# Date 2008-01-16 Time 05:19:46 PST -0800 (1200489586.79 s)
#phil __OFF__

Command line arguments: "../691.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32468
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 691

-------------------------------------------------------------------------------
  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: (70.25, 47.3993, 88.1178, 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: 3.27, 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: (70.25, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00069
Completeness in resolution range: 0.958413
Completeness with d_max=infinity: 0.955421

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   2.0007

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: (70.25, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 2.00069
Completeness in resolution range: 0.958413
Completeness with d_max=infinity: 0.955421

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0739 -  4.2805 [2156/2183]  1938   218  10.1%
  bin  2:  4.2805 -  3.4105 [2051/2067]  1849   202   9.8%
  bin  3:  3.4105 -  2.9832 [2043/2062]  1838   205  10.0%
  bin  4:  2.9832 -  2.7122 [2011/2041]  1809   202  10.0%
  bin  5:  2.7122 -  2.5187 [2000/2019]  1797   203  10.2%
  bin  6:  2.5187 -  2.3708 [1990/2015]  1793   197   9.9%
  bin  7:  2.3708 -  2.2525 [1997/2030]  1802   195   9.8%
  bin  8:  2.2525 -  2.1548 [1970/2001]  1770   200  10.2%
  bin  9:  2.1548 -  2.0720 [1967/2009]  1772   195   9.9%
  bin 10:  2.0720 -  2.0007 [1404/2012]  1262   142  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_691/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: 0.14 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:
        1.62 -     2.28: 9
        2.28 -     2.93: 1521
        2.93 -     3.59: 4389
        3.59 -     4.24: 9066
        4.24 -     4.90: 12899
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.619 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.882 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.882 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.905 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27879 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_691/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_691/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 70.25 47.3993 88.1178 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: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3780   r_free= 0.3708   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.159121                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1398  153 0.3038 0.3042      6.4003      6.3271|
|  2:  4.7741 -  3.8094 0.99   1334  153 0.2972 0.3158      6.5851       6.649|
|  3:  3.8094 -  3.3338 0.99   1321  145 0.3452 0.3072      6.5216      6.4576|
|  4:  3.3338 -  3.0317 0.99   1305  139 0.3600 0.3819      6.3749      6.3664|
|  5:  3.0317 -  2.8159 0.99   1304  147 0.3917 0.3240      6.2324      6.1518|
|  6:  2.8159 -  2.6509 0.99   1285  148 0.3945 0.4389      6.1417      6.1301|
|  7:  2.6509 -  2.5187 0.99   1284  145 0.3903 0.3899      6.1114      6.0507|
|  8:  2.5187 -  2.4096 0.98   1300  136 0.4317 0.4123      6.1105      6.0715|
|  9:  2.4096 -  2.3171 0.98   1271  146 0.4206 0.3743      5.9979      6.0035|
| 10:  2.3171 -  2.2374 0.98   1269  141 0.4466 0.4199      6.0599      5.9847|
| 11:  2.2374 -  2.1677 0.99   1277  141 0.4460 0.4507      5.9597      5.9929|
| 12:  2.1677 -  2.1059 0.97   1264  138 0.4338 0.4416       5.899      5.9996|
| 13:  2.1059 -  2.0506 0.99   1263  141 0.4491 0.4350      5.8334      5.7829|
| 14:  2.0506 -  2.0007 0.59    755   86 0.4162 0.4327      5.7766      5.7051|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1398   153  0.78  26.88   0.85     0.80      45887.74|
|  2:  4.7741 -  3.8094  1334   153  0.81  25.36   0.95     0.88      60944.81|
|  3:  3.8094 -  3.3338  1321   145  0.75  31.11   0.94     0.88      61484.43|
|  4:  3.3338 -  3.0317  1305   139  0.70  35.12   0.94     0.84      54477.60|
|  5:  3.0317 -  2.8159  1304   147  0.65  39.90   0.96     0.80      43732.01|
|  6:  2.8159 -  2.6509  1285   148  0.61  42.96   0.94     0.77      41170.82|
|  7:  2.6509 -  2.5187  1284   145  0.61  43.29   0.98     0.77      38040.17|
|  8:  2.5187 -  2.4096  1300   136  0.61  43.28   0.94     0.79      34908.00|
|  9:  2.4096 -  2.3171  1271   146  0.61  43.20   0.97     0.82      31075.60|
| 10:  2.3171 -  2.2374  1269   141  0.61  43.58   0.98     0.81      29085.02|
| 11:  2.2374 -  2.1677  1277   141  0.56  47.28   0.96     0.78      30209.96|
| 12:  2.1677 -  2.1059  1264   138  0.53  49.95   0.98     0.75      30595.42|
| 13:  2.1059 -  2.0506  1263   141  0.49  52.95   0.96     0.70      28352.24|
