# Date 2008-01-16 Time 03:46:07 PST -0800 (1200483967.19 s)
#phil __OFF__

Command line arguments: "../43.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14275
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 43

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.4607, 88.5498, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9001 1.95095
Completeness in resolution range: 0.926062
Completeness with d_max=infinity: 0.923313

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9001
                             d_min =   1.9510

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9001 1.95095
Completeness in resolution range: 0.926062
Completeness with d_max=infinity: 0.923313

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9005 -  4.1753 [2220/2248]  1995   225  10.1%
  bin  2:  4.1753 -  3.3262 [2138/2154]  1925   213  10.0%
  bin  3:  3.3262 -  2.9093 [2114/2133]  1908   206   9.7%
  bin  4:  2.9093 -  2.6449 [2077/2107]  1865   212  10.2%
  bin  5:  2.6449 -  2.4562 [2078/2097]  1862   216  10.4%
  bin  6:  2.4562 -  2.3120 [2062/2098]  1860   202   9.8%
  bin  7:  2.3120 -  2.1966 [2049/2083]  1853   196   9.6%
  bin  8:  2.1966 -  2.1012 [2049/2084]  1835   214  10.4%
  bin  9:  2.1012 -  2.0205 [1951/2057]  1766   185   9.5%
  bin 10:  2.0205 -  1.9510 [ 851/2092]   761    90  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_43/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:
        0.88 -     1.68: 9
        1.68 -     2.49: 71
        2.49 -     3.29: 3686
        3.29 -     4.10: 9551
        4.10 -     4.90: 15348
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  0.875 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  0.923 3.120 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.215 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.333 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.408 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28660 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_43/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_43/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.4607 88.54975 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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4714   r_free= 0.4671   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.276667                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9005 -  4.6572 0.99   1441  160 0.3603 0.3638      6.5464      6.5225|
|  2:  4.6572 -  3.7154 0.99   1394  155 0.3982 0.4254      6.7626      6.8313|
|  3:  3.7154 -  3.2513 0.99   1358  154 0.4539 0.4310      6.6716      6.6707|
|  4:  3.2513 -  2.9566 0.99   1347  142 0.4701 0.4955      6.5104       6.552|
|  5:  2.9566 -  2.7461 0.99   1337  155 0.4911 0.4804      6.3436      6.3957|
|  6:  2.7461 -  2.5851 0.99   1347  147 0.5124 0.4793      6.2668      6.1402|
|  7:  2.5851 -  2.4562 0.99   1331  159 0.5116 0.4689      6.2306      6.1553|
|  8:  2.4562 -  2.3497 0.98   1328  144 0.5162 0.5076      6.1652      6.1873|
|  9:  2.3497 -  2.2596 0.98   1329  140 0.5383 0.5467      6.1272      6.1707|
| 10:  2.2596 -  2.1819 0.98   1313  146 0.5301 0.4953      6.0904        6.07|
| 11:  2.1819 -  2.1138 1.00   1323  151 0.5293 0.4765      6.0112       5.981|
| 12:  2.1138 -  2.0536 0.97   1314  140 0.5237 0.5778      5.9499      5.9733|
| 13:  2.0536 -  1.9996 0.82   1090  118 0.5250 0.5311      5.8998      5.8427|
| 14:  1.9996 -  1.9510 0.29    378   48 0.5038 0.5032      5.8809      5.7806|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9005 -  4.6572  1441   160  0.72  32.39   0.83     0.77      67135.46|
|  2:  4.6572 -  3.7154  1394   155  0.69  36.29   0.92     0.79     110822.71|
|  3:  3.7154 -  3.2513  1358   154  0.57  46.54   0.91     0.75     120371.96|
|  4:  3.2513 -  2.9566  1347   142  0.47  54.05   0.90     0.67     109025.62|
|  5:  2.9566 -  2.7461  1337   155  0.44  56.93   0.89     0.62      78790.95|
|  6:  2.7461 -  2.5851  1347   147  0.42  58.36   0.89     0.60      65906.11|
|  7:  2.5851 -  2.4562  1331   159  0.43  57.60   0.89     0.59      58328.19|
|  8:  2.4562 -  2.3497  1328   144  0.38  61.65   0.93     0.56      55873.73|
|  9:  2.3497 -  2.2596  1329   140  0.37  62.10   0.90     0.56      52641.72|
| 10:  2.2596 -  2.1819  1313   146  0.38  61.24   0.92     0.56      45752.83|
| 11:  2.1819 -  2.1138  1323   151  0.36  62.76   0.91     0.60      45844.36|
| 12:  2.1138 -  2.0536  1314   140  0.33  65.36   0.94     0.55      42317.03|
| 13:  2.0536 -  1.9996  1090   118  0.30  67.88   0.94     0.49      39157.44|
| 14:  1.9996 -  1.9510   378    48  0.32  65.85   1.03     0.44      30489.85|
|alpha:            min =        0.44 max =            0.79 mean =         0.62|
|beta:             min =    30489.85 max =       120371.96 mean =     68519.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.43|
|phase err.(test): min =        0.00 max =           89.87 mean =        55.16|
|-----------------------------------------------------------------------------|

