# Date 2008-01-16 Time 03:25:31 PST -0800 (1200482731.28 s)
#phil __OFF__

Command line arguments: "../1228.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31900
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1228

-------------------------------------------------------------------------------
  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: (72.0062, 45.9914, 87.2539, 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: 3.23, per 1000 atoms: 1.14


================================== 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: (72.0062, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.96442
Completeness in resolution range: 0.921445
Completeness with d_max=infinity: 0.918852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   1.9644

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: (72.0062, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.96442
Completeness in resolution range: 0.921445
Completeness with d_max=infinity: 0.918852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.2057 [2231/2258]  2009   222  10.0%
  bin  2:  4.2057 -  3.3497 [2153/2173]  1940   213   9.9%
  bin  3:  3.3497 -  2.9296 [2114/2133]  1899   215  10.2%
  bin  4:  2.9296 -  2.6633 [2077/2107]  1867   210  10.1%
  bin  5:  2.6633 -  2.4733 [2101/2120]  1899   202   9.6%
  bin  6:  2.4733 -  2.3280 [2084/2109]  1870   214  10.3%
  bin  7:  2.3280 -  2.2118 [2069/2097]  1852   217  10.5%
  bin  8:  2.2118 -  2.1157 [2048/2084]  1848   200   9.8%
  bin  9:  2.1157 -  2.0345 [2012/2099]  1820   192   9.5%
  bin 10:  2.0345 -  1.9644 [ 700/2079]   626    74  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1228/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 34
        2.41 -     3.04: 2141
        3.04 -     3.66: 4649
        3.66 -     4.28: 9024
        4.28 -     4.90: 12298
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28141 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_1228/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1228/model_refine_001.geo

CPU time processing inputs: 9.02


============================ 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 = 72.00625 45.9914 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5107   r_free= 0.5027   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.309486                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6919 0.99   1447  163 0.4321 0.4269      6.6572      6.6737|
|  2:  4.6919 -  3.7420 0.99   1402  154 0.4504 0.4377      6.8753      6.8689|
|  3:  3.7420 -  3.2743 0.99   1362  148 0.4783 0.4614      6.6981       6.683|
|  4:  3.2743 -  2.9773 0.99   1362  157 0.5056 0.5011      6.5522      6.5335|
|  5:  2.9773 -  2.7653 0.99   1354  146 0.5397 0.5219      6.3852      6.3912|
|  6:  2.7653 -  2.6031 0.99   1346  153 0.5375 0.5362      6.2883      6.2292|
|  7:  2.6031 -  2.4733 0.99   1341  141 0.5599 0.4846      6.2522      6.1626|
|  8:  2.4733 -  2.3660 0.98   1331  155 0.5494 0.5503      6.1749      6.2374|
|  9:  2.3660 -  2.2752 0.98   1328  149 0.5537 0.5341      6.1378      6.1491|
| 10:  2.2752 -  2.1970 1.00   1322  152 0.5334 0.5264      6.0809      6.0495|
| 11:  2.1970 -  2.1284 0.98   1328  145 0.5357 0.5756       6.035      6.0872|
| 12:  2.1284 -  2.0678 0.98   1327  144 0.5468 0.5555      5.9411      5.9352|
| 13:  2.0678 -  2.0134 0.83   1100  123 0.5570 0.4922       5.881      5.7921|
| 14:  2.0134 -  1.9644 0.21    280   29 0.5683 0.5305      5.8841      5.9376|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.6919  1447   163  0.65  38.65   0.77     0.71      90741.42|
|  2:  4.6919 -  3.7420  1402   154  0.65  39.88   0.83     0.73     132806.18|
|  3:  3.7420 -  3.2743  1362   148  0.50  52.12   0.82     0.63     143669.32|
|  4:  3.2743 -  2.9773  1362   157  0.39  60.35   0.74     0.50     129287.23|
|  5:  2.9773 -  2.7653  1354   146  0.29  67.84   0.71     0.38     101217.01|
|  6:  2.7653 -  2.6031  1346   153  0.28  68.66   0.69     0.35      84087.66|
|  7:  2.6031 -  2.4733  1341   141  0.25  71.06   0.71     0.30      72993.25|
|  8:  2.4733 -  2.3660  1331   155  0.23  72.95   0.70     0.28      67401.21|
|  9:  2.3660 -  2.2752  1328   149  0.21  74.61   0.71     0.25      62675.23|
| 10:  2.2752 -  2.1970  1322   152  0.20  74.79   0.73     0.25      57336.11|
| 11:  2.1970 -  2.1284  1328   145  0.19  75.70   0.74     0.25      55114.09|
| 12:  2.1284 -  2.0678  1327   144  0.19  75.88   0.72     0.26      48874.07|
| 13:  2.0678 -  2.0134  1100   123  0.22  73.53   0.69     0.30      41351.88|
| 14:  2.0134 -  1.9644   280    29  0.36  63.17   0.71     0.40      29463.01|
|alpha:            min =        0.25 max =            0.73 mean =         0.40|
|beta:             min =    29463.01 max =       143669.32 mean =     83828.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.63|
|phase err.(test): min =        0.00 max =           89.99 mean =        64.66|
|-----------------------------------------------------------------------------|

