# Date 2008-01-16 Time 06:30:16 PST -0800 (1200493816.35 s)
#phil __OFF__

Command line arguments: "../1170.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7259
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1170

-------------------------------------------------------------------------------
  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: (71.655, 47.3993, 85.9581, 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: 3.32, per 1000 atoms: 1.18


================================== 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: (71.655, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99118
Completeness in resolution range: 0.949678
Completeness with d_max=infinity: 0.946832

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9912

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: (71.655, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99118
Completeness in resolution range: 0.949678
Completeness with d_max=infinity: 0.946832

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2613 [2165/2194]  1951   214   9.9%
  bin  2:  4.2613 -  3.3947 [2075/2091]  1865   210  10.1%
  bin  3:  3.3947 -  2.9692 [2048/2067]  1842   206  10.1%
  bin  4:  2.9692 -  2.6994 [2046/2076]  1848   198   9.7%
  bin  5:  2.6994 -  2.5068 [2034/2053]  1830   204  10.0%
  bin  6:  2.5068 -  2.3596 [2010/2046]  1802   208  10.3%
  bin  7:  2.3596 -  2.2418 [1986/2019]  1787   199  10.0%
  bin  8:  2.2418 -  2.1445 [2001/2035]  1805   196   9.8%
  bin  9:  2.1445 -  2.0622 [1986/2014]  1785   201  10.1%
  bin 10:  2.0622 -  1.9912 [1238/2032]  1115   123   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1170/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 4
        2.20 -     2.87: 1219
        2.87 -     3.55: 4372
        3.55 -     4.22: 9148
        4.22 -     4.90: 13235
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.525 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.129 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.177 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27973 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_1170/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1170/model_refine_001.geo

CPU time processing inputs: 8.89


============================ 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 = 71.655 47.3993 85.95805 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: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3640   r_free= 0.3602   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.126972                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7531 0.99   1401  157 0.3020 0.2991       6.386      6.3511|
|  2:  4.7531 -  3.7920 0.99   1360  145 0.2823 0.2902      6.5384      6.5085|
|  3:  3.7920 -  3.3184 0.99   1321  151 0.3157 0.3000      6.4219      6.4348|
|  4:  3.3184 -  3.0175 0.99   1328  150 0.3435 0.3196      6.3294      6.2637|
|  5:  3.0175 -  2.8027 0.99   1315  143 0.3632 0.3826       6.178      6.2653|
|  6:  2.8027 -  2.6384 0.99   1297  145 0.3946 0.3733      6.1323      6.0938|
|  7:  2.6384 -  2.5068 0.99   1314  141 0.4010 0.3748      6.1076      6.0721|
|  8:  2.5068 -  2.3982 0.98   1275  150 0.4092 0.4074      6.0407      6.1099|
|  9:  2.3982 -  2.3062 0.98   1295  146 0.4117 0.4020      6.0098      5.9967|
| 10:  2.3062 -  2.2268 0.98   1276  134 0.4169 0.4450      5.9922      6.0463|
| 11:  2.2268 -  2.1574 1.00   1289  144 0.4312 0.4404      5.9505      5.9626|
| 12:  2.1574 -  2.0959 0.97   1259  139 0.4383 0.4353      5.8895      5.9347|
| 13:  2.0959 -  2.0409 0.98   1282  142 0.4342 0.4148       5.803      5.7198|
| 14:  2.0409 -  1.9912 0.47    618   72 0.3945 0.4409      5.7161      5.7418|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7531  1401   157  0.78  26.73   0.85     0.80      44445.52|
|  2:  4.7531 -  3.7920  1360   145  0.82  24.01   0.96     0.88      52586.50|
|  3:  3.7920 -  3.3184  1321   151  0.77  29.45   0.96     0.90      55061.19|
|  4:  3.3184 -  3.0175  1328   150  0.72  33.37   0.96     0.87      50951.45|
|  5:  3.0175 -  2.8027  1315   143  0.65  39.80   0.95     0.82      44868.51|
|  6:  2.8027 -  2.6384  1297   145  0.63  41.41   0.98     0.81      39265.43|
|  7:  2.6384 -  2.5068  1314   141  0.63  41.22   0.96     0.81      36171.38|
|  8:  2.5068 -  2.3982  1275   150  0.60  43.89   0.96     0.81      35155.12|
|  9:  2.3982 -  2.3062  1295   146  0.58  45.54   0.99     0.79      34139.00|
| 10:  2.3062 -  2.2268  1276   134  0.57  46.75   0.99     0.77      33244.55|
| 11:  2.2268 -  2.1574  1289   144  0.56  47.28   1.00     0.79      30747.33|
| 12:  2.1574 -  2.0959  1259   139  0.57  47.05   0.98     0.82      28310.02|
| 13:  2.0959 -  2.0409  1282   142  0.56  47.27   0.95     0.80      23678.27|
| 14:  2.0409 -  1.9912   618    72  0.57  46.61   1.02     0.75      19162.62|
|alpha:            min =        0.75 max =            0.90 mean =         0.82|
|beta:             min =    19162.62 max =        55061.19 mean =     38602.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.65|
|phase err.(work): min =        0.00 max =           89.99 mean =        39.57|
|phase err.(test): min =        0.00 max =           89.92 mean =        39.37|
|-----------------------------------------------------------------------------|

