# Date 2008-01-16 Time 05:48:59 PST -0800 (1200491339.21 s)
#phil __OFF__

Command line arguments: "../893.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16239
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 893

-------------------------------------------------------------------------------
  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: (70.9525, 46.6953, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.9711
Completeness in resolution range: 0.954025
Completeness with d_max=infinity: 0.951153

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9711

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: (70.9525, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.9711
Completeness in resolution range: 0.954025
Completeness with d_max=infinity: 0.951153

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2183 [2153/2182]  1942   211   9.8%
  bin  2:  4.2183 -  3.3605 [2072/2088]  1862   210  10.1%
  bin  3:  3.3605 -  2.9393 [2036/2055]  1830   206  10.1%
  bin  4:  2.9393 -  2.6722 [2038/2068]  1837   201   9.9%
  bin  5:  2.6722 -  2.4816 [2020/2039]  1818   202  10.0%
  bin  6:  2.4816 -  2.3358 [2001/2026]  1795   206  10.3%
  bin  7:  2.3358 -  2.2192 [1984/2017]  1788   196   9.9%
  bin  8:  2.2192 -  2.1229 [1985/2016]  1791   194   9.8%
  bin  9:  2.1229 -  2.0414 [1985/2027]  1784   201  10.1%
  bin 10:  2.0414 -  1.9711 [1315/2015]  1183   132  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_893/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 23
        2.42 -     3.04: 2204
        3.04 -     3.66: 4725
        3.66 -     4.28: 9082
        4.28 -     4.90: 12384
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.000 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.048 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.125 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.163 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28413 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_893/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_893/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.69535 85.09415 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: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3312   r_free= 0.3346   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.052287                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7052 0.99   1396  155 0.2891 0.2831       6.354       6.317|
|  2:  4.7052 -  3.7538 0.99   1350  146 0.2610 0.2520      6.4378      6.4126|
|  3:  3.7538 -  3.2849 0.99   1322  149 0.2874 0.2734      6.3313      6.4433|
|  4:  3.2849 -  2.9871 0.99   1320  152 0.2931 0.3223      6.2214      6.2274|
|  5:  2.9871 -  2.7744 0.99   1306  141 0.3363 0.3344      6.1076      6.1168|
|  6:  2.7744 -  2.6118 0.99   1298  145 0.3570 0.3699      6.0557      6.0628|
|  7:  2.6118 -  2.4816 0.99   1297  142 0.3500 0.3430      6.0309      5.9999|
|  8:  2.4816 -  2.3740 0.98   1270  147 0.3748 0.3618      5.9836       5.953|
|  9:  2.3740 -  2.2829 0.98   1292  147 0.3560 0.3627      5.9177      5.8786|
| 10:  2.2829 -  2.2044 0.99   1270  136 0.3703 0.4519      5.9112      6.0298|
| 11:  2.2044 -  2.1357 0.99   1295  140 0.3892 0.3764      5.8791      5.9204|
| 12:  2.1357 -  2.0748 0.97   1254  136 0.3863 0.4219       5.823      5.9029|
| 13:  2.0748 -  2.0203 0.99   1271  143 0.3890 0.3818      5.7303      5.6574|
| 14:  2.0203 -  1.9711 0.53    689   80 0.4218 0.4285      5.7309      5.6896|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7052  1396   155  0.79  25.60   0.86     0.81      41163.98|
|  2:  4.7052 -  3.7538  1350   146  0.84  22.57   0.98     0.92      47325.98|
|  3:  3.7538 -  3.2849  1322   149  0.79  27.07   1.00     0.95      48006.24|
|  4:  3.2849 -  2.9871  1320   152  0.76  30.06   1.01     0.94      43618.19|
|  5:  2.9871 -  2.7744  1306   141  0.70  35.64   0.98     0.89      37081.01|
|  6:  2.7744 -  2.6118  1298   145  0.69  36.65   0.99     0.88      32556.48|
|  7:  2.6118 -  2.4816  1297   142  0.70  35.31   1.01     0.90      28759.49|
|  8:  2.4816 -  2.3740  1270   147  0.69  36.59   0.99     0.92      26368.53|
|  9:  2.3740 -  2.2829  1292   147  0.69  36.37   1.04     0.92      24681.76|
| 10:  2.2829 -  2.2044  1270   136  0.66  39.26   1.04     0.90      25713.27|
| 11:  2.2044 -  2.1357  1295   140  0.63  42.16   1.06     0.88      25286.20|
| 12:  2.1357 -  2.0748  1254   136  0.62  42.44   1.04     0.89      24059.96|
| 13:  2.0748 -  2.0203  1271   143  0.61  43.66   1.04     0.86      20232.79|
| 14:  2.0203 -  1.9711   689    80  0.61  43.55   1.02     0.79      16734.30|
|alpha:            min =        0.79 max =            0.95 mean =         0.89|
|beta:             min =    16734.30 max =        48006.24 mean =     32250.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.94 mean =        35.07|
|phase err.(test): min =        0.00 max =           89.88 mean =        35.30|
|-----------------------------------------------------------------------------|

============================== 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 = 6.263785              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 = 0.745659              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.023   (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 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      206 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1998 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1875 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2850 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4410 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5661 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6723 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.191 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    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: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3312   r_free= 0.3346   ksol= 0.00   Bsol= 0.00   scale= 0.973    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.052287                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3177   r_free= 0.3223   ksol= 0.33   Bsol= 41.22   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.54,-2.38,1.01,-0.00,0.00,0.00); trace/3= -0.97                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.034597                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.242594              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.458   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363470              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.864   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3177      final r-factor (work) = 0.1701          |
| start r-factor (free) = 0.3223      final r-factor (free) = 0.1936          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9928 = 5.24 * 0.50 * 6.0390 + 1.00 * 0.1628                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1272 = 5.24 * 0.50 * 5.7457 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1701      final r-factor (work) = 0.1624          |
| start r-factor (free) = 0.1936      final r-factor (free) = 0.1944          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0956 = 0.36 * 1.00 * 5.7457 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1122 = 0.36 * 1.00 * 5.4292 + 1.00 * 0.1388                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.36   16.20    None  None   None       |
|    all(noH): 2823   0      0.00    82.36   16.20    None  None   None       |
|    Sol.    : 438    0      5.73    62.41   37.11    None  None   None       |
|    Mac.    : 2385   0      0.00    82.36   12.36    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 -   8.236:  471   |   5:    41.179 -  49.415:   94        |
|      1:     8.236 -  16.472: 1582   |   6:    49.415 -  57.651:   78        |
|      2:    16.472 -  24.708:  305   |   7:    57.651 -  65.887:   14        |
