# Date 2008-01-16 Time 05:00:14 PST -0800 (1200488414.25 s)
#phil __OFF__

Command line arguments: "../550.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7685
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 550

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.1647, 84.2302, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95136
Completeness in resolution range: 0.940061
Completeness with d_max=infinity: 0.937228

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8359
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95136
Completeness in resolution range: 0.940061
Completeness with d_max=infinity: 0.937228

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8363 -  4.1758 [2193/2222]  1974   219  10.0%
  bin  2:  4.1758 -  3.3267 [2092/2115]  1885   207   9.9%
  bin  3:  3.3267 -  2.9098 [2065/2090]  1852   213  10.3%
  bin  4:  2.9098 -  2.6454 [2070/2086]  1871   199   9.6%
  bin  5:  2.6454 -  2.4567 [2033/2071]  1824   209  10.3%
  bin  6:  2.4567 -  2.3124 [2041/2074]  1840   201   9.8%
  bin  7:  2.3124 -  2.1970 [2008/2045]  1805   203  10.1%
  bin  8:  2.1970 -  2.1016 [2001/2043]  1803   198   9.9%
  bin  9:  2.1016 -  2.0209 [2011/2049]  1807   204  10.1%
  bin 10:  2.0209 -  1.9514 [1075/2043]   969   106   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_550/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:
        1.53 -     2.20: 26
        2.20 -     2.88: 1271
        2.88 -     3.55: 4506
        3.55 -     4.23: 9316
        4.23 -     4.90: 13581
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.526 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.592 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.614 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.746 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28695 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_550/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_550/model_refine_001.geo

CPU time processing inputs: 9.23


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.16465 84.23025 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 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3784   r_free= 0.3769   ksol= 0.00   Bsol= 0.00   scale= 0.952    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.169149                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6576 0.99   1418  161 0.3142 0.3207      6.4417      6.4568|
|  2:  4.6576 -  3.7160 0.99   1369  145 0.3102 0.2905      6.6145      6.5545|
|  3:  3.7160 -  3.2519 0.99   1335  154 0.3316 0.3458      6.4913      6.6554|
|  4:  3.2519 -  2.9571 0.99   1338  149 0.3533 0.3495      6.3637      6.3663|
|  5:  2.9571 -  2.7466 0.98   1324  146 0.3859 0.3477      6.2346      6.1917|
|  6:  2.7466 -  2.5856 0.99   1310  143 0.4006 0.4048      6.1516      6.0926|
|  7:  2.5856 -  2.4567 0.99   1312  149 0.4000 0.3391      6.1363      6.0592|
|  8:  2.4567 -  2.3502 0.99   1299  145 0.4070 0.4477      6.0605      6.1261|
|  9:  2.3502 -  2.2600 0.99   1305  147 0.4258 0.4174      6.0482      6.0369|
| 10:  2.2600 -  2.1823 0.98   1307  140 0.4276 0.4641      6.0211      6.0801|
| 11:  2.1823 -  2.1143 0.98   1283  138 0.4485 0.4692      5.9699      6.0359|
| 12:  2.1143 -  2.0540 1.00   1277  149 0.4251 0.4344      5.8882      5.9291|
| 13:  2.0540 -  2.0000 0.95   1274  144 0.4481 0.4562      5.8191      5.8091|
| 14:  2.0000 -  1.9514 0.36    479   49 0.5215 0.4953      5.8473      5.7193|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6576  1418   161  0.75  29.92   0.86     0.77      53609.07|
|  2:  4.6576 -  3.7160  1369   145  0.78  27.82   0.96     0.88      68623.20|
|  3:  3.7160 -  3.2519  1335   154  0.73  33.04   0.97     0.91      70855.38|
|  4:  3.2519 -  2.9571  1338   149  0.67  38.22   0.99     0.89      62701.01|
|  5:  2.9571 -  2.7466  1324   146  0.63  41.73   0.95     0.85      50278.14|
|  6:  2.7466 -  2.5856  1310   143  0.62  42.45   0.97     0.83      42242.52|
|  7:  2.5856 -  2.4567  1312   149  0.63  41.69   0.99     0.83      38264.28|
|  8:  2.4567 -  2.3502  1299   145  0.58  45.79   0.97     0.79      37534.16|
|  9:  2.3502 -  2.2600  1305   147  0.54  48.85   1.00     0.75      37295.40|
| 10:  2.2600 -  2.1823  1307   140  0.50  52.01   1.03     0.70      38134.18|
| 11:  2.1823 -  2.1143  1283   138  0.47  54.60   1.01     0.69      36662.61|
| 12:  2.1143 -  2.0540  1277   149  0.46  55.23   1.03     0.71      34889.07|
| 13:  2.0540 -  2.0000  1274   144  0.46  55.80   0.99     0.70      29687.46|
| 14:  2.0000 -  1.9514   479    49  0.45  55.81   0.96     0.66      24937.56|
|alpha:            min =        0.66 max =            0.91 mean =         0.79|
|beta:             min =    24937.56 max =        70855.38 mean =     45898.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.73|
|phase err.(test): min =        0.00 max =           89.98 mean =        43.51|
|-----------------------------------------------------------------------------|