============================== 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 = 4.385089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.001   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.998460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.059   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.525 -  1.862:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.862 -  2.200:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.200 -  2.537:       23 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.537 -  2.875:     1196 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.875 -  3.212:     1883 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.212 -  3.550:     2489 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.550 -  3.887:     4606 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.887 -  4.225:     4542 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.225 -  4.562:     6012 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.562 -  4.900:     7223 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.525 |       0.186 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    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: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3640   r_free= 0.3602   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.126972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3532   r_free= 0.3491   ksol= 0.30   Bsol= 50.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,0.20,-1.72,0.00,-0.00,-0.00); trace/3= -0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.112765                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.839603              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.281   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.541867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.674   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3532      final r-factor (work) = 0.2308          |
| start r-factor (free) = 0.3491      final r-factor (free) = 0.2573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9032 = 3.84 * 0.50 * 6.1145 + 1.00 * 0.1645                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3830 = 3.84 * 0.50 * 5.8885 + 1.00 * 0.0783                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2308      final r-factor (work) = 0.2103          |
| start r-factor (free) = 0.2573      final r-factor (free) = 0.2607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1971 = 0.54 * 1.00 * 5.8885 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0905 = 0.54 * 1.00 * 5.6821 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.56   17.61    None  None   None       |
|    all(noH): 2823   0      0.00    84.56   17.61    None  None   None       |
|    Sol.    : 438    0      4.61    84.56   40.52    None  None   None       |
|    Mac.    : 2385   0      0.00    78.76   13.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.456:  694   |   5:    42.280 -  50.736:  113        |
|      1:     8.456 -  16.912: 1187   |   6:    50.736 -  59.192:   69        |
|      2:    16.912 -  25.368:  413   |   7:    59.192 -  67.648:   41        |
|      3:    25.368 -  33.824:  154   |   8:    67.648 -  76.104:   22        |
|      4:    33.824 -  42.280:  120   |   9:    76.104 -  84.560:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2103 r_free = 0.2607             target_work(ml) = 5.687         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2100 r_free = 0.2602             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2100   r_free= 0.2602   ksol= 0.30   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,0.20,-1.72,0.00,-0.00,-0.00); trace/3= -0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.685165                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2086   r_free= 0.2579   ksol= 0.33   Bsol= 67.76   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,-1.34,-1.82,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.683490                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.471449              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.095   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340585              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.386  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2086      final r-factor (work) = 0.1495          |
| start r-factor (free) = 0.2579      final r-factor (free) = 0.1941          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9523 = 3.47 * 0.50 * 5.6887 + 1.00 * 0.0783                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6955 = 3.47 * 0.50 * 5.5492 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1495      final r-factor (work) = 0.1386          |
| start r-factor (free) = 0.1941      final r-factor (free) = 0.1819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9015 = 0.34 * 1.00 * 5.5492 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8331 = 0.34 * 1.00 * 5.3548 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    83.05   17.39    None  None   None       |
|    all(noH): 2823   0      1.47    83.05   17.39    None  None   None       |
|    Sol.    : 438    0      4.67    83.01   40.87    None  None   None       |
|    Mac.    : 2385   0      1.47    83.05   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.465 -   9.624:  939   |   5:    42.260 -  50.419:  102        |
|      1:     9.624 -  17.783: 1091   |   6:    50.419 -  58.578:   73        |
|      2:    17.783 -  25.942:  296   |   7:    58.578 -  66.737:   45        |
|      3:    25.942 -  34.101:  120   |   8:    66.737 -  74.896:   19        |
|      4:    34.101 -  42.260:  126   |   9:    74.896 -  83.055:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1386 r_free = 0.1819             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1384 r_free = 0.1819             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1819   ksol= 0.33   Bsol= 67.76   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,-1.34,-1.82,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.320499                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1817   ksol= 0.33   Bsol= 67.76   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.89,-1.64,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.391034              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.929  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.409947              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.404  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1384      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1450 = 3.39 * 0.50 * 5.3561 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9856 = 3.39 * 0.50 * 5.2574 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4221 = 1.41 * 1.00 * 5.2574 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3247 = 1.41 * 1.00 * 5.1875 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.33    90.67   17.51    None  None   None       |
|    all(noH): 2823   0      0.33    90.67   17.51    None  None   None       |
|    Sol.    : 438    0      5.40    85.84   41.86    None  None   None       |
|    Mac.    : 2385   0      0.33    90.67   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.330 -   9.364:  890   |   5:    45.500 -  54.534:  103        |
|      1:     9.364 -  18.398: 1199   |   6:    54.534 -  63.568:   73        |
|      2:    18.398 -  27.432:  262   |   7:    63.568 -  72.602:   36        |
|      3:    27.432 -  36.466:  128   |   8:    72.602 -  81.635:   13        |
|      4:    36.466 -  45.500:  110   |   9:    81.635 -  90.669:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1632             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1632             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1632   ksol= 0.33   Bsol= 67.76   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.89,-1.64,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.182693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1631   ksol= 0.33   Bsol= 67.76   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.91,-1.47,-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: 5.182653                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.298084              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.025  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.129077              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.062  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6259 = 3.30 * 0.50 * 5.1874 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5982 = 3.30 * 0.50 * 5.1670 + 1.00 * 0.0776                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8445 = 1.13 * 1.00 * 5.1670 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8334 = 1.13 * 1.00 * 5.1570 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.12   17.34    None  None   None       |
|    all(noH): 2823   0      0.00    97.12   17.34    None  None   None       |
|    Sol.    : 438    0      5.74    86.78   41.52    None  None   None       |