| 14:  2.0506 -  2.0007   755    86  0.50  52.22   1.00     0.64      23127.47|
|alpha:            min =        0.64 max =            0.88 mean =         0.79|
|beta:             min =    23127.47 max =        61484.43 mean =     40206.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.97 mean =        40.69|
|phase err.(test): min =        0.00 max =           89.76 mean =        40.90|
|-----------------------------------------------------------------------------|

============================== 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 = 5.536011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.484   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.957536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.427   (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 |  1.619 -  1.947:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.947 -  2.275:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.275 -  2.603:       30 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.603 -  2.932:     1491 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.932 -  3.260:     1880 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.260 -  3.588:     2509 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.588 -  3.916:     4667 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.916 -  4.244:     4399 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.244 -  4.572:     5875 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.572 -  4.900:     7024 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.619 |       0.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    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: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3780   r_free= 0.3708   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.159121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3642   r_free= 0.3579   ksol= 0.31   Bsol= 58.10   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.59,-0.06,4.05,-0.00,0.00,0.00); trace/3= 0.13                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.140250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.824144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.204   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.546608              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3642      final r-factor (work) = 0.2264          |
| start r-factor (free) = 0.3579      final r-factor (free) = 0.2501          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9770 = 4.82 * 0.50 * 6.1403 + 1.00 * 0.1662                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3012 = 4.82 * 0.50 * 5.8932 + 1.00 * 0.0863                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2264      final r-factor (work) = 0.2052          |
| start r-factor (free) = 0.2501      final r-factor (free) = 0.2547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2274 = 0.55 * 1.00 * 5.8932 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1023 = 0.55 * 1.00 * 5.6541 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.96   17.42    None  None   None       |
|    all(noH): 2823   0      0.00    79.96   17.42    None  None   None       |
|    Sol.    : 438    0      4.67    79.96   40.73    None  None   None       |
|    Mac.    : 2385   0      0.00    74.09   13.14    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 -   7.996:  633   |   5:    39.979 -  47.975:   86        |
|      1:     7.996 -  15.992: 1207   |   6:    47.975 -  55.971:   96        |
|      2:    15.992 -  23.988:  406   |   7:    55.971 -  63.967:   43        |
|      3:    23.988 -  31.983:  172   |   8:    63.967 -  71.963:   35        |
|      4:    31.983 -  39.979:  134   |   9:    71.963 -  79.959:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2052 r_free = 0.2547             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2050 r_free = 0.2550             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2050   r_free= 0.2550   ksol= 0.31   Bsol= 58.10   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.59,-0.06,4.05,-0.00,0.00,0.00); trace/3= 0.13                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.662286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2020   r_free= 0.2524   ksol= 0.33   Bsol= 75.22   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.16,0.77,-0.00,0.00,0.00); trace/3= -1.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.653676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.983008              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.616   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.242171              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.036  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2020      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2524      final r-factor (free) = 0.1912          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5211 = 2.98 * 0.50 * 5.6553 + 1.00 * 0.0863                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3104 = 2.98 * 0.50 * 5.5308 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1487      final r-factor (work) = 0.1409          |