============================== 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 = 11.936567             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.895   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.085409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.956   (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 |  0.875 -  1.278:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.278 -  1.680:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.680 -  2.083:       17 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.083 -  2.485:       54 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.485 -  2.888:     1335 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.888 -  3.290:     2351 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.290 -  3.693:     3697 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.693 -  4.095:     5854 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.095 -  4.498:     6749 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.498 -  4.900:     8599 |
|-----------------------------------------------------------------------------|
|-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 |        0.234 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  0.875 |       1.267 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4714   r_free= 0.4671   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.276667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4640   r_free= 0.4571   ksol= 0.30   Bsol= 23.66   scale= 0.942   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-1.11,4.08,-0.00,0.00,0.00); trace/3= 0.88                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.269590                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.865247              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.659   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.158627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.661   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4640      final r-factor (work) = 0.3407          |
| start r-factor (free) = 0.4571      final r-factor (free) = 0.3741          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.1459 = 9.87 * 0.50 * 6.2667 + 1.00 * 0.2344                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4201 = 9.87 * 0.50 * 6.1379 + 1.00 * 0.1440                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3407      final r-factor (work) = 0.3063          |
| start r-factor (free) = 0.3741      final r-factor (free) = 0.3816          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1177 = 1.16 * 1.00 * 6.1379 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9697 = 1.16 * 1.00 * 5.9999 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.94   19.09    None  None   None       |
|    all(noH): 2823   0      0.00    87.94   19.09    None  None   None       |
|    Sol.    : 438    0      0.00    87.94   39.48    None  None   None       |
|    Mac.    : 2385   0      0.00    83.18   15.35    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 -   8.794:  800   |   5:    43.970 -  52.763:   95        |
|      1:     8.794 -  17.588:  855   |   6:    52.763 -  61.557:   71        |
|      2:    17.588 -  26.382:  491   |   7:    61.557 -  70.351:   39        |
|      3:    26.382 -  35.176:  280   |   8:    70.351 -  79.145:   17        |
|      4:    35.176 -  43.970:  165   |   9:    79.145 -  87.939:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3063 r_free = 0.3816             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3062 r_free = 0.3818             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3062   r_free= 0.3818   ksol= 0.30   Bsol= 23.66   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-1.11,4.08,-0.00,0.00,0.00); trace/3= 0.88                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.006113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3035   r_free= 0.3784   ksol= 0.33   Bsol= 46.15   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.31,1.96,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.001594                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.222601              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.033   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.429630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.828  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3035      final r-factor (work) = 0.2197          |
| start r-factor (free) = 0.3784      final r-factor (free) = 0.2833          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8044 = 8.22 * 0.50 * 5.9982 + 1.00 * 0.1441                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3037 = 8.22 * 0.50 * 5.8905 + 1.00 * 0.0862                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2197      final r-factor (work) = 0.1984          |
| start r-factor (free) = 0.2833      final r-factor (free) = 0.2609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5490 = 0.43 * 1.00 * 5.8905 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4536 = 0.43 * 1.00 * 5.6862 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.22   18.45    None  None   None       |
|    all(noH): 2823   0      0.00    88.22   18.45    None  None   None       |
|    Sol.    : 438    0      4.46    88.22   41.56    None  None   None       |
|    Mac.    : 2385   0      0.00    82.40   14.20    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 -   8.822:  751   |   5:    44.108 -  52.929:  105        |
|      1:     8.822 -  17.643: 1105   |   6:    52.929 -  61.751:   75        |
|      2:    17.643 -  26.465:  382   |   7:    61.751 -  70.572:   33        |
|      3:    26.465 -  35.286:  191   |   8:    70.572 -  79.394:   17        |
|      4:    35.286 -  44.108:  159   |   9:    79.394 -  88.215:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1984 r_free = 0.2609             target_work(ml) = 5.641         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1983 r_free = 0.2607             target_work(ml) = 5.640         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1983   r_free= 0.2607   ksol= 0.33   Bsol= 46.15   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.31,1.96,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.640299                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1974   r_free= 0.2600   ksol= 0.33   Bsol= 53.11   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.97,0.52,-0.00,0.00,0.00); trace/3= -1.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.639109                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.167721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.591   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.892330              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.489  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1974      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2600      final r-factor (free) = 0.2063          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7864 = 5.17 * 0.50 * 5.6892 + 1.00 * 0.0862                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3901 = 5.17 * 0.50 * 5.5395 + 1.00 * 0.0767                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.2063      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4933 = 1.89 * 1.00 * 5.5395 + 1.00 * 0.0106                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1661 = 1.89 * 1.00 * 5.3658 + 1.00 * 0.0122                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.06   18.69    None  None   None       |
|    all(noH): 2823   0      0.00    99.06   18.69    None  None   None       |
|    Sol.    : 438    0      5.45    99.06   45.82    None  None   None       |
|    Mac.    : 2385   0      0.00    90.54   13.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.906:  950   |   5:    49.531 -  59.437:  120        |
|      1:     9.906 -  19.812: 1156   |   6:    59.437 -  69.343:   73        |
|      2:    19.812 -  29.718:  244   |   7:    69.343 -  79.249:   41        |
|      3:    29.718 -  39.625:  128   |   8:    79.249 -  89.155:   13        |
|      4:    39.625 -  49.531:   92   |   9:    89.155 -  99.061:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1373 r_free = 0.1908             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1372 r_free = 0.1908             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1908   ksol= 0.33   Bsol= 53.11   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.97,0.52,-0.00,0.00,0.00); trace/3= -1.41                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.326687                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1908   ksol= 0.33   Bsol= 57.50   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,-2.50,-0.32,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.576423              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.442  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.103270              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.034  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9948 = 2.58 * 0.50 * 5.3704 + 1.00 * 0.0767                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8767 = 2.58 * 0.50 * 5.2906 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5585 = 0.10 * 1.00 * 5.2906 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5499 = 0.10 * 1.00 * 5.2555 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.65    88.23   17.32    None  None   None       |