============================== 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 = 24.071452             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.314   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.109510              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.119   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       32 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2635 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3910 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5055 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6506 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7655 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.988 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       1.972 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    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 = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5135   r_free= 0.5037   ksol= 0.00   Bsol= 0.00   scale= 0.737    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.310080                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5029   r_free= 0.4906   ksol= 0.35   Bsol= 20.00   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.79,8.23,7.91,0.00,0.00,0.00); trace/3= 8.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.305685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.762593             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.997920              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.760   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5029      final r-factor (work) = 0.4421          |
| start r-factor (free) = 0.4906      final r-factor (free) = 0.4576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 116.2682 = 19.76 * 0.50 * 6.3028 + 1.00 * 53.9882                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.9790 = 19.76 * 0.50 * 6.2567 + 1.00 * 0.1549                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4421      final r-factor (work) = 0.4014          |
| start r-factor (free) = 0.4576      final r-factor (free) = 0.4647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5148 = 2.00 * 1.00 * 6.2567 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4221 = 2.00 * 1.00 * 6.2052 + 1.00 * 0.0246                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.87   17.29    None  None   None       |
|    all(noH): 2823   0      0.00    97.87   17.29    None  None   None       |
|    Sol.    : 438    0      0.00    97.87   25.45    None  None   None       |
|    Mac.    : 2385   0      0.00    95.28   15.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.787: 1015   |   5:    48.933 -  58.720:   70        |
|      1:     9.787 -  19.573:  825   |   6:    58.720 -  68.507:   23        |
|      2:    19.573 -  29.360:  475   |   7:    68.507 -  78.293:    3        |
|      3:    29.360 -  39.147:  268   |   8:    78.293 -  88.080:    2        |
|      4:    39.147 -  48.933:  139   |   9:    88.080 -  97.867:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4014 r_free = 0.4647             target_work(ml) = 6.203         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4009 r_free = 0.4642             target_work(ml) = 6.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4009   r_free= 0.4642   ksol= 0.35   Bsol= 20.00   scale= 1.122   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.79,8.23,7.91,0.00,0.00,0.00); trace/3= 8.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.202257                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3991   r_free= 0.4629   ksol= 0.34   Bsol= 50.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.24,4.35,4.39,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.203949                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.937953             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.021  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.710904              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.633  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3991      final r-factor (work) = 0.3383          |
| start r-factor (free) = 0.4629      final r-factor (free) = 0.4097          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.3723 = 13.94 * 0.50 * 6.2014 + 1.00 * 0.1549                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.9350 = 13.94 * 0.50 * 6.1457 + 1.00 * 0.1060                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3383      final r-factor (work) = 0.3179          |
| start r-factor (free) = 0.4097      final r-factor (free) = 0.3890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3933 = 0.71 * 1.00 * 6.1457 + 1.00 * 0.0243                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3222 = 0.71 * 1.00 * 6.0625 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.30   15.96    None  None   None       |
|    all(noH): 2823   0      0.00    80.30   15.96    None  None   None       |
|    Sol.    : 438    0      0.00    80.30   29.91    None  None   None       |
|    Mac.    : 2385   0      0.00    73.75   13.40    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 -   8.030:  870   |   5:    40.149 -  48.179:   87        |
|      1:     8.030 -  16.060:  841   |   6:    48.179 -  56.208:   42        |
|      2:    16.060 -  24.089:  503   |   7:    56.208 -  64.238:   20        |
|      3:    24.089 -  32.119:  311   |   8:    64.238 -  72.268:    1        |
|      4:    32.119 -  40.149:  144   |   9:    72.268 -  80.298:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3179 r_free = 0.3890             target_work(ml) = 6.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3176 r_free = 0.3886             target_work(ml) = 6.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3176   r_free= 0.3886   ksol= 0.34   Bsol= 50.00   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.24,4.35,4.39,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.041319                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3164   r_free= 0.3866   ksol= 0.33   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.62,1.83,2.72,0.00,0.00,0.00); trace/3= 2.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.040866                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.135774              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.943   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.382632              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.097  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3164      final r-factor (work) = 0.2485          |
| start r-factor (free) = 0.3866      final r-factor (free) = 0.3121          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7360 = 7.14 * 0.50 * 6.0624 + 1.00 * 0.1060                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3365 = 7.14 * 0.50 * 5.9555 + 1.00 * 0.0881                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2485      final r-factor (work) = 0.2281          |
| start r-factor (free) = 0.3121      final r-factor (free) = 0.2933          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2912 = 0.38 * 1.00 * 5.9555 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2611 = 0.38 * 1.00 * 5.7988 + 1.00 * 0.0423                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.97   15.74    None  None   None       |
|    all(noH): 2823   0      0.00    74.97   15.74    None  None   None       |
|    Sol.    : 438    0      1.69    72.51   34.59    None  None   None       |
|    Mac.    : 2385   0      0.00    74.97   12.28    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 -   7.497:  837   |   5:    37.487 -  44.984:  123        |
|      1:     7.497 -  14.995:  941   |   6:    44.984 -  52.481:   80        |
|      2:    14.995 -  22.492:  405   |   7:    52.481 -  59.979:   29        |
|      3:    22.492 -  29.989:  239   |   8:    59.979 -  67.476:    6        |
|      4:    29.989 -  37.487:  158   |   9:    67.476 -  74.973:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2281 r_free = 0.2933             target_work(ml) = 5.767         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2278 r_free = 0.2931             target_work(ml) = 5.765         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2278   r_free= 0.2931   ksol= 0.33   Bsol= 50.00   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.62,1.83,2.72,0.00,0.00,0.00); trace/3= 2.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.765212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2268   r_free= 0.2918   ksol= 0.32   Bsol= 51.76   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.83,0.16,1.43,0.00,0.00,0.00); trace/3= 0.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.764684                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.529348              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.361   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.721952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.403   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2268      final r-factor (work) = 0.1703          |
| start r-factor (free) = 0.2918      final r-factor (free) = 0.2246          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0312 = 6.53 * 0.50 * 5.8025 + 1.00 * 0.0881                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5357 = 6.53 * 0.50 * 5.6520 + 1.00 * 0.0838                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1703      final r-factor (work) = 0.1507          |
| start r-factor (free) = 0.2246      final r-factor (free) = 0.2070          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0990 = 0.72 * 1.00 * 5.6520 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9551 = 0.72 * 1.00 * 5.4613 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.06   16.37    None  None   None       |
