# Date 2008-01-16 Time 00:27:22 PST -0800 (1200472042.03 s)
#phil __OFF__

Command line arguments: "../17.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29011
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 17

-------------------------------------------------------------------------------
  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: (68.4938, 45.9914, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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: (68.4938, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7371 1.95075
Completeness in resolution range: 0.952494
Completeness with d_max=infinity: 0.94954

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7371
                             d_min =   1.9507

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: (68.4938, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7371 1.95075
Completeness in resolution range: 0.952494
Completeness with d_max=infinity: 0.94954

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7375 -  4.1739 [2167/2191]  1948   219  10.1%
  bin  2:  4.1739 -  3.3255 [2062/2081]  1857   205   9.9%
  bin  3:  3.3255 -  2.9088 [2050/2069]  1848   202   9.9%
  bin  4:  2.9088 -  2.6445 [2027/2057]  1817   210  10.4%
  bin  5:  2.6445 -  2.4559 [2013/2032]  1816   197   9.8%
  bin  6:  2.4559 -  2.3117 [2011/2036]  1808   203  10.1%
  bin  7:  2.3117 -  2.1963 [2009/2037]  1812   197   9.8%
  bin  8:  2.1963 -  2.1010 [1979/2015]  1776   203  10.3%
  bin  9:  2.1010 -  2.0203 [1981/2023]  1788   193   9.7%
  bin 10:  2.0203 -  1.9507 [1290/2025]  1160   130  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_17/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:
        1.37 -     2.08: 31
        2.08 -     2.78: 678
        2.78 -     3.49: 4652
        3.49 -     4.19: 9600
        4.19 -     4.90: 14048
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.374 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.384 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.524 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.558 3.040 -x+1/2,-y+1,z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.604 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 29004 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_17/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_17/model_refine_001.geo