|    Mac.    : 2385   0      0.00    97.12   12.89    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 -   9.712: 1011   |   5:    48.562 -  58.274:   99        |
|      1:     9.712 -  19.425: 1134   |   6:    58.274 -  67.987:   58        |
|      2:    19.425 -  29.137:  237   |   7:    67.987 -  77.699:   25        |
|      3:    29.137 -  38.850:  128   |   8:    77.699 -  87.412:    8        |
|      4:    38.850 -  48.562:  118   |   9:    87.412 -  97.124:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1619             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1619             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1619   ksol= 0.33   Bsol= 67.76   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.91,-1.47,-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: 5.157014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1619   ksol= 0.32   Bsol= 64.73   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-1.81,-1.29,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158064                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.404174              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.425  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.194200              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.817  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2774 = 2.40 * 0.50 * 5.1575 + 1.00 * 0.0776                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2717 = 2.40 * 0.50 * 5.1623 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0131 = 0.19 * 1.00 * 5.1623 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0126 = 0.19 * 1.00 * 5.1731 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    90.64   16.49    None  None   None       |
|    all(noH): 2823   0      0.87    90.64   16.49    None  None   None       |
|    Sol.    : 438    0      5.70    81.92   37.99    None  None   None       |
|    Mac.    : 2385   0      0.87    90.64   12.54    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:     0.872 -   9.849: 1069   |   5:    45.755 -  54.731:   92        |
|      1:     9.849 -  18.825: 1077   |   6:    54.731 -  63.708:   46        |
|      2:    18.825 -  27.802:  236   |   7:    63.708 -  72.685:   18        |
|      3:    27.802 -  36.778:  145   |   8:    72.685 -  81.661:    4        |
|      4:    36.778 -  45.755:  131   |   9:    81.661 -  90.638:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1612             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1611             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1611   ksol= 0.32   Bsol= 64.73   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-1.81,-1.29,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167770                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7531 0.99   1401  157 0.0999 0.1305      5.3935      5.5603|
|  2:  4.7531 -  3.7920 0.99   1360  145 0.0862 0.1082      5.4406       5.631|
|  3:  3.7920 -  3.3184 0.99   1321  151 0.1047 0.1533      5.4656      5.8576|
|  4:  3.3184 -  3.0175 0.99   1328  150 0.1202 0.1550      5.4638      5.6031|
|  5:  3.0175 -  2.8027 0.99   1315  143 0.1358 0.1857      5.3594      5.5775|
|  6:  2.8027 -  2.6384 0.99   1297  145 0.1259 0.1923      5.2413      5.4997|
|  7:  2.6384 -  2.5068 0.99   1314  141 0.1238 0.1703      5.1818       5.387|
|  8:  2.5068 -  2.3982 0.98   1275  150 0.1186 0.1753      5.0802      5.3468|
|  9:  2.3982 -  2.3062 0.98   1295  146 0.1171 0.1859      5.0459      5.3422|
| 10:  2.3062 -  2.2268 0.98   1276  134 0.1169 0.1802      4.9937      5.2459|
| 11:  2.2268 -  2.1574 1.00   1289  144 0.1182 0.1808      4.9708      5.2894|
| 12:  2.1574 -  2.0959 0.97   1259  139 0.1112 0.1662      4.9033      5.1391|
| 13:  2.0959 -  2.0409 0.98   1282  142 0.1229 0.1808      4.8188      5.0686|
| 14:  2.0409 -  1.9912 0.47    618   72 0.1046 0.1733      4.6594      4.9666|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7531  1401   157  0.94   9.31   0.97     0.94       7398.87|
|  2:  4.7531 -  3.7920  1360   145  0.95   8.12   1.00     0.98       9090.58|
|  3:  3.7920 -  3.3184  1321   151  0.93  11.52   1.01     1.01      10476.20|
|  4:  3.3184 -  3.0175  1328   150  0.92  14.10   1.00     0.98      10886.41|
|  5:  3.0175 -  2.8027  1315   143  0.89  17.03   0.99     0.96       9159.72|
|  6:  2.8027 -  2.6384  1297   145  0.90  16.67   0.98     0.95       7604.30|
|  7:  2.6384 -  2.5068  1314   141  0.90  15.90   0.99     0.96       6543.75|
|  8:  2.5068 -  2.3982  1275   150  0.90  15.94   0.99     0.96       5590.17|
|  9:  2.3982 -  2.3062  1295   146  0.90  15.92   0.99     0.96       5269.77|
| 10:  2.3062 -  2.2268  1276   134  0.90  16.14   0.98     0.94       4649.12|
| 11:  2.2268 -  2.1574  1289   144  0.90  16.74   0.98     0.95       4606.60|
| 12:  2.1574 -  2.0959  1259   139  0.91  15.61   0.99     0.98       4300.61|
| 13:  2.0959 -  2.0409  1282   142  0.89  17.10   0.98     0.97       3521.37|
| 14:  2.0409 -  1.9912   618    72  0.91  14.87   0.96     0.93       2552.92|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2552.92 max =        10886.41 mean =      6741.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.57|
|phase err.(test): min =        0.00 max =           88.46 mean =        14.05|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1612   ksol= 0.32   Bsol= 58.61   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-1.75,-1.15,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1612   ksol= 0.32   Bsol= 58.61   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-1.75,-1.15,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167832                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7531 0.99   1401  157 0.0996 0.1302       5.391      5.5567|
|  2:  4.7531 -  3.7920 0.99   1360  145 0.0858 0.1078      5.4367      5.6267|
|  3:  3.7920 -  3.3184 0.99   1321  151 0.1045 0.1532      5.4637      5.8574|
|  4:  3.3184 -  3.0175 0.99   1328  150 0.1203 0.1549      5.4647      5.6035|
|  5:  3.0175 -  2.8027 0.99   1315  143 0.1361 0.1859      5.3612      5.5792|
|  6:  2.8027 -  2.6384 0.99   1297  145 0.1261 0.1924      5.2427      5.5005|
|  7:  2.6384 -  2.5068 0.99   1314  141 0.1239 0.1705      5.1828      5.3883|
|  8:  2.5068 -  2.3982 0.98   1275  150 0.1187 0.1755      5.0811      5.3477|
|  9:  2.3982 -  2.3062 0.98   1295  146 0.1171 0.1856      5.0464      5.3415|
| 10:  2.3062 -  2.2268 0.98   1276  134 0.1170 0.1807      4.9947      5.2484|
| 11:  2.2268 -  2.1574 1.00   1289  144 0.1183 0.1812      4.9717      5.2902|
| 12:  2.1574 -  2.0959 0.97   1259  139 0.1112 0.1665      4.9043      5.1403|
| 13:  2.0959 -  2.0409 0.98   1282  142 0.1230 0.1812      4.8194      5.0695|
| 14:  2.0409 -  1.9912 0.47    618   72 0.1046 0.1732      4.6595      4.9656|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7531  1401   157  0.94   9.29   0.97     0.94       7351.66|
|  2:  4.7531 -  3.7920  1360   145  0.95   8.10   1.00     0.99       9031.70|
|  3:  3.7920 -  3.3184  1321   151  0.93  11.47   1.01     1.01      10426.60|
|  4:  3.3184 -  3.0175  1328   150  0.92  14.11   1.00     0.98      10896.92|
|  5:  3.0175 -  2.8027  1315   143  0.89  17.04   0.99     0.96       9174.16|
|  6:  2.8027 -  2.6384  1297   145  0.90  16.70   0.98     0.95       7626.74|
|  7:  2.6384 -  2.5068  1314   141  0.90  15.91   0.99     0.96       6557.32|
|  8:  2.5068 -  2.3982  1275   150  0.90  15.95   0.99     0.96       5600.15|
|  9:  2.3982 -  2.3062  1295   146  0.90  15.93   0.99     0.96       5274.54|
| 10:  2.3062 -  2.2268  1276   134  0.90  16.17   0.98     0.94       4656.95|
| 11:  2.2268 -  2.1574  1289   144  0.90  16.76   0.99     0.95       4617.62|
| 12:  2.1574 -  2.0959  1259   139  0.91  15.64   0.99     0.99       4313.86|
| 13:  2.0959 -  2.0409  1282   142  0.89  17.11   0.98     0.97       3525.74|
| 14:  2.0409 -  1.9912   618    72  0.91  14.88   0.97     0.94       2551.42|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     2551.42 max =        10896.92 mean =      6738.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.57|
|phase err.(test): min =        0.00 max =           88.22 mean =        14.06|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.205)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    90.61   16.46    None  None   None       |
|    all(noH): 2823   0      0.84    90.61   16.46    None  None   None       |
|    Sol.    : 438    0      5.67    81.89   37.96    None  None   None       |
|    Mac.    : 2385   0      0.84    90.61   12.51    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:     0.842 -   9.819: 1069   |   5:    45.725 -  54.702:   92        |
|      1:     9.819 -  18.795: 1077   |   6:    54.702 -  63.678:   46        |
|      2:    18.795 -  27.772:  236   |   7:    63.678 -  72.655:   18        |
|      3:    27.772 -  36.749:  145   |   8:    72.655 -  81.631:    4        |
|      4:    36.749 -  45.725:  131   |   9:    81.631 -  90.608:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 4.792
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 310
   mapped sites are within: 0.705 - 4.792