| start r-factor (free) = 0.1912      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3510 = 0.24 * 1.00 * 5.5308 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3051 = 0.24 * 1.00 * 5.3501 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    80.27   17.09    None  None   None       |
|    all(noH): 2823   0      1.14    80.27   17.09    None  None   None       |
|    Sol.    : 438    0      5.44    80.27   40.43    None  None   None       |
|    Mac.    : 2385   0      1.14    74.46   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.144 -   9.057:  865   |   5:    40.709 -  48.622:   86        |
|      1:     9.057 -  16.970: 1127   |   6:    48.622 -  56.535:   90        |
|      2:    16.970 -  24.883:  316   |   7:    56.535 -  64.448:   46        |
|      3:    24.883 -  32.796:  127   |   8:    64.448 -  72.362:   27        |
|      4:    32.796 -  40.709:  129   |   9:    72.362 -  80.275:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1409 r_free = 0.1813             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1408 r_free = 0.1811             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1408   r_free= 0.1811   ksol= 0.33   Bsol= 75.22   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.16,0.77,-0.00,0.00,0.00); trace/3= -1.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.323017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1407   r_free= 0.1804   ksol= 0.34   Bsol= 73.78   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-1.49,0.08,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.320776                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.520092              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.888  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.483495              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.350  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8019 = 2.52 * 0.50 * 5.3496 + 1.00 * 0.0612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6969 = 2.52 * 0.50 * 5.2628 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1189          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 44.6560 = 8.48 * 1.00 * 5.2628 + 1.00 * 0.0093                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 44.1085 = 8.48 * 1.00 * 5.1979 + 1.00 * 0.0122                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.35   17.38    None  None   None       |
|    all(noH): 2823   0      0.00    90.35   17.38    None  None   None       |
|    Sol.    : 438    0      5.30    90.35   42.84    None  None   None       |
|    Mac.    : 2385   0      0.00    90.00   12.70    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 -   9.035:  940   |   5:    45.176 -  54.211:   89        |
|      1:     9.035 -  18.070: 1153   |   6:    54.211 -  63.246:   84        |
|      2:    18.070 -  27.105:  254   |   7:    63.246 -  72.281:   40        |
|      3:    27.105 -  36.141:  126   |   8:    72.281 -  81.316:   26        |
|      4:    36.141 -  45.176:  101   |   9:    81.316 -  90.351:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1189 r_free = 0.1656             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1656             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1656   ksol= 0.34   Bsol= 73.78   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-1.49,0.08,-0.00,0.00,0.00); trace/3= -1.33                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.198622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1654   ksol= 0.33   Bsol= 70.30   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.43,0.02,-0.00,0.00,0.00); trace/3= -1.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.198298                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.793642              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.591  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.626  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3260 = 2.79 * 0.50 * 5.1979 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3075 = 2.79 * 0.50 * 5.1808 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4525 = 0.66 * 1.00 * 5.1808 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4436 = 0.66 * 1.00 * 5.1689 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.74   16.92    None  None   None       |