CPU time processing inputs: 11.46


============================ 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 = 68.49375 45.9914 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5054   r_free= 0.5046   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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.302576                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7375 -  4.6553 0.99   1406  155 0.4236 0.4159      6.6332      6.6665|
|  2:  4.6553 -  3.7145 0.99   1351  152 0.4295 0.4419      6.8311      6.8501|
|  3:  3.7145 -  3.2507 0.99   1310  148 0.4730 0.4552      6.7229      6.7237|
|  4:  3.2507 -  2.9561 0.99   1327  139 0.4986 0.4686      6.5666      6.5379|
|  5:  2.9561 -  2.7457 0.99   1298  149 0.5325 0.5107      6.3839      6.4255|
|  6:  2.7457 -  2.5847 0.99   1305  143 0.5388 0.5534      6.3025      6.2228|
|  7:  2.5847 -  2.4559 0.99   1289  147 0.5336 0.5428      6.2595      6.1763|
|  8:  2.4559 -  2.3494 0.98   1286  143 0.5537 0.5375      6.2028      6.2158|
|  9:  2.3494 -  2.2593 0.98   1286  138 0.5259 0.5819      6.1145      6.2114|
| 10:  2.2593 -  2.1816 0.99   1290  145 0.5569 0.5598      6.1192      6.1017|
| 11:  2.1816 -  2.1136 0.98   1274  143 0.5482 0.5402      6.0472      6.0569|
| 12:  2.1136 -  2.0533 0.97   1264  139 0.5503 0.5523      5.9656      6.0509|
| 13:  2.0533 -  1.9994 0.99   1274  138 0.5492 0.5180      5.9017       5.811|
| 14:  1.9994 -  1.9507 0.51    670   80 0.5612 0.5407      5.9128      5.8077|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7375 -  4.6553  1406   155  0.63  40.13   0.78     0.68      92338.74|
|  2:  4.6553 -  3.7145  1351   152  0.64  40.36   0.86     0.72     132242.13|
|  3:  3.7145 -  3.2507  1310   148  0.52  50.15   0.85     0.66     140157.38|
|  4:  3.2507 -  2.9561  1327   139  0.42  58.09   0.79     0.52     123429.06|
|  5:  2.9561 -  2.7457  1298   149  0.29  67.85   0.73     0.37      99313.63|
|  6:  2.7457 -  2.5847  1305   143  0.23  72.87   0.70     0.27      87299.77|
|  7:  2.5847 -  2.4559  1289   147  0.14  79.67   0.75     0.16      80817.14|
|  8:  2.4559 -  2.3494  1286   143  0.14  79.91   0.71     0.16      72873.83|
|  9:  2.3494 -  2.2593  1286   138  0.15  79.00   0.73     0.19      67089.78|
| 10:  2.2593 -  2.1816  1290   145  0.20  75.20   0.74     0.25      57198.15|
| 11:  2.1816 -  2.1136  1274   143  0.19  75.56   0.75     0.25      55453.94|
| 12:  2.1136 -  2.0533  1264   139  0.20  75.50   0.76     0.26      48289.86|
| 13:  2.0533 -  1.9994  1274   138  0.22  73.95   0.74     0.29      41904.81|
| 14:  1.9994 -  1.9507   670    80  0.32  66.20   0.72     0.35      30575.02|
|alpha:            min =        0.16 max =            0.72 mean =         0.37|
|beta:             min =    30575.02 max =       140157.38 mean =     82939.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           90.00 mean =        66.43|
|phase err.(test): min =        0.00 max =           90.00 mean =        66.56|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.362515             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.063   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.271456              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.358   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:       12 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       47 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      185 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      726 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1574 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2713 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4041 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5191 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6672 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7902 |
|-----------------------------------------------------------------------------|
|-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 |       52.752 |
| 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  1.196 |       3.577 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    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 = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5101   r_free= 0.5041   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.302594                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4970   r_free= 0.4922   ksol= 0.36   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.80,9.61,8.15,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.295661                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.731796             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.117945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.840   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4970      final r-factor (work) = 0.4365          |
| start r-factor (free) = 0.4922      final r-factor (free) = 0.4651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 111.7537 = 18.73 * 0.50 * 6.2996 + 1.00 * 52.7524                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.6704 = 18.73 * 0.50 * 6.2473 + 1.00 * 0.1586                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4365      final r-factor (work) = 0.3993          |
| start r-factor (free) = 0.4651      final r-factor (free) = 0.4654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.2459 = 2.12 * 1.00 * 6.2473 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1520 = 2.12 * 1.00 * 6.2001 + 1.00 * 0.0205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.24   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    64.24   13.80    None  None   None       |
|    Sol.    : 438    0      0.00    64.24   19.52    None  None   None       |
|    Mac.    : 2385   0      0.00    51.68   12.75    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 -   6.424:  747   |   5:    32.118 -  38.541:  116        |
|      1:     6.424 -  12.847:  777   |   6:    38.541 -  44.965:   47        |
|      2:    12.847 -  19.271:  555   |   7:    44.965 -  51.389:   16        |
|      3:    19.271 -  25.694:  359   |   8:    51.389 -  57.812:    4        |
|      4:    25.694 -  32.118:  200   |   9:    57.812 -  64.236:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3993 r_free = 0.4654             target_work(ml) = 6.194         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3989 r_free = 0.4647             target_work(ml) = 6.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3989   r_free= 0.4647   ksol= 0.36   Bsol= 0.00   scale= 1.100    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.80,9.61,8.15,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.193278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3975   r_free= 0.4606   ksol= 0.35   Bsol= 20.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,6.26,5.57,0.00,0.00,0.00); trace/3= 5.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.193667                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.686059              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.211  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.087606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3975      final r-factor (work) = 0.3436          |
| start r-factor (free) = 0.4606      final r-factor (free) = 0.4104          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1769 = 9.69 * 0.50 * 6.1983 + 1.00 * 0.1586                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8235 = 9.69 * 0.50 * 6.1391 + 1.00 * 0.0917                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3436      final r-factor (work) = 0.3240          |
| start r-factor (free) = 0.4104      final r-factor (free) = 0.3959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7009 = 1.09 * 1.00 * 6.1391 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6242 = 1.09 * 1.00 * 6.0640 + 1.00 * 0.0290                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.50   14.86    None  None   None       |
|    all(noH): 2823   0      0.00    78.50   14.86    None  None   None       |
|    Sol.    : 438    0      0.00    78.21   27.78    None  None   None       |
|    Mac.    : 2385   0      0.00    78.50   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.850: 1020   |   5:    39.249 -  47.099:   72        |
|      1:     7.850 -  15.700:  731   |   6:    47.099 -  54.949:   31        |
|      2:    15.700 -  23.550:  487   |   7:    54.949 -  62.799:   21        |
|      3:    23.550 -  31.400:  293   |   8:    62.799 -  70.649:   11        |
|      4:    31.400 -  39.249:  154   |   9:    70.649 -  78.499:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3240 r_free = 0.3959             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3238 r_free = 0.3960             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3238   r_free= 0.3960   ksol= 0.35   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.14,6.26,5.57,0.00,0.00,0.00); trace/3= 5.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.049768                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3225   r_free= 0.3953   ksol= 0.35   Bsol= 47.69   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.69,3.70,3.69,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.050019                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.718366              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.993  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.996  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3225      final r-factor (work) = 0.2500          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3139          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.5180 = 8.72 * 0.50 * 6.0622 + 1.00 * 0.0917                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0787 = 8.72 * 0.50 * 5.9599 + 1.00 * 0.0984                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2500      final r-factor (work) = 0.2215          |
| start r-factor (free) = 0.3139      final r-factor (free) = 0.2859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6883 = 0.78 * 1.00 * 5.9599 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9138 = 0.78 * 1.00 * 5.7874 + 1.00 * 0.3814                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.35   14.87    None  None   None       |
|    all(noH): 2823   0      0.00    84.35   14.87    None  None   None       |
|    Sol.    : 438    0      1.54    84.35   36.68    None  None   None       |
|    Mac.    : 2385   0      0.00    83.33   10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.435: 1231   |   5:    42.175 -  50.610:   96        |
|      1:     8.435 -  16.870:  790   |   6:    50.610 -  59.045:   66        |
|      2:    16.870 -  25.305:  290   |   7:    59.045 -  67.479:   28        |
|      3:    25.305 -  33.740:  179   |   8:    67.479 -  75.914:   12        |