============================== 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 = 5.134688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.809   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.265698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.006   (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 |  1.526 -  1.864:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.864 -  2.201:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.201 -  2.539:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.539 -  2.876:     1232 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.876 -  3.213:     1960 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.213 -  3.551:     2546 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.551 -  3.888:     4692 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.888 -  4.225:     4624 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.225 -  4.563:     6155 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.563 -  4.900:     7426 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.526 |       0.509 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    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 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3784   r_free= 0.3769   ksol= 0.00   Bsol= 0.00   scale= 0.952    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.169149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3637   r_free= 0.3597   ksol= 0.30   Bsol= 20.00   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-1.92,3.54,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.153455                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.254350              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.702   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.629329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.967   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3637      final r-factor (work) = 0.2629          |
| start r-factor (free) = 0.3597      final r-factor (free) = 0.2914          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2725 = 4.25 * 0.50 * 6.1535 + 1.00 * 0.1830                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7881 = 4.25 * 0.50 * 5.9705 + 1.00 * 0.0877                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2629      final r-factor (work) = 0.2434          |
| start r-factor (free) = 0.2914      final r-factor (free) = 0.3005          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7637 = 0.63 * 1.00 * 5.9705 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6998 = 0.63 * 1.00 * 5.8167 + 1.00 * 0.0392                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.21   17.14    None  None   None       |
|    all(noH): 2823   0      0.00    83.21   17.14    None  None   None       |
|    Sol.    : 438    0      4.34    63.57   37.87    None  None   None       |
|    Mac.    : 2385   0      0.00    83.21   13.33    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 -   8.321:  658   |   5:    41.604 -  49.925:  113        |
|      1:     8.321 -  16.642: 1128   |   6:    49.925 -  58.246:   76        |
|      2:    16.642 -  24.963:  497   |   7:    58.246 -  66.567:   12        |
|      3:    24.963 -  33.283:  184   |   8:    66.567 -  74.887:    0        |
|      4:    33.283 -  41.604:  154   |   9:    74.887 -  83.208:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2434 r_free = 0.3005             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2431 r_free = 0.3015             target_work(ml) = 5.826         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2431   r_free= 0.3015   ksol= 0.30   Bsol= 20.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-1.92,3.54,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.826326                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2405   r_free= 0.2964   ksol= 0.32   Bsol= 39.65   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-1.94,0.45,-0.00,0.00,0.00); trace/3= -1.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.819130                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.267406              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.443   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.393084              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.855   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2405      final r-factor (work) = 0.1650          |
| start r-factor (free) = 0.2964      final r-factor (free) = 0.2163          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4006 = 5.27 * 0.50 * 5.8142 + 1.00 * 0.0877                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9905 = 5.27 * 0.50 * 5.6667 + 1.00 * 0.0662                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1650      final r-factor (work) = 0.1481          |
| start r-factor (free) = 0.2163      final r-factor (free) = 0.1965          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2718 = 0.39 * 1.00 * 5.6667 + 1.00 * 0.0443                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1418 = 0.39 * 1.00 * 5.4269 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    74.76   17.37    None  None   None       |
|    all(noH): 2823   0      0.93    74.76   17.37    None  None   None       |
|    Sol.    : 438    0      2.47    74.76   39.87    None  None   None       |
|    Mac.    : 2385   0      0.93    73.64   13.24    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:     0.925 -   8.309:  608   |   5:    37.845 -  45.229:  116        |
|      1:     8.309 -  15.693: 1254   |   6:    45.229 -  52.613:  102        |
|      2:    15.693 -  23.077:  380   |   7:    52.613 -  59.997:   65        |
|      3:    23.077 -  30.461:  141   |   8:    59.997 -  67.381:   24        |
|      4:    30.461 -  37.845:  118   |   9:    67.381 -  74.765:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1481 r_free = 0.1965             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1478 r_free = 0.1965             target_work(ml) = 5.378         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1478   r_free= 0.1965   ksol= 0.32   Bsol= 39.65   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-1.94,0.45,-0.00,0.00,0.00); trace/3= -1.45                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.378452                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1471   r_free= 0.1944   ksol= 0.32   Bsol= 39.65   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.20,-1.34,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.370581                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.786472              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.695   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340953              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.619  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1471      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1944      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9146 = 1.79 * 0.50 * 5.4279 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7921 = 1.79 * 0.50 * 5.3107 + 1.00 * 0.0484                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1267      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8192 = 0.34 * 1.00 * 5.3107 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7899 = 0.34 * 1.00 * 5.2255 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.13   17.26    None  None   None       |
|    all(noH): 2823   0      0.00    80.13   17.26    None  None   None       |
|    Sol.    : 438    0      2.26    78.30   39.97    None  None   None       |
|    Mac.    : 2385   0      0.00    80.13   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.013:  511   |   5:    40.066 -  48.079:  131        |
|      1:     8.013 -  16.026: 1426   |   6:    48.079 -  56.092:   90        |
|      2:    16.026 -  24.039:  359   |   7:    56.092 -  64.105:   44        |
|      3:    24.039 -  32.053:  127   |   8:    64.105 -  72.118:   22        |
|      4:    32.053 -  40.066:  104   |   9:    72.118 -  80.131:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1654             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1215 r_free = 0.1653             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1653   ksol= 0.32   Bsol= 39.65   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,-2.20,-1.34,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.208860                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1652   ksol= 0.31   Bsol= 39.12   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.17,-1.82,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.207584                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.395111              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.586  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.661672              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.077  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3053 = 2.40 * 0.50 * 5.2247 + 1.00 * 0.0484                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2525 = 2.40 * 0.50 * 5.1692 + 1.00 * 0.0621                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4286 = 0.66 * 1.00 * 5.1692 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4038 = 0.66 * 1.00 * 5.1309 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    89.77   17.24    None  None   None       |
