# Date 2008-01-16 Time 04:49:09 PST -0800 (1200487749.20 s)
#phil __OFF__

Command line arguments: "../471.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1853
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 471

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.8686, 88.1178, 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: 3.39, per 1000 atoms: 1.20


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.98084
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927817

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0027
                             d_min =   1.9808

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.98084
Completeness in resolution range: 0.930638
Completeness with d_max=infinity: 0.927817

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0031 -  4.2385 [2210/2238]  1987   223  10.1%
  bin  2:  4.2385 -  3.3769 [2119/2142]  1903   216  10.2%
  bin  3:  3.3769 -  2.9537 [2083/2108]  1882   201   9.6%
  bin  4:  2.9537 -  2.6853 [2087/2103]  1874   213  10.2%
  bin  5:  2.6853 -  2.4938 [2037/2075]  1829   208  10.2%
  bin  6:  2.4938 -  2.3473 [2068/2101]  1864   204   9.9%
  bin  7:  2.3473 -  2.2302 [2042/2079]  1843   199   9.7%
  bin  8:  2.2302 -  2.1334 [2033/2075]  1826   207  10.2%
  bin  9:  2.1334 -  2.0515 [2018/2057]  1823   195   9.7%
  bin 10:  2.0515 -  1.9808 [ 892/2071]   799    93  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_471/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.64 -     2.29: 18
        2.29 -     2.94: 1588
        2.94 -     3.59: 4426
        3.59 -     4.25: 9062
        4.25 -     4.90: 12864
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.636 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.799 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.842 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.916 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27953 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 =====================


==================== 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/noshake/run_471/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_471/model_refine_001.geo

CPU time processing inputs: 9.30


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.8686 88.1178 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4612   r_free= 0.4558   ksol= 0.00   Bsol= 0.00   scale= 0.885    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.270058                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.7274 0.99   1436  159 0.3598 0.3654      6.5355      6.5258|
|  2:  4.7274 -  3.7719 0.99   1386  154 0.3982 0.4269      6.7995      6.8498|
|  3:  3.7719 -  3.3009 0.99   1346  149 0.4392 0.4063      6.6646      6.6013|
|  4:  3.3009 -  3.0018 0.99   1353  146 0.4496 0.4401      6.4879      6.4629|
|  5:  3.0018 -  2.7881 0.98   1324  152 0.4880 0.4499      6.3498      6.3591|
|  6:  2.7881 -  2.6246 0.99   1347  145 0.4949 0.5038      6.2659      6.1639|
|  7:  2.6246 -  2.4938 0.99   1283  156 0.4870 0.4563      6.2148      6.1352|
|  8:  2.4938 -  2.3857 0.99   1342  135 0.5111 0.4811      6.1666      6.1424|
|  9:  2.3857 -  2.2942 0.99   1328  150 0.5044 0.4866      6.1088      6.1688|
| 10:  2.2942 -  2.2153 0.98   1318  143 0.5157 0.4963      6.0807      6.0664|
| 11:  2.2153 -  2.1462 0.98   1278  153 0.5218 0.5025      6.0297      6.0262|
| 12:  2.1462 -  2.0850 1.00   1317  144 0.5095 0.5511      5.9352      5.9725|
| 13:  2.0850 -  2.0303 0.92   1243  131 0.5335 0.5720      5.8748      5.8422|
| 14:  2.0303 -  1.9808 0.25    329   42 0.4702 0.4201      5.8817      5.7273|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.7274  1436   159  0.71  32.96   0.83     0.74      65698.03|
|  2:  4.7274 -  3.7719  1386   154  0.72  33.92   0.91     0.80      98307.90|
|  3:  3.7719 -  3.3009  1346   149  0.63  41.62   0.88     0.79     102483.84|
|  4:  3.3009 -  3.0018  1353   146  0.55  48.17   0.90     0.72      89128.36|
|  5:  3.0018 -  2.7881  1324   152  0.49  53.06   0.87     0.65      69599.92|
|  6:  2.7881 -  2.6246  1347   145  0.45  56.05   0.89     0.61      61844.29|
|  7:  2.6246 -  2.4938  1283   156  0.45  55.97   0.92     0.60      56195.00|
|  8:  2.4938 -  2.3857  1342   135  0.43  57.38   0.89     0.60      51315.56|
|  9:  2.3857 -  2.2942  1328   150  0.43  57.43   0.90     0.62      48002.71|
| 10:  2.2942 -  2.2153  1318   143  0.42  58.31   0.91     0.61      43703.59|
| 11:  2.2153 -  2.1462  1278   153  0.36  63.02   0.92     0.55      45238.27|
| 12:  2.1462 -  2.0850  1317   144  0.29  68.00   0.90     0.46      44533.81|
| 13:  2.0850 -  2.0303  1243   131  0.24  72.16   0.89     0.38      40976.01|
| 14:  2.0303 -  1.9808   329    42  0.30  67.97   1.00     0.37      30933.59|
|alpha:            min =        0.37 max =            0.80 mean =         0.62|
|beta:             min =    30933.59 max =       102483.84 mean =     62647.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.62|
|phase err.(test): min =        0.00 max =           89.93 mean =        53.89|
|-----------------------------------------------------------------------------|

