# Date 2008-01-16 Time 03:49:18 PST -0800 (1200484158.23 s)
#phil __OFF__

Command line arguments: "../60.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2269
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 60

-------------------------------------------------------------------------------
  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: (68.4938, 46.93, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.718 1.95077
Completeness in resolution range: 0.9388
Completeness with d_max=infinity: 0.935929

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7180
                             d_min =   1.9508

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.718 1.95077
Completeness in resolution range: 0.9388
Completeness with d_max=infinity: 0.935929

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7184 -  4.1739 [2198/2226]  1975   223  10.1%
  bin  2:  4.1739 -  3.3255 [2088/2111]  1880   208  10.0%
  bin  3:  3.3255 -  2.9088 [2078/2100]  1873   205   9.9%
  bin  4:  2.9088 -  2.6445 [2070/2089]  1861   209  10.1%
  bin  5:  2.6445 -  2.4559 [2018/2047]  1814   204  10.1%
  bin  6:  2.4559 -  2.3117 [2041/2083]  1842   199   9.8%
  bin  7:  2.3117 -  2.1963 [2013/2049]  1811   202  10.0%
  bin  8:  2.1963 -  2.1010 [2021/2062]  1813   208  10.3%
  bin  9:  2.1010 -  2.0203 [2025/2053]  1831   194   9.6%
  bin 10:  2.0203 -  1.9508 [1037/2046]   930   107  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_60/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.22 -     1.96: 14
        1.96 -     2.69: 155
        2.69 -     3.43: 4590
        3.43 -     4.16: 9528
        4.16 -     4.90: 14476
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.225 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.416 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.420 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.586 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.620 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28758 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_60/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_60/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.93 86.39 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: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3317   r_free= 0.3317   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.095877                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6551 0.99   1425  158 0.2932 0.2878      6.3937      6.4344|
|  2:  4.6551 -  3.7145 0.99   1375  153 0.2624 0.2473      6.4777       6.485|
|  3:  3.7145 -  3.2507 0.99   1333  150 0.2883 0.2990      6.3947      6.4941|
|  4:  3.2507 -  2.9561 0.99   1336  140 0.3020 0.3409      6.2733      6.3657|
|  5:  2.9561 -  2.7457 0.98   1317  152 0.3315 0.3355      6.1403      6.1664|
|  6:  2.7457 -  2.5847 0.98   1315  147 0.3511 0.3807       6.093      6.0002|
|  7:  2.5847 -  2.4559 0.99   1302  149 0.3525 0.3021      6.0495      5.9589|
|  8:  2.4559 -  2.3495 0.99   1322  142 0.3604 0.3605      6.0032      6.0294|
|  9:  2.3495 -  2.2593 0.98   1309  144 0.3750 0.3829      5.9786      6.0437|
| 10:  2.2593 -  2.1816 0.98   1296  140 0.3687 0.3478      5.9469      5.8656|
| 11:  2.1816 -  2.1136 0.98   1304  149 0.3782 0.3693      5.8933      5.8847|
| 12:  2.1136 -  2.0534 0.99   1297  145 0.3870 0.3765      5.8449       5.874|
| 13:  2.0534 -  1.9994 0.97   1274  135 0.3849 0.3807        5.76      5.6785|
| 14:  1.9994 -  1.9508 0.33    425   55 0.4650 0.4580      5.8789      5.7092|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6551  1425   158  0.77  28.02   0.87     0.77      48261.66|
|  2:  4.6551 -  3.7145  1375   153  0.81  25.11   0.98     0.90      57661.82|
|  3:  3.7145 -  3.2507  1333   150  0.76  29.95   1.00     0.93      58098.24|
|  4:  3.2507 -  2.9561  1336   140  0.72  33.39   1.00     0.90      50559.39|
|  5:  2.9561 -  2.7457  1317   152  0.67  38.22   0.99     0.88      41850.61|
|  6:  2.7457 -  2.5847  1315   147  0.67  37.98   0.97     0.88      35152.41|
|  7:  2.5847 -  2.4559  1302   149  0.69  36.94   1.00     0.90      30853.57|
|  8:  2.4559 -  2.3495  1322   142  0.68  37.60   1.02     0.91      27634.96|
|  9:  2.3495 -  2.2593  1309   144  0.68  37.66   1.01     0.93      26077.02|
| 10:  2.2593 -  2.1816  1296   140  0.67  38.30   1.04     0.92      24052.85|
| 11:  2.1816 -  2.1136  1304   149  0.66  39.37   1.02     0.94      23139.52|
| 12:  2.1136 -  2.0534  1297   145  0.64  41.00   1.06     0.94      21911.07|
| 13:  2.0534 -  1.9994  1274   135  0.61  43.62   1.04     0.89      20417.87|
| 14:  1.9994 -  1.9508   425    55  0.61  43.53   0.99     0.78      17477.22|
|alpha:            min =        0.77 max =            0.94 mean =         0.90|
|beta:             min =    17477.22 max =        58098.24 mean =     35645.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           89.99 mean =        36.00|
|phase err.(test): min =        0.00 max =           89.97 mean =        35.84|
|-----------------------------------------------------------------------------|

============================== 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 = 3.622523              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.871   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.711483              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.632   (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 |  1.225 -  1.592:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.592 -  1.960:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.960 -  2.327:       25 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.327 -  2.695:      130 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.695 -  3.062:     2267 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.062 -  3.430:     2323 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.430 -  3.797:     4135 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.797 -  4.165:     5393 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.165 -  4.532:     6470 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.532 -  4.900:     8006 |
|-----------------------------------------------------------------------------|
|-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 |        0.213 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.225 |       0.954 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    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: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3317   r_free= 0.3317   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.095877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3168   r_free= 0.3188   ksol= 0.35   Bsol= 50.00   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,-2.80,-1.53,-0.00,-0.00,-0.00); trace/3= -0.81                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.072910                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.299216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.622   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376566              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.335   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3168      final r-factor (work) = 0.2185          |
| start r-factor (free) = 0.3188      final r-factor (free) = 0.2431          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2521 = 3.30 * 0.50 * 6.0859 + 1.00 * 0.2127                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7139 = 3.30 * 0.50 * 5.8400 + 1.00 * 0.0801                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2185      final r-factor (work) = 0.1993          |
| start r-factor (free) = 0.2431      final r-factor (free) = 0.2469          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2053 = 0.38 * 1.00 * 5.8400 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1329 = 0.38 * 1.00 * 5.6369 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.25   17.50    None  None   None       |
|    all(noH): 2823   0      0.00    77.25   17.50    None  None   None       |
|    Sol.    : 438    0      6.15    74.30   39.00    None  None   None       |
