# Date 2008-01-16 Time 03:56:14 PST -0800 (1200484574.25 s)
#phil __OFF__

Command line arguments: "../105.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17752
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 105

-------------------------------------------------------------------------------
  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, 47.8686, 86.822, 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, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9766 1.95088
Completeness in resolution range: 0.916573
Completeness with d_max=infinity: 0.913879

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9766
                             d_min =   1.9509

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, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9766 1.95088
Completeness in resolution range: 0.916573
Completeness with d_max=infinity: 0.913879

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9770 -  4.1755 [2243/2272]  2014   229  10.2%
  bin  2:  4.1755 -  3.3262 [2151/2174]  1935   216  10.0%
  bin  3:  3.3262 -  2.9092 [2126/2151]  1922   204   9.6%
  bin  4:  2.9092 -  2.6448 [2101/2128]  1887   214  10.2%
  bin  5:  2.6448 -  2.4561 [2079/2112]  1867   212  10.2%
  bin  6:  2.4561 -  2.3119 [2084/2112]  1878   206   9.9%
  bin  7:  2.3119 -  2.1965 [2072/2108]  1872   200   9.7%
  bin  8:  2.1965 -  2.1011 [2076/2118]  1866   210  10.1%
  bin  9:  2.1011 -  2.0204 [1995/2096]  1797   198   9.9%
  bin 10:  2.0204 -  1.9509 [ 662/2101]   592    70  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_105/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:
        0.99 -     1.77: 8
        1.77 -     2.55: 59
        2.55 -     3.33: 3966
        3.33 -     4.12: 9429
        4.12 -     4.90: 14970
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.985 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.036 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.204 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.460 3.040 -x+1/2,-y+1,z+1/2
  " N   TRP A  92 " - " O   HOH Z 401 "  1.565 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28427 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_105/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_105/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 47.8686 86.82195 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 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4573   r_free= 0.4496   ksol= 0.00   Bsol= 0.00   scale= 0.899    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.269766                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9770 -  4.6577 0.99   1461  161 0.3678 0.3915      6.5558      6.6187|
|  2:  4.6577 -  3.7156 0.99   1403  154 0.3913 0.3835      6.7828        6.77|
|  3:  3.7156 -  3.2514 0.99   1363  153 0.4326 0.4223      6.6439      6.6717|
|  4:  3.2514 -  2.9566 0.98   1375  148 0.4454 0.4000      6.4776      6.4481|
|  5:  2.9566 -  2.7461 0.99   1335  155 0.4865 0.4723      6.3418      6.3409|
|  6:  2.7461 -  2.5850 0.99   1377  150 0.4797 0.5015      6.2588       6.171|
|  7:  2.5850 -  2.4561 0.98   1311  154 0.4906 0.4286      6.2095      6.1219|
|  8:  2.4561 -  2.3497 0.98   1344  143 0.5111 0.5060      6.1614      6.1863|
|  9:  2.3497 -  2.2595 0.99   1341  140 0.5162 0.5115      6.1099      6.1506|
| 10:  2.2595 -  2.1818 0.99   1352  147 0.5027 0.4842      6.0767      6.0814|
| 11:  2.1818 -  2.1138 0.97   1308  156 0.5156 0.5357      6.0086      6.0573|
| 12:  2.1138 -  2.0535 0.98   1316  151 0.5148 0.4642       5.944      5.9282|
| 13:  2.0535 -  1.9996 0.80   1084  114 0.4992 0.5719      5.8557      5.7955|
| 14:  1.9996 -  1.9509 0.19    260   33 0.4932 0.4657      5.9041      5.7184|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9770 -  4.6577  1461   161  0.67  36.60   0.83     0.70      77431.88|
|  2:  4.6577 -  3.7156  1403   154  0.71  34.47   0.92     0.80     103468.81|
|  3:  3.7156 -  3.2514  1363   153  0.61  42.67   0.92     0.80     105459.43|
|  4:  3.2514 -  2.9566  1375   148  0.55  48.03   0.92     0.75      88458.37|
|  5:  2.9566 -  2.7461  1335   155  0.48  53.75   0.88     0.68      72152.20|
|  6:  2.7461 -  2.5850  1377   150  0.47  54.74   0.90     0.64      61567.00|
|  7:  2.5850 -  2.4561  1311   154  0.44  56.59   0.92     0.61      57287.93|
|  8:  2.4561 -  2.3497  1344   143  0.41  59.17   0.91     0.59      52605.09|
|  9:  2.3497 -  2.2595  1341   140  0.40  60.37   0.91     0.60      51382.92|
| 10:  2.2595 -  2.1818  1352   147  0.39  60.64   0.93     0.58      46945.32|
| 11:  2.1818 -  2.1138  1308   156  0.36  63.47   0.93     0.56      45817.87|
| 12:  2.1138 -  2.0535  1316   151  0.31  67.21   0.93     0.51      44090.02|
| 13:  2.0535 -  1.9996  1084   114  0.28  69.41   0.95     0.46      38950.35|
| 14:  1.9996 -  1.9509   260    33  0.32  65.69   0.96     0.41      29927.39|
|alpha:            min =        0.41 max =            0.80 mean =         0.64|
|beta:             min =    29927.39 max =       105459.43 mean =     65280.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.09|
|phase err.(test): min =        0.00 max =           89.97 mean =        54.26|
|-----------------------------------------------------------------------------|

============================== 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 = 9.552607              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.673   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.969831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.698   (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 |  0.985 -  1.377:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.377 -  1.768:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.768 -  2.160:       13 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.160 -  2.551:       46 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.551 -  2.943:     1615 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.943 -  3.334:     2351 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.334 -  3.726:     3805 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.726 -  4.117:     5624 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.117 -  4.509:     6583 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.509 -  4.900:     8387 |
|-----------------------------------------------------------------------------|
|-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 |        0.223 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  0.985 |       1.079 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    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 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4573   r_free= 0.4496   ksol= 0.00   Bsol= 0.00   scale= 0.899    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.269766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4495   r_free= 0.4398   ksol= 0.31   Bsol= 36.44   scale= 0.937   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,3.57,-1.31,0.00,-0.00,-0.00); trace/3= 0.69                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.262640                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.278404              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.294   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.056161              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.385   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4495      final r-factor (work) = 0.3446          |
| start r-factor (free) = 0.4398      final r-factor (free) = 0.3711          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.1479 = 8.28 * 0.50 * 6.2632 + 1.00 * 0.2232                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.5356 = 8.28 * 0.50 * 6.1396 + 1.00 * 0.1228                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3446      final r-factor (work) = 0.3103          |
| start r-factor (free) = 0.3711      final r-factor (free) = 0.3728          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4903 = 1.06 * 1.00 * 6.1396 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3782 = 1.06 * 1.00 * 6.0218 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.31   19.33    None  None   None       |
|    all(noH): 2823   0      0.00    95.31   19.33    None  None   None       |
|    Sol.    : 438    0      0.00    95.31   39.17    None  None   None       |
|    Mac.    : 2385   0      0.00    87.95   15.69    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 -   9.531:  887   |   5:    47.656 -  57.188:   94        |