|    all(noH): 2823   0      0.81    89.77   17.24    None  None   None       |
|    Sol.    : 438    0      1.78    80.83   40.31    None  None   None       |
|    Mac.    : 2385   0      0.81    89.77   13.01    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:     0.807 -   9.703:  939   |   5:    45.287 -  54.183:  110        |
|      1:     9.703 -  18.599: 1180   |   6:    54.183 -  63.079:   66        |
|      2:    18.599 -  27.495:  239   |   7:    63.079 -  71.975:   23        |
|      3:    27.495 -  36.391:  129   |   8:    71.975 -  80.871:   15        |
|      4:    36.391 -  45.287:  119   |   9:    80.871 -  89.767:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1093 r_free = 0.1570             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1568             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1568   ksol= 0.31   Bsol= 39.12   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.17,-1.82,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130419                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1568   ksol= 0.32   Bsol= 41.26   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.08,-1.87,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131992                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.378630              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.195  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420566              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.514  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1652 = 2.38 * 0.50 * 5.1316 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1532 = 2.38 * 0.50 * 5.1243 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1640 = 0.42 * 1.00 * 5.1243 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1633 = 0.42 * 1.00 * 5.1236 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.38    93.69   16.95    None  None   None       |
|    all(noH): 2823   0      1.38    93.69   16.95    None  None   None       |
|    Sol.    : 438    0      3.48    79.42   39.28    None  None   None       |
|    Mac.    : 2385   0      1.38    93.69   12.85    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:     1.381 -  10.611: 1169   |   5:    47.533 -  56.764:  101        |
|      1:    10.611 -  19.842: 1016   |   6:    56.764 -  65.994:   45        |
|      2:    19.842 -  29.072:  207   |   7:    65.994 -  75.225:   14        |
|      3:    29.072 -  38.303:  134   |   8:    75.225 -  84.455:    8        |
|      4:    38.303 -  47.533:  125   |   9:    84.455 -  93.686:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1070 r_free = 0.1565             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1070 r_free = 0.1565             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1565   ksol= 0.32   Bsol= 41.26   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.08,-1.87,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.123819                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6576 0.99   1418  161 0.0956 0.1257      5.3502      5.5305|
|  2:  4.6576 -  3.7160 0.99   1369  145 0.0818 0.1084      5.3973      5.6144|
|  3:  3.7160 -  3.2519 0.99   1335  154 0.1006 0.1499      5.4319      5.8147|
|  4:  3.2519 -  2.9571 0.99   1338  149 0.1182 0.1536      5.4376      5.6075|
|  5:  2.9571 -  2.7466 0.98   1324  146 0.1225 0.1733        5.28      5.4776|
|  6:  2.7466 -  2.5856 0.99   1310  143 0.1172 0.1875      5.1852      5.4309|
|  7:  2.5856 -  2.4567 0.99   1312  149 0.1165 0.1659       5.113      5.3553|
|  8:  2.4567 -  2.3502 0.99   1299  145 0.1124 0.1740       5.045      5.2762|
|  9:  2.3502 -  2.2600 0.99   1305  147 0.1133 0.1840      5.0053      5.3039|
| 10:  2.2600 -  2.1823 0.98   1307  140 0.1081 0.1696      4.9544      5.1927|
| 11:  2.1823 -  2.1143 0.98   1283  138 0.1096 0.1853      4.9107      5.2994|
| 12:  2.1143 -  2.0540 1.00   1277  149 0.1046 0.1601      4.8345      5.0415|
| 13:  2.0540 -  2.0000 0.95   1274  144 0.1103 0.1754      4.7639      5.0409|
| 14:  2.0000 -  1.9514 0.36    479   49 0.1049 0.1670      4.6655      4.9175|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6576  1418   161  0.94   8.49   0.98     0.96       6571.98|
|  2:  4.6576 -  3.7160  1369   145  0.95   7.64   1.02     1.01       8376.25|
|  3:  3.7160 -  3.2519  1335   154  0.94  10.92   1.03     1.03       9830.54|
|  4:  3.2519 -  2.9571  1338   149  0.92  13.83   1.01     0.99      10327.53|
|  5:  2.9571 -  2.7466  1324   146  0.90  15.58   1.00     0.97       7836.84|
|  6:  2.7466 -  2.5856  1310   143  0.90  15.78   0.99     0.96       6822.34|
|  7:  2.5856 -  2.4567  1312   149  0.91  14.66   0.99     0.96       5635.98|
|  8:  2.4567 -  2.3502  1299   145  0.91  15.39   1.00     0.97       5331.46|
|  9:  2.3502 -  2.2600  1305   147  0.91  15.55   1.00     0.97       4838.26|
| 10:  2.2600 -  2.1823  1307   140  0.91  15.25   1.00     0.96       4447.44|
| 11:  2.1823 -  2.1143  1283   138  0.90  16.23   1.00     0.97       4262.37|
| 12:  2.1143 -  2.0540  1277   149  0.92  14.70   1.00     0.99       3719.42|
| 13:  2.0540 -  2.0000  1274   144  0.90  16.35   1.00     1.00       3266.58|
| 14:  2.0000 -  1.9514   479    49  0.91  15.28   0.99     0.95       2636.16|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2636.16 max =        10327.53 mean =      6190.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.84|
|phase err.(test): min =        0.00 max =           89.07 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1565   ksol= 0.32   Bsol= 41.39   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.89,-1.71,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.124018                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1565   ksol= 0.32   Bsol= 41.39   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.89,-1.71,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.124018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6576 0.99   1418  161 0.0956 0.1258      5.3526       5.533|
|  2:  4.6576 -  3.7160 0.99   1369  145 0.0818 0.1083      5.3976      5.6137|
|  3:  3.7160 -  3.2519 0.99   1335  154 0.1006 0.1499      5.4316      5.8146|
|  4:  3.2519 -  2.9571 0.99   1338  149 0.1182 0.1536      5.4376      5.6076|
|  5:  2.9571 -  2.7466 0.98   1324  146 0.1225 0.1734        5.28      5.4774|
|  6:  2.7466 -  2.5856 0.99   1310  143 0.1172 0.1876      5.1854      5.4313|
|  7:  2.5856 -  2.4567 0.99   1312  149 0.1165 0.1659      5.1132      5.3556|
|  8:  2.4567 -  2.3502 0.99   1299  145 0.1125 0.1740      5.0451      5.2761|
|  9:  2.3502 -  2.2600 0.99   1305  147 0.1133 0.1839      5.0054      5.3037|
| 10:  2.2600 -  2.1823 0.98   1307  140 0.1081 0.1696      4.9544      5.1924|
| 11:  2.1823 -  2.1143 0.98   1283  138 0.1096 0.1853      4.9107      5.2994|
| 12:  2.1143 -  2.0540 1.00   1277  149 0.1046 0.1601      4.8343      5.0414|
| 13:  2.0540 -  2.0000 0.95   1274  144 0.1103 0.1753      4.7636      5.0403|
| 14:  2.0000 -  1.9514 0.36    479   49 0.1048 0.1671      4.6655      4.9182|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8363 -  4.6576  1418   161  0.94   8.52   0.98     0.96       6620.51|
|  2:  4.6576 -  3.7160  1369   145  0.95   7.65   1.02     1.01       8397.05|
|  3:  3.7160 -  3.2519  1335   154  0.94  10.91   1.04     1.03       9823.59|
|  4:  3.2519 -  2.9571  1338   149  0.92  13.83   1.01     0.99      10325.14|
|  5:  2.9571 -  2.7466  1324   146  0.90  15.58   1.00     0.98       7837.88|
|  6:  2.7466 -  2.5856  1310   143  0.90  15.78   0.99     0.96       6824.15|
|  7:  2.5856 -  2.4567  1312   149  0.91  14.67   0.99     0.96       5638.23|
|  8:  2.4567 -  2.3502  1299   145  0.91  15.39   1.00     0.98       5331.20|
|  9:  2.3502 -  2.2600  1305   147  0.91  15.55   1.01     0.98       4837.73|
| 10:  2.2600 -  2.1823  1307   140  0.91  15.25   1.00     0.97       4446.13|
| 11:  2.1823 -  2.1143  1283   138  0.90  16.23   1.01     0.98       4261.44|
| 12:  2.1143 -  2.0540  1277   149  0.92  14.69   1.01     0.99       3716.74|
| 13:  2.0540 -  2.0000  1274   144  0.90  16.35   1.01     1.01       3265.45|
| 14:  2.0000 -  1.9514   479    49  0.91  15.28   1.00     0.96       2637.11|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2637.11 max =        10325.14 mean =      6194.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.85|
|phase err.(test): min =        0.00 max =           89.07 mean =        13.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.599)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    93.64   16.90    None  None   None       |
|    all(noH): 2823   0      1.33    93.64   16.90    None  None   None       |
|    Sol.    : 438    0      3.43    79.37   39.23    None  None   None       |
|    Mac.    : 2385   0      1.33    93.64   12.80    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:     1.332 -  10.562: 1169   |   5:    47.484 -  56.715:  101        |
|      1:    10.562 -  19.793: 1016   |   6:    56.715 -  65.945:   45        |
|      2:    19.793 -  29.023:  207   |   7:    65.945 -  75.176:   14        |
|      3:    29.023 -  38.254:  134   |   8:    75.176 -  84.406:    8        |
|      4:    38.254 -  47.484:  125   |   9:    84.406 -  93.637:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.579 - 5.911
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 306
   mapped sites are within: 0.717 - 5.911