|      3:    24.708 -  32.944:  148   |   8:    65.887 -  74.123:    0        |
|      4:    32.944 -  41.179:  130   |   9:    74.123 -  82.359:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1624 r_free = 0.1944             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1618 r_free = 0.1945             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1618   r_free= 0.1945   ksol= 0.33   Bsol= 41.22   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.54,-2.38,1.01,-0.00,0.00,0.00); trace/3= -0.97                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.428861                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1603   r_free= 0.1915   ksol= 0.32   Bsol= 48.42   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.95,-1.51,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.422618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.630266              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.752  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.908800              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.204   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1603      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1915      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2387 = 2.63 * 0.50 * 5.4541 + 1.00 * 0.0659                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0296 = 2.63 * 0.50 * 5.2996 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1149          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8415 = 0.91 * 1.00 * 5.2996 + 1.00 * 0.0252                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6820 = 0.91 * 1.00 * 5.1422 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    80.58   17.23    None  None   None       |
|    all(noH): 2823   0      1.09    80.58   17.23    None  None   None       |
|    Sol.    : 438    0      1.61    75.68   40.28    None  None   None       |
|    Mac.    : 2385   0      1.09    80.58   13.00    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:     1.089 -   9.038:  738   |   5:    40.836 -  48.785:  107        |
|      1:     9.038 -  16.988: 1295   |   6:    48.785 -  56.735:   81        |
|      2:    16.988 -  24.937:  292   |   7:    56.735 -  64.684:   52        |
|      3:    24.937 -  32.887:  121   |   8:    64.684 -  72.634:   24        |
|      4:    32.887 -  40.836:  104   |   9:    72.634 -  80.583:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1149 r_free = 0.1542             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1542             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1542   ksol= 0.32   Bsol= 48.42   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.95,-1.51,-0.00,-0.00,-0.00); trace/3= -2.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141168                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1542   ksol= 0.32   Bsol= 48.42   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.68,-1.70,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142009                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.326469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.246  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188283              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.807  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0408 = 2.33 * 0.50 * 5.1416 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0162 = 2.33 * 0.50 * 5.1187 + 1.00 * 0.0619                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1518          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9725 = 0.19 * 1.00 * 5.1187 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9703 = 0.19 * 1.00 * 5.1145 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    81.01   16.71    None  None   None       |
|    all(noH): 2823   0      1.71    81.01   16.71    None  None   None       |
|    Sol.    : 438    0      2.77    75.99   37.82    None  None   None       |
|    Mac.    : 2385   0      1.71    81.01   12.83    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:     1.712 -   9.641:  907   |   5:    41.360 -  49.289:  101        |
|      1:     9.641 -  17.571: 1163   |   6:    49.289 -  57.219:   66        |
|      2:    17.571 -  25.501:  277   |   7:    57.219 -  65.148:   31        |
|      3:    25.501 -  33.430:  128   |   8:    65.148 -  73.078:   10        |
|      4:    33.430 -  41.360:  134   |   9:    73.078 -  81.007:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1518             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1517             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1517   ksol= 0.32   Bsol= 48.42   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.68,-1.70,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.113191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1517   ksol= 0.33   Bsol= 48.42   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.51,-1.67,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.113341                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.147397              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.191842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.952  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5536 = 2.15 * 0.50 * 5.1147 + 1.00 * 0.0619                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5456 = 2.15 * 0.50 * 5.1090 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9874 = 0.19 * 1.00 * 5.1090 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9876 = 0.19 * 1.00 * 5.1111 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    81.28   16.50    None  None   None       |
|    all(noH): 2823   0      1.69    81.28   16.50    None  None   None       |
|    Sol.    : 438    0      3.62    75.77   37.06    None  None   None       |
|    Mac.    : 2385   0      1.69    81.28   12.73    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:     1.687 -   9.646:  939   |   5:    41.481 -  49.440:  108        |
|      1:     9.646 -  17.605: 1141   |   6:    49.440 -  57.399:   62        |
|      2:    17.605 -  25.564:  277   |   7:    57.399 -  65.358:   21        |
|      3:    25.564 -  33.522:  128   |   8:    65.358 -  73.317:    8        |
|      4:    33.522 -  41.481:  133   |   9:    73.317 -  81.276:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1530             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1077 r_free = 0.1531             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1531   ksol= 0.33   Bsol= 48.42   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-2.51,-1.67,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113403                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1531   ksol= 0.33   Bsol= 48.42   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.41,-1.59,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113454                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.310715              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.595  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.098082              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.682  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9655 = 2.31 * 0.50 * 5.1113 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9656 = 2.31 * 0.50 * 5.1095 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5082 = 0.10 * 1.00 * 5.1095 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5081 = 0.10 * 1.00 * 5.1186 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.48    79.16   16.20    None  None   None       |
|    all(noH): 2823   0      2.48    79.16   16.20    None  None   None       |
|    Sol.    : 438    0      4.91    74.66   35.73    None  None   None       |
|    Mac.    : 2385   0      2.48    79.16   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.476 -  10.144: 1065   |   5:    40.818 -  48.486:   94        |
|      1:    10.144 -  17.812: 1047   |   6:    48.486 -  56.155:   63        |