|      1:     9.531 -  19.063:  868   |   6:    57.188 -  66.719:   54        |
|      2:    19.063 -  28.594:  471   |   7:    66.719 -  76.250:   34        |
|      3:    28.594 -  38.125:  258   |   8:    76.250 -  85.782:   12        |
|      4:    38.125 -  47.656:  138   |   9:    85.782 -  95.313:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3103 r_free = 0.3728             target_work(ml) = 6.023         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3100 r_free = 0.3728             target_work(ml) = 6.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3100   r_free= 0.3728   ksol= 0.31   Bsol= 36.44   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,3.57,-1.31,0.00,-0.00,-0.00); trace/3= 0.69                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.022541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3080   r_free= 0.3698   ksol= 0.31   Bsol= 48.97   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,1.58,-0.45,0.00,-0.00,-0.00); trace/3= -0.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.018157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.833201              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.890   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.603287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.071  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3080      final r-factor (work) = 0.2316          |
| start r-factor (free) = 0.3698      final r-factor (free) = 0.2842          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6934 = 6.83 * 0.50 * 6.0206 + 1.00 * 0.1233                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2770 = 6.83 * 0.50 * 5.9102 + 1.00 * 0.0844                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2316      final r-factor (work) = 0.2113          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2712          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5838 = 0.60 * 1.00 * 5.9102 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4691 = 0.60 * 1.00 * 5.7288 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   18.84    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   18.84    None  None   None       |
|    Sol.    : 438    0      3.47    90.51   41.69    None  None   None       |
|    Mac.    : 2385   0      0.00    86.81   14.64    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 -   9.051:  828   |   5:    45.253 -  54.303:   98        |
|      1:     9.051 -  18.101: 1058   |   6:    54.303 -  63.354:   69        |
|      2:    18.101 -  27.152:  357   |   7:    63.354 -  72.404:   36        |
|      3:    27.152 -  36.202:  197   |   8:    72.404 -  81.455:   30        |
|      4:    36.202 -  45.253:  138   |   9:    81.455 -  90.505:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2113 r_free = 0.2712             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2110 r_free = 0.2711             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2110   r_free= 0.2711   ksol= 0.31   Bsol= 48.97   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,1.58,-0.45,0.00,-0.00,-0.00); trace/3= -0.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.702991                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2105   r_free= 0.2701   ksol= 0.31   Bsol= 48.97   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.02,-0.68,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.700687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.187392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.589  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.862  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2105      final r-factor (work) = 0.1598          |
| start r-factor (free) = 0.2701      final r-factor (free) = 0.2094          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9475 = 5.19 * 0.50 * 5.7305 + 1.00 * 0.0844                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5796 = 5.19 * 0.50 * 5.5945 + 1.00 * 0.0692                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1598      final r-factor (work) = 0.1451          |
| start r-factor (free) = 0.2094      final r-factor (free) = 0.1930          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7580 = 0.49 * 1.00 * 5.5945 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6718 = 0.49 * 1.00 * 5.4102 + 1.00 * 0.0172                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.12   18.26    None  None   None       |
|    all(noH): 2823   0      0.00    95.12   18.26    None  None   None       |
|    Sol.    : 438    0      5.63    89.22   43.39    None  None   None       |
|    Mac.    : 2385   0      0.00    95.12   13.64    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 -   9.513:  904   |   5:    47.562 -  57.075:  104        |
|      1:     9.513 -  19.025: 1176   |   6:    57.075 -  66.587:   73        |
|      2:    19.025 -  28.537:  262   |   7:    66.587 -  76.100:   33        |
|      3:    28.537 -  38.050:  126   |   8:    76.100 -  85.612:   18        |
|      4:    38.050 -  47.562:  118   |   9:    85.612 -  95.125:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1451 r_free = 0.1930             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1450 r_free = 0.1928             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1928   ksol= 0.31   Bsol= 48.97   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-0.02,-0.68,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.369446                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1451   r_free= 0.1925   ksol= 0.32   Bsol= 55.32   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.10,-1.06,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.370027                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.940057              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.946  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616455              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.297   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1451      final r-factor (work) = 0.1307          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3225 = 1.94 * 0.50 * 5.4157 + 1.00 * 0.0692                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2222 = 1.94 * 0.50 * 5.3259 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1307      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1786      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2955 = 0.62 * 1.00 * 5.3259 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2595 = 0.62 * 1.00 * 5.2697 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    100.04  17.98    None  None   None       |
|    all(noH): 2823   0      1.21    100.04  17.98    None  None   None       |
|    Sol.    : 438    0      5.61    93.88   43.47    None  None   None       |
|    Mac.    : 2385   0      1.21    100.04  13.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.211 -  11.093: 1260   |   5:    50.624 -  60.507:   90        |
|      1:    11.093 -  20.976:  949   |   6:    60.507 -  70.389:   64        |
|      2:    20.976 -  30.859:  187   |   7:    70.389 -  80.272:   32        |
|      3:    30.859 -  40.741:  117   |   8:    80.272 -  90.155:   10        |
|      4:    40.741 -  50.624:  108   |   9:    90.155 - 100.037:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1270 r_free = 0.1753             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1269 r_free = 0.1753             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1753   ksol= 0.32   Bsol= 55.32   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.10,-1.06,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258672                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1754   ksol= 0.32   Bsol= 55.32   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-1.35,-1.00,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258677                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.259511              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.918  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.250681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.119  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1269      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0092 = 2.26 * 0.50 * 5.2696 + 1.00 * 0.0559                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9720 = 2.26 * 0.50 * 5.2309 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3221 = 0.25 * 1.00 * 5.2309 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3131 = 0.25 * 1.00 * 5.2022 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    98.95   17.28    None  None   None       |