|      4:    33.740 -  42.175:  126   |   9:    75.914 -  84.349:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2215 r_free = 0.2859             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2209 r_free = 0.2858             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2209   r_free= 0.2858   ksol= 0.35   Bsol= 47.69   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.69,3.70,3.69,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.737606                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2197   r_free= 0.2839   ksol= 0.34   Bsol= 47.69   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,2.08,2.90,0.00,0.00,0.00); trace/3= 2.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.732366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.708488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.977   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 29.318531             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.134   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2197      final r-factor (work) = 0.1798          |
| start r-factor (free) = 0.2839      final r-factor (free) = 0.2401          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9360 = 2.71 * 0.50 * 5.7875 + 1.00 * 0.0984                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7104 = 2.71 * 0.50 * 5.6528 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1798      final r-factor (work) = 0.1673          |
| start r-factor (free) = 0.2401      final r-factor (free) = 0.2380          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 165.7486 = 29.32 * 1.00 * 5.6528 + 1.00 * 0.0167                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 162.0439 = 29.32 * 1.00 * 5.5263 + 1.00 * 0.0205                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.20  16.20    None  None   None       |
|    all(noH): 2823   0      0.00    107.20  16.20    None  None   None       |
|    Sol.    : 438    0      2.04    107.20  46.04    None  None   None       |
|    Mac.    : 2385   0      0.00    104.35  10.71    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 -  10.720: 1637   |   5:    53.602 -  64.322:   89        |
|      1:    10.720 -  21.441:  574   |   6:    64.322 -  75.042:   74        |
|      2:    21.441 -  32.161:  177   |   7:    75.042 -  85.762:   30        |
|      3:    32.161 -  42.881:  118   |   8:    85.762 -  96.483:   14        |
|      4:    42.881 -  53.602:  105   |   9:    96.483 - 107.203:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1673 r_free = 0.2380             target_work(ml) = 5.519         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1671 r_free = 0.2378             target_work(ml) = 5.519         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2378   ksol= 0.34   Bsol= 47.69   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,2.08,2.90,0.00,0.00,0.00); trace/3= 2.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.518695                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1672   r_free= 0.2380   ksol= 0.31   Bsol= 44.43   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,1.53,2.81,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.517345                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.673466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.514  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.607390              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.776  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1672      final r-factor (work) = 0.1418          |
| start r-factor (free) = 0.2380      final r-factor (free) = 0.2035          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2048 = 3.67 * 0.50 * 5.5260 + 1.00 * 0.0550                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0793 = 3.67 * 0.50 * 5.4539 + 1.00 * 0.0619                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.2035      final r-factor (free) = 0.1873          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3347 = 0.61 * 1.00 * 5.4539 + 1.00 * 0.0220                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3200 = 0.61 * 1.00 * 5.3475 + 1.00 * 0.0720                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.24  15.06    None  None   None       |
|    all(noH): 2823   0      0.00    104.24  15.06    None  None   None       |
|    Sol.    : 438    0      2.04    104.24  43.50    None  None   None       |
|    Mac.    : 2385   0      0.00    103.66  9.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.424: 1724   |   5:    52.122 -  62.546:   75        |
|      1:    10.424 -  20.849:  545   |   6:    62.546 -  72.970:   57        |
|      2:    20.849 -  31.273:  152   |   7:    72.970 -  83.395:   24        |
|      3:    31.273 -  41.697:  112   |   8:    83.395 -  93.819:   22        |
|      4:    41.697 -  52.122:  109   |   9:    93.819 - 104.243:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1354 r_free = 0.1873             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1352 r_free = 0.1868             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1868   ksol= 0.31   Bsol= 44.43   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,1.53,2.81,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.300560                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7375 -  4.6553 0.99   1406  155 0.1036 0.1462      5.4592      5.6827|
|  2:  4.6553 -  3.7145 0.99   1351  152 0.0968 0.1425      5.5688      5.8205|
|  3:  3.7145 -  3.2507 0.99   1310  148 0.1288 0.1686      5.6552      5.9107|
|  4:  3.2507 -  2.9561 0.99   1327  139 0.1448 0.2199         5.6      5.8544|
|  5:  2.9561 -  2.7457 0.99   1298  149 0.1645 0.1856      5.5014      5.6579|
|  6:  2.7457 -  2.5847 0.99   1305  143 0.1506 0.2441      5.3698      5.6258|
|  7:  2.5847 -  2.4559 0.99   1289  147 0.1547 0.1994      5.3352      5.5047|
|  8:  2.4559 -  2.3494 0.98   1286  143 0.1487 0.1955      5.2744      5.4774|
|  9:  2.3494 -  2.2593 0.98   1286  138 0.1439 0.2151      5.1782      5.4836|
| 10:  2.2593 -  2.1816 0.99   1290  145 0.1388 0.1886      5.1103      5.2652|
| 11:  2.1816 -  2.1136 0.98   1274  143 0.1376 0.2084      5.0801      5.4156|
| 12:  2.1136 -  2.0533 0.97   1264  139 0.1459 0.1974      5.0557      5.3572|
| 13:  2.0533 -  1.9994 0.99   1274  138 0.1382 0.1768      4.9238      5.0548|
| 14:  1.9994 -  1.9507 0.51    670   80 0.1270 0.2041      4.7986      5.1248|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7375 -  4.6553  1406   155  0.92  11.29   0.98     0.96       9789.59|
|  2:  4.6553 -  3.7145  1351   152  0.94  10.34   1.04     1.02      12460.00|
|  3:  3.7145 -  3.2507  1310   148  0.91  14.90   1.06     1.05      15369.37|
|  4:  3.2507 -  2.9561  1327   139  0.89  16.91   1.03     1.02      14195.06|
|  5:  2.9561 -  2.7457  1298   149  0.87  19.12   1.02     0.98      11447.11|
|  6:  2.7457 -  2.5847  1305   143  0.87  19.83   0.99     0.95       9697.92|
|  7:  2.5847 -  2.4559  1289   147  0.87  19.85   1.01     0.96       8759.41|
|  8:  2.4559 -  2.3494  1286   143  0.87  19.61   1.01     0.99       8240.51|
|  9:  2.3494 -  2.2593  1286   138  0.88  18.48   1.01     0.96       6598.61|
| 10:  2.2593 -  2.1816  1290   145  0.87  19.08   1.01     0.97       5911.77|
| 11:  2.1816 -  2.1136  1274   143  0.87  19.41   1.02     0.97       5854.12|
| 12:  2.1136 -  2.0533  1264   139  0.87  19.44   1.02     1.02       5526.36|
| 13:  2.0533 -  1.9994  1274   138  0.88  18.87   1.02     0.99       4223.25|
| 14:  1.9994 -  1.9507   670    80  0.91  15.27   1.00     0.97       2971.25|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     2971.25 max =        15369.37 mean =      8899.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.84 mean =        17.31|
|phase err.(test): min =        0.00 max =           89.66 mean =        16.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1870   ksol= 0.31   Bsol= 43.66   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-0.29,1.17,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.301849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1355   r_free= 0.1870   ksol= 0.31   Bsol= 43.66   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-0.29,1.17,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.301849                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7375 -  4.6553 0.99   1406  155 0.1045 0.1463      5.4673      5.6839|
|  2:  4.6553 -  3.7145 0.99   1351  152 0.0977 0.1431      5.5753      5.8255|
|  3:  3.7145 -  3.2507 0.99   1310  148 0.1292 0.1678      5.6571      5.9082|
|  4:  3.2507 -  2.9561 0.99   1327  139 0.1451 0.2209      5.6005      5.8567|
|  5:  2.9561 -  2.7457 0.99   1298  149 0.1648 0.1855      5.5033      5.6587|
|  6:  2.7457 -  2.5847 0.99   1305  143 0.1509 0.2444      5.3703      5.6251|
|  7:  2.5847 -  2.4559 0.99   1289  147 0.1547 0.1998      5.3348      5.5053|
|  8:  2.4559 -  2.3494 0.98   1286  143 0.1486 0.1952      5.2729      5.4743|
|  9:  2.3494 -  2.2593 0.98   1286  138 0.1438 0.2149      5.1772      5.4825|
| 10:  2.2593 -  2.1816 0.99   1290  145 0.1387 0.1884      5.1096      5.2653|
| 11:  2.1816 -  2.1136 0.98   1274  143 0.1373 0.2087      5.0803       5.418|
| 12:  2.1136 -  2.0533 0.97   1264  139 0.1458 0.1974      5.0556      5.3568|
| 13:  2.0533 -  1.9994 0.99   1274  138 0.1382 0.1768      4.9242      5.0544|
| 14:  1.9994 -  1.9507 0.51    670   80 0.1269 0.2043      4.7991      5.1276|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7375 -  4.6553  1406   155  0.92  11.31   0.98     0.95       9793.93|
|  2:  4.6553 -  3.7145  1351   152  0.94  10.38   1.04     1.03      12543.14|
|  3:  3.7145 -  3.2507  1310   148  0.91  14.96   1.06     1.05      15445.44|
|  4:  3.2507 -  2.9561  1327   139  0.89  16.97   1.03     1.02      14230.81|
|  5:  2.9561 -  2.7457  1298   149  0.87  19.11   1.02     0.98      11456.35|
|  6:  2.7457 -  2.5847  1305   143  0.87  19.86   0.99     0.95       9704.93|
|  7:  2.5847 -  2.4559  1289   147  0.87  19.84   1.01     0.96       8744.33|
|  8:  2.4559 -  2.3494  1286   143  0.87  19.58   1.01     0.98       8208.21|
|  9:  2.3494 -  2.2593  1286   138  0.88  18.46   1.00     0.96       6583.03|
| 10:  2.2593 -  2.1816  1290   145  0.87  19.06   1.01     0.97       5900.06|
| 11:  2.1816 -  2.1136  1274   143  0.87  19.43   1.02     0.97       5865.20|
| 12:  2.1136 -  2.0533  1264   139  0.87  19.46   1.02     1.02       5531.33|
| 13:  2.0533 -  1.9994  1274   138  0.88  18.89   1.01     0.98       4234.42|
| 14:  1.9994 -  1.9507   670    80  0.91  15.29   0.99     0.97       2979.49|
|alpha:            min =        0.95 max =            1.05 mean =         0.99|
|beta:             min =     2979.49 max =        15445.44 mean =      8912.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.33|
|phase err.(test): min =        0.00 max =           89.48 mean =        16.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.321)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    105.95  16.77    None  None   None       |
|    all(noH): 2823   0      1.71    105.95  16.77    None  None   None       |
|    Sol.    : 438    0      3.75    105.95  45.21    None  None   None       |
|    Mac.    : 2385   0      1.71    105.38  11.54    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:     1.711 -  12.136: 1724   |   5:    53.833 -  64.257:   75        |
|      1:    12.136 -  22.560:  545   |   6:    64.257 -  74.682:   57        |
|      2:    22.560 -  32.984:  152   |   7:    74.682 -  85.106:   24        |
|      3:    32.984 -  43.409:  112   |   8:    85.106 -  95.530:   22        |
|      4:    43.409 -  53.833:  109   |   9:    95.530 - 105.955:    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)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.224 - 5.796
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 332
   mapped sites are within: 0.733 - 5.796