|    Mac.    : 2385   0      0.00    77.25   13.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.725:  521   |   5:    38.623 -  46.348:  120        |
|      1:     7.725 -  15.449: 1244   |   6:    46.348 -  54.073:   82        |
|      2:    15.449 -  23.174:  463   |   7:    54.073 -  61.797:   59        |
|      3:    23.174 -  30.899:  178   |   8:    61.797 -  69.522:   23        |
|      4:    30.899 -  38.623:  127   |   9:    69.522 -  77.247:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1993 r_free = 0.2469             target_work(ml) = 5.646         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1990 r_free = 0.2467             target_work(ml) = 5.645         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1990   r_free= 0.2467   ksol= 0.35   Bsol= 50.00   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,-2.80,-1.53,-0.00,-0.00,-0.00); trace/3= -0.81                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.644832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1934   r_free= 0.2418   ksol= 0.32   Bsol= 40.82   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.78,-1.67,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.623488                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.537842              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.646   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.193610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.968   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1934      final r-factor (work) = 0.1411          |
| start r-factor (free) = 0.2418      final r-factor (free) = 0.1814          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2284 = 2.54 * 0.50 * 5.6333 + 1.00 * 0.0801                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0250 = 2.54 * 0.50 * 5.4938 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1411      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0736 = 0.19 * 1.00 * 5.4938 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0349 = 0.19 * 1.00 * 5.3000 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.15   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    85.15   17.23    None  None   None       |
|    Sol.    : 438    0      6.26    73.57   38.54    None  None   None       |
|    Mac.    : 2385   0      0.00    85.15   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.516:  569   |   5:    42.578 -  51.093:  125        |
|      1:     8.516 -  17.031: 1420   |   6:    51.093 -  59.608:   71        |
|      2:    17.031 -  25.547:  326   |   7:    59.608 -  68.124:   24        |
|      3:    25.547 -  34.062:  143   |   8:    68.124 -  76.639:    5        |
|      4:    34.062 -  42.578:  138   |   9:    76.639 -  85.155:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1325 r_free = 0.1726             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1323 r_free = 0.1724             target_work(ml) = 5.272         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1724   ksol= 0.32   Bsol= 40.82   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.78,-1.67,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.272473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1715   ksol= 0.32   Bsol= 40.82   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-2.58,-1.56,-0.00,-0.00,-0.00); trace/3= -2.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.268193                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.457112              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.184083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.464  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1321      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9143 = 1.46 * 0.50 * 5.2988 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8522 = 1.46 * 0.50 * 5.2208 + 1.00 * 0.0485                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9690 = 0.18 * 1.00 * 5.2208 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9600 = 0.18 * 1.00 * 5.1760 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    88.89   17.08    None  None   None       |
|    all(noH): 2823   0      1.67    88.89   17.08    None  None   None       |
|    Sol.    : 438    0      3.54    72.44   38.35    None  None   None       |
|    Mac.    : 2385   0      1.67    88.89   13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.665 -  10.387: 1028   |   5:    45.276 -  53.998:  112        |
|      1:    10.387 -  19.109: 1123   |   6:    53.998 -  62.720:   44        |
|      2:    19.109 -  27.832:  223   |   7:    62.720 -  71.442:   17        |
|      3:    27.832 -  36.554:  131   |   8:    71.442 -  80.165:    3        |
|      4:    36.554 -  45.276:  140   |   9:    80.165 -  88.887:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1579             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1579             target_work(ml) = 5.173         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1579   ksol= 0.32   Bsol= 40.82   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-2.58,-1.56,-0.00,-0.00,-0.00); trace/3= -2.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1578   ksol= 0.32   Bsol= 40.82   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,-2.53,-1.50,-0.00,-0.00,-0.00); trace/3= -2.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172111                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.051098              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.215  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.151145              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.362  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1535          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9435 = 3.05 * 0.50 * 5.1752 + 1.00 * 0.0485                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9036 = 3.05 * 0.50 * 5.1350 + 1.00 * 0.0699                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1535      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7833 = 0.15 * 1.00 * 5.1350 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7799 = 0.15 * 1.00 * 5.1162 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.34    87.78   16.75    None  None   None       |
|    all(noH): 2823   0      2.34    87.78   16.75    None  None   None       |
|    Sol.    : 438    0      2.34    70.35   37.23    None  None   None       |
|    Mac.    : 2385   0      2.50    87.78   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.339 -  10.883: 1170   |   5:    45.058 -  53.601:  100        |
|      1:    10.883 -  19.427: 1020   |   6:    53.601 -  62.145:   36        |
|      2:    19.427 -  27.970:  199   |   7:    62.145 -  70.689:   16        |
|      3:    27.970 -  36.514:  133   |   8:    70.689 -  79.233:    2        |
|      4:    36.514 -  45.058:  145   |   9:    79.233 -  87.776:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1526             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1077 r_free = 0.1527             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1527   ksol= 0.32   Bsol= 40.82   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,-2.53,-1.50,-0.00,-0.00,-0.00); trace/3= -2.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113237                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1522   ksol= 0.32   Bsol= 40.81   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.45,-1.37,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.111272                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.381006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.040  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.401810              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.545  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6018 = 1.38 * 0.50 * 5.1150 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5900 = 1.38 * 0.50 * 5.1260 + 1.00 * 0.0504                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1923 = 1.40 * 1.00 * 5.1260 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1910 = 1.40 * 1.00 * 5.1236 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    94.30   17.23    None  None   None       |