|    all(noH): 2823   0      1.69    98.95   17.28    None  None   None       |
|    Sol.    : 438    0      5.35    91.50   40.80    None  None   None       |
|    Mac.    : 2385   0      1.69    98.95   12.97    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:     1.688 -  11.414: 1341   |   5:    50.319 -  60.045:   78        |
|      1:    11.414 -  21.140:  898   |   6:    60.045 -  69.771:   43        |
|      2:    21.140 -  30.866:  179   |   7:    69.771 -  79.497:   21        |
|      3:    30.866 -  40.593:  129   |   8:    79.497 -  89.223:    8        |
|      4:    40.593 -  50.319:  121   |   9:    89.223 -  98.949:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1620             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1184 r_free = 0.1619             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1619   ksol= 0.32   Bsol= 55.32   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,-1.35,-1.00,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.192519                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9770 -  4.6577 0.99   1461  161 0.0986 0.1332      5.3909      5.5927|
|  2:  4.6577 -  3.7156 0.99   1403  154 0.0849 0.1013      5.4274      5.5937|
|  3:  3.7156 -  3.2514 0.99   1363  153 0.1128 0.1532      5.4887      5.8143|
|  4:  3.2514 -  2.9566 0.98   1375  148 0.1328 0.1711       5.484      5.6631|
|  5:  2.9566 -  2.7461 0.99   1335  155 0.1432 0.1737      5.3848      5.5598|
|  6:  2.7461 -  2.5850 0.99   1377  150 0.1339 0.2114      5.2611      5.4841|
|  7:  2.5850 -  2.4561 0.98   1311  154 0.1343 0.1665      5.2172      5.3928|
|  8:  2.4561 -  2.3497 0.98   1344  143 0.1281 0.1835      5.1406      5.3658|
|  9:  2.3497 -  2.2595 0.99   1341  140 0.1250 0.1920      5.0659      5.3398|
| 10:  2.2595 -  2.1818 0.99   1352  147 0.1193 0.1778       4.991      5.1846|
| 11:  2.1818 -  2.1138 0.97   1308  156 0.1226 0.1800      4.9361      5.2509|
| 12:  2.1138 -  2.0535 0.98   1316  151 0.1190 0.1595      4.8739      5.0822|
| 13:  2.0535 -  1.9996 0.80   1084  114 0.1175 0.1948      4.7964      5.0709|
| 14:  1.9996 -  1.9509 0.19    260   33 0.1124 0.1927      4.7646      4.9494|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9770 -  4.6577  1461   161  0.94   9.49   0.97     0.95       7473.37|
|  2:  4.6577 -  3.7156  1403   154  0.95   7.88   1.02     1.00       8896.13|
|  3:  3.7156 -  3.2514  1363   153  0.93  11.58   1.02     1.02      10333.20|
|  4:  3.2514 -  2.9566  1375   148  0.91  14.96   1.01     1.00      10855.60|
|  5:  2.9566 -  2.7461  1335   155  0.89  16.87   1.01     0.98       9196.94|
|  6:  2.7461 -  2.5850  1377   150  0.89  17.16   0.98     0.95       7596.63|
|  7:  2.5850 -  2.4561  1311   154  0.90  16.70   0.99     0.97       6920.63|
|  8:  2.4561 -  2.3497  1344   143  0.89  17.14   1.00     0.96       6205.27|
|  9:  2.3497 -  2.2595  1341   140  0.89  16.93   0.99     0.95       5448.99|
| 10:  2.2595 -  2.1818  1352   147  0.90  16.60   1.00     0.97       4787.49|
| 11:  2.1818 -  2.1138  1308   156  0.90  16.54   0.99     0.96       4314.56|
| 12:  2.1138 -  2.0535  1316   151  0.90  16.33   1.00     1.00       3874.14|
| 13:  2.0535 -  1.9996  1084   114  0.89  17.08   0.99     0.98       3446.48|
| 14:  1.9996 -  1.9509   260    33  0.91  15.08   0.97     0.93       2937.30|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2937.30 max =        10855.60 mean =      6896.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.92|
|phase err.(test): min =        0.00 max =           88.49 mean =        14.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1623   ksol= 0.32   Bsol= 55.26   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.29,-0.94,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.194335                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1623   ksol= 0.32   Bsol= 55.26   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.29,-0.94,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.194335                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9770 -  4.6577 0.99   1461  161 0.1000 0.1329      5.3952      5.5911|
|  2:  4.6577 -  3.7156 0.99   1403  154 0.0865 0.1024      5.4375      5.6002|
|  3:  3.7156 -  3.2514 0.99   1363  153 0.1131 0.1544       5.494      5.8198|
|  4:  3.2514 -  2.9566 0.98   1375  148 0.1333 0.1718       5.485      5.6621|
|  5:  2.9566 -  2.7461 0.99   1335  155 0.1436 0.1741      5.3864      5.5592|
|  6:  2.7461 -  2.5850 0.99   1377  150 0.1340 0.2127      5.2623      5.4869|
|  7:  2.5850 -  2.4561 0.98   1311  154 0.1345 0.1669      5.2183      5.3962|
|  8:  2.4561 -  2.3497 0.98   1344  143 0.1277 0.1836      5.1411      5.3667|
|  9:  2.3497 -  2.2595 0.99   1341  140 0.1248 0.1916      5.0655      5.3378|
| 10:  2.2595 -  2.1818 0.99   1352  147 0.1192 0.1779      4.9907      5.1861|
| 11:  2.1818 -  2.1138 0.97   1308  156 0.1226 0.1798      4.9354      5.2494|
| 12:  2.1138 -  2.0535 0.98   1316  151 0.1190 0.1598      4.8735      5.0826|
| 13:  2.0535 -  1.9996 0.80   1084  114 0.1175 0.1946      4.7959      5.0699|
| 14:  1.9996 -  1.9509 0.19    260   33 0.1125 0.1923      4.7641      4.9473|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9770 -  4.6577  1461   161  0.94   9.49   0.97     0.95       7393.87|
|  2:  4.6577 -  3.7156  1403   154  0.95   7.92   1.02     1.00       8972.42|
|  3:  3.7156 -  3.2514  1363   153  0.93  11.69   1.02     1.02      10500.78|
|  4:  3.2514 -  2.9566  1375   148  0.91  14.97   1.01     1.00      10869.81|
|  5:  2.9566 -  2.7461  1335   155  0.89  16.89   1.01     0.98       9215.64|
|  6:  2.7461 -  2.5850  1377   150  0.89  17.20   0.98     0.95       7630.45|
|  7:  2.5850 -  2.4561  1311   154  0.90  16.76   0.99     0.96       6961.56|
|  8:  2.4561 -  2.3497  1344   143  0.89  17.17   1.00     0.96       6230.06|
|  9:  2.3497 -  2.2595  1341   140  0.89  16.92   0.99     0.95       5449.63|
| 10:  2.2595 -  2.1818  1352   147  0.90  16.60   1.00     0.97       4787.31|
| 11:  2.1818 -  2.1138  1308   156  0.90  16.53   0.99     0.96       4308.60|
| 12:  2.1138 -  2.0535  1316   151  0.90  16.33   1.00     1.00       3873.59|
| 13:  2.0535 -  1.9996  1084   114  0.89  17.07   0.99     0.98       3441.31|
| 14:  1.9996 -  1.9509   260    33  0.91  15.03   0.97     0.93       2929.14|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2929.14 max =        10869.81 mean =      6918.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.94|
|phase err.(test): min =        0.00 max =           89.34 mean =        14.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    98.89   17.22    None  None   None       |
|    all(noH): 2823   0      1.63    98.89   17.22    None  None   None       |
|    Sol.    : 438    0      5.29    91.44   40.74    None  None   None       |
|    Mac.    : 2385   0      1.63    98.89   12.90    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:     1.628 -  11.354: 1341   |   5:    50.258 -  59.984:   78        |
|      1:    11.354 -  21.080:  898   |   6:    59.984 -  69.711:   43        |
|      2:    21.080 -  30.806:  179   |   7:    69.711 -  79.437:   21        |
|      3:    30.806 -  40.532:  129   |   8:    79.437 -  89.163:    8        |
|      4:    40.532 -  50.258:  121   |   9:    89.163 -  98.889:    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)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.395 - 4.723
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 306
   mapped sites are within: 0.728 - 4.723

peak=   12.223 closest distance to " O  BHOH Z  74 " =    1.533
peak=    5.013 closest distance to " O   HOH Z 193 " =    1.791
peak=    5.005 closest distance to " O   HOH Z 402 " =    1.591
peak=    5.000 closest distance to " CG  PRO A  54 " =    1.288
peak=    4.990 closest distance to " NH2 ARG A  56 " =    2.152
peak=    4.919 closest distance to " O   HOH Z 102 " =    1.458
peak=    4.895 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.893 closest distance to " O   HOH Z 232 " =    2.305
peak=    4.891 closest distance to " O   HOH Z  49 " =    1.296
peak=    4.880 closest distance to " O   HOH Z 186 " =    2.461