peak=    9.048 closest distance to " CB  VAL A 296 " =    1.469
peak=    8.920 closest distance to " O   HOH Z 178 " =    1.313
peak=    8.883 closest distance to " CB  VAL A 230 " =    1.402
peak=    7.469 closest distance to " O   HOH Z 130 " =    1.985
peak=    6.895 closest distance to " OD1 ASP A  27 " =    1.044
peak=    6.821 closest distance to " CD2 LEU A   5 " =    1.417
peak=    6.759 closest distance to " O   HOH Z  41 " =    1.040
peak=    6.398 closest distance to " CG  ARG A 138 " =    1.173
peak=    6.309 closest distance to " O   HOH Z 227 " =    1.916
peak=    6.086 closest distance to " O   HOH Z 422 " =    1.228
peak=    6.059 closest distance to " CD  ARG A 138 " =    0.992
peak=    5.857 closest distance to " O   HOH Z  83 " =    1.332
peak=    5.855 closest distance to " CD1AILE A 234 " =    0.961
peak=    5.635 closest distance to " O   HOH Z 385 " =    1.207
peak=    5.599 closest distance to " O   HOH Z 347 " =    0.995
peak=    5.549 closest distance to " NH1 ARG A 138 " =    0.952
peak=    5.538 closest distance to " O   HOH Z  65 " =    1.881
peak=    5.445 closest distance to " O   HOH Z 124 " =    1.604
peak=    5.419 closest distance to " O   HOH Z 427 " =    1.245
peak=    5.417 closest distance to " O   HOH Z  69 " =    1.436
peak=    5.408 closest distance to " O   HOH Z 236 " =    1.795
peak=    5.407 closest distance to " CB  ARG A 275 " =    1.202
peak=    5.306 closest distance to " NE2 GLN A  11 " =    1.066
peak=    5.271 closest distance to " O   HOH Z 428 " =    1.335
peak=    5.120 closest distance to " O   HOH Z  43 " =    1.487
peak=    5.075 closest distance to " O   HOH Z 214 " =    1.362
peak=    5.006 closest distance to " O   HOH Z 418 " =    1.349
peak=    4.991 closest distance to " O   HOH Z 427 " =    1.974
peak=    4.918 closest distance to " O   HOH Z 358 " =    1.437
peak=    4.886 closest distance to " O   HOH Z 417 " =    1.531
peak=    4.884 closest distance to " CB  VAL A 230 " =    1.184
peak=    4.883 closest distance to " O   HOH Z 424 " =    1.535
peak=    4.857 closest distance to " O   HOH Z   9 " =    1.675
peak=    4.794 closest distance to " O   PRO A 198 " =    1.256
peak=    4.787 closest distance to " CB  GLN A 278 " =    0.905
peak=    4.765 closest distance to " O   HOH Z 193 " =    1.713
peak=    4.758 closest distance to " NE1 TRP A 274 " =    1.167
peak=    4.676 closest distance to " CG2 ILE A 234 " =    0.899
peak=    4.627 closest distance to " O   HOH Z 142 " =    1.807
peak=    4.623 closest distance to " NH1AARG A 275 " =    1.076
peak=    4.602 closest distance to " O   HOH Z 415 " =    1.126
peak=    4.602 closest distance to " O   HOH Z 222 " =    1.384
peak=    4.561 closest distance to " NE1 TRP A 266 " =    1.866
peak=    4.516 closest distance to " O   HOH Z 371 " =    2.195
peak=    4.509 closest distance to " CG  PRO A  54 " =    1.341
peak=    4.507 closest distance to " O   HOH Z 344 " =    1.536
peak=    4.501 closest distance to " O   HOH Z 103 " =    1.115
peak=    4.461 closest distance to " CG  LEU A   5 " =    1.166
peak=    4.440 closest distance to " O   HOH Z 245 " =    1.280
peak=    4.427 closest distance to " O   HOH Z  24 " =    1.797
peak=    4.404 closest distance to " O   HOH Z  28 " =    1.388
peak=    4.400 closest distance to " O   HOH Z 425 " =    1.483
peak=    4.396 closest distance to " O   HOH Z 406 " =    1.563
peak=    4.366 closest distance to " O   HOH Z 126 " =    1.702
peak=    4.361 closest distance to " O   HOH Z  63 " =    1.477
peak=    4.358 closest distance to " O   HOH Z  49 " =    1.076
peak=    4.356 closest distance to " O   HOH Z  45 " =    1.056
peak=    4.332 closest distance to " N   ARG A 275 " =    0.749
peak=    4.330 closest distance to " O   HOH Z 248 " =    1.099
peak=    4.324 closest distance to " O   HOH Z 123 " =    1.630
peak=    4.310 closest distance to " O   HOH Z 117 " =    1.340
peak=    4.272 closest distance to " OD1 ASP A 286 " =    1.113
peak=    4.269 closest distance to " O   HOH Z  51 " =    1.976
peak=    4.263 closest distance to " CB  PRO A  54 " =    1.132
peak=    4.251 closest distance to " O   HOH Z  46 " =    1.143
peak=    4.250 closest distance to " O   HOH Z 419 " =    1.984
peak=    4.245 closest distance to " O   HOH Z 414 " =    1.422
peak=    4.243 closest distance to " O   HOH Z 423 " =    1.675
peak=    4.238 closest distance to " O   HOH Z 403 " =    2.157
peak=    4.206 closest distance to " O   HOH Z   3 " =    2.167
peak=    4.184 closest distance to " O   HOH Z 211 " =    1.339
peak=    4.173 closest distance to " O   HOH Z 258 " =    1.218
peak=    4.164 closest distance to " CG  LEU A 228 " =    1.157
peak=    4.153 closest distance to " O   HOH Z 120 " =    1.123
peak=    4.151 closest distance to " O   HOH Z 410 " =    1.233
peak=    4.133 closest distance to " CD1 ILE A  49 " =    2.511
peak=    4.122 closest distance to " CB  SER A   3 " =    1.314
peak=    4.120 closest distance to " CB  GLN A 223 " =    1.628
peak=    4.118 closest distance to " O   HOH Z  39 " =    1.666
peak=    4.100 closest distance to " O   HOH Z 272 " =    1.880
peak=    4.092 closest distance to " CG  PRO A 213 " =    1.264
peak=    4.088 closest distance to " O   HOH Z  11 " =    1.410
peak=    4.087 closest distance to " O   HOH Z 238 " =    1.080
peak=    4.087 closest distance to " O   HOH Z  91 " =    0.938
peak=    4.081 closest distance to " NZ  LYS A 117 " =    3.007
peak=    4.079 closest distance to " CG2 ILE A 120 " =    1.202
peak=    4.076 closest distance to " O   HOH Z  92 " =    1.169
peak=    4.054 closest distance to " O   HOH Z   7 " =    1.198
peak=    4.053 closest distance to " O   HOH Z 291 " =    1.508
peak=    4.032 closest distance to " O   HOH Z 112 " =    1.378
peak=    4.024 closest distance to " O   HOH Z 218 " =    2.282
peak=    4.002 closest distance to " O   HOH Z 293 " =    1.450
peak=    4.000 closest distance to " O   HOH Z  22 " =    1.970
peak=    3.981 closest distance to " NH2 ARG A  56 " =    1.972
peak=    3.961 closest distance to " O   HOH Z 390 " =    1.190
peak=    3.954 closest distance to " CA  TRP A 150 " =    0.933
peak=    3.951 closest distance to " NH2AARG A 145 " =    1.091
peak=    3.939 closest distance to " CA  ASN A 127 " =    1.121
peak=    3.918 closest distance to " CG  LYS A  76 " =    1.737
peak=    3.916 closest distance to " O   HOH Z  69 " =    1.838
peak=    3.911 closest distance to " CB  ALA A   1 " =    1.193
peak=    3.891 closest distance to " NZ  LYS A 119 " =    2.530
peak=    3.883 closest distance to " CB  ASN A 148 " =    1.416
peak=    3.881 closest distance to " O   HOH Z 223 " =    1.002
peak=    3.874 closest distance to " O   HOH Z 366 " =    2.548
peak=    3.862 closest distance to " O   HOH Z  77 " =    1.252
peak=    3.861 closest distance to " O   HOH Z  59 " =    1.432
peak=    3.858 closest distance to " O   HOH Z 156 " =    3.015
peak=    3.854 closest distance to " O   HOH Z 371 " =    2.423
peak=    3.852 closest distance to " CB  THR A  31 " =    1.611
peak=    3.851 closest distance to " O   HOH Z 132 " =    1.013
peak=    3.846 closest distance to " CE AMET A  47 " =    1.434
peak=    3.830 closest distance to " O   HOH Z 392 " =    1.416
peak=    3.821 closest distance to " O   HOH Z 147 " =    1.074
peak=    3.820 closest distance to " O   HOH Z 250 " =    2.360
peak=    3.812 closest distance to " CB  ASN A 142 " =    1.189
peak=    3.802 closest distance to " O   HOH Z  47 " =    1.643
peak=    3.796 closest distance to " O   HOH Z 305 " =    3.223
peak=    3.789 closest distance to " CG2 THR A 221 " =    1.303
peak=    3.787 closest distance to " O   HOH Z 352 " =    1.539
peak=    3.776 closest distance to " O   HOH Z 137 " =    1.523
peak=    3.764 closest distance to " CB  SER A  63 " =    1.227
peak=    3.758 closest distance to " NE2 GLN A  73 " =    1.572
peak=    3.757 closest distance to " O   HOH Z 249 " =    1.175
peak=    3.753 closest distance to " NH2BARG A 190 " =    1.563
peak=    3.746 closest distance to " CE1 PHE A  38 " =    1.129
peak=    3.744 closest distance to " NH1 ARG A  14 " =    1.024
peak=    3.740 closest distance to " CB  ALA A 248 " =    1.379
peak=    3.738 closest distance to " O   HOH Z 316 " =    2.909
peak=    3.737 closest distance to " O   HOH Z 259 " =    2.127
peak=    3.722 closest distance to " O   HOH Z 257 " =    2.353
peak=    3.719 closest distance to " O   HOH Z  85 " =    1.474
peak=    3.706 closest distance to " CD  GLN A  58 " =    5.796
peak=    3.704 closest distance to " OD1 ASN A  45 " =    1.254
peak=    3.692 closest distance to " O  BHOH Z  74 " =    1.249
peak=    3.690 closest distance to " O   HOH Z 388 " =    1.155
peak=    3.679 closest distance to " O   HOH Z 150 " =    1.214
peak=    3.679 closest distance to " O   HOH Z 389 " =    1.621
peak=    3.678 closest distance to " CG  PRO A 243 " =    1.217
peak=    3.677 closest distance to " O   HOH Z 128 " =    1.893
peak=    3.670 closest distance to " OE1 GLU A  44 " =    1.070
peak=    3.667 closest distance to " CB  GLU A 277 " =    3.499
peak=    3.665 closest distance to " O   HOH Z 361 " =    1.319
peak=    3.655 closest distance to " CB  SER A 216 " =    0.976
peak=    3.653 closest distance to " O   HOH Z 248 " =    2.311
peak=    3.645 closest distance to " CZ3 TRP A 266 " =    1.227
peak=    3.638 closest distance to " O   HOH Z  76 " =    1.095
peak=    3.633 closest distance to " CD  GLN A  77 " =    1.264
peak=    3.625 closest distance to " O   HOH Z 119 " =    1.346
peak=    3.624 closest distance to " O   HOH Z 356 " =    1.371
peak=    3.621 closest distance to " O   HOH Z  65 " =    1.526
peak=    3.621 closest distance to " O   HOH Z 392 " =    1.667
peak=    3.621 closest distance to " O   HOH Z 153 " =    1.684
peak=    3.614 closest distance to " O   HOH Z 303 " =    2.185
peak=    3.613 closest distance to " O   HOH Z 244 " =    1.770
peak=    3.612 closest distance to " CB  SER A 276 " =    1.297
peak=    3.610 closest distance to " CB  ASN A 176 " =    1.064
peak=    3.605 closest distance to " O   HOH Z 130 " =    1.558
peak=    3.602 closest distance to " NH2BARG A 145 " =    1.708
peak=    3.601 closest distance to " CB  ASN A 110 " =    1.083
peak=    3.599 closest distance to " CA  TYR A  30 " =    0.992
peak=    3.597 closest distance to " CB  LEU A 300 " =    0.950
peak=    3.597 closest distance to " CA  ILE A 234 " =    1.086
peak=    3.597 closest distance to " CG  GLN A  58 " =    0.967