|    all(noH): 2823   0      0.00    84.06   16.37    None  None   None       |
|    Sol.    : 438    0      4.22    79.17   42.20    None  None   None       |
|    Mac.    : 2385   0      0.00    84.06   11.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.406: 1047   |   5:    42.029 -  50.435:  109        |
|      1:     8.406 -  16.812:  993   |   6:    50.435 -  58.840:   81        |
|      2:    16.812 -  25.217:  284   |   7:    58.840 -  67.246:   61        |
|      3:    25.217 -  33.623:  114   |   8:    67.246 -  75.652:   33        |
|      4:    33.623 -  42.029:   98   |   9:    75.652 -  84.058:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1507 r_free = 0.2070             target_work(ml) = 5.416         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1506 r_free = 0.2069             target_work(ml) = 5.415         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.2069   ksol= 0.32   Bsol= 51.76   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.83,0.16,1.43,0.00,0.00,0.00); trace/3= 0.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.415173                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.2065   ksol= 0.33   Bsol= 60.20   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,-0.69,0.98,-0.00,0.00,0.00); trace/3= 0.16                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.413014                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.132957              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.583  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.234149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.306  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1506      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2065      final r-factor (free) = 0.1921          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9108 = 2.13 * 0.50 * 5.4638 + 1.00 * 0.0838                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8015 = 2.13 * 0.50 * 5.3869 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1921      final r-factor (free) = 0.1865          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2736 = 0.23 * 1.00 * 5.3869 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2595 = 0.23 * 1.00 * 5.3367 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.37   15.76    None  None   None       |
|    all(noH): 2823   0      0.00    85.37   15.76    None  None   None       |
|    Sol.    : 438    0      4.70    78.78   40.63    None  None   None       |
|    Mac.    : 2385   0      0.00    85.37   11.19    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 -   8.537: 1114   |   5:    42.686 -  51.223:  100        |
|      1:     8.537 -  17.074: 1003   |   6:    51.223 -  59.760:   75        |
|      2:    17.074 -  25.612:  235   |   7:    59.760 -  68.297:   48        |
|      3:    25.612 -  34.149:  123   |   8:    68.297 -  76.834:   23        |
|      4:    34.149 -  42.686:  100   |   9:    76.834 -  85.372:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1865             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1861             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1861   ksol= 0.33   Bsol= 60.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,-0.69,0.98,-0.00,0.00,0.00); trace/3= 0.16                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322099                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6919 0.99   1447  163 0.1046 0.1402      5.4275      5.6442|
|  2:  4.6919 -  3.7420 0.99   1402  154 0.0962 0.1279      5.5514       5.784|
|  3:  3.7420 -  3.2743 0.99   1362  148 0.1271 0.1701      5.6145      5.8836|
|  4:  3.2743 -  2.9773 0.99   1362  157 0.1537 0.1890      5.6154      5.7425|
|  5:  2.9773 -  2.7653 0.99   1354  146 0.1646 0.2222      5.5057      5.7294|
|  6:  2.7653 -  2.6031 0.99   1346  153 0.1567 0.2280      5.3907      5.6245|
|  7:  2.6031 -  2.4733 0.99   1341  141 0.1572 0.2034      5.3446      5.4817|
|  8:  2.4733 -  2.3660 0.98   1331  155 0.1497 0.2043      5.2533      5.5089|
|  9:  2.3660 -  2.2752 0.98   1328  149 0.1528 0.2208      5.2359      5.4518|
| 10:  2.2752 -  2.1970 1.00   1322  152 0.1437 0.2023      5.1314      5.3331|
| 11:  2.1970 -  2.1284 0.98   1328  145 0.1410 0.1969      5.1013      5.4321|
| 12:  2.1284 -  2.0678 0.98   1327  144 0.1447 0.2248      5.0486      5.3021|
| 13:  2.0678 -  2.0134 0.83   1100  123 0.1457 0.1975      4.9656      5.1623|
| 14:  2.0134 -  1.9644 0.21    280   29 0.1243 0.1801      4.8346      5.0591|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.6919  1447   163  0.93   9.84   0.97     0.95       8038.43|
|  2:  4.6919 -  3.7420  1402   154  0.94   9.34   1.01     1.00      11364.13|
|  3:  3.7420 -  3.2743  1362   148  0.91  14.05   1.03     1.03      13674.03|
|  4:  3.2743 -  2.9773  1362   157  0.89  17.12   1.01     0.99      13745.09|
|  5:  2.9773 -  2.7653  1354   146  0.87  19.06   1.00     0.99      11707.73|
|  6:  2.7653 -  2.6031  1346   153  0.86  20.15   0.98     0.93       9910.82|
|  7:  2.6031 -  2.4733  1341   141  0.87  19.37   1.00     0.97       9013.20|
|  8:  2.4733 -  2.3660  1331   155  0.87  19.62   0.99     0.94       7654.28|
|  9:  2.3660 -  2.2752  1328   149  0.86  20.17   1.01     0.95       7385.53|
| 10:  2.2752 -  2.1970  1322   152  0.88  19.10   1.00     0.96       6152.90|
| 11:  2.1970 -  2.1284  1328   145  0.87  19.79   1.00     0.94       5925.78|
| 12:  2.1284 -  2.0678  1327   144  0.87  19.98   1.00     1.00       5673.62|
| 13:  2.0678 -  2.0134  1100   123  0.86  20.81   0.99     0.96       4837.27|
| 14:  2.0134 -  1.9644   280    29  0.90  16.88   0.99     0.96       3615.79|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3615.79 max =        13745.09 mean =      8851.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        17.43|
|phase err.(test): min =        0.00 max =           89.97 mean =        16.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1862   ksol= 0.32   Bsol= 60.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.91,0.86,-0.00,0.00,0.00); trace/3= -0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321963                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1862   ksol= 0.32   Bsol= 60.21   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.09,-0.91,0.86,-0.00,0.00,0.00); trace/3= -0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321963                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6919 0.99   1447  163 0.1044 0.1401      5.4257       5.644|
|  2:  4.6919 -  3.7420 0.99   1402  154 0.0962 0.1279      5.5516      5.7844|
|  3:  3.7420 -  3.2743 0.99   1362  148 0.1271 0.1700      5.6147      5.8833|
|  4:  3.2743 -  2.9773 0.99   1362  157 0.1537 0.1890      5.6153      5.7426|
|  5:  2.9773 -  2.7653 0.99   1354  146 0.1647 0.2224       5.506      5.7301|
|  6:  2.7653 -  2.6031 0.99   1346  153 0.1566 0.2280      5.3903      5.6237|
|  7:  2.6031 -  2.4733 0.99   1341  141 0.1572 0.2035      5.3442      5.4814|
|  8:  2.4733 -  2.3660 0.98   1331  155 0.1497 0.2043       5.253      5.5087|
|  9:  2.3660 -  2.2752 0.98   1328  149 0.1528 0.2209      5.2357      5.4514|
| 10:  2.2752 -  2.1970 1.00   1322  152 0.1437 0.2023      5.1315      5.3341|
| 11:  2.1970 -  2.1284 0.98   1328  145 0.1409 0.1969      5.1012      5.4323|
| 12:  2.1284 -  2.0678 0.98   1327  144 0.1448 0.2250      5.0494      5.3032|
| 13:  2.0678 -  2.0134 0.83   1100  123 0.1457 0.1974      4.9657      5.1627|
| 14:  2.0134 -  1.9644 0.21    280   29 0.1244 0.1802      4.8349      5.0593|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3073 -  4.6919  1447   163  0.93   9.82   0.96     0.94       8028.55|
|  2:  4.6919 -  3.7420  1402   154  0.94   9.33   1.01     1.00      11360.08|
|  3:  3.7420 -  3.2743  1362   148  0.91  14.05   1.03     1.03      13678.61|
|  4:  3.2743 -  2.9773  1362   157  0.89  17.12   1.00     0.98      13749.48|
|  5:  2.9773 -  2.7653  1354   146  0.87  19.06   1.00     0.98      11703.34|
|  6:  2.7653 -  2.6031  1346   153  0.86  20.14   0.97     0.93       9908.86|
|  7:  2.6031 -  2.4733  1341   141  0.87  19.36   0.99     0.96       9005.23|
|  8:  2.4733 -  2.3660  1331   155  0.87  19.61   0.98     0.93       7652.72|
|  9:  2.3660 -  2.2752  1328   149  0.86  20.16   1.00     0.94       7382.17|
| 10:  2.2752 -  2.1970  1322   152  0.88  19.10   0.99     0.95       6157.22|
| 11:  2.1970 -  2.1284  1328   145  0.87  19.80   0.99     0.93       5933.34|
| 12:  2.1284 -  2.0678  1327   144  0.87  19.99   0.99     0.99       5684.13|
| 13:  2.0678 -  2.0134  1100   123  0.86  20.83   0.98     0.95       4843.67|
| 14:  2.0134 -  1.9644   280    29  0.90  16.88   0.98     0.95       3619.43|
|alpha:            min =        0.93 max =            1.03 mean =         0.96|
|beta:             min =     3619.43 max =        13749.48 mean =      8851.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.92 mean =        17.43|
|phase err.(test): min =        0.00 max =           89.97 mean =        16.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.37   15.76    None  None   None       |
|    all(noH): 2823   0      0.00    85.37   15.76    None  None   None       |
|    Sol.    : 438    0      4.71    78.78   40.63    None  None   None       |
|    Mac.    : 2385   0      0.00    85.37   11.19    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:     0.003 -   8.540: 1114   |   5:    42.689 -  51.226:  100        |
|      1:     8.540 -  17.077: 1003   |   6:    51.226 -  59.763:   75        |
|      2:    17.077 -  25.614:  235   |   7:    59.763 -  68.300:   48        |
|      3:    25.614 -  34.152:  123   |   8:    68.300 -  76.837:   23        |
|      4:    34.152 -  42.689:  100   |   9:    76.837 -  85.375:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.547 - 5.764
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 340
   mapped sites are within: 0.710 - 5.764

