# Date 2008-01-16 Time 05:59:09 PST -0800 (1200491949.35 s)
#phil __OFF__

Command line arguments: "../961.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6352
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 961

-------------------------------------------------------------------------------
  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, 48.1033, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


================================== 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, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99137
Completeness in resolution range: 0.945598
Completeness with d_max=infinity: 0.942685

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9914

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, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.99137
Completeness in resolution range: 0.945598
Completeness with d_max=infinity: 0.942685

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2611 [2180/2208]  1962   218  10.0%
  bin  2:  4.2611 -  3.3948 [2080/2103]  1872   208  10.0%
  bin  3:  3.3948 -  2.9694 [2056/2081]  1848   208  10.1%
  bin  4:  2.9694 -  2.6996 [2049/2065]  1849   200   9.8%
  bin  5:  2.6996 -  2.5070 [2035/2072]  1827   208  10.2%
  bin  6:  2.5070 -  2.3598 [2017/2051]  1822   195   9.7%
  bin  7:  2.3598 -  2.2420 [1990/2027]  1788   202  10.2%
  bin  8:  2.2420 -  2.1447 [1998/2040]  1797   201  10.1%
  bin  9:  2.1447 -  2.0624 [2009/2044]  1809   200  10.0%
  bin 10:  2.0624 -  1.9914 [1175/2025]  1056   119  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_961/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:
        1.54 -     2.21: 7
        2.21 -     2.89: 1283
        2.89 -     3.56: 4389
        3.56 -     4.23: 9070
        4.23 -     4.90: 13162
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.544 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.563 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.656 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.802 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27906 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_961/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_961/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 48.10325 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4251   r_free= 0.4054   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.243219                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7525 0.99   1409  157 0.3513 0.3805      6.5189      6.5071|
|  2:  4.7525 -  3.7920 0.99   1368  147 0.3686 0.3802         6.8      6.7645|
|  3:  3.7920 -  3.3185 0.99   1323  155 0.3965 0.3495      6.6253      6.5582|
|  4:  3.3185 -  3.0177 0.99   1330  146 0.4100 0.4024      6.4722      6.4364|
|  5:  3.0177 -  2.8029 0.98   1316  147 0.4380 0.4179      6.3318      6.3182|
|  6:  2.8029 -  2.6386 0.99   1302  142 0.4644 0.3889      6.2613      6.0767|
|  7:  2.6386 -  2.5070 0.99   1310  148 0.4572 0.3965      6.2061      6.1122|
|  8:  2.5070 -  2.3984 0.99   1289  142 0.4720 0.4457      6.1297      6.1667|
|  9:  2.3984 -  2.3064 0.99   1295  142 0.4755 0.4671      6.0958      6.0732|
| 10:  2.3064 -  2.2270 0.98   1290  142 0.4481 0.4104      6.0576      5.9867|
| 11:  2.2270 -  2.1576 0.98   1279  143 0.4807 0.4148      6.0274      5.9747|
| 12:  2.1576 -  2.0961 1.00   1283  142 0.4619 0.4780      5.9258      5.9774|
| 13:  2.0961 -  2.0411 0.96   1272  139 0.4585 0.4282      5.8258      5.8051|
| 14:  2.0411 -  1.9914 0.43    564   67 0.4427 0.4463      5.7809      5.7151|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7525  1409   157  0.70  33.97   0.83     0.74      70961.26|
|  2:  4.7525 -  3.7920  1368   147  0.74  31.36   0.91     0.82      85952.06|
|  3:  3.7920 -  3.3185  1323   155  0.67  37.86   0.91     0.82      88159.15|
|  4:  3.3185 -  3.0177  1330   146  0.62  42.54   0.92     0.79      76324.81|
|  5:  3.0177 -  2.8029  1316   147  0.56  46.85   0.90     0.75      60753.27|
|  6:  2.8029 -  2.6386  1302   142  0.57  46.47   0.90     0.74      47817.78|
|  7:  2.6386 -  2.5070  1310   148  0.58  45.60   0.92     0.75      42015.25|
|  8:  2.5070 -  2.3984  1289   142  0.54  48.73   0.91     0.74      40802.55|
|  9:  2.3984 -  2.3064  1295   142  0.53  49.42   0.93     0.73      39255.45|
| 10:  2.3064 -  2.2270  1290   142  0.54  49.01   0.97     0.75      36631.23|
| 11:  2.2270 -  2.1576  1279   143  0.54  49.48   0.94     0.76      33289.70|
| 12:  2.1576 -  2.0961  1283   142  0.52  50.55   0.97     0.76      31183.75|
| 13:  2.0961 -  2.0411  1272   139  0.49  53.27   0.94     0.71      27396.62|
| 14:  2.0411 -  1.9914   564    67  0.49  53.26   0.98     0.66      23557.47|
|alpha:            min =        0.66 max =            0.82 mean =         0.75|
|beta:             min =    23557.47 max =        88159.15 mean =     51864.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.11|
|phase err.(test): min =        0.00 max =           89.74 mean =        45.04|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.282313              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.852   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.371946              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.593   (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 |  1.544 -  1.879:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.879 -  2.215:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.215 -  2.551:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.551 -  2.886:     1257 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.886 -  3.222:     1878 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.222 -  3.557:     2511 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.557 -  3.893:     4610 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.893 -  4.229:     4460 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.229 -  4.564:     5997 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7165 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.544 |       0.277 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4251   r_free= 0.4054   ksol= 0.00   Bsol= 0.00   scale= 0.902    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.243219                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4129   r_free= 0.3947   ksol= 0.29   Bsol= 28.69   scale= 0.934   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,5.71,-1.86,0.00,-0.00,-0.00); trace/3= 0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.231201                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.423702              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.471   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.704124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.504   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4129      final r-factor (work) = 0.3283          |
| start r-factor (free) = 0.3947      final r-factor (free) = 0.3604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.4089 = 8.42 * 0.50 * 6.2295 + 1.00 * 0.1711                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7502 = 8.42 * 0.50 * 6.0824 + 1.00 * 0.1319                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3283      final r-factor (work) = 0.3036          |
| start r-factor (free) = 0.3604      final r-factor (free) = 0.3676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2888 = 0.70 * 1.00 * 6.0824 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2488 = 0.70 * 1.00 * 6.0154 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.68   17.20    None  None   None       |
|    all(noH): 2823   0      0.00    79.68   17.20    None  None   None       |
|    Sol.    : 438    0      2.05    77.80   34.73    None  None   None       |
|    Mac.    : 2385   0      0.00    79.68   13.98    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 -   7.968:  733   |   5:    39.839 -  47.807:  118        |
|      1:     7.968 -  15.936:  944   |   6:    47.807 -  55.775:   60        |
|      2:    15.936 -  23.903:  506   |   7:    55.775 -  63.742:   39        |
|      3:    23.903 -  31.871:  268   |   8:    63.742 -  71.710:   12        |