peak=    4.857 closest distance to " O   HOH Z 401 " =    1.310
peak=    4.819 closest distance to " O   HOH Z 124 " =    1.268
peak=    4.796 closest distance to " CA  TYR A  30 " =    0.957
peak=    4.762 closest distance to " O   HOH Z 403 " =    1.889
peak=    4.695 closest distance to " CB  SER A  63 " =    1.080
peak=    4.661 closest distance to " CD2 TRP A 179 " =    1.344
peak=    4.632 closest distance to " CG  PRO A  90 " =    1.254
peak=    4.627 closest distance to " O   HOH Z 417 " =    2.142
peak=    4.566 closest distance to " O   HOH Z  63 " =    1.924
peak=    4.523 closest distance to " O   HOH Z 117 " =    1.217
peak=    4.504 closest distance to " NH2BARG A 145 " =    2.171
peak=    4.493 closest distance to " O   HOH Z 209 " =    2.298
peak=    4.484 closest distance to " O   HOH Z 433 " =    1.561
peak=    4.478 closest distance to " O   HOH Z  43 " =    2.216
peak=    4.465 closest distance to " O   HOH Z 414 " =    1.721
peak=    4.463 closest distance to " CB  ARG A 190 " =    1.761
peak=    4.427 closest distance to " CB  PRO A  54 " =    1.023
peak=    4.427 closest distance to " O   HOH Z  65 " =    1.121
peak=    4.377 closest distance to " CB  GLN A 223 " =    1.390
peak=    4.372 closest distance to " O   HOH Z  39 " =    1.629
peak=    4.370 closest distance to " O   HOH Z  80 " =    1.914
peak=    4.366 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.340 closest distance to " O   HOH Z  97 " =    1.564
peak=    4.322 closest distance to " O   HOH Z 248 " =    1.540
peak=    4.321 closest distance to " O   HOH Z 389 " =    1.927
peak=    4.289 closest distance to " O   HOH Z  15 " =    2.222
peak=    4.277 closest distance to " NH1AARG A 275 " =    1.035
peak=    4.265 closest distance to " O   HOH Z  44 " =    2.127
peak=    4.253 closest distance to " O   HOH Z 272 " =    1.929
peak=    4.249 closest distance to " O   HOH Z 423 " =    1.804
peak=    4.246 closest distance to " O   HOH Z 234 " =    3.569
peak=    4.242 closest distance to " CG1 ILE A  33 " =    1.238
peak=    4.229 closest distance to " CB  GLU A 152 " =    1.148
peak=    4.225 closest distance to " CB  PRO A 213 " =    1.304
peak=    4.194 closest distance to " O   HOH Z  59 " =    2.187
peak=    4.190 closest distance to " CG  PRO A 198 " =    1.300
peak=    4.185 closest distance to " CA  ALA A  51 " =    0.953
peak=    4.179 closest distance to " ND2 ASN A 187 " =    1.727
peak=    4.150 closest distance to " O   HOH Z 128 " =    1.539
peak=    4.128 closest distance to " O   HOH Z 346 " =    1.631
peak=    4.115 closest distance to " O   HOH Z 189 " =    2.595
peak=    4.108 closest distance to " O   PRO A 198 " =    1.551
peak=    4.104 closest distance to " O   SER A  87 " =    2.093
peak=    4.103 closest distance to " O   HOH Z 368 " =    2.107
peak=    4.085 closest distance to " O   HOH Z 375 " =    1.845
peak=    4.081 closest distance to " O   HOH Z 130 " =    2.553
peak=    4.073 closest distance to " O   HOH Z 298 " =    1.690
peak=    4.059 closest distance to " O   HOH Z 154 " =    1.670
peak=    4.059 closest distance to " NZ  LYS A 117 " =    3.018
peak=    4.056 closest distance to " O   HOH Z 203 " =    1.802
peak=    4.051 closest distance to " O   HOH Z 406 " =    1.542
peak=    4.049 closest distance to " O   HOH Z 134 " =    1.605
peak=    4.030 closest distance to " O   HOH Z  40 " =    1.908
peak=    4.019 closest distance to " O   HOH Z 369 " =    2.203
peak=    4.011 closest distance to " CB  SER A 141 " =    1.049
peak=    4.009 closest distance to " O   HOH Z 394 " =    1.595
peak=    4.006 closest distance to " O   HOH Z 210 " =    1.111
peak=    3.971 closest distance to " CD  LYS A 166 " =    1.431
peak=    3.966 closest distance to " O   HOH Z 250 " =    1.431
peak=    3.961 closest distance to " CG2BVAL A  41 " =    0.889
peak=    3.954 closest distance to " O   HOH Z 365 " =    2.416
peak=    3.943 closest distance to " O   HOH Z 265 " =    2.075
peak=    3.940 closest distance to " O   HOH Z  68 " =    1.757
peak=    3.931 closest distance to " CG  GLN A  11 " =    1.328
peak=    3.931 closest distance to " O   HOH Z  85 " =    1.566
peak=    3.916 closest distance to " O   HOH Z 345 " =    1.886
peak=    3.913 closest distance to " CG AARG A 275 " =    1.122
peak=    3.912 closest distance to " O   HOH Z 361 " =    3.305
peak=    3.907 closest distance to " CG2 ILE A  20 " =    1.413
peak=    3.851 closest distance to " CG2 ILE A 120 " =    1.258
peak=    3.849 closest distance to " O   HOH Z 246 " =    1.432
peak=    3.847 closest distance to " N   ASN A  39 " =    1.279
peak=    3.846 closest distance to " CD  ARG A 269 " =    1.046
peak=    3.834 closest distance to " CB  ARG A  79 " =    1.436
peak=    3.830 closest distance to " CB  TRP A 179 " =    1.220
peak=    3.830 closest distance to " CB  VAL A 202 " =    1.475
peak=    3.827 closest distance to " CD  PRO A  54 " =    1.055
peak=    3.825 closest distance to " O   ALA A 165 " =    1.360
peak=    3.819 closest distance to " CB  SER A   3 " =    1.216
peak=    3.812 closest distance to " OG BSER A 212 " =    2.520
peak=    3.795 closest distance to " CZ  PHE A 218 " =    1.176
peak=    3.784 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.783 closest distance to " CB  ASN A 148 " =    1.424
peak=    3.781 closest distance to " O   HOH Z 128 " =    1.930
peak=    3.764 closest distance to " O   HOH Z  51 " =    1.831
peak=    3.760 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.759 closest distance to " O   HOH Z 128 " =    2.340
peak=    3.759 closest distance to " O   HOH Z 173 " =    2.209
peak=    3.754 closest distance to " O   HOH Z 279 " =    2.075
peak=    3.751 closest distance to " O   HOH Z 422 " =    2.798
peak=    3.748 closest distance to " CB  GLU A 277 " =    3.649
peak=    3.746 closest distance to " O   HOH Z 132 " =    2.548
peak=    3.744 closest distance to " CB  SER A  26 " =    1.759
peak=    3.732 closest distance to " CD  LYS A  76 " =    1.785
peak=    3.728 closest distance to " O   HOH Z 214 " =    1.364
peak=    3.726 closest distance to " CA  ASN A 176 " =    1.195
peak=    3.721 closest distance to " CB  SER A  62 " =    0.878
peak=    3.718 closest distance to " CG  PRO A 243 " =    1.103
peak=    3.713 closest distance to " CB  ASN A 285 " =    0.946
peak=    3.694 closest distance to " CB  GLN A  88 " =    1.092
peak=    3.694 closest distance to " O   HOH Z 412 " =    3.741
peak=    3.677 closest distance to " O   HOH Z 380 " =    1.873
peak=    3.671 closest distance to " N   CYS A 260 " =    0.955
peak=    3.659 closest distance to " CD2 LEU A 297 " =    0.933
peak=    3.653 closest distance to " O   HOH Z 426 " =    1.408
peak=    3.653 closest distance to " O   HOH Z 245 " =    1.387
peak=    3.652 closest distance to " O   HOH Z 132 " =    2.345
peak=    3.651 closest distance to " O   HOH Z 421 " =    2.183
peak=    3.651 closest distance to " CB  TYR A 169 " =    0.796
peak=    3.647 closest distance to " CA  ARG A  36 " =    1.082
peak=    3.645 closest distance to " O   HOH Z 357 " =    2.036
peak=    3.638 closest distance to " O   HOH Z 126 " =    1.921
peak=    3.621 closest distance to " O   HOH Z 236 " =    1.582
peak=    3.610 closest distance to " CG  ARG A  66 " =    1.044
peak=    3.599 closest distance to " O   HOH Z 116 " =    1.301
peak=    3.599 closest distance to " CG AARG A 275 " =    1.183
peak=    3.594 closest distance to " CB  GLU A 175 " =    1.361
peak=    3.591 closest distance to " O   HOH Z 282 " =    2.010
peak=    3.588 closest distance to " O   HOH Z  63 " =    2.304
peak=    3.588 closest distance to " OE1 GLN A  11 " =    1.912
peak=    3.581 closest distance to " CD  LYS A 119 " =    2.002
peak=    3.571 closest distance to " O   HOH Z   9 " =    2.523
peak=    3.570 closest distance to " O   HOH Z 327 " =    1.710
peak=    3.567 closest distance to " CB  GLU A 128 " =    1.147
peak=    3.563 closest distance to " O   HOH Z 303 " =    2.263
peak=    3.562 closest distance to " CG  GLN A  58 " =    0.896
peak=    3.562 closest distance to " O   HOH Z 419 " =    2.489
peak=    3.546 closest distance to " O   HOH Z 358 " =    2.174
peak=    3.544 closest distance to " CZ3 TRP A 266 " =    1.050
peak=    3.540 closest distance to " CA  ALA A  84 " =    1.087
peak=    3.539 closest distance to " CA  THR A  82 " =    1.802
peak=    3.539 closest distance to " CD  ARG A 195 " =    0.902
peak=    3.538 closest distance to " CB  TRP A 266 " =    1.066
peak=    3.537 closest distance to " O   HOH Z 298 " =    2.287