|    all(noH): 2823   0      1.22    94.30   17.23    None  None   None       |
|    Sol.    : 438    0      3.21    79.56   39.84    None  None   None       |
|    Mac.    : 2385   0      1.22    94.30   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:     1.221 -  10.529: 1117   |   5:    47.759 -  57.066:  101        |
|      1:    10.529 -  19.836: 1075   |   6:    57.066 -  66.374:   51        |
|      2:    19.836 -  29.144:  194   |   7:    66.374 -  75.681:   18        |
|      3:    29.144 -  38.451:  130   |   8:    75.681 -  84.989:    6        |
|      4:    38.451 -  47.759:  128   |   9:    84.989 -  94.296:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1549             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1549             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1549   ksol= 0.32   Bsol= 40.81   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.45,-1.37,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131190                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6551 0.99   1425  158 0.0990 0.1293      5.3929      5.5467|
|  2:  4.6551 -  3.7145 0.99   1375  153 0.0843 0.1080      5.4163      5.5953|
|  3:  3.7145 -  3.2507 0.99   1333  150 0.1032 0.1510      5.4363      5.8054|
|  4:  3.2507 -  2.9561 0.99   1336  140 0.1174 0.1505      5.4181      5.5691|
|  5:  2.9561 -  2.7457 0.98   1317  152 0.1257 0.1609      5.2777      5.4849|
|  6:  2.7457 -  2.5847 0.98   1315  147 0.1201 0.1932      5.1845      5.4552|
|  7:  2.5847 -  2.4559 0.99   1302  149 0.1207 0.1582      5.1389      5.3215|
|  8:  2.4559 -  2.3495 0.99   1322  142 0.1121 0.1568      5.0613      5.2553|
|  9:  2.3495 -  2.2593 0.98   1309  144 0.1156 0.1937      5.0099      5.3724|
| 10:  2.2593 -  2.1816 0.98   1296  140 0.1079 0.1618      4.9265       5.131|
| 11:  2.1816 -  2.1136 0.98   1304  149 0.1108 0.1729      4.8946      5.2284|
| 12:  2.1136 -  2.0534 0.99   1297  145 0.1083 0.1705       4.847      5.1489|
| 13:  2.0534 -  1.9994 0.97   1274  135 0.1076 0.1712      4.7743      5.0001|
| 14:  1.9994 -  1.9508 0.33    425   55 0.1025 0.1760      4.7081      4.9482|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6551  1425   158  0.94   9.17   0.98     0.96       7248.71|
|  2:  4.6551 -  3.7145  1375   153  0.96   7.62   1.02     1.01       8580.67|
|  3:  3.7145 -  3.2507  1333   150  0.94  10.80   1.03     1.03       9502.59|
|  4:  3.2507 -  2.9561  1336   140  0.93  12.94   1.01     1.01       9657.92|
|  5:  2.9561 -  2.7457  1317   152  0.91  15.23   1.00     0.97       7690.20|
|  6:  2.7457 -  2.5847  1315   147  0.90  16.00   0.98     0.95       6675.16|
|  7:  2.5847 -  2.4559  1302   149  0.91  15.15   0.98     0.95       5894.26|
|  8:  2.4559 -  2.3495  1322   142  0.91  15.02   1.00     0.97       5415.34|
|  9:  2.3495 -  2.2593  1309   144  0.91  15.36   1.00     0.96       4769.75|
| 10:  2.2593 -  2.1816  1296   140  0.90  15.40   1.00     0.96       4268.76|
| 11:  2.1816 -  2.1136  1304   149  0.91  15.64   1.00     0.97       4055.79|
| 12:  2.1136 -  2.0534  1297   145  0.91  15.44   1.01     1.00       3780.83|
| 13:  2.0534 -  1.9994  1274   135  0.90  16.04   1.00     0.98       3368.09|
| 14:  1.9994 -  1.9508   425    55  0.91  15.23   0.98     0.93       2795.22|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     2795.22 max =         9657.92 mean =      6176.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.77 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1548   ksol= 0.32   Bsol= 41.85   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-2.21,-1.16,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131134                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.72 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1548   ksol= 0.32   Bsol= 41.85   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-2.21,-1.16,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131134                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7184 -  4.6551 0.99   1425  158 0.0991 0.1294      5.3932      5.5477|
|  2:  4.6551 -  3.7145 0.99   1375  153 0.0845 0.1081      5.4172      5.5953|
|  3:  3.7145 -  3.2507 0.99   1333  150 0.1033 0.1511      5.4365      5.8059|
|  4:  3.2507 -  2.9561 0.99   1336  140 0.1174 0.1503      5.4178      5.5684|
|  5:  2.9561 -  2.7457 0.98   1317  152 0.1256 0.1609      5.2773      5.4845|
|  6:  2.7457 -  2.5847 0.98   1315  147 0.1201 0.1931      5.1843      5.4544|
|  7:  2.5847 -  2.4559 0.99   1302  149 0.1207 0.1581      5.1386      5.3211|
|  8:  2.4559 -  2.3495 0.99   1322  142 0.1121 0.1567      5.0609      5.2544|
|  9:  2.3495 -  2.2593 0.98   1309  144 0.1156 0.1937      5.0098      5.3723|
| 10:  2.2593 -  2.1816 0.98   1296  140 0.1079 0.1617      4.9264      5.1309|
| 11:  2.1816 -  2.1136 0.98   1304  149 0.1108 0.1729      4.8945      5.2283|
| 12:  2.1136 -  2.0534 0.99   1297  145 0.1083 0.1705      4.8468      5.1487|
| 13:  2.0534 -  1.9994 0.97   1274  135 0.1076 0.1713      4.7741      4.9999|
| 14:  1.9994 -  1.9508 0.33    425   55 0.1025 0.1760       4.708       4.948|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7184 -  4.6551  1425   158  0.94   9.17   0.98     0.96       7245.58|
|  2:  4.6551 -  3.7145  1375   153  0.96   7.62   1.02     1.01       8586.52|
|  3:  3.7145 -  3.2507  1333   150  0.94  10.80   1.03     1.03       9507.48|
|  4:  3.2507 -  2.9561  1336   140  0.93  12.93   1.02     1.01       9652.46|
|  5:  2.9561 -  2.7457  1317   152  0.91  15.23   1.00     0.98       7685.81|
|  6:  2.7457 -  2.5847  1315   147  0.90  15.99   0.99     0.96       6669.42|
|  7:  2.5847 -  2.4559  1302   149  0.91  15.14   0.99     0.96       5887.54|
|  8:  2.4559 -  2.3495  1322   142  0.91  15.01   1.01     0.98       5408.35|
|  9:  2.3495 -  2.2593  1309   144  0.91  15.36   1.01     0.97       4764.84|
| 10:  2.2593 -  2.1816  1296   140  0.90  15.40   1.00     0.97       4266.66|
| 11:  2.1816 -  2.1136  1304   149  0.91  15.64   1.01     0.97       4053.56|
| 12:  2.1136 -  2.0534  1297   145  0.91  15.44   1.02     1.01       3780.21|
| 13:  2.0534 -  1.9994  1274   135  0.90  16.04   1.01     0.99       3368.25|
| 14:  1.9994 -  1.9508   425    55  0.91  15.23   0.99     0.94       2795.22|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2795.22 max =         9652.46 mean =      6173.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.515)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    94.25   17.19    None  None   None       |
|    all(noH): 2823   0      1.18    94.25   17.19    None  None   None       |
|    Sol.    : 438    0      3.17    79.52   39.80    None  None   None       |
|    Mac.    : 2385   0      1.18    94.25   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.178 -  10.486: 1117   |   5:    47.716 -  57.023:  101        |
|      1:    10.486 -  19.793: 1075   |   6:    57.023 -  66.331:   51        |
|      2:    19.793 -  29.101:  194   |   7:    66.331 -  75.638:   18        |
|      3:    29.101 -  38.408:  130   |   8:    75.638 -  84.946:    6        |
|      4:    38.408 -  47.716:  128   |   9:    84.946 -  94.253:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 273         
Filter by distance & map next to the model:
   mapped sites are within: 0.475 - 5.521
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 268 from: 273
   mapped sites are within: 0.710 - 5.521

peak=    6.140 closest distance to " CB  ARG A 275 " =    0.974
peak=    5.383 closest distance to " O   HOH Z 142 " =    1.656
peak=    5.213 closest distance to " O   HOH Z 126 " =    1.865
peak=    5.183 closest distance to " CG  PRO A  54 " =    1.261
peak=    5.121 closest distance to " NE2 GLN A  11 " =    1.072
peak=    5.032 closest distance to " NH2 ARG A  56 " =    2.097
peak=    4.886 closest distance to " CB  GLN A 223 " =    1.491
peak=    4.863 closest distance to " CG  PRO A  90 " =    1.208
peak=    4.849 closest distance to " CB  PRO A  54 " =    1.026