|      4:    31.871 -  39.839:  136   |   9:    71.710 -  79.678:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3036 r_free = 0.3676             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3035 r_free = 0.3667             target_work(ml) = 6.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3035   r_free= 0.3667   ksol= 0.29   Bsol= 28.69   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,5.71,-1.86,0.00,-0.00,-0.00); trace/3= 0.50                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.018075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3027   r_free= 0.3640   ksol= 0.31   Bsol= 49.18   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,3.11,-0.59,0.00,-0.00,-0.00); trace/3= 0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.018950                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.170883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.994   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631505              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.509  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3027      final r-factor (work) = 0.2417          |
| start r-factor (free) = 0.3640      final r-factor (free) = 0.2879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7156 = 8.17 * 0.50 * 6.0174 + 1.00 * 0.1319                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3087 = 8.17 * 0.50 * 5.9264 + 1.00 * 0.0968                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2417      final r-factor (work) = 0.2217          |
| start r-factor (free) = 0.2879      final r-factor (free) = 0.2788          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7557 = 0.63 * 1.00 * 5.9264 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6524 = 0.63 * 1.00 * 5.7621 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.85   17.54    None  None   None       |
|    all(noH): 2823   0      0.00    85.85   17.54    None  None   None       |
|    Sol.    : 438    0      0.91    83.62   39.26    None  None   None       |
|    Mac.    : 2385   0      0.00    85.85   13.55    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 -   8.585:  917   |   5:    42.924 -  51.508:  106        |
|      1:     8.585 -  17.169:  932   |   6:    51.508 -  60.093:   69        |
|      2:    17.169 -  25.754:  391   |   7:    60.093 -  68.678:   43        |
|      3:    25.754 -  34.339:  202   |   8:    68.678 -  77.262:   17        |
|      4:    34.339 -  42.924:  133   |   9:    77.262 -  85.847:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2217 r_free = 0.2788             target_work(ml) = 5.750         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2216 r_free = 0.2785             target_work(ml) = 5.749         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2216   r_free= 0.2785   ksol= 0.31   Bsol= 49.18   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,3.11,-0.59,0.00,-0.00,-0.00); trace/3= 0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.749398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2212   r_free= 0.2772   ksol= 0.32   Bsol= 62.90   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,1.57,-0.27,0.00,-0.00,-0.00); trace/3= 0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.747726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.437624              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.621  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.558927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.994  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2212      final r-factor (work) = 0.1774          |
| start r-factor (free) = 0.2772      final r-factor (free) = 0.2223          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0006 = 3.44 * 0.50 * 5.7620 + 1.00 * 0.0968                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7795 = 3.44 * 0.50 * 5.6506 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1774      final r-factor (work) = 0.1651          |
| start r-factor (free) = 0.2223      final r-factor (free) = 0.2104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1718 = 0.56 * 1.00 * 5.6506 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0882 = 0.56 * 1.00 * 5.5027 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.70   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    93.70   17.30    None  None   None       |
|    Sol.    : 438    0      3.99    93.70   41.83    None  None   None       |
|    Mac.    : 2385   0      0.00    92.48   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.371: 1099   |   5:    46.853 -  56.223:  106        |
|      1:     9.371 -  18.741:  976   |   6:    56.223 -  65.593:   57        |
|      2:    18.741 -  28.112:  267   |   7:    65.593 -  74.964:   33        |
|      3:    28.112 -  37.482:  130   |   8:    74.964 -  84.334:   15        |
|      4:    37.482 -  46.853:  130   |   9:    84.334 -  93.705:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1651 r_free = 0.2104             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1649 r_free = 0.2104             target_work(ml) = 5.479         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1649   r_free= 0.2104   ksol= 0.32   Bsol= 62.90   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.01,1.57,-0.27,0.00,-0.00,-0.00); trace/3= 0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.478590                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1652   r_free= 0.2105   ksol= 0.33   Bsol= 71.56   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,0.41,-0.47,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.480389                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.273873              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.102   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.968  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1652      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.2105      final r-factor (free) = 0.1838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8329 = 4.27 * 0.50 * 5.5059 + 1.00 * 0.0673                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6022 = 4.27 * 0.50 * 5.3925 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1356      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.1838      final r-factor (free) = 0.1782          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8843 = 0.90 * 1.00 * 5.3925 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7892 = 0.90 * 1.00 * 5.2869 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.33  17.15    None  None   None       |
|    all(noH): 2823   0      0.00    105.33  17.15    None  None   None       |
|    Sol.    : 438    0      1.84    105.33  43.51    None  None   None       |
|    Mac.    : 2385   0      0.00    103.08  12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.533: 1361   |   5:    52.666 -  63.199:   89        |
|      1:    10.533 -  21.066:  873   |   6:    63.199 -  73.732:   58        |
|      2:    21.066 -  31.600:  180   |   7:    73.732 -  84.265:   23        |
|      3:    31.600 -  42.133:  124   |   8:    84.265 -  94.798:    9        |
|      4:    42.133 -  52.666:  100   |   9:    94.798 - 105.332:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1281 r_free = 0.1782             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1281 r_free = 0.1780             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1780   ksol= 0.33   Bsol= 71.56   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.37,0.41,-0.47,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.266535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1784   ksol= 0.33   Bsol= 72.08   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-0.10,-0.37,-0.00,-0.00,-0.00); trace/3= -0.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.268543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.219170              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.407  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.312  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1784      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2339 = 4.22 * 0.50 * 5.2878 + 1.00 * 0.0789                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1301 = 4.22 * 0.50 * 5.2352 + 1.00 * 0.0860                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1704      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9170 = 0.36 * 1.00 * 5.2352 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9035 = 0.36 * 1.00 * 5.2035 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    107.74  16.44    None  None   None       |
|    all(noH): 2823   0      0.27    107.74  16.44    None  None   None       |
|    Sol.    : 438    0      2.55    107.74  41.33    None  None   None       |
|    Mac.    : 2385   0      0.27    101.38  11.87    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:     0.273 -  11.021: 1488   |   5:    54.009 -  64.756:   79        |
|      1:    11.021 -  21.768:  789   |   6:    64.756 -  75.503:   37        |
|      2:    21.768 -  32.515:  179   |   7:    75.503 -  86.250:   13        |