peak=    3.536 closest distance to " O   HOH Z 163 " =    1.533
peak=    3.536 closest distance to " O   HOH Z  78 " =    1.645
peak=    3.536 closest distance to " O   HOH Z 412 " =    3.389
peak=    3.531 closest distance to " CB  ASN A  39 " =    0.839
peak=    3.530 closest distance to " NH2 ARG A 156 " =    1.157
peak=    3.528 closest distance to " O   HOH Z 291 " =    1.422
peak=    3.522 closest distance to " O   HOH Z 214 " =    2.445
peak=    3.521 closest distance to " CA  SER A  87 " =    1.016
peak=    3.520 closest distance to " O   HOH Z 132 " =    1.116
peak=    3.509 closest distance to " CZ  PHE A  38 " =    1.205
peak=    3.509 closest distance to " O   HOH Z 142 " =    1.393
peak=    3.508 closest distance to " NE2 GLN A  77 " =    3.186
peak=    3.507 closest distance to " CA  ASP A 162 " =    1.180
peak=    3.504 closest distance to " O   HOH Z 435 " =    1.800
peak=    3.499 closest distance to " O   HOH Z 404 " =    1.586
peak=    3.496 closest distance to " O   HOH Z 193 " =    2.032
peak=    3.494 closest distance to " O   HOH Z 353 " =    2.743
peak=    3.486 closest distance to " CD  ARG A 139 " =    1.272
peak=    3.486 closest distance to " O   HOH Z 334 " =    1.488
peak=    3.479 closest distance to " O   HOH Z 427 " =    3.113
peak=    3.477 closest distance to " O   HOH Z 418 " =    3.108
peak=    3.477 closest distance to " O   HOH Z 427 " =    3.035
peak=    3.476 closest distance to " OH  TYR A 116 " =    1.124
peak=    3.472 closest distance to " O   HOH Z 403 " =    1.563
peak=    3.467 closest distance to " CA  ARG A 195 " =    1.238
peak=    3.466 closest distance to " CG2AVAL A 121 " =    2.113
peak=    3.463 closest distance to " O   HOH Z 162 " =    1.779
peak=    3.461 closest distance to " CD  ARG A 159 " =    0.835
peak=    3.452 closest distance to " O   THR A 220 " =    1.096
peak=    3.446 closest distance to " O   HOH Z 183 " =    1.897
peak=    3.446 closest distance to " ND2 ASN A 249 " =    0.924
peak=    3.435 closest distance to " CG1BVAL A  72 " =    1.849
peak=    3.434 closest distance to " CE  LYS A 119 " =    1.145
peak=    3.428 closest distance to " O   HOH Z 298 " =    4.148
peak=    3.428 closest distance to " O   HOH Z 419 " =    1.717
peak=    3.426 closest distance to " O   HOH Z  88 " =    3.174
peak=    3.417 closest distance to " NE2 GLN A  11 " =    1.116
peak=    3.417 closest distance to " O   HOH Z 251 " =    1.654
peak=    3.415 closest distance to " O   HOH Z  63 " =    2.078
peak=    3.409 closest distance to " CB  THR A  31 " =    1.580
peak=    3.407 closest distance to " O   HOH Z 336 " =    1.858
peak=    3.405 closest distance to " O   HOH Z 313 " =    1.821
peak=    3.397 closest distance to " CB  PRO A 198 " =    1.020
peak=    3.389 closest distance to " CB  GLN A 194 " =    0.883
peak=    3.385 closest distance to " O   HOH Z 244 " =    1.761
peak=    3.377 closest distance to " O   HOH Z  54 " =    1.606
peak=    3.373 closest distance to " O   HOH Z 316 " =    2.927
peak=    3.372 closest distance to " CG2 VAL A 197 " =    1.087
peak=    3.372 closest distance to " CB  SER A  62 " =    1.163
peak=    3.361 closest distance to " O   HOH Z 425 " =    1.307
peak=    3.361 closest distance to " CA  ALA A 295 " =    0.970
peak=    3.359 closest distance to " CB  VAL A 265 " =    1.270
peak=    3.359 closest distance to " O   ARG A  56 " =    2.917
peak=    3.359 closest distance to " O   HOH Z  22 " =    2.917
peak=    3.355 closest distance to " O   HOH Z  21 " =    1.871
peak=    3.351 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.347 closest distance to " CG  GLU A  37 " =    0.870
peak=    3.345 closest distance to " O   HOH Z 257 " =    2.220
peak=    3.345 closest distance to " O   HOH Z 299 " =    4.216
peak=    3.344 closest distance to " CB  PHE A  16 " =    1.106
peak=    3.341 closest distance to " O   HOH Z 111 " =    1.454
peak=    3.340 closest distance to " CB  PRO A  90 " =    0.914
peak=    3.332 closest distance to " O   HOH Z 371 " =    3.065
peak=    3.323 closest distance to " O   HOH Z 359 " =    1.650
peak=    3.320 closest distance to " O   HOH Z  20 " =    1.321
peak=    3.304 closest distance to " CA  ILE A 106 " =    0.813
peak=    3.304 closest distance to " NZ  LYS A 117 " =    2.024
peak=    3.303 closest distance to " CG2 THR A 220 " =    0.731
peak=    3.301 closest distance to " CG  MET A 185 " =    1.061
peak=    3.298 closest distance to " N   HIS A 108 " =    1.804
peak=    3.297 closest distance to " O   HOH Z 261 " =    2.137
peak=    3.297 closest distance to " CB  TYR A 247 " =    1.004
peak=    3.287 closest distance to " CB  LYS A 289 " =    1.133
peak=    3.284 closest distance to " O   GLU A   2 " =    1.757
peak=    3.282 closest distance to " NZ  LYS A 166 " =    2.895
peak=    3.282 closest distance to " CB  THR A  52 " =    0.802
peak=    3.281 closest distance to " OG BSER A 258 " =    3.060
peak=    3.280 closest distance to " CA  ARG A 156 " =    1.084
peak=    3.275 closest distance to " O   HOH Z  48 " =    1.652
peak=    3.272 closest distance to " O   HOH Z 344 " =    3.213
peak=    3.267 closest distance to " O   HOH Z 337 " =    3.703
peak=    3.265 closest distance to " CA  GLY A 241 " =    1.002
peak=    3.259 closest distance to " OG  SER A 245 " =    1.482
peak=    3.259 closest distance to " O   HOH Z 250 " =    1.878
peak=    3.256 closest distance to " O   HOH Z 293 " =    1.771
peak=    3.256 closest distance to " O   GLY A  91 " =    1.307
peak=    3.253 closest distance to " O   HOH Z 180 " =    2.328
peak=    3.251 closest distance to " CA  ASP A 191 " =    0.975
peak=    3.250 closest distance to " O   HOH Z 366 " =    2.608
peak=    3.247 closest distance to " O   HOH Z 234 " =    2.088
peak=    3.245 closest distance to " O   HOH Z 417 " =    2.812
peak=    3.244 closest distance to " CB  ARG A  79 " =    0.737
peak=    3.241 closest distance to " O   HOH Z  80 " =    1.992
peak=    3.236 closest distance to " CE  LYS A  76 " =    0.828
peak=    3.235 closest distance to " CD  GLN A 194 " =    1.596
peak=    3.233 closest distance to " O   HOH Z  89 " =    1.879
peak=    3.232 closest distance to " O   HOH Z 375 " =    2.056
peak=    3.231 closest distance to " CD1 LEU A  96 " =    0.751
peak=    3.229 closest distance to " CD1 ILE A 199 " =    1.287
peak=    3.228 closest distance to " CA  GLU A 152 " =    0.810
peak=    3.223 closest distance to " O   TRP A 274 " =    1.603
peak=    3.222 closest distance to " O   HOH Z  59 " =    1.889
peak=    3.221 closest distance to " O   HOH Z 284 " =    2.908
peak=    3.216 closest distance to " O   HOH Z 108 " =    2.821
peak=    3.213 closest distance to " CG1 ILE A  20 " =    1.287
peak=    3.212 closest distance to " CA  THR A  42 " =    0.978
peak=    3.205 closest distance to " CB  ASN A 142 " =    1.158
peak=    3.203 closest distance to " O   HOH Z  85 " =    1.573
peak=    3.202 closest distance to " O   HOH Z 189 " =    2.297
peak=    3.199 closest distance to " O   HOH Z 139 " =    4.723
peak=    3.199 closest distance to " O   HOH Z 287 " =    1.763
peak=    3.199 closest distance to " O   HOH Z 267 " =    1.934
peak=    3.185 closest distance to " N   TRP A 150 " =    1.380
peak=    3.178 closest distance to " O   HOH Z 158 " =    2.907
peak=    3.177 closest distance to " CB  ALA A 291 " =    1.226
peak=    3.173 closest distance to " O   THR A 182 " =    1.422
peak=    3.173 closest distance to " NH1AARG A 145 " =    1.399
peak=    3.171 closest distance to " O   HOH Z 109 " =    1.906
peak=    3.171 closest distance to " CB  ARG A 269 " =    1.864
peak=    3.171 closest distance to " O   HOH Z  85 " =    1.550
peak=    3.169 closest distance to " CA  ALA A 160 " =    0.902
peak=    3.165 closest distance to " CA  ASP A 191 " =    1.171
peak=    3.163 closest distance to " CA  ALA A 100 " =    1.116
peak=    3.163 closest distance to " CA  SER A  12 " =    1.473
peak=    3.156 closest distance to " O   HOH Z 255 " =    1.589
peak=    3.154 closest distance to " CZ3 TRP A  85 " =    0.961
peak=    3.148 closest distance to " O   HOH Z 123 " =    2.126
peak=    3.147 closest distance to " CG2 THR A 294 " =    1.326
peak=    3.146 closest distance to " O   HOH Z 365 " =    1.276
peak=    3.144 closest distance to " O   HOH Z 345 " =    2.322
peak=    3.142 closest distance to " OE1 GLU A   2 " =    2.174
peak=    3.140 closest distance to " O   HOH Z 194 " =    2.126
peak=    3.136 closest distance to " N   ARG A 156 " =    1.421