|    all(noH): 2823   0      2.65    88.23   17.32    None  None   None       |
|    Sol.    : 438    0      6.34    85.75   39.53    None  None   None       |
|    Mac.    : 2385   0      2.65    88.23   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:     2.649 -  11.207: 1206   |   5:    45.437 -  53.995:   83        |
|      1:    11.207 -  19.764:  966   |   6:    53.995 -  62.552:   61        |
|      2:    19.764 -  28.322:  222   |   7:    62.552 -  71.110:   22        |
|      3:    28.322 -  36.880:  126   |   8:    71.110 -  79.668:   12        |
|      4:    36.880 -  45.437:  118   |   9:    79.668 -  88.225:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1268 r_free = 0.1705             target_work(ml) = 5.243         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1265 r_free = 0.1703             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1703   ksol= 0.33   Bsol= 57.50   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.35,-2.50,-0.32,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.242150                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1705   ksol= 0.32   Bsol= 46.52   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.45,-2.64,-0.52,-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: 5.242252                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.380153              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.806  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.297  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6873 = 1.38 * 0.50 * 5.2543 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6628 = 1.38 * 0.50 * 5.2361 + 1.00 * 0.0495                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2071 = 0.42 * 1.00 * 5.2361 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2009 = 0.42 * 1.00 * 5.2175 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.91    92.19   17.54    None  None   None       |
|    all(noH): 2823   0      1.91    92.19   17.54    None  None   None       |
|    Sol.    : 438    0      6.35    85.04   41.28    None  None   None       |
|    Mac.    : 2385   0      1.91    92.19   13.19    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:     1.912 -  10.940: 1184   |   5:    47.053 -  56.081:  101        |
|      1:    10.940 -  19.969:  983   |   6:    56.081 -  65.109:   63        |
|      2:    19.969 -  28.997:  225   |   7:    65.109 -  74.137:   22        |
|      3:    28.997 -  38.025:  115   |   8:    74.137 -  83.165:   14        |
|      4:    38.025 -  47.053:  111   |   9:    83.165 -  92.193:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1670             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1670             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1670   ksol= 0.32   Bsol= 46.52   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.45,-2.64,-0.52,-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: 5.217215                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9005 -  4.6572 0.99   1441  160 0.1031 0.1363      5.4233      5.6248|
|  2:  4.6572 -  3.7154 0.99   1394  155 0.0911 0.1181      5.4897       5.688|
|  3:  3.7154 -  3.2513 0.99   1358  154 0.1181 0.1584      5.5542      5.8539|
|  4:  3.2513 -  2.9566 0.99   1347  142 0.1367 0.1729       5.518      5.6746|
|  5:  2.9566 -  2.7461 0.99   1337  155 0.1440 0.1618      5.4136      5.5621|
|  6:  2.7461 -  2.5851 0.99   1347  147 0.1388 0.2186       5.284      5.5827|
|  7:  2.5851 -  2.4562 0.99   1331  159 0.1390 0.1790      5.2396      5.3979|
|  8:  2.4562 -  2.3497 0.98   1328  144 0.1272 0.1799      5.1419      5.3856|
|  9:  2.3497 -  2.2596 0.98   1329  140 0.1264 0.1886       5.082        5.36|
| 10:  2.2596 -  2.1819 0.98   1313  146 0.1209 0.1705      4.9981      5.1721|
| 11:  2.1819 -  2.1138 1.00   1323  151 0.1246 0.2032      4.9666      5.3861|
| 12:  2.1138 -  2.0536 0.97   1314  140 0.1270 0.1682      4.9364      5.1349|
| 13:  2.0536 -  1.9996 0.82   1090  118 0.1116 0.1690      4.8029      5.0192|
| 14:  1.9996 -  1.9510 0.29    378   48 0.0957 0.1908      4.6819      5.0449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9005 -  4.6572  1441   160  0.94   9.62   0.98     0.95       7728.04|
|  2:  4.6572 -  3.7154  1394   155  0.95   8.53   1.02     1.02       9994.10|
|  3:  3.7154 -  3.2513  1358   154  0.93  12.47   1.03     1.03      11696.41|
|  4:  3.2513 -  2.9566  1347   142  0.91  14.88   1.02     1.00      11387.88|
|  5:  2.9566 -  2.7461  1337   155  0.88  17.97   0.99     0.97      10312.04|
|  6:  2.7461 -  2.5851  1347   147  0.89  17.48   0.97     0.93       7711.19|
|  7:  2.5851 -  2.4562  1331   159  0.89  17.33   0.99     0.95       7214.19|
|  8:  2.4562 -  2.3497  1328   144  0.90  16.33   1.00     0.97       6087.65|
|  9:  2.3497 -  2.2596  1329   140  0.89  17.17   1.00     0.96       5592.75|
| 10:  2.2596 -  2.1819  1313   146  0.90  16.51   1.00     0.97       4782.02|
| 11:  2.1819 -  2.1138  1323   151  0.89  17.56   1.00     0.96       4708.68|
| 12:  2.1138 -  2.0536  1314   140  0.89  17.40   1.01     1.01       4433.04|
| 13:  2.0536 -  1.9996  1090   118  0.90  16.99   0.99     0.95       3544.03|
| 14:  1.9996 -  1.9510   378    48  0.92  13.43   0.99     0.95       2663.80|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2663.80 max =        11696.41 mean =      7305.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.59 mean =        15.27|
|phase err.(test): min =        0.00 max =           89.74 mean =        14.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1670   ksol= 0.31   Bsol= 46.45   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.56,-0.42,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.217168                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1670   ksol= 0.31   Bsol= 46.45   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.32,-2.56,-0.42,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.217168                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9005 -  4.6572 0.99   1441  160 0.1030 0.1363      5.4224      5.6262|
|  2:  4.6572 -  3.7154 0.99   1394  155 0.0912 0.1181      5.4904      5.6881|
|  3:  3.7154 -  3.2513 0.99   1358  154 0.1181 0.1585      5.5546      5.8543|
|  4:  3.2513 -  2.9566 0.99   1347  142 0.1367 0.1729      5.5179      5.6745|
|  5:  2.9566 -  2.7461 0.99   1337  155 0.1439 0.1617      5.4134      5.5617|
|  6:  2.7461 -  2.5851 0.99   1347  147 0.1387 0.2185      5.2837      5.5825|
|  7:  2.5851 -  2.4562 0.99   1331  159 0.1390 0.1791      5.2395      5.3978|
|  8:  2.4562 -  2.3497 0.98   1328  144 0.1272 0.1799      5.1419      5.3855|
|  9:  2.3497 -  2.2596 0.98   1329  140 0.1264 0.1886      5.0819      5.3603|
| 10:  2.2596 -  2.1819 0.98   1313  146 0.1209 0.1705      4.9981      5.1722|
| 11:  2.1819 -  2.1138 1.00   1323  151 0.1246 0.2031      4.9666      5.3861|
| 12:  2.1138 -  2.0536 0.97   1314  140 0.1269 0.1681      4.9363      5.1348|
| 13:  2.0536 -  1.9996 0.82   1090  118 0.1116 0.1690      4.8028      5.0189|
| 14:  1.9996 -  1.9510 0.29    378   48 0.0957 0.1905      4.6819      5.0442|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9005 -  4.6572  1441   160  0.94   9.62   0.98     0.95       7730.53|
|  2:  4.6572 -  3.7154  1394   155  0.95   8.54   1.02     1.02      10003.39|
|  3:  3.7154 -  3.2513  1358   154  0.93  12.48   1.03     1.03      11708.71|
|  4:  3.2513 -  2.9566  1347   142  0.91  14.88   1.02     1.00      11388.73|
|  5:  2.9566 -  2.7461  1337   155  0.88  17.97   0.99     0.97      10309.94|
|  6:  2.7461 -  2.5851  1347   147  0.89  17.48   0.98     0.93       7707.53|
|  7:  2.5851 -  2.4562  1331   159  0.89  17.33   0.99     0.95       7212.40|
|  8:  2.4562 -  2.3497  1328   144  0.90  16.33   1.00     0.97       6086.67|
|  9:  2.3497 -  2.2596  1329   140  0.89  17.18   1.01     0.96       5593.94|
| 10:  2.2596 -  2.1819  1313   146  0.90  16.51   1.01     0.97       4781.42|
| 11:  2.1819 -  2.1138  1323   151  0.89  17.56   1.00     0.96       4708.30|
| 12:  2.1138 -  2.0536  1314   140  0.89  17.40   1.01     1.01       4432.39|
| 13:  2.0536 -  1.9996  1090   118  0.90  16.99   0.99     0.96       3542.26|
| 14:  1.9996 -  1.9510   378    48  0.92  13.43   0.99     0.95       2661.26|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     2661.26 max =        11708.71 mean =      7306.14|
|figures of merit: min =        0.01 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.50 mean =        15.27|
|phase err.(test): min =        0.00 max =           89.72 mean =        14.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.583)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.84    92.12   17.48    None  None   None       |
|    all(noH): 2823   0      1.84    92.12   17.48    None  None   None       |
|    Sol.    : 438    0      6.28    84.97   41.21    None  None   None       |
|    Mac.    : 2385   0      1.84    92.12   13.12    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:     1.843 -  10.872: 1184   |   5:    46.984 -  56.012:  101        |
|      1:    10.872 -  19.900:  983   |   6:    56.012 -  65.040:   63        |
|      2:    19.900 -  28.928:  225   |   7:    65.040 -  74.068:   22        |
|      3:    28.928 -  37.956:  115   |   8:    74.068 -  83.097:   14        |
|      4:    37.956 -  46.984:  111   |   9:    83.097 -  92.125:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.535 - 4.432
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 310
   mapped sites are within: 0.753 - 4.432