|      3:    32.515 -  43.262:  119   |   8:    86.250 -  96.997:    4        |
|      4:    43.262 -  54.009:  109   |   9:    96.997 - 107.745:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1664             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1666             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1666   ksol= 0.33   Bsol= 72.08   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-0.10,-0.37,-0.00,-0.00,-0.00); trace/3= -0.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193021                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7525 0.99   1409  157 0.1004 0.1335      5.4041      5.5834|
|  2:  4.7525 -  3.7920 0.99   1368  147 0.0852 0.1110      5.4418      5.6543|
|  3:  3.7920 -  3.3185 0.99   1323  155 0.1072 0.1576      5.4922       5.869|
|  4:  3.3185 -  3.0177 0.99   1330  146 0.1297 0.1648      5.5028      5.6622|
|  5:  3.0177 -  2.8029 0.98   1316  147 0.1382 0.1957      5.3892      5.6012|
|  6:  2.8029 -  2.6386 0.99   1302  142 0.1325 0.2078      5.2853      5.5089|
|  7:  2.6386 -  2.5070 0.99   1310  148 0.1303 0.1877      5.2151      5.4983|
|  8:  2.5070 -  2.3984 0.99   1289  142 0.1227 0.1672       5.124      5.3073|
|  9:  2.3984 -  2.3064 0.99   1295  142 0.1210 0.1843      5.0717      5.3619|
| 10:  2.3064 -  2.2270 0.98   1290  142 0.1217 0.1899      5.0239      5.2715|
| 11:  2.2270 -  2.1576 0.98   1279  143 0.1195 0.1907      4.9752      5.3035|
| 12:  2.1576 -  2.0961 1.00   1283  142 0.1136 0.1631      4.9076      5.1187|
| 13:  2.0961 -  2.0411 0.96   1272  139 0.1178 0.1869      4.8197      5.1296|
| 14:  2.0411 -  1.9914 0.43    564   67 0.1155 0.1788      4.7157      4.9485|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7525  1409   157  0.94   9.55   0.96     0.94       7794.06|
|  2:  4.7525 -  3.7920  1368   147  0.95   8.48   1.00     0.99       9491.84|
|  3:  3.7920 -  3.3185  1323   155  0.93  11.86   1.02     1.01      11141.37|
|  4:  3.3185 -  3.0177  1330   146  0.90  15.54   1.00     0.97      11778.81|
|  5:  3.0177 -  2.8029  1316   147  0.88  17.69   1.00     0.97       9829.69|
|  6:  2.8029 -  2.6386  1302   142  0.89  17.64   0.98     0.95       8327.06|
|  7:  2.6386 -  2.5070  1310   148  0.90  16.70   0.98     0.95       6971.50|
|  8:  2.5070 -  2.3984  1289   142  0.89  17.01   0.99     0.95       6269.16|
|  9:  2.3984 -  2.3064  1295   142  0.90  16.55   0.99     0.94       5506.12|
| 10:  2.3064 -  2.2270  1290   142  0.89  17.00   0.98     0.94       5048.76|
| 11:  2.2270 -  2.1576  1279   143  0.89  17.35   0.98     0.94       4754.17|
| 12:  2.1576 -  2.0961  1283   142  0.91  15.96   0.99     0.97       4267.51|
| 13:  2.0961 -  2.0411  1272   139  0.89  17.39   0.98     0.98       3668.92|
| 14:  2.0411 -  1.9914   564    67  0.89  16.62   0.96     0.93       2875.46|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2875.46 max =        11778.81 mean =      7195.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.26|
|phase err.(test): min =        0.00 max =           89.78 mean =        14.66|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1666   ksol= 0.33   Bsol= 67.31   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-0.26,-0.24,-0.00,-0.00,-0.00); trace/3= -0.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.192933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1666   ksol= 0.33   Bsol= 67.31   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,-0.26,-0.24,-0.00,-0.00,-0.00); trace/3= -0.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.192933                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7525 0.99   1409  157 0.1002 0.1333      5.4034      5.5822|
|  2:  4.7525 -  3.7920 0.99   1368  147 0.0850 0.1110      5.4401      5.6519|
|  3:  3.7920 -  3.3185 0.99   1323  155 0.1072 0.1576      5.4915      5.8702|
|  4:  3.3185 -  3.0177 0.99   1330  146 0.1297 0.1647      5.5035       5.662|
|  5:  3.0177 -  2.8029 0.98   1316  147 0.1384 0.1958      5.3894      5.6017|
|  6:  2.8029 -  2.6386 0.99   1302  142 0.1324 0.2072      5.2849      5.5074|
|  7:  2.6386 -  2.5070 0.99   1310  148 0.1304 0.1878      5.2152      5.4984|
|  8:  2.5070 -  2.3984 0.99   1289  142 0.1226 0.1674      5.1248      5.3077|
|  9:  2.3984 -  2.3064 0.99   1295  142 0.1209 0.1848      5.0719      5.3634|
| 10:  2.3064 -  2.2270 0.98   1290  142 0.1216 0.1902      5.0244       5.272|
| 11:  2.2270 -  2.1576 0.98   1279  143 0.1195 0.1904      4.9751      5.3033|
| 12:  2.1576 -  2.0961 1.00   1283  142 0.1135 0.1635      4.9081      5.1208|
| 13:  2.0961 -  2.0411 0.96   1272  139 0.1179 0.1867      4.8202      5.1292|
| 14:  2.0411 -  1.9914 0.43    564   67 0.1154 0.1783      4.7145      4.9461|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0824 -  4.7525  1409   157  0.94   9.55   0.96     0.94       7790.79|
|  2:  4.7525 -  3.7920  1368   147  0.95   8.48   1.00     0.99       9464.09|
|  3:  3.7920 -  3.3185  1323   155  0.93  11.84   1.02     1.01      11111.14|
|  4:  3.3185 -  3.0177  1330   146  0.90  15.54   1.00     0.97      11790.12|
|  5:  3.0177 -  2.8029  1316   147  0.88  17.67   1.00     0.97       9813.95|
|  6:  2.8029 -  2.6386  1302   142  0.89  17.62   0.98     0.95       8314.85|
|  7:  2.6386 -  2.5070  1310   148  0.90  16.70   0.99     0.95       6966.95|
|  8:  2.5070 -  2.3984  1289   142  0.89  17.03   0.99     0.95       6284.52|
|  9:  2.3984 -  2.3064  1295   142  0.90  16.57   0.99     0.94       5519.60|
| 10:  2.3064 -  2.2270  1290   142  0.89  17.03   0.98     0.94       5058.23|
| 11:  2.2270 -  2.1576  1279   143  0.89  17.35   0.98     0.94       4754.30|
| 12:  2.1576 -  2.0961  1283   142  0.91  15.98   0.99     0.97       4278.05|
| 13:  2.0961 -  2.0411  1272   139  0.89  17.38   0.98     0.98       3666.53|
| 14:  2.0411 -  1.9914   564    67  0.89  16.58   0.96     0.93       2862.10|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2862.10 max =        11790.12 mean =      7191.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.26|
|phase err.(test): min =        0.00 max =           89.64 mean =        14.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    107.74  16.44    None  None   None       |
|    all(noH): 2823   0      0.27    107.74  16.44    None  None   None       |
|    Sol.    : 438    0      2.55    107.74  41.32    None  None   None       |
|    Mac.    : 2385   0      0.27    101.37  11.87    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:     0.266 -  11.013: 1488   |   5:    54.002 -  64.749:   79        |
|      1:    11.013 -  21.760:  789   |   6:    64.749 -  75.496:   37        |
|      2:    21.760 -  32.508:  179   |   7:    75.496 -  86.243:   13        |
|      3:    32.508 -  43.255:  119   |   8:    86.243 -  96.990:    4        |
|      4:    43.255 -  54.002:  109   |   9:    96.990 - 107.737:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.583 - 5.278
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 304
   mapped sites are within: 0.753 - 5.278

peak=    5.992 closest distance to " O   HOH Z 111 " =    2.176
peak=    5.942 closest distance to " O   HOH Z 210 " =    1.321
peak=    5.625 closest distance to " CB  SER A  63 " =    1.229
peak=    5.126 closest distance to " CB  GLN A 223 " =    1.398
peak=    5.101 closest distance to " O   HOH Z 433 " =    1.714
peak=    4.934 closest distance to " O   PRO A 198 " =    1.532
peak=    4.801 closest distance to " O   HOH Z 134 " =    1.911
peak=    4.679 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.531 closest distance to " O   HOH Z  47 " =    1.505
peak=    4.502 closest distance to " O   HOH Z  15 " =    2.104
peak=    4.469 closest distance to " O   HOH Z  80 " =    1.924
peak=    4.459 closest distance to " O   HOH Z 232 " =    2.390
peak=    4.420 closest distance to " O   GLY A  23 " =    2.368
peak=    4.392 closest distance to " O   HOH Z  44 " =    2.424
peak=    4.387 closest distance to " O   HOH Z 418 " =    1.869
peak=    4.386 closest distance to " CB  ARG A 190 " =    1.720
peak=    4.349 closest distance to " O   HOH Z  20 " =    1.823
peak=    4.335 closest distance to " O   ALA A 165 " =    1.306
peak=    4.319 closest distance to " CG  PRO A 213 " =    1.171
peak=    4.319 closest distance to " O   HOH Z  40 " =    1.906
peak=    4.262 closest distance to " CG1 ILE A  33 " =    1.233
peak=    4.256 closest distance to " O   HOH Z 425 " =    1.549
peak=    4.241 closest distance to " O   HOH Z 357 " =    2.126
peak=    4.238 closest distance to " O   HOH Z 234 " =    3.764
peak=    4.232 closest distance to " CA  TYR A  30 " =    0.943
peak=    4.199 closest distance to " O   HOH Z 196 " =    1.723
peak=    4.189 closest distance to " O   HOH Z 133 " =    2.111