peak=    3.594 closest distance to " O   HOH Z 182 " =    0.958
peak=    3.589 closest distance to " O   HOH Z 422 " =    2.050
peak=    3.577 closest distance to " O   HOH Z 380 " =    2.096
peak=    3.574 closest distance to " O   HOH Z   4 " =    1.408
peak=    3.574 closest distance to " N   ARG A 156 " =    1.335
peak=    3.569 closest distance to " CB  GLU A 277 " =    1.069
peak=    3.562 closest distance to " O   HOH Z 289 " =    1.435
peak=    3.561 closest distance to " O   HOH Z   1 " =    1.769
peak=    3.561 closest distance to " O   HOH Z 429 " =    1.012
peak=    3.558 closest distance to " CG AARG A 275 " =    1.293
peak=    3.557 closest distance to " CB  ASN A 187 " =    1.010
peak=    3.556 closest distance to " O   HOH Z 426 " =    1.122
peak=    3.555 closest distance to " O   HOH Z 158 " =    2.832
peak=    3.555 closest distance to " O   HOH Z  44 " =    1.810
peak=    3.550 closest distance to " O   HOH Z  32 " =    2.030
peak=    3.548 closest distance to " O   HOH Z 407 " =    1.871
peak=    3.544 closest distance to " CG2 THR A  29 " =    1.112
peak=    3.542 closest distance to " O   HOH Z 125 " =    1.531
peak=    3.540 closest distance to " O   HOH Z 368 " =    2.090
peak=    3.538 closest distance to " CB  VAL A 202 " =    1.657
peak=    3.538 closest distance to " CB  GLN A 183 " =    1.192
peak=    3.533 closest distance to " O   HOH Z 425 " =    1.996
peak=    3.532 closest distance to " NE BARG A 145 " =    0.745
peak=    3.526 closest distance to " CG  LEU A 167 " =    1.216
peak=    3.511 closest distance to " CA  ARG A 159 " =    1.105
peak=    3.510 closest distance to " CA  ARG A 195 " =    1.376
peak=    3.509 closest distance to " CE  LYS A  48 " =    1.114
peak=    3.504 closest distance to " ND1 HIS A  81 " =    1.419
peak=    3.503 closest distance to " O   HOH Z  97 " =    1.089
peak=    3.499 closest distance to " O   HOH Z 189 " =    2.767
peak=    3.497 closest distance to " O   HOH Z 148 " =    1.644
peak=    3.494 closest distance to " O   HOH Z  85 " =    1.863
peak=    3.492 closest distance to " O   HOH Z  26 " =    1.525
peak=    3.490 closest distance to " CG2 ILE A  20 " =    1.855
peak=    3.488 closest distance to " O   HOH Z  61 " =    1.585
peak=    3.487 closest distance to " O   HOH Z 172 " =    2.714
peak=    3.484 closest distance to " O   HOH Z 164 " =    1.701
peak=    3.484 closest distance to " CG  PRO A 198 " =    1.412
peak=    3.481 closest distance to " CG  LYS A 166 " =    1.374
peak=    3.478 closest distance to " O   HOH Z 298 " =    1.632
peak=    3.476 closest distance to " CA  ALA A 129 " =    1.404
peak=    3.475 closest distance to " CB  VAL A 265 " =    1.454
peak=    3.475 closest distance to " O   HOH Z 362 " =    1.877
peak=    3.474 closest distance to " CB  ARG A 138 " =    0.770
peak=    3.471 closest distance to " CB  PHE A 204 " =    1.074
peak=    3.468 closest distance to " CD1 LEU A   5 " =    1.656
peak=    3.459 closest distance to " CB  ALA A 242 " =    1.334
peak=    3.458 closest distance to " CB  SER A 273 " =    0.923
peak=    3.458 closest distance to " O   HOH Z 185 " =    1.813
peak=    3.455 closest distance to " O   HOH Z 153 " =    3.100
peak=    3.451 closest distance to " N   GLU A 277 " =    0.967
peak=    3.449 closest distance to " O   VAL A  72 " =    0.918
peak=    3.443 closest distance to " CB  ARG A  79 " =    0.733
peak=    3.440 closest distance to " O   HOH Z 117 " =    1.884
peak=    3.435 closest distance to " O   HOH Z 350 " =    1.339
peak=    3.435 closest distance to " CB  ALA A 114 " =    1.477
peak=    3.432 closest distance to " O   HOH Z 403 " =    1.500
peak=    3.428 closest distance to " CG BARG A 102 " =    1.885
peak=    3.428 closest distance to " CE1 HIS A 115 " =    3.098
peak=    3.427 closest distance to " N   ALA A   1 " =    2.865
peak=    3.424 closest distance to " CG2BVAL A 121 " =    1.027
peak=    3.423 closest distance to " O   HOH Z 207 " =    2.658
peak=    3.423 closest distance to " CB  SER A  62 " =    1.112
peak=    3.421 closest distance to " N   PHE A 130 " =    1.300
peak=    3.420 closest distance to " C   GLN A  73 " =    1.020
peak=    3.419 closest distance to " O   HOH Z 188 " =    1.431
peak=    3.418 closest distance to " O   HOH Z 126 " =    1.438
peak=    3.416 closest distance to " O   HOH Z 227 " =    1.865
peak=    3.411 closest distance to " N   ASN A 148 " =    1.101
peak=    3.410 closest distance to " O   HOH Z 213 " =    1.626
peak=    3.405 closest distance to " CD2 LEU A 297 " =    1.029
peak=    3.404 closest distance to " CB  ASN A  74 " =    1.272
peak=    3.400 closest distance to " O   HOH Z 162 " =    1.454
peak=    3.399 closest distance to " CA  ALA A 184 " =    1.276
peak=    3.398 closest distance to " O   HOH Z 222 " =    2.073
peak=    3.391 closest distance to " CB  ALA A 114 " =    1.171
peak=    3.386 closest distance to " CG2 THR A 220 " =    0.963
peak=    3.373 closest distance to " OD2 ASP A 286 " =    2.103
peak=    3.370 closest distance to " CG2 ILE A  20 " =    1.194
peak=    3.369 closest distance to " O   HOH Z 384 " =    1.232
peak=    3.369 closest distance to " CD  GLN A 194 " =    1.420
peak=    3.365 closest distance to " O   HOH Z 225 " =    1.458
peak=    3.365 closest distance to " CD2 TRP A 179 " =    1.353
peak=    3.363 closest distance to " O   HOH Z 290 " =    1.091
peak=    3.361 closest distance to " CE3 TRP A 150 " =    1.137
peak=    3.355 closest distance to " CD1 ILE A  33 " =    1.760
peak=    3.352 closest distance to " O   HOH Z  80 " =    1.243
peak=    3.352 closest distance to " CB BVAL A  41 " =    1.043
peak=    3.348 closest distance to " C   ASN A 301 " =    1.017
peak=    3.343 closest distance to " O   HOH Z 145 " =    2.138
peak=    3.338 closest distance to " O   HOH Z 234 " =    3.484
peak=    3.331 closest distance to " N   ASN A  60 " =    0.935
peak=    3.329 closest distance to " O   HOH Z   6 " =    1.209
peak=    3.326 closest distance to " CE2 PHE A  16 " =    0.941
peak=    3.323 closest distance to " CB  SER A  99 " =    1.030
peak=    3.320 closest distance to " CA  PHE A 283 " =    1.277
peak=    3.318 closest distance to " O   HOH Z  89 " =    2.177
peak=    3.317 closest distance to " CB  GLN A 223 " =    1.619
peak=    3.313 closest distance to " ND2BASN A 224 " =    0.903
peak=    3.307 closest distance to " O   HOH Z 343 " =    2.821
peak=    3.301 closest distance to " NZ BLYS A 290 " =    1.094
peak=    3.300 closest distance to " O   HOH Z 281 " =    2.163
peak=    3.298 closest distance to " O   HOH Z  95 " =    1.489
peak=    3.297 closest distance to " O   HOH Z 423 " =    1.938
peak=    3.295 closest distance to " CG2 ILE A 151 " =    1.023
peak=    3.294 closest distance to " CB  TRP A 179 " =    1.312
peak=    3.294 closest distance to " O   HOH Z 337 " =    1.689
peak=    3.290 closest distance to " O   HOH Z  49 " =    2.998
peak=    3.287 closest distance to " NE2 GLN A  58 " =    4.307
peak=    3.286 closest distance to " CA  ASP A 253 " =    1.980
peak=    3.283 closest distance to " O   HOH Z 217 " =    2.333
peak=    3.280 closest distance to " O   HOH Z 223 " =    1.393
peak=    3.275 closest distance to " CG1 ILE A 120 " =    1.642
peak=    3.273 closest distance to " C   TRP A 274 " =    0.997
peak=    3.270 closest distance to " O   HOH Z 357 " =    1.812
peak=    3.268 closest distance to " O   HOH Z 411 " =    4.014
peak=    3.262 closest distance to " N   TYR A  15 " =    1.231
peak=    3.258 closest distance to " O   HOH Z 287 " =    1.516
peak=    3.254 closest distance to " O   HOH Z 116 " =    1.128
peak=    3.250 closest distance to " O   HOH Z 116 " =    5.630
peak=    3.245 closest distance to " CA  ASN A 284 " =    1.027
peak=    3.242 closest distance to " O   HOH Z 295 " =    1.198
peak=    3.235 closest distance to " O   HOH Z 342 " =    0.877
peak=    3.231 closest distance to " ND2 ASN A  60 " =    2.889
peak=    3.229 closest distance to " CD2 TYR A 186 " =    1.147
peak=    3.228 closest distance to " O   HOH Z 176 " =    1.817
peak=    3.228 closest distance to " O   HOH Z 419 " =    1.467
peak=    3.228 closest distance to " O   HOH Z  41 " =    2.091
peak=    3.227 closest distance to " O   HOH Z 212 " =    1.461
peak=    3.225 closest distance to " O   HOH Z 327 " =    1.606
peak=    3.221 closest distance to " O   HOH Z 129 " =    0.766
peak=    3.208 closest distance to " O   HOH Z 418 " =    1.992
peak=    3.207 closest distance to " CB  ALA A  10 " =    0.827
peak=    3.202 closest distance to " O   HOH Z 156 " =    2.908
peak=    3.193 closest distance to " OE1 GLU A   2 " =    2.189
peak=    3.193 closest distance to " CB  PHE A 130 " =    1.006
peak=    3.182 closest distance to " O   GLY A 147 " =    1.427
peak=    3.181 closest distance to " O   HOH Z 213 " =    1.528
peak=    3.180 closest distance to " CB  ASN A 215 " =    1.096
peak=    3.177 closest distance to " CB  TRP A  85 " =    1.686
peak=    3.165 closest distance to " O   HOH Z 400 " =    0.810
peak=    3.161 closest distance to " OG1 THR A 246 " =    1.093
peak=    3.161 closest distance to " CG  LYS A 119 " =    1.050
peak=    3.160 closest distance to " OE1 GLN A  73 " =    2.259
peak=    3.158 closest distance to " CG  ARG A  36 " =    1.107
peak=    3.157 closest distance to " CB  THR A  52 " =    0.957
peak=    3.149 closest distance to " C   ALA A 299 " =    0.980
peak=    3.126 closest distance to " CB  ASP A 191 " =    1.051
peak=    3.120 closest distance to " O   HOH Z 274 " =    1.900
peak=    3.118 closest distance to " O   HOH Z 436 " =    1.529
peak=    3.107 closest distance to " O   HOH Z 380 " =    1.519
peak=    3.105 closest distance to " CA  ASN A 215 " =    0.899
peak=    3.103 closest distance to " OG1 THR A 221 " =    1.303
peak=    3.095 closest distance to " O   HOH Z 381 " =    1.674
peak=    3.095 closest distance to " CB BSER A 164 " =    1.392
peak=    3.092 closest distance to " CG1 VAL A 126 " =    0.935
peak=    3.090 closest distance to " CB  MET A  40 " =    0.791
peak=    3.073 closest distance to " CZ3 TRP A 274 " =    1.289
peak=    3.071 closest distance to " O   HOH Z  33 " =    2.030
peak=    3.069 closest distance to " CE AMET A  47 " =    1.315
peak=    3.060 closest distance to " OE1 GLN A  58 " =    3.948
peak=    3.057 closest distance to " NH1AARG A 275 " =    1.291
peak=    3.053 closest distance to " O   HOH Z 408 " =    1.951
peak=    3.047 closest distance to " O   HOH Z 113 " =    2.266