|      2:    17.812 -  25.481:  253   |   7:    56.155 -  63.823:   17        |
|      3:    25.481 -  33.149:  135   |   8:    63.823 -  71.492:    6        |
|      4:    33.149 -  40.818:  136   |   9:    71.492 -  79.160:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1537             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1537             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1537   ksol= 0.33   Bsol= 48.42   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.26,-2.41,-1.59,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117929                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7052 0.99   1396  155 0.0995 0.1261      5.3811      5.5276|
|  2:  4.7052 -  3.7538 0.99   1350  146 0.0860 0.1106       5.441      5.6217|
|  3:  3.7538 -  3.2849 0.99   1322  149 0.1048 0.1519      5.4609      5.8577|
|  4:  3.2849 -  2.9871 0.99   1320  152 0.1152 0.1521      5.4326      5.5672|
|  5:  2.9871 -  2.7744 0.99   1306  141 0.1287 0.1716      5.3042      5.5287|
|  6:  2.7744 -  2.6118 0.99   1298  145 0.1171 0.1714      5.1787      5.4035|
|  7:  2.6118 -  2.4816 0.99   1297  142 0.1194 0.1539      5.1374      5.3308|
|  8:  2.4816 -  2.3740 0.98   1270  147 0.1106 0.1733      5.0011      5.3058|
|  9:  2.3740 -  2.2829 0.98   1292  147 0.1097 0.1715      4.9818      5.2826|
| 10:  2.2829 -  2.2044 0.99   1270  136 0.1071 0.1757      4.9139      5.1961|
| 11:  2.2044 -  2.1357 0.99   1295  140 0.1123 0.1743      4.9216      5.2526|
| 12:  2.1357 -  2.0748 0.97   1254  136 0.1060 0.1470      4.8423      5.0265|
| 13:  2.0748 -  2.0203 0.99   1271  143 0.1109 0.1737      4.7516      5.0628|
| 14:  2.0203 -  1.9711 0.53    689   80 0.0969 0.1496      4.5796      4.8435|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7052  1396   155  0.94   8.87   0.98     0.95       6888.30|
|  2:  4.7052 -  3.7538  1350   146  0.95   7.86   1.01     1.00       8893.11|
|  3:  3.7538 -  3.2849  1322   149  0.93  11.26   1.02     1.01      10180.78|
|  4:  3.2849 -  2.9871  1320   152  0.92  13.22   1.00     0.97      10043.25|
|  5:  2.9871 -  2.7744  1306   141  0.90  15.83   0.99     0.96       7999.21|
|  6:  2.7744 -  2.6118  1298   145  0.91  15.26   0.98     0.96       6630.86|
|  7:  2.6118 -  2.4816  1297   142  0.91  14.60   0.99     0.96       5773.27|
|  8:  2.4816 -  2.3740  1270   147  0.91  14.40   0.99     0.97       4648.84|
|  9:  2.3740 -  2.2829  1292   147  0.92  14.16   1.01     0.99       4501.86|
| 10:  2.2829 -  2.2044  1270   136  0.91  14.59   1.00     0.96       3950.67|
| 11:  2.2044 -  2.1357  1295   140  0.90  15.86   1.00     0.97       4207.73|
| 12:  2.1357 -  2.0748  1254   136  0.92  14.54   1.00     0.99       3756.75|
| 13:  2.0748 -  2.0203  1271   143  0.91  15.43   1.01     1.01       3037.27|
| 14:  2.0203 -  1.9711   689    80  0.93  12.88   0.98     0.95       2089.95|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2089.95 max =        10180.78 mean =      6073.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.12 mean =        13.04|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1538   ksol= 0.33   Bsol= 48.33   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-1.46,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117954                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1538   ksol= 0.33   Bsol= 48.33   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.28,-1.46,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117954                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7052 0.99   1396  155 0.0995 0.1261      5.3813      5.5278|
|  2:  4.7052 -  3.7538 0.99   1350  146 0.0861 0.1106       5.441      5.6216|
|  3:  3.7538 -  3.2849 0.99   1322  149 0.1048 0.1519      5.4608      5.8575|
|  4:  3.2849 -  2.9871 0.99   1320  152 0.1152 0.1521      5.4326      5.5672|
|  5:  2.9871 -  2.7744 0.99   1306  141 0.1287 0.1716      5.3043      5.5288|
|  6:  2.7744 -  2.6118 0.99   1298  145 0.1171 0.1714      5.1787      5.4035|
|  7:  2.6118 -  2.4816 0.99   1297  142 0.1194 0.1539      5.1374      5.3307|
|  8:  2.4816 -  2.3740 0.98   1270  147 0.1106 0.1733       5.001      5.3058|
|  9:  2.3740 -  2.2829 0.98   1292  147 0.1097 0.1714      4.9818      5.2825|
| 10:  2.2829 -  2.2044 0.99   1270  136 0.1071 0.1757      4.9139      5.1961|
| 11:  2.2044 -  2.1357 0.99   1295  140 0.1123 0.1744      4.9216      5.2527|
| 12:  2.1357 -  2.0748 0.97   1254  136 0.1060 0.1470      4.8424      5.0267|
| 13:  2.0748 -  2.0203 0.99   1271  143 0.1109 0.1737      4.7516      5.0628|
| 14:  2.0203 -  1.9711 0.53    689   80 0.0969 0.1496      4.5797      4.8435|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0399 -  4.7052  1396   155  0.94   8.88   0.98     0.95       6890.39|
|  2:  4.7052 -  3.7538  1350   146  0.95   7.86   1.01     1.00       8893.67|
|  3:  3.7538 -  3.2849  1322   149  0.93  11.25   1.02     1.02      10178.81|
|  4:  3.2849 -  2.9871  1320   152  0.92  13.22   1.00     0.97      10043.51|
|  5:  2.9871 -  2.7744  1306   141  0.90  15.83   0.99     0.96       7999.32|
|  6:  2.7744 -  2.6118  1298   145  0.91  15.26   0.98     0.96       6630.85|
|  7:  2.6118 -  2.4816  1297   142  0.91  14.60   0.99     0.96       5772.75|
|  8:  2.4816 -  2.3740  1270   147  0.91  14.40   0.99     0.97       4648.47|
|  9:  2.3740 -  2.2829  1292   147  0.92  14.16   1.01     0.99       4501.29|
| 10:  2.2829 -  2.2044  1270   136  0.91  14.59   1.00     0.97       3950.98|
| 11:  2.2044 -  2.1357  1295   140  0.90  15.86   1.00     0.97       4207.95|
| 12:  2.1357 -  2.0748  1254   136  0.92  14.54   1.01     0.99       3757.69|
| 13:  2.0748 -  2.0203  1271   143  0.91  15.43   1.01     1.01       3037.63|
| 14:  2.0203 -  1.9711   689    80  0.93  12.88   0.99     0.95       2090.34|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2090.34 max =        10178.81 mean =      6073.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.12 mean =        13.04|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.39    79.07   16.11    None  None   None       |
|    all(noH): 2823   0      2.39    79.07   16.11    None  None   None       |
|    Sol.    : 438    0      4.82    74.57   35.64    None  None   None       |
|    Mac.    : 2385   0      2.39    79.07   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.386 -  10.054: 1065   |   5:    40.728 -  48.396:   94        |
|      1:    10.054 -  17.723: 1047   |   6:    48.396 -  56.065:   63        |
|      2:    17.723 -  25.391:  253   |   7:    56.065 -  63.733:   17        |
|      3:    25.391 -  33.059:  135   |   8:    63.733 -  71.402:    6        |
|      4:    33.059 -  40.728:  136   |   9:    71.402 -  79.070:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.530 - 4.624
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 282 from: 288
   mapped sites are within: 0.724 - 4.624

peak=    5.703 closest distance to " O   HOH Z 126 " =    1.896
peak=    5.459 closest distance to " CG  PRO A  54 " =    1.266
peak=    5.433 closest distance to " NH2 ARG A  56 " =    2.164
peak=    5.317 closest distance to " CB  SER A  63 " =    1.205
peak=    5.167 closest distance to " NE2 GLN A  11 " =    1.168
peak=    5.098 closest distance to " O   HOH Z 232 " =    2.279
peak=    4.984 closest distance to " CB  GLN A 223 " =    1.433
peak=    4.980 closest distance to " O   HOH Z 236 " =    1.894
peak=    4.925 closest distance to " C   PRO A 198 " =    1.527
peak=    4.869 closest distance to " CB  GLU A 152 " =    1.154
peak=    4.820 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.729 closest distance to " CB  GLN A 183 " =    1.162
peak=    4.654 closest distance to " ND2 ASN A 187 " =    1.559
peak=    4.632 closest distance to " O   HOH Z 142 " =    1.717
peak=    4.586 closest distance to " CB  ASN A 187 " =    1.057
peak=    4.551 closest distance to " CB  PRO A  54 " =    0.873
peak=    4.546 closest distance to " O   HOH Z 193 " =    1.998