peak=    4.182 closest distance to " O   HOH Z 369 " =    2.205
peak=    4.178 closest distance to " O   HOH Z 403 " =    1.837
peak=    4.155 closest distance to " O   HOH Z 265 " =    2.009
peak=    4.149 closest distance to " O   HOH Z 154 " =    2.503
peak=    4.148 closest distance to " CB  GLU A 128 " =    1.104
peak=    4.126 closest distance to " O   HOH Z 154 " =    1.452
peak=    4.106 closest distance to " O   HOH Z  30 " =    1.966
peak=    4.097 closest distance to " CG  ARG A  66 " =    2.694
peak=    4.088 closest distance to " O   HOH Z 406 " =    1.616
peak=    4.084 closest distance to " O   HOH Z 298 " =    2.065
peak=    4.075 closest distance to " CB  TRP A 179 " =    1.384
peak=    4.074 closest distance to " O   HOH Z 374 " =    2.708
peak=    4.069 closest distance to " O   HOH Z 271 " =    2.808
peak=    4.060 closest distance to " O   HOH Z 163 " =    1.688
peak=    4.055 closest distance to " CB  ARG A  79 " =    1.376
peak=    4.042 closest distance to " CB  GLU A 277 " =    3.800
peak=    4.033 closest distance to " O   HOH Z  63 " =    1.694
peak=    4.028 closest distance to " CB  ARG A 275 " =    0.830
peak=    4.014 closest distance to " CB  VAL A 202 " =    1.515
peak=    4.013 closest distance to " CA  ALA A  51 " =    1.003
peak=    4.010 closest distance to " CB  SER A 141 " =    1.041
peak=    4.005 closest distance to " CB  SER A   3 " =    1.359
peak=    3.998 closest distance to " O   HOH Z  97 " =    2.014
peak=    3.997 closest distance to " O   HOH Z 352 " =    1.944
peak=    3.986 closest distance to " CB  TRP A 266 " =    1.004
peak=    3.957 closest distance to " O   HOH Z   7 " =    0.843
peak=    3.950 closest distance to " O   HOH Z 132 " =    2.714
peak=    3.947 closest distance to " O   HOH Z 118 " =    1.532
peak=    3.947 closest distance to " CB  GLU A 152 " =    1.160
peak=    3.947 closest distance to " O   HOH Z  67 " =    2.090
peak=    3.941 closest distance to " CA  ASN A 176 " =    1.756
peak=    3.930 closest distance to " CB  LEU A 228 " =    1.141
peak=    3.916 closest distance to " O   HOH Z 189 " =    2.422
peak=    3.914 closest distance to " CB  TYR A 169 " =    0.915
peak=    3.912 closest distance to " CA  ASP A 191 " =    0.906
peak=    3.898 closest distance to " O   HOH Z 258 " =    2.230
peak=    3.898 closest distance to " O   HOH Z  61 " =    1.583
peak=    3.895 closest distance to " OD1 ASN A  69 " =    2.516
peak=    3.893 closest distance to " OG BSER A 164 " =    2.339
peak=    3.892 closest distance to " O   SER A  87 " =    2.341
peak=    3.891 closest distance to " O   HOH Z 245 " =    1.391
peak=    3.883 closest distance to " O   HOH Z 394 " =    1.613
peak=    3.880 closest distance to " O   HOH Z 423 " =    1.941
peak=    3.880 closest distance to " O   HOH Z 247 " =    1.500
peak=    3.861 closest distance to " CA  ALA A  21 " =    1.432
peak=    3.856 closest distance to " CG2 VAL A 197 " =    1.146
peak=    3.855 closest distance to " O   THR A 251 " =    1.256
peak=    3.849 closest distance to " O   HOH Z 126 " =    1.665
peak=    3.839 closest distance to " O   HOH Z 214 " =    1.339
peak=    3.837 closest distance to " O   ALA A 158 " =    1.249
peak=    3.835 closest distance to " CD  LYS A 166 " =    1.399
peak=    3.832 closest distance to " O   HOH Z 412 " =    3.414
peak=    3.810 closest distance to " N   ASN A  39 " =    1.236
peak=    3.808 closest distance to " NH2 ARG A 156 " =    1.175
peak=    3.801 closest distance to " CB  ASN A 148 " =    1.347
peak=    3.800 closest distance to " CD1 LEU A 300 " =    1.187
peak=    3.793 closest distance to " O   HOH Z 336 " =    1.691
peak=    3.786 closest distance to " O   HOH Z 362 " =    3.523
peak=    3.780 closest distance to " C   ILE A 106 " =    1.873
peak=    3.777 closest distance to " CD2 LEU A 297 " =    1.011
peak=    3.776 closest distance to " NH2BARG A 145 " =    1.976
peak=    3.759 closest distance to " O   HOH Z 345 " =    1.694
peak=    3.753 closest distance to " NZ  LYS A 117 " =    3.265
peak=    3.753 closest distance to " CG  PRO A 198 " =    1.242
peak=    3.750 closest distance to " CG2 THR A 221 " =    1.087
peak=    3.748 closest distance to " O   HOH Z 422 " =    0.876
peak=    3.743 closest distance to " O   HOH Z 150 " =    1.917
peak=    3.739 closest distance to " O   HOH Z 126 " =    2.055
peak=    3.725 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.723 closest distance to " OG  SER A  62 " =    3.038
peak=    3.715 closest distance to " ND2 ASN A 187 " =    1.492
peak=    3.714 closest distance to " CG  PRO A  90 " =    1.132
peak=    3.701 closest distance to " O   HOH Z 193 " =    1.980
peak=    3.700 closest distance to " O   HOH Z 281 " =    4.626
peak=    3.695 closest distance to " O   HOH Z 128 " =    2.229
peak=    3.690 closest distance to " O   HOH Z 389 " =    2.008
peak=    3.689 closest distance to " O   HOH Z 133 " =    1.615
peak=    3.687 closest distance to " NZ  LYS A 117 " =    1.804
peak=    3.686 closest distance to " O   HOH Z  44 " =    1.886
peak=    3.681 closest distance to " O   HOH Z 176 " =    1.694
peak=    3.680 closest distance to " NE2 GLN A  11 " =    1.109
peak=    3.674 closest distance to " CZ3 TRP A  85 " =    0.972
peak=    3.672 closest distance to " O   HOH Z 327 " =    1.681
peak=    3.670 closest distance to " CD  ARG A 269 " =    0.945
peak=    3.670 closest distance to " CZ  PHE A 218 " =    1.190
peak=    3.665 closest distance to " O   HOH Z 174 " =    2.124
peak=    3.663 closest distance to " CB  ASN A  39 " =    0.848
peak=    3.661 closest distance to " O   HOH Z 368 " =    2.086
peak=    3.660 closest distance to " CG2BVAL A  41 " =    0.867
peak=    3.638 closest distance to " O   HOH Z 128 " =    2.157
peak=    3.631 closest distance to " CD2 LEU A 255 " =    1.257
peak=    3.623 closest distance to " CA  ALA A 295 " =    1.103
peak=    3.619 closest distance to " O   HOH Z 403 " =    1.558
peak=    3.619 closest distance to " O   HOH Z 402 " =    1.667
peak=    3.617 closest distance to " O   HOH Z 130 " =    1.181
peak=    3.615 closest distance to " O   HOH Z 180 " =    2.312
peak=    3.615 closest distance to " O   ASN A  74 " =    1.748
peak=    3.612 closest distance to " CB  SER A  62 " =    0.799
peak=    3.609 closest distance to " CA  THR A 221 " =    1.598
peak=    3.606 closest distance to " O   HOH Z 255 " =    1.797
peak=    3.604 closest distance to " CB  ASP A 140 " =    0.865
peak=    3.593 closest distance to " O   HOH Z  21 " =    1.824
peak=    3.575 closest distance to " O   HOH Z 303 " =    2.370
peak=    3.574 closest distance to " O   HOH Z 284 " =    2.896
peak=    3.574 closest distance to " CB  ALA A 100 " =    1.436
peak=    3.573 closest distance to " O   HOH Z 132 " =    1.016
peak=    3.571 closest distance to " CA  ARG A 195 " =    1.220
peak=    3.560 closest distance to " CA  GLY A 196 " =    1.043
peak=    3.553 closest distance to " O   HOH Z 437 " =    1.752
peak=    3.535 closest distance to " O   HOH Z 432 " =    1.901
peak=    3.529 closest distance to " CA  ALA A 160 " =    0.922
peak=    3.528 closest distance to " CA  LEU A  83 " =    1.416
peak=    3.525 closest distance to " O   HOH Z 279 " =    2.174
peak=    3.523 closest distance to " O   HOH Z 109 " =    2.115
peak=    3.522 closest distance to " O   HOH Z 346 " =    1.541
peak=    3.522 closest distance to " CG2 VAL A  78 " =    0.986
peak=    3.519 closest distance to " OG1 THR A 294 " =    2.485
peak=    3.517 closest distance to " O   HOH Z  78 " =    2.130
peak=    3.517 closest distance to " CD2 TRP A 179 " =    1.359
peak=    3.516 closest distance to " CG1BVAL A  72 " =    1.667
peak=    3.509 closest distance to " O   HOH Z 142 " =    1.360
peak=    3.502 closest distance to " O   HOH Z 383 " =    2.074
peak=    3.502 closest distance to " O   HOH Z 299 " =    2.297
peak=    3.497 closest distance to " CB  ALA A  71 " =    1.290
peak=    3.485 closest distance to " O   HOH Z 431 " =    1.145
peak=    3.481 closest distance to " CB  ASN A 187 " =    1.106
peak=    3.475 closest distance to " O   HOH Z 380 " =    1.753
peak=    3.466 closest distance to " CG  PRO A 243 " =    1.169
peak=    3.462 closest distance to " O   HOH Z 316 " =    3.067
peak=    3.456 closest distance to " CB  ASN A 285 " =    0.828
peak=    3.454 closest distance to " CD  PRO A  54 " =    0.915
peak=    3.451 closest distance to " OH  TYR A 169 " =    0.961
peak=    3.448 closest distance to " CA  ASP A 162 " =    1.192
peak=    3.447 closest distance to " O   HOH Z 250 " =    1.739
peak=    3.446 closest distance to " CD  ARG A 195 " =    1.024
peak=    3.440 closest distance to " C   SER A  32 " =    1.080