============================== 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 = 16.488099             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.347   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.975084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.073   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.636 -  1.962:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.962 -  2.288:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.288 -  2.615:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.615 -  2.941:     1549 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.941 -  3.268:     1875 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.268 -  3.594:     2551 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.594 -  3.921:     4693 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.921 -  4.247:     4369 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.574:     5817 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.574 -  4.900:     7047 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.636 |       0.304 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4612   r_free= 0.4558   ksol= 0.00   Bsol= 0.00   scale= 0.885    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.270058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4520   r_free= 0.4444   ksol= 0.29   Bsol= 34.41   scale= 0.931   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,3.41,2.81,0.00,0.00,0.00); trace/3= 1.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.262761                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.016998             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.859   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.050844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.731   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4520      final r-factor (work) = 0.3023          |
| start r-factor (free) = 0.4444      final r-factor (free) = 0.3307          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.0470 = 14.02 * 0.50 * 6.2602 + 1.00 * 0.1727                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.8223 = 14.02 * 0.50 * 6.0885 + 1.00 * 0.1512                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3023      final r-factor (work) = 0.2735          |
| start r-factor (free) = 0.3307      final r-factor (free) = 0.3434          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4042 = 1.05 * 1.00 * 6.0885 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2262 = 1.05 * 1.00 * 5.9084 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.47   18.38    None  None   None       |
|    all(noH): 2823   0      0.00    96.47   18.38    None  None   None       |
|    Sol.    : 438    0      1.40    96.47   41.05    None  None   None       |
|    Mac.    : 2385   0      0.00    86.31   14.22    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 -   9.647:  967   |   5:    48.237 -  57.884:   83        |
|      1:     9.647 -  19.295:  946   |   6:    57.884 -  67.531:   65        |
|      2:    19.295 -  28.942:  386   |   7:    67.531 -  77.179:   28        |
|      3:    28.942 -  38.589:  208   |   8:    77.179 -  86.826:    5        |
|      4:    38.589 -  48.237:  127   |   9:    86.826 -  96.473:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2735 r_free = 0.3434             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2733 r_free = 0.3434             target_work(ml) = 5.921         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2733   r_free= 0.3434   ksol= 0.29   Bsol= 34.41   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,3.41,2.81,0.00,0.00,0.00); trace/3= 1.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.921366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2702   r_free= 0.3397   ksol= 0.32   Bsol= 70.20   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,0.98,0.86,0.00,0.00,0.00); trace/3= -0.16                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.916462                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.305748              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.134   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332912              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.270  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2702      final r-factor (work) = 0.2016          |
| start r-factor (free) = 0.3397      final r-factor (free) = 0.2547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7799 = 6.31 * 0.50 * 5.9085 + 1.00 * 0.1512                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4150 = 6.31 * 0.50 * 5.8166 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2016      final r-factor (work) = 0.1863          |
| start r-factor (free) = 0.2547      final r-factor (free) = 0.2346          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9537 = 0.33 * 1.00 * 5.8166 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8805 = 0.33 * 1.00 * 5.6170 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.72   17.62    None  None   None       |
|    all(noH): 2823   0      0.00    93.72   17.62    None  None   None       |
|    Sol.    : 438    0      3.92    93.72   41.11    None  None   None       |
|    Mac.    : 2385   0      0.00    87.02   13.30    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 -   9.373:  932   |   5:    46.862 -  56.235:   97        |
|      1:     9.373 -  18.745: 1115   |   6:    56.235 -  65.607:   65        |
|      2:    18.745 -  28.117:  298   |   7:    65.607 -  74.980:   23        |
|      3:    28.117 -  37.490:  148   |   8:    74.980 -  84.352:    7        |
|      4:    37.490 -  46.862:  131   |   9:    84.352 -  93.725:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1863 r_free = 0.2346             target_work(ml) = 5.583         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1861 r_free = 0.2347             target_work(ml) = 5.582         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1861   r_free= 0.2347   ksol= 0.32   Bsol= 70.20   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,0.98,0.86,0.00,0.00,0.00); trace/3= -0.16                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.582137                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1858   r_free= 0.2339   ksol= 0.33   Bsol= 67.98   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-0.41,0.10,-0.00,0.00,0.00); trace/3= -0.95                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.580208                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.241391              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.481  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.098364              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.396  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.1954          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3723 = 2.24 * 0.50 * 5.6183 + 1.00 * 0.0759                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2199 = 2.24 * 0.50 * 5.5004 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.1954      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0520 = 1.10 * 1.00 * 5.5004 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9252 = 1.10 * 1.00 * 5.3824 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.09   18.06    None  None   None       |
|    all(noH): 2823   0      0.00    96.09   18.06    None  None   None       |
|    Sol.    : 438    0      4.76    96.09   45.17    None  None   None       |
|    Mac.    : 2385   0      0.00    91.25   13.08    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 -   9.609: 1004   |   5:    48.047 -  57.656:   98        |
|      1:     9.609 -  19.219: 1102   |   6:    57.656 -  67.266:   73        |
|      2:    19.219 -  28.828:  253   |   7:    67.266 -  76.875:   51        |
|      3:    28.828 -  38.438:  117   |   8:    76.875 -  86.484:   18        |
|      4:    38.438 -  48.047:   97   |   9:    86.484 -  96.094:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1455 r_free = 0.1939             target_work(ml) = 5.376         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1455 r_free = 0.1941             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1455   r_free= 0.1941   ksol= 0.33   Bsol= 67.98   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-0.41,0.10,-0.00,0.00,0.00); trace/3= -0.95                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.375488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1944   ksol= 0.34   Bsol= 80.81   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-0.93,-0.16,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.376854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.726167              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.027  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.036578              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1944      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3943 = 2.73 * 0.50 * 5.3839 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3181 = 2.73 * 0.50 * 5.3195 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1778      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5273 = 1.04 * 1.00 * 5.3195 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5159 = 1.04 * 1.00 * 5.2579 + 1.00 * 0.0656                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.52  17.72    None  None   None       |
|    all(noH): 2823   0      0.00    101.52  17.72    None  None   None       |
|    Sol.    : 438    0      0.00    101.52  44.99    None  None   None       |
|    Mac.    : 2385   0      0.00    99.84   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.152: 1187   |   5:    50.761 -  60.913:   85        |
|      1:    10.152 -  20.304:  996   |   6:    60.913 -  71.065:   67        |
|      2:    20.304 -  30.456:  207   |   7:    71.065 -  81.217:   48        |
|      3:    30.456 -  40.609:  121   |   8:    81.217 -  91.369:    6        |
|      4:    40.609 -  50.761:   94   |   9:    91.369 - 101.521:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1249 r_free = 0.1746             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1248 r_free = 0.1747             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1747   ksol= 0.34   Bsol= 80.81   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-0.93,-0.16,-0.00,-0.00,-0.00); trace/3= -1.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247105                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1744   ksol= 0.34   Bsol= 80.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.82,0.18,-0.00,0.00,0.00); trace/3= -0.94                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247424                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.030187              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.552790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.895   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1744      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4059 = 2.03 * 0.50 * 5.2591 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3775 = 2.03 * 0.50 * 5.2411 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1548 = 1.55 * 1.00 * 5.2411 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1300 = 1.55 * 1.00 * 5.2273 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.13  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    104.13  17.45    None  None   None       |
|    Sol.    : 438    0      0.00    104.13  44.53    None  None   None       |
|    Mac.    : 2385   0      0.00    101.90  12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.414: 1275   |   5:    52.067 -  62.481:   76        |
|      1:    10.414 -  20.827:  946   |   6:    62.481 -  72.894:   60        |
|      2:    20.827 -  31.240:  194   |   7:    72.894 -  83.307:   38        |
|      3:    31.240 -  41.654:  111   |   8:    83.307 -  93.721:    7        |
|      4:    41.654 -  52.067:  106   |   9:    93.721 - 104.134:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1697             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1214 r_free = 0.1698             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1698   ksol= 0.34   Bsol= 80.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-0.82,0.18,-0.00,0.00,0.00); trace/3= -0.94                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225573                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.7274 0.99   1436  159 0.0986 0.1310         5.4      5.5806|
|  2:  4.7274 -  3.7719 0.99   1386  154 0.0847 0.1036      5.4307      5.6247|
|  3:  3.7719 -  3.3009 0.99   1346  149 0.1124 0.1580      5.5108       5.871|
|  4:  3.3009 -  3.0018 0.99   1353  146 0.1352 0.1764      5.5219      5.6792|
|  5:  3.0018 -  2.7881 0.98   1324  152 0.1470 0.1833      5.4209      5.5916|
|  6:  2.7881 -  2.6246 0.99   1347  145 0.1423 0.2251      5.3253      5.5882|
|  7:  2.6246 -  2.4938 0.99   1283  156 0.1390 0.1821      5.2567       5.452|
|  8:  2.4938 -  2.3857 0.99   1342  135 0.1311 0.1869      5.1901      5.3695|
|  9:  2.3857 -  2.2942 0.99   1328  150 0.1310 0.2083      5.1178      5.4319|
| 10:  2.2942 -  2.2153 0.98   1318  143 0.1255 0.1772      5.0432      5.2061|
| 11:  2.2153 -  2.1462 0.98   1278  153 0.1273 0.2039      4.9916      5.3649|
| 12:  2.1462 -  2.0850 1.00   1317  144 0.1231 0.1646      4.9224      5.1351|
| 13:  2.0850 -  2.0303 0.92   1243  131 0.1206 0.1928      4.8408      5.0979|
| 14:  2.0303 -  1.9808 0.25    329   42 0.1080 0.1864      4.7855      5.0288|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.7274  1436   159  0.94   9.48   0.96     0.93       7636.35|
|  2:  4.7274 -  3.7719  1386   154  0.95   8.17   1.00     0.99       9171.96|
|  3:  3.7719 -  3.3009  1346   149  0.93  11.74   1.02     1.02      10855.32|
|  4:  3.3009 -  3.0018  1353   146  0.90  15.51   1.01     0.99      11879.28|
|  5:  3.0018 -  2.7881  1324   152  0.89  17.88   1.00     0.98      10220.05|
|  6:  2.7881 -  2.6246  1347   145  0.88  18.70   0.98     0.96       9001.65|
|  7:  2.6246 -  2.4938  1283   156  0.89  17.53   0.99     0.96       7528.14|
|  8:  2.4938 -  2.3857  1342   135  0.89  17.78   0.99     0.95       6962.11|
|  9:  2.3857 -  2.2942  1328   150  0.89  17.79   0.98     0.93       5854.38|
| 10:  2.2942 -  2.2153  1318   143  0.89  17.58   0.99     0.94       5350.07|
| 11:  2.2153 -  2.1462  1278   153  0.89  17.26   0.98     0.93       4717.90|
| 12:  2.1462 -  2.0850  1317   144  0.90  17.02   0.99     0.99       4333.19|
| 13:  2.0850 -  2.0303  1243   131  0.89  17.85   0.97     0.95       3815.54|
| 14:  2.0303 -  1.9808   329    42  0.90  15.93   0.96     0.90       3302.51|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     3302.51 max =        11879.28 mean =      7453.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.63|
|phase err.(test): min =        0.00 max =           90.00 mean =        15.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1700   ksol= 0.33   Bsol= 73.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.75,0.33,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.226220                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1700   ksol= 0.33   Bsol= 73.80   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-0.75,0.33,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.226220                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.7274 0.99   1436  159 0.0988 0.1327      5.3996      5.5781|
|  2:  4.7274 -  3.7719 0.99   1386  154 0.0851 0.1036      5.4341      5.6237|
|  3:  3.7719 -  3.3009 0.99   1346  149 0.1127 0.1579      5.5116      5.8713|
|  4:  3.3009 -  3.0018 0.99   1353  146 0.1356 0.1772      5.5242      5.6823|
|  5:  3.0018 -  2.7881 0.98   1324  152 0.1472 0.1834      5.4222      5.5914|
|  6:  2.7881 -  2.6246 0.99   1347  145 0.1422 0.2252      5.3253       5.589|
|  7:  2.6246 -  2.4938 0.99   1283  156 0.1390 0.1824      5.2575      5.4527|
|  8:  2.4938 -  2.3857 0.99   1342  135 0.1310 0.1867      5.1904      5.3698|
|  9:  2.3857 -  2.2942 0.99   1328  150 0.1309 0.2083      5.1177      5.4325|
| 10:  2.2942 -  2.2153 0.98   1318  143 0.1255 0.1773      5.0433      5.2061|
| 11:  2.2153 -  2.1462 0.98   1278  153 0.1273 0.2039      4.9915      5.3647|
| 12:  2.1462 -  2.0850 1.00   1317  144 0.1232 0.1647      4.9223      5.1351|
| 13:  2.0850 -  2.0303 0.92   1243  131 0.1206 0.1925      4.8407      5.0965|
| 14:  2.0303 -  1.9808 0.25    329   42 0.1079 0.1866      4.7861        5.03|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.7274  1436   159  0.94   9.52   0.96     0.93       7572.15|
|  2:  4.7274 -  3.7719  1386   154  0.95   8.16   1.01     0.99       9140.94|
|  3:  3.7719 -  3.3009  1346   149  0.93  11.71   1.03     1.02      10863.15|
|  4:  3.3009 -  3.0018  1353   146  0.90  15.55   1.01     0.99      11926.20|
|  5:  3.0018 -  2.7881  1324   152  0.88  17.91   1.00     0.98      10240.85|
|  6:  2.7881 -  2.6246  1347   145  0.88  18.70   0.99     0.96       9007.76|
|  7:  2.6246 -  2.4938  1283   156  0.89  17.55   1.00     0.96       7545.32|
|  8:  2.4938 -  2.3857  1342   135  0.89  17.79   1.00     0.95       6969.54|
|  9:  2.3857 -  2.2942  1328   150  0.89  17.80   0.99     0.94       5861.00|
| 10:  2.2942 -  2.2153  1318   143  0.89  17.58   0.99     0.95       5350.69|
| 11:  2.2153 -  2.1462  1278   153  0.89  17.26   0.98     0.93       4716.40|
| 12:  2.1462 -  2.0850  1317   144  0.90  17.02   1.00     0.99       4333.35|
| 13:  2.0850 -  2.0303  1243   131  0.89  17.85   0.98     0.96       3812.68|
| 14:  2.0303 -  1.9808   329    42  0.90  15.93   0.97     0.91       3299.57|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3299.57 max =        11926.20 mean =      7454.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.64|
|phase err.(test): min =        0.00 max =           89.90 mean =        15.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.143)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.14  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    104.14  17.45    None  None   None       |
|    Sol.    : 438    0      0.00    104.14  44.53    None  None   None       |
|    Mac.    : 2385   0      0.00    101.91  12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.416: 1275   |   5:    52.070 -  62.484:   76        |
|      1:    10.416 -  20.830:  946   |   6:    62.484 -  72.897:   60        |
|      2:    20.830 -  31.243:  194   |   7:    72.897 -  83.310:   38        |
|      3:    31.243 -  41.657:  111   |   8:    83.310 -  93.724:    7        |
|      4:    41.657 -  52.070:  106   |   9:    93.724 - 104.137:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.488 - 5.354
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 330 from: 333
   mapped sites are within: 0.742 - 5.354