peak=    3.135 closest distance to " N   ASP A 162 " =    1.171
peak=    3.132 closest distance to " O   HOH Z 392 " =    2.070
peak=    3.129 closest distance to " CB  ARG A 219 " =    1.066
peak=    3.129 closest distance to " CD  PRO A 213 " =    1.373
peak=    3.124 closest distance to " CB  MET A  47 " =    1.112
peak=    3.123 closest distance to " O   HOH Z 408 " =    1.824
peak=    3.121 closest distance to " O   TYR A 116 " =    1.463
peak=    3.117 closest distance to " CD1 LEU A 228 " =    1.612
peak=    3.114 closest distance to " O   HOH Z  28 " =    2.006
peak=    3.108 closest distance to " CA  ALA A 129 " =    1.222
peak=    3.106 closest distance to " O   HOH Z 147 " =    1.779
peak=    3.101 closest distance to " O   HOH Z  11 " =    1.221
peak=    3.082 closest distance to " CG  MET A 185 " =    0.994
peak=    3.077 closest distance to " CB  ALA A 114 " =    0.937
peak=    3.076 closest distance to " O   HOH Z 128 " =    1.541
peak=    3.065 closest distance to " NE  ARG A  24 " =    0.981
peak=    3.063 closest distance to " CB  LEU A  83 " =    0.728
peak=    3.063 closest distance to " CG  GLN A  89 " =    1.485
peak=    3.054 closest distance to " O   HOH Z  78 " =    1.906
peak=    3.053 closest distance to " OE1 GLN A 223 " =    2.311
peak=    3.052 closest distance to " ND1 HIS A  81 " =    1.463
peak=    3.049 closest distance to " CB  PHE A 283 " =    0.832
peak=    3.037 closest distance to " CA  LYS A 117 " =    1.255
peak=    3.037 closest distance to " CB  ASP A 140 " =    0.899

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.697 - 5.855
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 211
   mapped sites are within: 0.705 - 5.855

peak=   -4.827 closest distance to " O   HOH Z 422 " =    1.079
peak=   -4.763 closest distance to " O   HOH Z 266 " =    5.074
peak=   -4.505 closest distance to " O   HOH Z 210 " =    0.825
peak=   -4.289 closest distance to " CA  VAL A  67 " =    2.990
peak=   -4.248 closest distance to " C   HIS A 108 " =    1.047
peak=   -4.188 closest distance to " CG2 ILE A  49 " =    2.796
peak=   -4.151 closest distance to " C   THR A 279 " =    1.173
peak=   -4.150 closest distance to " O   HOH Z 290 " =    0.911
peak=   -4.106 closest distance to " CD2 TYR A  30 " =    2.778
peak=   -4.028 closest distance to " O   HOH Z 401 " =    0.705
peak=   -4.022 closest distance to " CD  GLN A  58 " =    0.964
peak=   -4.009 closest distance to " O   HOH Z 165 " =    1.854
peak=   -3.994 closest distance to " CD  ARG A 156 " =    2.007
peak=   -3.988 closest distance to " OXT GLY A 302 " =    2.943
peak=   -3.957 closest distance to " O   HOH Z  13 " =    1.805
peak=   -3.934 closest distance to " OG BSER A 134 " =    1.463
peak=   -3.924 closest distance to " O   HOH Z 183 " =    1.420
peak=   -3.923 closest distance to " SG  CYS A 254 " =    3.367
peak=   -3.916 closest distance to " O   PHE A 218 " =    1.553
peak=   -3.913 closest distance to " NE2 GLN A 223 " =    1.100
peak=   -3.867 closest distance to " O   PRO A 163 " =    2.032
peak=   -3.864 closest distance to " O   HOH Z 366 " =    1.477
peak=   -3.842 closest distance to " O   PRO A 198 " =    1.331
peak=   -3.839 closest distance to " CG  MET A  93 " =    2.401
peak=   -3.809 closest distance to " O   VAL A  67 " =    2.841
peak=   -3.807 closest distance to " O   HOH Z  15 " =    1.460
peak=   -3.795 closest distance to " CD2 LEU A 237 " =    2.408
peak=   -3.791 closest distance to " ND2 ASN A  45 " =    1.736
peak=   -3.790 closest distance to " O   GLY A 241 " =    2.228
peak=   -3.785 closest distance to " CD1 ILE A 106 " =    2.149
peak=   -3.772 closest distance to " O   HOH Z 377 " =    2.120
peak=   -3.754 closest distance to " CZ  ARG A  66 " =    0.968
peak=   -3.742 closest distance to " O   HOH Z 119 " =    2.179
peak=   -3.734 closest distance to " CD1 PHE A  59 " =    2.002
peak=   -3.723 closest distance to " O   TRP A  92 " =    2.029
peak=   -3.715 closest distance to " O   HOH Z 171 " =    2.394
peak=   -3.710 closest distance to " CB  ALA A 161 " =    2.532
peak=   -3.710 closest distance to " CD  GLN A  58 " =    1.164
peak=   -3.710 closest distance to " CD  GLN A 223 " =    1.575
peak=   -3.695 closest distance to " O   GLY A  80 " =    2.535
peak=   -3.686 closest distance to " ND2 ASN A  69 " =    1.684
peak=   -3.681 closest distance to " O   HOH Z 418 " =    1.274
peak=   -3.666 closest distance to " CH2 TRP A 150 " =    1.035
peak=   -3.664 closest distance to " CA  GLY A 133 " =    2.093
peak=   -3.652 closest distance to " O   HOH Z 372 " =    2.363
peak=   -3.645 closest distance to " CG  GLU A  53 " =    1.413
peak=   -3.642 closest distance to " O   HOH Z 174 " =    3.728
peak=   -3.640 closest distance to " CG  ASP A 132 " =    2.288
peak=   -3.638 closest distance to " NE2 GLN A  88 " =    1.508
peak=   -3.637 closest distance to " O   HOH Z 221 " =    0.933
peak=   -3.633 closest distance to " CB  ALA A 248 " =    2.214
peak=   -3.632 closest distance to " NE2 GLN A  88 " =    1.024
peak=   -3.627 closest distance to " O   HOH Z 166 " =    1.822
peak=   -3.625 closest distance to " O   HOH Z  56 " =    0.929
peak=   -3.624 closest distance to " O   ALA A  34 " =    2.375
peak=   -3.615 closest distance to " O   HOH Z 423 " =    2.330
peak=   -3.597 closest distance to " O   HOH Z 102 " =    1.363
peak=   -3.594 closest distance to " O   HOH Z 234 " =    3.857
peak=   -3.578 closest distance to " O   VAL A 174 " =    2.041
peak=   -3.577 closest distance to " CZ  TYR A 169 " =    1.869
peak=   -3.571 closest distance to " O   HOH Z  10 " =    1.629
peak=   -3.569 closest distance to " CD1 TRP A 179 " =    1.085
peak=   -3.568 closest distance to " CB  ALA A  43 " =    2.451
peak=   -3.563 closest distance to " CH2 TRP A 179 " =    1.273
peak=   -3.560 closest distance to " OG  SER A  26 " =    1.018
peak=   -3.559 closest distance to " CZ  PHE A  38 " =    2.189
peak=   -3.549 closest distance to " CB  TRP A  85 " =    2.676
peak=   -3.546 closest distance to " O   SER A 146 " =    1.114
peak=   -3.542 closest distance to " O   HOH Z 166 " =    1.564
peak=   -3.536 closest distance to " OG  SER A  97 " =    2.212
peak=   -3.533 closest distance to " O   SER A  95 " =    1.744
peak=   -3.521 closest distance to " CD2 TYR A 293 " =    1.893
peak=   -3.521 closest distance to " CB  PRO A 243 " =    2.728
peak=   -3.520 closest distance to " OE2 GLU A   2 " =    1.530
peak=   -3.519 closest distance to " OD1 ASP A 171 " =    1.445
peak=   -3.517 closest distance to " CG  GLN A  11 " =    1.409
peak=   -3.509 closest distance to " O   HOH Z 351 " =    1.544
peak=   -3.506 closest distance to " CD1 PHE A 130 " =    2.288
peak=   -3.505 closest distance to " CG1AVAL A  41 " =    2.573
peak=   -3.493 closest distance to " O   HOH Z  97 " =    1.199
peak=   -3.491 closest distance to " CZ  TYR A 172 " =    1.831
peak=   -3.467 closest distance to " OD1 ASN A 148 " =    1.480
peak=   -3.461 closest distance to " O   HOH Z 428 " =    1.161
peak=   -3.456 closest distance to " O   HOH Z  11 " =    1.860
peak=   -3.456 closest distance to " O   HOH Z 244 " =    1.386
peak=   -3.447 closest distance to " CB  PHE A 208 " =    2.315
peak=   -3.444 closest distance to " CG1 VAL A  78 " =    2.587
peak=   -3.440 closest distance to " CD  GLN A  73 " =    0.787
peak=   -3.440 closest distance to " O   HOH Z 252 " =    4.168
peak=   -3.432 closest distance to " O   HOH Z 198 " =    1.234
peak=   -3.430 closest distance to " O   HOH Z 150 " =    2.013
peak=   -3.427 closest distance to " N   THR A  52 " =    1.741
peak=   -3.427 closest distance to " O   SER A  26 " =    1.446
peak=   -3.426 closest distance to " OD2 ASP A 171 " =    2.295
peak=   -3.425 closest distance to " N   ALA A 248 " =    1.764
peak=   -3.423 closest distance to " O   SER A 210 " =    1.795
peak=   -3.415 closest distance to " N   ALA A 226 " =    1.910
peak=   -3.406 closest distance to " O   HOH Z  38 " =    1.496
peak=   -3.406 closest distance to " OG BSER A 258 " =    5.149
peak=   -3.405 closest distance to " OD1 ASN A 301 " =    1.992
peak=   -3.404 closest distance to " CG1 VAL A 112 " =    2.553
peak=   -3.401 closest distance to " O   HOH Z 150 " =    1.180
peak=   -3.400 closest distance to " O   HOH Z 377 " =    1.771
peak=   -3.396 closest distance to " CG  PHE A 283 " =    2.600
peak=   -3.394 closest distance to " O   HOH Z 374 " =    1.999
peak=   -3.393 closest distance to " N   SER A 276 " =    1.491
peak=   -3.390 closest distance to " O   HOH Z 210 " =    1.081