peak=    3.433 closest distance to " O   HOH Z  22 " =    2.570
peak=    3.432 closest distance to " O  BHOH Z 338 " =    2.241
peak=    3.430 closest distance to " O   HOH Z 334 " =    1.527
peak=    3.429 closest distance to " O   HOH Z 214 " =    2.358
peak=    3.426 closest distance to " O   HOH Z 404 " =    1.524
peak=    3.425 closest distance to " O   HOH Z 155 " =    3.203
peak=    3.423 closest distance to " CG2 ILE A  20 " =    1.411
peak=    3.420 closest distance to " O   HOH Z 435 " =    2.955
peak=    3.419 closest distance to " O   HOH Z 227 " =    1.764
peak=    3.416 closest distance to " CG  GLU A  37 " =    0.985
peak=    3.412 closest distance to " O   HOH Z 313 " =    1.866
peak=    3.400 closest distance to " O   HOH Z 345 " =    3.049
peak=    3.393 closest distance to " O   HOH Z 145 " =    2.288
peak=    3.387 closest distance to " CD BLYS A 290 " =    1.052
peak=    3.384 closest distance to " CB  ALA A   9 " =    1.608
peak=    3.383 closest distance to " O   HOH Z 185 " =    1.693
peak=    3.383 closest distance to " O   HOH Z 417 " =    3.190
peak=    3.382 closest distance to " O   HOH Z 104 " =    2.612
peak=    3.380 closest distance to " OD2 ASP A 286 " =    2.916
peak=    3.380 closest distance to " CA  GLU A 152 " =    0.914
peak=    3.375 closest distance to " CB  ASN A 142 " =    1.190
peak=    3.374 closest distance to " OE1 GLU A   2 " =    2.161
peak=    3.372 closest distance to " CB  ARG A 190 " =    1.091
peak=    3.371 closest distance to " O   HOH Z 146 " =    1.527
peak=    3.371 closest distance to " O   HOH Z 371 " =    3.416
peak=    3.365 closest distance to " OG  SER A 245 " =    1.666
peak=    3.363 closest distance to " NZ  LYS A 166 " =    3.036
peak=    3.361 closest distance to " O   HOH Z 339 " =    1.265
peak=    3.359 closest distance to " O   HOH Z 409 " =    3.006
peak=    3.358 closest distance to " O   HOH Z  88 " =    3.657
peak=    3.355 closest distance to " O   ASP A 124 " =    1.465
peak=    3.355 closest distance to " O   HOH Z 386 " =    2.334
peak=    3.350 closest distance to " CD  ARG A 159 " =    0.876
peak=    3.349 closest distance to " CZ  PHE A  38 " =    1.408
peak=    3.345 closest distance to " CB  GLN A  88 " =    1.162
peak=    3.343 closest distance to " CD  ARG A  66 " =    2.562
peak=    3.340 closest distance to " CG  ARG A 219 " =    1.295
peak=    3.339 closest distance to " OE1 GLN A  11 " =    2.040
peak=    3.339 closest distance to " CA  ILE A 106 " =    0.777
peak=    3.339 closest distance to " O   HOH Z 387 " =    2.518
peak=    3.337 closest distance to " O   HOH Z  66 " =    2.191
peak=    3.325 closest distance to " O   HOH Z   1 " =    3.149
peak=    3.318 closest distance to " CB  MET A 105 " =    1.146
peak=    3.316 closest distance to " O  BHOH Z  74 " =    1.491
peak=    3.315 closest distance to " CA  TYR A 116 " =    1.351
peak=    3.315 closest distance to " CA  ALA A 100 " =    1.215
peak=    3.314 closest distance to " O   HOH Z 123 " =    2.135
peak=    3.308 closest distance to " O   HOH Z  48 " =    1.989
peak=    3.303 closest distance to " CB  MET A  40 " =    0.774
peak=    3.302 closest distance to " CA  ALA A 158 " =    1.138
peak=    3.301 closest distance to " NZ  LYS A  76 " =    1.295
peak=    3.297 closest distance to " O   HOH Z 344 " =    3.037
peak=    3.297 closest distance to " CA  LYS A 117 " =    1.290
peak=    3.292 closest distance to " O   HOH Z 244 " =    1.685
peak=    3.286 closest distance to " O   HOH Z  49 " =    1.869
peak=    3.286 closest distance to " O   HOH Z  64 " =    2.355
peak=    3.283 closest distance to " CG AARG A 275 " =    1.204
peak=    3.279 closest distance to " O   HOH Z 214 " =    2.249
peak=    3.278 closest distance to " O   HOH Z 234 " =    1.897
peak=    3.278 closest distance to " O   HOH Z 173 " =    2.278
peak=    3.267 closest distance to " CE  LYS A 119 " =    1.002
peak=    3.264 closest distance to " CA  PRO A  90 " =    0.971
peak=    3.262 closest distance to " O   HOH Z 365 " =    2.877
peak=    3.259 closest distance to " O   HOH Z  54 " =    1.545
peak=    3.251 closest distance to " CB  TYR A 116 " =    1.250
peak=    3.250 closest distance to " O   HOH Z 416 " =    2.979
peak=    3.249 closest distance to " O   HOH Z  11 " =    1.292
peak=    3.248 closest distance to " CG2 THR A  29 " =    1.397
peak=    3.247 closest distance to " CA  SER A  12 " =    1.642
peak=    3.232 closest distance to " CD2 HIS A  81 " =    1.135
peak=    3.228 closest distance to " O   HOH Z 156 " =    2.684
peak=    3.224 closest distance to " CB  GLN A  89 " =    1.210
peak=    3.224 closest distance to " O   HOH Z 130 " =    2.216
peak=    3.221 closest distance to " ND1 HIS A  81 " =    1.640
peak=    3.218 closest distance to " O   HOH Z 395 " =    1.406
peak=    3.216 closest distance to " CG  GLN A  58 " =    2.531
peak=    3.213 closest distance to " CG  GLN A  11 " =    1.234
peak=    3.212 closest distance to " O   HOH Z  19 " =    1.699
peak=    3.209 closest distance to " O   HOH Z  88 " =    3.420
peak=    3.209 closest distance to " N   ARG A 156 " =    1.464
peak=    3.207 closest distance to " O   HOH Z  88 " =    1.679
peak=    3.205 closest distance to " O   HOH Z  43 " =    1.228
peak=    3.205 closest distance to " O   HOH Z 287 " =    1.877
peak=    3.203 closest distance to " CB  ALA A 291 " =    1.225
peak=    3.202 closest distance to " O   HOH Z 355 " =    1.771
peak=    3.201 closest distance to " O   HOH Z 162 " =    1.820
peak=    3.201 closest distance to " CA  ASP A 132 " =    1.190
peak=    3.197 closest distance to " O   HOH Z 358 " =    2.075
peak=    3.197 closest distance to " CB  ALA A 242 " =    1.016
peak=    3.195 closest distance to " CG  GLN A  77 " =    0.819
peak=    3.193 closest distance to " O   HOH Z 167 " =    1.764
peak=    3.192 closest distance to " O   HOH Z 261 " =    1.806
peak=    3.185 closest distance to " CB  LEU A  83 " =    0.812
peak=    3.183 closest distance to " CD  ARG A  56 " =    1.396
peak=    3.181 closest distance to " CA  THR A 221 " =    0.957
peak=    3.177 closest distance to " O   HOH Z 423 " =    3.284
peak=    3.172 closest distance to " CB  GLN A 103 " =    0.869
peak=    3.172 closest distance to " O   HOH Z 272 " =    1.965
peak=    3.169 closest distance to " O   HOH Z 419 " =    1.752
peak=    3.165 closest distance to " CA  ARG A  36 " =    1.091
peak=    3.162 closest distance to " O   HOH Z 343 " =    2.431
peak=    3.161 closest distance to " NH2AARG A 275 " =    3.199
peak=    3.157 closest distance to " O   HOH Z 298 " =    4.453
peak=    3.155 closest distance to " O   HOH Z 428 " =    1.187
peak=    3.153 closest distance to " O   HOH Z 435 " =    1.660
peak=    3.152 closest distance to " CB  THR A  52 " =    1.065
peak=    3.152 closest distance to " O   HOH Z 377 " =    1.288
peak=    3.151 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.148 closest distance to " O   THR A 251 " =    2.016
peak=    3.143 closest distance to " CA  SER A  32 " =    1.624
peak=    3.141 closest distance to " O   HOH Z 189 " =    2.963
peak=    3.136 closest distance to " O   HOH Z 325 " =    3.918
peak=    3.135 closest distance to " O   HOH Z 192 " =    1.644
peak=    3.135 closest distance to " CA  GLU A  46 " =    0.771
peak=    3.134 closest distance to " CB  LEU A   5 " =    1.144
peak=    3.134 closest distance to " CG  MET A 185 " =    1.162
peak=    3.133 closest distance to " CA  ASP A 124 " =    0.792
peak=    3.132 closest distance to " CZ3 TRP A 266 " =    1.056
peak=    3.121 closest distance to " O   TRP A 274 " =    1.841
peak=    3.119 closest distance to " CB  THR A 157 " =    1.114
peak=    3.112 closest distance to " CG2 ILE A 151 " =    0.793
peak=    3.111 closest distance to " CD  LYS A 119 " =    1.906
peak=    3.108 closest distance to " O   HOH Z 124 " =    1.297
peak=    3.106 closest distance to " CA  SER A  87 " =    0.938
peak=    3.100 closest distance to " O   HOH Z  48 " =    1.594
peak=    3.097 closest distance to " CA  VAL A  41 " =    0.809
peak=    3.096 closest distance to " O   HOH Z  83 " =    1.606
peak=    3.093 closest distance to " CA  ALA A  84 " =    1.262
peak=    3.091 closest distance to " O   GLY A  91 " =    1.098
peak=    3.090 closest distance to " CB  VAL A 257 " =    0.871
peak=    3.071 closest distance to " O   HOH Z 131 " =    5.278
peak=    3.055 closest distance to " O   HOH Z  99 " =    2.296
peak=    3.042 closest distance to " CA  ARG A  66 " =    1.022
peak=    3.040 closest distance to " O   HOH Z 420 " =    2.092
peak=    3.037 closest distance to " O   HOH Z 327 " =    2.148
peak=    3.033 closest distance to " OD2 ASP A 298 " =    3.993