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.555 - 4.905
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.721 - 4.905

peak=   -5.228 closest distance to " CD  ARG A 138 " =    1.044
peak=   -4.962 closest distance to " O   PRO A 198 " =    1.063
peak=   -4.858 closest distance to " O   HOH Z  69 " =    1.654
peak=   -4.600 closest distance to " O   HOH Z  24 " =    1.009
peak=   -4.473 closest distance to " OD1 ASP A  27 " =    0.723
peak=   -4.316 closest distance to " OG BSER A 134 " =    1.417
peak=   -4.214 closest distance to " O   HOH Z 385 " =    1.097
peak=   -4.163 closest distance to " CE3 TRP A 274 " =    2.206
peak=   -4.148 closest distance to " OG  SER A  97 " =    2.229
peak=   -4.143 closest distance to " O   HOH Z 131 " =    4.055
peak=   -4.014 closest distance to " OG  SER A  63 " =    1.296
peak=   -4.001 closest distance to " O   HOH Z  65 " =    1.226
peak=   -4.000 closest distance to " O   HOH Z  56 " =    2.075
peak=   -3.983 closest distance to " O   HOH Z 415 " =    1.053
peak=   -3.946 closest distance to " CB  GLN A  55 " =    1.311
peak=   -3.928 closest distance to " OD2 ASP A  50 " =    1.304
peak=   -3.917 closest distance to " N   ARG A 275 " =    0.721
peak=   -3.875 closest distance to " O   HOH Z 134 " =    3.586
peak=   -3.869 closest distance to " O   HOH Z 429 " =    1.561
peak=   -3.864 closest distance to " N   GLN A  58 " =    1.186
peak=   -3.863 closest distance to " O   SER A 135 " =    1.620
peak=   -3.839 closest distance to " C   ASN A 285 " =    2.008
peak=   -3.827 closest distance to " CG2 ILE A  20 " =    2.646
peak=   -3.825 closest distance to " C   LEU A 222 " =    1.412
peak=   -3.811 closest distance to " O   MET A  40 " =    2.784
peak=   -3.798 closest distance to " O   HOH Z 428 " =    1.462
peak=   -3.765 closest distance to " CG2 ILE A 120 " =    0.983
peak=   -3.763 closest distance to " ND2 ASN A  39 " =    1.233
peak=   -3.756 closest distance to " CB  ALA A  43 " =    2.359
peak=   -3.748 closest distance to " OG  SER A  87 " =    1.744
peak=   -3.746 closest distance to " NH2 ARG A  79 " =    2.094
peak=   -3.731 closest distance to " CE2 TYR A  30 " =    2.728
peak=   -3.727 closest distance to " CD2 LEU A   5 " =    0.922
peak=   -3.723 closest distance to " CG2 ILE A 120 " =    1.332
peak=   -3.720 closest distance to " CG  ARG A 219 " =    2.119
peak=   -3.720 closest distance to " O   HOH Z 185 " =    1.819
peak=   -3.717 closest distance to " CD1 TRP A 179 " =    1.254
peak=   -3.713 closest distance to " N   THR A 157 " =    1.505
peak=   -3.695 closest distance to " OD2 ASP A 171 " =    1.754
peak=   -3.695 closest distance to " CG  PRO A 243 " =    1.491
peak=   -3.687 closest distance to " N   ALA A   1 " =    2.816
peak=   -3.686 closest distance to " CA  GLY A 133 " =    2.121
peak=   -3.679 closest distance to " CD1 LEU A 255 " =    2.828
peak=   -3.663 closest distance to " O   ALA A 292 " =    2.320
peak=   -3.661 closest distance to " O   HOH Z 412 " =    4.823
peak=   -3.656 closest distance to " O   HOH Z 359 " =    3.299
peak=   -3.655 closest distance to " C   GLU A   2 " =    1.794
peak=   -3.642 closest distance to " O   HOH Z 427 " =    1.558
peak=   -3.628 closest distance to " O   HOH Z  45 " =    1.010
peak=   -3.626 closest distance to " O   PHE A 218 " =    1.443
peak=   -3.602 closest distance to " O   SER A 273 " =    1.513
peak=   -3.601 closest distance to " O   HOH Z  41 " =    0.831
peak=   -3.600 closest distance to " N   ALA A   1 " =    1.335
peak=   -3.599 closest distance to " O   SER A  95 " =    1.421
peak=   -3.599 closest distance to " O   HOH Z  52 " =    0.916
peak=   -3.591 closest distance to " N   VAL A  72 " =    2.068
peak=   -3.584 closest distance to " O   HOH Z  37 " =    1.502
peak=   -3.578 closest distance to " ND2 ASN A 187 " =    1.671
peak=   -3.576 closest distance to " O   HOH Z 423 " =    2.814
peak=   -3.569 closest distance to " O   HOH Z 244 " =    1.305
peak=   -3.564 closest distance to " C   PHE A  59 " =    0.970
peak=   -3.556 closest distance to " NE2 GLN A  94 " =    1.658
peak=   -3.555 closest distance to " O   HOH Z 107 " =    1.945
peak=   -3.555 closest distance to " O   HOH Z 257 " =    1.071
peak=   -3.552 closest distance to " O   GLY A 136 " =    1.473
peak=   -3.551 closest distance to " OE1 GLN A 183 " =    1.509
peak=   -3.539 closest distance to " ND2 ASN A  45 " =    2.113
peak=   -3.536 closest distance to " O   TRP A  92 " =    1.724
peak=   -3.526 closest distance to " O   HOH Z 377 " =    1.112
peak=   -3.525 closest distance to " CD1 TRP A 274 " =    1.024
peak=   -3.521 closest distance to " OE1 GLU A 277 " =    1.855
peak=   -3.512 closest distance to " O   HOH Z  52 " =    1.547
peak=   -3.507 closest distance to " O   HOH Z 147 " =    0.885
peak=   -3.504 closest distance to " NE1 TRP A  70 " =    1.528
peak=   -3.502 closest distance to " CA  ASN A 127 " =    1.238
peak=   -3.489 closest distance to " O   ILE A  49 " =    1.512
peak=   -3.489 closest distance to " O   ASP A 191 " =    1.819
peak=   -3.485 closest distance to " O   ALA A  51 " =    1.136
peak=   -3.485 closest distance to " O   HOH Z 416 " =    0.892
peak=   -3.472 closest distance to " O   HOH Z 217 " =    1.879
peak=   -3.461 closest distance to " CE1 TYR A 247 " =    2.578
peak=   -3.460 closest distance to " CG2 ILE A 151 " =    2.481
peak=   -3.456 closest distance to " CG1BVAL A  72 " =    2.115
peak=   -3.450 closest distance to " O   HOH Z  89 " =    2.832
peak=   -3.447 closest distance to " CD1 PHE A  59 " =    1.068
peak=   -3.445 closest distance to " O   HOH Z 398 " =    1.128
peak=   -3.439 closest distance to " CD2 LEU A 167 " =    1.862
peak=   -3.434 closest distance to " O   HOH Z 397 " =    1.450
peak=   -3.433 closest distance to " O   SER A  22 " =    2.361
peak=   -3.430 closest distance to " ND2 ASN A 209 " =    1.823
peak=   -3.430 closest distance to " CG  ASP A 286 " =    1.503
peak=   -3.427 closest distance to " O   HOH Z 178 " =    0.721
peak=   -3.426 closest distance to " O   HOH Z 100 " =    0.975
peak=   -3.424 closest distance to " CE2 PHE A 218 " =    2.348
peak=   -3.423 closest distance to " CD1 TYR A 214 " =    1.421
peak=   -3.418 closest distance to " CD  LYS A 289 " =    2.335
peak=   -3.416 closest distance to " O   TRP A 179 " =    1.607
peak=   -3.411 closest distance to " O   HOH Z 286 " =    1.441
peak=   -3.407 closest distance to " CD  PRO A 243 " =    1.847
peak=   -3.407 closest distance to " N   ALA A   1 " =    1.561