peak=    8.872 closest distance to " CB  VAL A 230 " =    1.491
peak=    6.902 closest distance to " CG2 VAL A 296 " =    1.228
peak=    6.591 closest distance to " O   HOH Z 130 " =    1.366
peak=    6.461 closest distance to " CD2 LEU A   5 " =    1.369
peak=    6.418 closest distance to " CG  ARG A 138 " =    1.268
peak=    6.234 closest distance to " O   HOH Z  41 " =    1.185
peak=    5.903 closest distance to " O   HOH Z 268 " =    1.151
peak=    5.896 closest distance to " NH1 ARG A 138 " =    1.079
peak=    5.862 closest distance to " CD  ARG A 138 " =    1.059
peak=    5.516 closest distance to " O   HOH Z 222 " =    1.711
peak=    5.471 closest distance to " O   HOH Z  63 " =    1.674
peak=    5.291 closest distance to " O   HOH Z  65 " =    1.390
peak=    5.279 closest distance to " O   HOH Z   7 " =    1.958
peak=    5.275 closest distance to " O   HOH Z 403 " =    1.533
peak=    5.152 closest distance to " CD1AILE A 234 " =    1.094
peak=    5.116 closest distance to " NE2 GLN A  11 " =    1.200
peak=    4.986 closest distance to " O   HOH Z 232 " =    2.084
peak=    4.940 closest distance to " NH1 ARG A  56 " =    1.241
peak=    4.932 closest distance to " CB  PRO A  54 " =    1.518
peak=    4.894 closest distance to " CB  PRO A  54 " =    1.160
peak=    4.868 closest distance to " O   HOH Z 117 " =    1.185
peak=    4.841 closest distance to " CA  VAL A 230 " =    1.258
peak=    4.834 closest distance to " O   HOH Z  97 " =    1.589
peak=    4.748 closest distance to " O   HOH Z 139 " =    1.403
peak=    4.748 closest distance to " O   HOH Z 287 " =    2.064
peak=    4.738 closest distance to " O   HOH Z 401 " =    1.296
peak=    4.620 closest distance to " CB  ASN A 148 " =    1.322
peak=    4.588 closest distance to " NZ ALYS A 290 " =    1.049
peak=    4.587 closest distance to " O   HOH Z 425 " =    1.810
peak=    4.555 closest distance to " CB  SER A 216 " =    1.086
peak=    4.523 closest distance to " O   HOH Z 316 " =    3.054
peak=    4.509 closest distance to " O   HOH Z 410 " =    1.786
peak=    4.498 closest distance to " O   HOH Z  69 " =    2.424
peak=    4.490 closest distance to " CD2 TRP A 179 " =    2.217
peak=    4.442 closest distance to " CB  ASP A 124 " =    0.797
peak=    4.419 closest distance to " O   HOH Z 255 " =    1.163
peak=    4.416 closest distance to " CG  LEU A   5 " =    1.238
peak=    4.393 closest distance to " CB  SER A  63 " =    1.405
peak=    4.382 closest distance to " CG  LEU A 228 " =    1.217
peak=    4.370 closest distance to " CB  GLN A 223 " =    1.471
peak=    4.353 closest distance to " O   HOH Z 245 " =    1.178
peak=    4.351 closest distance to " CB  TRP A 266 " =    1.010
peak=    4.306 closest distance to " CZ  PHE A 192 " =    1.024
peak=    4.305 closest distance to " ND2 ASN A 285 " =    1.024
peak=    4.300 closest distance to " CG  PRO A 198 " =    1.334
peak=    4.289 closest distance to " CB  SER A   3 " =    1.668
peak=    4.272 closest distance to " CA  ALA A  51 " =    1.070
peak=    4.252 closest distance to " O   HOH Z 144 " =    2.030
peak=    4.251 closest distance to " C   ASN A 209 " =    1.531
peak=    4.245 closest distance to " O   HOH Z 183 " =    1.406
peak=    4.236 closest distance to " O   HOH Z  56 " =    2.204
peak=    4.227 closest distance to " CG  PRO A 280 " =    1.143
peak=    4.207 closest distance to " NH1AARG A 145 " =    1.149
peak=    4.205 closest distance to " O   HOH Z 417 " =    1.464
peak=    4.199 closest distance to " O   HOH Z  57 " =    1.664
peak=    4.186 closest distance to " CD BLYS A 290 " =    1.073
peak=    4.163 closest distance to " O   HOH Z 186 " =    1.731
peak=    4.154 closest distance to " CB  MET A  40 " =    0.862
peak=    4.134 closest distance to " CD2 LEU A 228 " =    1.369
peak=    4.126 closest distance to " N   GLN A 278 " =    1.195
peak=    4.095 closest distance to " CG2 THR A 221 " =    1.189
peak=    4.086 closest distance to " O   HOH Z 218 " =    2.153
peak=    4.084 closest distance to " O   HOH Z 369 " =    1.998
peak=    4.077 closest distance to " O   PRO A 198 " =    1.364
peak=    4.077 closest distance to " CB  LYS A 290 " =    0.893
peak=    4.075 closest distance to " CZ3 TRP A 123 " =    1.466
peak=    4.074 closest distance to " O   HOH Z 411 " =    3.110
peak=    4.072 closest distance to " O   HOH Z 423 " =    1.880
peak=    4.069 closest distance to " O   HOH Z 126 " =    2.144
peak=    4.065 closest distance to " O   HOH Z 148 " =    1.732
peak=    4.059 closest distance to " CG  LEU A 167 " =    1.326
peak=    4.047 closest distance to " O   HOH Z  55 " =    2.000
peak=    4.044 closest distance to " O   HOH Z  59 " =    1.928
peak=    4.039 closest distance to " CA  ILE A 234 " =    1.127
peak=    4.038 closest distance to " CZ  PHE A 218 " =    1.193
peak=    4.032 closest distance to " O   HOH Z 170 " =    1.638
peak=    4.026 closest distance to " O   HOH Z 272 " =    2.030
peak=    4.014 closest distance to " CB  ASN A  39 " =    0.962
peak=    3.999 closest distance to " O   HOH Z 425 " =    2.070
peak=    3.992 closest distance to " O   HOH Z 427 " =    2.768
peak=    3.983 closest distance to " O   HOH Z 360 " =    1.273
peak=    3.980 closest distance to " O   HOH Z 133 " =    2.726
peak=    3.972 closest distance to " O   HOH Z   9 " =    1.781
peak=    3.965 closest distance to " NH2AARG A 145 " =    1.100
peak=    3.950 closest distance to " O   HOH Z 332 " =    1.662
peak=    3.948 closest distance to " CE3 TRP A 274 " =    1.389
peak=    3.941 closest distance to " O   HOH Z 102 " =    0.953
peak=    3.921 closest distance to " CG  ASN A  60 " =    0.994
peak=    3.918 closest distance to " CA  SER A  87 " =    0.916
peak=    3.907 closest distance to " CB  SER A 210 " =    0.957
peak=    3.902 closest distance to " OE1 GLN A 240 " =    1.750
peak=    3.901 closest distance to " O   HOH Z 273 " =    1.577
peak=    3.854 closest distance to " O   HOH Z 350 " =    1.514
peak=    3.852 closest distance to " O   HOH Z 258 " =    2.197
peak=    3.844 closest distance to " CE3 TRP A 274 " =    2.467
peak=    3.842 closest distance to " N   TYR A  15 " =    0.959
peak=    3.828 closest distance to " CA  ASP A  50 " =    1.205
peak=    3.822 closest distance to " ND2 ASN A 249 " =    0.793
peak=    3.815 closest distance to " CD  ARG A 269 " =    1.021
peak=    3.812 closest distance to " CG  PRO A 213 " =    1.406
peak=    3.805 closest distance to " O   HOH Z 172 " =    2.121
peak=    3.798 closest distance to " N   CYS A 260 " =    0.848
peak=    3.797 closest distance to " CB  ALA A 104 " =    0.811
peak=    3.790 closest distance to " CG  GLN A  88 " =    0.945
peak=    3.786 closest distance to " O   HOH Z 145 " =    2.309
peak=    3.785 closest distance to " O   HOH Z 424 " =    1.253
peak=    3.776 closest distance to " O   HOH Z 132 " =    1.161
peak=    3.776 closest distance to " CB  GLU A 152 " =    1.223
peak=    3.776 closest distance to " O   HOH Z 143 " =    1.494
peak=    3.767 closest distance to " NH1 ARG A  14 " =    1.123
peak=    3.763 closest distance to " O   HOH Z  30 " =    1.384
peak=    3.757 closest distance to " CB  ASN A  60 " =    1.049
peak=    3.755 closest distance to " CA  VAL A 296 " =    1.128
peak=    3.747 closest distance to " CG  PRO A 243 " =    1.110
peak=    3.736 closest distance to " O   THR A 182 " =    1.691
peak=    3.733 closest distance to " O   HOH Z  61 " =    1.936
peak=    3.731 closest distance to " O   HOH Z 215 " =    1.449
peak=    3.728 closest distance to " O   HOH Z 147 " =    1.484
peak=    3.723 closest distance to " O   HOH Z 414 " =    1.619
peak=    3.721 closest distance to " O   HOH Z   2 " =    1.829
peak=    3.716 closest distance to " CB  LEU A 237 " =    0.919
peak=    3.716 closest distance to " CD1 LEU A 300 " =    1.282
peak=    3.708 closest distance to " O   HOH Z 290 " =    1.332
peak=    3.702 closest distance to " O   HOH Z 193 " =    1.757
peak=    3.691 closest distance to " CG1 VAL A 296 " =    1.224
peak=    3.688 closest distance to " CD  ARG A 159 " =    0.757
peak=    3.688 closest distance to " OD1 ASN A 217 " =    1.633
peak=    3.686 closest distance to " O   HOH Z 153 " =    4.101
peak=    3.680 closest distance to " NH2BARG A 190 " =    1.419
peak=    3.678 closest distance to " O   HOH Z  26 " =    1.561
peak=    3.678 closest distance to " CB  ARG A 138 " =    1.317
peak=    3.674 closest distance to " N   GLY A 136 " =    1.135
peak=    3.673 closest distance to " CA  ASN A 127 " =    1.189
peak=    3.671 closest distance to " CB  VAL A 265 " =    1.395
peak=    3.666 closest distance to " O   HOH Z 298 " =    2.128
peak=    3.661 closest distance to " CE  MET A  93 " =    1.534
peak=    3.656 closest distance to " NE2 GLN A  58 " =    3.872
peak=    3.644 closest distance to " CB  GLN A 183 " =    1.163
peak=    3.635 closest distance to " O   HOH Z 373 " =    2.033
peak=    3.634 closest distance to " O   HOH Z  39 " =    1.184
peak=    3.634 closest distance to " CE3 TRP A  85 " =    1.106
peak=    3.629 closest distance to " O   HOH Z 353 " =    2.571
peak=    3.623 closest distance to " O   HOH Z 217 " =    2.823
peak=    3.620 closest distance to " CA  ALA A 295 " =    1.018
peak=    3.616 closest distance to " CZ3 TRP A 266 " =    1.183
peak=    3.613 closest distance to " O   HOH Z 225 " =    1.490
peak=    3.612 closest distance to " CB  ALA A  10 " =    1.111
peak=    3.606 closest distance to " O   ASP A 132 " =    3.835
peak=    3.605 closest distance to " O   TYR A 116 " =    1.194
peak=    3.600 closest distance to " O   HOH Z  78 " =    1.589
peak=    3.589 closest distance to " OG ASER A 212 " =    1.760
peak=    3.584 closest distance to " OG  SER A 276 " =    1.021
peak=    3.575 closest distance to " CA  ILE A 106 " =    0.824
peak=    3.568 closest distance to " CD1 ILE A  33 " =    1.795
peak=    3.563 closest distance to " CG  LYS A  76 " =    1.759
peak=    3.561 closest distance to " CB  ASN A 142 " =    0.838
peak=    3.559 closest distance to " CB  GLU A 128 " =    1.126
peak=    3.559 closest distance to " O   HOH Z  85 " =    1.976
peak=    3.556 closest distance to " CD1 LEU A   5 " =    1.283
peak=    3.556 closest distance to " CD  ARG A  66 " =    2.234
peak=    3.545 closest distance to " CG1 ILE A  33 " =    1.253
peak=    3.543 closest distance to " NE AARG A 275 " =    1.679
peak=    3.541 closest distance to " CB  ARG A 275 " =    1.050
peak=    3.533 closest distance to " CG1 ILE A 151 " =    1.170
peak=    3.531 closest distance to " CA  MET A  47 " =    1.237
peak=    3.528 closest distance to " O   HOH Z 146 " =    1.654
peak=    3.528 closest distance to " ND1 HIS A  81 " =    1.723
peak=    3.526 closest distance to " O   HOH Z 438 " =    2.148