peak=    5.912 closest distance to " CB  GLN A 223 " =    1.441
peak=    5.699 closest distance to " O   HOH Z 111 " =    2.053
peak=    5.006 closest distance to " CB  SER A  63 " =    1.280
peak=    4.880 closest distance to " O   HOH Z 232 " =    2.278
peak=    4.810 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.708 closest distance to " CB  GLN A 183 " =    1.201
peak=    4.655 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.636 closest distance to " CB  LEU A 228 " =    1.047
peak=    4.487 closest distance to " C   PRO A 198 " =    1.514
peak=    4.455 closest distance to " O   HOH Z 126 " =    1.881
peak=    4.449 closest distance to " CG  PRO A  90 " =    1.147
peak=    4.434 closest distance to " NH2 ARG A 156 " =    1.218
peak=    4.427 closest distance to " CB  GLU A 152 " =    1.166
peak=    4.398 closest distance to " CB  GLU A 128 " =    1.076
peak=    4.396 closest distance to " O   HOH Z 298 " =    1.925
peak=    4.386 closest distance to " CG  PRO A 198 " =    1.308
peak=    4.358 closest distance to " CA  TYR A  30 " =    0.966
peak=    4.355 closest distance to " CG  PRO A 243 " =    1.157
peak=    4.346 closest distance to " O   HOH Z 369 " =    1.999
peak=    4.271 closest distance to " O   HOH Z 261 " =    2.120
peak=    4.268 closest distance to " O   HOH Z 236 " =    2.001
peak=    4.241 closest distance to " CB  ARG A 190 " =    1.658
peak=    4.232 closest distance to " CZ  PHE A 218 " =    1.071
peak=    4.227 closest distance to " CB  ASN A 148 " =    1.359
peak=    4.172 closest distance to " O   HOH Z 368 " =    2.104
peak=    4.155 closest distance to " CB  TRP A 266 " =    0.910
peak=    4.146 closest distance to " O   HOH Z  15 " =    2.029
peak=    4.145 closest distance to " NE2 GLN A  11 " =    1.082
peak=    4.144 closest distance to " O   HOH Z  78 " =    1.647
peak=    4.136 closest distance to " CB  SER A   3 " =    1.378
peak=    4.117 closest distance to " CD1 LEU A 300 " =    1.247
peak=    4.115 closest distance to " ND2 ASN A 187 " =    1.487
peak=    4.107 closest distance to " O   HOH Z 234 " =    3.895
peak=    4.102 closest distance to " CB  GLU A 277 " =    3.672
peak=    4.097 closest distance to " CB  ARG A  79 " =    1.343
peak=    4.058 closest distance to " O   HOH Z 193 " =    1.988
peak=    4.055 closest distance to " O   HOH Z  21 " =    1.776
peak=    4.050 closest distance to " O   HOH Z 133 " =    2.305
peak=    4.045 closest distance to " O   HOH Z 303 " =    2.068
peak=    4.037 closest distance to " CZ  PHE A 192 " =    0.938
peak=    4.034 closest distance to " CB  TYR A 169 " =    0.722
peak=    4.032 closest distance to " CB  VAL A 265 " =    1.254
peak=    3.990 closest distance to " OD1 ASN A  69 " =    2.686
peak=    3.989 closest distance to " O   HOH Z  54 " =    2.326
peak=    3.983 closest distance to " O   HOH Z 189 " =    2.531
peak=    3.974 closest distance to " CG1 ILE A  33 " =    1.288
peak=    3.937 closest distance to " CD  ARG A 159 " =    0.805
peak=    3.935 closest distance to " CB  VAL A 202 " =    1.589
peak=    3.935 closest distance to " O   MET A 105 " =    1.851
peak=    3.932 closest distance to " O   HOH Z 316 " =    3.168
peak=    3.925 closest distance to " CB  ASN A 187 " =    1.209
peak=    3.917 closest distance to " CG2 THR A 221 " =    0.967
peak=    3.915 closest distance to " CD  ARG A 269 " =    0.949
peak=    3.909 closest distance to " NH1AARG A 145 " =    1.254
peak=    3.880 closest distance to " CA  THR A 264 " =    0.877
peak=    3.878 closest distance to " CB  ASN A  39 " =    0.914
peak=    3.874 closest distance to " ND2 ASN A 110 " =    1.704
peak=    3.866 closest distance to " CA  ASP A 191 " =    0.753
peak=    3.859 closest distance to " O   HOH Z 180 " =    2.139
peak=    3.845 closest distance to " O   HOH Z 158 " =    3.051
peak=    3.832 closest distance to " CB  TRP A 179 " =    1.466
peak=    3.832 closest distance to " O   HOH Z 403 " =    1.710
peak=    3.830 closest distance to " O   HOH Z  68 " =    1.786
peak=    3.829 closest distance to " CD  LYS A 166 " =    1.312
peak=    3.828 closest distance to " CB  ASP A 124 " =    0.718
peak=    3.811 closest distance to " O   HOH Z  88 " =    3.600
peak=    3.797 closest distance to " O   ALA A 165 " =    1.423
peak=    3.790 closest distance to " O   HOH Z 272 " =    1.949
peak=    3.789 closest distance to " O   HOH Z  20 " =    1.966
peak=    3.782 closest distance to " O   HOH Z 147 " =    1.779
peak=    3.768 closest distance to " O   HOH Z  40 " =    1.682
peak=    3.759 closest distance to " O   HOH Z 427 " =    3.109
peak=    3.756 closest distance to " CA  ALA A  21 " =    1.287
peak=    3.755 closest distance to " CG2BVAL A  41 " =    0.897
peak=    3.754 closest distance to " O   HOH Z 134 " =    1.439
peak=    3.753 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.744 closest distance to " O   HOH Z 368 " =    3.678
peak=    3.742 closest distance to " O   HOH Z 214 " =    1.998
peak=    3.732 closest distance to " CA  THR A 221 " =    0.948
peak=    3.721 closest distance to " O   HOH Z 135 " =    1.814
peak=    3.717 closest distance to " CD ALYS A 290 " =    1.010
peak=    3.716 closest distance to " OD2 ASP A 286 " =    2.924
peak=    3.712 closest distance to " CD1 ILE A 106 " =    0.909
peak=    3.707 closest distance to " CD2 LEU A 297 " =    0.851
peak=    3.694 closest distance to " O   HOH Z 108 " =    2.669
peak=    3.692 closest distance to " O   HOH Z 132 " =    2.685
peak=    3.685 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.685 closest distance to " O   HOH Z  92 " =    2.510
peak=    3.672 closest distance to " O   HOH Z 411 " =    3.806
peak=    3.671 closest distance to " CA  MET A  40 " =    1.131
peak=    3.669 closest distance to " O   HOH Z 426 " =    1.506
peak=    3.669 closest distance to " OD1 ASN A 217 " =    1.682
peak=    3.662 closest distance to " O   HOH Z 128 " =    2.173
peak=    3.657 closest distance to " N   ASN A  39 " =    1.350
peak=    3.652 closest distance to " O   HOH Z 213 " =    1.849
peak=    3.645 closest distance to " CB  ASP A 140 " =    0.831
peak=    3.635 closest distance to " O   HOH Z 163 " =    1.701
peak=    3.629 closest distance to " O   HOH Z 406 " =    1.655
peak=    3.625 closest distance to " O   HOH Z 344 " =    3.204
peak=    3.618 closest distance to " N   ARG A 156 " =    1.424
peak=    3.616 closest distance to " CA  SER A  87 " =    0.970
peak=    3.615 closest distance to " CG BARG A 275 " =    1.445
peak=    3.610 closest distance to " O   HOH Z 142 " =    1.618
peak=    3.605 closest distance to " CA  ALA A  51 " =    0.905
peak=    3.603 closest distance to " CZ  PHE A 208 " =    1.183
peak=    3.600 closest distance to " O   HOH Z 423 " =    1.879
peak=    3.597 closest distance to " ND1 HIS A  86 " =    1.759
peak=    3.588 closest distance to " CB  LEU A 143 " =    1.081
peak=    3.586 closest distance to " CA  ASP A 124 " =    0.739
peak=    3.584 closest distance to " O   HOH Z 193 " =    2.169
peak=    3.584 closest distance to " O   HOH Z  80 " =    1.606
peak=    3.581 closest distance to " CA  ARG A 195 " =    1.189
peak=    3.578 closest distance to " O   HOH Z  66 " =    2.143
peak=    3.578 closest distance to " ND2 ASN A 249 " =    1.923
peak=    3.578 closest distance to " CB  ILE A 120 " =    1.229
peak=    3.572 closest distance to " CB  SER A 141 " =    0.971
peak=    3.569 closest distance to " NZ  LYS A 117 " =    3.399
peak=    3.564 closest distance to " CG1BVAL A  72 " =    1.740
peak=    3.559 closest distance to " CB  GLU A  46 " =    0.975
peak=    3.558 closest distance to " CD  ARG A  66 " =    2.320
peak=    3.556 closest distance to " O   HOH Z 171 " =    3.852
peak=    3.553 closest distance to " CB  SER A 216 " =    0.811
peak=    3.552 closest distance to " CB  SER A 212 " =    1.148
peak=    3.550 closest distance to " NZ  LYS A 166 " =    3.059
peak=    3.543 closest distance to " CG2 VAL A 257 " =    0.933
peak=    3.542 closest distance to " O   SER A  87 " =    2.258
peak=    3.537 closest distance to " CG1 ILE A 151 " =    1.026
peak=    3.530 closest distance to " CB  TYR A 169 " =    0.829
peak=    3.529 closest distance to " O   HOH Z 313 " =    1.845
peak=    3.517 closest distance to " O   HOH Z 281 " =    4.640
peak=    3.510 closest distance to " O   HOH Z 209 " =    2.262
peak=    3.509 closest distance to " O   HOH Z 133 " =    1.711
peak=    3.509 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.507 closest distance to " CA  ARG A  36 " =    1.181
peak=    3.501 closest distance to " CD1 LEU A  96 " =    0.705
peak=    3.498 closest distance to " O   HOH Z  10 " =    1.874
peak=    3.497 closest distance to " NH2BARG A 145 " =    2.193
peak=    3.497 closest distance to " ND1 HIS A  81 " =    1.685
peak=    3.494 closest distance to " CB  PHE A  16 " =    1.052
peak=    3.492 closest distance to " O   HOH Z 197 " =    2.758
peak=    3.491 closest distance to " O   HOH Z  97 " =    2.026
peak=    3.491 closest distance to " CG  LEU A 167 " =    1.186
peak=    3.489 closest distance to " O   HOH Z 193 " =    1.688
peak=    3.485 closest distance to " CB  ALA A 100 " =    1.274
peak=    3.485 closest distance to " CG2 ILE A 120 " =    1.065
peak=    3.481 closest distance to " O   HOH Z   1 " =    2.123
peak=    3.480 closest distance to " CA  ASN A 215 " =    1.207
peak=    3.478 closest distance to " O   TRP A 274 " =    1.856
peak=    3.467 closest distance to " O   HOH Z 305 " =    3.762
peak=    3.466 closest distance to " O   HOH Z 425 " =    1.339
peak=    3.460 closest distance to " O   HOH Z 352 " =    1.917
peak=    3.456 closest distance to " O   HOH Z 345 " =    1.812
peak=    3.445 closest distance to " CB  TYR A 116 " =    0.923