|    all(noH): 2823   0      0.00    91.74   16.92    None  None   None       |
|    Sol.    : 438    0      4.67    90.93   41.43    None  None   None       |
|    Mac.    : 2385   0      0.00    91.74   12.42    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 -   9.174: 1005   |   5:    45.872 -  55.046:   91        |
|      1:     9.174 -  18.349: 1124   |   6:    55.046 -  64.220:   71        |
|      2:    18.349 -  27.523:  228   |   7:    64.220 -  73.395:   32        |
|      3:    27.523 -  36.697:  132   |   8:    73.395 -  82.569:   19        |
|      4:    36.697 -  45.872:  112   |   9:    82.569 -  91.743:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1612             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1613             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1613   ksol= 0.33   Bsol= 70.30   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.43,0.02,-0.00,0.00,0.00); trace/3= -1.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.163725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1606   ksol= 0.32   Bsol= 66.07   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.32,0.09,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.161961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.031916              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.704  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.009275              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9067 = 3.03 * 0.50 * 5.1690 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8865 = 3.03 * 0.50 * 5.1518 + 1.00 * 0.0766                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3623 = 2.01 * 1.00 * 5.1518 + 1.00 * 0.0109                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3623 = 2.01 * 1.00 * 5.1516 + 1.00 * 0.0113                              |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.65   16.72    None  None   None       |
|    all(noH): 2823   0      0.00    92.65   16.72    None  None   None       |
|    Sol.    : 438    0      4.40    91.57   41.24    None  None   None       |
|    Mac.    : 2385   0      0.00    92.65   12.21    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 -   9.265: 1084   |   5:    46.324 -  55.589:   91        |
|      1:     9.265 -  18.530: 1054   |   6:    55.589 -  64.853:   63        |
|      2:    18.530 -  27.794:  231   |   7:    64.853 -  74.118:   34        |
|      3:    27.794 -  37.059:  130   |   8:    74.118 -  83.383:   16        |
|      4:    37.059 -  46.324:  111   |   9:    83.383 -  92.648:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1615             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1103 r_free = 0.1615             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1615   ksol= 0.32   Bsol= 66.07   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-1.32,0.09,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.152886                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1398  153 0.0975 0.1295        5.39      5.5297|
|  2:  4.7741 -  3.8094 0.99   1334  153 0.0820 0.1095      5.4169      5.6316|
|  3:  3.8094 -  3.3338 0.99   1321  145 0.1022 0.1509      5.4558      5.8471|
|  4:  3.3338 -  3.0317 0.99   1305  139 0.1173 0.1579      5.4366      5.5963|
|  5:  3.0317 -  2.8159 0.99   1304  147 0.1316 0.1715      5.3267      5.5525|
|  6:  2.8159 -  2.6509 0.99   1285  148 0.1237 0.2095      5.2332      5.5405|
|  7:  2.6509 -  2.5187 0.99   1284  145 0.1249 0.1669       5.181      5.3485|
|  8:  2.5187 -  2.4096 0.98   1300  136 0.1123 0.1697      5.0801      5.3546|
|  9:  2.4096 -  2.3171 0.98   1271  146 0.1187 0.1915      5.0465      5.3485|
| 10:  2.3171 -  2.2374 0.98   1269  141 0.1126 0.1667      4.9893      5.2019|
| 11:  2.2374 -  2.1677 0.99   1277  141 0.1152 0.1930      4.9579      5.3074|
| 12:  2.1677 -  2.1059 0.97   1264  138 0.1137 0.1706      4.9017      5.2126|
| 13:  2.1059 -  2.0506 0.99   1263  141 0.1087 0.1792      4.7945      5.0506|
| 14:  2.0506 -  2.0007 0.59    755   86 0.0982 0.1841      4.6716      4.9933|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1398   153  0.94   9.57   0.96     0.93       7571.98|
|  2:  4.7741 -  3.8094  1334   153  0.95   7.98   1.00     0.98       9095.16|
|  3:  3.8094 -  3.3338  1321   145  0.94  11.14   1.02     1.01      10190.11|
|  4:  3.3338 -  3.0317  1305   139  0.92  13.40   1.00     0.99      10212.25|
|  5:  3.0317 -  2.8159  1304   147  0.90  15.91   0.99     0.97       8434.31|
|  6:  2.8159 -  2.6509  1285   148  0.89  16.85   0.98     0.95       7591.75|
|  7:  2.6509 -  2.5187  1284   145  0.90  16.10   0.98     0.95       6564.67|