peak=    6.393 closest distance to " O   HOH Z 103 " =    1.092
peak=    5.399 closest distance to " CB  ARG A 275 " =    0.978
peak=    5.345 closest distance to " CG  PRO A 280 " =    0.962
peak=    5.337 closest distance to " O   HOH Z 142 " =    1.741
peak=    5.222 closest distance to " OE1 GLN A  55 " =    2.127
peak=    5.071 closest distance to " CG  PRO A  54 " =    1.386
peak=    5.038 closest distance to " O   HOH Z 417 " =    1.659
peak=    4.996 closest distance to " NE2 GLN A  11 " =    1.186
peak=    4.974 closest distance to " CB  GLN A 223 " =    1.395
peak=    4.971 closest distance to " O   HOH Z 375 " =    1.249
peak=    4.968 closest distance to " CG2 VAL A 257 " =    0.936
peak=    4.935 closest distance to " O   HOH Z 402 " =    1.471
peak=    4.910 closest distance to " O   HOH Z 112 " =    1.288
peak=    4.905 closest distance to " O   HOH Z 403 " =    1.148
peak=    4.803 closest distance to " O   HOH Z 117 " =    1.313
peak=    4.710 closest distance to " CG  PRO A  90 " =    1.304
peak=    4.706 closest distance to " O   HOH Z 287 " =    1.888
peak=    4.637 closest distance to " O   HOH Z 126 " =    2.110
peak=    4.635 closest distance to " O   HOH Z 232 " =    2.442
peak=    4.572 closest distance to " O   HOH Z  70 " =    1.114
peak=    4.560 closest distance to " CG  PRO A 243 " =    1.117
peak=    4.559 closest distance to " CZ  PHE A 218 " =    1.202
peak=    4.536 closest distance to " O   HOH Z 236 " =    1.445
peak=    4.525 closest distance to " NH2 ARG A  56 " =    2.044
peak=    4.443 closest distance to " CB  ARG A  79 " =    1.325
peak=    4.439 closest distance to " O   HOH Z 369 " =    2.162
peak=    4.436 closest distance to " CB  PRO A  54 " =    1.037
peak=    4.436 closest distance to " O   HOH Z 188 " =    1.561
peak=    4.413 closest distance to " CA  ARG A 195 " =    1.315
peak=    4.394 closest distance to " O   HOH Z 248 " =    1.483
peak=    4.386 closest distance to " O   HOH Z  43 " =    2.246
peak=    4.383 closest distance to " O   HOH Z  49 " =    1.150
peak=    4.372 closest distance to " CD2 TRP A 179 " =    1.342
peak=    4.369 closest distance to " O   SER A  87 " =    2.347
peak=    4.358 closest distance to " O   HOH Z 132 " =    1.217
peak=    4.323 closest distance to " CB  ASN A 148 " =    1.456
peak=    4.256 closest distance to " CB  VAL A 265 " =    1.313
peak=    4.222 closest distance to " CG  GLN A  58 " =    1.216
peak=    4.198 closest distance to " CB  THR A  31 " =    1.606
peak=    4.190 closest distance to " O   HOH Z 188 " =    2.525
peak=    4.167 closest distance to " O   HOH Z 303 " =    2.193
peak=    4.147 closest distance to " O   HOH Z 371 " =    2.051
peak=    4.139 closest distance to " CB  ILE A 120 " =    1.294
peak=    4.137 closest distance to " O   HOH Z 406 " =    1.688
peak=    4.136 closest distance to " CB  ASN A 110 " =    1.047
peak=    4.127 closest distance to " CA  ARG A  36 " =    0.995
peak=    4.118 closest distance to " ND2 ASN A 187 " =    1.622
peak=    4.115 closest distance to " O   HOH Z 427 " =    2.844
peak=    4.106 closest distance to " CA  TYR A  30 " =    1.018
peak=    4.090 closest distance to " O   HOH Z 272 " =    1.830
peak=    4.083 closest distance to " CB  GLU A  46 " =    1.252
peak=    4.082 closest distance to " O   HOH Z 298 " =    1.868
peak=    4.059 closest distance to " CG  PRO A 198 " =    1.317
peak=    4.047 closest distance to " O   HOH Z  40 " =    2.042
peak=    4.039 closest distance to " O   HOH Z 126 " =    1.990
peak=    4.038 closest distance to " OG ASER A 258 " =    2.905
peak=    4.037 closest distance to " CB  ASN A 142 " =    1.000
peak=    4.027 closest distance to " NH1BARG A 145 " =    1.604
peak=    4.022 closest distance to " CB  ASN A  39 " =    0.857
peak=    4.021 closest distance to " CB  ALA A 114 " =    0.812
peak=    4.011 closest distance to " O   HOH Z 365 " =    2.595
peak=    4.003 closest distance to " CG  GLN A  11 " =    2.231
peak=    4.000 closest distance to " O   HOH Z 234 " =    3.400
peak=    3.995 closest distance to " CG  PRO A 213 " =    1.270
peak=    3.987 closest distance to " NZ  LYS A 117 " =    3.087
peak=    3.981 closest distance to " CB  GLN A  88 " =    1.228
peak=    3.966 closest distance to " CG2AVAL A 121 " =    2.295
peak=    3.965 closest distance to " O   HOH Z 126 " =    1.575
peak=    3.948 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.946 closest distance to " O   HOH Z 120 " =    1.132
peak=    3.946 closest distance to " CE  LYS A  76 " =    0.924
peak=    3.944 closest distance to " CB  PRO A  90 " =    1.122
peak=    3.942 closest distance to " CB  GLU A 152 " =    1.193
peak=    3.925 closest distance to " CB  SER A  63 " =    1.178
peak=    3.915 closest distance to " O   HOH Z 250 " =    1.434
peak=    3.914 closest distance to " O   HOH Z 185 " =    1.506
peak=    3.881 closest distance to " O   HOH Z 261 " =    2.066
peak=    3.878 closest distance to " CE  LYS A 119 " =    1.267
peak=    3.875 closest distance to " CB  ASP A 191 " =    1.163
peak=    3.858 closest distance to " O  BHOH Z  74 " =    1.245
peak=    3.851 closest distance to " CG2 ILE A 120 " =    1.235
peak=    3.844 closest distance to " O   HOH Z 327 " =    1.781
peak=    3.843 closest distance to " N   TYR A 116 " =    1.447
peak=    3.833 closest distance to " O   HOH Z 419 " =    2.047
peak=    3.826 closest distance to " CB  GLN A 183 " =    1.219
peak=    3.809 closest distance to " CG2 ILE A 239 " =    0.775
peak=    3.790 closest distance to " CA  ALA A  51 " =    0.957
peak=    3.782 closest distance to " OG1 THR A 264 " =    0.811
peak=    3.780 closest distance to " O   HOH Z 132 " =    2.082
peak=    3.765 closest distance to " O   THR A 220 " =    1.259
peak=    3.760 closest distance to " O   HOH Z 193 " =    1.215
peak=    3.739 closest distance to " O   HOH Z 213 " =    2.237
peak=    3.738 closest distance to " CB  TRP A 266 " =    1.197
peak=    3.736 closest distance to " CB  PRO A 198 " =    1.131
peak=    3.722 closest distance to " NH2AARG A 190 " =    2.091
peak=    3.720 closest distance to " O   HOH Z  97 " =    1.329
peak=    3.711 closest distance to " O   HOH Z 425 " =    1.363
peak=    3.707 closest distance to " O   HOH Z 251 " =    1.682
peak=    3.706 closest distance to " CB  ARG A 156 " =    1.035
peak=    3.702 closest distance to " CZ3 TRP A 266 " =    1.051
peak=    3.700 closest distance to " CA  ASN A 127 " =    1.151
peak=    3.692 closest distance to " NH2 ARG A  56 " =    1.118
peak=    3.687 closest distance to " O   PRO A 198 " =    1.647
peak=    3.674 closest distance to " O   HOH Z  78 " =    1.652
peak=    3.667 closest distance to " CA  ASP A 162 " =    1.045
peak=    3.666 closest distance to " O   HOH Z 415 " =    3.623
peak=    3.666 closest distance to " CB  SER A  26 " =    1.866
peak=    3.664 closest distance to " O   HOH Z 357 " =    2.014
peak=    3.654 closest distance to " O   HOH Z 180 " =    2.279
peak=    3.650 closest distance to " O   HOH Z 124 " =    1.217
peak=    3.650 closest distance to " CB  SER A  99 " =    0.834
peak=    3.636 closest distance to " CB  ALA A 291 " =    1.002
peak=    3.635 closest distance to " CB  ARG A 102 " =    0.867
peak=    3.623 closest distance to " CB  SER A  62 " =    0.898
peak=    3.619 closest distance to " O   HOH Z   1 " =    1.584
peak=    3.617 closest distance to " O   HOH Z 359 " =    1.692
peak=    3.610 closest distance to " CB  VAL A 202 " =    1.601
peak=    3.595 closest distance to " O   HOH Z 153 " =    3.842
peak=    3.592 closest distance to " O   HOH Z   9 " =    2.025
peak=    3.592 closest distance to " CZ  PHE A  38 " =    1.208
peak=    3.592 closest distance to " O   GLN A 194 " =    1.417
peak=    3.584 closest distance to " CG AARG A 275 " =    1.183
peak=    3.583 closest distance to " O   HOH Z 422 " =    1.079
peak=    3.582 closest distance to " O   HOH Z  44 " =    2.014
peak=    3.578 closest distance to " O   HOH Z   9 " =    1.191
peak=    3.576 closest distance to " N   ASN A  39 " =    1.159
peak=    3.573 closest distance to " CB  GLU A 277 " =    3.575
peak=    3.569 closest distance to " CG  ARG A  66 " =    2.470
peak=    3.566 closest distance to " O   HOH Z 346 " =    1.700
peak=    3.562 closest distance to " CG  LYS A  76 " =    1.856
peak=    3.555 closest distance to " CB  PHE A 204 " =    0.761
peak=    3.547 closest distance to " O   HOH Z   1 " =    1.930
peak=    3.544 closest distance to " O   ARG A 275 " =    1.455
peak=    3.540 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.536 closest distance to " O   HOH Z 246 " =    1.084
peak=    3.532 closest distance to " O   HOH Z  69 " =    0.905
peak=    3.530 closest distance to " CD1 ILE A 199 " =    1.313
peak=    3.530 closest distance to " CB  THR A  52 " =    0.753
peak=    3.529 closest distance to " CB  SER A 216 " =    1.000
peak=    3.528 closest distance to " CB  ASN A 285 " =    1.041
peak=    3.527 closest distance to " O   HOH Z 421 " =    2.271
peak=    3.527 closest distance to " O   HOH Z 394 " =    1.704
peak=    3.526 closest distance to " O   HOH Z 233 " =    1.675
peak=    3.523 closest distance to " CB  SER A 273 " =    0.923
peak=    3.522 closest distance to " O   HOH Z 368 " =    3.486
peak=    3.520 closest distance to " N   ASP A 162 " =    1.156
peak=    3.516 closest distance to " OG BSER A 164 " =    2.329
peak=    3.500 closest distance to " CB  GLN A  89 " =    1.302
peak=    3.490 closest distance to " O   HOH Z 395 " =    3.319
peak=    3.488 closest distance to " O   HOH Z 257 " =    1.294
peak=    3.487 closest distance to " N   PHE A 130 " =    1.291
peak=    3.479 closest distance to " O   HOH Z 218 " =    1.569