peak=    3.519 closest distance to " CB  ALA A 233 " =    1.119
peak=    3.514 closest distance to " O   HOH Z 422 " =    2.563
peak=    3.507 closest distance to " O   HOH Z  80 " =    1.768
peak=    3.504 closest distance to " CA  ASN A 284 " =    0.865
peak=    3.504 closest distance to " N   SER A 271 " =    0.989
peak=    3.502 closest distance to " O   HOH Z 102 " =    1.507
peak=    3.501 closest distance to " O   HOH Z  30 " =    2.198
peak=    3.501 closest distance to " O   HOH Z 365 " =    5.721
peak=    3.500 closest distance to " CE2 TYR A 186 " =    0.952
peak=    3.499 closest distance to " CG2 THR A 279 " =    1.020
peak=    3.496 closest distance to " O   HOH Z   1 " =    2.138
peak=    3.496 closest distance to " O   HOH Z 167 " =    1.778
peak=    3.494 closest distance to " O   HOH Z 281 " =    4.766
peak=    3.488 closest distance to " O   HOH Z 361 " =    1.437
peak=    3.486 closest distance to " O   PRO A 198 " =    1.505
peak=    3.485 closest distance to " CB  ALA A  43 " =    0.999
peak=    3.478 closest distance to " O   ALA A 165 " =    1.410
peak=    3.475 closest distance to " OG BSER A 212 " =    2.234
peak=    3.471 closest distance to " CB  VAL A 202 " =    1.576
peak=    3.469 closest distance to " NE2 HIS A 207 " =    0.998
peak=    3.462 closest distance to " O   HOH Z 415 " =    1.076
peak=    3.455 closest distance to " O   HOH Z 424 " =    3.028
peak=    3.447 closest distance to " O   HOH Z 154 " =    1.966
peak=    3.445 closest distance to " CB  VAL A 250 " =    1.107
peak=    3.442 closest distance to " OE2 GLU A   2 " =    2.040
peak=    3.436 closest distance to " O   HOH Z 328 " =    1.726
peak=    3.430 closest distance to " CA  VAL A 153 " =    0.996
peak=    3.430 closest distance to " OG BSER A 134 " =    2.483
peak=    3.430 closest distance to " CH2 TRP A 150 " =    1.115
peak=    3.427 closest distance to " CB  ALA A 114 " =    0.850
peak=    3.427 closest distance to " N   ARG A 156 " =    1.434
peak=    3.424 closest distance to " O   HOH Z 236 " =    1.746
peak=    3.421 closest distance to " O   HOH Z 359 " =    1.388
peak=    3.417 closest distance to " CB  THR A  31 " =    1.545
peak=    3.416 closest distance to " O   HOH Z 257 " =    1.162
peak=    3.413 closest distance to " CA  PRO A  54 " =    0.925
peak=    3.409 closest distance to " O   HOH Z  91 " =    2.459
peak=    3.405 closest distance to " CB  ASN A 187 " =    1.082
peak=    3.398 closest distance to " O   HOH Z 392 " =    1.263
peak=    3.397 closest distance to " O   HOH Z 389 " =    1.787
peak=    3.392 closest distance to " O   HOH Z  68 " =    1.844
peak=    3.391 closest distance to " O   HOH Z 368 " =    3.558
peak=    3.388 closest distance to " CB  SER A 276 " =    1.274
peak=    3.386 closest distance to " N   PHE A 130 " =    1.361
peak=    3.383 closest distance to " CG  ARG A 159 " =    1.014
peak=    3.378 closest distance to " N   SER A  97 " =    0.838
peak=    3.367 closest distance to " CA  ALA A  21 " =    1.124
peak=    3.365 closest distance to " CB  MET A  47 " =    1.063
peak=    3.363 closest distance to " OE2 GLU A   2 " =    2.333
peak=    3.362 closest distance to " CA  ALA A 299 " =    0.967
peak=    3.360 closest distance to " O   HOH Z 222 " =    1.989
peak=    3.360 closest distance to " OH  TYR A 186 " =    1.020
peak=    3.357 closest distance to " CB  GLU A 277 " =    3.763
peak=    3.355 closest distance to " O   HOH Z  57 " =    1.653
peak=    3.351 closest distance to " CE  LYS A  76 " =    0.838
peak=    3.347 closest distance to " NH2 ARG A 219 " =    1.865
peak=    3.346 closest distance to " CG2 VAL A 268 " =    0.978
peak=    3.345 closest distance to " O   HOH Z 175 " =    3.824
peak=    3.335 closest distance to " NH2AARG A 190 " =    1.584
peak=    3.333 closest distance to " O   HOH Z 313 " =    1.755
peak=    3.327 closest distance to " O   HOH Z  51 " =    2.054
peak=    3.324 closest distance to " C   GLN A  88 " =    1.543
peak=    3.319 closest distance to " O   HOH Z 204 " =    1.551
peak=    3.303 closest distance to " CB  ARG A 259 " =    1.938
peak=    3.303 closest distance to " CB  LEU A 228 " =    1.243
peak=    3.298 closest distance to " O   GLN A  55 " =    1.848
peak=    3.297 closest distance to " O   HOH Z  44 " =    2.492
peak=    3.293 closest distance to " CA  GLY A 196 " =    0.853
peak=    3.290 closest distance to " O   HOH Z 368 " =    1.949
peak=    3.290 closest distance to " OE2 GLU A  53 " =    1.736
peak=    3.290 closest distance to " CG2 ILE A 234 " =    1.215
peak=    3.289 closest distance to " O   HOH Z 244 " =    1.817
peak=    3.287 closest distance to " O   HOH Z 188 " =    3.107
peak=    3.284 closest distance to " O   HOH Z 362 " =    2.137
peak=    3.277 closest distance to " CA  ARG A  36 " =    1.178
peak=    3.274 closest distance to " CD  LYS A 119 " =    1.560
peak=    3.274 closest distance to " CB  GLU A 175 " =    0.829
peak=    3.269 closest distance to " N   ALA A   1 " =    1.475
peak=    3.268 closest distance to " CD  ARG A  56 " =    0.750
peak=    3.267 closest distance to " CB  ALA A  21 " =    1.124
peak=    3.264 closest distance to " OG  SER A  22 " =    3.039
peak=    3.261 closest distance to " O   HOH Z 248 " =    2.024
peak=    3.261 closest distance to " O   HOH Z 409 " =    3.670
peak=    3.260 closest distance to " O   HOH Z  46 " =    1.032
peak=    3.259 closest distance to " CG2 ILE A 109 " =    0.981
peak=    3.258 closest distance to " O   HOH Z 109 " =    2.299
peak=    3.254 closest distance to " CB  ASN A 110 " =    1.051
peak=    3.254 closest distance to " O   HOH Z 374 " =    1.109
peak=    3.253 closest distance to " ND2BASN A 224 " =    0.853
peak=    3.252 closest distance to " NE2 GLN A  89 " =    1.611
peak=    3.249 closest distance to " CB  ALA A 184 " =    1.066
peak=    3.245 closest distance to " O   HOH Z   9 " =    1.946
peak=    3.243 closest distance to " O   HOH Z 171 " =    1.977
peak=    3.238 closest distance to " O   HOH Z 145 " =    2.090
peak=    3.238 closest distance to " O   HOH Z   7 " =    3.279
peak=    3.237 closest distance to " CG  MET A 113 " =    1.476
peak=    3.236 closest distance to " CG  GLN A  89 " =    1.547
peak=    3.235 closest distance to " OG  SER A  28 " =    1.588
peak=    3.232 closest distance to " O   HOH Z 158 " =    2.755
peak=    3.231 closest distance to " O   HOH Z 184 " =    1.759
peak=    3.229 closest distance to " CA  ALA A 184 " =    1.176
peak=    3.225 closest distance to " CB  ARG A  79 " =    1.317
peak=    3.218 closest distance to " O   HOH Z 356 " =    1.428
peak=    3.218 closest distance to " C   ASP A 298 " =    1.600
peak=    3.216 closest distance to " O   HOH Z 195 " =    1.678
peak=    3.214 closest distance to " O   HOH Z 384 " =    2.021
peak=    3.211 closest distance to " O   HOH Z 411 " =    1.477
peak=    3.209 closest distance to " O   THR A 294 " =    1.038
peak=    3.206 closest distance to " O   HOH Z 139 " =    1.924
peak=    3.205 closest distance to " CA  LEU A 282 " =    0.988
peak=    3.204 closest distance to " O   HOH Z 434 " =    1.587
peak=    3.200 closest distance to " O   HOH Z 124 " =    1.796
peak=    3.195 closest distance to " O   HOH Z 409 " =    2.119
peak=    3.181 closest distance to " CA  THR A 264 " =    0.802
peak=    3.180 closest distance to " CA  ALA A 160 " =    1.196
peak=    3.177 closest distance to " ND2 ASN A  60 " =    1.379
peak=    3.176 closest distance to " O   HOH Z 153 " =    3.810
peak=    3.174 closest distance to " O   HOH Z 143 " =    1.114
peak=    3.174 closest distance to " O   HOH Z 115 " =    2.229
peak=    3.171 closest distance to " O   HOH Z 380 " =    1.773
peak=    3.167 closest distance to " O   HOH Z 284 " =    3.121
peak=    3.165 closest distance to " CG  GLN A 144 " =    0.888
peak=    3.163 closest distance to " OD1 ASP A 200 " =    1.688
peak=    3.160 closest distance to " O   THR A 251 " =    1.254
peak=    3.159 closest distance to " O   HOH Z 271 " =    1.687
peak=    3.158 closest distance to " NE2 GLN A  58 " =    5.764
peak=    3.157 closest distance to " CG1 ILE A  49 " =    1.637
peak=    3.157 closest distance to " CB  GLU A 277 " =    0.879
peak=    3.155 closest distance to " O   ALA A 180 " =    1.327
peak=    3.153 closest distance to " OD2 ASP A 286 " =    2.806
peak=    3.151 closest distance to " CG1 ILE A 120 " =    1.389
peak=    3.150 closest distance to " NH2BARG A 145 " =    1.991
peak=    3.150 closest distance to " CA  ALA A 154 " =    1.051
peak=    3.142 closest distance to " CD  LYS A 166 " =    1.367
peak=    3.139 closest distance to " OE1 GLU A   2 " =    1.457
peak=    3.138 closest distance to " O   HOH Z  55 " =    1.729
peak=    3.137 closest distance to " NE  ARG A  56 " =    3.728
peak=    3.137 closest distance to " CB  TRP A 274 " =    1.016
peak=    3.136 closest distance to " N   SER A 134 " =    1.251
peak=    3.133 closest distance to " O   HOH Z 418 " =    0.927
peak=    3.132 closest distance to " O   HOH Z 127 " =    1.057
peak=    3.123 closest distance to " CB  ALA A 248 " =    1.259
peak=    3.122 closest distance to " CA  THR A 221 " =    0.860
peak=    3.122 closest distance to " CD1 LEU A 167 " =    1.304
peak=    3.119 closest distance to " CB  SER A  62 " =    1.210
peak=    3.117 closest distance to " O   HOH Z 406 " =    1.632
peak=    3.116 closest distance to " O   GLY A 302 " =    2.373
peak=    3.111 closest distance to " CA  TRP A  92 " =    1.186
peak=    3.111 closest distance to " CA  VAL A 121 " =    0.992
peak=    3.110 closest distance to " O   HOH Z 425 " =    2.029
peak=    3.110 closest distance to " O   HOH Z  99 " =    2.322
peak=    3.107 closest distance to " CA  ARG A 159 " =    1.373
peak=    3.104 closest distance to " OG  SER A  62 " =    3.876
peak=    3.103 closest distance to " CA  ASP A 149 " =    1.378
peak=    3.101 closest distance to " O   HOH Z 411 " =    3.913
peak=    3.098 closest distance to " O   HOH Z 217 " =    1.651
peak=    3.094 closest distance to " CB  ARG A 156 " =    1.223
peak=    3.087 closest distance to " OG BSER A 258 " =    0.918
peak=    3.078 closest distance to " CA  TYR A 116 " =    1.426
peak=    3.075 closest distance to " NH2BARG A 190 " =    1.872
peak=    3.074 closest distance to " O   HOH Z 409 " =    1.897
peak=    3.070 closest distance to " O   HOH Z 186 " =    2.844
peak=    3.069 closest distance to " ND2 ASN A 249 " =    0.710
peak=    3.069 closest distance to " CA  LEU A 222 " =    1.048
peak=    3.068 closest distance to " O   HOH Z  88 " =    2.955
peak=    3.062 closest distance to " CG2 THR A 220 " =    1.017
peak=    3.059 closest distance to " O   ALA A 233 " =    1.851
peak=    3.051 closest distance to " O   HOH Z 285 " =    2.636