peak=    4.798 closest distance to " O   HOH Z  78 " =    1.859
peak=    4.755 closest distance to " CG  PRO A 213 " =    1.306
peak=    4.730 closest distance to " CA  TYR A  30 " =    0.924
peak=    4.636 closest distance to " CB  SER A  63 " =    1.152
peak=    4.628 closest distance to " O   HOH Z 232 " =    2.387
peak=    4.597 closest distance to " O   HOH Z 402 " =    1.434
peak=    4.576 closest distance to " O  BHOH Z  74 " =    1.189
peak=    4.561 closest distance to " O   HOH Z 287 " =    1.829
peak=    4.512 closest distance to " CB  GLN A 183 " =    1.263
peak=    4.507 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.486 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.445 closest distance to " O   HOH Z 209 " =    2.249
peak=    4.432 closest distance to " O   HOH Z 427 " =    2.871
peak=    4.414 closest distance to " O   HOH Z 298 " =    1.819
peak=    4.413 closest distance to " CB  ASN A 148 " =    1.460
peak=    4.380 closest distance to " O   HOH Z  40 " =    1.741
peak=    4.375 closest distance to " O   HOH Z 193 " =    1.681
peak=    4.374 closest distance to " C   PRO A 198 " =    1.494
peak=    4.367 closest distance to " CG  PRO A 243 " =    1.059
peak=    4.343 closest distance to " O   HOH Z 250 " =    1.504
peak=    4.328 closest distance to " O   SER A  87 " =    2.256
peak=    4.300 closest distance to " ND2 ASN A 187 " =    1.399
peak=    4.297 closest distance to " O   HOH Z  97 " =    2.001
peak=    4.267 closest distance to " O   HOH Z  43 " =    2.043
peak=    4.260 closest distance to " O   HOH Z 369 " =    2.210
peak=    4.260 closest distance to " CG  ARG A  66 " =    2.576
peak=    4.246 closest distance to " CD2 TRP A 179 " =    1.370
peak=    4.243 closest distance to " O   HOH Z 316 " =    3.041
peak=    4.225 closest distance to " CG2 VAL A 257 " =    0.849
peak=    4.206 closest distance to " O   HOH Z 109 " =    1.418
peak=    4.203 closest distance to " O   HOH Z 126 " =    2.032
peak=    4.194 closest distance to " O   HOH Z 234 " =    3.585
peak=    4.145 closest distance to " O   HOH Z 417 " =    1.252
peak=    4.144 closest distance to " O   HOH Z 203 " =    1.746
peak=    4.132 closest distance to " O   HOH Z  44 " =    1.967
peak=    4.110 closest distance to " CB  VAL A 265 " =    1.173
peak=    4.108 closest distance to " NZ  LYS A 117 " =    2.896
peak=    4.106 closest distance to " O   HOH Z 327 " =    1.577
peak=    4.103 closest distance to " CB  GLU A 152 " =    1.203
peak=    4.090 closest distance to " O   HOH Z 346 " =    1.676
peak=    4.083 closest distance to " CB  ARG A  79 " =    1.333
peak=    4.080 closest distance to " O   HOH Z  97 " =    2.315
peak=    4.069 closest distance to " O   HOH Z 303 " =    2.096
peak=    4.028 closest distance to " O   HOH Z 128 " =    1.874
peak=    4.012 closest distance to " CG1 ILE A  33 " =    1.236
peak=    4.011 closest distance to " CB  ARG A 190 " =    1.713
peak=    4.004 closest distance to " O   HOH Z  54 " =    1.747
peak=    4.002 closest distance to " O   HOH Z 189 " =    2.149
peak=    3.988 closest distance to " O   HOH Z  68 " =    2.177
peak=    3.986 closest distance to " OE1 GLU A   2 " =    2.242
peak=    3.951 closest distance to " O   HOH Z 368 " =    2.042
peak=    3.933 closest distance to " NH2BARG A 145 " =    2.037
peak=    3.930 closest distance to " O   HOH Z  61 " =    1.668
peak=    3.930 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.927 closest distance to " CB  TRP A 266 " =    1.057
peak=    3.925 closest distance to " CA  ARG A  36 " =    1.000
peak=    3.911 closest distance to " CZ  PHE A 218 " =    1.062
peak=    3.909 closest distance to " O   HOH Z 423 " =    1.914
peak=    3.908 closest distance to " CB  GLU A 128 " =    1.049
peak=    3.869 closest distance to " O   HOH Z 392 " =    2.715
peak=    3.835 closest distance to " O   HOH Z  59 " =    1.876
peak=    3.835 closest distance to " O   HOH Z 406 " =    1.520
peak=    3.829 closest distance to " CB  THR A  31 " =    1.605
peak=    3.829 closest distance to " O   HOH Z 245 " =    1.354
peak=    3.828 closest distance to " O   HOH Z  15 " =    2.224
peak=    3.815 closest distance to " CG AARG A 275 " =    1.088
peak=    3.805 closest distance to " O   HOH Z 227 " =    1.588
peak=    3.800 closest distance to " O   HOH Z 236 " =    1.375
peak=    3.799 closest distance to " CB  VAL A 202 " =    1.556
peak=    3.793 closest distance to " O   HOH Z 344 " =    3.074
peak=    3.786 closest distance to " CA  ALA A  84 " =    1.183
peak=    3.777 closest distance to " O   HOH Z 389 " =    1.809
peak=    3.775 closest distance to " O   HOH Z 132 " =    2.650
peak=    3.761 closest distance to " O   HOH Z 365 " =    2.736
peak=    3.755 closest distance to " O   HOH Z 173 " =    2.072
peak=    3.754 closest distance to " O   HOH Z 416 " =    2.658
peak=    3.746 closest distance to " CA  ALA A  21 " =    1.060
peak=    3.739 closest distance to " O   HOH Z 403 " =    1.741
peak=    3.736 closest distance to " O   HOH Z 357 " =    1.910
peak=    3.734 closest distance to " CG2 ILE A 120 " =    1.213
peak=    3.733 closest distance to " CB  SER A  26 " =    1.697
peak=    3.731 closest distance to " CD  ARG A 269 " =    0.957
peak=    3.726 closest distance to " OG BSER A 164 " =    2.091
peak=    3.708 closest distance to " CE  LYS A 119 " =    1.119
peak=    3.706 closest distance to " O   HOH Z 265 " =    2.283
peak=    3.703 closest distance to " O   HOH Z 124 " =    1.302
peak=    3.702 closest distance to " CB  SER A   3 " =    1.156
peak=    3.689 closest distance to " CG2AVAL A 121 " =    2.245
peak=    3.685 closest distance to " CA  ASN A 215 " =    0.994
peak=    3.675 closest distance to " O   HOH Z 415 " =    3.479
peak=    3.675 closest distance to " N   ASN A  39 " =    1.149
peak=    3.671 closest distance to " CD2 LEU A 297 " =    0.960
peak=    3.666 closest distance to " N   TYR A 116 " =    1.587
peak=    3.664 closest distance to " CA  ARG A 195 " =    1.296
peak=    3.654 closest distance to " O   HOH Z 361 " =    3.639
peak=    3.653 closest distance to " CA  MET A  40 " =    1.102
peak=    3.636 closest distance to " CB  ASN A 110 " =    1.058
peak=    3.633 closest distance to " O   HOH Z 280 " =    2.999
peak=    3.622 closest distance to " CB  HIS A 108 " =    0.886
peak=    3.606 closest distance to " O   HOH Z 305 " =    3.535
peak=    3.603 closest distance to " N   ARG A 156 " =    1.331
peak=    3.602 closest distance to " CB  GLU A 277 " =    3.512
peak=    3.598 closest distance to " O   HOH Z  88 " =    2.727
peak=    3.595 closest distance to " O   HOH Z   3 " =    1.804
peak=    3.581 closest distance to " CB  TRP A 179 " =    1.157
peak=    3.578 closest distance to " O   HOH Z 214 " =    2.172
peak=    3.576 closest distance to " O   HOH Z 158 " =    2.994
peak=    3.568 closest distance to " CG2BVAL A  41 " =    0.793
peak=    3.565 closest distance to " O   HOH Z 227 " =    2.193
peak=    3.560 closest distance to " CE  LYS A  76 " =    0.837
peak=    3.560 closest distance to " O   HOH Z 371 " =    1.536
peak=    3.559 closest distance to " CB  ASN A  39 " =    0.829
peak=    3.557 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.554 closest distance to " O   HOH Z  61 " =    1.505
peak=    3.551 closest distance to " O   HOH Z 132 " =    2.376
peak=    3.539 closest distance to " O   HOH Z  47 " =    1.588
peak=    3.534 closest distance to " O   HOH Z 102 " =    1.261
peak=    3.531 closest distance to " O   HOH Z 342 " =    0.881
peak=    3.531 closest distance to " CB  ALA A 291 " =    1.220
peak=    3.528 closest distance to " CA  ASN A 176 " =    1.140
peak=    3.527 closest distance to " CB  TYR A 169 " =    0.710
peak=    3.526 closest distance to " O   HOH Z 425 " =    2.004
peak=    3.519 closest distance to " CB  ALA A 114 " =    1.079
peak=    3.515 closest distance to " O   HOH Z 261 " =    2.042
peak=    3.511 closest distance to " CA  ALA A  51 " =    0.940
peak=    3.510 closest distance to " O   HOH Z 353 " =    2.587
peak=    3.506 closest distance to " CD  LYS A  76 " =    1.917
peak=    3.491 closest distance to " O   HOH Z 291 " =    1.388