peak=   -3.376 closest distance to " CG  PRO A 243 " =    1.610
peak=   -3.364 closest distance to " O   HOH Z  59 " =    3.849
peak=   -3.364 closest distance to " O   ALA A  10 " =    1.808
peak=   -3.361 closest distance to " CG1 VAL A  78 " =    2.663
peak=   -3.351 closest distance to " CD2 PHE A 192 " =    2.131
peak=   -3.343 closest distance to " N   GLN A  58 " =    1.700
peak=   -3.343 closest distance to " OE1 GLN A 223 " =    2.274
peak=   -3.336 closest distance to " CD2 LEU A 237 " =    2.540
peak=   -3.336 closest distance to " OD1 ASN A 173 " =    1.642
peak=   -3.335 closest distance to " NE  ARG A  79 " =    1.374
peak=   -3.334 closest distance to " OH  TYR A 169 " =    0.905
peak=   -3.333 closest distance to " O   HOH Z 378 " =    1.132
peak=   -3.327 closest distance to " CD  ARG A 139 " =    1.493
peak=   -3.325 closest distance to " CD1 LEU A  25 " =    2.490
peak=   -3.322 closest distance to " O   LEU A 300 " =    2.497
peak=   -3.312 closest distance to " O   HOH Z 174 " =    2.143
peak=   -3.311 closest distance to " O   HOH Z 149 " =    1.818
peak=   -3.311 closest distance to " O   HOH Z 198 " =    1.321
peak=   -3.310 closest distance to " O   ASN A 187 " =    1.572
peak=   -3.300 closest distance to " OD2 ASP A 191 " =    1.559
peak=   -3.295 closest distance to " CB  ALA A  10 " =    2.222
peak=   -3.290 closest distance to " O   HOH Z 215 " =    2.348
peak=   -3.284 closest distance to " O   GLN A  11 " =    1.290
peak=   -3.279 closest distance to " NH2 ARG A  56 " =    1.870
peak=   -3.274 closest distance to " O   HOH Z  52 " =    1.692
peak=   -3.260 closest distance to " O  BHOH Z 338 " =    1.205
peak=   -3.260 closest distance to " CB  SER A 210 " =    1.222
peak=   -3.259 closest distance to " O   HOH Z 196 " =    1.735
peak=   -3.257 closest distance to " O   HOH Z 252 " =    4.990
peak=   -3.254 closest distance to " O   HOH Z 109 " =    2.550
peak=   -3.254 closest distance to " CB  PRO A 213 " =    1.756
peak=   -3.252 closest distance to " CG  MET A 105 " =    0.989
peak=   -3.250 closest distance to " OE1 GLN A 183 " =    1.516
peak=   -3.249 closest distance to " CA  LYS A 289 " =    2.171
peak=   -3.247 closest distance to " CG2 VAL A 189 " =    2.205
peak=   -3.242 closest distance to " CB  ASP A 132 " =    2.406
peak=   -3.239 closest distance to " CE1 TYR A 247 " =    2.695
peak=   -3.237 closest distance to " O   HOH Z  41 " =    2.001
peak=   -3.236 closest distance to " O   HOH Z 196 " =    1.950
peak=   -3.232 closest distance to " O   HOH Z 215 " =    3.949
peak=   -3.229 closest distance to " CG  ARG A 219 " =    2.323
peak=   -3.222 closest distance to " C   SER A 206 " =    1.504
peak=   -3.221 closest distance to " O   HOH Z   1 " =    4.439
peak=   -3.218 closest distance to " C   GLN A 144 " =    0.873
peak=   -3.211 closest distance to " NH2 ARG A  66 " =    5.855
peak=   -3.209 closest distance to " O   HOH Z 214 " =    2.596
peak=   -3.208 closest distance to " O   HOH Z 392 " =    1.465
peak=   -3.208 closest distance to " ND2 ASN A  45 " =    1.238
peak=   -3.206 closest distance to " CG  PHE A 225 " =    1.377
peak=   -3.200 closest distance to " N   SER A 206 " =    1.788
peak=   -3.199 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.199 closest distance to " O   TYR A  15 " =    1.765
peak=   -3.194 closest distance to " O   HOH Z 426 " =    1.720
peak=   -3.193 closest distance to " CE BMET A  47 " =    1.612
peak=   -3.189 closest distance to " O   HOH Z 200 " =    1.201
peak=   -3.188 closest distance to " O   HOH Z 126 " =    2.007
peak=   -3.183 closest distance to " O   HOH Z 281 " =    2.415
peak=   -3.182 closest distance to " O   HOH Z 139 " =    3.398
peak=   -3.179 closest distance to " CB  PRO A 163 " =    2.554
peak=   -3.177 closest distance to " OXT GLY A 302 " =    3.247
peak=   -3.176 closest distance to " SD  MET A 105 " =    2.195
peak=   -3.171 closest distance to " O   ALA A 256 " =    1.620
peak=   -3.170 closest distance to " O   HOH Z 172 " =    5.252
peak=   -3.163 closest distance to " O   HOH Z 434 " =    2.745
peak=   -3.157 closest distance to " O   ASN A  45 " =    1.822
peak=   -3.148 closest distance to " O   HOH Z 116 " =    1.226
peak=   -3.147 closest distance to " O   HOH Z 157 " =    3.446
peak=   -3.146 closest distance to " CA  GLY A 241 " =    3.188
peak=   -3.145 closest distance to " C   ASN A 148 " =    1.689
peak=   -3.144 closest distance to " CD2 TYR A 247 " =    2.351
peak=   -3.143 closest distance to " ND2 ASN A  39 " =    1.137
peak=   -3.136 closest distance to " NH2 ARG A  66 " =    5.144
peak=   -3.134 closest distance to " O   HOH Z 301 " =    2.420
peak=   -3.123 closest distance to " NH1 ARG A 195 " =    2.687
peak=   -3.120 closest distance to " OE1 GLN A  55 " =    1.261
peak=   -3.118 closest distance to " CD2 LEU A 300 " =    2.715
peak=   -3.116 closest distance to " O   HOH Z  11 " =    1.759
peak=   -3.116 closest distance to " CD  LYS A 289 " =    2.332
peak=   -3.115 closest distance to " O   HOH Z 265 " =    2.382
peak=   -3.114 closest distance to " CZ  TYR A  68 " =    1.099
peak=   -3.112 closest distance to " OG  SER A  63 " =    1.101
peak=   -3.110 closest distance to " CG2 THR A  18 " =    2.942
peak=   -3.110 closest distance to " O   HOH Z 111 " =    3.792
peak=   -3.109 closest distance to " O   HOH Z 280 " =    1.548
peak=   -3.100 closest distance to " O   HOH Z 297 " =    2.841
peak=   -3.098 closest distance to " OG  SER A  87 " =    1.638
peak=   -3.092 closest distance to " CZ3 TRP A 274 " =    2.102
peak=   -3.085 closest distance to " O   HOH Z 198 " =    1.009
peak=   -3.080 closest distance to " O   HOH Z 287 " =    2.027
peak=   -3.070 closest distance to " O   ASN A 110 " =    2.294
peak=   -3.067 closest distance to " CE3 TRP A 150 " =    2.340
peak=   -3.067 closest distance to " O   PRO A 198 " =    1.229
peak=   -3.065 closest distance to " O   HOH Z 145 " =    2.795
peak=   -3.063 closest distance to " O   LYS A 117 " =    1.634
peak=   -3.056 closest distance to " O   HOH Z 393 " =    1.307
peak=   -3.047 closest distance to " OG BSER A 134 " =    1.793
peak=   -3.039 closest distance to " N   VAL A 189 " =    1.710
peak=   -3.037 closest distance to " O   ASN A 301 " =    1.295
peak=   -3.027 closest distance to " CD  GLN A  88 " =    0.858
peak=   -3.020 closest distance to " O   HOH Z 185 " =    2.453

================= 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    :  0.4573 0.4496   6.269766e+00   6.260197e+00
   1_bss:  0.4495 0.4398   6.262640e+00   6.251219e+00
   1_xyz:  0.3446 0.3711   6.082618e+00   6.133819e+00
   1_adp:  0.3103 0.3728   6.023200e+00   6.142091e+00
   1_occ:  0.3100 0.3728   6.022541e+00   6.142254e+00
   2_bss:  0.3080 0.3698   6.018157e+00   6.139712e+00
   2_xyz:  0.2316 0.2842   5.768404e+00   5.933992e+00
   2_adp:  0.2113 0.2712   5.703428e+00   5.890540e+00
   2_occ:  0.2110 0.2711   5.702991e+00   5.890547e+00
   3_bss:  0.2105 0.2701   5.700687e+00   5.887724e+00
   3_xyz:  0.1598 0.2094   5.451125e+00   5.664839e+00
   3_adp:  0.1451 0.1930   5.369737e+00   5.584576e+00
   3_occ:  0.1450 0.1928   5.369446e+00   5.584310e+00
   4_bss:  0.1451 0.1925   5.370027e+00   5.581035e+00
   4_xyz:  0.1307 0.1786   5.282649e+00   5.503946e+00
   4_adp:  0.1270 0.1753   5.258943e+00   5.483478e+00
   4_occ:  0.1269 0.1753   5.258672e+00   5.483234e+00
   5_bss:  0.1269 0.1754   5.258677e+00   5.483299e+00
   5_xyz:  0.1187 0.1651   5.202074e+00   5.432340e+00
   5_adp:  0.1184 0.1620   5.192965e+00   5.416067e+00
   5_occ:  0.1184 0.1619   5.192519e+00   5.415748e+00
   5_bss:  0.1189 0.1623   5.194335e+00   5.416762e+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:  0.310  36.437  -0.182   3.571  -1.310   0.000  -0.000  -0.000
   1_xyz:  0.310  36.437  -0.182   3.571  -1.310   0.000  -0.000  -0.000
   1_adp:  0.310  36.437  -0.182   3.571  -1.310   0.000  -0.000  -0.000
   1_occ:  0.310  36.437  -0.182   3.571  -1.310   0.000  -0.000  -0.000
   2_bss:  0.312  48.971  -1.448   1.580  -0.451   0.000  -0.000  -0.000
   2_xyz:  0.312  48.971  -1.448   1.580  -0.451   0.000  -0.000  -0.000
   2_adp:  0.312  48.971  -1.448   1.580  -0.451   0.000  -0.000  -0.000
   2_occ:  0.312  48.971  -1.448   1.580  -0.451   0.000  -0.000  -0.000
   3_bss:  0.312  48.971  -2.365  -0.024  -0.675  -0.000  -0.000  -0.000
   3_xyz:  0.312  48.971  -2.365  -0.024  -0.675  -0.000  -0.000  -0.000
   3_adp:  0.312  48.971  -2.365  -0.024  -0.675  -0.000  -0.000  -0.000