peak=   -3.405 closest distance to " CG  GLN A  88 " =    1.267
peak=   -3.400 closest distance to " N   ALA A 248 " =    1.633
peak=   -3.386 closest distance to " N   GLU A 277 " =    1.450
peak=   -3.385 closest distance to " O   HOH Z 422 " =    3.226
peak=   -3.381 closest distance to " CD2 TYR A 293 " =    1.867
peak=   -3.375 closest distance to " O   HOH Z 238 " =    0.724
peak=   -3.372 closest distance to " O   HOH Z 331 " =    1.738
peak=   -3.371 closest distance to " CG2 THR A 235 " =    2.580
peak=   -3.363 closest distance to " C   HIS A 108 " =    1.300
peak=   -3.362 closest distance to " CD1 TRP A  85 " =    1.071
peak=   -3.359 closest distance to " CB  ALA A 291 " =    2.118
peak=   -3.354 closest distance to " C   GLN A 205 " =    1.978
peak=   -3.346 closest distance to " OG  SER A  62 " =    3.932
peak=   -3.329 closest distance to " CG BARG A 275 " =    0.779
peak=   -3.321 closest distance to " CB  ALA A 114 " =    2.346
peak=   -3.319 closest distance to " NE2 GLN A 223 " =    1.607
peak=   -3.315 closest distance to " O   HOH Z 412 " =    3.210
peak=   -3.313 closest distance to " CG  TRP A 266 " =    1.745
peak=   -3.311 closest distance to " OG  SER A   3 " =    1.206
peak=   -3.305 closest distance to " O   HOH Z 298 " =    3.714
peak=   -3.296 closest distance to " O   HOH Z 359 " =    1.816
peak=   -3.296 closest distance to " O   HOH Z 335 " =    1.310
peak=   -3.296 closest distance to " CZ  PHE A 130 " =    1.027
peak=   -3.295 closest distance to " O   HOH Z  60 " =    1.835
peak=   -3.293 closest distance to " O   HOH Z 308 " =    1.957
peak=   -3.283 closest distance to " O   HOH Z 235 " =    1.104
peak=   -3.283 closest distance to " CA  GLY A  57 " =    2.202
peak=   -3.281 closest distance to " OG  SER A  87 " =    1.299
peak=   -3.280 closest distance to " CD  ARG A  14 " =    2.855
peak=   -3.277 closest distance to " CG  LEU A  83 " =    2.230
peak=   -3.277 closest distance to " CA  GLY A  23 " =    1.752
peak=   -3.276 closest distance to " CE  MET A 188 " =    2.197
peak=   -3.272 closest distance to " O   HOH Z 151 " =    1.412
peak=   -3.265 closest distance to " CB  SER A 210 " =    1.147
peak=   -3.265 closest distance to " O   HOH Z 234 " =    4.110
peak=   -3.263 closest distance to " O   HOH Z 113 " =    1.109
peak=   -3.260 closest distance to " O   HOH Z 414 " =    2.392
peak=   -3.259 closest distance to " O   GLU A 152 " =    1.529
peak=   -3.259 closest distance to " O   HOH Z 298 " =    2.847
peak=   -3.253 closest distance to " O   ASP A 298 " =    1.875
peak=   -3.251 closest distance to " O   HOH Z 313 " =    1.486
peak=   -3.250 closest distance to " CD2 PHE A  61 " =    1.849
peak=   -3.248 closest distance to " O   HOH Z 288 " =    1.204
peak=   -3.244 closest distance to " O   HOH Z 266 " =    4.905
peak=   -3.243 closest distance to " O   HOH Z 126 " =    1.967
peak=   -3.243 closest distance to " O   HOH Z 265 " =    1.915
peak=   -3.238 closest distance to " N   ALA A 244 " =    1.317
peak=   -3.237 closest distance to " O   HOH Z 165 " =    2.293
peak=   -3.237 closest distance to " CG  ARG A 138 " =    0.817
peak=   -3.236 closest distance to " OE2 GLU A 152 " =    1.192
peak=   -3.236 closest distance to " CB  PHE A  59 " =    1.609
peak=   -3.234 closest distance to " O   HOH Z 231 " =    1.807
peak=   -3.229 closest distance to " CG1 VAL A 112 " =    3.044
peak=   -3.228 closest distance to " O   HOH Z 388 " =    1.927
peak=   -3.227 closest distance to " ND2 ASN A 249 " =    2.059
peak=   -3.226 closest distance to " O   HOH Z 421 " =    2.632
peak=   -3.223 closest distance to " O   HOH Z 224 " =    0.843
peak=   -3.219 closest distance to " OG  SER A 245 " =    1.378
peak=   -3.208 closest distance to " O   HOH Z  11 " =    1.955
peak=   -3.208 closest distance to " OXT GLY A 302 " =    3.118
peak=   -3.201 closest distance to " CD2 HIS A 115 " =    1.832
peak=   -3.199 closest distance to " O   HOH Z 100 " =    1.209
peak=   -3.199 closest distance to " CG1 ILE A 109 " =    2.672
peak=   -3.187 closest distance to " O   HOH Z 339 " =    1.279
peak=   -3.176 closest distance to " OG  SER A 135 " =    1.402
peak=   -3.175 closest distance to " O   HOH Z 102 " =    1.667
peak=   -3.170 closest distance to " O   HOH Z 407 " =    2.222
peak=   -3.168 closest distance to " O   HOH Z  34 " =    2.068
peak=   -3.168 closest distance to " CB  ASP A 132 " =    2.585
peak=   -3.164 closest distance to " CB  ASN A 301 " =    2.007
peak=   -3.163 closest distance to " CD2 PHE A  61 " =    2.209
peak=   -3.162 closest distance to " CB  ASN A  45 " =    1.895
peak=   -3.161 closest distance to " CD1 TRP A 266 " =    1.739
peak=   -3.160 closest distance to " ND2 ASN A 285 " =    1.969
peak=   -3.147 closest distance to " O   HOH Z 394 " =    1.305
peak=   -3.143 closest distance to " OD1 ASN A  60 " =    1.563
peak=   -3.140 closest distance to " CE  MET A  93 " =    1.107
peak=   -3.139 closest distance to " CD2 LEU A 237 " =    2.593
peak=   -3.138 closest distance to " O   HOH Z 357 " =    2.127
peak=   -3.135 closest distance to " O   HOH Z 298 " =    1.214
peak=   -3.126 closest distance to " O   HOH Z 256 " =    1.224
peak=   -3.119 closest distance to " CG  GLN A  11 " =    1.912
peak=   -3.116 closest distance to " ND2 ASN A 127 " =    1.653
peak=   -3.113 closest distance to " O   VAL A  67 " =    2.236
peak=   -3.113 closest distance to " O   HOH Z  64 " =    2.129
peak=   -3.110 closest distance to " CA  GLN A  58 " =    1.204
peak=   -3.109 closest distance to " O   HOH Z  63 " =    2.192
peak=   -3.106 closest distance to " O   HOH Z 184 " =    0.990
peak=   -3.096 closest distance to " OXT GLY A 302 " =    4.339
peak=   -3.092 closest distance to " O   HOH Z 339 " =    1.353
peak=   -3.086 closest distance to " NZ  LYS A 119 " =    0.815
peak=   -3.083 closest distance to " CB  ALA A 248 " =    2.181
peak=   -3.079 closest distance to " CZ  ARG A  66 " =    1.756
peak=   -3.077 closest distance to " O   HOH Z 323 " =    1.900
peak=   -3.076 closest distance to " NH2AARG A 275 " =    4.630
peak=   -3.075 closest distance to " OG1 THR A 235 " =    1.338
peak=   -3.070 closest distance to " C   HIS A 207 " =    1.218
peak=   -3.063 closest distance to " O   HOH Z 116 " =    4.695
peak=   -3.063 closest distance to " O   HOH Z 368 " =    1.391
peak=   -3.052 closest distance to " CG  HIS A 108 " =    0.983
peak=   -3.050 closest distance to " CD2 HIS A 207 " =    1.871
peak=   -3.029 closest distance to " C   ILE A 120 " =    1.751
peak=   -3.023 closest distance to " CB  ALA A 131 " =    1.835