peak=    6.013 closest distance to " O   HOH Z 210 " =    1.294
peak=    5.161 closest distance to " CG  PRO A 280 " =    0.890
peak=    5.046 closest distance to " O   HOH Z 117 " =    1.181
peak=    5.036 closest distance to " O   HOH Z  49 " =    1.470
peak=    4.962 closest distance to " O   HOH Z  65 " =    0.982
peak=    4.957 closest distance to " CG  PRO A  54 " =    1.404
peak=    4.901 closest distance to " O   HOH Z 113 " =    1.924
peak=    4.899 closest distance to " CG  PRO A  90 " =    1.209
peak=    4.837 closest distance to " O   HOH Z 403 " =    1.920
peak=    4.759 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.717 closest distance to " CB  ARG A 190 " =    1.738
peak=    4.699 closest distance to " CA  TYR A  30 " =    0.922
peak=    4.686 closest distance to " CB  ARG A 275 " =    0.873
peak=    4.661 closest distance to " O   HOH Z 248 " =    1.348
peak=    4.651 closest distance to " O   HOH Z  43 " =    2.250
peak=    4.589 closest distance to " CG  PRO A 198 " =    1.179
peak=    4.573 closest distance to " CD2 TRP A 179 " =    1.317
peak=    4.550 closest distance to " CA  ARG A  36 " =    1.075
peak=    4.477 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.426 closest distance to " CB  SER A  63 " =    1.116
peak=    4.401 closest distance to " O   HOH Z 369 " =    2.234
peak=    4.383 closest distance to " O   PRO A 198 " =    1.540
peak=    4.339 closest distance to " CB  PRO A  54 " =    0.961
peak=    4.338 closest distance to " CZ  PHE A 218 " =    1.098
peak=    4.299 closest distance to " O   HOH Z 232 " =    2.363
peak=    4.288 closest distance to " CZ3 TRP A 266 " =    1.101
peak=    4.207 closest distance to " CZ  PHE A  38 " =    1.223
peak=    4.189 closest distance to " O   HOH Z 188 " =    2.870
peak=    4.177 closest distance to " O   HOH Z 402 " =    1.532
peak=    4.155 closest distance to " O   HOH Z  40 " =    1.894
peak=    4.126 closest distance to " O   HOH Z 346 " =    1.645
peak=    4.115 closest distance to " O   HOH Z 214 " =    1.276
peak=    4.109 closest distance to " O   HOH Z 433 " =    1.551
peak=    4.104 closest distance to " CB  GLU A 152 " =    1.111
peak=    4.080 closest distance to " O   HOH Z 261 " =    2.376
peak=    4.066 closest distance to " O   HOH Z  54 " =    1.049
peak=    4.050 closest distance to " O   HOH Z 298 " =    1.871
peak=    4.049 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.030 closest distance to " O   HOH Z  59 " =    2.403
peak=    4.030 closest distance to " CA  ARG A 195 " =    1.180
peak=    4.023 closest distance to " O   SER A  87 " =    2.285
peak=    4.017 closest distance to " O   HOH Z 234 " =    3.771
peak=    4.016 closest distance to " CB  GLU A 277 " =    3.770
peak=    4.011 closest distance to " O   HOH Z 203 " =    1.644
peak=    4.005 closest distance to " NZ  LYS A 117 " =    3.016
peak=    4.001 closest distance to " CG  GLN A  58 " =    0.916
peak=    3.999 closest distance to " CG  PRO A 243 " =    1.123
peak=    3.991 closest distance to " CB  ASN A 148 " =    1.431
peak=    3.991 closest distance to " O   HOH Z 134 " =    1.580
peak=    3.971 closest distance to " CB  TRP A 179 " =    1.363
peak=    3.966 closest distance to " O   HOH Z 412 " =    3.696
peak=    3.963 closest distance to " O   HOH Z 176 " =    1.568
peak=    3.962 closest distance to " O   HOH Z  63 " =    1.919
peak=    3.937 closest distance to " CG  ARG A  66 " =    2.623
peak=    3.926 closest distance to " O   HOH Z 316 " =    3.029
peak=    3.926 closest distance to " CB  GLU A 128 " =    1.157
peak=    3.924 closest distance to " CD  ARG A 269 " =    0.994
peak=    3.918 closest distance to " O   HOH Z 251 " =    1.604
peak=    3.910 closest distance to " CB  THR A  52 " =    0.801
peak=    3.890 closest distance to " O   HOH Z 362 " =    3.469
peak=    3.887 closest distance to " CG2BVAL A  41 " =    0.869
peak=    3.880 closest distance to " CB  SER A 141 " =    1.170
peak=    3.875 closest distance to " CB  ARG A  79 " =    1.371
peak=    3.875 closest distance to " ND2 ASN A 249 " =    0.927
peak=    3.872 closest distance to " O   HOH Z  76 " =    0.978
peak=    3.871 closest distance to " O   HOH Z 132 " =    2.577
peak=    3.870 closest distance to " O   HOH Z 423 " =    1.811
peak=    3.867 closest distance to " CB  VAL A 202 " =    1.533
peak=    3.862 closest distance to " O   HOH Z 368 " =    2.076
peak=    3.861 closest distance to " CA  ALA A 160 " =    0.915
peak=    3.857 closest distance to " NE2 GLN A  77 " =    3.225
peak=    3.851 closest distance to " CG  GLN A  11 " =    1.330
peak=    3.851 closest distance to " CA  ALA A  51 " =    0.998
peak=    3.839 closest distance to " O   HOH Z 394 " =    1.447
peak=    3.834 closest distance to " O   HOH Z 209 " =    2.295
peak=    3.831 closest distance to " O   HOH Z 406 " =    1.600
peak=    3.807 closest distance to " CB  GLU A  46 " =    1.058
peak=    3.793 closest distance to " NE2 GLN A  11 " =    1.087
peak=    3.773 closest distance to " O   HOH Z 102 " =    1.328
peak=    3.772 closest distance to " CD  LYS A 166 " =    1.409
peak=    3.765 closest distance to " CA  VAL A 125 " =    1.338
peak=    3.749 closest distance to " O  BHOH Z  74 " =    1.360
peak=    3.730 closest distance to " O   HOH Z 258 " =    2.087
peak=    3.727 closest distance to " O   HOH Z  78 " =    1.714
peak=    3.712 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.711 closest distance to " O   HOH Z 193 " =    1.808
peak=    3.707 closest distance to " ND2 ASN A 249 " =    2.020
peak=    3.706 closest distance to " CB  ARG A  79 " =    0.949
peak=    3.699 closest distance to " O   HOH Z  15 " =    2.385
peak=    3.698 closest distance to " NH1AARG A 145 " =    1.365
peak=    3.696 closest distance to " O   HOH Z 357 " =    2.147
peak=    3.690 closest distance to " O   HOH Z 365 " =    2.648
peak=    3.690 closest distance to " CB  TYR A 169 " =    0.795
peak=    3.687 closest distance to " O   HOH Z 265 " =    2.059
peak=    3.685 closest distance to " CA  ASN A 176 " =    1.279
peak=    3.680 closest distance to " O   TYR A 116 " =    1.389
peak=    3.678 closest distance to " O   ALA A 165 " =    1.378
peak=    3.677 closest distance to " O   HOH Z 287 " =    1.697
peak=    3.675 closest distance to " CB  SER A  62 " =    0.874
peak=    3.670 closest distance to " CB  VAL A 265 " =    1.159
peak=    3.670 closest distance to " NH2 ARG A 156 " =    1.153
peak=    3.663 closest distance to " ND2 ASN A 187 " =    1.498
peak=    3.661 closest distance to " OH  TYR A 116 " =    1.138
peak=    3.655 closest distance to " CB  ASN A 285 " =    0.950
peak=    3.654 closest distance to " N   ASN A  39 " =    1.275
peak=    3.642 closest distance to " CB  ASN A  39 " =    0.894
peak=    3.636 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.633 closest distance to " O   HOH Z 417 " =    2.953
peak=    3.631 closest distance to " O   HOH Z 418 " =    1.154
peak=    3.623 closest distance to " CA  ALA A 100 " =    1.067