peak=    5.533 closest distance to " NH2 ARG A  56 " =    2.139
peak=    5.520 closest distance to " CG  PRO A  54 " =    1.217
peak=    5.319 closest distance to " CB  GLN A 223 " =    1.423
peak=    5.257 closest distance to " O   HOH Z 142 " =    1.718
peak=    5.227 closest distance to " O   HOH Z 126 " =    1.839
peak=    5.223 closest distance to " CB  SER A  63 " =    1.171
peak=    5.220 closest distance to " CG  PRO A 213 " =    1.230
peak=    5.176 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.878 closest distance to " O   HOH Z 193 " =    1.826
peak=    4.857 closest distance to " NE2 GLN A  11 " =    1.068
peak=    4.819 closest distance to " CB  GLN A 183 " =    1.290
peak=    4.763 closest distance to " O   HOH Z 272 " =    1.844
peak=    4.746 closest distance to " O   HOH Z  78 " =    1.762
peak=    4.726 closest distance to " C   PRO A 198 " =    1.524
peak=    4.693 closest distance to " O   HOH Z 124 " =    1.431
peak=    4.680 closest distance to " O   HOH Z 234 " =    3.722
peak=    4.662 closest distance to " O   HOH Z 232 " =    2.302
peak=    4.609 closest distance to " CB  ASN A 148 " =    1.616
peak=    4.550 closest distance to " CB  PRO A  54 " =    0.919
peak=    4.547 closest distance to " CG  PRO A  90 " =    1.110
peak=    4.456 closest distance to " O   HOH Z 427 " =    2.819
peak=    4.440 closest distance to " CB  GLU A 152 " =    1.157
peak=    4.409 closest distance to " O   HOH Z 236 " =    1.959
peak=    4.400 closest distance to " CB  SER A   3 " =    1.311
peak=    4.372 closest distance to " O   HOH Z 368 " =    1.962
peak=    4.354 closest distance to " CB  TYR A 169 " =    0.778
peak=    4.335 closest distance to " OD2 ASP A 286 " =    2.755
peak=    4.313 closest distance to " OD1 ASN A  69 " =    2.613
peak=    4.301 closest distance to " O   HOH Z 298 " =    1.880
peak=    4.284 closest distance to " O   HOH Z 209 " =    2.227
peak=    4.284 closest distance to " O   HOH Z 203 " =    1.801
peak=    4.254 closest distance to " O   HOH Z  15 " =    2.114
peak=    4.254 closest distance to " CA  TYR A  30 " =    0.947
peak=    4.254 closest distance to " O   HOH Z  97 " =    1.900
peak=    4.224 closest distance to " ND2 ASN A 187 " =    1.537
peak=    4.215 closest distance to " CB  GLU A 128 " =    1.107
peak=    4.208 closest distance to " CB  ARG A  79 " =    1.410
peak=    4.192 closest distance to " O   HOH Z 344 " =    2.936
peak=    4.179 closest distance to " O   HOH Z 108 " =    1.351
peak=    4.177 closest distance to " O   HOH Z 316 " =    2.929
peak=    4.176 closest distance to " O   HOH Z 389 " =    1.852
peak=    4.173 closest distance to " CA  ALA A  21 " =    1.116
peak=    4.149 closest distance to " CB  TRP A 179 " =    1.277
peak=    4.129 closest distance to " O   SER A  87 " =    2.251
peak=    4.113 closest distance to " O   HOH Z 134 " =    1.467
peak=    4.103 closest distance to " O   HOH Z  93 " =    2.468
peak=    4.098 closest distance to " CB  GLU A 277 " =    3.482
peak=    4.089 closest distance to " O   HOH Z  54 " =    1.675
peak=    4.075 closest distance to " OE1 GLU A   2 " =    2.242
peak=    4.073 closest distance to " O   HOH Z 371 " =    3.326
peak=    4.033 closest distance to " CB  LEU A 228 " =    1.096
peak=    4.033 closest distance to " O   HOH Z 128 " =    2.048
peak=    4.032 closest distance to " NZ  LYS A 117 " =    3.198
peak=    4.002 closest distance to " O   HOH Z 278 " =    0.968
peak=    3.992 closest distance to " O   HOH Z 261 " =    2.182
peak=    3.972 closest distance to " CG1 ILE A  33 " =    1.293
peak=    3.962 closest distance to " O   HOH Z 207 " =    1.822
peak=    3.943 closest distance to " NH2BARG A 145 " =    2.024
peak=    3.933 closest distance to " NZ  LYS A 119 " =    1.640
peak=    3.932 closest distance to " O   HOH Z 346 " =    1.713
peak=    3.925 closest distance to " CG  PRO A 198 " =    1.244
peak=    3.918 closest distance to " CG  ARG A  66 " =    2.583
peak=    3.915 closest distance to " O   HOH Z 426 " =    1.506
peak=    3.896 closest distance to " CA  THR A 221 " =    0.942
peak=    3.890 closest distance to " O   HOH Z  40 " =    1.504
peak=    3.883 closest distance to " O   HOH Z 369 " =    1.891
peak=    3.873 closest distance to " O   HOH Z 132 " =    2.527
peak=    3.863 closest distance to " O   HOH Z 279 " =    2.092
peak=    3.860 closest distance to " O   HOH Z 303 " =    1.906
peak=    3.854 closest distance to " O   HOH Z 173 " =    1.928
peak=    3.844 closest distance to " CB  TYR A 169 " =    0.863
peak=    3.841 closest distance to " O   HOH Z 193 " =    2.082
peak=    3.840 closest distance to " O   HOH Z  21 " =    1.743
peak=    3.839 closest distance to " O   HOH Z 214 " =    2.112
peak=    3.828 closest distance to " O   HOH Z 403 " =    1.714
peak=    3.814 closest distance to " CA  ASN A 215 " =    1.203
peak=    3.813 closest distance to " O   HOH Z  49 " =    2.118
peak=    3.812 closest distance to " O   HOH Z  10 " =    1.889
peak=    3.807 closest distance to " O   HOH Z 284 " =    2.892
peak=    3.798 closest distance to " O   HOH Z  59 " =    2.231
peak=    3.779 closest distance to " CG2BVAL A  41 " =    0.807
peak=    3.775 closest distance to " O   HOH Z 326 " =    1.508
peak=    3.770 closest distance to " O   HOH Z 411 " =    3.725
peak=    3.766 closest distance to " OG BSER A 164 " =    2.478
peak=    3.763 closest distance to " CG  PRO A 243 " =    1.168
peak=    3.761 closest distance to " O   HOH Z 197 " =    2.877
peak=    3.752 closest distance to " CB  ASN A 148 " =    1.155
peak=    3.743 closest distance to " O   HOH Z 313 " =    1.739
peak=    3.737 closest distance to " O   HOH Z 128 " =    2.181
peak=    3.730 closest distance to " O   HOH Z 368 " =    3.689
peak=    3.729 closest distance to " CD BLYS A 290 " =    1.197
peak=    3.727 closest distance to " O   HOH Z 273 " =    2.712
peak=    3.723 closest distance to " O   HOH Z 261 " =    1.571
peak=    3.722 closest distance to " CB  ARG A 190 " =    1.724
peak=    3.716 closest distance to " O   HOH Z  44 " =    1.890
peak=    3.716 closest distance to " O   HOH Z 327 " =    1.715
peak=    3.713 closest distance to " CG1BVAL A  72 " =    1.551
peak=    3.709 closest distance to " CB  VAL A 202 " =    1.662
peak=    3.706 closest distance to " NH1BARG A 145 " =    1.178
peak=    3.706 closest distance to " O   HOH Z  88 " =    3.179
peak=    3.691 closest distance to " O   HOH Z 374 " =    2.504
peak=    3.686 closest distance to " O   HOH Z 423 " =    1.997
peak=    3.673 closest distance to " CG2 ILE A 120 " =    1.213
peak=    3.673 closest distance to " NH1AARG A 145 " =    1.053
peak=    3.672 closest distance to " OG  SER A  22 " =    2.710
peak=    3.671 closest distance to " O   HOH Z  85 " =    1.702
peak=    3.667 closest distance to " O   MET A 105 " =    1.799
peak=    3.667 closest distance to " O   HOH Z 180 " =    2.241
peak=    3.666 closest distance to " O   HOH Z  43 " =    2.025
peak=    3.649 closest distance to " O   HOH Z  68 " =    1.628
peak=    3.647 closest distance to " O   HOH Z 172 " =    3.885
peak=    3.640 closest distance to " CB  SER A 141 " =    1.086
peak=    3.627 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.626 closest distance to " O   HOH Z 250 " =    1.321
peak=    3.624 closest distance to " O   HOH Z 125 " =    2.282
peak=    3.624 closest distance to " O   HOH Z 189 " =    1.677
peak=    3.620 closest distance to " CA  ASN A 176 " =    1.138
peak=    3.615 closest distance to " O   HOH Z 227 " =    1.603
peak=    3.613 closest distance to " O   HOH Z 334 " =    1.407
peak=    3.613 closest distance to " O   HOH Z 353 " =    2.572
peak=    3.613 closest distance to " N   ASN A  39 " =    1.218
peak=    3.611 closest distance to " O   HOH Z 260 " =    1.207
peak=    3.610 closest distance to " CA  MET A  40 " =    1.018
peak=    3.601 closest distance to " O   HOH Z 183 " =    1.514
peak=    3.597 closest distance to " CB  ARG A 139 " =    0.932
peak=    3.596 closest distance to " O   HOH Z 345 " =    3.133
peak=    3.591 closest distance to " CB  VAL A 265 " =    1.277
peak=    3.577 closest distance to " CA  ARG A  36 " =    1.072
peak=    3.575 closest distance to " O   ALA A 165 " =    1.386
peak=    3.572 closest distance to " NH2 ARG A 156 " =    1.176
peak=    3.567 closest distance to " CD  ARG A 159 " =    0.748
peak=    3.567 closest distance to " O   HOH Z  19 " =    2.202
peak=    3.556 closest distance to " O   HOH Z  66 " =    2.206
peak=    3.556 closest distance to " O   HOH Z 108 " =    2.003
peak=    3.554 closest distance to " O   HOH Z   3 " =    1.654
peak=    3.552 closest distance to " CD2 LEU A 297 " =    0.896
peak=    3.542 closest distance to " O   HOH Z 402 " =    1.410
peak=    3.539 closest distance to " O   HOH Z  71 " =    1.197
peak=    3.533 closest distance to " O   HOH Z 427 " =    3.041
peak=    3.533 closest distance to " CA  ASP A 140 " =    1.070
peak=    3.526 closest distance to " CB  SER A  26 " =    1.582
peak=    3.526 closest distance to " CA  ALA A 248 " =    1.207
peak=    3.518 closest distance to " CG2 ILE A  20 " =    1.418
peak=    3.504 closest distance to " O   HOH Z 132 " =    2.327
peak=    3.499 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.498 closest distance to " O   HOH Z 291 " =    1.463
peak=    3.486 closest distance to " O   HOH Z  63 " =    1.842
peak=    3.484 closest distance to " CD  LYS A 119 " =    1.249
peak=    3.483 closest distance to " O   HOH Z 158 " =    3.015
peak=    3.476 closest distance to " O   HOH Z  61 " =    1.623
peak=    3.468 closest distance to " O   HOH Z 281 " =    4.372