peak=    3.443 closest distance to " O   HOH Z 126 " =    1.574
peak=    3.442 closest distance to " CA  ALA A 295 " =    1.110
peak=    3.441 closest distance to " O   HOH Z 346 " =    1.592
peak=    3.438 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.438 closest distance to " O   HOH Z 172 " =    3.708
peak=    3.437 closest distance to " O   HOH Z  68 " =    2.211
peak=    3.434 closest distance to " O   HOH Z 263 " =    1.722
peak=    3.432 closest distance to " NE1 TRP A 266 " =    1.380
peak=    3.429 closest distance to " CG AARG A 275 " =    1.205
peak=    3.426 closest distance to " CD  ARG A 219 " =    1.028
peak=    3.426 closest distance to " CE1 TYR A 186 " =    1.337
peak=    3.425 closest distance to " O   THR A 251 " =    1.298
peak=    3.425 closest distance to " O   HOH Z 371 " =    3.337
peak=    3.424 closest distance to " O   HOH Z 245 " =    1.359
peak=    3.423 closest distance to " N   ASN A 127 " =    1.252
peak=    3.422 closest distance to " CB  ALA A   9 " =    1.568
peak=    3.415 closest distance to " O   HOH Z 128 " =    2.252
peak=    3.414 closest distance to " CD  LYS A 119 " =    1.458
peak=    3.413 closest distance to " O   HOH Z 183 " =    1.499
peak=    3.413 closest distance to " CB  MET A  40 " =    0.787
peak=    3.400 closest distance to " CB  ASN A 142 " =    0.966
peak=    3.393 closest distance to " CA  ASP A 140 " =    1.219
peak=    3.385 closest distance to " CB  ALA A 291 " =    1.207
peak=    3.384 closest distance to " CG1 VAL A 153 " =    0.958
peak=    3.379 closest distance to " CD2 LEU A 255 " =    1.490
peak=    3.379 closest distance to " CA  GLN A 223 " =    0.958
peak=    3.378 closest distance to " O   HOH Z  62 " =    2.339
peak=    3.366 closest distance to " O   HOH Z  49 " =    2.301
peak=    3.366 closest distance to " CA  ASP A 162 " =    1.163
peak=    3.363 closest distance to " NE2 GLN A  77 " =    3.459
peak=    3.362 closest distance to " CB  ALA A 248 " =    1.026
peak=    3.354 closest distance to " O   HOH Z 329 " =    3.705
peak=    3.354 closest distance to " O   HOH Z 425 " =    2.075
peak=    3.349 closest distance to " OG  SER A 245 " =    1.747
peak=    3.349 closest distance to " CG2 VAL A 197 " =    1.171
peak=    3.346 closest distance to " CA  ALA A 154 " =    0.960
peak=    3.345 closest distance to " O   HOH Z  97 " =    2.598
peak=    3.342 closest distance to " O   HOH Z 327 " =    1.949
peak=    3.341 closest distance to " N   VAL A 126 " =    1.336
peak=    3.339 closest distance to " O   HOH Z 402 " =    1.446
peak=    3.338 closest distance to " CG  LYS A  76 " =    0.932
peak=    3.333 closest distance to " NH1 ARG A 138 " =    1.116
peak=    3.327 closest distance to " CG BARG A 102 " =    1.907
peak=    3.324 closest distance to " CB  ALA A 242 " =    0.841
peak=    3.324 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.322 closest distance to " O   HOH Z 247 " =    1.416
peak=    3.319 closest distance to " CA  GLY A 241 " =    0.723
peak=    3.318 closest distance to " CB  MET A  47 " =    0.956
peak=    3.315 closest distance to " O   HOH Z 334 " =    1.523
peak=    3.314 closest distance to " O   HOH Z  43 " =    1.828
peak=    3.314 closest distance to " O   HOH Z 126 " =    1.908
peak=    3.311 closest distance to " O   HOH Z 273 " =    2.810
peak=    3.305 closest distance to " CA  ALA A 158 " =    1.058
peak=    3.304 closest distance to " CB  GLN A  88 " =    1.247
peak=    3.304 closest distance to " O   HOH Z   4 " =    1.866
peak=    3.304 closest distance to " O   HOH Z 295 " =    1.481
peak=    3.301 closest distance to " CA  GLY A 267 " =    1.028
peak=    3.301 closest distance to " CD1AILE A 234 " =    0.959
peak=    3.286 closest distance to " CD1 TRP A 266 " =    1.129
peak=    3.280 closest distance to " CA  LYS A 117 " =    1.223
peak=    3.275 closest distance to " CB  ARG A 138 " =    1.084
peak=    3.270 closest distance to " O   HOH Z 298 " =    2.550
peak=    3.269 closest distance to " CA  MET A 105 " =    1.036
peak=    3.267 closest distance to " O   HOH Z 383 " =    1.971
peak=    3.265 closest distance to " N   TYR A  15 " =    0.756
peak=    3.263 closest distance to " CD  ARG A  14 " =    1.253
peak=    3.261 closest distance to " CB  ALA A 104 " =    0.724
peak=    3.260 closest distance to " CA  ILE A  33 " =    1.647
peak=    3.255 closest distance to " O   HOH Z 281 " =    3.990
peak=    3.246 closest distance to " NE2 HIS A 115 " =    0.987
peak=    3.246 closest distance to " O   HOH Z 419 " =    3.092
peak=    3.245 closest distance to " CG  MET A 185 " =    1.194
peak=    3.242 closest distance to " O   HOH Z 148 " =    3.226
peak=    3.241 closest distance to " CG2 THR A 220 " =    0.827
peak=    3.239 closest distance to " CG  GLU A  37 " =    0.883
peak=    3.238 closest distance to " CB  PRO A 198 " =    0.959
peak=    3.237 closest distance to " O   HOH Z 234 " =    1.770
peak=    3.236 closest distance to " CZ  PHE A  38 " =    1.297
peak=    3.235 closest distance to " OE1 GLN A  11 " =    2.087
peak=    3.233 closest distance to " OE1 GLU A   2 " =    2.202
peak=    3.233 closest distance to " CA  GLU A 152 " =    0.874
peak=    3.233 closest distance to " CG  GLN A  58 " =    2.751
peak=    3.232 closest distance to " OG BSER A 164 " =    2.355
peak=    3.228 closest distance to " CG  MET A 113 " =    1.713
peak=    3.227 closest distance to " O  BHOH Z 338 " =    2.407
peak=    3.226 closest distance to " CB  ALA A  34 " =    1.065
peak=    3.219 closest distance to " CB  GLN A  89 " =    1.259
peak=    3.219 closest distance to " O   HOH Z 280 " =    3.006
peak=    3.219 closest distance to " CB  TRP A 150 " =    1.407
peak=    3.219 closest distance to " O   HOH Z 411 " =    1.830
peak=    3.218 closest distance to " O   HOH Z 387 " =    2.804
peak=    3.214 closest distance to " CA  LEU A 282 " =    1.093
peak=    3.213 closest distance to " CA  ALA A 233 " =    1.492
peak=    3.210 closest distance to " CD  ARG A  66 " =    2.320
peak=    3.210 closest distance to " O   HOH Z 261 " =    2.179
peak=    3.207 closest distance to " O   HOH Z 421 " =    1.662
peak=    3.205 closest distance to " C   TYR A 214 " =    1.512
peak=    3.205 closest distance to " N   SER A 135 " =    1.361
peak=    3.203 closest distance to " OD1 ASP A 231 " =    1.881
peak=    3.202 closest distance to " CB  LYS A 193 " =    1.013
peak=    3.201 closest distance to " O   HOH Z 437 " =    1.401
peak=    3.201 closest distance to " O   HOH Z 116 " =    1.843
peak=    3.200 closest distance to " O   ALA A 158 " =    1.306
peak=    3.200 closest distance to " O   HOH Z  44 " =    1.771
peak=    3.198 closest distance to " CB  PRO A  54 " =    1.251
peak=    3.195 closest distance to " O   HOH Z  88 " =    1.810
peak=    3.193 closest distance to " CB  GLU A 236 " =    1.057
peak=    3.191 closest distance to " O   HOH Z 250 " =    1.459
peak=    3.189 closest distance to " O   HOH Z 391 " =    2.947
peak=    3.187 closest distance to " O   HOH Z 359 " =    1.507
peak=    3.182 closest distance to " CG  MET A 185 " =    1.089
peak=    3.181 closest distance to " CA  ASN A 217 " =    1.306
peak=    3.176 closest distance to " CG  ARG A 159 " =    0.966
peak=    3.173 closest distance to " CA  TYR A 116 " =    1.422
peak=    3.172 closest distance to " CB  GLN A 103 " =    0.850
peak=    3.171 closest distance to " NH2AARG A 275 " =    3.609
peak=    3.165 closest distance to " O   TYR A 116 " =    1.277
peak=    3.163 closest distance to " O   HOH Z 392 " =    2.002
peak=    3.163 closest distance to " OG1 THR A 294 " =    1.676
peak=    3.160 closest distance to " O   HOH Z 294 " =    1.571
peak=    3.158 closest distance to " CB  ARG A 139 " =    0.879
peak=    3.156 closest distance to " O   HOH Z 409 " =    3.206
peak=    3.155 closest distance to " CG2 ILE A 151 " =    0.716
peak=    3.153 closest distance to " CB  ALA A  71 " =    1.328
peak=    3.151 closest distance to " O   HOH Z 353 " =    2.757
peak=    3.151 closest distance to " O   HOH Z 287 " =    2.304
peak=    3.150 closest distance to " N   GLY A  98 " =    1.170
peak=    3.148 closest distance to " CA  ALA A  84 " =    1.426
peak=    3.145 closest distance to " CD2 HIS A  81 " =    1.165
peak=    3.135 closest distance to " NH2AARG A 190 " =    1.228
peak=    3.135 closest distance to " O   HOH Z 384 " =    2.804
peak=    3.133 closest distance to " O   HOH Z 350 " =    1.624
peak=    3.129 closest distance to " CB  ASN A 110 " =    1.182
peak=    3.127 closest distance to " O   HOH Z 218 " =    4.792
peak=    3.112 closest distance to " O   HOH Z 417 " =    2.084
peak=    3.111 closest distance to " OG  SER A  28 " =    1.534
peak=    3.103 closest distance to " O   HOH Z  59 " =    2.153
peak=    3.103 closest distance to " O   HOH Z 355 " =    1.629
peak=    3.100 closest distance to " CD2 TRP A 179 " =    1.348
peak=    3.090 closest distance to " CB  SER A  62 " =    1.225
peak=    3.084 closest distance to " CA  GLU A  46 " =    0.766
peak=    3.080 closest distance to " CB  ALA A 248 " =    1.227
peak=    3.078 closest distance to " OG  SER A 206 " =    1.289
peak=    3.075 closest distance to " NH1BARG A 145 " =    1.148
peak=    3.074 closest distance to " CB  GLU A 152 " =    1.521
peak=    3.067 closest distance to " O   THR A 251 " =    1.960
peak=    3.061 closest distance to " O   HOH Z 213 " =    2.539
peak=    3.058 closest distance to " CA  GLN A  88 " =    1.333
peak=    3.047 closest distance to " O   ASN A 209 " =    1.295
peak=    3.046 closest distance to " O   HOH Z 302 " =    2.043
peak=    3.038 closest distance to " O   HOH Z 153 " =    1.833
peak=    3.032 closest distance to " CB  ALA A 114 " =    1.126

