 closest distance to " O   ALA A  51 " =    1.180
peak=   -3.086 closest distance to " O   GLN A 194 " =    1.406
peak=   -3.082 closest distance to " CD2 PHE A 225 " =    0.891
peak=   -3.079 closest distance to " O   ASN A 187 " =    1.167
peak=   -3.076 closest distance to " OE1 GLN A 183 " =    1.565
peak=   -3.072 closest distance to " CE3 TRP A 179 " =    2.364
peak=   -3.069 closest distance to " N   GLN A 223 " =    1.543
peak=   -3.059 closest distance to " O   HOH Z 390 " =    2.004
peak=   -3.058 closest distance to " O   HOH Z 265 " =    1.899
peak=   -3.049 closest distance to " O   HOH Z 414 " =    2.253
peak=   -3.012 closest distance to " O   HOH Z 249 " =    0.834

================= 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    :  0.5104 0.5091   6.303581e+00   6.297697e+00
   1_bss:  0.5013 0.4969   6.296304e+00   6.288821e+00
   1_xyz:  0.4431 0.4675   6.234246e+00   6.259266e+00
   1_adp:  0.4033 0.4599   6.191640e+00   6.252788e+00
   1_occ:  0.4029 0.4599   6.190879e+00   6.252979e+00
   2_bss:  0.4019 0.4554   6.191266e+00   6.251169e+00
   2_xyz:  0.3216 0.3816   6.026968e+00   6.147044e+00
   2_adp:  0.2911 0.3570   5.957683e+00   6.097267e+00
   2_occ:  0.2907 0.3578   5.958040e+00   6.098453e+00
   3_bss:  0.2878 0.3566   5.954457e+00   6.094533e+00
   3_xyz:  0.2366 0.3016   5.791389e+00   5.958673e+00
   3_adp:  0.2209 0.2836   5.736789e+00   5.906249e+00
   3_occ:  0.2205 0.2831   5.735069e+00   5.904196e+00
   4_bss:  0.2203 0.2818   5.734100e+00   5.902188e+00
   4_xyz:  0.1721 0.2193   5.499122e+00   5.689369e+00
   4_adp:  0.1602 0.2096   5.439681e+00   5.647905e+00
   4_occ:  0.1599 0.2091   5.437993e+00   5.645375e+00
   5_bss:  0.1601 0.2090   5.437407e+00   5.644348e+00
   5_xyz:  0.1362 0.1810   5.294427e+00   5.513949e+00
   5_adp:  0.1295 0.1767   5.259677e+00   5.490943e+00
   5_occ:  0.1294 0.1768   5.259392e+00   5.490334e+00
   5_bss:  0.1296 0.1764   5.258020e+00   5.488570e+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:  0.378   0.000   6.971   9.338   7.920   0.000   0.000   0.000
   1_xyz:  0.378   0.000   6.971   9.338   7.920   0.000   0.000   0.000
   1_adp:  0.378   0.000   6.971   9.338   7.920   0.000   0.000   0.000
   1_occ:  0.378   0.000   6.971   9.338   7.920   0.000   0.000   0.000
   2_bss:  0.358  22.642   4.301   5.957   5.593   0.000   0.000   0.000
   2_xyz:  0.358  22.642   4.301   5.957   5.593   0.000   0.000   0.000
   2_adp:  0.358  22.642   4.301   5.957   5.593   0.000   0.000   0.000
   2_occ:  0.358  22.642   4.301   5.957   5.593   0.000   0.000   0.000
   3_bss:  0.347  43.382   2.118   2.956   3.143   0.000   0.000   0.000
   3_xyz:  0.347  43.382   2.118   2.956   3.143   0.000   0.000   0.000
   3_adp:  0.347  43.382   2.118   2.956   3.143   0.000   0.000   0.000
   3_occ:  0.347  43.382   2.118   2.956   3.143   0.000   0.000   0.000
   4_bss:  0.333  36.757   1.259   1.886   2.420   0.000   0.000   0.000
   4_xyz:  0.333  36.757   1.259   1.886   2.420   0.000   0.000   0.000
   4_adp:  0.333  36.757   1.259   1.886   2.420   0.000   0.000   0.000
   4_occ:  0.333  36.757   1.259   1.886   2.420   0.000   0.000   0.000
   5_bss:  0.333  36.757   0.749   1.065   2.033   0.000   0.000   0.000
   5_xyz:  0.333  36.757   0.749   1.065   2.033   0.000   0.000   0.000
   5_adp:  0.333  36.757   0.749   1.065   2.033   0.000   0.000   0.000
   5_occ:  0.333  36.757   0.749   1.065   2.033   0.000   0.000   0.000
   5_bss:  0.318  34.963  -0.533  -0.218   0.751   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.475 0.3096  0.3711    82866.150
   1_bss:  66.384 0.3093  0.4596    80114.935
   1_xyz:  58.771 0.4075  0.6020    68108.719
   1_adp:  55.738 0.4472  0.7168    65718.816
   1_occ:  55.717 0.4474  0.7161    65705.452