peak=    3.484 closest distance to " O   HOH Z 313 " =    1.941
peak=    3.466 closest distance to " OD2 ASP A 286 " =    2.716
peak=    3.465 closest distance to " O   HOH Z 180 " =    2.316
peak=    3.459 closest distance to " CG  MET A 185 " =    1.133
peak=    3.457 closest distance to " N   PHE A 130 " =    1.262
peak=    3.457 closest distance to " O   HOH Z 411 " =    3.790
peak=    3.454 closest distance to " O   THR A 220 " =    1.257
peak=    3.453 closest distance to " O   HOH Z 371 " =    3.169
peak=    3.453 closest distance to " O   HOH Z  21 " =    1.774
peak=    3.453 closest distance to " O   HOH Z  49 " =    2.096
peak=    3.452 closest distance to " N   HIS A 108 " =    1.854
peak=    3.449 closest distance to " O   HOH Z 234 " =    2.169
peak=    3.448 closest distance to " CG2 ILE A  20 " =    1.398
peak=    3.444 closest distance to " O   HOH Z 345 " =    3.035
peak=    3.443 closest distance to " O   HOH Z 337 " =    3.432
peak=    3.443 closest distance to " OD1 ASN A  69 " =    2.531
peak=    3.434 closest distance to " NH1AARG A 145 " =    1.214
peak=    3.432 closest distance to " O   HOH Z  85 " =    1.353
peak=    3.432 closest distance to " O   ALA A   1 " =    1.640
peak=    3.421 closest distance to " O   HOH Z  19 " =    2.146
peak=    3.420 closest distance to " O   HOH Z  80 " =    1.662
peak=    3.403 closest distance to " CB  LEU A 228 " =    1.124
peak=    3.400 closest distance to " O   HOH Z 273 " =    2.724
peak=    3.397 closest distance to " CB  ALA A 248 " =    1.344
peak=    3.392 closest distance to " O   HOH Z 407 " =    1.320
peak=    3.390 closest distance to " CB  TYR A 169 " =    0.936
peak=    3.390 closest distance to " O   HOH Z 261 " =    1.704
peak=    3.379 closest distance to " CB  ILE A 120 " =    1.307
peak=    3.378 closest distance to " CG  LEU A 167 " =    1.287
peak=    3.376 closest distance to " O   HOH Z   1 " =    1.915
peak=    3.375 closest distance to " O   GLY A  91 " =    1.542
peak=    3.368 closest distance to " O   HOH Z 172 " =    3.653
peak=    3.364 closest distance to " CB  ASP A 140 " =    1.040
peak=    3.360 closest distance to " CG2 THR A 294 " =    1.612
peak=    3.360 closest distance to " O   HOH Z 435 " =    1.852
peak=    3.358 closest distance to " CA  ASP A 140 " =    1.066
peak=    3.356 closest distance to " O  BHOH Z 338 " =    2.306
peak=    3.354 closest distance to " ND2 ASN A 249 " =    0.924
peak=    3.352 closest distance to " CB  GLU A  46 " =    1.042
peak=    3.343 closest distance to " O   HOH Z 185 " =    1.740
peak=    3.342 closest distance to " O   HOH Z 433 " =    1.890
peak=    3.340 closest distance to " CA  ILE A 234 " =    0.987
peak=    3.336 closest distance to " O   HOH Z   9 " =    2.156
peak=    3.335 closest distance to " O   HOH Z 299 " =    4.280
peak=    3.333 closest distance to " CG  GLN A  77 " =    2.161
peak=    3.333 closest distance to " CB  SER A 141 " =    1.063
peak=    3.332 closest distance to " CD  LYS A 166 " =    1.230
peak=    3.331 closest distance to " O   HOH Z  88 " =    2.541
peak=    3.326 closest distance to " CG1BVAL A  72 " =    1.578
peak=    3.318 closest distance to " O   HOH Z 163 " =    1.938
peak=    3.305 closest distance to " CA  MET A 105 " =    1.034
peak=    3.305 closest distance to " CD2 HIS A  81 " =    1.042
peak=    3.301 closest distance to " CE BMET A  47 " =    1.295
peak=    3.300 closest distance to " CA  VAL A 125 " =    1.008
peak=    3.291 closest distance to " CG  LYS A  76 " =    0.953
peak=    3.280 closest distance to " O   ASN A  74 " =    1.687
peak=    3.276 closest distance to " CA  LEU A 300 " =    0.974
peak=    3.270 closest distance to " O   HOH Z 272 " =    2.333
peak=    3.264 closest distance to " O   HOH Z 148 " =    3.327
peak=    3.260 closest distance to " CA  SER A 146 " =    1.841
peak=    3.259 closest distance to " CG  ARG A 269 " =    1.224
peak=    3.258 closest distance to " OG  SER A  62 " =    2.719
peak=    3.254 closest distance to " O   HOH Z 261 " =    2.293
peak=    3.251 closest distance to " CD1 ILE A 106 " =    0.861
peak=    3.250 closest distance to " O   HOH Z 267 " =    2.000
peak=    3.248 closest distance to " O   HOH Z 298 " =    2.253
peak=    3.245 closest distance to " O   HOH Z 421 " =    1.861
peak=    3.245 closest distance to " CA  GLY A  80 " =    0.731
peak=    3.234 closest distance to " CA  LYS A 117 " =    1.201
peak=    3.232 closest distance to " CD  ARG A  66 " =    2.694
peak=    3.232 closest distance to " CA  ALA A 248 " =    1.246
peak=    3.228 closest distance to " CA  ARG A 159 " =    1.299
peak=    3.222 closest distance to " CG  MET A 113 " =    0.894
peak=    3.222 closest distance to " O   HOH Z 207 " =    1.655
peak=    3.221 closest distance to " O   HOH Z 380 " =    2.007
peak=    3.216 closest distance to " CA  ASP A 162 " =    1.088
peak=    3.215 closest distance to " CB  TYR A 116 " =    0.817
peak=    3.213 closest distance to " CB  SER A  62 " =    0.960
peak=    3.206 closest distance to " CB  ASN A 215 " =    1.100
peak=    3.205 closest distance to " CA  ASN A 217 " =    1.204
peak=    3.203 closest distance to " O   HOH Z 234 " =    1.930
peak=    3.197 closest distance to " O   HOH Z 329 " =    3.914
peak=    3.195 closest distance to " O   HOH Z 183 " =    1.708
peak=    3.191 closest distance to " O   HOH Z  44 " =    3.181
peak=    3.191 closest distance to " O   HOH Z 426 " =    1.583
peak=    3.190 closest distance to " O   HOH Z 332 " =    1.466
peak=    3.179 closest distance to " O   HOH Z 345 " =    1.499
peak=    3.175 closest distance to " O   HOH Z 248 " =    1.536
peak=    3.174 closest distance to " CB  ARG A 156 " =    1.040
peak=    3.173 closest distance to " O   HOH Z 193 " =    2.011
peak=    3.173 closest distance to " O   HOH Z 112 " =    1.093
peak=    3.169 closest distance to " CB  GLN A 278 " =    0.877
peak=    3.168 closest distance to " CG  LYS A 119 " =    1.160
peak=    3.167 closest distance to " CD2 TYR A 186 " =    1.093
peak=    3.167 closest distance to " CA  ALA A 158 " =    1.467
peak=    3.163 closest distance to " OG1 THR A 264 " =    0.786
peak=    3.163 closest distance to " CB  LYS A 290 " =    1.168
peak=    3.163 closest distance to " CB  VAL A 268 " =    0.866
peak=    3.160 closest distance to " OE1 GLU A 236 " =    1.423
peak=    3.159 closest distance to " O   HOH Z 286 " =    2.328
peak=    3.159 closest distance to " CB  VAL A 126 " =    1.110
peak=    3.156 closest distance to " CA  ALA A 291 " =    0.776
peak=    3.152 closest distance to " CG2 VAL A 197 " =    1.053
peak=    3.146 closest distance to " O   HOH Z 310 " =    3.645
peak=    3.146 closest distance to " CG2 VAL A  78 " =    0.845
peak=    3.144 closest distance to " O   HOH Z 126 " =    1.511
peak=    3.142 closest distance to " OG  SER A  62 " =    3.639
peak=    3.138 closest distance to " O   THR A 182 " =    1.439
peak=    3.135 closest distance to " CG2 VAL A 202 " =    1.107
peak=    3.131 closest distance to " O   HOH Z 430 " =    5.521
peak=    3.127 closest distance to " CA  THR A 264 " =    0.778
peak=    3.125 closest distance to " O   HOH Z  85 " =    2.434
peak=    3.125 closest distance to " O   HOH Z 291 " =    1.685
peak=    3.123 closest distance to " OG BSER A 134 " =    2.941
peak=    3.117 closest distance to " NH1BARG A 145 " =    1.392
peak=    3.113 closest distance to " NH1 ARG A  14 " =    1.156
peak=    3.112 closest distance to " CB  LEU A 300 " =    0.953
peak=    3.111 closest distance to " O   HOH Z  62 " =    2.203
peak=    3.111 closest distance to " CB  MET A  47 " =    1.158
peak=    3.101 closest distance to " N   ASP A 162 " =    1.198
peak=    3.098 closest distance to " CB  THR A 279 " =    1.664
peak=    3.094 closest distance to " CB  ARG A  79 " =    0.773
peak=    3.092 closest distance to " CA  TYR A 116 " =    1.429
peak=    3.087 closest distance to " CD1AILE A 234 " =    0.939
peak=    3.086 closest distance to " N   VAL A 265 " =    1.160
peak=    3.085 closest distance to " CB  ARG A 138 " =    0.835
peak=    3.070 closest distance to " CG1 ILE A 120 " =    1.135