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.466 - 5.515
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 199
   mapped sites are within: 0.730 - 5.515

peak=   -4.573 closest distance to " O   HOH Z 290 " =    1.139
peak=   -4.506 closest distance to " O   HOH Z 266 " =    4.860
peak=   -4.401 closest distance to " CB  PRO A 243 " =    2.634
peak=   -4.266 closest distance to " O   HOH Z  10 " =    1.574
peak=   -4.210 closest distance to " O   VAL A  67 " =    2.676
peak=   -4.170 closest distance to " CD  ARG A 156 " =    2.048
peak=   -4.128 closest distance to " N   ALA A  43 " =    2.548
peak=   -4.126 closest distance to " O   ILE A 109 " =    2.676
peak=   -4.092 closest distance to " O   HOH Z 372 " =    2.510
peak=   -4.090 closest distance to " O   HOH Z  52 " =    1.516
peak=   -4.082 closest distance to " CZ3 TRP A 179 " =    1.156
peak=   -4.074 closest distance to " CE2 TYR A  30 " =    2.768
peak=   -3.973 closest distance to " CD  GLN A 223 " =    1.815
peak=   -3.921 closest distance to " O   HOH Z  38 " =    1.223
peak=   -3.915 closest distance to " OG  SER A  97 " =    2.239
peak=   -3.874 closest distance to " CG1 VAL A 112 " =    2.584
peak=   -3.857 closest distance to " CG1 VAL A 250 " =    2.714
peak=   -3.847 closest distance to " O   HOH Z 118 " =    3.223
peak=   -3.822 closest distance to " OD1 ASN A 148 " =    1.630
peak=   -3.816 closest distance to " CD1 LEU A 101 " =    2.536
peak=   -3.796 closest distance to " CD  ARG A  14 " =    3.406
peak=   -3.793 closest distance to " O   HOH Z 185 " =    2.474
peak=   -3.790 closest distance to " CD1 LEU A 228 " =    2.414
peak=   -3.789 closest distance to " NH2AARG A 275 " =    5.515
peak=   -3.787 closest distance to " O   PRO A 163 " =    2.151
peak=   -3.779 closest distance to " ND2 ASN A  45 " =    1.019
peak=   -3.757 closest distance to " O   HOH Z 377 " =    1.883
peak=   -3.743 closest distance to " CD  GLN A  58 " =    1.090
peak=   -3.741 closest distance to " O   HOH Z  73 " =    2.275
peak=   -3.726 closest distance to " CD1 PHE A 130 " =    2.214
peak=   -3.716 closest distance to " O   VAL A 189 " =    2.601
peak=   -3.710 closest distance to " C   ALA A 158 " =    1.351
peak=   -3.706 closest distance to " O   HOH Z 353 " =    2.219
peak=   -3.701 closest distance to " CA  GLY A 241 " =    3.125
peak=   -3.698 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.692 closest distance to " O   HOH Z 196 " =    2.102
peak=   -3.690 closest distance to " CD2 TYR A 293 " =    2.018
peak=   -3.685 closest distance to " CD2 LEU A 300 " =    2.925
peak=   -3.680 closest distance to " C   HIS A 108 " =    1.112
peak=   -3.679 closest distance to " O   HOH Z 407 " =    3.547
peak=   -3.670 closest distance to " OXT GLY A 302 " =    2.953
peak=   -3.669 closest distance to " CG  LEU A 101 " =    2.523
peak=   -3.664 closest distance to " ND2 ASN A  45 " =    1.802
peak=   -3.650 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.646 closest distance to " CG  ARG A  66 " =    2.280
peak=   -3.645 closest distance to " O   HOH Z  43 " =    1.547
peak=   -3.642 closest distance to " O   HOH Z 394 " =    1.513
peak=   -3.640 closest distance to " O   HOH Z 241 " =    1.172
peak=   -3.640 closest distance to " O   HOH Z 377 " =    1.055
peak=   -3.637 closest distance to " N   ALA A 226 " =    2.119
peak=   -3.637 closest distance to " C   ASN A 187 " =    1.926
peak=   -3.630 closest distance to " C   ASN A 285 " =    2.544
peak=   -3.627 closest distance to " CD1 ILE A 151 " =    2.371
peak=   -3.612 closest distance to " ND2 ASN A  60 " =    1.383
peak=   -3.608 closest distance to " OG BSER A 134 " =    1.902
peak=   -3.585 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.576 closest distance to " CB  ASN A  39 " =    2.181
peak=   -3.575 closest distance to " C   SER A 206 " =    1.464
peak=   -3.575 closest distance to " O   HOH Z 426 " =    1.685
peak=   -3.563 closest distance to " CD1 ILE A 239 " =    2.040
peak=   -3.562 closest distance to " SG  CYS A 254 " =    3.331
peak=   -3.560 closest distance to " O   HOH Z 389 " =    1.883
peak=   -3.558 closest distance to " CG2 ILE A 263 " =    2.353
peak=   -3.553 closest distance to " CD2 PHE A  61 " =    2.506
peak=   -3.541 closest distance to " O   HOH Z 351 " =    1.464
peak=   -3.527 closest distance to " CG  GLU A  53 " =    1.436
peak=   -3.520 closest distance to " CD  GLN A  88 " =    0.730
peak=   -3.512 closest distance to " O   HOH Z 222 " =    1.241
peak=   -3.502 closest distance to " CB  ALA A  43 " =    2.590
peak=   -3.499 closest distance to " O   HOH Z 393 " =    1.399
peak=   -3.494 closest distance to " O   GLY A 211 " =    1.546
peak=   -3.480 closest distance to " O   ASN A 209 " =    2.087
peak=   -3.476 closest distance to " OD1 ASP A 191 " =    1.651
peak=   -3.471 closest distance to " O   HOH Z 176 " =    0.847
peak=   -3.471 closest distance to " NH1 ARG A 195 " =    2.600
peak=   -3.468 closest distance to " CA  GLY A 241 " =    2.300
peak=   -3.468 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.456 closest distance to " O   HOH Z 275 " =    1.565
peak=   -3.451 closest distance to " O   HOH Z 166 " =    1.774
peak=   -3.447 closest distance to " CG  PHE A 283 " =    2.783
peak=   -3.444 closest distance to " SG  CYS A 168 " =    1.141
peak=   -3.441 closest distance to " NH2 ARG A  66 " =    1.932
peak=   -3.437 closest distance to " CB  ASP A 286 " =    2.172
peak=   -3.426 closest distance to " NE2 GLN A 103 " =    1.763
peak=   -3.424 closest distance to " CH2 TRP A 177 " =    2.130
peak=   -3.418 closest distance to " CD2 LEU A 237 " =    2.875
peak=   -3.417 closest distance to " C   LEU A 143 " =    1.158
peak=   -3.417 closest distance to " CG  ASP A 231 " =    0.799
peak=   -3.414 closest distance to " O   HOH Z  19 " =    2.360
peak=   -3.412 closest distance to " CB  TRP A  85 " =    2.446
peak=   -3.405 closest distance to " CA  ASP A 298 " =    1.123
peak=   -3.404 closest distance to " SG ACYS A 201 " =    2.066
peak=   -3.402 closest distance to " CG  ARG A 269 " =    2.449
peak=   -3.399 closest distance to " CD  ARG A 195 " =    5.106
peak=   -3.397 closest distance to " CD  ARG A 139 " =    1.611
peak=   -3.397 closest distance to " O   HOH Z 311 " =    3.753
peak=   -3.394 closest distance to " OG  SER A  62 " =    1.622