peak=    4.494 closest distance to " CB  LEU A 228 " =    1.029
peak=    4.471 closest distance to " CB  ASN A 148 " =    1.482
peak=    4.442 closest distance to " O   HOH Z  15 " =    2.184
peak=    4.421 closest distance to " O   HOH Z  78 " =    1.737
peak=    4.396 closest distance to " OD1 ASN A  69 " =    2.603
peak=    4.393 closest distance to " O   HOH Z 298 " =    1.905
peak=    4.370 closest distance to " CB  SER A   3 " =    1.433
peak=    4.368 closest distance to " O   HOH Z 234 " =    3.765
peak=    4.326 closest distance to " CA  TYR A  30 " =    0.965
peak=    4.289 closest distance to " CB  GLU A 128 " =    0.993
peak=    4.192 closest distance to " O   HOH Z 369 " =    2.015
peak=    4.165 closest distance to " CB  TYR A 169 " =    0.748
peak=    4.148 closest distance to " O   HOH Z 303 " =    1.994
peak=    4.124 closest distance to " OD2 ASP A 286 " =    2.866
peak=    4.095 closest distance to " CB  ARG A  79 " =    1.344
peak=    4.089 closest distance to " CG  PRO A  90 " =    1.133
peak=    4.086 closest distance to " O   HOH Z 132 " =    2.475
peak=    4.069 closest distance to " O   HOH Z 368 " =    1.925
peak=    4.065 closest distance to " O   HOH Z 272 " =    1.849
peak=    4.029 closest distance to " O   HOH Z 158 " =    2.978
peak=    4.014 closest distance to " O   HOH Z 427 " =    2.843
peak=    4.008 closest distance to " CA  ASN A 215 " =    1.182
peak=    4.008 closest distance to " O   HOH Z  10 " =    1.874
peak=    4.004 closest distance to " CA  THR A 264 " =    0.881
peak=    3.988 closest distance to " O   HOH Z  21 " =    1.699
peak=    3.973 closest distance to " O   HOH Z  61 " =    1.642
peak=    3.948 closest distance to " O   HOH Z 346 " =    1.621
peak=    3.948 closest distance to " CG  PRO A 243 " =    1.116
peak=    3.941 closest distance to " CA  ALA A  21 " =    1.161
peak=    3.922 closest distance to " O   HOH Z 219 " =    2.131
peak=    3.912 closest distance to " O   HOH Z 133 " =    1.631
peak=    3.897 closest distance to " O   HOH Z 316 " =    3.093
peak=    3.885 closest distance to " O   HOH Z 344 " =    3.140
peak=    3.878 closest distance to " CB  VAL A 265 " =    1.254
peak=    3.863 closest distance to " O   HOH Z 203 " =    1.874
peak=    3.860 closest distance to " O   HOH Z 207 " =    1.823
peak=    3.854 closest distance to " O   HOH Z 144 " =    2.201
peak=    3.845 closest distance to " O   HOH Z 214 " =    1.996
peak=    3.836 closest distance to " O   HOH Z 197 " =    3.113
peak=    3.829 closest distance to " O   HOH Z 189 " =    2.086
peak=    3.813 closest distance to " O   SER A  87 " =    2.241
peak=    3.792 closest distance to " CD  ARG A 159 " =    0.724
peak=    3.780 closest distance to " O   HOH Z  44 " =    1.771
peak=    3.778 closest distance to " CG2 VAL A 257 " =    0.984
peak=    3.760 closest distance to " CB  SER A 216 " =    0.731
peak=    3.757 closest distance to " CG1 ILE A  33 " =    1.296
peak=    3.753 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.753 closest distance to " O   HOH Z 273 " =    2.659
peak=    3.749 closest distance to " NH1AARG A 145 " =    1.143
peak=    3.748 closest distance to " O   HOH Z 213 " =    1.755
peak=    3.742 closest distance to " O   HOH Z  61 " =    1.549
peak=    3.740 closest distance to " O   HOH Z  66 " =    2.126
peak=    3.730 closest distance to " CB  TRP A 179 " =    1.327
peak=    3.730 closest distance to " CE  LYS A  76 " =    0.906
peak=    3.726 closest distance to " CB  SER A 212 " =    1.151
peak=    3.719 closest distance to " O   HOH Z 389 " =    1.923
peak=    3.719 closest distance to " O   HOH Z  59 " =    2.006
peak=    3.714 closest distance to " O   HOH Z  54 " =    1.692
peak=    3.705 closest distance to " O   HOH Z 193 " =    2.021
peak=    3.704 closest distance to " O   HOH Z 425 " =    1.871
peak=    3.692 closest distance to " CG  PRO A 198 " =    1.350
peak=    3.691 closest distance to " O   HOH Z   1 " =    1.923
peak=    3.688 closest distance to " CB  TRP A 266 " =    0.915
peak=    3.684 closest distance to " O   HOH Z 248 " =    1.696
peak=    3.684 closest distance to " O   HOH Z 403 " =    1.678
peak=    3.682 closest distance to " CB  TYR A 169 " =    0.754
peak=    3.669 closest distance to " O   HOH Z  40 " =    1.848
peak=    3.665 closest distance to " CA  SER A  87 " =    0.931
peak=    3.662 closest distance to " O   HOH Z   9 " =    2.033
peak=    3.653 closest distance to " OD1BASN A 224 " =    2.352
peak=    3.647 closest distance to " CD1 LEU A 300 " =    1.252
peak=    3.644 closest distance to " O   HOH Z  40 " =    2.326
peak=    3.642 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.639 closest distance to " CB  ARG A 190 " =    1.691
peak=    3.636 closest distance to " CA  THR A 221 " =    0.973
peak=    3.630 closest distance to " NH2BARG A 145 " =    2.067
peak=    3.629 closest distance to " O   HOH Z 175 " =    2.231
peak=    3.628 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.627 closest distance to " NH2 ARG A 156 " =    1.198
peak=    3.627 closest distance to " N   ARG A 156 " =    1.298
peak=    3.625 closest distance to " CB  ASN A 142 " =    0.906
peak=    3.622 closest distance to " O   HOH Z 402 " =    1.490
peak=    3.603 closest distance to " O   HOH Z 128 " =    2.156
peak=    3.597 closest distance to " CB  LEU A 143 " =    1.100
peak=    3.596 closest distance to " O   HOH Z 368 " =    3.576
peak=    3.590 closest distance to " CG1BVAL A  72 " =    1.561
peak=    3.590 closest distance to " ND1 HIS A  86 " =    1.604
peak=    3.589 closest distance to " NZ  LYS A 117 " =    3.325
peak=    3.583 closest distance to " O   HOH Z 407 " =    2.317
peak=    3.580 closest distance to " O   HOH Z 263 " =    2.293
peak=    3.576 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.569 closest distance to " O   HOH Z  97 " =    1.916
peak=    3.569 closest distance to " O   HOH Z 193 " =    1.712
peak=    3.568 closest distance to " CD2 LEU A 255 " =    1.378
peak=    3.547 closest distance to " O   HOH Z 291 " =    1.625
peak=    3.544 closest distance to " CA  ALA A  51 " =    0.900
peak=    3.540 closest distance to " O   HOH Z 173 " =    1.867
peak=    3.538 closest distance to " CB  ILE A 120 " =    1.135
peak=    3.536 closest distance to " O   HOH Z 258 " =    1.810
peak=    3.536 closest distance to " CB  ASN A 224 " =    1.152
peak=    3.535 closest distance to " CZ  PHE A 218 " =    1.053
peak=    3.535 closest distance to " O   HOH Z 305 " =    3.627
peak=    3.524 closest distance to " OE1 GLU A   2 " =    2.130
peak=    3.524 closest distance to " O   HOH Z 406 " =    1.680
peak=    3.517 closest distance to " CE BLYS A 290 " =    1.135
peak=    3.514 closest distance to " O   HOH Z 295 " =    1.540
peak=    3.505 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.501 closest distance to " CG2 THR A 221 " =    1.111
peak=    3.497 closest distance to " CA  MET A  40 " =    1.165
peak=    3.496 closest distance to " CD2 TRP A 179 " =    1.320
peak=    3.493 closest distance to " O   HOH Z 345 " =    3.506
peak=    3.491 closest distance to " O   HOH Z   3 " =    1.796
peak=    3.491 closest distance to " O   HOH Z 280 " =    3.035
peak=    3.490 closest distance to " O   HOH Z 180 " =    2.098
peak=    3.488 closest distance to " O   HOH Z 163 " =    1.883
peak=    3.480 closest distance to " CB  MET A  40 " =    0.889
peak=    3.472 closest distance to " CB  ARG A 139 " =    1.036
peak=    3.471 closest distance to " O   HOH Z 411 " =    3.845
peak=    3.467 closest distance to " CD2 LEU A 297 " =    0.859
peak=    3.467 closest distance to " O   HOH Z 281 " =    4.624
peak=    3.461 closest distance to " O   HOH Z  93 " =    2.462
peak=    3.459 closest distance to " CA  ALA A  84 " =    1.404
peak=    3.458 closest distance to " CG  LYS A  76 " =    0.947
peak=    3.458 closest distance to " CA  ALA A 233 " =    1.235
peak=    3.458 closest distance to " OG  SER A  97 " =    3.604
peak=    3.457 closest distance to " CD1 ILE A 106 " =    0.892