================= 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    :  0.5054 0.5046   6.302576e+00   6.298162e+00
   1_bss:  0.4970 0.4922   6.295661e+00   6.290200e+00
   1_xyz:  0.4365 0.4651   6.231742e+00   6.261100e+00
   1_adp:  0.3993 0.4654   6.194281e+00   6.257886e+00
   1_occ:  0.3989 0.4647   6.193278e+00   6.258143e+00
   2_bss:  0.3975 0.4606   6.193667e+00   6.256986e+00
   2_xyz:  0.3436 0.4104   6.084198e+00   6.190392e+00
   2_adp:  0.3240 0.3959   6.049536e+00   6.169595e+00
   2_occ:  0.3238 0.3960   6.049768e+00   6.170052e+00
   3_bss:  0.3225 0.3953   6.050019e+00   6.169135e+00
   3_xyz:  0.2500 0.3139   5.840190e+00   6.007821e+00
   3_adp:  0.2215 0.2859   5.739084e+00   5.927255e+00
   3_occ:  0.2209 0.2858   5.737606e+00   5.926184e+00
   4_bss:  0.2197 0.2839   5.732366e+00   5.922239e+00
   4_xyz:  0.1798 0.2401   5.560660e+00   5.774431e+00
   4_adp:  0.1673 0.2380   5.519281e+00   5.753932e+00
   4_occ:  0.1671 0.2378   5.518695e+00   5.753262e+00
   5_bss:  0.1672 0.2380   5.517345e+00   5.753109e+00
   5_xyz:  0.1418 0.2035   5.364359e+00   5.612660e+00
   5_adp:  0.1354 0.1873   5.302404e+00   5.536627e+00
   5_occ:  0.1352 0.1868   5.300560e+00   5.533887e+00
   5_bss:  0.1355 0.1870   5.301849e+00   5.534320e+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:  0.361   0.000   7.801   9.613   8.147   0.000   0.000   0.000
   1_xyz:  0.361   0.000   7.801   9.613   8.147   0.000   0.000   0.000
   1_adp:  0.361   0.000   7.801   9.613   8.147   0.000   0.000   0.000
   1_occ:  0.361   0.000   7.801   9.613   8.147   0.000   0.000   0.000
   2_bss:  0.348  20.001   5.137   6.259   5.571   0.000   0.000   0.000
   2_xyz:  0.348  20.001   5.137   6.259   5.571   0.000   0.000   0.000
   2_adp:  0.348  20.001   5.137   6.259   5.571   0.000   0.000   0.000
   2_occ:  0.348  20.001   5.137   6.259   5.571   0.000   0.000   0.000
   3_bss:  0.353  47.690   2.690   3.702   3.686   0.000   0.000   0.000
   3_xyz:  0.353  47.690   2.690   3.702   3.686   0.000   0.000   0.000
   3_adp:  0.353  47.690   2.690   3.702   3.686   0.000   0.000   0.000
   3_occ:  0.353  47.690   2.690   3.702   3.686   0.000   0.000   0.000
   4_bss:  0.336  47.690   1.243   2.076   2.898   0.000   0.000   0.000
   4_xyz:  0.336  47.690   1.243   2.076   2.898   0.000   0.000   0.000
   4_adp:  0.336  47.690   1.243   2.076   2.898   0.000   0.000   0.000
   4_occ:  0.336  47.690   1.243   2.076   2.898   0.000   0.000   0.000
   5_bss:  0.313  44.426   0.881   1.526   2.806   0.000   0.000   0.000
   5_xyz:  0.313  44.426   0.881   1.526   2.806   0.000   0.000   0.000
   5_adp:  0.313  44.426   0.881   1.526   2.806   0.000   0.000   0.000
   5_occ:  0.313  44.426   0.881   1.526   2.806   0.000   0.000   0.000
   5_bss:  0.313  43.663  -0.888  -0.286   1.174   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.445 0.3094  0.3719    82931.702
   1_bss:  65.584 0.3194  0.4836    79921.378
   1_xyz:  58.669 0.4083  0.6122    68137.060
   1_adp:  56.675 0.4345  0.6979    67165.748
   1_occ:  56.676 0.4344  0.6961    67160.145
   2_bss:  56.309 0.4387  0.6406    66229.789
   2_xyz:  46.432 0.5636  0.8234    49631.140
   2_adp:  43.987 0.5940  0.8792    45614.614
   2_occ:  44.053 0.5932  0.8777    45707.112
   3_bss:  43.765 0.5968  0.8151    45460.251
   3_xyz:  33.067 0.7232  0.9610    27368.063
   3_adp:  28.924 0.7704  0.9938    22088.175
   3_occ:  28.863 0.7710  0.9941    21965.138
   4_bss:  28.645 0.7731  0.9498    21544.452
   4_xyz:  23.378 0.8285  0.9860    14892.792
   4_adp:  22.792 0.8347  0.9760    14405.818
   4_occ:  22.769 0.8349  0.9758    14362.620
   5_bss:  22.743 0.8351  0.9639    14327.022
   5_xyz:  19.225 0.8689  0.9865    10435.027
   5_adp:  17.287 0.8871  0.9870     8962.408
   5_occ:  17.236 0.8875  0.9869     8898.284
   5_bss:  17.250 0.8874  0.9854     8911.370
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2752e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2752e+01
   1_xyz:   1.779  0.014  0.109 18.290  0.007  4.102   1.5855e-01
   1_adp:   1.779  0.014  0.109 18.290  0.007  4.102   1.5855e-01
   1_occ:   1.779  0.014  0.109 18.290  0.007  4.102   1.5855e-01
   2_bss:   1.779  0.014  0.109 18.290  0.007  4.102   1.5855e-01
   2_xyz:   1.202  0.008  0.079 16.175  0.005  4.116   9.1665e-02
   2_adp:   1.202  0.008  0.079 16.175  0.005  4.116   9.1665e-02
   2_occ:   1.202  0.008  0.079 16.175  0.005  4.116   9.1665e-02
   3_bss:   1.202  0.008  0.079 16.175  0.005  4.116   9.1665e-02
   3_xyz:   1.263  0.010  0.089 16.476  0.005  4.108   9.8375e-02
   3_adp:   1.263  0.010  0.089 16.476  0.005  4.108   9.8375e-02
   3_occ:   1.263  0.010  0.089 16.476  0.005  4.108   9.8375e-02
   4_bss:   1.263  0.010  0.089 16.476  0.005  4.108   9.8375e-02
   4_xyz:   0.915  0.005  0.064 15.456  0.003  4.116   5.5138e-02
   4_adp:   0.915  0.005  0.064 15.456  0.003  4.116   5.5138e-02
   4_occ:   0.915  0.005  0.064 15.456  0.003  4.116   5.5138e-02
   5_bss:   0.915  0.005  0.064 15.456  0.003  4.116   5.5138e-02
   5_xyz:   1.017  0.006  0.071 15.516  0.004  4.112   6.1851e-02
   5_adp:   1.017  0.006  0.071 15.516  0.004  4.112   6.1851e-02
   5_occ:   1.017  0.006  0.071 15.516  0.004  4.112   6.1851e-02
   5_bss:   1.017  0.006  0.071 15.516  0.004  4.112   6.1851e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8253e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8253e+00
   1_xyz:  15.176  0.170  0.478 87.832  0.033  2.103   1.0156e-01
   1_adp:  15.176  0.170  0.478 87.832  0.033  2.103   1.0156e-01
   1_occ:  15.176  0.170  0.478 87.832  0.033  2.103   1.0156e-01
   2_bss:  15.176  0.170  0.478 87.832  0.033  2.103   1.0156e-01
   2_xyz:   6.742  0.119  0.284 83.792  0.047  2.114   6.8566e-02
   2_adp:   6.742  0.119  0.284 83.792  0.047  2.114   6.8566e-02
   2_occ:   6.742  0.119  0.284 83.792  0.047  2.114   6.8566e-02
   3_bss:   6.742  0.119  0.284 83.792  0.047  2.114   6.8566e-02
   3_xyz:   7.577  0.068  0.284 84.506  0.042  2.157   1.5565e-01
   3_adp:   7.577  0.068  0.284 84.506  0.042  2.157   1.5565e-01
   3_occ:   7.577  0.068  0.284 84.506  0.042  2.157   1.5565e-01
   4_bss:   7.577  0.068  0.284 84.506  0.042  2.157   1.5565e-01
   4_xyz:   7.327  0.048  0.233 80.624  0.033  2.349   3.4352e-02
   4_adp:   7.327  0.048  0.233 80.624  0.033  2.349   3.4352e-02
   4_occ:   7.327  0.048  0.233 80.624  0.033  2.349   3.4352e-02
   5_bss:   7.327  0.048  0.233 80.624  0.033  2.349   3.4352e-02
   5_xyz:   9.046  0.050  0.276 84.106  0.032  2.389   4.8646e-02
   5_adp:   9.046  0.050  0.276 84.106  0.032  2.389   4.8646e-02
   5_occ:   9.046  0.050  0.276 84.106  0.032  2.389   4.8646e-02
   5_bss:   9.046  0.050  0.276 84.106  0.032  2.389   4.8646e-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:  64.24   0.00  13.80  51.68   0.00  12.75  64.24   0.00  19.52
   1_occ:  64.24   0.00  13.80  51.68   0.00  12.75  64.24   0.00  19.52
   2_bss:  64.24   0.00  13.80  51.68   0.00  12.75  64.24   0.00  19.52
   2_xyz:  64.24   0.00  13.80  51.68   0.00  12.75  64.24   0.00  19.52
   2_adp:  78.50   0.00  14.86  78.50   0.00  12.48  78.21   0.00  27.78
   2_occ:  78.50   0.00  14.86  78.50   0.00  12.48  78.21   0.00  27.78
   3_bss:  78.50   0.00  14.86  78.50   0.00  12.48  78.21   0.00  27.78
   3_xyz:  78.50   0.00  14.86  78.50   0.00  12.48  78.21   0.00  27.78
   3_adp:  84.35   0.00  14.87  83.33   0.00  10.87  84.35   1.54  36.68
   3_occ:  84.35   0.00  14.87  83.33   0.00  10.87  84.35   1.54  36.68
   4_bss:  84.35   0.00  14.87  83.33   0.00  10.87  84.35   1.54  36.68
   4_xyz:  84.35   0.00  14.87  83.33   0.00  10.87  84.35   1.54  36.68
   4_adp: 107.20   0.00  16.20 104.35   0.00  10.71 107.20   2.04  46.04
   4_occ: 107.20   0.00  16.20 104.35   0.00  10.71 107.20   2.04  46.04
   5_bss: 107.20   0.00  16.20 104.35   0.00  10.71 107.20   2.04  46.04
   5_xyz: 107.20   0.00  16.20 104.35   0.00  10.71 107.20   2.04  46.04
   5_adp: 104.24   0.00  15.06 103.66   0.00   9.83 104.24   2.04  43.50
   5_occ: 104.24   0.00  15.06 103.66   0.00   9.83 104.24   2.04  43.50
   5_bss: 105.95   1.71  16.77 105.38   1.71  11.54 105.95   3.75  45.21
------------------------------------------------------------------------
 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:    1.266    0.027    0.417
   1_adp:    1.266    0.027    0.417
   1_occ:    1.266    0.027    0.417
   2_bss:    1.266    0.027    0.417
   2_xyz:    1.607    0.045    0.560
   2_adp:    1.607    0.045    0.560
   2_occ:    1.607    0.045    0.560
   3_bss:    1.607    0.045    0.560
   3_xyz:    1.743    0.039    0.733
   3_adp:    1.743    0.039    0.733
   3_occ:    1.743    0.039    0.733
   4_bss:    1.743    0.039    0.733
   4_xyz:    1.813    0.065    0.795
   4_adp:    1.813    0.065    0.795
   4_occ:    1.813    0.065    0.795
   5_bss:    1.813    0.065    0.795
   5_xyz:    1.793    0.057    0.849
   5_adp:    1.793    0.057    0.849
   5_occ:    1.793    0.057    0.849
   5_bss:    1.793    0.057    0.849
------------------------------------------------------------------------

CPU time actual refinement: 348.31


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_17/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_17/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_17/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_17/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_17/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.15 
  Macro-tasks:
    bulk solvent and scale       = 47.25  
    individual site refinement   = 144.24 
    weights calculation          = 32.11  
    collect and process          = 6.34   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 230.05 
  Micro-tasks:
    mask                            = 2.96   
    f_calc                          = 107.11 
    alpha_beta                      = 8.22   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 118.12 
    fmodel                         = 7.84   
    r_factors                      = 0.32   
    phase_errors                   = 9.81   
    foms                           = 0.32   
    TOTAL for micro-tasks          = 255.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.936 micro seconds
Total CPU time: 6.07 minutes
from_scatterers_fft:    642 calls, 106.80 s
gradients_fft:          586 calls, 105.16 s

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

# Date 2008-01-16 Time 00:33:30 PST -0800 (1200472410.75 s)
Start R-work = 0.5054, R-free = 0.5046 (no bulk solvent and anisotropic scale)
Final R-work = 0.1510, R-free = 0.2001 (no bulk solvent and anisotropic scale)

Start R-work = 0.4970, R-free = 0.4922
Final R-work = 0.1355, R-free = 0.1870