|  8:  2.5187 -  2.4096  1300   136  0.91  15.42   0.98     0.96       5651.94|
|  9:  2.4096 -  2.3171  1271   146  0.90  16.07   0.99     0.94       5284.04|
| 10:  2.3171 -  2.2374  1269   141  0.89  16.54   0.98     0.93       4775.55|
| 11:  2.2374 -  2.1677  1277   141  0.90  16.76   0.97     0.93       4641.22|
| 12:  2.1677 -  2.1059  1264   138  0.90  16.15   0.99     0.98       4248.95|
| 13:  2.1059 -  2.0506  1263   141  0.90  16.32   0.97     0.95       3497.77|
| 14:  2.0506 -  2.0007   755    86  0.91  14.71   0.95     0.91       2659.86|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2659.86 max =        10212.25 mean =      6610.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.42|
|phase err.(test): min =        0.00 max =           88.81 mean =        13.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1613   ksol= 0.32   Bsol= 63.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.11,0.27,-0.00,0.00,0.00); trace/3= -0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.152944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1613   ksol= 0.32   Bsol= 63.47   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.11,0.27,-0.00,0.00,0.00); trace/3= -0.86                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.152944                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0739 -  4.7741 0.99   1398  153 0.0973 0.1295      5.3889      5.5294|
|  2:  4.7741 -  3.8094 0.99   1334  153 0.0819 0.1094      5.4165      5.6303|
|  3:  3.8094 -  3.3338 0.99   1321  145 0.1021 0.1510      5.4554       5.848|
|  4:  3.3338 -  3.0317 0.99   1305  139 0.1174 0.1580      5.4373      5.5969|
|  5:  3.0317 -  2.8159 0.99   1304  147 0.1316 0.1714      5.3273      5.5527|
|  6:  2.8159 -  2.6509 0.99   1285  148 0.1237 0.2097      5.2336      5.5413|
|  7:  2.6509 -  2.5187 0.99   1284  145 0.1250 0.1669      5.1815      5.3489|
|  8:  2.5187 -  2.4096 0.98   1300  136 0.1124 0.1697      5.0804      5.3546|
|  9:  2.4096 -  2.3171 0.98   1271  146 0.1186 0.1915      5.0466      5.3484|
| 10:  2.3171 -  2.2374 0.98   1269  141 0.1126 0.1667      4.9894      5.2021|
| 11:  2.2374 -  2.1677 0.99   1277  141 0.1152 0.1929      4.9578      5.3071|
| 12:  2.1677 -  2.1059 0.97   1264  138 0.1137 0.1703      4.9015      5.2118|
| 13:  2.1059 -  2.0506 0.99   1263  141 0.1086 0.1794      4.7946      5.0514|
| 14:  2.0506 -  2.0007 0.59    755   86 0.0982 0.1839      4.6721      4.9931|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0739 -  4.7741  1398   153  0.94   9.55   0.97     0.93       7558.62|
|  2:  4.7741 -  3.8094  1334   153  0.95   7.98   1.00     0.99       9085.69|
|  3:  3.8094 -  3.3338  1321   145  0.94  11.13   1.02     1.02      10187.62|
|  4:  3.3338 -  3.0317  1305   139  0.92  13.42   1.01     0.99      10222.72|
|  5:  3.0317 -  2.8159  1304   147  0.90  15.92   1.00     0.97       8445.77|
|  6:  2.8159 -  2.6509  1285   148  0.89  16.86   0.98     0.96       7597.60|
|  7:  2.6509 -  2.5187  1284   145  0.90  16.11   0.99     0.96       6572.27|
|  8:  2.5187 -  2.4096  1300   136  0.91  15.43   0.99     0.96       5654.44|
|  9:  2.4096 -  2.3171  1271   146  0.90  16.08   1.00     0.95       5287.74|
| 10:  2.3171 -  2.2374  1269   141  0.89  16.54   0.99     0.94       4772.65|
| 11:  2.2374 -  2.1677  1277   141  0.90  16.75   0.98     0.95       4637.82|
| 12:  2.1677 -  2.1059  1264   138  0.90  16.14   1.00     0.99       4247.24|
| 13:  2.1059 -  2.0506  1263   141  0.90  16.32   0.98     0.96       3498.17|
| 14:  2.0506 -  2.0007   755    86  0.91  14.71   0.96     0.92       2661.40|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2661.40 max =        10222.72 mean =      6610.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.42|
|phase err.(test): min =        0.00 max =           88.81 mean =        13.90|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.212)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.65   16.72    None  None   None       |
|    all(noH): 2823   0      0.00    92.65   16.72    None  None   None       |
|    Sol.    : 438    0      4.41    91.57   41.24    None  None   None       |
|    Mac.    : 2385   0      0.00    92.65   12.22    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:     0.003 -   9.268: 1084   |   5:    46.327 -  55.592:   91        |
|      1:     9.268 -  18.533: 1054   |   6:    55.592 -  64.856:   63        |
|      2:    18.533 -  27.797:  231   |   7:    64.856 -  74.121:   34        |
|      3:    27.797 -  37.062:  130   |   8:    74.121 -  83.386:   16        |
|      4:    37.062 -  46.327:  111   |   9:    83.386 -  92.651:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.439 - 4.957