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.386 - 5.823
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 218
   mapped sites are within: 0.736 - 5.823

peak=   -5.796 closest distance to " CD  ARG A 138 " =    1.052
peak=   -4.808 closest distance to " CG2 VAL A 230 " =    0.852
peak=   -4.684 closest distance to " O   HOH Z  39 " =    0.785
peak=   -4.449 closest distance to " OE1 GLN A  88 " =    0.936
peak=   -4.264 closest distance to " CD  ARG A  14 " =    3.117
peak=   -4.247 closest distance to " CB  PHE A 130 " =    1.310
peak=   -4.199 closest distance to " O   PRO A 198 " =    1.253
peak=   -4.118 closest distance to " O   HOH Z 102 " =    1.215
peak=   -4.087 closest distance to " O   HOH Z 290 " =    1.266
peak=   -4.066 closest distance to " CB  ASP A  27 " =    2.527
peak=   -4.029 closest distance to " CG  GLN A  88 " =    0.877
peak=   -4.021 closest distance to " CG  MET A 105 " =    0.941
peak=   -3.958 closest distance to " O   HOH Z 255 " =    0.947
peak=   -3.949 closest distance to " O   HOH Z 359 " =    1.517
peak=   -3.899 closest distance to " CD  GLU A 277 " =    0.919
peak=   -3.873 closest distance to " CB  ALA A   9 " =    2.526
peak=   -3.867 closest distance to " OG  SER A  87 " =    1.447
peak=   -3.839 closest distance to " OG  SER A  97 " =    2.024
peak=   -3.836 closest distance to " CA  GLY A  91 " =    2.341
peak=   -3.820 closest distance to " O   HOH Z  32 " =    1.362
peak=   -3.803 closest distance to " CG2 ILE A 151 " =    2.590
peak=   -3.801 closest distance to " O   HOH Z 166 " =    1.509
peak=   -3.798 closest distance to " CG2 VAL A 296 " =    1.866
peak=   -3.796 closest distance to " CB  ALA A  43 " =    2.566
peak=   -3.788 closest distance to " O   HOH Z 198 " =    2.644
peak=   -3.778 closest distance to " OG  SER A  63 " =    1.182
peak=   -3.728 closest distance to " O   HOH Z 401 " =    0.815
peak=   -3.725 closest distance to " O   HOH Z 389 " =    1.070
peak=   -3.724 closest distance to " CG BLYS A 290 " =    0.856
peak=   -3.723 closest distance to " O   HOH Z 286 " =    1.673
peak=   -3.710 closest distance to " N   THR A 157 " =    1.736
peak=   -3.681 closest distance to " CD2 LEU A   5 " =    0.872
peak=   -3.670 closest distance to " CG1 VAL A 296 " =    1.392
peak=   -3.666 closest distance to " O   HOH Z 108 " =    1.347
peak=   -3.666 closest distance to " OG BSER A 134 " =    1.869
peak=   -3.664 closest distance to " O   HOH Z 163 " =    1.606
peak=   -3.658 closest distance to " OE1 GLN A  88 " =    1.296
peak=   -3.658 closest distance to " O   HOH Z 389 " =    2.309
peak=   -3.657 closest distance to " O   TRP A  70 " =    1.510
peak=   -3.636 closest distance to " N   ALA A  43 " =    2.685
peak=   -3.628 closest distance to " CB  ALA A 291 " =    1.871
peak=   -3.622 closest distance to " CZ3 TRP A 179 " =    1.175
peak=   -3.618 closest distance to " CA  GLY A 203 " =    2.322
peak=   -3.618 closest distance to " NE1 TRP A  70 " =    2.444
peak=   -3.609 closest distance to " CB  PRO A 243 " =    2.575
peak=   -3.597 closest distance to " O   SER A 135 " =    1.360
peak=   -3.587 closest distance to " CD  ARG A 156 " =    1.984
peak=   -3.583 closest distance to " CB  PRO A 163 " =    2.334
peak=   -3.580 closest distance to " O   GLY A 203 " =    2.424
peak=   -3.573 closest distance to " CB  ASP A 132 " =    2.356
peak=   -3.570 closest distance to " CD  LYS A 289 " =    2.342
peak=   -3.569 closest distance to " CB  VAL A 230 " =    0.963
peak=   -3.567 closest distance to " CD1 PHE A  59 " =    2.053
peak=   -3.549 closest distance to " O   HOH Z 245 " =    1.115
peak=   -3.544 closest distance to " N   ASP A 191 " =    1.146
peak=   -3.541 closest distance to " O   HOH Z  60 " =    1.671
peak=   -3.524 closest distance to " O   HOH Z 313 " =    1.553
peak=   -3.523 closest distance to " O   SER A  32 " =    1.050
peak=   -3.519 closest distance to " O   HOH Z 371 " =    2.436
peak=   -3.514 closest distance to " O   HOH Z 350 " =    1.598
peak=   -3.501 closest distance to " O   HOH Z 359 " =    3.330
peak=   -3.496 closest distance to " O   HOH Z 231 " =    1.867
peak=   -3.496 closest distance to " C   ASP A  50 " =    1.666
peak=   -3.492 closest distance to " CG  ARG A 219 " =    2.300
peak=   -3.481 closest distance to " CD  PRO A 213 " =    2.061
peak=   -3.480 closest distance to " O   HOH Z 368 " =    1.299
peak=   -3.477 closest distance to " OD2 ASP A  27 " =    1.749
peak=   -3.474 closest distance to " CG  TRP A 266 " =    1.835
peak=   -3.473 closest distance to " C   ASN A 285 " =    2.381
peak=   -3.473 closest distance to " OG  SER A  28 " =    1.940
peak=   -3.471 closest distance to " OE1 GLU A 277 " =    2.480
peak=   -3.468 closest distance to " NH2 ARG A  79 " =    2.019
peak=   -3.466 closest distance to " O   HOH Z 275 " =    1.613
peak=   -3.462 closest distance to " O   HOH Z 413 " =    3.446
peak=   -3.461 closest distance to " O   ILE A 106 " =    2.243
peak=   -3.460 closest distance to " O   HOH Z 415 " =    0.946
peak=   -3.459 closest distance to " OE1 GLN A 278 " =    1.104
peak=   -3.458 closest distance to " O   HOH Z 411 " =    5.104
peak=   -3.457 closest distance to " OG ASER A 134 " =    1.143
peak=   -3.457 closest distance to " O   HOH Z 111 " =    2.054
peak=   -3.443 closest distance to " O   HOH Z  52 " =    1.642
peak=   -3.436 closest distance to " CB  SER A  63 " =    3.422
peak=   -3.434 closest distance to " CB  ARG A 138 " =    1.446
peak=   -3.431 closest distance to " O   THR A 178 " =    0.845
peak=   -3.426 closest distance to " O   HOH Z 282 " =    4.581
peak=   -3.424 closest distance to " CG  PRO A 163 " =    2.535
peak=   -3.423 closest distance to " CZ2 TRP A  92 " =    2.848
peak=   -3.417 closest distance to " O   VAL A 125 " =    2.308
peak=   -3.414 closest distance to " O   HOH Z 211 " =    1.277
peak=   -3.412 closest distance to " CG  LEU A   5 " =    0.891
peak=   -3.411 closest distance to " N   ALA A 226 " =    2.166
peak=   -3.403 closest distance to " CG1 VAL A  78 " =    2.269
peak=   -3.402 closest distance to " O   HOH Z 216 " =    1.284
peak=   -3.400 closest distance to " O   HOH Z 201 " =    1.334
peak=   -3.389 closest distance to " CA  GLY A 133 " =    2.134
peak=   -3.386 closest distance to " O   HOH Z  51 " =    0.984
peak=   -3.385 closest distance to " CA  GLY A 133 " =    2.261
peak=   -3.383 closest distance to " CB  ALA A 248 " =    2.027
peak=   -3.381 closest distance to " O   SER A  22 " =    2.919
peak=   -3.379 closest distance to " NH2AARG A 275 " =    5.823
peak=   -3.374 closest distance to " CB  ALA A 248 " =    2.547
peak=   -3.372 closest distance to " CB  GLN A  55 " =    1.409
peak=   -3.364 closest distance to " CD2 TYR A 293 " =    1.969
peak=   -3.364 closest distance to " NH1 ARG A 138 " =    1.039
peak=   -3.364 closest distance to " CB  ALA A 161 " =    1.710