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 241         
Filter by distance & map next to the model:
   mapped sites are within: 0.645 - 5.896
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 239 from: 241
   mapped sites are within: 0.798 - 5.896

peak=   -4.830 closest distance to " O   HOH Z 266 " =    4.863
peak=   -4.382 closest distance to " O   VAL A  67 " =    2.834
peak=   -4.372 closest distance to " OXT GLY A 302 " =    2.980
peak=   -4.305 closest distance to " O   HOH Z 377 " =    0.967
peak=   -4.302 closest distance to " CD  ARG A 156 " =    2.151
peak=   -4.291 closest distance to " O   HOH Z 166 " =    1.703
peak=   -4.281 closest distance to " O   HOH Z 155 " =    1.725
peak=   -4.236 closest distance to " O   PRO A 163 " =    2.147
peak=   -4.142 closest distance to " CD2 LEU A 237 " =    2.664
peak=   -4.136 closest distance to " OG  SER A  97 " =    2.159
peak=   -4.135 closest distance to " CE2 TYR A  30 " =    2.701
peak=   -4.113 closest distance to " O   HOH Z   5 " =    1.600
peak=   -4.062 closest distance to " CD1 PHE A  59 " =    1.948
peak=   -4.058 closest distance to " NH2 ARG A  66 " =    1.438
peak=   -4.045 closest distance to " CB  PHE A 208 " =    2.350
peak=   -3.991 closest distance to " O   HOH Z 150 " =    1.063
peak=   -3.986 closest distance to " CB  PRO A 243 " =    2.720
peak=   -3.957 closest distance to " C   HIS A 108 " =    1.117
peak=   -3.903 closest distance to " O   HOH Z 252 " =    4.095
peak=   -3.896 closest distance to " OE1 GLN A  88 " =    0.848
peak=   -3.884 closest distance to " OD1 ASP A 191 " =    1.809
peak=   -3.860 closest distance to " N   ALA A  43 " =    2.659
peak=   -3.855 closest distance to " O   PRO A 198 " =    1.381
peak=   -3.842 closest distance to " O   HOH Z 290 " =    1.001
peak=   -3.829 closest distance to " CD  GLN A 223 " =    1.310
peak=   -3.826 closest distance to " O   HOH Z 109 " =    3.586
peak=   -3.818 closest distance to " OG BSER A 210 " =    1.206
peak=   -3.814 closest distance to " CG2 ILE A  49 " =    2.748
peak=   -3.803 closest distance to " CD  GLN A  88 " =    0.798
peak=   -3.790 closest distance to " CG1 VAL A 112 " =    2.574
peak=   -3.779 closest distance to " O   HOH Z 185 " =    2.536
peak=   -3.772 closest distance to " CD  GLN A  58 " =    1.185
peak=   -3.771 closest distance to " CD1 LEU A 167 " =    2.070
peak=   -3.769 closest distance to " CG  ARG A 269 " =    2.383
peak=   -3.757 closest distance to " O   HOH Z 111 " =    1.320
peak=   -3.751 closest distance to " O   VAL A  67 " =    2.971
peak=   -3.749 closest distance to " O   HOH Z  52 " =    1.790
peak=   -3.747 closest distance to " O   HOH Z 283 " =    2.151
peak=   -3.739 closest distance to " CD  ARG A  14 " =    3.430
peak=   -3.726 closest distance to " O   HOH Z 165 " =    1.997
peak=   -3.722 closest distance to " CH2 TRP A 179 " =    1.182
peak=   -3.712 closest distance to " CG  MET A  93 " =    2.542
peak=   -3.700 closest distance to " CA  SER A 276 " =    1.523
peak=   -3.697 closest distance to " CB  SER A 146 " =    2.200
peak=   -3.658 closest distance to " O   HOH Z 377 " =    2.199
peak=   -3.657 closest distance to " O   HOH Z  19 " =    2.303
peak=   -3.656 closest distance to " C   ALA A 158 " =    1.303
peak=   -3.656 closest distance to " C   ASN A 285 " =    2.444
peak=   -3.653 closest distance to " O   HOH Z 234 " =    4.333
peak=   -3.652 closest distance to " ND2 ASN A  45 " =    1.893
peak=   -3.650 closest distance to " CD2 LEU A 300 " =    2.900
peak=   -3.638 closest distance to " O   PHE A 218 " =    1.468
peak=   -3.635 closest distance to " O   HOH Z 117 " =    4.535
peak=   -3.632 closest distance to " O   HOH Z 422 " =    1.376
peak=   -3.630 closest distance to " O   HOH Z 166 " =    2.638
peak=   -3.623 closest distance to " O   HOH Z  71 " =    1.631
peak=   -3.619 closest distance to " O   HOH Z  58 " =    1.171
peak=   -3.597 closest distance to " CD1 PHE A 130 " =    2.375
peak=   -3.595 closest distance to " CD2 TYR A 293 " =    1.902
peak=   -3.593 closest distance to " OD1 ASN A 148 " =    1.629
peak=   -3.591 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.587 closest distance to " CB  ALA A  43 " =    2.517
peak=   -3.583 closest distance to " ND2 ASN A  45 " =    1.095
peak=   -3.563 closest distance to " ND2 ASN A  60 " =    1.594
peak=   -3.563 closest distance to " CB  ALA A  10 " =    2.040
peak=   -3.562 closest distance to " O   ALA A   1 " =    1.960
peak=   -3.555 closest distance to " CA  GLY A 203 " =    2.349
peak=   -3.554 closest distance to " C   SER A 206 " =    1.480
peak=   -3.547 closest distance to " O   HOH Z 407 " =    1.701
peak=   -3.546 closest distance to " O   HOH Z 308 " =    1.716
peak=   -3.535 closest distance to " OE1 GLN A 223 " =    2.380
peak=   -3.534 closest distance to " CA  GLY A 241 " =    2.289
peak=   -3.507 closest distance to " O   HOH Z 236 " =    1.687
peak=   -3.506 closest distance to " O   HOH Z   6 " =    1.525
peak=   -3.503 closest distance to " O   HOH Z  37 " =    1.819
peak=   -3.502 closest distance to " OG  SER A  26 " =    1.430
peak=   -3.498 closest distance to " OD2 ASP A 171 " =    1.867
peak=   -3.497 closest distance to " O   HOH Z 292 " =    4.575
peak=   -3.493 closest distance to " O   HOH Z 136 " =    1.896
peak=   -3.493 closest distance to " NE2 GLN A 223 " =    1.084
peak=   -3.484 closest distance to " CB  ASP A 132 " =    2.436
peak=   -3.482 closest distance to " CB  ARG A 219 " =    2.310
peak=   -3.480 closest distance to " CD2 LEU A 167 " =    1.821
peak=   -3.472 closest distance to " OG BSER A 210 " =    2.207
peak=   -3.467 closest distance to " NH2 ARG A  66 " =    1.190
peak=   -3.462 closest distance to " O   HOH Z 350 " =    1.629
peak=   -3.457 closest distance to " O   HOH Z 351 " =    1.470
peak=   -3.456 closest distance to " CB  ALA A 248 " =    2.095
peak=   -3.456 closest distance to " O   ALA A  10 " =    1.781
peak=   -3.453 closest distance to " O   HOH Z  15 " =    1.566
peak=   -3.452 closest distance to " O   HOH Z 407 " =    0.840
peak=   -3.452 closest distance to " N   THR A 235 " =    1.363
peak=   -3.443 closest distance to " O   HOH Z 150 " =    1.951
peak=   -3.442 closest distance to " CB  ASP A 162 " =    2.656
peak=   -3.437 closest distance to " C   THR A 279 " =    1.128
peak=   -3.434 closest distance to " CG  PRO A 243 " =    1.719
peak=   -3.433 closest distance to " OD1 ASN A  39 " =    2.302
peak=   -3.432 closest distance to " CD  ARG A 195 " =    5.066
peak=   -3.427 closest distance to " CE3 TRP A 274 " =    2.394
peak=   -3.420 closest distance to " CD2 PHE A 225 " =    1.324
peak=   -3.417 closest distance to " O   HOH Z 150 " =    2.119
peak=   -3.416 closest distance to " CA  GLY A 133 " =    2.327
peak=   -3.407 closest distance to " CD1 LEU A  25 " =    2.543
peak=   -3.405 closest distance to " O   HOH Z 372 " =    2.563
peak=   -3.399 closest distance to " CG  MET A 105 " =    0.909
peak=   -3.393 closest distance to " O   HOH Z 422 " =    1.596
peak=   -3.391 closest distance to " NH2 ARG A  79 " =    1.991
peak=   -3.387 closest distance to " O   HOH Z 128 " =    4.325
peak=   -3.385 closest distance to " O   HOH Z   7 " =    1.278
peak=   -3.384 closest distance to " CB  ARG A 219 " =    2.429
peak=   -3.384 closest distance to " O   HOH Z 426 " =    1.670
peak=   -3.381 closest distance to " O   ASN A 187 " =    1.614
peak=   -3.381 closest distance to " C   LEU A 143 " =    1.147
peak=   -3.379 closest distance to " CH2 TRP A 177 " =    1.917
peak=   -3.375 closest distance to " O   HOH Z  91 " =    2.128
peak=   -3.369 closest distance to " O   ALA A  34 " =    2.517
peak=   -3.360 closest distance to " CG  TRP A 266 " =    1.940
peak=   -3.358 closest distance to " O   HOH Z 418 " =    1.318
peak=   -3.358 closest distance to " OD2 ASP A 171 " =    2.308
peak=   -3.354 closest distance to " CB  ALA A 291 " =    2.492
peak=   -3.350 closest distance to " O   HOH Z 388 " =    1.980
peak=   -3.348 closest distance to " O   VAL A 189 " =    2.604
peak=   -3.344 closest distance to " CG2 VAL A 189 " =    2.197
peak=   -3.342 closest distance to " O   HOH Z 275 " =    1.535
peak=   -3.342 closest distance to " CG  GLU A 277 " =    1.134
peak=   -3.341 closest distance to " O   TRP A  92 " =    1.896
peak=   -3.341 closest distance to " O   HOH Z 171 " =    2.421
peak=   -3.341 closest distance to " O  BHOH Z 338 " =    1.150
peak=   -3.336 closest distance to " O   HOH Z  90 " =    2.003
peak=   -3.334 closest distance to " CD2 PHE A  59 " =    2.426
peak=   -3.332 closest distance to " CB  ALA A 131 " =    2.371
peak=   -3.324 closest distance to " OE2 GLU A 152 " =    2.257
peak=   -3.322 closest distance to " O   HOH Z 392 " =    1.228