peak=    3.479 closest distance to " CB  ARG A 190 " =    1.586
peak=    3.474 closest distance to " O   HOH Z 325 " =    2.498
peak=    3.472 closest distance to " O   HOH Z  78 " =    2.152
peak=    3.471 closest distance to " CA  GLY A 241 " =    4.015
peak=    3.469 closest distance to " CD  ARG A 269 " =    0.968
peak=    3.461 closest distance to " CA  ASN A 215 " =    0.992
peak=    3.457 closest distance to " O   HOH Z  97 " =    1.887
peak=    3.455 closest distance to " O   HOH Z  92 " =    2.315
peak=    3.454 closest distance to " O   HOH Z 132 " =    2.573
peak=    3.450 closest distance to " O   HOH Z 258 " =    1.885
peak=    3.442 closest distance to " CG2 THR A 220 " =    0.911
peak=    3.441 closest distance to " CA  ASN A 217 " =    1.119
peak=    3.437 closest distance to " O   HOH Z 109 " =    1.721
peak=    3.437 closest distance to " O   HOH Z  80 " =    1.665
peak=    3.428 closest distance to " O   HOH Z 191 " =    2.806
peak=    3.427 closest distance to " O   HOH Z 407 " =    2.383
peak=    3.427 closest distance to " O   HOH Z  88 " =    2.435
peak=    3.426 closest distance to " O   HOH Z 353 " =    2.505
peak=    3.424 closest distance to " O   HOH Z 193 " =    1.872
peak=    3.419 closest distance to " CB  SER A  62 " =    0.931
peak=    3.418 closest distance to " O   HOH Z 298 " =    2.445
peak=    3.416 closest distance to " ND2BASN A 224 " =    0.900
peak=    3.412 closest distance to " CB  SER A 212 " =    1.315
peak=    3.409 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.403 closest distance to " O   HOH Z  85 " =    2.220
peak=    3.396 closest distance to " CA  VAL A 125 " =    1.035
peak=    3.395 closest distance to " O   HOH Z  88 " =    2.549
peak=    3.394 closest distance to " CB  ASP A 140 " =    1.034
peak=    3.384 closest distance to " CB  SER A 210 " =    0.814
peak=    3.383 closest distance to " O   HOH Z  21 " =    1.801
peak=    3.383 closest distance to " O   HOH Z  59 " =    1.760
peak=    3.382 closest distance to " O   HOH Z 380 " =    1.810
peak=    3.380 closest distance to " O   HOH Z   6 " =    1.543
peak=    3.375 closest distance to " N   TYR A  15 " =    1.146
peak=    3.375 closest distance to " O   HOH Z 143 " =    1.392
peak=    3.372 closest distance to " O   HOH Z  85 " =    1.506
peak=    3.370 closest distance to " CB  LYS A 166 " =    0.864
peak=    3.369 closest distance to " CB  GLU A 128 " =    0.947
peak=    3.363 closest distance to " CG2 ILE A  20 " =    1.600
peak=    3.363 closest distance to " O   HOH Z 193 " =    1.628
peak=    3.358 closest distance to " CA  GLN A  58 " =    0.964
peak=    3.357 closest distance to " O   HOH Z 425 " =    1.826
peak=    3.349 closest distance to " CA  ALA A 129 " =    1.466
peak=    3.344 closest distance to " OG BSER A 258 " =    2.963
peak=    3.343 closest distance to " CB  ASP A 107 " =    1.242
peak=    3.343 closest distance to " CE3 TRP A 150 " =    1.119
peak=    3.341 closest distance to " CB  GLU A 152 " =    1.581
peak=    3.337 closest distance to " O   HOH Z 128 " =    1.473
peak=    3.335 closest distance to " O   ASN A  74 " =    1.332
peak=    3.331 closest distance to " CB  LEU A 228 " =    1.072
peak=    3.330 closest distance to " CB  ASN A 173 " =    0.991
peak=    3.328 closest distance to " CA  ASP A 149 " =    1.190
peak=    3.320 closest distance to " CB  TRP A 179 " =    1.363
peak=    3.315 closest distance to " O   HOH Z  43 " =    1.823
peak=    3.310 closest distance to " CD2 LEU A 297 " =    0.997
peak=    3.305 closest distance to " CA  THR A 264 " =    0.914
peak=    3.303 closest distance to " O   HOH Z 119 " =    4.324
peak=    3.300 closest distance to " CG2 VAL A 197 " =    1.037
peak=    3.299 closest distance to " O   HOH Z 137 " =    1.581
peak=    3.296 closest distance to " O   HOH Z 394 " =    3.728
peak=    3.294 closest distance to " CB  ASP A 124 " =    0.771
peak=    3.293 closest distance to " CB  ASP A 272 " =    1.115
peak=    3.292 closest distance to " CG BARG A 275 " =    1.920
peak=    3.289 closest distance to " NE2 HIS A 207 " =    1.103
peak=    3.284 closest distance to " OG  SER A  62 " =    2.760
peak=    3.282 closest distance to " CA  ALA A 158 " =    1.489
peak=    3.278 closest distance to " O   HOH Z 148 " =    3.444
peak=    3.278 closest distance to " O   HOH Z 141 " =    1.652
peak=    3.271 closest distance to " O   HOH Z 111 " =    1.466
peak=    3.270 closest distance to " CA  ILE A 234 " =    1.000
peak=    3.266 closest distance to " O   HOH Z 244 " =    1.791
peak=    3.266 closest distance to " O   HOH Z 142 " =    1.634
peak=    3.264 closest distance to " O   HOH Z 385 " =    3.944
peak=    3.262 closest distance to " ND2 ASN A 209 " =    3.577
peak=    3.261 closest distance to " CG  MET A 113 " =    1.002
peak=    3.257 closest distance to " CB  HIS A 108 " =    0.881
peak=    3.257 closest distance to " O   HOH Z 305 " =    3.633
peak=    3.255 closest distance to " O   HOH Z  41 " =    1.861
peak=    3.249 closest distance to " O   HOH Z 173 " =    1.972
peak=    3.249 closest distance to " CA  SER A  32 " =    1.794
peak=    3.248 closest distance to " O   HOH Z 344 " =    3.063
peak=    3.248 closest distance to " O   HOH Z 203 " =    1.638
peak=    3.241 closest distance to " CG  MET A 185 " =    1.094
peak=    3.241 closest distance to " CA  ALA A 100 " =    1.037
peak=    3.235 closest distance to " O   HOH Z 280 " =    2.861
peak=    3.234 closest distance to " CB  ARG A 219 " =    1.234
peak=    3.234 closest distance to " CG2BVAL A  41 " =    0.841
peak=    3.232 closest distance to " O   HOH Z  61 " =    1.473
peak=    3.232 closest distance to " O   HOH Z 130 " =    2.156
peak=    3.231 closest distance to " O   HOH Z 389 " =    1.378
peak=    3.229 closest distance to " O   HOH Z  26 " =    1.242
peak=    3.225 closest distance to " O   HOH Z 214 " =    2.503
peak=    3.221 closest distance to " CB  ALA A 292 " =    1.003
peak=    3.218 closest distance to " CA  PHE A  59 " =    0.861
peak=    3.215 closest distance to " CD2 LEU A   5 " =    1.221
peak=    3.215 closest distance to " OD2 ASP A 286 " =    3.175
peak=    3.214 closest distance to " CA  ILE A 263 " =    1.115
peak=    3.211 closest distance to " N   ALA A 292 " =    1.069
peak=    3.203 closest distance to " O   HOH Z   1 " =    1.816
peak=    3.200 closest distance to " O   HOH Z  28 " =    1.857
peak=    3.195 closest distance to " N   VAL A 296 " =    1.814
peak=    3.193 closest distance to " O   HOH Z  44 " =    2.734
peak=    3.193 closest distance to " O   HOH Z   7 " =    1.331
peak=    3.193 closest distance to " O   HOH Z 293 " =    1.953
peak=    3.193 closest distance to " O   HOH Z 216 " =    3.876
peak=    3.192 closest distance to " CB  PHE A 130 " =    0.921
peak=    3.192 closest distance to " O   HOH Z 438 " =    2.678
peak=    3.188 closest distance to " O   HOH Z 198 " =    1.551
peak=    3.186 closest distance to " N   CYS A 260 " =    0.873
peak=    3.185 closest distance to " CB  TRP A 179 " =    1.677
peak=    3.179 closest distance to " O   HOH Z   5 " =    2.158
peak=    3.177 closest distance to " O   THR A 182 " =    1.483
peak=    3.174 closest distance to " CB  SER A  99 " =    1.307
peak=    3.173 closest distance to " OE1 GLN A  11 " =    2.062
peak=    3.173 closest distance to " O   HOH Z  85 " =    1.850
peak=    3.170 closest distance to " NZ  LYS A 117 " =    1.317
peak=    3.161 closest distance to " CA  ALA A 233 " =    1.099
peak=    3.154 closest distance to " O   HOH Z 299 " =    4.432
peak=    3.153 closest distance to " OG BSER A  99 " =    2.352
peak=    3.152 closest distance to " O   ASP A 124 " =    1.080
peak=    3.147 closest distance to " O   HOH Z 291 " =    1.392
peak=    3.144 closest distance to " CG1 ILE A 151 " =    0.919
peak=    3.141 closest distance to " CB  ARG A 156 " =    0.860
peak=    3.134 closest distance to " OD1 ASN A  69 " =    2.378
peak=    3.131 closest distance to " CB  LEU A 300 " =    1.061
peak=    3.130 closest distance to " O   HOH Z 281 " =    1.548
peak=    3.129 closest distance to " O   ARG A 275 " =    0.905
peak=    3.124 closest distance to " O   HOH Z 156 " =    2.580
peak=    3.121 closest distance to " CB  SER A 271 " =    1.567
peak=    3.119 closest distance to " NH1AARG A 145 " =    1.259
peak=    3.117 closest distance to " O   HOH Z  95 " =    1.129
peak=    3.113 closest distance to " O   HOH Z  24 " =    1.628
peak=    3.108 closest distance to " CB  ASN A 215 " =    1.041
peak=    3.107 closest distance to " O   HOH Z  47 " =    1.690
peak=    3.103 closest distance to " O   HOH Z 411 " =    1.583
peak=    3.102 closest distance to " CD  LYS A 166 " =    1.234
peak=    3.102 closest distance to " O   HOH Z  10 " =    2.378
peak=    3.094 closest distance to " CA  PRO A 280 " =    1.264
peak=    3.085 closest distance to " CB  GLU A 175 " =    1.061
peak=    3.083 closest distance to " CD1 LEU A 261 " =    1.183
peak=    3.080 closest distance to " CE1 TYR A  30 " =    1.129
peak=    3.076 closest distance to " CB  ALA A  10 " =    0.779
peak=    3.072 closest distance to " N   SER A 135 " =    1.257
peak=    3.065 closest distance to " CB  PRO A 243 " =    1.121
peak=    3.065 closest distance to " CD  ARG A  79 " =    0.893
peak=    3.063 closest distance to " O   ALA A   1 " =    1.734
peak=    3.061 closest distance to " CG2 THR A 221 " =    1.204
peak=    3.060 closest distance to " CG1BVAL A  72 " =    1.646
peak=    3.044 closest distance to " O   HOH Z 234 " =    2.243
peak=    3.025 closest distance to " CE1 HIS A 115 " =    3.217
peak=    3.023 closest distance to " O   HOH Z 174 " =    2.224
peak=    3.013 closest distance to " O   HOH Z 213 " =    1.982