peak=    3.620 closest distance to " O   HOH Z 285 " =    2.555
peak=    3.619 closest distance to " O   HOH Z 425 " =    1.425
peak=    3.619 closest distance to " O   HOH Z  80 " =    1.947
peak=    3.614 closest distance to " OG BSER A 164 " =    2.239
peak=    3.593 closest distance to " O   HOH Z 427 " =    3.009
peak=    3.592 closest distance to " O   HOH Z  44 " =    1.972
peak=    3.582 closest distance to " O   HOH Z 128 " =    1.476
peak=    3.581 closest distance to " O   HOH Z 196 " =    1.295
peak=    3.580 closest distance to " O   HOH Z  48 " =    1.843
peak=    3.579 closest distance to " O   HOH Z 132 " =    2.722
peak=    3.577 closest distance to " O   HOH Z 126 " =    2.068
peak=    3.576 closest distance to " O   HOH Z 126 " =    1.594
peak=    3.570 closest distance to " O   HOH Z 345 " =    1.674
peak=    3.561 closest distance to " CG  GLU A  37 " =    0.974
peak=    3.558 closest distance to " O   THR A 220 " =    1.104
peak=    3.554 closest distance to " CG1 ILE A  20 " =    1.235
peak=    3.552 closest distance to " NH2BARG A 145 " =    2.238
peak=    3.551 closest distance to " N   CYS A 260 " =    0.894
peak=    3.549 closest distance to " O   HOH Z 280 " =    3.021
peak=    3.549 closest distance to " CB  PRO A 243 " =    1.380
peak=    3.548 closest distance to " CD2 LEU A 297 " =    0.878
peak=    3.542 closest distance to " O   ASN A  74 " =    1.702
peak=    3.534 closest distance to " O   HOH Z  19 " =    1.546
peak=    3.531 closest distance to " O   HOH Z 325 " =    2.061
peak=    3.520 closest distance to " O   THR A 251 " =    1.207
peak=    3.520 closest distance to " CG2 VAL A 197 " =    1.154
peak=    3.515 closest distance to " O   HOH Z 142 " =    1.510
peak=    3.514 closest distance to " O   HOH Z 213 " =    2.380
peak=    3.513 closest distance to " CB  ASN A 142 " =    1.141
peak=    3.511 closest distance to " O   HOH Z 336 " =    1.953
peak=    3.505 closest distance to " CA  ALA A 295 " =    1.074
peak=    3.499 closest distance to " CB  TRP A 266 " =    1.106
peak=    3.498 closest distance to " CA  ASP A 162 " =    1.130
peak=    3.492 closest distance to " O   HOH Z  21 " =    1.847
peak=    3.492 closest distance to " CG2AVAL A 121 " =    2.182
peak=    3.492 closest distance to " CD1 LEU A  96 " =    0.806
peak=    3.489 closest distance to " O   HOH Z 246 " =    1.444
peak=    3.485 closest distance to " CA  GLU A 152 " =    0.883
peak=    3.480 closest distance to " CB  SER A   3 " =    1.339
peak=    3.480 closest distance to " CB  ASP A 124 " =    0.762
peak=    3.479 closest distance to " O   HOH Z  20 " =    1.370
peak=    3.475 closest distance to " CB  ALA A 291 " =    1.120
peak=    3.474 closest distance to " O   HOH Z 353 " =    2.792
peak=    3.473 closest distance to " CB  LEU A  83 " =    0.798
peak=    3.472 closest distance to " CG2 ILE A 120 " =    1.227
peak=    3.471 closest distance to " CA  TYR A 116 " =    1.317
peak=    3.464 closest distance to " O   HOH Z 214 " =    2.656
peak=    3.459 closest distance to " O   HOH Z 180 " =    2.226
peak=    3.456 closest distance to " O   HOH Z 299 " =    4.389
peak=    3.453 closest distance to " O   HOH Z  35 " =    2.346
peak=    3.450 closest distance to " CB  ALA A 248 " =    1.401
peak=    3.450 closest distance to " CB  PRO A 198 " =    1.128
peak=    3.449 closest distance to " CD  PRO A  54 " =    0.934
peak=    3.448 closest distance to " O   HOH Z 154 " =    3.107
peak=    3.445 closest distance to " O   HOH Z 366 " =    2.411
peak=    3.441 closest distance to " O   HOH Z 426 " =    1.315
peak=    3.440 closest distance to " N   TYR A 116 " =    1.625
peak=    3.434 closest distance to " O   HOH Z 393 " =    3.232
peak=    3.432 closest distance to " CA  SER A  87 " =    1.060
peak=    3.427 closest distance to " CB  GLN A  89 " =    1.344
peak=    3.424 closest distance to " O   HOH Z 391 " =    3.039
peak=    3.423 closest distance to " OG BSER A 134 " =    2.782
peak=    3.422 closest distance to " O   HOH Z 313 " =    1.808
peak=    3.422 closest distance to " CB  SER A 273 " =    0.887
peak=    3.413 closest distance to " O   HOH Z 291 " =    1.412
peak=    3.411 closest distance to " CB  LEU A 228 " =    1.116
peak=    3.409 closest distance to " O   THR A 182 " =    1.420
peak=    3.408 closest distance to " O   HOH Z 162 " =    1.787
peak=    3.404 closest distance to " CB  ALA A 114 " =    0.794
peak=    3.403 closest distance to " CG2AVAL A  72 " =    1.942
peak=    3.403 closest distance to " CB  SER A  26 " =    1.795
peak=    3.403 closest distance to " O   HOH Z 193 " =    1.273
peak=    3.403 closest distance to " O   HOH Z 394 " =    3.903
peak=    3.402 closest distance to " CA  ARG A 156 " =    1.030
peak=    3.402 closest distance to " O   HOH Z 285 " =    1.819
peak=    3.402 closest distance to " CG  LEU A 167 " =    1.128
peak=    3.398 closest distance to " CA  MET A 188 " =    0.987
peak=    3.394 closest distance to " CG2 ILE A  20 " =    1.396
peak=    3.394 closest distance to " O   HOH Z 422 " =    2.655
peak=    3.391 closest distance to " O   ASP A 124 " =    1.565
peak=    3.390 closest distance to " CB  MET A  40 " =    0.996
peak=    3.387 closest distance to " O   HOH Z 227 " =    1.654
peak=    3.386 closest distance to " O   HOH Z  78 " =    1.906
peak=    3.386 closest distance to " OG  SER A 135 " =    1.295
peak=    3.384 closest distance to " CD1 ILE A 199 " =    1.247
peak=    3.383 closest distance to " CG2 THR A  29 " =    1.389
peak=    3.378 closest distance to " O   HOH Z 359 " =    1.691
peak=    3.378 closest distance to " CB  PRO A  90 " =    1.115
peak=    3.371 closest distance to " CG2 THR A 221 " =    1.210
peak=    3.370 closest distance to " CD  ARG A 159 " =    0.822
peak=    3.359 closest distance to " O   HOH Z 361 " =    2.514
peak=    3.351 closest distance to " CA  ASN A 127 " =    1.190
peak=    3.348 closest distance to " CB  ASP A 140 " =    1.083
peak=    3.347 closest distance to " N   HIS A 108 " =    1.759
peak=    3.344 closest distance to " O   HOH Z 380 " =    1.751
peak=    3.341 closest distance to " CB  PHE A  16 " =    1.106
peak=    3.339 closest distance to " CG  MET A 185 " =    1.132
peak=    3.337 closest distance to " CG1 VAL A 153 " =    1.096
peak=    3.336 closest distance to " CG  ARG A 138 " =    1.323
peak=    3.336 closest distance to " O   HOH Z 371 " =    2.843
peak=    3.333 closest distance to " N   THR A  52 " =    1.096
peak=    3.327 closest distance to " CB  GLU A  37 " =    0.824
peak=    3.325 closest distance to " CA  ILE A 106 " =    0.819
peak=    3.324 closest distance to " O   HOH Z 250 " =    1.360
peak=    3.323 closest distance to " O   HOH Z 290 " =    1.072
peak=    3.322 closest distance to " CA  MET A 105 " =    1.151
peak=    3.321 closest distance to " O   HOH Z 403 " =    1.532
peak=    3.321 closest distance to " O   HOH Z 383 " =    2.292
peak=    3.318 closest distance to " O   HOH Z 189 " =    2.586
peak=    3.318 closest distance to " O   HOH Z  30 " =    1.025