peak=   -3.363 closest distance to " CG  MET A  40 " =    2.294
peak=   -3.343 closest distance to " O   HOH Z 398 " =    0.874
peak=   -3.343 closest distance to " OD1 ASP A 171 " =    1.614
peak=   -3.337 closest distance to " CG1 VAL A 112 " =    3.146
peak=   -3.336 closest distance to " O   GLY A  91 " =    1.600
peak=   -3.336 closest distance to " CA  THR A  18 " =    1.380
peak=   -3.329 closest distance to " O   HOH Z  43 " =    1.405
peak=   -3.321 closest distance to " O   HOH Z 181 " =    2.219
peak=   -3.320 closest distance to " CD1 LEU A 297 " =    2.282
peak=   -3.320 closest distance to " NE2 GLN A 223 " =    1.647
peak=   -3.319 closest distance to " CD  LYS A 166 " =    2.494
peak=   -3.318 closest distance to " O   TYR A 247 " =    2.776
peak=   -3.313 closest distance to " O   HOH Z 131 " =    3.770
peak=   -3.310 closest distance to " O   HOH Z 297 " =    3.745
peak=   -3.310 closest distance to " O   HOH Z 377 " =    0.949
peak=   -3.307 closest distance to " N   THR A  29 " =    1.267
peak=   -3.306 closest distance to " CE  MET A 188 " =    2.240
peak=   -3.303 closest distance to " CB  ALA A 114 " =    2.446
peak=   -3.302 closest distance to " O   THR A  18 " =    1.617
peak=   -3.299 closest distance to " NE2 GLN A  58 " =    3.167
peak=   -3.299 closest distance to " O   HOH Z 298 " =    2.692
peak=   -3.294 closest distance to " O   HOH Z 139 " =    3.045
peak=   -3.293 closest distance to " O   HOH Z  49 " =    1.777
peak=   -3.289 closest distance to " OE1 GLU A   2 " =    1.742
peak=   -3.289 closest distance to " O   PRO A 163 " =    2.009
peak=   -3.281 closest distance to " CA  TYR A  68 " =    1.204
peak=   -3.281 closest distance to " CG  GLN A 278 " =    2.254
peak=   -3.278 closest distance to " OH  TYR A 214 " =    1.103
peak=   -3.278 closest distance to " CE2 TYR A  30 " =    2.558
peak=   -3.274 closest distance to " CD  GLN A  58 " =    0.738
peak=   -3.272 closest distance to " CB  ASN A  39 " =    2.135
peak=   -3.270 closest distance to " CG1BVAL A  72 " =    2.175
peak=   -3.268 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.268 closest distance to " O   HOH Z 268 " =    0.877
peak=   -3.266 closest distance to " O   HOH Z   2 " =    1.695
peak=   -3.265 closest distance to " O   GLN A 194 " =    1.428
peak=   -3.264 closest distance to " O   HOH Z 105 " =    1.981
peak=   -3.264 closest distance to " O   HOH Z 103 " =    2.148
peak=   -3.263 closest distance to " CB  PRO A  54 " =    2.529
peak=   -3.250 closest distance to " O   VAL A 174 " =    2.173
peak=   -3.250 closest distance to " CA  ARG A  56 " =    1.128
peak=   -3.248 closest distance to " OG  SER A 206 " =    1.771
peak=   -3.246 closest distance to " O   HOH Z 259 " =    4.022
peak=   -3.246 closest distance to " OH  TYR A 247 " =    1.685
peak=   -3.246 closest distance to " OE1 GLU A  44 " =    0.786
peak=   -3.243 closest distance to " O   ARG A 145 " =    1.494
peak=   -3.242 closest distance to " CA  GLY A  98 " =    1.880
peak=   -3.242 closest distance to " CB  CYS A 254 " =    1.640
peak=   -3.241 closest distance to " O   HOH Z 275 " =    1.804
peak=   -3.236 closest distance to " CA  GLY A 241 " =    2.216
peak=   -3.234 closest distance to " C   PHE A 155 " =    0.882
peak=   -3.234 closest distance to " O   HOH Z 185 " =    2.336
peak=   -3.231 closest distance to " O   HOH Z 156 " =    2.196
peak=   -3.228 closest distance to " CB  TYR A  15 " =    2.081
peak=   -3.226 closest distance to " O   ASN A 301 " =    1.378
peak=   -3.221 closest distance to " OD1 ASN A  60 " =    1.015
peak=   -3.218 closest distance to " O   HOH Z 133 " =    1.610
peak=   -3.217 closest distance to " O   HOH Z 292 " =    1.902
peak=   -3.205 closest distance to " C   LEU A 101 " =    1.155
peak=   -3.203 closest distance to " OG  SER A 245 " =    1.505
peak=   -3.202 closest distance to " OG  SER A 141 " =    1.763
peak=   -3.201 closest distance to " C   SER A 206 " =    1.575
peak=   -3.197 closest distance to " O   HOH Z 246 " =    0.736
peak=   -3.192 closest distance to " O   SER A  12 " =    1.692
peak=   -3.186 closest distance to " O   HOH Z 407 " =    3.429
peak=   -3.186 closest distance to " N   MET A 105 " =    2.519
peak=   -3.179 closest distance to " CB  ALA A 158 " =    1.684
peak=   -3.174 closest distance to " O   HOH Z 244 " =    1.900
peak=   -3.173 closest distance to " O   HOH Z 389 " =    4.801
peak=   -3.173 closest distance to " N   PRO A  54 " =    1.114
peak=   -3.171 closest distance to " CD2 LEU A 143 " =    2.605
peak=   -3.170 closest distance to " O   HOH Z 118 " =    4.976
peak=   -3.167 closest distance to " O   HOH Z 241 " =    1.390
peak=   -3.166 closest distance to " O   HOH Z  83 " =    1.396
peak=   -3.166 closest distance to " O   HOH Z 165 " =    2.114
peak=   -3.164 closest distance to " CD2 TYR A 116 " =    2.325
peak=   -3.163 closest distance to " O   TYR A 186 " =    2.359
peak=   -3.162 closest distance to " O   HOH Z 362 " =    4.148
peak=   -3.160 closest distance to " SD  MET A 105 " =    2.457
peak=   -3.158 closest distance to " N   ARG A 138 " =    1.559
peak=   -3.158 closest distance to " C   MET A 188 " =    1.479
peak=   -3.154 closest distance to " CD2 LEU A 237 " =    2.328
peak=   -3.154 closest distance to " CG2BVAL A  41 " =    2.230
peak=   -3.149 closest distance to " O   HOH Z 384 " =    0.821
peak=   -3.148 closest distance to " CG  ASP A 231 " =    0.762
peak=   -3.144 closest distance to " C   SER A 135 " =    1.233
peak=   -3.140 closest distance to " O   HOH Z  10 " =    1.651
peak=   -3.134 closest distance to " O   HOH Z 417 " =    3.084
peak=   -3.121 closest distance to " O   HOH Z  52 " =    1.841
peak=   -3.116 closest distance to " CD2 HIS A 207 " =    2.267
peak=   -3.113 closest distance to " C   GLU A   2 " =    1.775
peak=   -3.109 closest distance to " O   HOH Z 318 " =    1.714
peak=   -3.106 closest distance to " O   HOH Z 117 " =    0.937
peak=   -3.098 closest distance to " O   HOH Z 376 " =    2.504
peak=   -3.095 closest distance to " ND2 ASN A  60 " =    4.112
peak=   -3.095 closest distance to " CG  PRO A 213 " =    2.049
peak=   -3.092 closest distance to " O   HOH Z 135 " =    0.817
peak=   -3.080 closest distance to " CD1 TRP A 179 " =    0.980
peak=   -3.077 closest distance to " C   PHE A  59 " =    1.026
peak=   -3.068 closest distance to " O   HOH Z  38 " =    1.221
peak=   -3.064 closest distance to " O   HOH Z 352 " =    0.954
peak=   -3.064 closest distance to " CG1 VAL A 112 " =    2.467
peak=   -3.055 closest distance to " CE1 TYR A 247 " =    2.612
peak=   -3.044 closest distance to " O   GLY A  80 " =    2.523
peak=   -3.036 closest distance to " CG2 VAL A 296 " =    0.779
peak=   -3.034 closest distance to " O   HOH Z 166 " =    1.327
peak=   -3.021 closest distance to " O   HOH Z 351 " =    1.368
peak=   -3.006 closest distance to " ND2 ASN A 285 " =    1.574