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.694 - 5.832
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.802 - 5.832

peak=   -4.947 closest distance to " CD  ARG A  14 " =    3.140
peak=   -4.767 closest distance to " O   PRO A 198 " =    1.225
peak=   -4.643 closest distance to " NE2 GLN A  55 " =    1.024
peak=   -4.427 closest distance to " O   HOH Z  69 " =    1.455
peak=   -4.318 closest distance to " CE  MET A 105 " =    2.546
peak=   -4.271 closest distance to " O   HOH Z 193 " =    0.802
peak=   -4.271 closest distance to " OG BSER A 134 " =    1.424
peak=   -4.177 closest distance to " CG  GLN A  58 " =    0.936
peak=   -4.122 closest distance to " CG2 ILE A  20 " =    2.895
peak=   -4.096 closest distance to " O   HOH Z 211 " =    1.071
peak=   -4.067 closest distance to " O   HOH Z 198 " =    0.814
peak=   -4.023 closest distance to " CD1 LEU A 255 " =    2.760
peak=   -4.005 closest distance to " O   HOH Z 377 " =    2.090
peak=   -3.985 closest distance to " CB  PHE A 192 " =    2.047
peak=   -3.975 closest distance to " CG2 ILE A  49 " =    2.823
peak=   -3.969 closest distance to " O   HOH Z 394 " =    1.573
peak=   -3.962 closest distance to " O   HOH Z  91 " =    1.392
peak=   -3.945 closest distance to " C   HIS A 108 " =    1.069
peak=   -3.940 closest distance to " O   HOH Z 131 " =    4.095
peak=   -3.890 closest distance to " CB  GLN A  55 " =    1.240
peak=   -3.889 closest distance to " O   HOH Z 290 " =    0.901
peak=   -3.843 closest distance to " O   GLY A 241 " =    2.278
peak=   -3.827 closest distance to " CG2 THR A  18 " =    2.731
peak=   -3.806 closest distance to " CD1 LEU A 101 " =    2.242
peak=   -3.803 closest distance to " CG1 VAL A 112 " =    3.002
peak=   -3.796 closest distance to " CB  ALA A  43 " =    2.353
peak=   -3.776 closest distance to " O   HOH Z 231 " =    2.220
peak=   -3.770 closest distance to " CB  ASN A  39 " =    2.402
peak=   -3.738 closest distance to " O   HOH Z 119 " =    2.370
peak=   -3.723 closest distance to " O   HOH Z 387 " =    2.659
peak=   -3.722 closest distance to " O   ALA A 227 " =    1.370
peak=   -3.715 closest distance to " O   HOH Z 278 " =    1.005
peak=   -3.710 closest distance to " O   HOH Z 100 " =    0.902
peak=   -3.682 closest distance to " CG1 VAL A 265 " =    2.627
peak=   -3.674 closest distance to " CD2 TYR A 293 " =    1.991
peak=   -3.666 closest distance to " O   HOH Z 137 " =    1.394
peak=   -3.663 closest distance to " O   HOH Z  35 " =    2.416
peak=   -3.658 closest distance to " O   ALA A  10 " =    1.590
peak=   -3.649 closest distance to " O   HOH Z 313 " =    1.732
peak=   -3.649 closest distance to " O   HOH Z  20 " =    1.317
peak=   -3.637 closest distance to " CE BMET A  47 " =    1.163
peak=   -3.636 closest distance to " O   HOH Z 281 " =    3.005
peak=   -3.632 closest distance to " CB  ASP A 132 " =    2.393
peak=   -3.614 closest distance to " N   ALA A  43 " =    2.463
peak=   -3.607 closest distance to " NE2 GLN A  11 " =    1.756
peak=   -3.606 closest distance to " O   HOH Z 369 " =    2.173
peak=   -3.584 closest distance to " OG  SER A  97 " =    2.254
peak=   -3.583 closest distance to " CG  GLN A  88 " =    0.920
peak=   -3.578 closest distance to " O   HOH Z 116 " =    1.405
peak=   -3.576 closest distance to " O   PRO A 163 " =    1.420
peak=   -3.567 closest distance to " O   HOH Z 351 " =    1.430
peak=   -3.557 closest distance to " O   GLU A 152 " =    1.331
peak=   -3.549 closest distance to " O   HOH Z 103 " =    1.139
peak=   -3.541 closest distance to " O   HOH Z 359 " =    3.219
peak=   -3.536 closest distance to " CG  GLN A 223 " =    1.968
peak=   -3.527 closest distance to " CB  SER A 210 " =    1.115
peak=   -3.526 closest distance to " NH2 ARG A  66 " =    0.998
peak=   -3.526 closest distance to " O   HOH Z 187 " =    1.709
peak=   -3.523 closest distance to " CE2 TYR A  30 " =    2.776
peak=   -3.519 closest distance to " OXT GLY A 302 " =    2.904
peak=   -3.498 closest distance to " OD1 ASP A 171 " =    1.475
peak=   -3.495 closest distance to " CZ  PHE A 155 " =    1.080
peak=   -3.491 closest distance to " O   HOH Z  63 " =    1.645
peak=   -3.491 closest distance to " NZ  LYS A 166 " =    1.264
peak=   -3.489 closest distance to " CZ  TYR A 169 " =    1.707
peak=   -3.487 closest distance to " OH  TYR A 172 " =    1.921
peak=   -3.479 closest distance to " CB  ASN A  45 " =    2.013
peak=   -3.479 closest distance to " O   HOH Z  70 " =    0.975
peak=   -3.477 closest distance to " CG  GLU A 277 " =    1.439
peak=   -3.475 closest distance to " CA  GLY A  57 " =    2.107
peak=   -3.474 closest distance to " O   HOH Z 428 " =    2.877
peak=   -3.470 closest distance to " O   SER A  95 " =    1.547
peak=   -3.470 closest distance to " O   HOH Z 185 " =    2.017
peak=   -3.468 closest distance to " CB  ALA A 244 " =    2.066
peak=   -3.465 closest distance to " O   HOH Z 301 " =    2.555
peak=   -3.461 closest distance to " CD2 HIS A 207 " =    2.111
peak=   -3.456 closest distance to " O   HOH Z 276 " =    1.480
peak=   -3.455 closest distance to " OD2 ASP A 191 " =    1.392
peak=   -3.455 closest distance to " O   HOH Z 142 " =    1.085
peak=   -3.452 closest distance to " C   ARG A 195 " =    1.666
peak=   -3.452 closest distance to " CB  ALA A 100 " =    2.403
peak=   -3.448 closest distance to " OE1 GLN A 183 " =    1.539
peak=   -3.446 closest distance to " CB  TRP A  85 " =    2.513
peak=   -3.439 closest distance to " O   TYR A 247 " =    2.814
peak=   -3.435 closest distance to " CA  GLY A 241 " =    3.209
peak=   -3.434 closest distance to " CE2 PHE A  61 " =    2.710
peak=   -3.432 closest distance to " O   HOH Z  64 " =    1.415
peak=   -3.432 closest distance to " CB  ALA A   7 " =    2.034
peak=   -3.429 closest distance to " CD2 TYR A 247 " =    2.465
peak=   -3.420 closest distance to " CG  PRO A 198 " =    1.718
peak=   -3.419 closest distance to " O   VAL A  67 " =    2.590
peak=   -3.416 closest distance to " O   ASN A 187 " =    1.489
peak=   -3.415 closest distance to " CD  ARG A 156 " =    2.062
peak=   -3.412 closest distance to " O   ALA A 161 " =    1.766
peak=   -3.412 closest distance to " CA  GLY A 133 " =    2.013
peak=   -3.411 closest distance to " ND2 ASN A 249 " =    2.239
peak=   -3.409 closest distance to " O   HOH Z 236 " =    1.677