peak=    3.456 closest distance to " CB  ASP A 140 " =    0.797
peak=    3.454 closest distance to " O   HOH Z 263 " =    1.691
peak=    3.450 closest distance to " O   HOH Z 329 " =    3.714
peak=    3.449 closest distance to " O   HOH Z 148 " =    3.210
peak=    3.443 closest distance to " CB  GLU A 277 " =    3.526
peak=    3.442 closest distance to " CB  GLN A  88 " =    1.216
peak=    3.439 closest distance to " O   HOH Z 245 " =    1.413
peak=    3.438 closest distance to " O   HOH Z 337 " =    3.710
peak=    3.436 closest distance to " CD  LYS A 166 " =    1.215
peak=    3.432 closest distance to " O   HOH Z 426 " =    1.547
peak=    3.426 closest distance to " O   HOH Z 327 " =    1.768
peak=    3.422 closest distance to " O   HOH Z 423 " =    1.877
peak=    3.419 closest distance to " O   HOH Z 280 " =    1.850
peak=    3.406 closest distance to " O   HOH Z  88 " =    3.283
peak=    3.403 closest distance to " CA  ALA A 291 " =    0.979
peak=    3.397 closest distance to " O   HOH Z 261 " =    2.138
peak=    3.396 closest distance to " NH1BARG A 145 " =    1.311
peak=    3.393 closest distance to " OG  SER A  22 " =    2.739
peak=    3.392 closest distance to " CB  ALA A  34 " =    1.078
peak=    3.391 closest distance to " O   HOH Z 371 " =    3.042
peak=    3.390 closest distance to " O   HOH Z  89 " =    2.144
peak=    3.390 closest distance to " OD1 ASN A 217 " =    1.657
peak=    3.385 closest distance to " O   HOH Z 437 " =    1.611
peak=    3.375 closest distance to " O   HOH Z 166 " =    3.749
peak=    3.375 closest distance to " O   HOH Z 419 " =    1.898
peak=    3.370 closest distance to " O   HOH Z 411 " =    1.823
peak=    3.367 closest distance to " CD BLYS A 290 " =    1.264
peak=    3.361 closest distance to " CG2 ILE A 120 " =    1.263
peak=    3.361 closest distance to " CG  LEU A 167 " =    1.228
peak=    3.358 closest distance to " O   HOH Z  19 " =    2.494
peak=    3.355 closest distance to " N   VAL A 126 " =    1.322
peak=    3.351 closest distance to " O   HOH Z 188 " =    2.117
peak=    3.349 closest distance to " O   HOH Z 234 " =    1.716
peak=    3.340 closest distance to " ND1 HIS A  81 " =    1.618
peak=    3.340 closest distance to " O   HOH Z 209 " =    2.452
peak=    3.340 closest distance to " O   HOH Z 199 " =    1.578
peak=    3.339 closest distance to " O   HOH Z 353 " =    2.698
peak=    3.336 closest distance to " O   HOH Z 108 " =    2.222
peak=    3.334 closest distance to " O   HOH Z  44 " =    3.190
peak=    3.330 closest distance to " CG  GLU A 277 " =    2.258
peak=    3.327 closest distance to " OG  SER A 206 " =    1.296
peak=    3.324 closest distance to " CB  ALA A 291 " =    1.384
peak=    3.321 closest distance to " OG BSER A 164 " =    2.394
peak=    3.318 closest distance to " OE1 GLU A 277 " =    1.882
peak=    3.316 closest distance to " O   HOH Z  49 " =    2.594
peak=    3.316 closest distance to " O   HOH Z 345 " =    1.799
peak=    3.316 closest distance to " CB  ALA A  71 " =    1.370
peak=    3.315 closest distance to " CA  ASP A 162 " =    1.045
peak=    3.314 closest distance to " N   PHE A 130 " =    1.360
peak=    3.309 closest distance to " CA  ILE A  33 " =    1.486
peak=    3.308 closest distance to " O   HOH Z 281 " =    4.091
peak=    3.303 closest distance to " CB  SER A 141 " =    0.988
peak=    3.301 closest distance to " O   HOH Z 144 " =    1.788
peak=    3.301 closest distance to " CZ2 TRP A 179 " =    1.702
peak=    3.298 closest distance to " CD  ARG A 219 " =    1.033
peak=    3.297 closest distance to " CA  ALA A 248 " =    1.298
peak=    3.297 closest distance to " N   SER A 135 " =    1.299
peak=    3.297 closest distance to " CB  ALA A   9 " =    1.524
peak=    3.295 closest distance to " O   HOH Z  43 " =    1.849
peak=    3.286 closest distance to " CB  LEU A 255 " =    0.744
peak=    3.285 closest distance to " O   HOH Z 172 " =    3.322
peak=    3.284 closest distance to " O   HOH Z  85 " =    2.267
peak=    3.278 closest distance to " O   HOH Z   1 " =    1.720
peak=    3.275 closest distance to " O   HOH Z 359 " =    3.962
peak=    3.271 closest distance to " CD  PRO A 243 " =    1.609
peak=    3.266 closest distance to " O   TRP A 274 " =    1.829
peak=    3.261 closest distance to " O   HOH Z 287 " =    1.830
peak=    3.259 closest distance to " O   HOH Z 133 " =    2.364
peak=    3.249 closest distance to " O   HOH Z  49 " =    2.179
peak=    3.246 closest distance to " CG2 THR A 220 " =    0.862
peak=    3.245 closest distance to " CB  GLN A 278 " =    0.834
peak=    3.240 closest distance to " O   HOH Z 255 " =    1.638
peak=    3.240 closest distance to " CB  HIS A 108 " =    0.793
peak=    3.239 closest distance to " O   HOH Z 374 " =    2.626
peak=    3.231 closest distance to " CB  SER A  62 " =    1.263
peak=    3.229 closest distance to " O   GLN A 240 " =    2.241
peak=    3.226 closest distance to " OE1 GLN A  11 " =    2.166
peak=    3.219 closest distance to " CG1 VAL A 153 " =    0.919
peak=    3.217 closest distance to " O   HOH Z 128 " =    2.036
peak=    3.214 closest distance to " O   MET A 105 " =    1.717
peak=    3.213 closest distance to " O   HOH Z 319 " =    2.101
peak=    3.210 closest distance to " N   ASN A  39 " =    1.229
peak=    3.209 closest distance to " O   HOH Z 313 " =    1.817
peak=    3.204 closest distance to " O   HOH Z 292 " =    1.753
peak=    3.200 closest distance to " O   HOH Z 334 " =    1.487
peak=    3.199 closest distance to " CG  MET A 185 " =    1.045
peak=    3.198 closest distance to " O   HOH Z 151 " =    1.841
peak=    3.186 closest distance to " OD1 ASP A 231 " =    1.896
peak=    3.186 closest distance to " CB  PHE A  16 " =    1.097
peak=    3.184 closest distance to " CB  THR A 157 " =    1.066
peak=    3.179 closest distance to " CG  MET A 185 " =    1.116
peak=    3.177 closest distance to " O   GLY A 229 " =    1.793
peak=    3.175 closest distance to " O   ALA A   1 " =    1.494
peak=    3.175 closest distance to " O   HOH Z 302 " =    1.960
peak=    3.174 closest distance to " O   PHE A 192 " =    1.409
peak=    3.173 closest distance to " O   HOH Z 286 " =    2.230
peak=    3.173 closest distance to " O   HOH Z 433 " =    1.856
peak=    3.171 closest distance to " OG1 THR A 294 " =    1.631
peak=    3.170 closest distance to " CA  ARG A 195 " =    1.164
peak=    3.170 closest distance to " O   HOH Z 409 " =    2.843
peak=    3.167 closest distance to " N   ASN A 127 " =    1.277
peak=    3.166 closest distance to " O   HOH Z 267 " =    2.063
peak=    3.166 closest distance to " O   HOH Z 383 " =    1.724
peak=    3.166 closest distance to " O   HOH Z 216 " =    2.623
peak=    3.165 closest distance to " CB  ALA A 233 " =    1.428
peak=    3.163 closest distance to " O   HOH Z 171 " =    2.107
peak=    3.159 closest distance to " CB  TRP A 150 " =    1.489
peak=    3.157 closest distance to " CA  GLN A 223 " =    0.900
peak=    3.151 closest distance to " CA  ILE A 234 " =    0.908
peak=    3.150 closest distance to " CZ3 TRP A 123 " =    1.251
peak=    3.150 closest distance to " NZ  LYS A  76 " =    1.154
peak=    3.148 closest distance to " N   SER A 134 " =    1.284
peak=    3.146 closest distance to " NH2AARG A 190 " =    1.237
peak=    3.141 closest distance to " O   HOH Z 116 " =    1.685
peak=    3.139 closest distance to " O   HOH Z 227 " =    1.673
peak=    3.133 closest distance to " CG  GLN A  77 " =    1.794
peak=    3.126 closest distance to " CA  ASP A 140 " =    1.168
peak=    3.125 closest distance to " O   GLY A  57 " =    2.554
peak=    3.124 closest distance to " CB  LYS A 193 " =    0.950
peak=    3.123 closest distance to " O   HOH Z 423 " =    2.907
peak=    3.121 closest distance to " CA  ALA A 158 " =    1.140
peak=    3.117 closest distance to " NH1 ARG A 138 " =    1.155
peak=    3.116 closest distance to " O   HOH Z 387 " =    3.203
peak=    3.116 closest distance to " CG2BVAL A  41 " =    0.788
peak=    3.111 closest distance to " CA  ASP A 191 " =    0.753