peak=   -3.393 closest distance to " O   HOH Z  93 " =    2.356
peak=   -3.392 closest distance to " CG1 VAL A 112 " =    2.973
peak=   -3.391 closest distance to " N   THR A  18 " =    1.299
peak=   -3.385 closest distance to " O   HOH Z 128 " =    2.495
peak=   -3.385 closest distance to " O   VAL A 125 " =    2.328
peak=   -3.384 closest distance to " O   HOH Z 111 " =    1.999
peak=   -3.371 closest distance to " NH2 ARG A 159 " =    2.398
peak=   -3.371 closest distance to " CG1 VAL A 125 " =    2.034
peak=   -3.370 closest distance to " O   HOH Z  51 " =    1.488
peak=   -3.363 closest distance to " N   MET A 105 " =    2.819
peak=   -3.363 closest distance to " NH2 ARG A  79 " =    1.576
peak=   -3.354 closest distance to " CB  ALA A 291 " =    2.304
peak=   -3.354 closest distance to " OG ASER A 134 " =    1.328
peak=   -3.346 closest distance to " ND2 ASN A 249 " =    2.399
peak=   -3.346 closest distance to " O   HOH Z 177 " =    1.622
peak=   -3.345 closest distance to " O   HOH Z 435 " =    2.715
peak=   -3.344 closest distance to " CE  MET A  93 " =    1.381
peak=   -3.344 closest distance to " O   HOH Z 313 " =    1.081
peak=   -3.340 closest distance to " O   HOH Z 166 " =    1.649
peak=   -3.335 closest distance to " O   HOH Z 211 " =    1.577
peak=   -3.332 closest distance to " CA  GLY A 203 " =    2.327
peak=   -3.328 closest distance to " O   VAL A  67 " =    2.741
peak=   -3.322 closest distance to " ND2BASN A 224 " =    1.743
peak=   -3.321 closest distance to " CG  GLU A 152 " =    0.856
peak=   -3.318 closest distance to " O   GLY A 196 " =    1.254
peak=   -3.309 closest distance to " CG  TRP A 266 " =    1.845
peak=   -3.309 closest distance to " CB  PRO A 163 " =    2.598
peak=   -3.306 closest distance to " O   HOH Z 232 " =    1.695
peak=   -3.299 closest distance to " OD2 ASP A 171 " =    1.854
peak=   -3.298 closest distance to " O   HOH Z  13 " =    1.457
peak=   -3.295 closest distance to " CB  ASP A 132 " =    2.324
peak=   -3.294 closest distance to " CE  MET A 105 " =    2.035
peak=   -3.292 closest distance to " O   HOH Z 103 " =    1.922
peak=   -3.291 closest distance to " CD2 PHE A  59 " =    2.591
peak=   -3.279 closest distance to " CG  LEU A  83 " =    1.963
peak=   -3.279 closest distance to " OG BSER A 134 " =    1.295
peak=   -3.278 closest distance to " O   HOH Z 252 " =    4.169
peak=   -3.274 closest distance to " O   HOH Z  76 " =    1.968
peak=   -3.272 closest distance to " O   HOH Z  60 " =    2.619
peak=   -3.267 closest distance to " CG2 THR A 221 " =    2.226
peak=   -3.267 closest distance to " OE1 GLN A  88 " =    1.262
peak=   -3.263 closest distance to " O   HOH Z 436 " =    1.531
peak=   -3.261 closest distance to " O   HOH Z  11 " =    1.843
peak=   -3.258 closest distance to " CE3 TRP A 150 " =    2.016
peak=   -3.258 closest distance to " O   HOH Z 298 " =    2.691
peak=   -3.254 closest distance to " O   HOH Z 198 " =    1.306
peak=   -3.242 closest distance to " NH2 ARG A  79 " =    1.919
peak=   -3.241 closest distance to " NE2 GLN A  58 " =    1.222
peak=   -3.239 closest distance to " CB  PHE A 192 " =    2.045
peak=   -3.234 closest distance to " O   HOH Z 348 " =    2.282
peak=   -3.233 closest distance to " O   GLY A  80 " =    2.644
peak=   -3.231 closest distance to " OG BSER A 210 " =    2.118
peak=   -3.230 closest distance to " CD  GLN A  88 " =    0.956
peak=   -3.225 closest distance to " CZ  ARG A  66 " =    0.969
peak=   -3.224 closest distance to " CB  ALA A 248 " =    2.514
peak=   -3.223 closest distance to " CB  CYS A 254 " =    2.388
peak=   -3.222 closest distance to " O   HOH Z 252 " =    4.205
peak=   -3.221 closest distance to " CE1 TYR A 169 " =    2.510
peak=   -3.218 closest distance to " CG1 VAL A 197 " =    2.294
peak=   -3.217 closest distance to " O   ASN A 301 " =    1.472
peak=   -3.215 closest distance to " O   HOH Z 323 " =    1.341
peak=   -3.215 closest distance to " CG  GLU A 277 " =    1.148
peak=   -3.204 closest distance to " CG  ASN A 301 " =    1.921
peak=   -3.204 closest distance to " O   HOH Z 292 " =    4.650
peak=   -3.203 closest distance to " C   ILE A 234 " =    1.230
peak=   -3.201 closest distance to " CZ  TYR A 169 " =    1.796
peak=   -3.201 closest distance to " O   ALA A  10 " =    1.748
peak=   -3.195 closest distance to " CD  PRO A 213 " =    2.222
peak=   -3.187 closest distance to " OD2 ASP A  65 " =    1.894
peak=   -3.182 closest distance to " NE2 GLN A 194 " =    1.806
peak=   -3.182 closest distance to " CG2 VAL A 189 " =    2.186
peak=   -3.182 closest distance to " N   SER A   3 " =    2.092
peak=   -3.181 closest distance to " CD  ARG A  79 " =    1.170
peak=   -3.174 closest distance to " O   GLY A 203 " =    2.400
peak=   -3.168 closest distance to " O   HOH Z 390 " =    2.300
peak=   -3.167 closest distance to " CE BMET A  47 " =    2.278
peak=   -3.166 closest distance to " CE3 TRP A 274 " =    2.543
peak=   -3.164 closest distance to " CA  GLY A 133 " =    2.261
peak=   -3.163 closest distance to " O   HOH Z 417 " =    2.633
peak=   -3.161 closest distance to " N   THR A 157 " =    1.604
peak=   -3.150 closest distance to " O   HOH Z 243 " =    2.028
peak=   -3.148 closest distance to " CE2 PHE A 218 " =    2.450
peak=   -3.145 closest distance to " O   HOH Z 350 " =    1.849
peak=   -3.144 closest distance to " N   SER A 276 " =    1.410
peak=   -3.129 closest distance to " O   HOH Z 396 " =    1.839
peak=   -3.127 closest distance to " CG  PRO A 163 " =    2.486
peak=   -3.126 closest distance to " OD1 ASP A 171 " =    1.557
peak=   -3.126 closest distance to " O   HOH Z   6 " =    1.557
peak=   -3.125 closest distance to " O   HOH Z 184 " =    1.749
peak=   -3.123 closest distance to " CD2 LEU A 222 " =    2.064
peak=   -3.121 closest distance to " CA  SER A 135 " =    1.313
peak=   -3.120 closest distance to " O   HOH Z 234 " =    4.410
peak=   -3.117 closest distance to " O   ALA A  34 " =    2.659
peak=   -3.113 closest distance to " O   HOH Z 193 " =    1.891
peak=   -3.108 closest distance to " O   HOH Z 354 " =    1.722
peak=   -3.062 closest distance to " O   HOH Z 398 " =    0.751
peak=   -3.060 closest distance to " O   HOH Z  90 " =    1.732
peak=   -3.047 closest distance to " O   PHE A 218 " =    1.566
peak=   -3.021 closest distance to " CB  ALA A 291 " =    1.887
peak=   -2.972 closest distance to " NH2 ARG A  66 " =    1.483