peak=    3.466 closest distance to " CD2 TRP A 179 " =    1.399
peak=    3.463 closest distance to " CB  TRP A 266 " =    0.972
peak=    3.458 closest distance to " O   HOH Z 403 " =    1.331
peak=    3.455 closest distance to " O   HOH Z 366 " =    2.903
peak=    3.451 closest distance to " O   SER A  26 " =    1.710
peak=    3.444 closest distance to " CD2 LEU A 255 " =    1.150
peak=    3.439 closest distance to " CD  LYS A 166 " =    1.301
peak=    3.439 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.438 closest distance to " NH2AARG A 190 " =    1.264
peak=    3.438 closest distance to " CA  ALA A 233 " =    1.225
peak=    3.437 closest distance to " O  BHOH Z  74 " =    1.521
peak=    3.434 closest distance to " CA  THR A 264 " =    0.822
peak=    3.433 closest distance to " O   HOH Z   1 " =    1.967
peak=    3.425 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.419 closest distance to " O   HOH Z 185 " =    1.678
peak=    3.418 closest distance to " CZ2 TRP A 179 " =    1.637
peak=    3.413 closest distance to " O   TRP A 274 " =    1.858
peak=    3.408 closest distance to " CG  GLU A 277 " =    2.211
peak=    3.408 closest distance to " O   HOH Z 247 " =    1.255
peak=    3.407 closest distance to " O   HOH Z 163 " =    1.900
peak=    3.405 closest distance to " N   ARG A 156 " =    1.324
peak=    3.404 closest distance to " CB  GLN A  88 " =    1.168
peak=    3.403 closest distance to " CE1 TYR A 186 " =    1.241
peak=    3.400 closest distance to " CB  ALA A 291 " =    1.350
peak=    3.395 closest distance to " O   HOH Z 337 " =    3.639
peak=    3.384 closest distance to " O   HOH Z 407 " =    2.711
peak=    3.383 closest distance to " NE2 GLN A  58 " =    4.339
peak=    3.379 closest distance to " O   HOH Z 392 " =    1.865
peak=    3.377 closest distance to " O   HOH Z 286 " =    2.165
peak=    3.376 closest distance to " CB  SER A 216 " =    0.757
peak=    3.373 closest distance to " O   HOH Z  48 " =    1.413
peak=    3.372 closest distance to " CB  MET A  47 " =    1.023
peak=    3.371 closest distance to " CG  GLN A  77 " =    1.913
peak=    3.361 closest distance to " CG  MET A 185 " =    1.192
peak=    3.360 closest distance to " CB  SER A  62 " =    1.278
peak=    3.353 closest distance to " NH2 ARG A 219 " =    1.867
peak=    3.351 closest distance to " O   HOH Z 227 " =    1.607
peak=    3.351 closest distance to " O   HOH Z 295 " =    1.509
peak=    3.350 closest distance to " CG  LEU A 167 " =    1.182
peak=    3.348 closest distance to " O   HOH Z 227 " =    2.190
peak=    3.345 closest distance to " O   HOH Z  20 " =    2.342
peak=    3.341 closest distance to " O   HOH Z 147 " =    1.663
peak=    3.333 closest distance to " O   HOH Z 133 " =    1.448
peak=    3.330 closest distance to " CA  ALA A  84 " =    1.347
peak=    3.328 closest distance to " O   HOH Z 106 " =    2.263
peak=    3.325 closest distance to " O   HOH Z 194 " =    1.887
peak=    3.323 closest distance to " CD1 LEU A 300 " =    1.197
peak=    3.323 closest distance to " O   ALA A   1 " =    1.474
peak=    3.313 closest distance to " O   HOH Z 357 " =    1.907
peak=    3.310 closest distance to " O   HOH Z 425 " =    1.958
peak=    3.309 closest distance to " O   HOH Z 135 " =    1.664
peak=    3.303 closest distance to " O   HOH Z 409 " =    3.145
peak=    3.303 closest distance to " O   HOH Z 411 " =    1.731
peak=    3.301 closest distance to " CG AARG A 275 " =    0.948
peak=    3.299 closest distance to " O   ALA A   1 " =    1.647
peak=    3.298 closest distance to " OD1 ASP A 231 " =    1.877
peak=    3.298 closest distance to " CB  LEU A 255 " =    0.717
peak=    3.297 closest distance to " O   HOH Z 267 " =    2.062
peak=    3.297 closest distance to " CG  MET A 185 " =    1.085
peak=    3.294 closest distance to " CA  VAL A 126 " =    1.080
peak=    3.294 closest distance to " O   HOH Z 263 " =    2.268
peak=    3.293 closest distance to " CB  ASP A 140 " =    0.873
peak=    3.289 closest distance to " CA  ASN A 217 " =    1.272
peak=    3.280 closest distance to " CG2 THR A 221 " =    1.100
peak=    3.275 closest distance to " O   HOH Z 248 " =    1.573
peak=    3.273 closest distance to " O   HOH Z 358 " =    2.214
peak=    3.271 closest distance to " O   HOH Z  59 " =    2.205
peak=    3.268 closest distance to " O   HOH Z 422 " =    2.686
peak=    3.265 closest distance to " CA  LYS A 117 " =    1.233
peak=    3.260 closest distance to " O   HOH Z 367 " =    3.511
peak=    3.254 closest distance to " O   HOH Z  80 " =    1.620
peak=    3.253 closest distance to " O   HOH Z 211 " =    2.458
peak=    3.253 closest distance to " CA  ALA A  51 " =    0.863
peak=    3.251 closest distance to " OE1 GLU A 277 " =    1.932
peak=    3.249 closest distance to " O   HOH Z 250 " =    1.617
peak=    3.247 closest distance to " CA  ALA A  43 " =    1.247
peak=    3.244 closest distance to " ND1 HIS A  81 " =    1.513
peak=    3.234 closest distance to " CZ  PHE A 218 " =    0.990
peak=    3.234 closest distance to " CB  SER A 212 " =    1.001
peak=    3.231 closest distance to " O   HOH Z 214 " =    2.363
peak=    3.231 closest distance to " CB  PHE A  16 " =    0.992
peak=    3.228 closest distance to " N   ASN A 127 " =    1.226
peak=    3.227 closest distance to " O   HOH Z 145 " =    3.727
peak=    3.226 closest distance to " CG2 VAL A 257 " =    0.850
peak=    3.225 closest distance to " O   HOH Z 189 " =    1.378
peak=    3.223 closest distance to " O   HOH Z 106 " =    2.227
peak=    3.222 closest distance to " O   HOH Z 266 " =    2.870
peak=    3.221 closest distance to " OG  SER A  62 " =    2.974
peak=    3.220 closest distance to " CG  GLN A  89 " =    1.459
peak=    3.217 closest distance to " O   HOH Z 192 " =    1.866
peak=    3.214 closest distance to " O   HOH Z 291 " =    1.829
peak=    3.207 closest distance to " O   HOH Z 258 " =    2.299
peak=    3.204 closest distance to " O   HOH Z 261 " =    1.944
peak=    3.202 closest distance to " CG  LYS A  76 " =    1.064
peak=    3.195 closest distance to " O   HOH Z 163 " =    1.666
peak=    3.194 closest distance to " CA  ILE A  33 " =    1.487
peak=    3.193 closest distance to " O   HOH Z 430 " =    5.559
peak=    3.192 closest distance to " O   HOH Z 336 " =    1.711
peak=    3.188 closest distance to " CD1 LEU A  96 " =    0.814
peak=    3.186 closest distance to " CB  ALA A   9 " =    1.581
peak=    3.178 closest distance to " O   HOH Z 102 " =    1.207
peak=    3.178 closest distance to " OG  SER A 206 " =    1.278
peak=    3.173 closest distance to " O   HOH Z 437 " =    1.632
peak=    3.170 closest distance to " CB  ASN A  39 " =    0.876
peak=    3.170 closest distance to " CG  MET A 113 " =    1.186
peak=    3.170 closest distance to " CB  SER A  62 " =    0.887
peak=    3.169 closest distance to " OD1 ASP A 238 " =    0.974
peak=    3.166 closest distance to " CA  ASP A 162 " =    1.159
peak=    3.165 closest distance to " O   HOH Z 175 " =    2.135
peak=    3.163 closest distance to " CB  ALA A  71 " =    1.285
peak=    3.159 closest distance to " CB  GLU A 152 " =    1.494
peak=    3.158 closest distance to " CZ2 TRP A 274 " =    1.610
peak=    3.158 closest distance to " O   HOH Z 380 " =    2.053
peak=    3.155 closest distance to " O   ALA A 158 " =    1.259
peak=    3.155 closest distance to " O   HOH Z 106 " =    1.638
peak=    3.149 closest distance to " O   HOH Z 329 " =    3.506
peak=    3.149 closest distance to " O   HOH Z 148 " =    3.052
peak=    3.148 closest distance to " CG2 THR A 294 " =    1.612
peak=    3.144 closest distance to " O   HOH Z  14 " =    1.957
peak=    3.141 closest distance to " CA  ASP A 191 " =    0.784
peak=    3.141 closest distance to " O   HOH Z 126 " =    1.642
peak=    3.138 closest distance to " O   HOH Z 285 " =    1.865
peak=    3.136 closest distance to " O   HOH Z 280 " =    2.463
peak=    3.135 closest distance to " CB  LEU A 143 " =    1.052
peak=    3.133 closest distance to " O   HOH Z 287 " =    1.770
peak=    3.132 closest distance to " C   ALA A 299 " =    0.928
peak=    3.121 closest distance to " OD1 ASP A 286 " =    1.524
peak=    3.118 closest distance to " CB  ASN A 215 " =    1.088
peak=    3.118 closest distance to " O   HOH Z 425 " =    1.274
peak=    3.117 closest distance to " CB  GLN A 205 " =    1.228
peak=    3.115 closest distance to " OH  TYR A  30 " =    1.127
peak=    3.103 closest distance to " CD  GLN A  58 " =    5.911
peak=    3.098 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.095 closest distance to " O   HOH Z  40 " =    2.607
peak=    3.094 closest distance to " O   HOH Z 189 " =    1.762
peak=    3.090 closest distance to " O   HOH Z 126 " =    2.101
peak=    3.090 closest distance to " CG  ARG A  66 " =    0.923
peak=    3.089 closest distance to " CA  ALA A 158 " =    1.128
peak=    3.089 closest distance to " CA  ARG A 195 " =    1.204
peak=    3.086 closest distance to " OE1 GLN A  11 " =    1.886
peak=    3.080 closest distance to " CB  SER A 273 " =    0.772
peak=    3.079 closest distance to " N   TYR A 116 " =    1.650
peak=    3.077 closest distance to " O   HOH Z 151 " =    1.525
peak=    3.069 closest distance to " O   HOH Z 132 " =    0.864
peak=    3.067 closest distance to " O   HOH Z  66 " =    2.047
peak=    3.056 closest distance to " OG ASER A  99 " =    1.675
peak=    3.047 closest distance to " OG BSER A  99 " =    2.186
peak=    3.042 closest distance to " O   HOH Z  30 " =    2.103
peak=    3.039 closest distance to " O   HOH Z 368 " =    2.479
peak=    2.985 closest distance to " O   HOH Z 286 " =    2.193