peak=    3.313 closest distance to " N   ILE A  33 " =    0.916
peak=    3.309 closest distance to " CB  ASN A 187 " =    1.413
peak=    3.306 closest distance to " O   HOH Z 298 " =    2.316
peak=    3.306 closest distance to " NZ  LYS A  48 " =    1.205
peak=    3.302 closest distance to " CG AARG A 275 " =    1.303
peak=    3.302 closest distance to " O   HOH Z 216 " =    5.096
peak=    3.301 closest distance to " CD  ARG A 195 " =    0.960
peak=    3.296 closest distance to " CD  GLN A 194 " =    1.629
peak=    3.294 closest distance to " O  BHOH Z 338 " =    0.960
peak=    3.294 closest distance to " OG  SER A 245 " =    1.623
peak=    3.293 closest distance to " CA  GLY A 133 " =    3.717
peak=    3.290 closest distance to " O   HOH Z 139 " =    4.795
peak=    3.287 closest distance to " CE1 TYR A 186 " =    1.278
peak=    3.287 closest distance to " CA  ARG A 195 " =    1.518
peak=    3.286 closest distance to " OD1 ASN A  69 " =    2.439
peak=    3.284 closest distance to " CA  SER A  32 " =    1.665
peak=    3.283 closest distance to " O   HOH Z 299 " =    4.188
peak=    3.278 closest distance to " CA  THR A 246 " =    0.987
peak=    3.271 closest distance to " CB  PHE A 204 " =    0.886
peak=    3.270 closest distance to " O   HOH Z  88 " =    3.365
peak=    3.269 closest distance to " CB  ASP A 191 " =    1.188
peak=    3.267 closest distance to " O   HOH Z 293 " =    2.121
peak=    3.265 closest distance to " NE2 GLN A  58 " =    3.507
peak=    3.263 closest distance to " O   HOH Z 240 " =    2.473
peak=    3.261 closest distance to " O   HOH Z 271 " =    2.512
peak=    3.260 closest distance to " O   ASP A 191 " =    1.540
peak=    3.256 closest distance to " O   HOH Z 163 " =    1.417
peak=    3.255 closest distance to " O   GLY A  91 " =    1.225
peak=    3.254 closest distance to " O   HOH Z  85 " =    1.330
peak=    3.253 closest distance to " O   HOH Z 313 " =    1.610
peak=    3.248 closest distance to " CA  GLY A 196 " =    1.074
peak=    3.248 closest distance to " CD  LYS A 193 " =    1.923
peak=    3.241 closest distance to " CE  LYS A 119 " =    1.089
peak=    3.241 closest distance to " CE1 PHE A 218 " =    0.742
peak=    3.239 closest distance to " N   SER A 164 " =    1.045
peak=    3.234 closest distance to " O   HOH Z 420 " =    1.748
peak=    3.234 closest distance to " CA  ALA A 154 " =    1.054
peak=    3.233 closest distance to " CG2 THR A 220 " =    0.810
peak=    3.231 closest distance to " N   GLU A  44 " =    1.268
peak=    3.229 closest distance to " CA  LEU A  83 " =    1.310
peak=    3.229 closest distance to " O   ALA A 242 " =    1.336
peak=    3.225 closest distance to " O   HOH Z 272 " =    1.849
peak=    3.222 closest distance to " CB  SER A 210 " =    0.867
peak=    3.219 closest distance to " CD  LYS A 119 " =    1.868
peak=    3.217 closest distance to " OE1 GLN A  11 " =    2.064
peak=    3.215 closest distance to " CA  GLU A  46 " =    0.856
peak=    3.215 closest distance to " CB  MET A 105 " =    1.035
peak=    3.211 closest distance to " O   HOH Z  47 " =    2.487
peak=    3.207 closest distance to " O   HOH Z  63 " =    2.077
peak=    3.206 closest distance to " CB  ASN A 110 " =    1.133
peak=    3.203 closest distance to " O   HOH Z 298 " =    4.203
peak=    3.202 closest distance to " O   HOH Z 327 " =    1.767
peak=    3.200 closest distance to " O   HOH Z 199 " =    1.647
peak=    3.199 closest distance to " CB  ALA A   9 " =    1.667
peak=    3.197 closest distance to " O   HOH Z 146 " =    2.166
peak=    3.193 closest distance to " CA  ARG A 139 " =    1.153
peak=    3.191 closest distance to " O   HOH Z 279 " =    2.159
peak=    3.190 closest distance to " O   HOH Z 193 " =    0.986
peak=    3.189 closest distance to " O   HOH Z 193 " =    1.751
peak=    3.186 closest distance to " CB  ARG A 269 " =    0.843
peak=    3.184 closest distance to " NH2AARG A 275 " =    3.621
peak=    3.183 closest distance to " CB  THR A  31 " =    1.584
peak=    3.183 closest distance to " CA  SER A  12 " =    1.488
peak=    3.181 closest distance to " CB  TYR A 247 " =    0.934
peak=    3.180 closest distance to " OD1 ASN A 301 " =    1.156
peak=    3.179 closest distance to " O   HOH Z 303 " =    2.278
peak=    3.173 closest distance to " O   HOH Z  22 " =    2.521
peak=    3.169 closest distance to " O   HOH Z 345 " =    3.650
peak=    3.168 closest distance to " CD1 LEU A 300 " =    1.098
peak=    3.167 closest distance to " OG1 THR A  82 " =    0.911
peak=    3.167 closest distance to " CB  GLU A 175 " =    1.421
peak=    3.167 closest distance to " O   HOH Z  80 " =    1.838
peak=    3.166 closest distance to " N   TYR A 247 " =    1.192
peak=    3.166 closest distance to " CG  GLN A 205 " =    1.058
peak=    3.165 closest distance to " OE1 GLU A   2 " =    1.863
peak=    3.163 closest distance to " CE3 TRP A 150 " =    1.102
peak=    3.158 closest distance to " CG2 VAL A 257 " =    0.777
peak=    3.156 closest distance to " C   GLY A  80 " =    1.059
peak=    3.154 closest distance to " CD  ARG A 139 " =    1.260
peak=    3.150 closest distance to " ND2AASN A 224 " =    0.900
peak=    3.145 closest distance to " CG2 ILE A 234 " =    1.094
peak=    3.141 closest distance to " O   HOH Z 173 " =    2.120
peak=    3.140 closest distance to " CE1 HIS A 108 " =    1.042
peak=    3.140 closest distance to " N   ARG A 156 " =    1.581
peak=    3.138 closest distance to " O   HOH Z   6 " =    2.513
peak=    3.138 closest distance to " O   ALA A 158 " =    1.174
peak=    3.135 closest distance to " CE1 TYR A  30 " =    1.004
peak=    3.132 closest distance to " O   HOH Z 200 " =    2.991
peak=    3.132 closest distance to " CB  GLN A  88 " =    1.141
peak=    3.129 closest distance to " O   HOH Z 132 " =    0.929
peak=    3.127 closest distance to " CG  ARG A 219 " =    1.207
peak=    3.119 closest distance to " O   HOH Z 150 " =    1.408
peak=    3.108 closest distance to " CZ3 TRP A  85 " =    0.917
peak=    3.103 closest distance to " O   HOH Z 409 " =    3.178
peak=    3.097 closest distance to " CB  VAL A 257 " =    0.913
peak=    3.087 closest distance to " O   HOH Z 109 " =    2.284
peak=    3.085 closest distance to " NE2 GLN A  58 " =    4.783
peak=    3.081 closest distance to " OD2 ASP A 298 " =    3.854
peak=    3.078 closest distance to " CD2 TYR A 186 " =    1.074
peak=    3.077 closest distance to " O   HOH Z 227 " =    1.974
peak=    3.075 closest distance to " O   HOH Z 147 " =    1.643
peak=    3.071 closest distance to " CB  LYS A 117 " =    1.201
peak=    3.062 closest distance to " CG2BVAL A 121 " =    0.820
peak=    3.061 closest distance to " O   HOH Z 141 " =    1.680
peak=    3.050 closest distance to " O   HOH Z 420 " =    5.354
peak=    3.047 closest distance to " CA  ALA A 299 " =    1.091
peak=    3.040 closest distance to " O   HOH Z 365 " =    2.866
peak=    3.034 closest distance to " OG  SER A  22 " =    2.730
peak=    3.031 closest distance to " CB  ASN A 148 " =    2.034
peak=    3.025 closest distance to " CD  PRO A 213 " =    1.436