   3_occ:  0.312  48.971  -2.365  -0.024  -0.675  -0.000  -0.000  -0.000
   4_bss:  0.323  55.324  -3.056  -1.096  -1.057  -0.000  -0.000  -0.000
   4_xyz:  0.323  55.324  -3.056  -1.096  -1.057  -0.000  -0.000  -0.000
   4_adp:  0.323  55.324  -3.056  -1.096  -1.057  -0.000  -0.000  -0.000
   4_occ:  0.323  55.324  -3.056  -1.096  -1.057  -0.000  -0.000  -0.000
   5_bss:  0.325  55.324  -3.122  -1.351  -0.997  -0.000  -0.000  -0.000
   5_xyz:  0.325  55.324  -3.122  -1.351  -0.997  -0.000  -0.000  -0.000
   5_adp:  0.325  55.324  -3.122  -1.351  -0.997  -0.000  -0.000  -0.000
   5_occ:  0.325  55.324  -3.122  -1.351  -0.997  -0.000  -0.000  -0.000
   5_bss:  0.325  55.263  -3.062  -1.291  -0.937  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.107 0.4698  0.6363    65272.451
   1_bss:  52.996 0.4827  0.6737    62211.212
   1_xyz:  40.981 0.6313  0.8493    39998.252
   1_adp:  41.280 0.6271  0.8521    40653.441
   1_occ:  41.273 0.6272  0.8512    40591.431
   2_bss:  40.882 0.6317  0.8356    39814.607
   2_xyz:  30.354 0.7520  0.9589    21994.099
   2_adp:  27.992 0.7790  0.9672    19598.521
   2_occ:  27.978 0.7792  0.9668    19578.018
   3_bss:  27.780 0.7812  0.9374    19309.057
   3_xyz:  20.623 0.8546  0.9941    11205.847
   3_adp:  18.590 0.8748  0.9998     9702.267
   3_occ:  18.588 0.8749  0.9999     9703.558
   4_bss:  18.522 0.8754  0.9758     9631.747
   4_xyz:  16.745 0.8915  0.9808     8121.670
   4_adp:  16.253 0.8961  0.9757     7880.194
   4_occ:  16.248 0.8962  0.9758     7876.018
   5_bss:  16.248 0.8962  0.9730     7876.637
   5_xyz:  15.249 0.9046  0.9779     7097.540
   5_adp:  14.882 0.9078  0.9744     6904.429
   5_occ:  14.873 0.9079  0.9744     6895.529
   5_bss:  14.892 0.9077  0.9741     6917.194
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.2315e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.2315e-01
   1_xyz:   1.513  0.011  0.088 15.450  0.005  4.103   1.2276e-01
   1_adp:   1.513  0.011  0.088 15.450  0.005  4.103   1.2276e-01
   1_occ:   1.513  0.011  0.088 15.450  0.005  4.103   1.2276e-01
   2_bss:   1.513  0.011  0.088 15.450  0.005  4.103   1.2276e-01
   2_xyz:   1.252  0.009  0.087 14.800  0.005  4.121   8.4361e-02
   2_adp:   1.252  0.009  0.087 14.800  0.005  4.121   8.4361e-02
   2_occ:   1.252  0.009  0.087 14.800  0.005  4.121   8.4361e-02
   3_bss:   1.252  0.009  0.087 14.800  0.005  4.121   8.4361e-02
   3_xyz:   1.089  0.008  0.071 14.690  0.004  4.112   6.9156e-02
   3_adp:   1.089  0.008  0.071 14.690  0.004  4.112   6.9156e-02
   3_occ:   1.089  0.008  0.071 14.690  0.004  4.112   6.9156e-02
   4_bss:   1.089  0.008  0.071 14.690  0.004  4.112   6.9156e-02
   4_xyz:   0.972  0.006  0.069 14.458  0.004  4.110   5.5891e-02
   4_adp:   0.972  0.006  0.069 14.458  0.004  4.110   5.5891e-02
   4_occ:   0.972  0.006  0.069 14.458  0.004  4.110   5.5891e-02
   5_bss:   0.972  0.006  0.069 14.458  0.004  4.110   5.5891e-02
   5_xyz:   1.052  0.007  0.074 14.580  0.004  4.113   6.2401e-02
   5_adp:   1.052  0.007  0.074 14.580  0.004  4.113   6.2401e-02
   5_occ:   1.052  0.007  0.074 14.580  0.004  4.113   6.2401e-02
   5_bss:   1.052  0.007  0.074 14.580  0.004  4.113   6.2401e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.985   2.4516e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.985   2.4516e-01
   1_xyz:   8.499  0.078  0.339 82.275  0.020  1.751   8.0368e-02
   1_adp:   8.499  0.078  0.339 82.275  0.020  1.751   8.0368e-02
   1_occ:   8.499  0.078  0.339 82.275  0.020  1.751   8.0368e-02
   2_bss:   8.499  0.078  0.339 82.275  0.020  1.751   8.0368e-02
   2_xyz:   8.435  0.043  0.258 80.671  0.028  2.134   8.5023e-02
   2_adp:   8.435  0.043  0.258 80.671  0.028  2.134   8.5023e-02
   2_occ:   8.435  0.043  0.258 80.671  0.028  2.134   8.5023e-02
   3_bss:   8.435  0.043  0.258 80.671  0.028  2.134   8.5023e-02
   3_xyz:   7.555  0.060  0.218 78.105  0.041  2.129   5.5865e-02
   3_adp:   7.555  0.060  0.218 78.105  0.041  2.129   5.5865e-02
   3_occ:   7.555  0.060  0.218 78.105  0.041  2.129   5.5865e-02
   4_bss:   7.555  0.060  0.218 78.105  0.041  2.129   5.5865e-02
   4_xyz:   6.682  0.044  0.226 79.550  0.038  2.289   5.3819e-02
   4_adp:   6.682  0.044  0.226 79.550  0.038  2.289   5.3819e-02
   4_occ:   6.682  0.044  0.226 79.550  0.038  2.289   5.3819e-02
   5_bss:   6.682  0.044  0.226 79.550  0.038  2.289   5.3819e-02
   5_xyz:   7.751  0.050  0.237 82.845  0.036  2.296   4.2095e-02
   5_adp:   7.751  0.050  0.237 82.845  0.036  2.296   4.2095e-02
   5_occ:   7.751  0.050  0.237 82.845  0.036  2.296   4.2095e-02
   5_bss:   7.751  0.050  0.237 82.845  0.036  2.296   4.2095e-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:  95.31   0.00  19.33  87.95   0.00  15.69  95.31   0.00  39.17
   1_occ:  95.31   0.00  19.33  87.95   0.00  15.69  95.31   0.00  39.17
   2_bss:  95.31   0.00  19.33  87.95   0.00  15.69  95.31   0.00  39.17
   2_xyz:  95.31   0.00  19.33  87.95   0.00  15.69  95.31   0.00  39.17
   2_adp:  90.51   0.00  18.84  86.81   0.00  14.64  90.51   3.47  41.69
   2_occ:  90.51   0.00  18.84  86.81   0.00  14.64  90.51   3.47  41.69
   3_bss:  90.51   0.00  18.84  86.81   0.00  14.64  90.51   3.47  41.69
   3_xyz:  90.51   0.00  18.84  86.81   0.00  14.64  90.51   3.47  41.69
   3_adp:  95.12   0.00  18.26  95.12   0.00  13.64  89.22   5.63  43.39
   3_occ:  95.12   0.00  18.26  95.12   0.00  13.64  89.22   5.63  43.39
   4_bss:  95.12   0.00  18.26  95.12   0.00  13.64  89.22   5.63  43.39
   4_xyz:  95.12   0.00  18.26  95.12   0.00  13.64  89.22   5.63  43.39
   4_adp: 100.04   1.21  17.98 100.04   1.21  13.30  93.88   5.61  43.47
   4_occ: 100.04   1.21  17.98 100.04   1.21  13.30  93.88   5.61  43.47
   5_bss: 100.04   1.21  17.98 100.04   1.21  13.30  93.88   5.61  43.47
   5_xyz: 100.04   1.21  17.98 100.04   1.21  13.30  93.88   5.61  43.47
   5_adp:  98.95   1.69  17.28  98.95   1.69  12.97  91.50   5.35  40.80
   5_occ:  98.95   1.69  17.28  98.95   1.69  12.97  91.50   5.35  40.80
   5_bss:  98.89   1.63  17.22  98.89   1.63  12.90  91.44   5.29  40.74
------------------------------------------------------------------------
 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:    3.412    0.019    0.368
   1_adp:    3.412    0.019    0.368
   1_occ:    3.412    0.019    0.368
   2_bss:    3.412    0.019    0.368
   2_xyz:    3.407    0.018    0.572
   2_adp:    3.407    0.018    0.572
   2_occ:    3.407    0.018    0.572
   3_bss:    3.407    0.018    0.572
   3_xyz:    3.450    0.063    0.702
   3_adp:    3.450    0.063    0.702
   3_occ:    3.450    0.063    0.702
   4_bss:    3.450    0.063    0.702
   4_xyz:    3.474    0.094    0.742
   4_adp:    3.474    0.094    0.742
   4_occ:    3.474    0.094    0.742
   5_bss:    3.474    0.094    0.742
   5_xyz:    3.478    0.078    0.765
   5_adp:    3.478    0.078    0.765
   5_occ:    3.478    0.078    0.765
   5_bss:    3.478    0.078    0.765
------------------------------------------------------------------------

CPU time actual refinement: 334.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_105/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_105/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_105/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_105/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_105/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.38 
  Macro-tasks:
    bulk solvent and scale       = 37.54  
    individual site refinement   = 135.87 
    weights calculation          = 30.34  
    collect and process          = 6.59   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.46 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 107.40 
    alpha_beta                      = 8.24   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 114.99 
    fmodel                         = 6.71   
    r_factors                      = 0.19   
    phase_errors                   = 10.69  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 252.09 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.817 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    633 calls, 107.09 s
gradients_fft:          578 calls, 102.50 s

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

# Date 2008-01-16 Time 04:02:01 PST -0800 (1200484921.19 s)
Start R-work = 0.4573, R-free = 0.4496 (no bulk solvent and anisotropic scale)
Final R-work = 0.1424, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4495, R-free = 0.4398
Final R-work = 0.1189, R-free = 0.1623