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 292
   mapped sites are within: 0.742 - 4.957

peak=    5.530 closest distance to " O   HOH Z 113 " =    2.141
peak=    5.230 closest distance to " CB  GLN A 223 " =    1.474
peak=    4.895 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.889 closest distance to " CG  PRO A  54 " =    1.335
peak=    4.877 closest distance to " NE2 GLN A  11 " =    1.087
peak=    4.697 closest distance to " CB  ARG A  79 " =    1.379
peak=    4.685 closest distance to " CB  ARG A 190 " =    1.657
peak=    4.636 closest distance to " O   HOH Z 142 " =    1.606
peak=    4.565 closest distance to " CB  SER A  63 " =    1.164
peak=    4.546 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.545 closest distance to " CB  ARG A 275 " =    0.974
peak=    4.527 closest distance to " O   HOH Z 126 " =    1.847
peak=    4.486 closest distance to " CA  TYR A  30 " =    0.957
peak=    4.465 closest distance to " O   HOH Z 369 " =    2.282
peak=    4.410 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.396 closest distance to " C   PRO A 198 " =    1.507
peak=    4.382 closest distance to " O   HOH Z 189 " =    2.692
peak=    4.311 closest distance to " O   HOH Z 298 " =    1.904
peak=    4.272 closest distance to " O   HOH Z 427 " =    3.088
peak=    4.249 closest distance to " O   HOH Z  15 " =    2.164
peak=    4.224 closest distance to " CG  PRO A 213 " =    1.184
peak=    4.177 closest distance to " CB  GLU A 277 " =    3.738
peak=    4.163 closest distance to " O   HOH Z  78 " =    1.626
peak=    4.151 closest distance to " O   HOH Z 406 " =    1.621
peak=    4.121 closest distance to " ND2 ASN A 187 " =    1.467
peak=    4.119 closest distance to " CB  ASN A 148 " =    1.433
peak=    4.107 closest distance to " CB  GLU A 152 " =    1.172
peak=    4.102 closest distance to " O   SER A  87 " =    2.227
peak=    4.100 closest distance to " O   HOH Z  19 " =    2.156
peak=    4.092 closest distance to " CB  PRO A  54 " =    0.916
peak=    4.084 closest distance to " O   HOH Z 346 " =    1.701
peak=    4.064 closest distance to " O   HOH Z  40 " =    1.807
peak=    4.057 closest distance to " CD2 TRP A 179 " =    1.316
peak=    4.056 closest distance to " O   HOH Z 287 " =    1.920
peak=    4.054 closest distance to " CG  PRO A 198 " =    1.255
peak=    4.045 closest distance to " CE  LYS A  76 " =    0.876
peak=    4.039 closest distance to " O   HOH Z 303 " =    2.221
peak=    4.037 closest distance to " O   HOH Z 158 " =    3.151
peak=    4.032 closest distance to " CA  ALA A  51 " =    0.945
peak=    4.026 closest distance to " O   HOH Z 180 " =    2.165
peak=    4.018 closest distance to " CB  LEU A 228 " =    1.095
peak=    4.004 closest distance to " O   HOH Z 234 " =    3.815
peak=    4.002 closest distance to " CD  ARG A 269 " =    0.947
peak=    3.982 closest distance to " O   HOH Z 392 " =    2.794
peak=    3.975 closest distance to " NZ  LYS A 117 " =    3.204
peak=    3.973 closest distance to " CB  VAL A 265 " =    1.271
peak=    3.945 closest distance to " CB  TRP A 266 " =    1.028
peak=    3.943 closest distance to " O   HOH Z 265 " =    2.107
peak=    3.924 closest distance to " O   HOH Z 209 " =    2.279
peak=    3.915 closest distance to " CZ3 TRP A 266 " =    1.134
peak=    3.909 closest distance to " CA  ARG A 195 " =    1.268
peak=    3.906 closest distance to " O   HOH Z 250 " =    1.427
peak=    3.891 closest distance to " O   HOH Z 126 " =    1.649
peak=    3.882 closest distance to " CB  VAL A 202 " =    1.585
peak=    3.879 closest distance to " CG  MET A 185 " =    1.166
peak=    3.878 closest distance to " O  BHOH Z 338 " =    2.323
peak=    3.876 closest distance to " O   HOH Z 368 " =    2.195
peak=    3.871 closest distance to " CA  ASN A 215 " =    1.079
peak=    3.870 closest distance to " OG BSER A 164 " =    2.321
peak=    3.835 closest distance to " CG  ARG A  66 " =    2.414
peak=    3.831 closest distance to " CD  LYS A 166 " =    1.277
peak=    3.824 closest distance to " O   ASN A  74 " =    1.523
peak=    3.819 closest distance to " CA  ARG A  36 " =    1.108
peak=    3.815 closest distance to " O   HOH Z 133 " =    2.800
peak=    3.809 closest distance to " CG  PRO A 243 " =    1.068
peak=    3.800 closest distance to " CB  TYR A 169 " =    0.771
peak=    3.797 closest distance to " O   HOH Z 214 " =    2.241
peak=    3.792 closest distance to " CD  ARG A 159 " =    0.778
peak=    3.791 closest distance to " CG2 VAL A 257 " =    0.769
peak=    3.790 closest distance to " O   HOH Z 316 " =    3.143
peak=    3.789 closest distance to " O   HOH Z 368 " =    3.753
peak=    3.786 closest distance to " N   HIS A 108 " =    1.907
peak=    3.779 closest distance to " ND2 ASN A 249 " =    0.878