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.817 - 5.145
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.817 - 5.145

peak=   -4.719 closest distance to " O   HOH Z 266 " =    4.197
peak=   -4.516 closest distance to " O   HOH Z 372 " =    2.302
peak=   -4.314 closest distance to " OXT GLY A 302 " =    2.744
peak=   -4.285 closest distance to " CB  ALA A 161 " =    2.569
peak=   -4.253 closest distance to " CB  PRO A 243 " =    2.558
peak=   -4.234 closest distance to " C   HIS A 108 " =    1.065
peak=   -4.165 closest distance to " CD  ARG A 156 " =    1.995
peak=   -4.161 closest distance to " O   HOH Z 198 " =    2.185
peak=   -4.157 closest distance to " SG  CYS A 254 " =    3.247
peak=   -4.126 closest distance to " O   VAL A  67 " =    2.796
peak=   -4.081 closest distance to " O   HOH Z 377 " =    1.971
peak=   -4.050 closest distance to " OG  SER A  97 " =    2.049
peak=   -4.037 closest distance to " O   HOH Z  13 " =    1.482
peak=   -4.037 closest distance to " O   PRO A 163 " =    2.020
peak=   -4.021 closest distance to " N   GLN A  58 " =    1.664
peak=   -4.018 closest distance to " O   HOH Z  10 " =    1.467
peak=   -3.968 closest distance to " OE1 GLN A 223 " =    2.127
peak=   -3.963 closest distance to " O   HOH Z 290 " =    1.009
peak=   -3.948 closest distance to " N   ALA A 248 " =    1.622
peak=   -3.943 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.939 closest distance to " ND2 ASN A  45 " =    0.921
peak=   -3.923 closest distance to " O   VAL A  67 " =    2.839
peak=   -3.910 closest distance to " C   ALA A 158 " =    1.189
peak=   -3.905 closest distance to " O   HOH Z 231 " =    2.204
peak=   -3.888 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.882 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.873 closest distance to " CD1 LEU A 101 " =    2.484
peak=   -3.852 closest distance to " O   HOH Z  11 " =    1.877
peak=   -3.822 closest distance to " CB  TYR A  15 " =    2.202
peak=   -3.793 closest distance to " O   HOH Z 102 " =    1.669
peak=   -3.788 closest distance to " O   HOH Z 126 " =    1.872
peak=   -3.779 closest distance to " O   HOH Z 185 " =    2.197
peak=   -3.775 closest distance to " CZ3 TRP A 179 " =    1.345
peak=   -3.761 closest distance to " O   HOH Z 407 " =    2.998
peak=   -3.752 closest distance to " CD1 LEU A 228 " =    2.194
peak=   -3.741 closest distance to " O   HOH Z  52 " =    1.445
peak=   -3.740 closest distance to " CD1 PHE A  59 " =    1.840
peak=   -3.740 closest distance to " CE  MET A 105 " =    2.010
peak=   -3.734 closest distance to " CZ  PHE A  59 " =    1.594
peak=   -3.727 closest distance to " N   ALA A  43 " =    2.458
peak=   -3.722 closest distance to " O   HOH Z 234 " =    4.139
peak=   -3.708 closest distance to " O   HOH Z  43 " =    1.586
peak=   -3.697 closest distance to " OG BSER A 134 " =    1.238
peak=   -3.690 closest distance to " CB  ALA A 291 " =    2.401
peak=   -3.676 closest distance to " O   HOH Z 166 " =    1.490
peak=   -3.669 closest distance to " N   ASP A 286 " =    2.382
peak=   -3.667 closest distance to " O   HOH Z 388 " =    1.997
peak=   -3.664 closest distance to " NH2 ARG A  79 " =    1.882
peak=   -3.631 closest distance to " NE2 GLN A  58 " =    1.182
peak=   -3.630 closest distance to " O   HOH Z 292 " =    4.493
peak=   -3.626 closest distance to " O   HOH Z 353 " =    2.211
peak=   -3.623 closest distance to " CG  ASP A  50 " =    2.385
peak=   -3.620 closest distance to " CD2 LEU A 300 " =    2.847
peak=   -3.613 closest distance to " O   SER A 135 " =    1.576
peak=   -3.610 closest distance to " CG  PHE A 283 " =    2.614
peak=   -3.608 closest distance to " O   HOH Z 118 " =    2.914
peak=   -3.604 closest distance to " O   HOH Z 385 " =    2.028
peak=   -3.596 closest distance to " CG  ASP A 231 " =    0.817
peak=   -3.594 closest distance to " C   LEU A 143 " =    1.126
peak=   -3.578 closest distance to " O   SER A 210 " =    1.890
peak=   -3.575 closest distance to " OG  SER A   3 " =    1.661
peak=   -3.572 closest distance to " O   VAL A 153 " =    2.329
peak=   -3.570 closest distance to " CB  ASN A  39 " =    2.234
peak=   -3.569 closest distance to " O   ALA A 161 " =    1.620
peak=   -3.560 closest distance to " O   HOH Z 283 " =    1.738
peak=   -3.555 closest distance to " OG ASER A 134 " =    1.218
peak=   -3.554 closest distance to " CG  GLU A   2 " =    2.005
peak=   -3.551 closest distance to " ND2 ASN A 187 " =    1.476
peak=   -3.548 closest distance to " O   HOH Z  11 " =    1.819
peak=   -3.545 closest distance to " N   SER A 276 " =    1.293
peak=   -3.541 closest distance to " O   HOH Z 351 " =    1.454
peak=   -3.540 closest distance to " CE2 TYR A  30 " =    2.852
peak=   -3.531 closest distance to " O   HOH Z  15 " =    1.580
peak=   -3.531 closest distance to " OG BSER A 134 " =    1.717
peak=   -3.530 closest distance to " O   SER A 146 " =    0.951
peak=   -3.516 closest distance to " O   HOH Z  38 " =    1.591
peak=   -3.516 closest distance to " O   VAL A 174 " =    2.023
peak=   -3.502 closest distance to " CB  PHE A 192 " =    1.884
peak=   -3.502 closest distance to " O   GLY A 196 " =    0.950
peak=   -3.489 closest distance to " O   HOH Z 148 " =    3.433
peak=   -3.480 closest distance to " CG  GLU A  53 " =    1.422
peak=   -3.479 closest distance to " O   HOH Z 165 " =    2.000
peak=   -3.471 closest distance to " O   HOH Z  93 " =    1.516
peak=   -3.458 closest distance to " CB  ASP A 132 " =    2.304
peak=   -3.455 closest distance to " O   HOH Z 311 " =    3.356
peak=   -3.444 closest distance to " O   HOH Z  19 " =    2.169
peak=   -3.442 closest distance to " CB  ALA A  51 " =    1.860
peak=   -3.427 closest distance to " O   HOH Z  24 " =    1.465
peak=   -3.427 closest distance to " O   MET A  40 " =    2.705
peak=   -3.427 closest distance to " CD1 ILE A 239 " =    2.516
peak=   -3.426 closest distance to " ND2 ASN A 209 " =    1.731
peak=   -3.423 closest distance to " CD2 LEU A 237 " =    2.381
peak=   -3.420 closest distance to " CB  CYS A 254 " =    2.492
peak=   -3.416 closest distance to " NH2AARG A 275 " =    5.145
peak=   -3.414 closest distance to " NH2 ARG A  66 " =    4.787
peak=   -3.402 closest distance to " OD2 ASP A 171 " =    2.371
peak=   -3.402 closest distance to " O   HOH Z 395 " =    5.080
peak=   -3.397 closest distance to " O   HOH Z 427 " =    1.310
peak=   -3.396 closest distance to " CA  GLY A 133 " =    1.864
peak=   -3.392 closest distance to " OE1 GLN A  88 " =    1.150
peak=   -3.391 closest distance to " O   HOH Z  63 " =    1.353