   2_bss:  55.344 0.4520  0.6622    65006.603
   2_xyz:  42.318 0.6145  0.8970    42284.594
   2_adp:  38.120 0.6653  0.9610    35746.329
   2_occ:  38.210 0.6642  0.9593    35884.008
   3_bss:  37.883 0.6678  0.8791    35322.666
   3_xyz:  30.403 0.7529  0.9600    23304.257
   3_adp:  27.745 0.7830  0.9806    20521.549
   3_occ:  27.653 0.7840  0.9810    20387.987
   4_bss:  27.613 0.7844  0.9490    20283.102
   4_xyz:  20.791 0.8545  0.9988    12128.268
   4_adp:  19.605 0.8662  0.9983    11181.993
   4_occ:  19.548 0.8667  0.9986    11106.552
   5_bss:  19.503 0.8670  0.9773    11044.410
   5_xyz:  16.583 0.8935  0.9925     8306.602
   5_adp:  16.020 0.8987  0.9881     7976.502
   5_occ:  16.015 0.8987  0.9880     7961.389
   5_bss:  15.981 0.8989  0.9879     7913.076
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2508e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2508e+01
   1_xyz:   1.828  0.015  0.112 18.383  0.007  4.102   1.6602e-01
   1_adp:   1.828  0.015  0.112 18.383  0.007  4.102   1.6602e-01
   1_occ:   1.828  0.015  0.112 18.383  0.007  4.102   1.6602e-01
   2_bss:   1.828  0.015  0.112 18.383  0.007  4.102   1.6602e-01
   2_xyz:   1.498  0.013  0.098 17.286  0.007  4.097   1.3282e-01
   2_adp:   1.498  0.013  0.098 17.286  0.007  4.097   1.3282e-01
   2_occ:   1.498  0.013  0.098 17.286  0.007  4.097   1.3282e-01
   3_bss:   1.498  0.013  0.098 17.286  0.007  4.097   1.3282e-01
   3_xyz:   1.003  0.006  0.069 16.068  0.003  4.114   6.5472e-02
   3_adp:   1.003  0.006  0.069 16.068  0.003  4.114   6.5472e-02
   3_occ:   1.003  0.006  0.069 16.068  0.003  4.114   6.5472e-02
   4_bss:   1.003  0.006  0.069 16.068  0.003  4.114   6.5472e-02
   4_xyz:   0.993  0.006  0.069 15.794  0.004  4.108   6.2473e-02
   4_adp:   0.993  0.006  0.069 15.794  0.004  4.108   6.2473e-02
   4_occ:   0.993  0.006  0.069 15.794  0.004  4.108   6.2473e-02
   5_bss:   0.993  0.006  0.069 15.794  0.004  4.108   6.2473e-02
   5_xyz:   0.963  0.006  0.067 15.633  0.003  4.105   5.9941e-02
   5_adp:   0.963  0.006  0.067 15.633  0.003  4.105   5.9941e-02
   5_occ:   0.963  0.006  0.067 15.633  0.003  4.105   5.9941e-02
   5_bss:   0.963  0.006  0.067 15.633  0.003  4.105   5.9941e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.867   6.7965e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.867   6.7965e+00
   1_xyz:  15.776  0.181  0.503 88.050  0.048  1.958   1.0743e-01
   1_adp:  15.776  0.181  0.503 88.050  0.048  1.958   1.0743e-01
   1_occ:  15.776  0.181  0.503 88.050  0.048  1.958   1.0743e-01
   2_bss:  15.776  0.181  0.503 88.050  0.048  1.958   1.0743e-01
   2_xyz:   9.561  0.171  0.418 83.589  0.063  2.094   1.0442e-01
   2_adp:   9.561  0.171  0.418 83.589  0.063  2.094   1.0442e-01
   2_occ:   9.561  0.171  0.418 83.589  0.063  2.094   1.0442e-01
   3_bss:   9.561  0.171  0.418 83.589  0.063  2.094   1.0442e-01
   3_xyz:   7.437  0.042  0.240 78.353  0.023  2.310   4.5095e-02
   3_adp:   7.437  0.042  0.240 78.353  0.023  2.310   4.5095e-02
   3_occ:   7.437  0.042  0.240 78.353  0.023  2.310   4.5095e-02
   4_bss:   7.437  0.042  0.240 78.353  0.023  2.310   4.5095e-02
   4_xyz:   7.873  0.047  0.246 82.484  0.027  2.343   4.9994e-02
   4_adp:   7.873  0.047  0.246 82.484  0.027  2.343   4.9994e-02
   4_occ:   7.873  0.047  0.246 82.484  0.027  2.343   4.9994e-02
   5_bss:   7.873  0.047  0.246 82.484  0.027  2.343   4.9994e-02
   5_xyz:   7.520  0.042  0.251 84.154  0.026  2.319   9.9462e-02
   5_adp:   7.520  0.042  0.251 84.154  0.026  2.319   9.9462e-02
   5_occ:   7.520  0.042  0.251 84.154  0.026  2.319   9.9462e-02
   5_bss:   7.520  0.042  0.251 84.154  0.026  2.319   9.9462e-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:  92.55   0.00  15.76  89.21   0.00  14.26  92.55   0.00  23.92