peak=    3.775 closest distance to " NH1AARG A 145 " =    1.334
peak=    3.770 closest distance to " CD1 LEU A  96 " =    0.751
peak=    3.768 closest distance to " CG  PRO A  90 " =    1.190
peak=    3.759 closest distance to " CA  TYR A  30 " =    1.049
peak=    3.744 closest distance to " CB  ASP A 140 " =    1.084
peak=    3.740 closest distance to " O   HOH Z 412 " =    3.802
peak=    3.739 closest distance to " OD1 ASN A  69 " =    2.602
peak=    3.737 closest distance to " O   HOH Z  43 " =    1.883
peak=    3.726 closest distance to " O   HOH Z 359 " =    1.578
peak=    3.718 closest distance to " CB  GLU A  46 " =    0.998
peak=    3.709 closest distance to " O   HOH Z 280 " =    2.890
peak=    3.693 closest distance to " O   HOH Z  21 " =    1.861
peak=    3.690 closest distance to " O   HOH Z 203 " =    1.689
peak=    3.683 closest distance to " O   ASN A  74 " =    2.078
peak=    3.677 closest distance to " CZ  PHE A  38 " =    1.263
peak=    3.673 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.666 closest distance to " O   HOH Z 403 " =    1.533
peak=    3.657 closest distance to " ND2 ASN A 249 " =    1.929
peak=    3.649 closest distance to " O   HOH Z  59 " =    2.225
peak=    3.647 closest distance to " O   HOH Z 423 " =    2.030
peak=    3.647 closest distance to " CA  ALA A 160 " =    0.945
peak=    3.646 closest distance to " O   HOH Z 248 " =    1.657
peak=    3.643 closest distance to " CB  GLU A 128 " =    1.028
peak=    3.642 closest distance to " O   HOH Z 147 " =    1.855
peak=    3.634 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.629 closest distance to " O   HOH Z  61 " =    1.635
peak=    3.628 closest distance to " NH2AARG A 275 " =    3.574
peak=    3.627 closest distance to " O   HOH Z   1 " =    2.240
peak=    3.602 closest distance to " CB  ASN A 148 " =    1.984
peak=    3.602 closest distance to " CD2 LEU A 297 " =    0.882
peak=    3.601 closest distance to " CB  THR A  31 " =    1.647
peak=    3.596 closest distance to " O   HOH Z 313 " =    1.956
peak=    3.595 closest distance to " CD1 LEU A 300 " =    1.157
peak=    3.573 closest distance to " O   HOH Z  97 " =    1.991
peak=    3.565 closest distance to " O   HOH Z 299 " =    4.380
peak=    3.564 closest distance to " CA  THR A 264 " =    0.960
peak=    3.562 closest distance to " O   HOH Z 193 " =    1.738
peak=    3.562 closest distance to " O   HOH Z 426 " =    1.599
peak=    3.556 closest distance to " CB  ASN A 142 " =    1.075
peak=    3.552 closest distance to " N   ASN A  39 " =    1.307
peak=    3.543 closest distance to " CG  LEU A 167 " =    1.233
peak=    3.540 closest distance to " CA  ASN A 176 " =    1.560
peak=    3.539 closest distance to " O   HOH Z 353 " =    2.648
peak=    3.535 closest distance to " O   HOH Z 430 " =    3.978
peak=    3.533 closest distance to " CA  MET A 105 " =    1.025
peak=    3.533 closest distance to " O   HOH Z 272 " =    1.866
peak=    3.533 closest distance to " O   HOH Z  80 " =    1.706
peak=    3.532 closest distance to " CA  VAL A 125 " =    1.140
peak=    3.531 closest distance to " O   HOH Z 126 " =    1.624
peak=    3.527 closest distance to " NE2 HIS A 207 " =    1.191
peak=    3.527 closest distance to " CG2AVAL A  72 " =    1.843
peak=    3.516 closest distance to " CB  GLN A  88 " =    1.187
peak=    3.514 closest distance to " CG1 ILE A  33 " =    1.214
peak=    3.512 closest distance to " O   HOH Z 128 " =    2.300
peak=    3.498 closest distance to " O   HOH Z 403 " =    1.596
peak=    3.498 closest distance to " CB  GLN A  89 " =    1.304
peak=    3.494 closest distance to " OG BSER A 134 " =    2.840
peak=    3.490 closest distance to " CB  TYR A 116 " =    0.762
peak=    3.481 closest distance to " O   HOH Z 148 " =    3.428
peak=    3.479 closest distance to " CG  GLU A  37 " =    0.911
peak=    3.477 closest distance to " CG2 VAL A 197 " =    1.127
peak=    3.477 closest distance to " NE  ARG A  79 " =    1.050
peak=    3.473 closest distance to " O   HOH Z 290 " =    0.992
peak=    3.471 closest distance to " O   HOH Z 285 " =    1.903
peak=    3.470 closest distance to " O   HOH Z 185 " =    1.869
peak=    3.465 closest distance to " O   HOH Z 294 " =    1.497
peak=    3.465 closest distance to " O   HOH Z 271 " =    2.669
peak=    3.463 closest distance to " CG  GLN A  11 " =    1.631
peak=    3.463 closest distance to " O   HOH Z 421 " =    2.087
peak=    3.462 closest distance to " CA  ALA A 154 " =    0.994
peak=    3.453 closest distance to " CA  PRO A  54 " =    1.372
peak=    3.453 closest distance to " CG2 ILE A 120 " =    1.041
peak=    3.446 closest distance to " O   HOH Z  62 " =    2.218
peak=    3.440 closest distance to " O   HOH Z 261 " =    1.880
peak=    3.427 closest distance to " CA  ASN A 127 " =    1.171