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 222         
Filter by distance & map next to the model:
   mapped sites are within: 0.817 - 5.966
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 222
   mapped sites are within: 0.817 - 5.966

peak=   -4.582 closest distance to " O   PRO A 198 " =    1.331
peak=   -4.456 closest distance to " O   HOH Z 266 " =    5.481
peak=   -4.432 closest distance to " CD  GLN A  58 " =    0.980
peak=   -4.265 closest distance to " CG2 ILE A  49 " =    2.795
peak=   -4.228 closest distance to " CG1 VAL A 250 " =    2.711
peak=   -4.211 closest distance to " CD  ARG A  14 " =    3.482
peak=   -4.053 closest distance to " O   HOH Z 374 " =    1.991
peak=   -4.049 closest distance to " CD2 TYR A 293 " =    1.816
peak=   -4.047 closest distance to " CD1 LEU A 101 " =    2.391
peak=   -4.042 closest distance to " CG  GLN A  11 " =    1.493
peak=   -4.036 closest distance to " O   HOH Z 166 " =    1.622
peak=   -4.026 closest distance to " CD  ARG A 156 " =    2.074
peak=   -4.021 closest distance to " CD  GLN A 223 " =    1.482
peak=   -3.990 closest distance to " O   HOH Z  10 " =    1.626
peak=   -3.979 closest distance to " OXT GLY A 302 " =    2.959
peak=   -3.978 closest distance to " C   HIS A 108 " =    1.067
peak=   -3.967 closest distance to " O   VAL A  67 " =    2.827
peak=   -3.955 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.927 closest distance to " CD1 LEU A  25 " =    2.503
peak=   -3.920 closest distance to " O   HOH Z 165 " =    1.897
peak=   -3.920 closest distance to " CB  PRO A 243 " =    2.739
peak=   -3.898 closest distance to " CG  GLN A 103 " =    2.513
peak=   -3.887 closest distance to " O   SER A 210 " =    1.790
peak=   -3.873 closest distance to " ND2BASN A 224 " =    1.897
peak=   -3.860 closest distance to " CG  GLU A  53 " =    1.508
peak=   -3.845 closest distance to " OG  SER A  97 " =    2.184
peak=   -3.838 closest distance to " O   HOH Z 377 " =    2.063
peak=   -3.830 closest distance to " CE2 PHE A  61 " =    2.666
peak=   -3.822 closest distance to " CZ  TYR A 169 " =    1.867
peak=   -3.814 closest distance to " CE3 TRP A 150 " =    2.262
peak=   -3.801 closest distance to " CD2 PHE A  61 " =    2.166
peak=   -3.793 closest distance to " CE2 TYR A  30 " =    2.809
peak=   -3.793 closest distance to " CG2 ILE A  20 " =    3.020
peak=   -3.764 closest distance to " CD  GLN A  58 " =    0.917
peak=   -3.740 closest distance to " CD1 PHE A  59 " =    2.078
peak=   -3.719 closest distance to " O   HOH Z 348 " =    2.285
peak=   -3.692 closest distance to " CD  ARG A  79 " =    1.255
peak=   -3.683 closest distance to " CG  ARG A 269 " =    2.286
peak=   -3.668 closest distance to " CA  GLY A 241 " =    3.202
peak=   -3.664 closest distance to " CG  PRO A 243 " =    1.640
peak=   -3.663 closest distance to " O   HOH Z 150 " =    1.104
peak=   -3.662 closest distance to " O   HOH Z 193 " =    1.263
peak=   -3.659 closest distance to " NE2 GLN A 223 " =    1.135
peak=   -3.659 closest distance to " O   HOH Z 150 " =    2.044
peak=   -3.651 closest distance to " CZ  PHE A  38 " =    2.310
peak=   -3.647 closest distance to " O   HOH Z 418 " =    1.216
peak=   -3.643 closest distance to " O   ALA A  34 " =    2.443
peak=   -3.640 closest distance to " C   THR A 279 " =    1.176
peak=   -3.621 closest distance to " O   HOH Z  90 " =    4.024
peak=   -3.618 closest distance to " ND2 ASN A  45 " =    1.997
peak=   -3.617 closest distance to " CG1 VAL A 112 " =    2.653
peak=   -3.610 closest distance to " CB  ALA A 184 " =    2.405
peak=   -3.592 closest distance to " O   HOH Z 283 " =    2.269
peak=   -3.591 closest distance to " O   HOH Z 185 " =    2.479
peak=   -3.591 closest distance to " N   ALA A  43 " =    2.694
peak=   -3.585 closest distance to " SG  CYS A 254 " =    3.205
peak=   -3.584 closest distance to " O   HOH Z 102 " =    1.614
peak=   -3.582 closest distance to " O   HOH Z 154 " =    1.518
peak=   -3.578 closest distance to " CA  GLY A 241 " =    2.321
peak=   -3.576 closest distance to " O   PHE A 218 " =    1.488
peak=   -3.576 closest distance to " O   HOH Z 285 " =    1.426
peak=   -3.574 closest distance to " CB  ALA A 161 " =    2.616
peak=   -3.574 closest distance to " OG BSER A 134 " =    1.407
peak=   -3.565 closest distance to " O   HOH Z 106 " =    1.980
peak=   -3.565 closest distance to " OD1 ASP A 171 " =    1.511
peak=   -3.553 closest distance to " O   HOH Z 171 " =    2.435
peak=   -3.535 closest distance to " O   HOH Z 287 " =    1.948
peak=   -3.534 closest distance to " CB  ALA A  10 " =    2.212
peak=   -3.529 closest distance to " O   HOH Z 366 " =    1.628
peak=   -3.526 closest distance to " O   HOH Z 191 " =    5.966
peak=   -3.526 closest distance to " O   HOH Z 145 " =    2.916
peak=   -3.525 closest distance to " OD1 ASN A 148 " =    1.404
peak=   -3.513 closest distance to " O   PRO A 163 " =    2.081
peak=   -3.512 closest distance to " OD1 ASP A 191 " =    1.502
peak=   -3.502 closest distance to " CH2 TRP A 150 " =    1.137
peak=   -3.501 closest distance to " CG2 VAL A 189 " =    2.216
peak=   -3.496 closest distance to " CH2 TRP A 179 " =    1.223
peak=   -3.492 closest distance to " O   HOH Z 196 " =    2.340
peak=   -3.490 closest distance to " O   GLU A 152 " =    1.347
peak=   -3.489 closest distance to " CD2 HIS A 207 " =    2.191
peak=   -3.481 closest distance to " O   HOH Z 394 " =    1.727
peak=   -3.480 closest distance to " O   HOH Z 128 " =    2.618
peak=   -3.473 closest distance to " ND2 ASN A 249 " =    2.245
peak=   -3.471 closest distance to " CA  GLY A 203 " =    2.415
peak=   -3.463 closest distance to " CE  MET A  93 " =    1.561
peak=   -3.457 closest distance to " CB  TRP A  85 " =    2.403
peak=   -3.455 closest distance to " C   ASN A 285 " =    2.267
peak=   -3.453 closest distance to " CD1 ILE A 109 " =    2.957
peak=   -3.449 closest distance to " O   HOH Z 103 " =    1.891
peak=   -3.446 closest distance to " O   HOH Z 198 " =    1.521
peak=   -3.445 closest distance to " CD  LYS A 289 " =    2.320
peak=   -3.442 closest distance to " CG1AVAL A  41 " =    2.599
peak=   -3.442 closest distance to " O   TRP A  92 " =    2.018
peak=   -3.441 closest distance to " O   HOH Z 422 " =    1.494
peak=   -3.437 closest distance to " OE1 GLN A 223 " =    2.326
peak=   -3.437 closest distance to " O   HOH Z 211 " =    1.362
peak=   -3.429 closest distance to " CB  ALA A 291 " =    2.433
peak=   -3.425 closest distance to " SD  MET A 105 " =    2.555
peak=   -3.422 closest distance to " CB  ALA A  43 " =    2.638
peak=   -3.422 closest distance to " N   SER A 276 " =    1.560
peak=   -3.419 closest distance to " O   ALA A  10 " =    1.837
peak=   -3.414 closest distance to " O   HOH Z  71 " =    2.466
peak=   -3.413 closest distance to " O   TRP A  70 " =    1.701
peak=   -3.412 closest distance to " O   HOH Z 252 " =    3.633
peak=   -3.407 closest distance to " O   HOH Z 351 " =    1.687
peak=   -3.404 closest distance to " O   HOH Z  13 " =    1.945
peak=   -3.403 closest distance to " C   SER A 206 " =    1.468
peak=   -3.401 closest distance to " CD1 ILE A 106 " =    2.194
peak=   -3.393 closest distance to " NE  ARG A  66 " =    4.448