peak=    3.050 closest distance to " O   HOH Z 336 " =    1.575
peak=    3.047 closest distance to " CB  ARG A 139 " =    1.051
peak=    3.031 closest distance to " N   SER A 135 " =    1.273
peak=    3.031 closest distance to " C   ALA A  21 " =    0.969

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.818 - 5.726
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 211
   mapped sites are within: 0.818 - 5.726

peak=   -4.583 closest distance to " O   HOH Z 266 " =    5.032
peak=   -4.478 closest distance to " CG  GLN A  58 " =    1.072
peak=   -4.434 closest distance to " C   HIS A 108 " =    1.077
peak=   -4.431 closest distance to " OG BSER A 134 " =    1.287
peak=   -4.306 closest distance to " CG1 VAL A 112 " =    2.837
peak=   -4.279 closest distance to " CA  VAL A  67 " =    2.833
peak=   -4.270 closest distance to " CG  GLN A 223 " =    2.115
peak=   -4.227 closest distance to " CD  ARG A 156 " =    2.097
peak=   -4.209 closest distance to " CD  ARG A  14 " =    3.304
peak=   -4.148 closest distance to " N   ALA A 248 " =    1.728
peak=   -4.138 closest distance to " O   PRO A 198 " =    1.232
peak=   -4.114 closest distance to " OXT GLY A 302 " =    2.818
peak=   -4.103 closest distance to " ND2 ASN A  45 " =    0.987
peak=   -4.100 closest distance to " CB  PRO A 280 " =    2.137
peak=   -4.092 closest distance to " CB  PRO A 243 " =    2.658
peak=   -4.043 closest distance to " O   HOH Z 198 " =    1.668
peak=   -4.011 closest distance to " O   VAL A  67 " =    2.659
peak=   -4.006 closest distance to " CB  PHE A 192 " =    1.968
peak=   -4.005 closest distance to " CE2 TYR A  30 " =    2.844
peak=   -4.003 closest distance to " OD2 ASP A 171 " =    2.351
peak=   -4.002 closest distance to " CB  ASN A  39 " =    2.245
peak=   -3.994 closest distance to " O   HOH Z 231 " =    2.350
peak=   -3.948 closest distance to " O   HOH Z 351 " =    1.446
peak=   -3.941 closest distance to " OD2 ASP A 191 " =    1.396
peak=   -3.909 closest distance to " CZ  TYR A 169 " =    1.812
peak=   -3.907 closest distance to " O   HOH Z 165 " =    2.060
peak=   -3.905 closest distance to " O   HOH Z  13 " =    1.632
peak=   -3.857 closest distance to " OG  SER A   3 " =    1.673
peak=   -3.855 closest distance to " N   GLN A  58 " =    1.747
peak=   -3.838 closest distance to " O   HOH Z 372 " =    2.148
peak=   -3.794 closest distance to " CE  MET A 105 " =    2.389
peak=   -3.780 closest distance to " O   HOH Z 102 " =    1.765
peak=   -3.780 closest distance to " O   PHE A 218 " =    1.670
peak=   -3.775 closest distance to " O   HOH Z 407 " =    2.516
peak=   -3.759 closest distance to " O   PRO A 163 " =    1.966
peak=   -3.755 closest distance to " O   HOH Z 353 " =    2.231
peak=   -3.745 closest distance to " CD  ARG A 139 " =    1.520
peak=   -3.743 closest distance to " CB  ALA A 161 " =    2.476
peak=   -3.731 closest distance to " CD1 LEU A 101 " =    2.387
peak=   -3.727 closest distance to " O   HOH Z 185 " =    2.317
peak=   -3.718 closest distance to " CB  PHE A 208 " =    2.241
peak=   -3.713 closest distance to " O   HOH Z   6 " =    2.060
peak=   -3.693 closest distance to " O   ALA A 161 " =    1.587
peak=   -3.689 closest distance to " O   HOH Z 313 " =    1.867
peak=   -3.682 closest distance to " O   VAL A 174 " =    2.179
peak=   -3.680 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.641 closest distance to " CG  PHE A 283 " =    2.645
peak=   -3.639 closest distance to " CD2 TYR A 247 " =    2.462
peak=   -3.638 closest distance to " CG1 VAL A  78 " =    3.007
peak=   -3.629 closest distance to " O   HOH Z 109 " =    5.726
peak=   -3.628 closest distance to " ND2 ASN A  39 " =    1.202
peak=   -3.619 closest distance to " C   GLN A 205 " =    1.801
peak=   -3.615 closest distance to " CZ  ARG A  66 " =    1.122
peak=   -3.605 closest distance to " CD1 LEU A 255 " =    2.690
peak=   -3.604 closest distance to " N   ALA A 248 " =    2.194
peak=   -3.599 closest distance to " ND2 ASN A 187 " =    1.547
peak=   -3.596 closest distance to " CA  GLY A 203 " =    2.388
peak=   -3.591 closest distance to " O   SER A  95 " =    1.499
peak=   -3.586 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.584 closest distance to " O   HOH Z 183 " =    1.540
peak=   -3.574 closest distance to " O   GLN A  89 " =    1.460
peak=   -3.571 closest distance to " CB  ALA A 248 " =    2.175
peak=   -3.568 closest distance to " CZ3 TRP A 179 " =    1.283
peak=   -3.558 closest distance to " CG2 ILE A 263 " =    2.215
peak=   -3.549 closest distance to " CA  GLY A 241 " =    2.292
peak=   -3.535 closest distance to " NE  ARG A 156 " =    1.909
peak=   -3.532 closest distance to " O   HOH Z 196 " =    2.036
peak=   -3.509 closest distance to " O   HOH Z 139 " =    5.088
peak=   -3.507 closest distance to " O   HOH Z  63 " =    1.516
peak=   -3.506 closest distance to " C   ASP A 231 " =    2.547
peak=   -3.505 closest distance to " CB  ASP A 132 " =    2.237
peak=   -3.499 closest distance to " O   HOH Z 211 " =    1.822
peak=   -3.491 closest distance to " O   SER A 210 " =    1.987
peak=   -3.482 closest distance to " O   ILE A  49 " =    1.737
peak=   -3.479 closest distance to " N   ASP A 286 " =    2.184
peak=   -3.469 closest distance to " OD1 ASP A 191 " =    1.534
peak=   -3.452 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.451 closest distance to " O   ALA A  34 " =    2.257
peak=   -3.451 closest distance to " O   HOH Z 369 " =    2.153
peak=   -3.449 closest distance to " O   HOH Z 126 " =    1.908
peak=   -3.448 closest distance to " O   HOH Z 417 " =    2.282
peak=   -3.447 closest distance to " O   HOH Z 243 " =    1.949
peak=   -3.443 closest distance to " O   HOH Z 200 " =    4.843
peak=   -3.436 closest distance to " O   HOH Z 281 " =    2.696
peak=   -3.436 closest distance to " OG  SER A  97 " =    2.125
peak=   -3.424 closest distance to " N   THR A 235 " =    1.333
peak=   -3.419 closest distance to " O   MET A  40 " =    2.705
peak=   -3.417 closest distance to " O   HOH Z 394 " =    1.496
peak=   -3.413 closest distance to " O   HOH Z 166 " =    2.017
peak=   -3.412 closest distance to " O   HOH Z 427 " =    1.472
peak=   -3.397 closest distance to " CB  GLN A  11 " =    1.834
peak=   -3.392 closest distance to " O   HOH Z 421 " =    3.274
peak=   -3.386 closest distance to " CD  GLU A 236 " =    1.034
peak=   -3.382 closest distance to " O   TRP A  92 " =    1.775
peak=   -3.380 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.379 closest distance to " O   HOH Z 309 " =    2.552
peak=   -3.379 closest distance to " OE1 GLN A 183 " =    1.474
peak=   -3.377 closest distance to " CD1 LEU A  25 " =    2.509
peak=   -3.376 closest distance to " O   HOH Z  11 " =    1.787
peak=   -3.374 closest distance to " O   HOH Z 197 " =    5.067
peak=   -3.372 closest distance to " C   MET A 188 " =    1.507
peak=   -3.370 closest distance to " NE2 GLN A  88 " =    1.744
peak=   -3.370 closest distance to " O   HOH Z 114 " =    3.202
peak=   -3.369 closest distance to " C   THR A 279 " =    1.277
peak=   -3.368 closest distance to " NH1 ARG A 195 " =    2.613
peak=   -3.360 closest distance to " O   GLU A 152 " =    1.362
peak=   -3.359 closest distance to " O   HOH Z 326 " =    1.671
peak=   -3.353 closest distance to " CG  TRP A 266 " =    2.023
peak=   -3.351 closest distance to " OXT GLY A 302 " =    3.364
peak=   -3.348 closest distance to " O   HOH Z  15 " =    1.520
peak=   -3.347 closest distance to " N   ALA A  43 " =    2.582
peak=   -3.346 closest distance to " CD2 PHE A 225 " =    1.279
peak=   -3.346 closest distance to " O  BHOH Z 338 " =    1.374
peak=   -3.341 closest distance to " CG2 ILE A  49 " =    2.627
peak=   -3.339 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.338 closest distance to " CD2 LEU A 237 " =    2.355
peak=   -3.337 closest distance to " CD2 TYR A 293 " =    1.996
peak=   -3.335 closest distance to " CB  ALA A 248 " =    2.201
peak=   -3.333 closest distance to " O   PRO A 198 " =    1.229
peak=   -3.333 closest distance to " O   HOH Z 389 " =    1.768
peak=   -3.330 closest distance to " O   HOH Z 423 " =    2.199
peak=   -3.329 closest distance to " CB  ASP A 286 " =    1.836