peak=   -3.401 closest distance to " CD1 TRP A  70 " =    1.061
peak=   -3.396 closest distance to " C   LEU A   5 " =    1.004
peak=   -3.395 closest distance to " CA  GLY A 203 " =    2.511
peak=   -3.394 closest distance to " O   ALA A   7 " =    1.576
peak=   -3.394 closest distance to " O   SER A 210 " =    1.995
peak=   -3.383 closest distance to " O   HOH Z 362 " =    5.832
peak=   -3.380 closest distance to " O   HOH Z 266 " =    5.474
peak=   -3.380 closest distance to " O   HOH Z 372 " =    2.363
peak=   -3.380 closest distance to " O   HOH Z   9 " =    1.634
peak=   -3.377 closest distance to " CB  PHE A 208 " =    2.270
peak=   -3.373 closest distance to " CZ2 TRP A 274 " =    1.041
peak=   -3.368 closest distance to " O   TRP A  70 " =    1.423
peak=   -3.354 closest distance to " N   THR A  52 " =    1.665
peak=   -3.347 closest distance to " N   ASP A 286 " =    2.122
peak=   -3.340 closest distance to " OG  SER A  63 " =    1.233
peak=   -3.336 closest distance to " O   HOH Z 298 " =    2.496
peak=   -3.336 closest distance to " O   HOH Z 295 " =    1.726
peak=   -3.334 closest distance to " CZ3 TRP A 179 " =    1.319
peak=   -3.332 closest distance to " CG  PHE A 283 " =    2.655
peak=   -3.331 closest distance to " OD1 ASN A 187 " =    1.681
peak=   -3.329 closest distance to " O   HIS A  81 " =    1.233
peak=   -3.325 closest distance to " CD  GLN A  88 " =    1.239
peak=   -3.321 closest distance to " O   HOH Z 165 " =    2.176
peak=   -3.320 closest distance to " CG  GLU A  46 " =    2.573
peak=   -3.319 closest distance to " O   ALA A 180 " =    1.002
peak=   -3.317 closest distance to " CD  PRO A 213 " =    2.071
peak=   -3.316 closest distance to " CD1 ILE A 199 " =    2.406
peak=   -3.314 closest distance to " O   SER A 146 " =    1.271
peak=   -3.313 closest distance to " O   HOH Z 390 " =    2.389
peak=   -3.309 closest distance to " NE  ARG A  79 " =    1.243
peak=   -3.303 closest distance to " O   HOH Z  49 " =    1.110
peak=   -3.303 closest distance to " O   HOH Z 140 " =    1.191
peak=   -3.301 closest distance to " O   HOH Z 201 " =    1.902
peak=   -3.301 closest distance to " CG  LEU A  83 " =    2.109
peak=   -3.300 closest distance to " O   HOH Z 102 " =    1.699
peak=   -3.300 closest distance to " O   HOH Z  63 " =    1.855
peak=   -3.291 closest distance to " O   HOH Z 374 " =    1.803
peak=   -3.282 closest distance to " O   HOH Z 357 " =    2.251
peak=   -3.280 closest distance to " O   HOH Z 166 " =    1.973
peak=   -3.279 closest distance to " O   SER A 276 " =    1.764
peak=   -3.278 closest distance to " CD2 PHE A 225 " =    0.988
peak=   -3.267 closest distance to " O   HOH Z 407 " =    2.514
peak=   -3.258 closest distance to " O   HOH Z 421 " =    3.128
peak=   -3.257 closest distance to " O   ASN A 252 " =    1.258
peak=   -3.251 closest distance to " CA  ASN A 127 " =    1.478
peak=   -3.247 closest distance to " O   GLN A 240 " =    2.104
peak=   -3.246 closest distance to " CE1 TYR A 247 " =    2.667
peak=   -3.242 closest distance to " CB  ALA A 129 " =    2.477
peak=   -3.242 closest distance to " N   ALA A 226 " =    1.954
peak=   -3.238 closest distance to " O   HOH Z 318 " =    1.807
peak=   -3.234 closest distance to " O   HOH Z 351 " =    1.586
peak=   -3.232 closest distance to " C   ALA A 114 " =    2.285
peak=   -3.232 closest distance to " NE2 GLN A 278 " =    1.496
peak=   -3.231 closest distance to " CG2 VAL A 296 " =    2.088
peak=   -3.230 closest distance to " O   HOH Z  60 " =    1.741
peak=   -3.223 closest distance to " CB  ALA A 291 " =    2.222
peak=   -3.215 closest distance to " O   HOH Z 250 " =    1.825
peak=   -3.209 closest distance to " OE2 GLU A 152 " =    1.351
peak=   -3.205 closest distance to " ND2 ASN A  45 " =    1.114
peak=   -3.200 closest distance to " ND2 ASN A 285 " =    2.173
peak=   -3.199 closest distance to " CG  PRO A 243 " =    1.775
peak=   -3.197 closest distance to " CB  ALA A 161 " =    2.350
peak=   -3.195 closest distance to " CZ  ARG A 259 " =    0.931
peak=   -3.193 closest distance to " CG2 THR A 178 " =    2.468
peak=   -3.185 closest distance to " O   HOH Z 139 " =    4.943
peak=   -3.181 closest distance to " O   HOH Z 397 " =    1.152
peak=   -3.178 closest distance to " O   HOH Z 309 " =    2.483
peak=   -3.176 closest distance to " O   VAL A 174 " =    2.193
peak=   -3.169 closest distance to " CZ3 TRP A 274 " =    2.233
peak=   -3.168 closest distance to " N   GLN A  58 " =    1.374
peak=   -3.163 closest distance to " CD1 LEU A 297 " =    2.515
peak=   -3.158 closest distance to " CG  MET A 105 " =    1.069
peak=   -3.157 closest distance to " O   HOH Z  37 " =    1.732
peak=   -3.148 closest distance to " ND2 ASN A 215 " =    2.133
peak=   -3.147 closest distance to " O   ARG A 219 " =    1.770
peak=   -3.142 closest distance to " CG  ARG A  66 " =    2.319
peak=   -3.142 closest distance to " CG  ARG A 138 " =    1.228
peak=   -3.135 closest distance to " CB  ASP A 200 " =    2.637
peak=   -3.128 closest distance to " CG1 VAL A 125 " =    1.737
peak=   -3.127 closest distance to " O   VAL A 189 " =    2.606
peak=   -3.122 closest distance to " O   GLN A 278 " =    1.390
peak=   -3.121 closest distance to " O   HOH Z 191 " =    5.798
peak=   -3.120 closest distance to " O   LYS A  76 " =    1.954
peak=   -3.117 closest distance to " O   HOH Z 423 " =    2.235
peak=   -3.116 closest distance to " O   PHE A 218 " =    1.534
peak=   -3.115 closest distance to " CG1 VAL A 126 " =    2.477
peak=   -3.112 closest distance to " CG1 VAL A 250 " =    2.558
peak=   -3.108 closest distance to " NZ  LYS A 119 " =    0.971
peak=   -3.106 closest distance to " O   HOH Z  60 " =    1.130
peak=   -3.103 closest distance to " N   ALA A 248 " =    1.622
peak=   -3.090 closest distance to " N   SER A 276 " =    1.386
peak=   -3.087 closest distance to " CD  GLN A  77 " =    1.193
peak=   -3.074 closest distance to " CD2 LEU A 237 " =    2.374
peak=   -3.074 closest distance to " CB  ALA A 248 " =    2.260
peak=   -3.068 closest distance to " CB  PRO A 163 " =    2.626
peak=   -3.066 closest distance to " O   HOH Z 252 " =    3.592
peak=   -3.065 closest distance to " O   HOH Z 371 " =    1.759
peak=   -3.065 closest distance to " O   HOH Z  11 " =    1.689
peak=   -3.051 closest distance to " CA  ASP A  27 " =    2.314
peak=   -3.033 closest distance to " O   HOH Z   5 " =    1.180