================= 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    :  0.3640 0.3602   6.126972e+00   6.125137e+00
   1_bss:  0.3532 0.3491   6.112765e+00   6.105493e+00
   1_xyz:  0.2308 0.2573   5.745948e+00   5.834211e+00
   1_adp:  0.2103 0.2607   5.686670e+00   5.850194e+00
   1_occ:  0.2100 0.2602   5.685165e+00   5.848863e+00
   2_bss:  0.2086 0.2579   5.683490e+00   5.845502e+00
   2_xyz:  0.1495 0.1941   5.387568e+00   5.596137e+00
   2_adp:  0.1386 0.1819   5.321065e+00   5.532628e+00
   2_occ:  0.1384 0.1819   5.320499e+00   5.532337e+00
   3_bss:  0.1384 0.1817   5.321063e+00   5.531141e+00
   3_xyz:  0.1192 0.1642   5.201327e+00   5.435454e+00
   3_adp:  0.1156 0.1632   5.182733e+00   5.425930e+00
   3_occ:  0.1156 0.1632   5.182693e+00   5.426019e+00
   4_bss:  0.1156 0.1631   5.182653e+00   5.425981e+00
   4_xyz:  0.1110 0.1620   5.160216e+00   5.413853e+00
   4_adp:  0.1103 0.1619   5.157063e+00   5.413086e+00
   4_occ:  0.1103 0.1619   5.157014e+00   5.413189e+00
   5_bss:  0.1105 0.1619   5.158064e+00   5.413583e+00
   5_xyz:  0.1115 0.1628   5.167297e+00   5.421072e+00
   5_adp:  0.1129 0.1612   5.167833e+00   5.414512e+00
   5_occ:  0.1128 0.1611   5.167770e+00   5.414650e+00
   5_bss:  0.1128 0.1612   5.167832e+00   5.414698e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000   1.384   0.197  -1.719   0.000  -0.000  -0.000
   1_xyz:  0.300  50.000   1.384   0.197  -1.719   0.000  -0.000  -0.000
   1_adp:  0.300  50.000   1.384   0.197  -1.719   0.000  -0.000  -0.000
   1_occ:  0.300  50.000   1.384   0.197  -1.719   0.000  -0.000  -0.000
   2_bss:  0.328  67.765  -1.091  -1.336  -1.816  -0.000  -0.000  -0.000
   2_xyz:  0.328  67.765  -1.091  -1.336  -1.816  -0.000  -0.000  -0.000
   2_adp:  0.328  67.765  -1.091  -1.336  -1.816  -0.000  -0.000  -0.000
   2_occ:  0.328  67.765  -1.091  -1.336  -1.816  -0.000  -0.000  -0.000
   3_bss:  0.333  67.765  -1.855  -1.885  -1.644  -0.000  -0.000  -0.000
   3_xyz:  0.333  67.765  -1.855  -1.885  -1.644  -0.000  -0.000  -0.000
   3_adp:  0.333  67.765  -1.855  -1.885  -1.644  -0.000  -0.000  -0.000
   3_occ:  0.333  67.765  -1.855  -1.885  -1.644  -0.000  -0.000  -0.000
   4_bss:  0.333  67.765  -1.907  -1.909  -1.473  -0.000  -0.000  -0.000
   4_xyz:  0.333  67.765  -1.907  -1.909  -1.473  -0.000  -0.000  -0.000
   4_adp:  0.333  67.765  -1.907  -1.909  -1.473  -0.000  -0.000  -0.000
   4_occ:  0.333  67.765  -1.907  -1.909  -1.473  -0.000  -0.000  -0.000
   5_bss:  0.325  64.725  -1.805  -1.809  -1.286  -0.000  -0.000  -0.000
   5_xyz:  0.325  64.725  -1.805  -1.809  -1.286  -0.000  -0.000  -0.000
   5_adp:  0.325  64.725  -1.805  -1.809  -1.286  -0.000  -0.000  -0.000
   5_occ:  0.325  64.725  -1.805  -1.809  -1.286  -0.000  -0.000  -0.000
   5_bss:  0.320  58.610  -1.778  -1.753  -1.152  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  39.554 0.6500  0.8177    38601.105
   1_bss:  38.499 0.6607  0.8342    35826.276
   1_xyz:  25.540 0.8069  0.9734    17121.624
   1_adp:  26.198 0.7990  0.9658    17765.400
   1_occ:  26.167 0.7992  0.9658    17700.958
   2_bss:  25.997 0.8010  0.9232    17538.896
   2_xyz:  18.891 0.8714  0.9724     9799.649
   2_adp:  17.149 0.8881  0.9761     8560.055
   2_occ:  17.137 0.8882  0.9760     8553.708
   3_bss:  17.128 0.8883  0.9631     8546.561
   3_xyz:  15.069 0.9060  0.9736     7008.287
   3_adp:  14.816 0.9084  0.9692     6882.803
   3_occ:  14.819 0.9084  0.9691     6884.182
   4_bss:  14.818 0.9084  0.9703     6882.580
   4_xyz:  14.556 0.9106  0.9706     6696.710
   4_adp:  14.512 0.9110  0.9643     6687.419
   4_occ:  14.513 0.9110  0.9642     6686.040
   5_bss:  14.549 0.9107  0.9682     6703.237
   5_xyz:  14.692 0.9095  0.9671     6790.601
   5_adp:  14.514 0.9111  0.9636     6742.780
   5_occ:  14.515 0.9111  0.9636     6741.832
   5_bss:  14.521 0.9110  0.9650     6738.010
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6448e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6448e-01
   1_xyz:   1.180  0.009  0.076 15.375  0.004  4.117   7.8347e-02
   1_adp:   1.180  0.009  0.076 15.375  0.004  4.117   7.8347e-02
   1_occ:   1.180  0.009  0.076 15.375  0.004  4.117   7.8347e-02
   2_bss:   1.180  0.009  0.076 15.375  0.004  4.117   7.8347e-02
   2_xyz:   1.035  0.007  0.075 14.731  0.004  4.133   6.3672e-02
   2_adp:   1.035  0.007  0.075 14.731  0.004  4.133   6.3672e-02
   2_occ:   1.035  0.007  0.075 14.731  0.004  4.133   6.3672e-02
   3_bss:   1.035  0.007  0.075 14.731  0.004  4.133   6.3672e-02
   3_xyz:   1.083  0.010  0.079 15.049  0.004  4.114   7.1585e-02
   3_adp:   1.083  0.010  0.079 15.049  0.004  4.114   7.1585e-02
   3_occ:   1.083  0.010  0.079 15.049  0.004  4.114   7.1585e-02
   4_bss:   1.083  0.010  0.079 15.049  0.004  4.114   7.1585e-02
   4_xyz:   1.125  0.011  0.082 15.131  0.005  4.117   7.7592e-02
   4_adp:   1.125  0.011  0.082 15.131  0.005  4.117   7.7592e-02
   4_occ:   1.125  0.011  0.082 15.131  0.005  4.117   7.7592e-02
   5_bss:   1.125  0.011  0.082 15.131  0.005  4.117   7.7592e-02
   5_xyz:   1.041  0.009  0.077 14.911  0.004  4.118   6.6194e-02
   5_adp:   1.041  0.009  0.077 14.911  0.004  4.118   6.6194e-02
   5_occ:   1.041  0.009  0.077 14.911  0.004  4.118   6.6194e-02
   5_bss:   1.041  0.009  0.077 14.911  0.004  4.118   6.6194e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.525   2.4325e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.525   2.4325e-01
   1_xyz:   7.592  0.062  0.296 87.060  0.018  2.128   8.0218e-02
   1_adp:   7.592  0.062  0.296 87.060  0.018  2.128   8.0218e-02
   1_occ:   7.592  0.062  0.296 87.060  0.018  2.128   8.0218e-02
   2_bss:   7.592  0.062  0.296 87.060  0.018  2.128   8.0218e-02
   2_xyz:   7.300  0.046  0.216 84.424  0.041  2.278   1.0307e-01
   2_adp:   7.300  0.046  0.216 84.424  0.041  2.278   1.0307e-01
   2_occ:   7.300  0.046  0.216 84.424  0.041  2.278   1.0307e-01
   3_bss:   7.300  0.046  0.216 84.424  0.041  2.278   1.0307e-01
   3_xyz:   7.643  0.049  0.237 83.420  0.041  2.292   5.8108e-02
   3_adp:   7.643  0.049  0.237 83.420  0.041  2.292   5.8108e-02
   3_occ:   7.643  0.049  0.237 83.420  0.041  2.292   5.8108e-02
   4_bss:   7.643  0.049  0.237 83.420  0.041  2.292   5.8108e-02
   4_xyz:   7.659  0.048  0.257 82.510  0.043  2.300   5.8318e-02
   4_adp:   7.659  0.048  0.257 82.510  0.043  2.300   5.8318e-02
   4_occ:   7.659  0.048  0.257 82.510  0.043  2.300   5.8318e-02
   5_bss:   7.659  0.048  0.257 82.510  0.043  2.300   5.8318e-02
   5_xyz:   7.505  0.045  0.229 82.440  0.041  2.365   4.5726e-02
   5_adp:   7.505  0.045  0.229 82.440  0.041  2.365   4.5726e-02
   5_occ:   7.505  0.045  0.229 82.440  0.041  2.365   4.5726e-02
   5_bss:   7.505  0.045  0.229 82.440  0.041  2.365   4.5726e-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:  84.56   0.00  17.61  78.76   0.00  13.40  84.56   4.61  40.52
   1_occ:  84.56   0.00  17.61  78.76   0.00  13.40  84.56   4.61  40.52
   2_bss:  84.56   0.00  17.61  78.76   0.00  13.40  84.56   4.61  40.52
   2_xyz:  84.56   0.00  17.61  78.76   0.00  13.40  84.56   4.61  40.52
   2_adp:  83.05   1.47  17.39  83.05   1.47  13.08  83.01   4.67  40.87
   2_occ:  83.05   1.47  17.39  83.05   1.47  13.08  83.01   4.67  40.87
   3_bss:  83.05   1.47  17.39  83.05   1.47  13.08  83.01   4.67  40.87
   3_xyz:  83.05   1.47  17.39  83.05   1.47  13.08  83.01   4.67  40.87
   3_adp:  90.67   0.33  17.51  90.67   0.33  13.04  85.84   5.40  41.86
   3_occ:  90.67   0.33  17.51  90.67   0.33  13.04  85.84   5.40  41.86
   4_bss:  90.67   0.33  17.51  90.67   0.33  13.04  85.84   5.40  41.86
   4_xyz:  90.67   0.33  17.51  90.67   0.33  13.04  85.84   5.40  41.86
   4_adp:  97.12   0.00  17.34  97.12   0.00  12.89  86.78   5.74  41.52
   4_occ:  97.12   0.00  17.34  97.12   0.00  12.89  86.78   5.74  41.52
   5_bss:  97.12   0.00  17.34  97.12   0.00  12.89  86.78   5.74  41.52
   5_xyz:  97.12   0.00  17.34  97.12   0.00  12.89  86.78   5.74  41.52
   5_adp:  90.64   0.87  16.49  90.64   0.87  12.54  81.92   5.70  37.99
   5_occ:  90.64   0.87  16.49  90.64   0.87  12.54  81.92   5.70  37.99
   5_bss:  90.61   0.84  16.46  90.61   0.84  12.51  81.89   5.67  37.96
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.609    0.023    0.298
   1_adp:    1.609    0.023    0.298
   1_occ:    1.609    0.023    0.298
   2_bss:    1.609    0.023    0.298
   2_xyz:    0.964    0.013    0.421
   2_adp:    0.964    0.013    0.421
   2_occ:    0.964    0.013    0.421
   3_bss:    0.964    0.013    0.421
   3_xyz:    0.912    0.027    0.476
   3_adp:    0.912    0.027    0.476
   3_occ:    0.912    0.027    0.476
   4_bss:    0.912    0.027    0.476
   4_xyz:    0.966    0.048    0.493
   4_adp:    0.966    0.048    0.493
   4_occ:    0.966    0.048    0.493
   5_bss:    0.966    0.048    0.493
   5_xyz:    1.035    0.047    0.503
   5_adp:    1.035    0.047    0.503
   5_occ:    1.035    0.047    0.503
   5_bss:    1.035    0.047    0.503
------------------------------------------------------------------------

CPU time actual refinement: 331.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1170/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_1170/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1170/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1170/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1170/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.61 
  Macro-tasks:
    bulk solvent and scale       = 40.85  
    individual site refinement   = 130.80 
    weights calculation          = 29.04  
    collect and process          = 6.69   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 207.47 
  Micro-tasks:
    mask                            = 1.65   
    f_calc                          = 106.85 
    alpha_beta                      = 8.15   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 110.59 
    fmodel                         = 6.72   
    r_factors                      = 0.20   
    phase_errors                   = 12.06  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 247.66 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.712 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    662 calls, 106.41 s
gradients_fft:          607 calls,  99.14 s

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

# Date 2008-01-16 Time 06:36:01 PST -0800 (1200494161.14 s)
Start R-work = 0.3640, R-free = 0.3602 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1794 (no bulk solvent and anisotropic scale)

Start R-work = 0.3532, R-free = 0.3491
Final R-work = 0.1128, R-free = 0.1612