peak=   -3.328 closest distance to " O   HOH Z 377 " =    1.484
peak=   -3.325 closest distance to " CZ  PHE A  59 " =    1.470
peak=   -3.324 closest distance to " CB  ASP A 286 " =    2.171
peak=   -3.319 closest distance to " NH2AARG A 275 " =    4.917
peak=   -3.318 closest distance to " O   SER A 146 " =    1.090
peak=   -3.318 closest distance to " CB  SER A 210 " =    1.185
peak=   -3.314 closest distance to " O   LEU A 167 " =    1.526
peak=   -3.314 closest distance to " O   ALA A 292 " =    2.105
peak=   -3.310 closest distance to " O   HOH Z  38 " =    1.717
peak=   -3.310 closest distance to " CG1 VAL A 230 " =    1.921
peak=   -3.309 closest distance to " CB  PRO A 163 " =    2.515
peak=   -3.297 closest distance to " CZ  PHE A 130 " =    0.907
peak=   -3.296 closest distance to " O   HOH Z 250 " =    1.385
peak=   -3.295 closest distance to " CG  GLU A   2 " =    1.930
peak=   -3.291 closest distance to " C   LEU A 143 " =    1.006
peak=   -3.289 closest distance to " OG BSER A 134 " =    1.674
peak=   -3.283 closest distance to " O   ASN A 187 " =    1.482
peak=   -3.282 closest distance to " CZ3 TRP A 274 " =    2.291
peak=   -3.278 closest distance to " N   PRO A 163 " =    1.657
peak=   -3.272 closest distance to " O   HOH Z 139 " =    3.151
peak=   -3.268 closest distance to " CG  GLU A  53 " =    1.418
peak=   -3.268 closest distance to " ND2 ASN A 249 " =    2.360
peak=   -3.259 closest distance to " O   HOH Z 256 " =    1.339
peak=   -3.258 closest distance to " OH  TYR A 169 " =    0.940
peak=   -3.257 closest distance to " O   HOH Z 263 " =    2.923
peak=   -3.252 closest distance to " NE2 GLN A 194 " =    1.787
peak=   -3.248 closest distance to " O   ASN A  45 " =    1.844
peak=   -3.247 closest distance to " O   HOH Z 385 " =    1.985
peak=   -3.242 closest distance to " ND2 ASN A  69 " =    1.676
peak=   -3.241 closest distance to " OD1 ASN A 301 " =    1.936
peak=   -3.239 closest distance to " OD1 ASP A 191 " =    1.570
peak=   -3.239 closest distance to " CG2 THR A 178 " =    2.167
peak=   -3.239 closest distance to " OD2 ASP A  50 " =    1.387
peak=   -3.237 closest distance to " O   HOH Z 148 " =    3.700
peak=   -3.237 closest distance to " OH  TYR A 172 " =    1.841
peak=   -3.230 closest distance to " OD1 ASP A 171 " =    1.494
peak=   -3.227 closest distance to " O   ILE A 106 " =    1.801
peak=   -3.216 closest distance to " N   THR A 157 " =    1.519
peak=   -3.216 closest distance to " C   ALA A 158 " =    1.364
peak=   -3.214 closest distance to " CA  GLY A 241 " =    3.155
peak=   -3.211 closest distance to " OE2 GLU A 152 " =    1.315
peak=   -3.209 closest distance to " C   ALA A 114 " =    2.141
peak=   -3.208 closest distance to " O   SER A   3 " =    1.001
peak=   -3.208 closest distance to " NE2 GLN A  88 " =    1.194
peak=   -3.208 closest distance to " ND2 ASN A 209 " =    1.847
peak=   -3.208 closest distance to " CG  GLU A 152 " =    1.038
peak=   -3.207 closest distance to " O   SER A 135 " =    1.476
peak=   -3.207 closest distance to " O   HOH Z 414 " =    1.527
peak=   -3.206 closest distance to " CD1 ILE A 106 " =    2.219
peak=   -3.201 closest distance to " CD1 PHE A  59 " =    1.915
peak=   -3.199 closest distance to " CE1 TYR A 247 " =    2.698
peak=   -3.199 closest distance to " CZ  ARG A 259 " =    0.923
peak=   -3.194 closest distance to " CA  ASN A 127 " =    1.299
peak=   -3.192 closest distance to " O   ALA A  10 " =    1.777
peak=   -3.183 closest distance to " O   HOH Z 119 " =    2.356
peak=   -3.181 closest distance to " N   GLY A  23 " =    2.477
peak=   -3.180 closest distance to " N   ALA A 226 " =    1.869
peak=   -3.175 closest distance to " CB  ASP A 132 " =    2.362
peak=   -3.175 closest distance to " O   HOH Z 123 " =    2.363
peak=   -3.174 closest distance to " O   ARG A 145 " =    1.610
peak=   -3.173 closest distance to " NH2 ARG A  66 " =    5.215
peak=   -3.171 closest distance to " O   ASN A 249 " =    1.254
peak=   -3.169 closest distance to " O   SER A  26 " =    1.180
peak=   -3.166 closest distance to " O   TRP A  70 " =    1.408
peak=   -3.161 closest distance to " O   HOH Z 422 " =    1.569
peak=   -3.158 closest distance to " O   SER A 146 " =    1.074
peak=   -3.157 closest distance to " OD2 ASP A  50 " =    2.199
peak=   -3.157 closest distance to " CA  GLY A 133 " =    1.866
peak=   -3.149 closest distance to " O   GLN A  11 " =    1.271
peak=   -3.148 closest distance to " CE3 TRP A 150 " =    2.225
peak=   -3.146 closest distance to " O   ILE A 120 " =    1.390
peak=   -3.144 closest distance to " O   HOH Z 174 " =    4.049
peak=   -3.138 closest distance to " CZ2 TRP A 274 " =    1.028
peak=   -3.137 closest distance to " N   PHE A  59 " =    1.754
peak=   -3.130 closest distance to " O   HOH Z 397 " =    1.183
peak=   -3.129 closest distance to " O   HOH Z 265 " =    2.272
peak=   -3.125 closest distance to " O   HOH Z  37 " =    1.628
peak=   -3.121 closest distance to " O   HOH Z 134 " =    3.006
peak=   -3.118 closest distance to " O   HOH Z 198 " =    1.543
peak=   -3.113 closest distance to " O   HOH Z 137 " =    1.474
peak=   -3.099 closest distance to " O   HOH Z 234 " =    3.816
peak=   -3.099 closest distance to " OD1 ASN A  39 " =    2.227
peak=   -3.095 closest distance to " OE1 GLN A  88 " =    1.072
peak=   -3.085 closest distance to " ND2 ASN A  60 " =    1.397
peak=   -3.059 closest distance to " CB  LYS A 117 " =    2.456
peak=   -3.058 closest distance to " O   HOH Z  97 " =    1.309
peak=   -3.054 closest distance to " CG1 VAL A 268 " =    2.404
peak=   -3.041 closest distance to " O   HOH Z 210 " =    1.010
peak=   -3.008 closest distance to " CD2 LEU A 300 " =    2.634

================= 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    :  0.3317 0.3317   6.095877e+00   6.094007e+00
   1_bss:  0.3168 0.3188   6.072910e+00   6.072289e+00
   1_xyz:  0.2185 0.2431   5.703084e+00   5.792201e+00
   1_adp:  0.1993 0.2469   5.645500e+00   5.813118e+00
   1_occ:  0.1990 0.2467   5.644832e+00   5.812713e+00
   2_bss:  0.1934 0.2418   5.623488e+00   5.795044e+00
   2_xyz:  0.1411 0.1814   5.331054e+00   5.524629e+00
   2_adp:  0.1325 0.1726   5.273721e+00   5.471055e+00
   2_occ:  0.1323 0.1724   5.272473e+00   5.469951e+00
   3_bss:  0.1321 0.1715   5.268193e+00   5.462543e+00
   3_xyz:  0.1197 0.1587   5.184565e+00   5.393381e+00
   3_adp:  0.1177 0.1579   5.173050e+00   5.386203e+00
   3_occ:  0.1176 0.1579   5.172526e+00   5.385991e+00
   4_bss:  0.1176 0.1578   5.172111e+00   5.385441e+00
   4_xyz:  0.1080 0.1535   5.117389e+00   5.356719e+00
   4_adp:  0.1078 0.1526   5.113446e+00   5.351076e+00
   4_occ:  0.1077 0.1527   5.113237e+00   5.351359e+00
   5_bss:  0.1073 0.1522   5.111272e+00   5.348449e+00
   5_xyz:  0.1104 0.1533   5.131538e+00   5.359600e+00
   5_adp:  0.1090 0.1549   5.131083e+00   5.371013e+00
   5_occ:  0.1090 0.1549   5.131190e+00   5.371342e+00
   5_bss:  0.1089 0.1548   5.131134e+00   5.371173e+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:  0.349  50.000   1.900  -2.796  -1.533  -0.000  -0.000  -0.000
   1_xyz:  0.349  50.000   1.900  -2.796  -1.533  -0.000  -0.000  -0.000
   1_adp:  0.349  50.000   1.900  -2.796  -1.533  -0.000  -0.000  -0.000
   1_occ:  0.349  50.000   1.900  -2.796  -1.533  -0.000  -0.000  -0.000
   2_bss:  0.323  40.818  -2.072  -2.780  -1.673  -0.000  -0.000  -0.000
   2_xyz:  0.323  40.818  -2.072  -2.780  -1.673  -0.000  -0.000  -0.000
   2_adp:  0.323  40.818  -2.072  -2.780  -1.673  -0.000  -0.000  -0.000
   2_occ:  0.323  40.818  -2.072  -2.780  -1.673  -0.000  -0.000  -0.000
   3_bss:  0.318  40.818  -3.091  -2.578  -1.557  -0.000  -0.000  -0.000
   3_xyz:  0.318  40.818  -3.091  -2.578  -1.557  -0.000  -0.000  -0.000
   3_adp:  0.318  40.818  -3.091  -2.578  -1.557  -0.000  -0.000  -0.000
   3_occ:  0.318  40.818  -3.091  -2.578  -1.557  -0.000  -0.000  -0.000
   4_bss:  0.318  40.818  -3.332  -2.534  -1.495  -0.000  -0.000  -0.000
   4_xyz:  0.318  40.818  -3.332  -2.534  -1.495  -0.000  -0.000  -0.000
   4_adp:  0.318  40.818  -3.332  -2.534  -1.495  -0.000  -0.000  -0.000