peak=    3.108 closest distance to " CG  GLN A  89 " =    1.496
peak=    3.086 closest distance to " NZ ALYS A 290 " =    1.109
peak=    3.083 closest distance to " CB  ALA A 114 " =    1.255
peak=    3.081 closest distance to " O   HOH Z 357 " =    1.881
peak=    3.078 closest distance to " CB  ASN A 215 " =    1.073
peak=    3.074 closest distance to " O   PRO A  90 " =    1.319
peak=    3.072 closest distance to " O   HOH Z 391 " =    2.924
peak=    3.064 closest distance to " O   HOH Z  71 " =    2.316
peak=    3.064 closest distance to " O   HOH Z  66 " =    1.944
peak=    3.058 closest distance to " O   ALA A 158 " =    1.295
peak=    3.057 closest distance to " CB  ARG A 138 " =    1.009
peak=    3.048 closest distance to " CB  PHE A 283 " =    0.769
peak=    3.015 closest distance to " O   HOH Z 389 " =    1.737
peak=    3.014 closest distance to " O   SER A  26 " =    2.017

                           ----------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: 0.257 - 5.628
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 199
   mapped sites are within: 0.710 - 5.628

peak=   -4.890 closest distance to " O   HOH Z 290 " =    1.049
peak=   -4.736 closest distance to " CB  PRO A 243 " =    2.620
peak=   -4.503 closest distance to " O   HOH Z 266 " =    4.573
peak=   -4.341 closest distance to " O   VAL A  67 " =    2.692
peak=   -4.228 closest distance to " CG  GLN A 223 " =    1.807
peak=   -4.186 closest distance to " CB  ALA A 161 " =    2.592
peak=   -4.182 closest distance to " CD  ARG A 156 " =    1.978
peak=   -4.145 closest distance to " O   HOH Z 372 " =    2.424
peak=   -4.105 closest distance to " SG  CYS A 254 " =    3.264
peak=   -3.973 closest distance to " O   HOH Z 389 " =    1.856
peak=   -3.973 closest distance to " CG  ASP A 231 " =    0.752
peak=   -3.971 closest distance to " O   HOH Z 353 " =    2.186
peak=   -3.964 closest distance to " N   ALA A  43 " =    2.473
peak=   -3.932 closest distance to " C   ALA A 158 " =    1.320
peak=   -3.905 closest distance to " O   HOH Z 185 " =    2.319
peak=   -3.894 closest distance to " CE2 TYR A  30 " =    2.816
peak=   -3.889 closest distance to " CD  GLN A 223 " =    1.065
peak=   -3.874 closest distance to " N   GLN A  58 " =    1.887
peak=   -3.862 closest distance to " O   HOH Z  10 " =    1.464
peak=   -3.849 closest distance to " CZ3 TRP A 179 " =    1.085
peak=   -3.848 closest distance to " O   HOH Z 126 " =    1.910
peak=   -3.843 closest distance to " C   HIS A 108 " =    1.141
peak=   -3.838 closest distance to " O   HOH Z 211 " =    1.669
peak=   -3.833 closest distance to " CG1 VAL A 112 " =    2.769
peak=   -3.830 closest distance to " CD1 LEU A 228 " =    2.290
peak=   -3.824 closest distance to " ND2 ASN A  45 " =    1.610
peak=   -3.805 closest distance to " O   HOH Z 198 " =    2.142
peak=   -3.805 closest distance to " O   HOH Z 435 " =    2.768
peak=   -3.801 closest distance to " O   HOH Z 351 " =    1.425
peak=   -3.786 closest distance to " OG BSER A 134 " =    1.229
peak=   -3.784 closest distance to " O   PRO A 198 " =    1.270
peak=   -3.780 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.778 closest distance to " CG  PHE A 283 " =    2.785
peak=   -3.773 closest distance to " O   HOH Z 198 " =    1.118
peak=   -3.772 closest distance to " CG1 VAL A 112 " =    2.944
peak=   -3.761 closest distance to " CD1 PHE A  59 " =    1.825
peak=   -3.756 closest distance to " CD2 PHE A 192 " =    2.132
peak=   -3.734 closest distance to " O   HOH Z  52 " =    1.330
peak=   -3.732 closest distance to " O   HOH Z 377 " =    2.109
peak=   -3.717 closest distance to " CE  MET A 105 " =    2.085
peak=   -3.716 closest distance to " CD  ARG A 139 " =    1.624
peak=   -3.713 closest distance to " O   HOH Z 118 " =    3.051
peak=   -3.709 closest distance to " O   HOH Z 231 " =    2.106
peak=   -3.700 closest distance to " C   ASP A 231 " =    2.697
peak=   -3.699 closest distance to " O   HOH Z  43 " =    1.554
peak=   -3.693 closest distance to " CD  GLN A  58 " =    1.019
peak=   -3.691 closest distance to " CD1 LEU A 101 " =    2.391
peak=   -3.677 closest distance to " N   SER A 212 " =    2.005
peak=   -3.660 closest distance to " CB  ALA A 291 " =    2.364
peak=   -3.656 closest distance to " NH2AARG A 275 " =    5.375
peak=   -3.656 closest distance to " CG  GLU A 152 " =    0.806
peak=   -3.651 closest distance to " OG BSER A 134 " =    1.675
peak=   -3.645 closest distance to " NH1 ARG A 195 " =    2.488
peak=   -3.642 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.640 closest distance to " O   PRO A 163 " =    2.017
peak=   -3.638 closest distance to " CZ  TYR A 169 " =    1.631
peak=   -3.626 closest distance to " N   ASP A 286 " =    2.473
peak=   -3.616 closest distance to " O   HOH Z 313 " =    2.038
peak=   -3.610 closest distance to " O   GLY A 196 " =    1.118
peak=   -3.609 closest distance to " CD2 LEU A 300 " =    2.862
peak=   -3.595 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.583 closest distance to " CE2 PHE A 218 " =    2.505
peak=   -3.579 closest distance to " CG2 ILE A 263 " =    2.268
peak=   -3.566 closest distance to " O   HOH Z 407 " =    3.182
peak=   -3.563 closest distance to " ND2 ASN A  45 " =    1.061
peak=   -3.554 closest distance to " O   HOH Z 311 " =    3.585
peak=   -3.541 closest distance to " O   HOH Z  47 " =    1.603
peak=   -3.541 closest distance to " SG ACYS A 201 " =    1.901
peak=   -3.539 closest distance to " CB  ASN A  39 " =    2.175
peak=   -3.518 closest distance to " CB  ALA A 291 " =    2.218
peak=   -3.509 closest distance to " CD2 PHE A  61 " =    2.410
peak=   -3.505 closest distance to " NH2 ARG A  79 " =    1.683
peak=   -3.501 closest distance to " NH2 ARG A  79 " =    1.881
peak=   -3.497 closest distance to " CA  GLY A  98 " =    1.937
peak=   -3.485 closest distance to " CB  ASP A 286 " =    2.129
peak=   -3.482 closest distance to " CD  GLN A  88 " =    0.714
peak=   -3.479 closest distance to " OD1 ASP A 171 " =    1.643
peak=   -3.475 closest distance to " CD1 LEU A 297 " =    2.359
peak=   -3.475 closest distance to " OXT GLY A 302 " =    2.703
peak=   -3.470 closest distance to " CD1 ILE A 239 " =    2.064
peak=   -3.456 closest distance to " O   VAL A 189 " =    2.543
peak=   -3.452 closest distance to " N   PHE A  59 " =    2.136
peak=   -3.444 closest distance to " CZ  PHE A  59 " =    1.540
peak=   -3.437 closest distance to " OG  SER A  62 " =    1.432
peak=   -3.435 closest distance to " CE  LYS A  76 " =    2.820
peak=   -3.428 closest distance to " O   HOH Z 290 " =    0.936
peak=   -3.425 closest distance to " O   HOH Z 222 " =    1.133
peak=   -3.424 closest distance to " CG  ARG A 269 " =    2.364
peak=   -3.421 closest distance to " O   HOH Z 417 " =    2.407
peak=   -3.420 closest distance to " O   PRO A 198 " =    1.191
peak=   -3.420 closest distance to " N   THR A 235 " =    1.364
peak=   -3.412 closest distance to " CG1 VAL A 197 " =    2.208
peak=   -3.411 closest distance to " O   LEU A 101 " =    2.866
peak=   -3.408 closest distance to " O   GLN A 240 " =    2.124
peak=   -3.406 closest distance to " O   SER A 135 " =    1.488
peak=   -3.402 closest distance to " CG1 VAL A 112 " =    2.591
peak=   -3.394 closest distance to " ND2 ASN A 249 " =    2.061
peak=   -3.369 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.367 closest distance to " O   HOH Z 210 " =    0.967
peak=   -3.366 closest distance to " CD2 LEU A 237 " =    2.756
peak=   -3.366 closest distance to " O   HOH Z  60 " =    2.475
peak=   -3.365 closest distance to " C   LEU A 143 " =    1.163
peak=   -3.364 closest distance to " OD1 ASP A 191 " =    1.738
peak=   -3.358 closest distance to " CA  GLY A 241 " =    3.002
peak=   -3.356 closest distance to " CB  CYS A 254 " =    2.387
peak=   -3.355 closest distance to " CZ3 TRP A 274 " =    1.065
peak=   -3.349 closest distance to " CD2 LEU A 300 " =    3.056
peak=   -3.348 closest distance to " O   HOH Z  76 " =    1.862