================= 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    :  0.4714 0.4671   6.276667e+00   6.268578e+00
   1_bss:  0.4640 0.4571   6.269590e+00   6.258528e+00
   1_xyz:  0.3407 0.3741   6.058721e+00   6.129618e+00
   1_adp:  0.3063 0.3816   6.006073e+00   6.142225e+00
   1_occ:  0.3062 0.3818   6.006113e+00   6.142849e+00
   2_bss:  0.3035 0.3784   6.001594e+00   6.142773e+00
   2_xyz:  0.2197 0.2833   5.726664e+00   5.928765e+00
   2_adp:  0.1984 0.2609   5.641191e+00   5.847739e+00
   2_occ:  0.1983 0.2607   5.640299e+00   5.846937e+00
   3_bss:  0.1974 0.2600   5.639109e+00   5.846724e+00
   3_xyz:  0.1518 0.2063   5.410216e+00   5.634487e+00
   3_adp:  0.1373 0.1908   5.326885e+00   5.566625e+00
   3_occ:  0.1372 0.1908   5.326687e+00   5.566705e+00
   4_bss:  0.1372 0.1908   5.324662e+00   5.564967e+00
   4_xyz:  0.1257 0.1751   5.245972e+00   5.489661e+00
   4_adp:  0.1268 0.1705   5.243315e+00   5.465717e+00
   4_occ:  0.1265 0.1703   5.242150e+00   5.465325e+00
   5_bss:  0.1264 0.1705   5.242252e+00   5.465676e+00
   5_xyz:  0.1242 0.1671   5.229229e+00   5.451542e+00
   5_adp:  0.1217 0.1670   5.217505e+00   5.450595e+00
   5_occ:  0.1216 0.1670   5.217215e+00   5.450547e+00
   5_bss:  0.1216 0.1670   5.217168e+00   5.450607e+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:  0.297  23.663  -0.331  -1.109   4.081  -0.000   0.000   0.000
   1_xyz:  0.297  23.663  -0.331  -1.109   4.081  -0.000   0.000   0.000
   1_adp:  0.297  23.663  -0.331  -1.109   4.081  -0.000   0.000   0.000
   1_occ:  0.297  23.663  -0.331  -1.109   4.081  -0.000   0.000   0.000
   2_bss:  0.328  46.149  -1.671  -1.311   1.961  -0.000   0.000   0.000
   2_xyz:  0.328  46.149  -1.671  -1.311   1.961  -0.000   0.000   0.000
   2_adp:  0.328  46.149  -1.671  -1.311   1.961  -0.000   0.000   0.000
   2_occ:  0.328  46.149  -1.671  -1.311   1.961  -0.000   0.000   0.000
   3_bss:  0.327  53.111  -2.773  -1.967   0.524  -0.000   0.000   0.000
   3_xyz:  0.327  53.111  -2.773  -1.967   0.524  -0.000   0.000   0.000
   3_adp:  0.327  53.111  -2.773  -1.967   0.524  -0.000   0.000   0.000
   3_occ:  0.327  53.111  -2.773  -1.967   0.524  -0.000   0.000   0.000
   4_bss:  0.326  57.499  -3.352  -2.505  -0.319  -0.000  -0.000  -0.000
   4_xyz:  0.326  57.499  -3.352  -2.505  -0.319  -0.000  -0.000  -0.000
   4_adp:  0.326  57.499  -3.352  -2.505  -0.319  -0.000  -0.000  -0.000
   4_occ:  0.326  57.499  -3.352  -2.505  -0.319  -0.000  -0.000  -0.000
   5_bss:  0.318  46.522  -3.452  -2.642  -0.516  -0.000  -0.000  -0.000
   5_xyz:  0.318  46.522  -3.452  -2.642  -0.516  -0.000  -0.000  -0.000
   5_adp:  0.318  46.522  -3.452  -2.642  -0.516  -0.000  -0.000  -0.000
   5_occ:  0.318  46.522  -3.452  -2.642  -0.516  -0.000  -0.000  -0.000
   5_bss:  0.313  46.453  -3.323  -2.562  -0.419  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.405 0.4532  0.6235    68515.148
   1_bss:  53.885 0.4717  0.6739    65429.136
   1_xyz:  40.241 0.6401  0.8728    39372.933
   1_adp:  41.265 0.6272  0.8608    41256.778
   1_occ:  41.328 0.6264  0.8595    41328.311
   2_bss:  40.976 0.6303  0.8301    40700.474
   2_xyz:  29.193 0.7654  0.9754    21505.679
   2_adp:  25.719 0.8040  1.0104    17830.274
   2_occ:  25.700 0.8041  1.0105    17782.812
   3_bss:  25.592 0.8052  0.9730    17712.480
   3_xyz:  19.773 0.8634  1.0007    10889.146
   3_adp:  18.034 0.8800  0.9991     9420.440
   3_occ:  18.032 0.8801  0.9991     9423.933
   4_bss:  17.942 0.8808  0.9765     9345.536
   4_xyz:  16.143 0.8969  0.9853     7869.486
   4_adp:  15.655 0.9014  0.9852     7633.643
   4_occ:  15.645 0.9015  0.9853     7624.496
   5_bss:  15.655 0.9014  0.9799     7627.519
   5_xyz:  15.287 0.9048  0.9795     7379.078
   5_adp:  15.231 0.9053  0.9741     7307.565
   5_occ:  15.224 0.9053  0.9741     7305.433
   5_bss:  15.225 0.9053  0.9752     7306.540
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.3443e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.3443e-01
   1_xyz:   1.634  0.012  0.104 16.026  0.007  4.103   1.4401e-01
   1_adp:   1.634  0.012  0.104 16.026  0.007  4.103   1.4401e-01
   1_occ:   1.634  0.012  0.104 16.026  0.007  4.103   1.4401e-01
   2_bss:   1.634  0.012  0.104 16.026  0.007  4.103   1.4401e-01
   2_xyz:   1.240  0.009  0.085 15.296  0.005  4.120   8.6188e-02
   2_adp:   1.240  0.009  0.085 15.296  0.005  4.120   8.6188e-02
   2_occ:   1.240  0.009  0.085 15.296  0.005  4.120   8.6188e-02
   3_bss:   1.240  0.009  0.085 15.296  0.005  4.120   8.6188e-02
   3_xyz:   1.146  0.009  0.079 14.950  0.004  4.114   7.6677e-02
   3_adp:   1.146  0.009  0.079 14.950  0.004  4.114   7.6677e-02
   3_occ:   1.146  0.009  0.079 14.950  0.004  4.114   7.6677e-02
   4_bss:   1.146  0.009  0.079 14.950  0.004  4.114   7.6677e-02
   4_xyz:   1.018  0.007  0.073 14.659  0.004  4.119   6.1354e-02
   4_adp:   1.018  0.007  0.073 14.659  0.004  4.119   6.1354e-02
   4_occ:   1.018  0.007  0.073 14.659  0.004  4.119   6.1354e-02
   5_bss:   1.018  0.007  0.073 14.659  0.004  4.119   6.1354e-02
   5_xyz:   0.903  0.005  0.068 14.299  0.004  4.117   4.9513e-02
   5_adp:   0.903  0.005  0.068 14.299  0.004  4.117   4.9513e-02
   5_occ:   0.903  0.005  0.068 14.299  0.004  4.117   4.9513e-02
   5_bss:   0.903  0.005  0.068 14.299  0.004  4.117   4.9513e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.875   2.4527e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.875   2.4527e-01
   1_xyz:  10.089  0.077  0.408 86.193  0.047  1.911   9.7135e-02
   1_adp:  10.089  0.077  0.408 86.193  0.047  1.911   9.7135e-02
   1_occ:  10.089  0.077  0.408 86.193  0.047  1.911   9.7135e-02
   2_bss:  10.089  0.077  0.408 86.193  0.047  1.911   9.7135e-02
   2_xyz:   8.456  0.072  0.320 87.481  0.039  2.249   1.1599e-01
   2_adp:   8.456  0.072  0.320 87.481  0.039  2.249   1.1599e-01
   2_occ:   8.456  0.072  0.320 87.481  0.039  2.249   1.1599e-01
   3_bss:   8.456  0.072  0.320 87.481  0.039  2.249   1.1599e-01
   3_xyz:   7.491  0.053  0.261 85.388  0.033  2.201   1.3186e-01
   3_adp:   7.491  0.053  0.261 85.388  0.033  2.201   1.3186e-01
   3_occ:   7.491  0.053  0.261 85.388  0.033  2.201   1.3186e-01
   4_bss:   7.491  0.053  0.261 85.388  0.033  2.201   1.3186e-01
   4_xyz:   6.724  0.043  0.242 82.841  0.038  2.278   8.5096e-02
   4_adp:   6.724  0.043  0.242 82.841  0.038  2.278   8.5096e-02
   4_occ:   6.724  0.043  0.242 82.841  0.038  2.278   8.5096e-02
   5_bss:   6.724  0.043  0.242 82.841  0.038  2.278   8.5096e-02
   5_xyz:   6.402  0.037  0.218 82.612  0.033  2.339   3.1097e-02
   5_adp:   6.402  0.037  0.218 82.612  0.033  2.339   3.1097e-02
   5_occ:   6.402  0.037  0.218 82.612  0.033  2.339   3.1097e-02
   5_bss:   6.402  0.037  0.218 82.612  0.033  2.339   3.1097e-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:  87.94   0.00  19.09  83.18   0.00  15.35  87.94   0.00  39.48
   1_occ:  87.94   0.00  19.09  83.18   0.00  15.35  87.94   0.00  39.48
   2_bss:  87.94   0.00  19.09  83.18   0.00  15.35  87.94   0.00  39.48
   2_xyz:  87.94   0.00  19.09  83.18   0.00  15.35  87.94   0.00  39.48
   2_adp:  88.22   0.00  18.45  82.40   0.00  14.20  88.22   4.46  41.56
   2_occ:  88.22   0.00  18.45  82.40   0.00  14.20  88.22   4.46  41.56
   3_bss:  88.22   0.00  18.45  82.40   0.00  14.20  88.22   4.46  41.56
   3_xyz:  88.22   0.00  18.45  82.40   0.00  14.20  88.22   4.46  41.56
   3_adp:  99.06   0.00  18.69  90.54   0.00  13.71  99.06   5.45  45.82
   3_occ:  99.06   0.00  18.69  90.54   0.00  13.71  99.06   5.45  45.82
   4_bss:  99.06   0.00  18.69  90.54   0.00  13.71  99.06   5.45  45.82
   4_xyz:  99.06   0.00  18.69  90.54   0.00  13.71  99.06   5.45  45.82
   4_adp:  88.23   2.65  17.32  88.23   2.65  13.24  85.75   6.34  39.53
   4_occ:  88.23   2.65  17.32  88.23   2.65  13.24  85.75   6.34  39.53
   5_bss:  88.23   2.65  17.32  88.23   2.65  13.24  85.75   6.34  39.53
   5_xyz:  88.23   2.65  17.32  88.23   2.65  13.24  85.75   6.34  39.53
   5_adp:  92.19   1.91  17.54  92.19   1.91  13.19  85.04   6.35  41.28
   5_occ:  92.19   1.91  17.54  92.19   1.91  13.19  85.04   6.35  41.28
   5_bss:  92.12   1.84  17.48  92.12   1.84  13.12  84.97   6.28  41.21
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    3.326    0.026    0.409
   1_adp:    3.326    0.026    0.409
   1_occ:    3.326    0.026    0.409
   2_bss:    3.326    0.026    0.409
   2_xyz:    3.334    0.048    0.606
   2_adp:    3.334    0.048    0.606
   2_occ:    3.334    0.048    0.606
   3_bss:    3.334    0.048    0.606
   3_xyz:    3.324    0.052    0.709
   3_adp:    3.324    0.052    0.709
   3_occ:    3.324    0.052    0.709
   4_bss:    3.324    0.052    0.709
   4_xyz:    3.262    0.106    0.730
   4_adp:    3.262    0.106    0.730
   4_occ:    3.262    0.106    0.730
   5_bss:    3.262    0.106    0.730
   5_xyz:    3.228    0.028    0.745
   5_adp:    3.228    0.028    0.745
   5_occ:    3.228    0.028    0.745
   5_bss:    3.228    0.028    0.745
------------------------------------------------------------------------

CPU time actual refinement: 337.76


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_43/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_43/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_43/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_43/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_43/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.61 
  Macro-tasks:
    bulk solvent and scale       = 40.56  
    individual site refinement   = 138.78 
    weights calculation          = 29.93  
    collect and process          = 6.43   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.80 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 107.44 
    alpha_beta                      = 8.00   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.03 
    fmodel                         = 7.09   
    r_factors                      = 0.16   
    phase_errors                   = 10.67  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 253.61 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.789 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    645 calls, 107.07 s
gradients_fft:          590 calls, 103.82 s

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

# Date 2008-01-16 Time 03:51:57 PST -0800 (1200484317.63 s)
Start R-work = 0.4714, R-free = 0.4671 (no bulk solvent and anisotropic scale)
Final R-work = 0.1480, R-free = 0.1859 (no bulk solvent and anisotropic scale)

Start R-work = 0.4640, R-free = 0.4571
Final R-work = 0.1216, R-free = 0.1670