   4_occ:  0.318  40.818  -3.332  -2.534  -1.495  -0.000  -0.000  -0.000
   5_bss:  0.320  40.810  -3.323  -2.448  -1.370  -0.000  -0.000  -0.000
   5_xyz:  0.320  40.810  -3.323  -2.448  -1.370  -0.000  -0.000  -0.000
   5_adp:  0.320  40.810  -3.323  -2.448  -1.370  -0.000  -0.000  -0.000
   5_occ:  0.320  40.810  -3.323  -2.448  -1.370  -0.000  -0.000  -0.000
   5_bss:  0.319  41.845  -3.130  -2.212  -1.157  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.979 0.6937  0.8962    35642.117
   1_bss:  34.829 0.7054  0.8924    32356.418
   1_xyz:  23.848 0.8245  0.9938    15503.380
   1_adp:  24.704 0.8148  0.9918    16160.855
   1_occ:  24.713 0.8148  0.9918    16181.330
   2_bss:  24.033 0.8214  0.9477    15331.718
   2_xyz:  17.133 0.8879  0.9879     8377.764
   2_adp:  15.861 0.8996  0.9920     7633.055
   2_occ:  15.835 0.8998  0.9920     7606.815
   3_bss:  15.708 0.9007  0.9827     7461.254
   3_xyz:  14.316 0.9123  0.9865     6440.295
   3_adp:  14.140 0.9139  0.9842     6387.226
   3_occ:  14.138 0.9139  0.9840     6377.323
   4_bss:  14.133 0.9139  0.9821     6370.408
   4_xyz:  13.575 0.9182  0.9839     6029.131
   4_adp:  13.456 0.9193  0.9811     5984.516
   4_occ:  13.458 0.9193  0.9810     5983.840
   5_bss:  13.425 0.9195  0.9838     5939.762
   5_xyz:  13.559 0.9188  0.9830     6072.247
   5_adp:  13.769 0.9171  0.9776     6171.819
   5_occ:  13.772 0.9171  0.9775     6175.036
   5_bss:  13.770 0.9171  0.9835     6172.702
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.1272e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.1272e-01
   1_xyz:   1.205  0.009  0.074 15.036  0.005  4.107   8.0139e-02
   1_adp:   1.205  0.009  0.074 15.036  0.005  4.107   8.0139e-02
   1_occ:   1.205  0.009  0.074 15.036  0.005  4.107   8.0139e-02
   2_bss:   1.205  0.009  0.074 15.036  0.005  4.107   8.0139e-02
   2_xyz:   0.979  0.005  0.069 14.309  0.004  4.116   5.3789e-02
   2_adp:   0.979  0.005  0.069 14.309  0.004  4.116   5.3789e-02
   2_occ:   0.979  0.005  0.069 14.309  0.004  4.116   5.3789e-02
   3_bss:   0.979  0.005  0.069 14.309  0.004  4.116   5.3789e-02
   3_xyz:   0.899  0.005  0.066 14.381  0.004  4.110   4.8547e-02
   3_adp:   0.899  0.005  0.066 14.381  0.004  4.110   4.8547e-02
   3_occ:   0.899  0.005  0.066 14.381  0.004  4.110   4.8547e-02
   4_bss:   0.899  0.005  0.066 14.381  0.004  4.110   4.8547e-02
   4_xyz:   1.109  0.008  0.081 14.954  0.005  4.110   6.9890e-02
   4_adp:   1.109  0.008  0.081 14.954  0.005  4.110   6.9890e-02
   4_occ:   1.109  0.008  0.081 14.954  0.005  4.110   6.9890e-02
   5_bss:   1.109  0.008  0.081 14.954  0.005  4.110   6.9890e-02
   5_xyz:   0.911  0.005  0.069 14.435  0.004  4.110   5.0425e-02
   5_adp:   0.911  0.005  0.069 14.435  0.004  4.110   5.0425e-02
   5_occ:   0.911  0.005  0.069 14.435  0.004  4.110   5.0425e-02
   5_bss:   0.911  0.005  0.069 14.435  0.004  4.110   5.0425e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.225   2.4159e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.225   2.4159e-01
   1_xyz:   8.212  0.055  0.285 82.920  0.046  2.097   9.1309e-02
   1_adp:   8.212  0.055  0.285 82.920  0.046  2.097   9.1309e-02
   1_occ:   8.212  0.055  0.285 82.920  0.046  2.097   9.1309e-02
   2_bss:   8.212  0.055  0.285 82.920  0.046  2.097   9.1309e-02
   2_xyz:   7.165  0.033  0.201 80.470  0.041  2.305   4.3074e-02
   2_adp:   7.165  0.033  0.201 80.470  0.041  2.305   4.3074e-02
   2_occ:   7.165  0.033  0.201 80.470  0.041  2.305   4.3074e-02
   3_bss:   7.165  0.033  0.201 80.470  0.041  2.305   4.3074e-02
   3_xyz:   6.599  0.038  0.194 82.478  0.036  2.379   3.3232e-02
   3_adp:   6.599  0.038  0.194 82.478  0.036  2.379   3.3232e-02
   3_occ:   6.599  0.038  0.194 82.478  0.036  2.379   3.3232e-02
   4_bss:   6.599  0.038  0.194 82.478  0.036  2.379   3.3232e-02
   4_xyz:   7.362  0.049  0.259 83.117  0.040  2.280   5.5516e-02
   4_adp:   7.362  0.049  0.259 83.117  0.040  2.280   5.5516e-02
   4_occ:   7.362  0.049  0.259 83.117  0.040  2.280   5.5516e-02
   5_bss:   7.362  0.049  0.259 83.117  0.040  2.280   5.5516e-02
   5_xyz:   6.277  0.041  0.213 83.446  0.042  2.393   3.2301e-02
   5_adp:   6.277  0.041  0.213 83.446  0.042  2.393   3.2301e-02
   5_occ:   6.277  0.041  0.213 83.446  0.042  2.393   3.2301e-02
   5_bss:   6.277  0.041  0.213 83.446  0.042  2.393   3.2301e-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:  77.25   0.00  17.50  77.25   0.00  13.55  74.30   6.15  39.00
   1_occ:  77.25   0.00  17.50  77.25   0.00  13.55  74.30   6.15  39.00
   2_bss:  77.25   0.00  17.50  77.25   0.00  13.55  74.30   6.15  39.00
   2_xyz:  77.25   0.00  17.50  77.25   0.00  13.55  74.30   6.15  39.00
   2_adp:  85.15   0.00  17.23  85.15   0.00  13.32  73.57   6.26  38.54
   2_occ:  85.15   0.00  17.23  85.15   0.00  13.32  73.57   6.26  38.54
   3_bss:  85.15   0.00  17.23  85.15   0.00  13.32  73.57   6.26  38.54
   3_xyz:  85.15   0.00  17.23  85.15   0.00  13.32  73.57   6.26  38.54
   3_adp:  88.89   1.67  17.08  88.89   1.67  13.17  72.44   3.54  38.35
   3_occ:  88.89   1.67  17.08  88.89   1.67  13.17  72.44   3.54  38.35
   4_bss:  88.89   1.67  17.08  88.89   1.67  13.17  72.44   3.54  38.35
   4_xyz:  88.89   1.67  17.08  88.89   1.67  13.17  72.44   3.54  38.35
   4_adp:  87.78   2.34  16.75  87.78   2.50  12.98  70.35   2.34  37.23
   4_occ:  87.78   2.34  16.75  87.78   2.50  12.98  70.35   2.34  37.23
   5_bss:  87.78   2.34  16.75  87.78   2.50  12.98  70.35   2.34  37.23
   5_xyz:  87.78   2.34  16.75  87.78   2.50  12.98  70.35   2.34  37.23
   5_adp:  94.30   1.22  17.23  94.30   1.22  13.08  79.56   3.21  39.84
   5_occ:  94.30   1.22  17.23  94.30   1.22  13.08  79.56   3.21  39.84
   5_bss:  94.25   1.18  17.19  94.25   1.18  13.04  79.52   3.17  39.80
------------------------------------------------------------------------
 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:    2.257    0.014    0.302
   1_adp:    2.257    0.014    0.302
   1_occ:    2.257    0.014    0.302
   2_bss:    2.257    0.014    0.302
   2_xyz:    1.813    0.009    0.378
   2_adp:    1.813    0.009    0.378
   2_occ:    1.813    0.009    0.378
   3_bss:    1.813    0.009    0.378
   3_xyz:    1.633    0.007    0.414
   3_adp:    1.633    0.007    0.414
   3_occ:    1.633    0.007    0.414
   4_bss:    1.633    0.007    0.414
   4_xyz:    1.567    0.005    0.433
   4_adp:    1.567    0.005    0.433
   4_occ:    1.567    0.005    0.433
   5_bss:    1.567    0.005    0.433
   5_xyz:    1.522    0.013    0.437
   5_adp:    1.522    0.013    0.437
   5_occ:    1.522    0.013    0.437
   5_bss:    1.522    0.013    0.437
------------------------------------------------------------------------

CPU time actual refinement: 320.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_60/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_60/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_60/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_60/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_60/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.21 
  Macro-tasks:
    bulk solvent and scale       = 36.10  
    individual site refinement   = 131.18 
    weights calculation          = 28.70  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 202.58 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 102.76 
    alpha_beta                      = 8.16   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 110.87 
    fmodel                         = 6.42   
    r_factors                      = 0.11   
    phase_errors                   = 11.23  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 242.74 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.600 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    630 calls, 102.35 s
gradients_fft:          575 calls,  98.01 s

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

# Date 2008-01-16 Time 03:54:51 PST -0800 (1200484491.27 s)
Start R-work = 0.3317, R-free = 0.3317 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1759 (no bulk solvent and anisotropic scale)

Start R-work = 0.3168, R-free = 0.3188
Final R-work = 0.1089, R-free = 0.1548