   1_occ:  92.55   0.00  15.76  89.21   0.00  14.26  92.55   0.00  23.92
   2_bss:  92.55   0.00  15.76  89.21   0.00  14.26  92.55   0.00  23.92
   2_xyz:  92.55   0.00  15.76  89.21   0.00  14.26  92.55   0.00  23.92
   2_adp: 101.28   0.00  14.79  95.89   0.00  11.88 101.28   0.00  30.64
   2_occ: 101.28   0.00  14.79  95.89   0.00  11.88 101.28   0.00  30.64
   3_bss: 101.28   0.00  14.79  95.89   0.00  11.88 101.28   0.00  30.64
   3_xyz: 101.28   0.00  14.79  95.89   0.00  11.88 101.28   0.00  30.64
   3_adp:  96.80   0.00  13.98  96.80   0.00  10.39  88.57   1.52  33.49
   3_occ:  96.80   0.00  13.98  96.80   0.00  10.39  88.57   1.52  33.49
   4_bss:  96.80   0.00  13.98  96.80   0.00  10.39  88.57   1.52  33.49
   4_xyz:  96.80   0.00  13.98  96.80   0.00  10.39  88.57   1.52  33.49
   4_adp:  94.96   0.00  13.88  94.96   0.00   9.74  84.14   3.19  36.39
   4_occ:  94.96   0.00  13.88  94.96   0.00   9.74  84.14   3.19  36.39
   5_bss:  94.96   0.00  13.88  94.96   0.00   9.74  84.14   3.19  36.39
   5_xyz:  94.96   0.00  13.88  94.96   0.00   9.74  84.14   3.19  36.39
   5_adp:  98.44   0.00  14.38  98.44   0.00   9.62  87.04   3.03  40.29
   5_occ:  98.44   0.00  14.38  98.44   0.00   9.62  87.04   3.03  40.29
   5_bss:  99.72   1.28  15.66  99.72   1.28  10.90  88.32   4.31  41.57
------------------------------------------------------------------------
 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:    1.268    0.019    0.423
   1_adp:    1.268    0.019    0.423
   1_occ:    1.268    0.019    0.423
   2_bss:    1.268    0.019    0.423
   2_xyz:    1.808    0.061    0.647
   2_adp:    1.808    0.061    0.647
   2_occ:    1.808    0.061    0.647
   3_bss:    1.808    0.061    0.647
   3_xyz:    1.713    0.051    0.727
   3_adp:    1.713    0.051    0.727
   3_occ:    1.713    0.051    0.727
   4_bss:    1.713    0.051    0.727
   4_xyz:    1.788    0.037    0.830
   4_adp:    1.788    0.037    0.830
   4_occ:    1.788    0.037    0.830
   5_bss:    1.788    0.037    0.830
   5_xyz:    1.902    0.047    0.869
   5_adp:    1.902    0.047    0.869
   5_occ:    1.902    0.047    0.869
   5_bss:    1.902    0.047    0.869
------------------------------------------------------------------------

CPU time actual refinement: 340.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_134/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_134/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_134/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_134/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_134/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.89 
  Macro-tasks:
    bulk solvent and scale       = 47.66  
    individual site refinement   = 132.92 
    weights calculation          = 32.56  
    collect and process          = 6.38   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 219.66 
  Micro-tasks:
    mask                            = 2.98   
    f_calc                          = 103.17 
    alpha_beta                      = 8.11   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 111.64 
    fmodel                         = 7.66   
    r_factors                      = 0.29   
    phase_errors                   = 10.16  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 245.43 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.849 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    632 calls, 102.87 s
gradients_fft:          578 calls,  99.23 s

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

# Date 2008-01-16 Time 00:51:16 PST -0800 (1200473476.97 s)
Start R-work = 0.5104, R-free = 0.5091 (no bulk solvent and anisotropic scale)
Final R-work = 0.1456, R-free = 0.1901 (no bulk solvent and anisotropic scale)

Start R-work = 0.5013, R-free = 0.4969
Final R-work = 0.1296, R-free = 0.1764