peak=   -3.390 closest distance to " CG2 ILE A 263 " =    2.274
peak=   -3.390 closest distance to " CB  ASP A 132 " =    2.365
peak=   -3.389 closest distance to " O   HOH Z 149 " =    2.048
peak=   -3.384 closest distance to " CB  SER A 210 " =    1.113
peak=   -3.383 closest distance to " O   HOH Z 174 " =    2.308
peak=   -3.382 closest distance to " O   HOH Z 156 " =    3.633
peak=   -3.378 closest distance to " O   HOH Z 197 " =    1.875
peak=   -3.376 closest distance to " CG1 VAL A 189 " =    2.594
peak=   -3.375 closest distance to " O   HOH Z  19 " =    2.398
peak=   -3.375 closest distance to " O   SER A 276 " =    1.740
peak=   -3.362 closest distance to " OD2 ASP A 270 " =    1.077
peak=   -3.356 closest distance to " NH2 ARG A  79 " =    2.249
peak=   -3.347 closest distance to " CG  LEU A  83 " =    2.127
peak=   -3.339 closest distance to " O   HOH Z 166 " =    1.661
peak=   -3.336 closest distance to " O   HOH Z 264 " =    1.816
peak=   -3.335 closest distance to " O   HOH Z   6 " =    1.797
peak=   -3.335 closest distance to " N   SER A 134 " =    1.156
peak=   -3.325 closest distance to " N   THR A  52 " =    1.713
peak=   -3.320 closest distance to " O   HOH Z 234 " =    4.241
peak=   -3.320 closest distance to " O   SER A 271 " =    2.101
peak=   -3.319 closest distance to " CG  MET A 105 " =    1.034
peak=   -3.311 closest distance to " ND2 ASN A 187 " =    1.688
peak=   -3.306 closest distance to " O   HOH Z 423 " =    2.455
peak=   -3.301 closest distance to " CG  ASP A 286 " =    1.556
peak=   -3.293 closest distance to " CB  ALA A 248 " =    2.208
peak=   -3.292 closest distance to " ND2 ASN A  45 " =    1.231
peak=   -3.292 closest distance to " O   HOH Z  91 " =    1.978
peak=   -3.287 closest distance to " O   HOH Z 278 " =    1.254
peak=   -3.286 closest distance to " CA  ASP A  65 " =    1.363
peak=   -3.285 closest distance to " O   HOH Z 131 " =    4.173
peak=   -3.283 closest distance to " O   GLN A  11 " =    1.248
peak=   -3.280 closest distance to " OG BSER A 210 " =    1.389
peak=   -3.280 closest distance to " CG2 THR A 221 " =    2.393
peak=   -3.278 closest distance to " NE2 GLN A 103 " =    1.851
peak=   -3.278 closest distance to " O   HOH Z 210 " =    1.746
peak=   -3.268 closest distance to " O   HOH Z 435 " =    2.203
peak=   -3.266 closest distance to " CD  ARG A 195 " =    5.097
peak=   -3.266 closest distance to " O   HOH Z  78 " =    1.842
peak=   -3.265 closest distance to " O   HOH Z 407 " =    3.264
peak=   -3.264 closest distance to " O   HOH Z  56 " =    1.477
peak=   -3.264 closest distance to " NH1 ARG A 195 " =    2.360
peak=   -3.262 closest distance to " NE2 GLN A  88 " =    1.888
peak=   -3.259 closest distance to " CB  PHE A 192 " =    2.023
peak=   -3.254 closest distance to " O   SER A   3 " =    1.101
peak=   -3.253 closest distance to " CD2 PHE A 225 " =    1.293
peak=   -3.253 closest distance to " O   GLN A 240 " =    2.673
peak=   -3.251 closest distance to " O   HOH Z 201 " =    2.086
peak=   -3.249 closest distance to " O   HOH Z 200 " =    1.383
peak=   -3.249 closest distance to " NH2 ARG A  79 " =    1.618
peak=   -3.247 closest distance to " O   HOH Z 174 " =    3.586
peak=   -3.246 closest distance to " O   HOH Z 392 " =    1.527
peak=   -3.244 closest distance to " O   HOH Z 163 " =    5.094
peak=   -3.242 closest distance to " NH2 ARG A  66 " =    2.113
peak=   -3.240 closest distance to " O   HOH Z 210 " =    0.817
peak=   -3.235 closest distance to " O   HOH Z 301 " =    2.446
peak=   -3.230 closest distance to " O   HOH Z 135 " =    1.605
peak=   -3.229 closest distance to " CA  VAL A 197 " =    0.995
peak=   -3.228 closest distance to " OD1 ASN A 301 " =    1.871
peak=   -3.227 closest distance to " CG1 VAL A 112 " =    2.720
peak=   -3.225 closest distance to " ND2 ASN A  69 " =    1.798
peak=   -3.223 closest distance to " N   ALA A 226 " =    1.971
peak=   -3.223 closest distance to " O   HOH Z 290 " =    0.984
peak=   -3.223 closest distance to " O   HOH Z   6 " =    1.672
peak=   -3.221 closest distance to " CG1 VAL A  78 " =    2.576
peak=   -3.217 closest distance to " CB  ALA A 131 " =    2.444
peak=   -3.217 closest distance to " O   HOH Z 196 " =    1.703
peak=   -3.211 closest distance to " OD2 ASP A 171 " =    1.839
peak=   -3.208 closest distance to " O   HOH Z  64 " =    1.551
peak=   -3.208 closest distance to " O   HOH Z 259 " =    1.932
peak=   -3.206 closest distance to " CD2 TYR A 247 " =    2.440
peak=   -3.204 closest distance to " CA  GLY A 133 " =    2.136
peak=   -3.204 closest distance to " CE BMET A  47 " =    1.615
peak=   -3.200 closest distance to " N   ALA A 248 " =    1.821
peak=   -3.196 closest distance to " NE2 GLN A  88 " =    1.024
peak=   -3.196 closest distance to " C   ARG A  79 " =    2.714
peak=   -3.192 closest distance to " CE1 TYR A 247 " =    2.743
peak=   -3.192 closest distance to " O   HOH Z 331 " =    1.203
peak=   -3.191 closest distance to " C   LEU A 143 " =    1.151
peak=   -3.191 closest distance to " O   HOH Z 345 " =    2.908
peak=   -3.189 closest distance to " CG2BVAL A  41 " =    1.690
peak=   -3.180 closest distance to " OG1 THR A  82 " =    1.265
peak=   -3.175 closest distance to " O   HOH Z 275 " =    1.596
peak=   -3.172 closest distance to " CD  GLN A  88 " =    0.955
peak=   -3.167 closest distance to " O   HOH Z 252 " =    4.122
peak=   -3.165 closest distance to " O   HOH Z  60 " =    1.929
peak=   -3.165 closest distance to " O   HOH Z 397 " =    1.185
peak=   -3.164 closest distance to " O   HOH Z 434 " =    2.467
peak=   -3.158 closest distance to " O   HOH Z 113 " =    1.959
peak=   -3.155 closest distance to " O   HOH Z 281 " =    2.399
peak=   -3.154 closest distance to " CZ  TYR A  68 " =    1.098
peak=   -3.153 closest distance to " NE2 GLN A  94 " =    1.830
peak=   -3.147 closest distance to " O  BHOH Z 338 " =    1.169
peak=   -3.137 closest distance to " O   HOH Z  55 " =    1.947
peak=   -3.137 closest distance to " O   HOH Z 114 " =    3.459
peak=   -3.134 closest distance to " NE2 GLN A 278 " =    1.629
peak=   -3.132 closest distance to " CB  ALA A   9 " =    2.544
peak=   -3.126 closest distance to " O   HOH Z 109 " =    3.688
peak=   -3.118 closest distance to " CZ3 TRP A 274 " =    2.282
peak=   -3.116 closest distance to " O   HOH Z 396 " =    1.818
peak=   -3.114 closest distance to " C   GLY A  17 " =    1.109
peak=   -3.114 closest distance to " CD1 ILE A 263 " =    1.973
peak=   -3.113 closest distance to " OH  TYR A 172 " =    1.802
peak=   -3.112 closest distance to " NH2 ARG A  66 " =    1.103
peak=   -3.106 closest distance to " CB  PRO A 213 " =    2.096
peak=   -3.089 closest distance to " CD  PRO A 243 " =    1.966
peak=   -3.088 closest distance to " CE1 HIS A  81 " =    1.591
peak=   -3.088 closest distance to " O   HOH Z 134 " =    2.753
peak=   -3.086 closest distance to " CB  HIS A  86 " =    1.177
peak=   -3.054 closest distance to " CB  SER A  62 " =    5.569
peak=   -3.050 closest distance to " CD1 ILE A 109 " =    2.846
peak=   -3.047 closest distance to " CB  ASN A  45 " =    2.097
peak=   -3.001 closest distance to " O   HOH Z 198 " =    1.152