peak=   -3.321 closest distance to " OG BSER A 134 " =    1.849
peak=   -3.321 closest distance to " CB  ALA A 291 " =    2.258
peak=   -3.319 closest distance to " N   THR A 157 " =    1.682
peak=   -3.315 closest distance to " CB  CYS A 254 " =    2.363
peak=   -3.312 closest distance to " O   ALA A  34 " =    2.036
peak=   -3.310 closest distance to " CD1 LEU A 228 " =    2.369
peak=   -3.310 closest distance to " NE2 GLN A 103 " =    1.712
peak=   -3.309 closest distance to " CG  ASP A 231 " =    0.809
peak=   -3.306 closest distance to " CD  PRO A 213 " =    2.250
peak=   -3.305 closest distance to " O   HOH Z 394 " =    1.578
peak=   -3.304 closest distance to " O   HOH Z   7 " =    1.776
peak=   -3.302 closest distance to " CD2 LEU A 300 " =    2.701
peak=   -3.302 closest distance to " O   HOH Z 151 " =    1.430
peak=   -3.300 closest distance to " CG2 THR A   4 " =    1.771
peak=   -3.300 closest distance to " CE2 PHE A  38 " =    1.915
peak=   -3.300 closest distance to " CG2 THR A 221 " =    2.304
peak=   -3.299 closest distance to " O   HOH Z 298 " =    2.942
peak=   -3.291 closest distance to " CD  ARG A 139 " =    1.549
peak=   -3.290 closest distance to " ND2 ASN A  69 " =    1.462
peak=   -3.287 closest distance to " CG1 VAL A  78 " =    2.684
peak=   -3.286 closest distance to " CG  GLN A  58 " =    1.248
peak=   -3.283 closest distance to " CB  ALA A 161 " =    2.613
peak=   -3.282 closest distance to " CG1 VAL A 197 " =    2.324
peak=   -3.280 closest distance to " CG2AVAL A  41 " =    2.898
peak=   -3.277 closest distance to " O   HOH Z 414 " =    1.489
peak=   -3.277 closest distance to " O   HOH Z 166 " =    2.114
peak=   -3.276 closest distance to " O   SER A 210 " =    1.715
peak=   -3.274 closest distance to " CG  GLU A  53 " =    1.448
peak=   -3.265 closest distance to " O   HOH Z 397 " =    1.132
peak=   -3.260 closest distance to " O   HOH Z 174 " =    1.949
peak=   -3.259 closest distance to " O   HOH Z  17 " =    1.261
peak=   -3.254 closest distance to " NH1 ARG A 195 " =    1.106
peak=   -3.248 closest distance to " O   VAL A 174 " =    2.167
peak=   -3.248 closest distance to " CE3 TRP A 150 " =    2.177
peak=   -3.247 closest distance to " CA  GLY A 241 " =    3.193
peak=   -3.247 closest distance to " O   HOH Z 198 " =    2.480
peak=   -3.245 closest distance to " CG2 ILE A 263 " =    2.315
peak=   -3.242 closest distance to " O   HOH Z  78 " =    1.691
peak=   -3.239 closest distance to " C   ARG A  79 " =    2.706
peak=   -3.233 closest distance to " O   HOH Z 417 " =    2.683
peak=   -3.231 closest distance to " O   HOH Z 128 " =    2.629
peak=   -3.226 closest distance to " NH2BARG A 145 " =    2.399
peak=   -3.223 closest distance to " O   HOH Z 106 " =    2.261
peak=   -3.223 closest distance to " O   HOH Z 146 " =    1.553
peak=   -3.217 closest distance to " O   HOH Z 378 " =    1.267
peak=   -3.216 closest distance to " CD  GLN A 223 " =    0.893
peak=   -3.214 closest distance to " CB  PHE A 283 " =    2.967
peak=   -3.213 closest distance to " NH2 ARG A 159 " =    2.423
peak=   -3.209 closest distance to " CD2 LEU A 237 " =    2.793
peak=   -3.208 closest distance to " O   HOH Z 126 " =    2.017
peak=   -3.207 closest distance to " NH2 ARG A  66 " =    4.247
peak=   -3.205 closest distance to " NE2 GLN A  94 " =    1.821
peak=   -3.205 closest distance to " CA  VAL A 197 " =    0.949
peak=   -3.201 closest distance to " N   GLN A  58 " =    1.436
peak=   -3.200 closest distance to " O   HOH Z  88 " =    2.476
peak=   -3.200 closest distance to " CD2 PHE A  61 " =    2.005
peak=   -3.197 closest distance to " OG  SER A  62 " =    1.468
peak=   -3.195 closest distance to " ND2 ASN A 249 " =    2.202
peak=   -3.195 closest distance to " OE2 GLU A   2 " =    1.534
peak=   -3.194 closest distance to " O   HOH Z  40 " =    3.051
peak=   -3.191 closest distance to " CZ  TYR A 169 " =    1.893
peak=   -3.186 closest distance to " CG2BVAL A  41 " =    1.425
peak=   -3.183 closest distance to " O   HOH Z 396 " =    1.685
peak=   -3.182 closest distance to " CD1 TRP A 179 " =    0.994
peak=   -3.182 closest distance to " OH  TYR A 169 " =    0.946
peak=   -3.180 closest distance to " CB  PRO A 163 " =    2.624
peak=   -3.177 closest distance to " OG  SER A  87 " =    1.610
peak=   -3.176 closest distance to " O   HOH Z 384 " =    2.041
peak=   -3.175 closest distance to " SG ACYS A 201 " =    1.962
peak=   -3.174 closest distance to " N   ALA A 226 " =    2.004
peak=   -3.174 closest distance to " O   HOH Z 385 " =    3.881
peak=   -3.172 closest distance to " CG  LYS A 119 " =    2.946
peak=   -3.170 closest distance to " O   SER A   3 " =    1.218
peak=   -3.170 closest distance to " ND2 ASN A  60 " =    1.835
peak=   -3.167 closest distance to " O   HOH Z  43 " =    1.382
peak=   -3.164 closest distance to " O   HOH Z 111 " =    1.961
peak=   -3.164 closest distance to " CE2 PHE A  61 " =    2.627
peak=   -3.159 closest distance to " OE1 GLN A  88 " =    1.383
peak=   -3.157 closest distance to " CG2BVAL A  41 " =    1.845
peak=   -3.144 closest distance to " O   HOH Z  48 " =    1.006
peak=   -3.141 closest distance to " O   HOH Z 139 " =    3.193
peak=   -3.140 closest distance to " CB  ALA A 291 " =    2.326
peak=   -3.138 closest distance to " O   HOH Z 252 " =    3.730
peak=   -3.137 closest distance to " CB  ASP A 286 " =    2.054
peak=   -3.136 closest distance to " OE1 GLN A 223 " =    2.166
peak=   -3.134 closest distance to " CG1 VAL A 112 " =    2.419
peak=   -3.129 closest distance to " O   GLY A 118 " =    2.330
peak=   -3.129 closest distance to " O   ASN A 301 " =    1.276
peak=   -3.123 closest distance to " O   HOH Z 157 " =    3.624
peak=   -3.119 closest distance to " O   HOH Z 191 " =    5.896
peak=   -3.116 closest distance to " OG ASER A 134 " =    1.253
peak=   -3.116 closest distance to " O   PRO A 198 " =    1.300
peak=   -3.103 closest distance to " O   HOH Z 177 " =    1.924
peak=   -3.094 closest distance to " O   HOH Z  77 " =    2.018
peak=   -3.092 closest distance to " O   HOH Z 134 " =    2.119
peak=   -3.087 closest distance to " O   HOH Z 424 " =    3.027
peak=   -3.086 closest distance to " CB  TRP A  85 " =    2.496
peak=   -3.079 closest distance to " CG  GLN A  11 " =    1.460
peak=   -3.066 closest distance to " NH2BARG A 275 " =    1.784
peak=   -3.064 closest distance to " CG  ASN A 301 " =    1.939
peak=   -3.059 closest distance to " C   TRP A 274 " =    1.385
peak=   -3.057 closest distance to " OG1 THR A  82 " =    1.582
peak=   -3.056 closest distance to " O   HOH Z 380 " =    4.533
peak=   -3.049 closest distance to " N   ASP A 272 " =    1.223
peak=   -3.020 closest distance to " O   HOH Z 118 " =    1.564
peak=   -3.009 closest distance to " CG  PRO A 163 " =    2.235

================= 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    :  0.4251 0.4054   6.243219e+00   6.201997e+00
   1_bss:  0.4129 0.3947   6.231201e+00   6.186145e+00
   1_xyz:  0.3283 0.3604   6.063276e+00   6.124089e+00
   1_adp:  0.3036 0.3676   6.019266e+00   6.130709e+00
   1_occ:  0.3035 0.3667   6.018075e+00   6.129821e+00
   2_bss:  0.3027 0.3640   6.018950e+00   6.129418e+00
   2_xyz:  0.2417 0.2879   5.802345e+00   5.941003e+00
   2_adp:  0.2217 0.2788   5.749903e+00   5.914710e+00
   2_occ:  0.2216 0.2785   5.749398e+00   5.914226e+00
   3_bss:  0.2212 0.2772   5.747726e+00   5.911925e+00
   3_xyz:  0.1774 0.2223   5.537860e+00   5.723753e+00
   3_adp:  0.1651 0.2104   5.479052e+00   5.674210e+00
   3_occ:  0.1649 0.2104   5.478590e+00   5.673755e+00
   4_bss:  0.1652 0.2105   5.480389e+00   5.674009e+00
   4_xyz:  0.1356 0.1838   5.310393e+00   5.535752e+00
   4_adp:  0.1281 0.1782   5.266765e+00   5.500694e+00
   4_occ:  0.1281 0.1780   5.266535e+00   5.500683e+00
   5_bss:  0.1285 0.1784   5.268543e+00   5.501685e+00
   5_xyz:  0.1177 0.1704   5.207998e+00   5.457926e+00
   5_adp:  0.1162 0.1664   5.193126e+00   5.439499e+00
   5_occ:  0.1161 0.1666   5.193021e+00   5.439985e+00
   5_bss:  0.1160 0.1666   5.192933e+00   5.439927e+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:  0.288  28.688  -2.338   5.710  -1.864   0.000  -0.000  -0.000
   1_xyz:  0.288  28.688  -2.338   5.710  -1.864   0.000  -0.000  -0.000
   1_adp:  0.288  28.688  -2.338   5.710  -1.864   0.000  -0.000  -0.000
   1_occ:  0.288  28.688  -2.338   5.710  -1.864   0.000  -0.000  -0.000
   2_bss:  0.307  49.181  -1.372   3.113  -0.593   0.000  -0.000  -0.000
   2_xyz:  0.307  49.181  -1.372   3.113  -0.593   0.000  -0.000  -0.000
   2_adp:  0.307  49.181  -1.372   3.113  -0.593   0.000  -0.000  -0.000
   2_occ:  0.307  49.181  -1.372   3.113  -0.593   0.000  -0.000  -0.000