peak=   -3.390 closest distance to " N   HIS A 115 " =    1.903
peak=   -3.387 closest distance to " O   HOH Z  76 " =    1.938
peak=   -3.386 closest distance to " OD1 ASP A 191 " =    1.629
peak=   -3.382 closest distance to " CG1 VAL A 112 " =    2.759
peak=   -3.381 closest distance to " CA  GLY A 203 " =    2.178
peak=   -3.380 closest distance to " CD  GLN A  88 " =    1.857
peak=   -3.377 closest distance to " O   HOH Z 435 " =    2.701
peak=   -3.375 closest distance to " O   GLY A  80 " =    2.413
peak=   -3.372 closest distance to " CG  GLU A 152 " =    2.254
peak=   -3.369 closest distance to " CD2 LEU A 237 " =    2.259
peak=   -3.367 closest distance to " O   SER A  95 " =    1.498
peak=   -3.364 closest distance to " N   GLN A 122 " =    1.525
peak=   -3.361 closest distance to " NH1 ARG A  56 " =    2.589
peak=   -3.360 closest distance to " OXT GLY A 302 " =    3.131
peak=   -3.359 closest distance to " O   HOH Z 417 " =    2.504
peak=   -3.353 closest distance to " O   HOH Z 198 " =    1.489
peak=   -3.345 closest distance to " CD1 ILE A 239 " =    1.998
peak=   -3.342 closest distance to " CG  GLU A 277 " =    1.150
peak=   -3.341 closest distance to " O   HOH Z 166 " =    1.847
peak=   -3.340 closest distance to " OD1 ASN A 249 " =    1.251
peak=   -3.339 closest distance to " O   HOH Z 263 " =    2.893
peak=   -3.331 closest distance to " NH1 ARG A 195 " =    2.593
peak=   -3.328 closest distance to " O   HOH Z  98 " =    2.039
peak=   -3.328 closest distance to " O   ALA A  34 " =    2.533
peak=   -3.320 closest distance to " CB  ALA A 248 " =    1.939
peak=   -3.318 closest distance to " O   TRP A  92 " =    1.745
peak=   -3.317 closest distance to " O   HOH Z  90 " =    2.796
peak=   -3.314 closest distance to " CG2 VAL A 189 " =    2.101
peak=   -3.312 closest distance to " CE  LYS A  76 " =    2.891
peak=   -3.312 closest distance to " O   PHE A 218 " =    1.539
peak=   -3.310 closest distance to " CD  LYS A 289 " =    2.494
peak=   -3.301 closest distance to " O   ALA A 160 " =    1.520
peak=   -3.293 closest distance to " CE2 TYR A 186 " =    2.163
peak=   -3.287 closest distance to " O   ASP A 231 " =    2.478
peak=   -3.284 closest distance to " O   HOH Z 436 " =    1.466
peak=   -3.278 closest distance to " OD1 ASP A 200 " =    1.280
peak=   -3.276 closest distance to " O   HOH Z 281 " =    2.767
peak=   -3.276 closest distance to " CE3 TRP A 150 " =    1.923
peak=   -3.273 closest distance to " N   SER A 206 " =    1.911
peak=   -3.263 closest distance to " CB  SER A 245 " =    2.459
peak=   -3.263 closest distance to " CA  TRP A 274 " =    1.541
peak=   -3.253 closest distance to " ND2 ASN A  39 " =    1.393
peak=   -3.250 closest distance to " O   HOH Z 396 " =    1.494
peak=   -3.249 closest distance to " CB  SER A 258 " =    2.047
peak=   -3.243 closest distance to " O   HOH Z  97 " =    1.745
peak=   -3.243 closest distance to " CB  CYS A 201 " =    2.577
peak=   -3.243 closest distance to " CB  PRO A 163 " =    2.573
peak=   -3.242 closest distance to " CG  LEU A  83 " =    1.959
peak=   -3.242 closest distance to " CD1 LEU A  25 " =    2.449
peak=   -3.241 closest distance to " CG  PRO A 163 " =    2.503
peak=   -3.240 closest distance to " N   VAL A 189 " =    1.657
peak=   -3.239 closest distance to " CG2 ILE A 263 " =    2.237
peak=   -3.236 closest distance to " CB  PHE A 208 " =    2.207
peak=   -3.234 closest distance to " SG ACYS A 201 " =    2.183
peak=   -3.227 closest distance to " O   HOH Z  60 " =    1.973
peak=   -3.224 closest distance to " O   TRP A  70 " =    1.630
peak=   -3.223 closest distance to " OG BSER A 210 " =    1.969
peak=   -3.219 closest distance to " CE2 PHE A 192 " =    2.009
peak=   -3.219 closest distance to " O   HOH Z 222 " =    1.189
peak=   -3.219 closest distance to " N   GLN A  58 " =    1.304
peak=   -3.213 closest distance to " OE1 GLN A  77 " =    1.753
peak=   -3.207 closest distance to " OG  SER A  87 " =    1.283
peak=   -3.206 closest distance to " O   HOH Z  41 " =    2.323
peak=   -3.205 closest distance to " O   HOH Z  47 " =    1.492
peak=   -3.199 closest distance to " O   LEU A 167 " =    1.490
peak=   -3.196 closest distance to " OD1 ASN A 148 " =    1.655
peak=   -3.194 closest distance to " OG1 THR A 178 " =    1.228
peak=   -3.193 closest distance to " CG2AVAL A  41 " =    2.654
peak=   -3.192 closest distance to " CB  ASP A 132 " =    2.334
peak=   -3.190 closest distance to " O   ASN A 249 " =    1.545
peak=   -3.178 closest distance to " CE3 TRP A 274 " =    2.436
peak=   -3.177 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.176 closest distance to " N   THR A 157 " =    1.572
peak=   -3.174 closest distance to " O   HOH Z 210 " =    1.070
peak=   -3.174 closest distance to " O   ALA A  51 " =    1.370
peak=   -3.173 closest distance to " O   ALA A 292 " =    1.950
peak=   -3.170 closest distance to " CG  ARG A 259 " =    2.833
peak=   -3.170 closest distance to " O   ALA A   1 " =    1.808
peak=   -3.170 closest distance to " OE1 GLN A 223 " =    1.941
peak=   -3.164 closest distance to " OD1 ASP A 171 " =    1.599
peak=   -3.161 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.160 closest distance to " O   HOH Z 423 " =    2.289
peak=   -3.142 closest distance to " CD2 TYR A 293 " =    2.066
peak=   -3.138 closest distance to " O   ALA A 256 " =    1.511
peak=   -3.138 closest distance to " O   HOH Z 137 " =    1.490
peak=   -3.137 closest distance to " CD2 LEU A 300 " =    2.599
peak=   -3.133 closest distance to " CD  GLU A 236 " =    1.057
peak=   -3.130 closest distance to " OH  TYR A 214 " =    1.285
peak=   -3.125 closest distance to " ND2 ASN A 249 " =    2.275
peak=   -3.123 closest distance to " O   HOH Z  71 " =    1.487
peak=   -3.121 closest distance to " CB  ALA A  10 " =    2.177
peak=   -3.120 closest distance to " O   HOH Z 211 " =    1.727
peak=   -3.111 closest distance to " OG1 THR A 279 " =    1.288
peak=   -3.107 closest distance to " N   ALA A 226 " =    2.001
peak=   -3.094 closest distance to " CG  GLU A 152 " =    0.925
peak=   -3.081 closest distance to " O   HOH Z  88 " =    2.360
peak=   -3.079 closest distance to " O   HOH Z 361 " =    3.428
peak=   -3.078 closest distance to " N   ALA A 248 " =    2.209
peak=   -3.075 closest distance to " CA  GLY A 241 " =    3.158
peak=   -3.069 closest distance to " O   HOH Z 378 " =    1.672
peak=   -3.063 closest distance to " CD1 TYR A 247 " =    2.426
peak=   -3.040 closest distance to " O   HOH Z 148 " =    2.728
peak=   -3.014 closest distance to " N   THR A  52 " =    1.765