================= 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    :  0.4612 0.4558   6.270058e+00   6.251685e+00
   1_bss:  0.4520 0.4444   6.262761e+00   6.240774e+00
   1_xyz:  0.3023 0.3307   5.967739e+00   6.042303e+00
   1_adp:  0.2735 0.3434   5.921426e+00   6.066320e+00
   1_occ:  0.2733 0.3434   5.921366e+00   6.066612e+00
   2_bss:  0.2702 0.3397   5.916462e+00   6.062597e+00
   2_xyz:  0.2016 0.2547   5.650399e+00   5.836067e+00
   2_adp:  0.1863 0.2346   5.582633e+00   5.770097e+00
   2_occ:  0.1861 0.2347   5.582137e+00   5.770039e+00
   3_bss:  0.1858 0.2339   5.580208e+00   5.767827e+00
   3_xyz:  0.1543 0.1954   5.411505e+00   5.606477e+00
   3_adp:  0.1455 0.1939   5.375598e+00   5.587768e+00
   3_occ:  0.1455 0.1941   5.375488e+00   5.587829e+00
   4_bss:  0.1459 0.1944   5.376854e+00   5.587975e+00
   4_xyz:  0.1278 0.1778   5.269072e+00   5.500595e+00
   4_adp:  0.1249 0.1746   5.247286e+00   5.478960e+00
   4_occ:  0.1248 0.1747   5.247105e+00   5.478850e+00
   5_bss:  0.1247 0.1744   5.247424e+00   5.479039e+00
   5_xyz:  0.1225 0.1702   5.230719e+00   5.461375e+00
   5_adp:  0.1216 0.1697   5.225750e+00   5.457629e+00
   5_occ:  0.1214 0.1698   5.225573e+00   5.457724e+00
   5_bss:  0.1216 0.1700   5.226220e+00   5.457762e+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:  0.293  34.414  -3.135   3.411   2.814   0.000   0.000   0.000
   1_xyz:  0.293  34.414  -3.135   3.411   2.814   0.000   0.000   0.000
   1_adp:  0.293  34.414  -3.135   3.411   2.814   0.000   0.000   0.000
   1_occ:  0.293  34.414  -3.135   3.411   2.814   0.000   0.000   0.000
   2_bss:  0.323  70.201  -2.327   0.979   0.863   0.000   0.000   0.000
   2_xyz:  0.323  70.201  -2.327   0.979   0.863   0.000   0.000   0.000
   2_adp:  0.323  70.201  -2.327   0.979   0.863   0.000   0.000   0.000
   2_occ:  0.323  70.201  -2.327   0.979   0.863   0.000   0.000   0.000
   3_bss:  0.328  67.985  -2.528  -0.406   0.098  -0.000   0.000   0.000
   3_xyz:  0.328  67.985  -2.528  -0.406   0.098  -0.000   0.000   0.000
   3_adp:  0.328  67.985  -2.528  -0.406   0.098  -0.000   0.000   0.000
   3_occ:  0.328  67.985  -2.528  -0.406   0.098  -0.000   0.000   0.000
   4_bss:  0.338  80.808  -2.599  -0.933  -0.163  -0.000  -0.000  -0.000
   4_xyz:  0.338  80.808  -2.599  -0.933  -0.163  -0.000  -0.000  -0.000
   4_adp:  0.338  80.808  -2.599  -0.933  -0.163  -0.000  -0.000  -0.000
   4_occ:  0.338  80.808  -2.599  -0.933  -0.163  -0.000  -0.000  -0.000
   5_bss:  0.339  80.000  -2.171  -0.823   0.176  -0.000   0.000   0.000
   5_xyz:  0.339  80.000  -2.171  -0.823   0.176  -0.000   0.000   0.000
   5_adp:  0.339  80.000  -2.171  -0.823   0.176  -0.000   0.000   0.000
   5_occ:  0.339  80.000  -2.171  -0.823   0.176  -0.000   0.000   0.000
   5_bss:  0.329  73.800  -1.981  -0.750   0.330  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.650 0.4751  0.6239    62638.947
   1_bss:  52.519 0.4879  0.6647    59594.873
   1_xyz:  35.718 0.6933  0.9040    30621.094
   1_adp:  37.379 0.6730  0.8803    33017.500
   1_occ:  37.416 0.6725  0.8795    33068.597
   2_bss:  36.860 0.6791  0.8558    32392.614
   2_xyz:  26.107 0.7988  0.9613    17084.623
   2_adp:  23.592 0.8260  0.9677    14643.824
   2_occ:  23.590 0.8260  0.9676    14646.186
   3_bss:  23.459 0.8272  0.9431    14503.134
   3_xyz:  18.945 0.8715  0.9726     9974.594
   3_adp:  18.476 0.8761  0.9673     9742.877
   3_occ:  18.478 0.8761  0.9673     9744.694
   4_bss:  18.463 0.8763  0.9582     9756.983
   4_xyz:  16.593 0.8930  0.9643     8121.754
   4_adp:  16.111 0.8974  0.9557     7825.653
   4_occ:  16.106 0.8974  0.9555     7823.562
   5_bss:  16.114 0.8974  0.9655     7828.576
   5_xyz:  15.690 0.9011  0.9694     7502.415
   5_adp:  15.583 0.9021  0.9615     7457.031
   5_occ:  15.579 0.9022  0.9613     7452.699
   5_bss:  15.591 0.9020  0.9657     7453.269
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7267e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7267e-01
   1_xyz:   1.690  0.015  0.105 15.890  0.007  4.115   1.5121e-01
   1_adp:   1.690  0.015  0.105 15.890  0.007  4.115   1.5121e-01
   1_occ:   1.690  0.015  0.105 15.890  0.007  4.115   1.5121e-01
   2_bss:   1.690  0.015  0.105 15.890  0.007  4.115   1.5121e-01
   2_xyz:   1.170  0.008  0.081 14.659  0.005  4.113   7.5933e-02
   2_adp:   1.170  0.008  0.081 14.659  0.005  4.113   7.5933e-02
   2_occ:   1.170  0.008  0.081 14.659  0.005  4.113   7.5933e-02
   3_bss:   1.170  0.008  0.081 14.659  0.005  4.113   7.5933e-02
   3_xyz:   0.972  0.007  0.067 14.239  0.003  4.124   5.5614e-02
   3_adp:   0.972  0.007  0.067 14.239  0.003  4.124   5.5614e-02
   3_occ:   0.972  0.007  0.067 14.239  0.003  4.124   5.5614e-02
   4_bss:   0.972  0.007  0.067 14.239  0.003  4.124   5.5614e-02
   4_xyz:   1.102  0.009  0.079 14.512  0.004  4.135   6.7120e-02
   4_adp:   1.102  0.009  0.079 14.512  0.004  4.135   6.7120e-02
   4_occ:   1.102  0.009  0.079 14.512  0.004  4.135   6.7120e-02
   5_bss:   1.102  0.009  0.079 14.512  0.004  4.135   6.7120e-02
   5_xyz:   0.989  0.008  0.074 14.212  0.003  4.127   5.7289e-02
   5_adp:   0.989  0.008  0.074 14.212  0.003  4.127   5.7289e-02
   5_occ:   0.989  0.008  0.074 14.212  0.003  4.127   5.7289e-02
   5_bss:   0.989  0.008  0.074 14.212  0.003  4.127   5.7289e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.636   2.4359e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.636   2.4359e-01
   1_xyz:  12.074  0.097  0.362 82.459  0.038  1.906   1.3325e-01
   1_adp:  12.074  0.097  0.362 82.459  0.038  1.906   1.3325e-01
   1_occ:  12.074  0.097  0.362 82.459  0.038  1.906   1.3325e-01
   2_bss:  12.074  0.097  0.362 82.459  0.038  1.906   1.3325e-01
   2_xyz:   7.466  0.056  0.263 85.411  0.055  2.258   5.8410e-02
   2_adp:   7.466  0.056  0.263 85.411  0.055  2.258   5.8410e-02
   2_occ:   7.466  0.056  0.263 85.411  0.055  2.258   5.8410e-02
   3_bss:   7.466  0.056  0.263 85.411  0.055  2.258   5.8410e-02
   3_xyz:   6.520  0.047  0.221 79.517  0.032  2.353   4.3662e-02
   3_adp:   6.520  0.047  0.221 79.517  0.032  2.353   4.3662e-02
   3_occ:   6.520  0.047  0.221 79.517  0.032  2.353   4.3662e-02
   4_bss:   6.520  0.047  0.221 79.517  0.032  2.353   4.3662e-02
   4_xyz:   8.007  0.043  0.271 83.326  0.039  2.308   4.5199e-02
   4_adp:   8.007  0.043  0.271 83.326  0.039  2.308   4.5199e-02
   4_occ:   8.007  0.043  0.271 83.326  0.039  2.308   4.5199e-02
   5_bss:   8.007  0.043  0.271 83.326  0.039  2.308   4.5199e-02
   5_xyz:   7.533  0.046  0.252 79.731  0.028  2.400   3.5723e-02
   5_adp:   7.533  0.046  0.252 79.731  0.028  2.400   3.5723e-02
   5_occ:   7.533  0.046  0.252 79.731  0.028  2.400   3.5723e-02
   5_bss:   7.533  0.046  0.252 79.731  0.028  2.400   3.5723e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  96.47   0.00  18.38  86.31   0.00  14.22  96.47   1.40  41.05
   1_occ:  96.47   0.00  18.38  86.31   0.00  14.22  96.47   1.40  41.05
   2_bss:  96.47   0.00  18.38  86.31   0.00  14.22  96.47   1.40  41.05
   2_xyz:  96.47   0.00  18.38  86.31   0.00  14.22  96.47   1.40  41.05
   2_adp:  93.72   0.00  17.62  87.02   0.00  13.30  93.72   3.92  41.11
   2_occ:  93.72   0.00  17.62  87.02   0.00  13.30  93.72   3.92  41.11
   3_bss:  93.72   0.00  17.62  87.02   0.00  13.30  93.72   3.92  41.11
   3_xyz:  93.72   0.00  17.62  87.02   0.00  13.30  93.72   3.92  41.11
   3_adp:  96.09   0.00  18.06  91.25   0.00  13.08  96.09   4.76  45.17
   3_occ:  96.09   0.00  18.06  91.25   0.00  13.08  96.09   4.76  45.17
   4_bss:  96.09   0.00  18.06  91.25   0.00  13.08  96.09   4.76  45.17
   4_xyz:  96.09   0.00  18.06  91.25   0.00  13.08  96.09   4.76  45.17
   4_adp: 101.52   0.00  17.72  99.84   0.00  12.71 101.52   0.00  44.99
   4_occ: 101.52   0.00  17.72  99.84   0.00  12.71 101.52   0.00  44.99
   5_bss: 101.52   0.00  17.72  99.84   0.00  12.71 101.52   0.00  44.99
   5_xyz: 101.52   0.00  17.72  99.84   0.00  12.71 101.52   0.00  44.99
   5_adp: 104.13   0.00  17.45 101.90   0.00  12.48 104.13   0.00  44.53
   5_occ: 104.13   0.00  17.45 101.90   0.00  12.48 104.13   0.00  44.53
   5_bss: 104.14   0.00  17.45 101.91   0.00  12.48 104.14   0.00  44.53
------------------------------------------------------------------------
 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:    1.487    0.037    0.506
   1_adp:    1.487    0.037    0.506
   1_occ:    1.487    0.037    0.506
   2_bss:    1.487    0.037    0.506
   2_xyz:    1.298    0.045    0.612
   2_adp:    1.298    0.045    0.612
   2_occ:    1.298    0.045    0.612
   3_bss:    1.298    0.045    0.612
   3_xyz:    1.329    0.032    0.699
   3_adp:    1.329    0.032    0.699
   3_occ:    1.329    0.032    0.699
   4_bss:    1.329    0.032    0.699
   4_xyz:    1.411    0.014    0.742
   4_adp:    1.411    0.014    0.742
   4_occ:    1.411    0.014    0.742
   5_bss:    1.411    0.014    0.742
   5_xyz:    1.383    0.038    0.759
   5_adp:    1.383    0.038    0.759
   5_occ:    1.383    0.038    0.759
   5_bss:    1.383    0.038    0.759
------------------------------------------------------------------------

CPU time actual refinement: 341.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_471/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/noshake/run_471/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_471/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_471/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_471/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.82 
  Macro-tasks:
    bulk solvent and scale       = 50.96  
    individual site refinement   = 127.57 
    weights calculation          = 30.18  
    collect and process          = 6.72   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 215.55 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 105.52 
    alpha_beta                      = 8.68   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 112.43 
    fmodel                         = 7.98   
    r_factors                      = 0.35   
    phase_errors                   = 10.81  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 249.64 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.919 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    634 calls, 105.15 s
gradients_fft:          579 calls,  99.83 s

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

# Date 2008-01-16 Time 04:55:04 PST -0800 (1200488104.71 s)
Start R-work = 0.4612, R-free = 0.4558 (no bulk solvent and anisotropic scale)
Final R-work = 0.1401, R-free = 0.1846 (no bulk solvent and anisotropic scale)

Start R-work = 0.4520, R-free = 0.4444
Final R-work = 0.1216, R-free = 0.1700