peak=   -3.347 closest distance to " CG  MET A 105 " =    0.997
peak=   -3.347 closest distance to " O   HOH Z  98 " =    2.365
peak=   -3.346 closest distance to " O   HOH Z 395 " =    5.235
peak=   -3.346 closest distance to " O   HOH Z 111 " =    2.261
peak=   -3.339 closest distance to " O   ALA A 161 " =    1.560
peak=   -3.337 closest distance to " CG1 VAL A 230 " =    2.027
peak=   -3.331 closest distance to " O   HOH Z 196 " =    2.116
peak=   -3.331 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.328 closest distance to " CE BMET A  47 " =    2.244
peak=   -3.320 closest distance to " OG1 THR A 178 " =    1.275
peak=   -3.319 closest distance to " O   HOH Z 241 " =    1.292
peak=   -3.310 closest distance to " O   HOH Z  38 " =    1.573
peak=   -3.306 closest distance to " CA  GLY A 203 " =    2.156
peak=   -3.305 closest distance to " OD1 ASN A 148 " =    1.664
peak=   -3.304 closest distance to " CG  TRP A 266 " =    1.805
peak=   -3.294 closest distance to " CB  ALA A 248 " =    2.063
peak=   -3.291 closest distance to " O   GLY A 211 " =    1.477
peak=   -3.281 closest distance to " O   HOH Z 281 " =    2.686
peak=   -3.280 closest distance to " C   MET A 188 " =    1.482
peak=   -3.277 closest distance to " CG  LEU A 101 " =    2.339
peak=   -3.272 closest distance to " O   HOH Z  11 " =    1.747
peak=   -3.270 closest distance to " N   GLN A 122 " =    1.472
peak=   -3.268 closest distance to " CE3 TRP A 123 " =    1.213
peak=   -3.265 closest distance to " O   TRP A  70 " =    1.581
peak=   -3.258 closest distance to " O   HOH Z 282 " =    1.115
peak=   -3.251 closest distance to " O   HOH Z 388 " =    2.049
peak=   -3.247 closest distance to " O   LYS A 117 " =    1.683
peak=   -3.244 closest distance to " CB  ALA A  43 " =    2.398
peak=   -3.243 closest distance to " OD2 ASP A 171 " =    2.274
peak=   -3.242 closest distance to " O   HOH Z 137 " =    1.480
peak=   -3.236 closest distance to " O   SER A  22 " =    2.399
peak=   -3.234 closest distance to " O   HOH Z 317 " =    2.458
peak=   -3.233 closest distance to " NH2BARG A 275 " =    1.859
peak=   -3.230 closest distance to " CB  TYR A  15 " =    2.156
peak=   -3.226 closest distance to " O   HOH Z 323 " =    1.201
peak=   -3.220 closest distance to " CB  ALA A   1 " =    2.751
peak=   -3.216 closest distance to " O   HOH Z 298 " =    2.660
peak=   -3.216 closest distance to " ND2 ASN A  60 " =    1.470
peak=   -3.214 closest distance to " ND2 ASN A 187 " =    1.469
peak=   -3.214 closest distance to " CB  TRP A  85 " =    2.485
peak=   -3.213 closest distance to " OD1 ASP A 191 " =    1.549
peak=   -3.213 closest distance to " CG1 VAL A 250 " =    2.730
peak=   -3.212 closest distance to " OE1 GLN A  88 " =    1.234
peak=   -3.211 closest distance to " O   HOH Z  51 " =    1.202
peak=   -3.202 closest distance to " N   ALA A 226 " =    2.105
peak=   -3.197 closest distance to " CE3 TRP A 274 " =    2.447
peak=   -3.192 closest distance to " O   HOH Z 252 " =    4.287
peak=   -3.189 closest distance to " O   VAL A 174 " =    2.021
peak=   -3.184 closest distance to " O   ALA A  34 " =    2.841
peak=   -3.173 closest distance to " CB  ALA A 248 " =    2.438
peak=   -3.170 closest distance to " OG  SER A   3 " =    1.535
peak=   -3.166 closest distance to " O   HOH Z 385 " =    2.085
peak=   -3.165 closest distance to " O   HOH Z 359 " =    3.121
peak=   -3.162 closest distance to " CB  PHE A 208 " =    2.268
peak=   -3.156 closest distance to " O   HOH Z  88 " =    2.170
peak=   -3.156 closest distance to " O   HOH Z 184 " =    1.819
peak=   -3.155 closest distance to " CE  MET A  93 " =    1.176
peak=   -3.148 closest distance to " O   HOH Z 176 " =    0.710
peak=   -3.145 closest distance to " O   HOH Z 174 " =    2.422
peak=   -3.143 closest distance to " O   HOH Z 394 " =    1.402
peak=   -3.140 closest distance to " O   HOH Z 166 " =    1.400
peak=   -3.138 closest distance to " O   HOH Z  63 " =    1.495
peak=   -3.138 closest distance to " CD  GLU A 277 " =    1.170
peak=   -3.132 closest distance to " N   ALA A 248 " =    1.562
peak=   -3.131 closest distance to " O   HOH Z 390 " =    2.411
peak=   -3.129 closest distance to " O   HOH Z  13 " =    1.481
peak=   -3.128 closest distance to " OE1 GLN A 223 " =    1.800
peak=   -3.127 closest distance to " O   HOH Z 414 " =    1.792
peak=   -3.120 closest distance to " CG  ARG A  66 " =    2.357
peak=   -3.119 closest distance to " CA  TRP A 274 " =    1.457
peak=   -3.117 closest distance to " O   HOH Z  73 " =    2.319
peak=   -3.105 closest distance to " CG  ASN A 301 " =    1.866
peak=   -3.102 closest distance to " O   HOH Z  89 " =    2.998
peak=   -3.097 closest distance to " O   PHE A 218 " =    1.596
peak=   -3.088 closest distance to " O   HOH Z 281 " =    3.253
peak=   -3.082 closest distance to " O   HOH Z 283 " =    5.628
peak=   -3.080 closest distance to " CA  ASP A 298 " =    1.097
peak=   -3.080 closest distance to " O   HOH Z 436 " =    1.246
peak=   -3.072 closest distance to " CB  ASP A 132 " =    2.277
peak=   -3.047 closest distance to " CD2 TYR A 293 " =    2.080
peak=   -3.036 closest distance to " O   ALA A 292 " =    1.914
peak=   -3.032 closest distance to " O   HOH Z 198 " =    1.542
peak=   -3.032 closest distance to " O   LYS A 289 " =    3.035
peak=   -3.030 closest distance to " OXT GLY A 302 " =    3.381
peak=   -3.026 closest distance to " O   HOH Z 175 " =    4.244

================= 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    :  0.3312 0.3346   6.052287e+00   6.059555e+00
   1_bss:  0.3177 0.3223   6.034597e+00   6.031028e+00
   1_xyz:  0.1701 0.1936   5.465417e+00   5.585345e+00
   1_adp:  0.1624 0.1944   5.431671e+00   5.593021e+00
   1_occ:  0.1618 0.1945   5.428861e+00   5.591143e+00
   2_bss:  0.1603 0.1915   5.422618e+00   5.582664e+00
   2_xyz:  0.1231 0.1543   5.181830e+00   5.369536e+00
   2_adp:  0.1149 0.1542   5.141340e+00   5.364803e+00
   2_occ:  0.1149 0.1542   5.141168e+00   5.364882e+00
   3_bss:  0.1150 0.1542   5.142009e+00   5.365886e+00
   3_xyz:  0.1088 0.1527   5.113653e+00   5.355689e+00
   3_adp:  0.1089 0.1518   5.113318e+00   5.353517e+00
   3_occ:  0.1088 0.1517   5.113191e+00   5.353798e+00
   4_bss:  0.1088 0.1517   5.113341e+00   5.353876e+00
   4_xyz:  0.1077 0.1525   5.111171e+00   5.357828e+00
   4_adp:  0.1078 0.1530   5.113430e+00   5.361383e+00
   4_occ:  0.1077 0.1531   5.113403e+00   5.361630e+00
   5_bss:  0.1077 0.1531   5.113454e+00   5.361655e+00
   5_xyz:  0.1068 0.1538   5.111626e+00   5.365433e+00
   5_adp:  0.1083 0.1537   5.117889e+00   5.364695e+00
   5_occ:  0.1083 0.1537   5.117929e+00   5.365073e+00
   5_bss:  0.1083 0.1538   5.117954e+00   5.365081e+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:  0.328  41.220  -1.536  -2.383   1.007  -0.000   0.000   0.000
   1_xyz:  0.328  41.220  -1.536  -2.383   1.007  -0.000   0.000   0.000
   1_adp:  0.328  41.220  -1.536  -2.383   1.007  -0.000   0.000   0.000
   1_occ:  0.328  41.220  -1.536  -2.383   1.007  -0.000   0.000   0.000
   2_bss:  0.320  48.420  -2.511  -2.949  -1.509  -0.000  -0.000  -0.000
   2_xyz:  0.320  48.420  -2.511  -2.949  -1.509  -0.000  -0.000  -0.000
   2_adp:  0.320  48.420  -2.511  -2.949  -1.509  -0.000  -0.000  -0.000
   2_occ:  0.320  48.420  -2.511  -2.949  -1.509  -0.000  -0.000  -0.000
   3_bss:  0.320  48.420  -2.437  -2.676  -1.700  -0.000  -0.000  -0.000
   3_xyz:  0.320  48.420  -2.437  -2.676  -1.700  -0.000  -0.000  -0.000
   3_adp:  0.320  48.420  -2.437  -2.676  -1.700  -0.000  -0.000  -0.000
   3_occ:  0.320  48.420  -2.437  -2.676  -1.700  -0.000  -0.000  -0.000
   4_bss:  0.326  48.420  -2.350  -2.509  -1.670  -0.000  -0.000  -0.000
   4_xyz:  0.326  48.420  -2.350  -2.509  -1.670  -0.000  -0.000  -0.000
   4_adp:  0.326  48.420  -2.350  -2.509  -1.670  -0.000  -0.000  -0.000
   4_occ:  0.326  48.420  -2.350  -2.509  -1.670  -0.000  -0.000  -0.000
   5_bss:  0.326  48.420  -2.265  -2.411  -1.593  -0.000  -0.000  -0.000