================= 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    :  0.3784 0.3769   6.169149e+00   6.177441e+00
   1_bss:  0.3637 0.3597   6.153455e+00   6.148508e+00
   1_xyz:  0.2629 0.2914   5.871430e+00   5.948996e+00
   1_adp:  0.2434 0.3005   5.826983e+00   5.969260e+00
   1_occ:  0.2431 0.3015   5.826326e+00   5.969092e+00
   2_bss:  0.2405 0.2964   5.819130e+00   5.961387e+00
   2_xyz:  0.1650 0.2163   5.477815e+00   5.678533e+00
   2_adp:  0.1481 0.1965   5.379325e+00   5.592230e+00
   2_occ:  0.1478 0.1965   5.378452e+00   5.591694e+00
   3_bss:  0.1471 0.1944   5.370581e+00   5.582315e+00
   3_xyz:  0.1267 0.1701   5.242436e+00   5.460141e+00
   3_adp:  0.1216 0.1654   5.209400e+00   5.429874e+00
   3_occ:  0.1215 0.1653   5.208860e+00   5.429626e+00
   4_bss:  0.1214 0.1652   5.207584e+00   5.428882e+00
   4_xyz:  0.1112 0.1567   5.138369e+00   5.374305e+00
   4_adp:  0.1093 0.1570   5.130870e+00   5.372485e+00
   4_occ:  0.1092 0.1568   5.130419e+00   5.372215e+00
   5_bss:  0.1097 0.1568   5.131992e+00   5.372797e+00
   5_xyz:  0.1073 0.1569   5.124826e+00   5.374949e+00
   5_adp:  0.1070 0.1565   5.124112e+00   5.375614e+00
   5_occ:  0.1070 0.1565   5.123819e+00   5.375612e+00
   5_bss:  0.1069 0.1565   5.124018e+00   5.375736e+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:  0.300  20.000  -3.098  -1.920   3.543  -0.000   0.000   0.000
   1_xyz:  0.300  20.000  -3.098  -1.920   3.543  -0.000   0.000   0.000
   1_adp:  0.300  20.000  -3.098  -1.920   3.543  -0.000   0.000   0.000
   1_occ:  0.300  20.000  -3.098  -1.920   3.543  -0.000   0.000   0.000
   2_bss:  0.324  39.649  -2.863  -1.945   0.454  -0.000   0.000   0.000
   2_xyz:  0.324  39.649  -2.863  -1.945   0.454  -0.000   0.000   0.000
   2_adp:  0.324  39.649  -2.863  -1.945   0.454  -0.000   0.000   0.000
   2_occ:  0.324  39.649  -2.863  -1.945   0.454  -0.000   0.000   0.000
   3_bss:  0.324  39.649  -2.779  -2.201  -1.343  -0.000  -0.000  -0.000
   3_xyz:  0.324  39.649  -2.779  -2.201  -1.343  -0.000  -0.000  -0.000
   3_adp:  0.324  39.649  -2.779  -2.201  -1.343  -0.000  -0.000  -0.000
   3_occ:  0.324  39.649  -2.779  -2.201  -1.343  -0.000  -0.000  -0.000
   4_bss:  0.315  39.121  -2.759  -2.174  -1.820  -0.000  -0.000  -0.000
   4_xyz:  0.315  39.121  -2.759  -2.174  -1.820  -0.000  -0.000  -0.000
   4_adp:  0.315  39.121  -2.759  -2.174  -1.820  -0.000  -0.000  -0.000
   4_occ:  0.315  39.121  -2.759  -2.174  -1.820  -0.000  -0.000  -0.000
   5_bss:  0.316  41.261  -2.647  -2.081  -1.873  -0.000  -0.000  -0.000
   5_xyz:  0.316  41.261  -2.647  -2.081  -1.873  -0.000  -0.000  -0.000
   5_adp:  0.316  41.261  -2.647  -2.081  -1.873  -0.000  -0.000  -0.000
   5_occ:  0.316  41.261  -2.647  -2.081  -1.873  -0.000  -0.000  -0.000
   5_bss:  0.319  41.387  -2.459  -1.886  -1.711  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.706 0.5995  0.7894    45899.295
   1_bss:  41.919 0.6192  0.8011    41250.420
   1_xyz:  29.885 0.7595  0.9449    22610.017
   1_adp:  31.348 0.7420  0.9299    24053.777
   1_occ:  31.378 0.7417  0.9299    24065.495
   2_bss:  30.777 0.7483  0.9082    23381.674
   2_xyz:  21.162 0.8494  0.9914    11779.270
   2_adp:  18.736 0.8734  1.0017     9829.960
   2_occ:  18.721 0.8735  1.0013     9814.680
   3_bss:  18.413 0.8763  0.9795     9574.288
   3_xyz:  15.657 0.9009  0.9899     7351.280
   3_adp:  14.908 0.9077  0.9890     6964.595
   3_occ:  14.897 0.9078  0.9889     6962.170
   4_bss:  14.877 0.9080  0.9836     6953.371
   4_xyz:  13.921 0.9153  0.9869     6185.392
   4_adp:  13.840 0.9162  0.9836     6159.125
   4_occ:  13.830 0.9163  0.9835     6156.582
   5_bss:  13.854 0.9161  0.9849     6180.251
   5_xyz:  13.830 0.9164  0.9839     6195.697
   5_adp:  13.811 0.9166  0.9793     6192.160
   5_occ:  13.806 0.9167  0.9793     6190.440
   5_bss:  13.809 0.9166  0.9840     6195.157
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8299e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8299e-01
   1_xyz:   1.232  0.010  0.076 15.466  0.005  4.108   8.7708e-02
   1_adp:   1.232  0.010  0.076 15.466  0.005  4.108   8.7708e-02
   1_occ:   1.232  0.010  0.076 15.466  0.005  4.108   8.7708e-02
   2_bss:   1.232  0.010  0.076 15.466  0.005  4.108   8.7708e-02
   2_xyz:   1.083  0.007  0.068 14.331  0.004  4.108   6.6209e-02
   2_adp:   1.083  0.007  0.068 14.331  0.004  4.108   6.6209e-02
   2_occ:   1.083  0.007  0.068 14.331  0.004  4.108   6.6209e-02
   3_bss:   1.083  0.007  0.068 14.331  0.004  4.108   6.6209e-02
   3_xyz:   0.890  0.005  0.063 14.215  0.003  4.110   4.8399e-02
   3_adp:   0.890  0.005  0.063 14.215  0.003  4.110   4.8399e-02
   3_occ:   0.890  0.005  0.063 14.215  0.003  4.110   4.8399e-02
   4_bss:   0.890  0.005  0.063 14.215  0.003  4.110   4.8399e-02
   4_xyz:   1.046  0.007  0.074 14.623  0.004  4.111   6.2082e-02
   4_adp:   1.046  0.007  0.074 14.623  0.004  4.111   6.2082e-02
   4_occ:   1.046  0.007  0.074 14.623  0.004  4.111   6.2082e-02
   5_bss:   1.046  0.007  0.074 14.623  0.004  4.111   6.2082e-02
   5_xyz:   1.009  0.007  0.072 14.503  0.004  4.107   5.8850e-02
   5_adp:   1.009  0.007  0.072 14.503  0.004  4.107   5.8850e-02
   5_occ:   1.009  0.007  0.072 14.503  0.004  4.107   5.8850e-02
   5_bss:   1.009  0.007  0.072 14.503  0.004  4.107   5.8850e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.526   2.3935e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.526   2.3935e-01
   1_xyz:   8.189  0.050  0.289 87.652  0.034  2.008   8.6571e-02
   1_adp:   8.189  0.050  0.289 87.652  0.034  2.008   8.6571e-02
   1_occ:   8.189  0.050  0.289 87.652  0.034  2.008   8.6571e-02
   2_bss:   8.189  0.050  0.289 87.652  0.034  2.008   8.6571e-02
   2_xyz:   7.655  0.043  0.251 80.777  0.036  2.318   1.1253e-01
   2_adp:   7.655  0.043  0.251 80.777  0.036  2.318   1.1253e-01
   2_occ:   7.655  0.043  0.251 80.777  0.036  2.318   1.1253e-01
   3_bss:   7.655  0.043  0.251 80.777  0.036  2.318   1.1253e-01
   3_xyz:   6.348  0.047  0.237 82.652  0.033  2.409   3.8008e-02
   3_adp:   6.348  0.047  0.237 82.652  0.033  2.409   3.8008e-02
   3_occ:   6.348  0.047  0.237 82.652  0.033  2.409   3.8008e-02
   4_bss:   6.348  0.047  0.237 82.652  0.033  2.409   3.8008e-02
   4_xyz:   6.905  0.038  0.233 82.270  0.035  2.292   4.9579e-02
   4_adp:   6.905  0.038  0.233 82.270  0.035  2.292   4.9579e-02
   4_occ:   6.905  0.038  0.233 82.270  0.035  2.292   4.9579e-02
   5_bss:   6.905  0.038  0.233 82.270  0.035  2.292   4.9579e-02
   5_xyz:   6.755  0.034  0.234 82.024  0.038  2.327   4.3956e-02
   5_adp:   6.755  0.034  0.234 82.024  0.038  2.327   4.3956e-02
   5_occ:   6.755  0.034  0.234 82.024  0.038  2.327   4.3956e-02
   5_bss:   6.755  0.034  0.234 82.024  0.038  2.327   4.3956e-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:  83.21   0.00  17.14  83.21   0.00  13.33  63.57   4.34  37.87
   1_occ:  83.21   0.00  17.14  83.21   0.00  13.33  63.57   4.34  37.87
   2_bss:  83.21   0.00  17.14  83.21   0.00  13.33  63.57   4.34  37.87
   2_xyz:  83.21   0.00  17.14  83.21   0.00  13.33  63.57   4.34  37.87
   2_adp:  74.76   0.93  17.37  73.64   0.93  13.24  74.76   2.47  39.87
   2_occ:  74.76   0.93  17.37  73.64   0.93  13.24  74.76   2.47  39.87
   3_bss:  74.76   0.93  17.37  73.64   0.93  13.24  74.76   2.47  39.87
   3_xyz:  74.76   0.93  17.37  73.64   0.93  13.24  74.76   2.47  39.87
   3_adp:  80.13   0.00  17.26  80.13   0.00  13.08  78.30   2.26  39.97
   3_occ:  80.13   0.00  17.26  80.13   0.00  13.08  78.30   2.26  39.97
   4_bss:  80.13   0.00  17.26  80.13   0.00  13.08  78.30   2.26  39.97
   4_xyz:  80.13   0.00  17.26  80.13   0.00  13.08  78.30   2.26  39.97
   4_adp:  89.77   0.81  17.24  89.77   0.81  13.01  80.83   1.78  40.31
   4_occ:  89.77   0.81  17.24  89.77   0.81  13.01  80.83   1.78  40.31
   5_bss:  89.77   0.81  17.24  89.77   0.81  13.01  80.83   1.78  40.31
   5_xyz:  89.77   0.81  17.24  89.77   0.81  13.01  80.83   1.78  40.31
   5_adp:  93.69   1.38  16.95  93.69   1.38  12.85  79.42   3.48  39.28
   5_occ:  93.69   1.38  16.95  93.69   1.38  12.85  79.42   3.48  39.28
   5_bss:  93.64   1.33  16.90  93.64   1.33  12.80  79.37   3.43  39.23
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.890    0.013    0.293
   1_adp:    1.890    0.013    0.293
   1_occ:    1.890    0.013    0.293
   2_bss:    1.890    0.013    0.293
   2_xyz:    1.375    0.029    0.452
   2_adp:    1.375    0.029    0.452
   2_occ:    1.375    0.029    0.452
   3_bss:    1.375    0.029    0.452
   3_xyz:    1.464    0.009    0.498
   3_adp:    1.464    0.009    0.498
   3_occ:    1.464    0.009    0.498
   4_bss:    1.464    0.009    0.498
   4_xyz:    1.580    0.029    0.522
   4_adp:    1.580    0.029    0.522
   4_occ:    1.580    0.029    0.522
   5_bss:    1.580    0.029    0.522
   5_xyz:    1.683    0.084    0.534
   5_adp:    1.683    0.084    0.534
   5_occ:    1.683    0.084    0.534
   5_bss:    1.683    0.084    0.534
------------------------------------------------------------------------

CPU time actual refinement: 353.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_550/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_550/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_550/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_550/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_550/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.10 
  Macro-tasks:
    bulk solvent and scale       = 42.87  
    individual site refinement   = 153.85 
    weights calculation          = 29.59  
    collect and process          = 6.60   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 233.03 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 112.55 
    alpha_beta                      = 8.21   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 123.80 
    fmodel                         = 7.40   
    r_factors                      = 0.28   
    phase_errors                   = 10.92  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 266.43 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.838 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    672 calls, 112.25 s
gradients_fft:          617 calls, 108.96 s

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

# Date 2008-01-16 Time 05:06:21 PST -0800 (1200488781.62 s)
Start R-work = 0.3784, R-free = 0.3769 (no bulk solvent and anisotropic scale)
Final R-work = 0.1322, R-free = 0.1772 (no bulk solvent and anisotropic scale)

Start R-work = 0.3637, R-free = 0.3597
Final R-work = 0.1069, R-free = 0.1565