================= 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    :  0.5107 0.5027   6.309486e+00   6.299154e+00
   1_bss:  0.5029 0.4906   6.305685e+00   6.294632e+00
   1_xyz:  0.4421 0.4576   6.242763e+00   6.262804e+00
   1_adp:  0.4014 0.4647   6.203005e+00   6.265659e+00
   1_occ:  0.4009 0.4642   6.202257e+00   6.265359e+00
   2_bss:  0.3991 0.4629   6.203949e+00   6.265393e+00
   2_xyz:  0.3383 0.4097   6.077964e+00   6.189247e+00
   2_adp:  0.3179 0.3890   6.042231e+00   6.159660e+00
   2_occ:  0.3176 0.3886   6.041319e+00   6.159146e+00
   3_bss:  0.3164 0.3866   6.040866e+00   6.156832e+00
   3_xyz:  0.2485 0.3121   5.835070e+00   5.995233e+00
   3_adp:  0.2281 0.2933   5.766608e+00   5.944671e+00
   3_occ:  0.2278 0.2931   5.765212e+00   5.943664e+00
   4_bss:  0.2268 0.2918   5.764684e+00   5.942869e+00
   4_xyz:  0.1703 0.2246   5.514162e+00   5.730843e+00
   4_adp:  0.1507 0.2070   5.415861e+00   5.651670e+00
   4_occ:  0.1506 0.2069   5.415173e+00   5.650888e+00
   5_bss:  0.1506 0.2065   5.413014e+00   5.648451e+00
   5_xyz:  0.1390 0.1921   5.340188e+00   5.570176e+00
   5_adp:  0.1369 0.1865   5.323071e+00   5.546213e+00
   5_occ:  0.1368 0.1861   5.322099e+00   5.545040e+00
   5_bss:  0.1367 0.1862   5.321963e+00   5.545145e+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:  0.347  20.001   8.793   8.228   7.915   0.000   0.000   0.000
   1_xyz:  0.347  20.001   8.793   8.228   7.915   0.000   0.000   0.000
   1_adp:  0.347  20.001   8.793   8.228   7.915   0.000   0.000   0.000
   1_occ:  0.347  20.001   8.793   8.228   7.915   0.000   0.000   0.000
   2_bss:  0.344  50.001   5.244   4.353   4.390   0.000   0.000   0.000
   2_xyz:  0.344  50.001   5.244   4.353   4.390   0.000   0.000   0.000
   2_adp:  0.344  50.001   5.244   4.353   4.390   0.000   0.000   0.000
   2_occ:  0.344  50.001   5.244   4.353   4.390   0.000   0.000   0.000
   3_bss:  0.332  50.001   2.624   1.830   2.718   0.000   0.000   0.000
   3_xyz:  0.332  50.001   2.624   1.830   2.718   0.000   0.000   0.000
   3_adp:  0.332  50.001   2.624   1.830   2.718   0.000   0.000   0.000
   3_occ:  0.332  50.001   2.624   1.830   2.718   0.000   0.000   0.000
   4_bss:  0.319  51.759   0.826   0.164   1.427   0.000   0.000   0.000
   4_xyz:  0.319  51.759   0.826   0.164   1.427   0.000   0.000   0.000
   4_adp:  0.319  51.759   0.826   0.164   1.427   0.000   0.000   0.000
   4_occ:  0.319  51.759   0.826   0.164   1.427   0.000   0.000   0.000
   5_bss:  0.325  60.205   0.195  -0.694   0.983  -0.000   0.000   0.000
   5_xyz:  0.325  60.205   0.195  -0.694   0.983  -0.000   0.000   0.000
   5_adp:  0.325  60.205   0.195  -0.694   0.983  -0.000   0.000   0.000
   5_occ:  0.325  60.205   0.195  -0.694   0.983  -0.000   0.000   0.000
   5_bss:  0.321  60.208  -0.088  -0.912   0.860  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.634 0.3333  0.4036    83828.381
   1_bss:  64.012 0.3409  0.5251    82803.583
   1_xyz:  57.195 0.4281  0.6421    68767.629
   1_adp:  57.979 0.4174  0.6979    70245.675
   1_occ:  57.953 0.4178  0.6976    70167.928
   2_bss:  57.761 0.4202  0.6243    69913.053
   2_xyz:  47.552 0.5491  0.8136    50321.746
   2_adp:  44.076 0.5927  0.8657    45030.870
   2_occ:  44.036 0.5931  0.8653    44859.610
   3_bss:  43.770 0.5962  0.8041    44411.979
   3_xyz:  32.812 0.7247  0.9484    26443.385
   3_adp:  29.797 0.7594  0.9795    22806.261
   3_occ:  29.753 0.7598  0.9789    22709.253
   4_bss:  29.683 0.7606  0.9269    22632.984
   4_xyz:  22.436 0.8369  0.9811    13337.421
   4_adp:  20.312 0.8582  0.9852    11271.619
   4_occ:  20.289 0.8584  0.9850    11237.483
   5_bss:  20.218 0.8590  0.9634    11148.274
   5_xyz:  18.111 0.8791  0.9712     9332.176
   5_adp:  17.397 0.8862  0.9690     8894.158
   5_occ:  17.370 0.8864  0.9689     8851.214
   5_bss:  17.368 0.8864  0.9619     8851.451
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3988e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3988e+01
   1_xyz:   1.759  0.014  0.111 18.568  0.007  4.106   1.5492e-01
   1_adp:   1.759  0.014  0.111 18.568  0.007  4.106   1.5492e-01
   1_occ:   1.759  0.014  0.111 18.568  0.007  4.106   1.5492e-01
   2_bss:   1.759  0.014  0.111 18.568  0.007  4.106   1.5492e-01
   2_xyz:   1.272  0.009  0.088 16.995  0.005  4.104   1.0598e-01
   2_adp:   1.272  0.009  0.088 16.995  0.005  4.104   1.0598e-01
   2_occ:   1.272  0.009  0.088 16.995  0.005  4.104   1.0598e-01
   3_bss:   1.272  0.009  0.088 16.995  0.005  4.104   1.0598e-01
   3_xyz:   1.209  0.009  0.086 15.960  0.005  4.128   8.8068e-02
   3_adp:   1.209  0.009  0.086 15.960  0.005  4.128   8.8068e-02
   3_occ:   1.209  0.009  0.086 15.960  0.005  4.128   8.8068e-02
   4_bss:   1.209  0.009  0.086 15.960  0.005  4.128   8.8068e-02
   4_xyz:   1.159  0.010  0.086 15.603  0.004  4.114   8.3753e-02
   4_adp:   1.159  0.010  0.086 15.603  0.004  4.114   8.3753e-02
   4_occ:   1.159  0.010  0.086 15.603  0.004  4.114   8.3753e-02
   5_bss:   1.159  0.010  0.086 15.603  0.004  4.114   8.3753e-02
   5_xyz:   0.946  0.006  0.072 15.167  0.003  4.122   5.6566e-02
   5_adp:   0.946  0.006  0.072 15.167  0.003  4.122   5.6566e-02
   5_occ:   0.946  0.006  0.072 15.167  0.003  4.122   5.6566e-02
   5_bss:   0.946  0.006  0.072 15.167  0.003  4.122   5.6566e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9979e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9979e+00
   1_xyz:  13.642  0.178  0.434 87.681  0.040  2.164   1.0627e-01
   1_adp:  13.642  0.178  0.434 87.681  0.040  2.164   1.0627e-01
   1_occ:  13.642  0.178  0.434 87.681  0.040  2.164   1.0627e-01
   2_bss:  13.642  0.178  0.434 87.681  0.040  2.164   1.0627e-01
   2_xyz:   7.109  0.085  0.293 88.678  0.049  2.045   9.8827e-02
   2_adp:   7.109  0.085  0.293 88.678  0.049  2.045   9.8827e-02
   2_occ:   7.109  0.085  0.293 88.678  0.049  2.045   9.8827e-02
   3_bss:   7.109  0.085  0.293 88.678  0.049  2.045   9.8827e-02
   3_xyz:   8.794  0.068  0.395 81.590  0.050  2.216   9.1816e-02
   3_adp:   8.794  0.068  0.395 81.590  0.050  2.216   9.1816e-02
   3_occ:   8.794  0.068  0.395 81.590  0.050  2.216   9.1816e-02
   4_bss:   8.794  0.068  0.395 81.590  0.050  2.216   9.1816e-02
   4_xyz:   8.684  0.080  0.401 85.539  0.039  2.213   7.5337e-02
   4_adp:   8.684  0.080  0.401 85.539  0.039  2.213   7.5337e-02
   4_occ:   8.684  0.080  0.401 85.539  0.039  2.213   7.5337e-02
   5_bss:   8.684  0.080  0.401 85.539  0.039  2.213   7.5337e-02
   5_xyz:   8.234  0.051  0.352 80.410  0.034  2.394   3.3710e-02
   5_adp:   8.234  0.051  0.352 80.410  0.034  2.394   3.3710e-02
   5_occ:   8.234  0.051  0.352 80.410  0.034  2.394   3.3710e-02
   5_bss:   8.234  0.051  0.352 80.410  0.034  2.394   3.3710e-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:  97.87   0.00  17.29  95.28   0.00  15.79  97.87   0.00  25.45
   1_occ:  97.87   0.00  17.29  95.28   0.00  15.79  97.87   0.00  25.45
   2_bss:  97.87   0.00  17.29  95.28   0.00  15.79  97.87   0.00  25.45
   2_xyz:  97.87   0.00  17.29  95.28   0.00  15.79  97.87   0.00  25.45
   2_adp:  80.30   0.00  15.96  73.75   0.00  13.40  80.30   0.00  29.91
   2_occ:  80.30   0.00  15.96  73.75   0.00  13.40  80.30   0.00  29.91
   3_bss:  80.30   0.00  15.96  73.75   0.00  13.40  80.30   0.00  29.91
   3_xyz:  80.30   0.00  15.96  73.75   0.00  13.40  80.30   0.00  29.91
   3_adp:  74.97   0.00  15.74  74.97   0.00  12.28  72.51   1.69  34.59
   3_occ:  74.97   0.00  15.74  74.97   0.00  12.28  72.51   1.69  34.59
   4_bss:  74.97   0.00  15.74  74.97   0.00  12.28  72.51   1.69  34.59
   4_xyz:  74.97   0.00  15.74  74.97   0.00  12.28  72.51   1.69  34.59
   4_adp:  84.06   0.00  16.37  84.06   0.00  11.62  79.17   4.22  42.20
   4_occ:  84.06   0.00  16.37  84.06   0.00  11.62  79.17   4.22  42.20
   5_bss:  84.06   0.00  16.37  84.06   0.00  11.62  79.17   4.22  42.20
   5_xyz:  84.06   0.00  16.37  84.06   0.00  11.62  79.17   4.22  42.20
   5_adp:  85.37   0.00  15.76  85.37   0.00  11.19  78.78   4.70  40.63
   5_occ:  85.37   0.00  15.76  85.37   0.00  11.19  78.78   4.70  40.63
   5_bss:  85.37   0.00  15.76  85.37   0.00  11.19  78.78   4.71  40.63
------------------------------------------------------------------------
 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:    1.280    0.016    0.412
   1_adp:    1.280    0.016    0.412
   1_occ:    1.280    0.016    0.412
   2_bss:    1.280    0.016    0.412
   2_xyz:    1.580    0.050    0.607
   2_adp:    1.580    0.050    0.607
   2_occ:    1.580    0.050    0.607
   3_bss:    1.580    0.050    0.607
   3_xyz:    1.752    0.057    0.741
   3_adp:    1.752    0.057    0.741
   3_occ:    1.752    0.057    0.741
   4_bss:    1.752    0.057    0.741
   4_xyz:    2.027    0.035    0.861
   4_adp:    2.027    0.035    0.861
   4_occ:    2.027    0.035    0.861
   5_bss:    2.027    0.035    0.861
   5_xyz:    2.162    0.048    0.875
   5_adp:    2.162    0.048    0.875
   5_occ:    2.162    0.048    0.875
   5_bss:    2.162    0.048    0.875
------------------------------------------------------------------------

CPU time actual refinement: 349.09


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1228/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_1228/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1228/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1228/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1228/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.93 
  Macro-tasks:
    bulk solvent and scale       = 41.38  
    individual site refinement   = 150.08 
    weights calculation          = 31.61  
    collect and process          = 6.25   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 229.42 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 111.93 
    alpha_beta                      = 8.27   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.64 
    fmodel                         = 6.99   
    r_factors                      = 0.21   
    phase_errors                   = 10.01  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 262.86 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.893 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    639 calls, 111.62 s
gradients_fft:          583 calls, 108.28 s

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

# Date 2008-01-16 Time 03:31:32 PST -0800 (1200483092.35 s)
Start R-work = 0.5107, R-free = 0.5027 (no bulk solvent and anisotropic scale)
Final R-work = 0.1525, R-free = 0.2022 (no bulk solvent and anisotropic scale)

Start R-work = 0.5029, R-free = 0.4906
Final R-work = 0.1367, R-free = 0.1862