   5_xyz:  0.326  48.420  -2.265  -2.411  -1.593  -0.000  -0.000  -0.000
   5_adp:  0.326  48.420  -2.265  -2.411  -1.593  -0.000  -0.000  -0.000
   5_occ:  0.326  48.420  -2.265  -2.411  -1.593  -0.000  -0.000  -0.000
   5_bss:  0.326  48.330  -2.150  -2.281  -1.464  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.090 0.7032  0.8936    32249.186
   1_bss:  33.714 0.7166  0.8836    28815.120
   1_xyz:  18.050 0.8817  1.0115     9789.202
   1_adp:  18.285 0.8793  1.0077     9946.268
   1_occ:  18.255 0.8795  1.0077     9877.287
   2_bss:  17.984 0.8818  0.9611     9649.709
   2_xyz:  13.511 0.9189  0.9793     6142.338
   2_adp:  13.516 0.9187  0.9784     6030.018
   2_occ:  13.516 0.9187  0.9783     6029.463
   3_bss:  13.549 0.9185  0.9796     6066.940
   3_xyz:  13.310 0.9206  0.9796     5936.962
   3_adp:  13.243 0.9212  0.9769     5916.908
   3_occ:  13.244 0.9212  0.9768     5917.641
   4_bss:  13.251 0.9211  0.9802     5921.820
   4_xyz:  13.310 0.9207  0.9794     5967.027
   4_adp:  13.362 0.9203  0.9759     6007.440
   4_occ:  13.365 0.9203  0.9758     6008.527
   5_bss:  13.367 0.9202  0.9789     6009.318
   5_xyz:  13.429 0.9198  0.9788     6060.308
   5_adp:  13.401 0.9201  0.9769     6072.212
   5_occ:  13.407 0.9200  0.9768     6073.838
   5_bss:  13.409 0.9200  0.9780     6073.967
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6279e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6279e-01
   1_xyz:   1.066  0.008  0.072 15.103  0.005  4.110   6.5919e-02
   1_adp:   1.066  0.008  0.072 15.103  0.005  4.110   6.5919e-02
   1_occ:   1.066  0.008  0.072 15.103  0.005  4.110   6.5919e-02
   2_bss:   1.066  0.008  0.072 15.103  0.005  4.110   6.5919e-02
   2_xyz:   0.993  0.007  0.075 14.943  0.004  4.117   5.9907e-02
   2_adp:   0.993  0.007  0.075 14.943  0.004  4.117   5.9907e-02
   2_occ:   0.993  0.007  0.075 14.943  0.004  4.117   5.9907e-02
   3_bss:   0.993  0.007  0.075 14.943  0.004  4.117   5.9907e-02
   3_xyz:   1.008  0.007  0.076 15.042  0.004  4.118   6.1932e-02
   3_adp:   1.008  0.007  0.076 15.042  0.004  4.118   6.1932e-02
   3_occ:   1.008  0.007  0.076 15.042  0.004  4.118   6.1932e-02
   4_bss:   1.008  0.007  0.076 15.042  0.004  4.118   6.1932e-02
   4_xyz:   0.989  0.007  0.075 14.933  0.004  4.119   6.0094e-02
   4_adp:   0.989  0.007  0.075 14.933  0.004  4.119   6.0094e-02
   4_occ:   0.989  0.007  0.075 14.933  0.004  4.119   6.0094e-02
   5_bss:   0.989  0.007  0.075 14.933  0.004  4.119   6.0094e-02
   5_xyz:   1.010  0.007  0.075 14.998  0.004  4.119   6.2236e-02
   5_adp:   1.010  0.007  0.075 14.998  0.004  4.119   6.2236e-02
   5_occ:   1.010  0.007  0.075 14.998  0.004  4.119   6.2236e-02
   5_bss:   1.010  0.007  0.075 14.998  0.004  4.119   6.2236e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4014e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4014e-01
   1_xyz:   8.024  0.043  0.351 84.092  0.040  2.335   5.8784e-02
   1_adp:   8.024  0.043  0.351 84.092  0.040  2.335   5.8784e-02
   1_occ:   8.024  0.043  0.351 84.092  0.040  2.335   5.8784e-02
   2_bss:   8.024  0.043  0.351 84.092  0.040  2.335   5.8784e-02
   2_xyz:   7.268  0.040  0.226 85.506  0.041  2.287   5.4173e-02
   2_adp:   7.268  0.040  0.226 85.506  0.041  2.287   5.4173e-02
   2_occ:   7.268  0.040  0.226 85.506  0.041  2.287   5.4173e-02
   3_bss:   7.268  0.040  0.226 85.506  0.041  2.287   5.4173e-02
   3_xyz:   7.155  0.039  0.236 84.050  0.039  2.294   4.9031e-02
   3_adp:   7.155  0.039  0.236 84.050  0.039  2.294   4.9031e-02
   3_occ:   7.155  0.039  0.236 84.050  0.039  2.294   4.9031e-02
   4_bss:   7.155  0.039  0.236 84.050  0.039  2.294   4.9031e-02
   4_xyz:   6.942  0.038  0.232 84.178  0.038  2.280   4.3672e-02
   4_adp:   6.942  0.038  0.232 84.178  0.038  2.280   4.3672e-02
   4_occ:   6.942  0.038  0.232 84.178  0.038  2.280   4.3672e-02
   5_bss:   6.942  0.038  0.232 84.178  0.038  2.280   4.3672e-02
   5_xyz:   6.830  0.040  0.230 84.058  0.038  2.293   4.5076e-02
   5_adp:   6.830  0.040  0.230 84.058  0.038  2.293   4.5076e-02
   5_occ:   6.830  0.040  0.230 84.058  0.038  2.293   4.5076e-02
   5_bss:   6.830  0.040  0.230 84.058  0.038  2.293   4.5076e-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:  82.36   0.00  16.20  82.36   0.00  12.36  62.41   5.73  37.11
   1_occ:  82.36   0.00  16.20  82.36   0.00  12.36  62.41   5.73  37.11
   2_bss:  82.36   0.00  16.20  82.36   0.00  12.36  62.41   5.73  37.11
   2_xyz:  82.36   0.00  16.20  82.36   0.00  12.36  62.41   5.73  37.11
   2_adp:  80.58   1.09  17.23  80.58   1.09  13.00  75.68   1.61  40.28
   2_occ:  80.58   1.09  17.23  80.58   1.09  13.00  75.68   1.61  40.28
   3_bss:  80.58   1.09  17.23  80.58   1.09  13.00  75.68   1.61  40.28
   3_xyz:  80.58   1.09  17.23  80.58   1.09  13.00  75.68   1.61  40.28
   3_adp:  81.01   1.71  16.71  81.01   1.71  12.83  75.99   2.77  37.82
   3_occ:  81.01   1.71  16.71  81.01   1.71  12.83  75.99   2.77  37.82
   4_bss:  81.01   1.71  16.71  81.01   1.71  12.83  75.99   2.77  37.82
   4_xyz:  81.01   1.71  16.71  81.01   1.71  12.83  75.99   2.77  37.82
   4_adp:  81.28   1.69  16.50  81.28   1.69  12.73  75.77   3.62  37.06
   4_occ:  81.28   1.69  16.50  81.28   1.69  12.73  75.77   3.62  37.06
   5_bss:  81.28   1.69  16.50  81.28   1.69  12.73  75.77   3.62  37.06
   5_xyz:  81.28   1.69  16.50  81.28   1.69  12.73  75.77   3.62  37.06
   5_adp:  79.16   2.48  16.20  79.16   2.48  12.62  74.66   4.91  35.73
   5_occ:  79.16   2.48  16.20  79.16   2.48  12.62  74.66   4.91  35.73
   5_bss:  79.07   2.39  16.11  79.07   2.39  12.53  74.57   4.82  35.64
------------------------------------------------------------------------
 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:    1.136    0.006    0.321
   1_adp:    1.136    0.006    0.321
   1_occ:    1.136    0.006    0.321
   2_bss:    1.136    0.006    0.321
   2_xyz:    0.799    0.012    0.376
   2_adp:    0.799    0.012    0.376
   2_occ:    0.799    0.012    0.376
   3_bss:    0.799    0.012    0.376
   3_xyz:    0.893    0.030    0.389
   3_adp:    0.893    0.030    0.389
   3_occ:    0.893    0.030    0.389
   4_bss:    0.893    0.030    0.389
   4_xyz:    0.996    0.027    0.402
   4_adp:    0.996    0.027    0.402
   4_occ:    0.996    0.027    0.402
   5_bss:    0.996    0.027    0.402
   5_xyz:    1.108    0.041    0.406
   5_adp:    1.108    0.041    0.406
   5_occ:    1.108    0.041    0.406
   5_bss:    1.108    0.041    0.406
------------------------------------------------------------------------

CPU time actual refinement: 320.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_893/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_893/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_893/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_893/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_893/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.87 
  Macro-tasks:
    bulk solvent and scale       = 37.30  
    individual site refinement   = 134.49 
    weights calculation          = 29.31  
    collect and process          = 6.64   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 207.85 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 99.95  
    alpha_beta                      = 8.16   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.52 
    fmodel                         = 6.64   
    r_factors                      = 0.22   
    phase_errors                   = 11.22  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 239.26 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.504 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    645 calls, 99.57 s
gradients_fft:          590 calls, 96.61 s

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

# Date 2008-01-16 Time 05:54:31 PST -0800 (1200491671.21 s)
Start R-work = 0.3312, R-free = 0.3346 (no bulk solvent and anisotropic scale)
Final R-work = 0.1335, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.3177, R-free = 0.3223
Final R-work = 0.1083, R-free = 0.1538