   3_bss:  0.318  62.898  -1.013   1.569  -0.268   0.000  -0.000  -0.000
   3_xyz:  0.318  62.898  -1.013   1.569  -0.268   0.000  -0.000  -0.000
   3_adp:  0.318  62.898  -1.013   1.569  -0.268   0.000  -0.000  -0.000
   3_occ:  0.318  62.898  -1.013   1.569  -0.268   0.000  -0.000  -0.000
   4_bss:  0.326  71.563  -1.375   0.405  -0.472   0.000  -0.000  -0.000
   4_xyz:  0.326  71.563  -1.375   0.405  -0.472   0.000  -0.000  -0.000
   4_adp:  0.326  71.563  -1.375   0.405  -0.472   0.000  -0.000  -0.000
   4_occ:  0.326  71.563  -1.375   0.405  -0.472   0.000  -0.000  -0.000
   5_bss:  0.329  72.078  -1.345  -0.099  -0.371  -0.000  -0.000  -0.000
   5_xyz:  0.329  72.078  -1.345  -0.099  -0.371  -0.000  -0.000  -0.000
   5_adp:  0.329  72.078  -1.345  -0.099  -0.371  -0.000  -0.000  -0.000
   5_occ:  0.329  72.078  -1.345  -0.099  -0.371  -0.000  -0.000  -0.000
   5_bss:  0.325  67.311  -1.214  -0.256  -0.238  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.103 0.5843  0.7550    51867.739
   1_bss:  44.254 0.5932  0.7754    48431.073
   1_xyz:  41.036 0.6302  0.8114    39471.839
   1_adp:  41.578 0.6232  0.7910    40067.537
   1_occ:  41.514 0.6240  0.7911    39933.102
   2_bss:  41.221 0.6277  0.7972    39652.900
   2_xyz:  30.557 0.7506  0.9206    22439.334
   2_adp:  28.963 0.7688  0.9215    20906.085
   2_occ:  28.941 0.7691  0.9214    20867.984
   3_bss:  28.757 0.7710  0.9159    20643.860
   3_xyz:  22.332 0.8383  0.9697    13070.117
   3_adp:  20.714 0.8549  0.9701    11776.623
   3_occ:  20.701 0.8551  0.9703    11773.104
   4_bss:  20.663 0.8555  0.9519    11757.412
   4_xyz:  17.439 0.8852  0.9702     8646.231
   4_adp:  16.529 0.8937  0.9670     8107.394
   4_occ:  16.526 0.8937  0.9670     8105.042
   5_bss:  16.553 0.8935  0.9630     8140.356
   5_xyz:  15.603 0.9017  0.9671     7395.758
   5_adp:  15.191 0.9053  0.9613     7190.772
   5_occ:  15.199 0.9052  0.9612     7195.561
   5_bss:  15.200 0.9052  0.9624     7192.288
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7110e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7110e-01
   1_xyz:   1.592  0.013  0.098 16.242  0.006  4.116   1.3190e-01
   1_adp:   1.592  0.013  0.098 16.242  0.006  4.116   1.3190e-01
   1_occ:   1.592  0.013  0.098 16.242  0.006  4.116   1.3190e-01
   2_bss:   1.592  0.013  0.098 16.242  0.006  4.116   1.3190e-01
   2_xyz:   1.360  0.010  0.086 15.171  0.007  4.119   9.6799e-02
   2_adp:   1.360  0.010  0.086 15.171  0.007  4.119   9.6799e-02
   2_occ:   1.360  0.010  0.086 15.171  0.007  4.119   9.6799e-02
   3_bss:   1.360  0.010  0.086 15.171  0.007  4.119   9.6799e-02
   3_xyz:   1.019  0.008  0.071 14.675  0.005  4.113   6.7253e-02
   3_adp:   1.019  0.008  0.071 14.675  0.005  4.113   6.7253e-02
   3_occ:   1.019  0.008  0.071 14.675  0.005  4.113   6.7253e-02
   4_bss:   1.019  0.008  0.071 14.675  0.005  4.113   6.7253e-02
   4_xyz:   1.155  0.010  0.080 14.941  0.004  4.125   7.8886e-02
   4_adp:   1.155  0.010  0.080 14.941  0.004  4.125   7.8886e-02
   4_occ:   1.155  0.010  0.080 14.941  0.004  4.125   7.8886e-02
   5_bss:   1.155  0.010  0.080 14.941  0.004  4.125   7.8886e-02
   5_xyz:   1.196  0.012  0.086 15.181  0.005  4.134   8.5973e-02
   5_adp:   1.196  0.012  0.086 15.181  0.005  4.134   8.5973e-02
   5_occ:   1.196  0.012  0.086 15.181  0.005  4.134   8.5973e-02
   5_bss:   1.196  0.012  0.086 15.181  0.005  4.134   8.5973e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.544   2.4406e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.544   2.4406e-01
   1_xyz:  10.425  0.077  0.365 86.263  0.052  2.049   1.4566e-01
   1_adp:  10.425  0.077  0.365 86.263  0.052  2.049   1.4566e-01
   1_occ:  10.425  0.077  0.365 86.263  0.052  2.049   1.4566e-01
   2_bss:  10.425  0.077  0.365 86.263  0.052  2.049   1.4566e-01
   2_xyz:   8.390  0.054  0.272 82.950  0.079  2.218   8.8728e-02
   2_adp:   8.390  0.054  0.272 82.950  0.079  2.218   8.8728e-02
   2_occ:   8.390  0.054  0.272 82.950  0.079  2.218   8.8728e-02
   3_bss:   8.390  0.054  0.272 82.950  0.079  2.218   8.8728e-02
   3_xyz:   7.283  0.077  0.186 86.918  0.034  2.332   1.1808e-01
   3_adp:   7.283  0.077  0.186 86.918  0.034  2.332   1.1808e-01
   3_occ:   7.283  0.077  0.186 86.918  0.034  2.332   1.1808e-01
   4_bss:   7.283  0.077  0.186 86.918  0.034  2.332   1.1808e-01
   4_xyz:   8.186  0.062  0.236 83.219  0.037  2.209   8.3513e-02
   4_adp:   8.186  0.062  0.236 83.219  0.037  2.209   8.3513e-02
   4_occ:   8.186  0.062  0.236 83.219  0.037  2.209   8.3513e-02
   5_bss:   8.186  0.062  0.236 83.219  0.037  2.209   8.3513e-02
   5_xyz:   8.698  0.054  0.273 82.479  0.036  2.299   6.5085e-02
   5_adp:   8.698  0.054  0.273 82.479  0.036  2.299   6.5085e-02
   5_occ:   8.698  0.054  0.273 82.479  0.036  2.299   6.5085e-02
   5_bss:   8.698  0.054  0.273 82.479  0.036  2.299   6.5085e-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:  79.68   0.00  17.20  79.68   0.00  13.98  77.80   2.05  34.73
   1_occ:  79.68   0.00  17.20  79.68   0.00  13.98  77.80   2.05  34.73
   2_bss:  79.68   0.00  17.20  79.68   0.00  13.98  77.80   2.05  34.73
   2_xyz:  79.68   0.00  17.20  79.68   0.00  13.98  77.80   2.05  34.73
   2_adp:  85.85   0.00  17.54  85.85   0.00  13.55  83.62   0.91  39.26
   2_occ:  85.85   0.00  17.54  85.85   0.00  13.55  83.62   0.91  39.26
   3_bss:  85.85   0.00  17.54  85.85   0.00  13.55  83.62   0.91  39.26
   3_xyz:  85.85   0.00  17.54  85.85   0.00  13.55  83.62   0.91  39.26
   3_adp:  93.70   0.00  17.30  92.48   0.00  12.79  93.70   3.99  41.83
   3_occ:  93.70   0.00  17.30  92.48   0.00  12.79  93.70   3.99  41.83
   4_bss:  93.70   0.00  17.30  92.48   0.00  12.79  93.70   3.99  41.83
   4_xyz:  93.70   0.00  17.30  92.48   0.00  12.79  93.70   3.99  41.83
   4_adp: 105.33   0.00  17.15 103.08   0.00  12.30 105.33   1.84  43.51
   4_occ: 105.33   0.00  17.15 103.08   0.00  12.30 105.33   1.84  43.51
   5_bss: 105.33   0.00  17.15 103.08   0.00  12.30 105.33   1.84  43.51
   5_xyz: 105.33   0.00  17.15 103.08   0.00  12.30 105.33   1.84  43.51
   5_adp: 107.74   0.27  16.44 101.38   0.27  11.87 107.74   2.55  41.33
   5_occ: 107.74   0.27  16.44 101.38   0.27  11.87 107.74   2.55  41.33
   5_bss: 107.74   0.27  16.44 101.37   0.27  11.87 107.74   2.55  41.32
------------------------------------------------------------------------
 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:    1.592    0.011    0.366
   1_adp:    1.592    0.011    0.366
   1_occ:    1.592    0.011    0.366
   2_bss:    1.592    0.011    0.366
   2_xyz:    1.462    0.053    0.552
   2_adp:    1.462    0.053    0.552
   2_occ:    1.462    0.053    0.552
   3_bss:    1.462    0.053    0.552
   3_xyz:    1.578    0.062    0.674
   3_adp:    1.578    0.062    0.674
   3_occ:    1.578    0.062    0.674
   4_bss:    1.578    0.062    0.674
   4_xyz:    1.661    0.026    0.747
   4_adp:    1.661    0.026    0.747
   4_occ:    1.661    0.026    0.747
   5_bss:    1.661    0.026    0.747
   5_xyz:    1.572    0.018    0.779
   5_adp:    1.572    0.018    0.779
   5_occ:    1.572    0.018    0.779
   5_bss:    1.572    0.018    0.779
------------------------------------------------------------------------

CPU time actual refinement: 330.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_961/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_961/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_961/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_961/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_961/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.52 
  Macro-tasks:
    bulk solvent and scale       = 38.31  
    individual site refinement   = 129.11 
    weights calculation          = 29.30  
    collect and process          = 6.60   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.45 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 106.10 
    alpha_beta                      = 8.23   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 113.35 
    fmodel                         = 6.52   
    r_factors                      = 0.15   
    phase_errors                   = 10.95  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 249.12 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.775 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    642 calls, 105.67 s
gradients_fft:          587 calls, 100.91 s

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

# Date 2008-01-16 Time 06:04:53 PST -0800 (1200492293.03 s)
Start R-work = 0.4251, R-free = 0.4054 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1813 (no bulk solvent and anisotropic scale)

Start R-work = 0.4129, R-free = 0.3947
Final R-work = 0.1160, R-free = 0.1666