peak=    3.423 closest distance to " NZ  LYS A  48 " =    1.234
peak=    3.421 closest distance to " N   ARG A 156 " =    1.383
peak=    3.420 closest distance to " CA  ALA A 295 " =    1.086
peak=    3.417 closest distance to " CB  LEU A  83 " =    0.803
peak=    3.416 closest distance to " O   HOH Z 285 " =    2.413
peak=    3.413 closest distance to " OG  SER A  22 " =    2.715
peak=    3.411 closest distance to " O   HOH Z 193 " =    1.848
peak=    3.411 closest distance to " O   HOH Z  88 " =    3.742
peak=    3.410 closest distance to " O   HOH Z 213 " =    1.958
peak=    3.409 closest distance to " CB  ASP A 298 " =    1.182
peak=    3.404 closest distance to " CB  PRO A  90 " =    1.161
peak=    3.400 closest distance to " O   HOH Z 163 " =    1.993
peak=    3.395 closest distance to " CB  PHE A 204 " =    0.874
peak=    3.392 closest distance to " CB  THR A  52 " =    0.765
peak=    3.389 closest distance to " O   HOH Z 371 " =    3.171
peak=    3.386 closest distance to " NE2 GLN A  77 " =    3.394
peak=    3.386 closest distance to " CB  SER A 212 " =    1.099
peak=    3.383 closest distance to " CA  ALA A  21 " =    1.200
peak=    3.381 closest distance to " CG1 VAL A 153 " =    1.022
peak=    3.370 closest distance to " O   HOH Z 394 " =    3.869
peak=    3.369 closest distance to " CB  ASN A 215 " =    1.192
peak=    3.368 closest distance to " O   HOH Z 325 " =    2.400
peak=    3.367 closest distance to " O   HOH Z 383 " =    2.278
peak=    3.365 closest distance to " CA  ALA A 158 " =    1.303
peak=    3.363 closest distance to " CG  PHE A 204 " =    0.803
peak=    3.362 closest distance to " O   HOH Z 425 " =    2.052
peak=    3.360 closest distance to " CB  ASN A 110 " =    1.149
peak=    3.354 closest distance to " O   HOH Z 106 " =    4.071
peak=    3.354 closest distance to " CA  LEU A  83 " =    1.276
peak=    3.352 closest distance to " CD BLYS A 290 " =    0.968
peak=    3.349 closest distance to " O   HOH Z 422 " =    2.693
peak=    3.347 closest distance to " CA  SER A  87 " =    1.101
peak=    3.346 closest distance to " OH  TYR A 116 " =    1.083
peak=    3.346 closest distance to " NH2 ARG A 156 " =    1.156
peak=    3.346 closest distance to " O   HOH Z 365 " =    2.849
peak=    3.343 closest distance to " O   ALA A 165 " =    1.537
peak=    3.333 closest distance to " CA  TYR A 116 " =    1.359
peak=    3.326 closest distance to " O   THR A 182 " =    1.425
peak=    3.319 closest distance to " O   THR A 251 " =    1.117
peak=    3.318 closest distance to " CE1 TYR A 186 " =    1.345
peak=    3.316 closest distance to " CB  SER A   3 " =    1.334
peak=    3.313 closest distance to " CA  THR A 221 " =    1.039
peak=    3.310 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.309 closest distance to " O   HOH Z  44 " =    1.611
peak=    3.307 closest distance to " O   HOH Z 273 " =    2.850
peak=    3.304 closest distance to " O   HOH Z 391 " =    2.903
peak=    3.294 closest distance to " O   ASP A 191 " =    1.529
peak=    3.288 closest distance to " O   HOH Z 291 " =    1.499
peak=    3.288 closest distance to " OG BSER A  99 " =    2.339
peak=    3.280 closest distance to " CB  ALA A 248 " =    1.263
peak=    3.277 closest distance to " O   THR A 220 " =    1.233
peak=    3.275 closest distance to " CG  ARG A  66 " =    2.998
peak=    3.273 closest distance to " O   HOH Z  88 " =    2.506
peak=    3.273 closest distance to " CB  LYS A 117 " =    1.161
peak=    3.272 closest distance to " O   HOH Z 417 " =    3.233
peak=    3.272 closest distance to " O   HOH Z 279 " =    2.287
peak=    3.268 closest distance to " CB  ARG A 138 " =    0.969
peak=    3.264 closest distance to " O   HOH Z 402 " =    1.358
peak=    3.262 closest distance to " O   HOH Z 258 " =    2.084
peak=    3.257 closest distance to " CB  ALA A   9 " =    1.637
peak=    3.255 closest distance to " CA  ASN A 252 " =    1.932
peak=    3.253 closest distance to " CG2 ILE A  20 " =    1.309
peak=    3.252 closest distance to " O   HOH Z 361 " =    3.820
peak=    3.252 closest distance to " O   HOH Z 245 " =    1.292
peak=    3.250 closest distance to " CB  SER A 141 " =    1.035
peak=    3.248 closest distance to " CB  TRP A 179 " =    1.412
peak=    3.246 closest distance to " O   HOH Z 171 " =    2.068
peak=    3.245 closest distance to " CA  ILE A 106 " =    0.816
peak=    3.243 closest distance to " CA  ASP A 162 " =    1.064
peak=    3.243 closest distance to " CA  GLY A 241 " =    0.889
peak=    3.242 closest distance to " CA  LYS A 117 " =    1.236
peak=    3.242 closest distance to " CB  GLN A 205 " =    1.105
peak=    3.232 closest distance to " N   CYS A 260 " =    0.846
peak=    3.229 closest distance to " O   HOH Z 183 " =    1.394
peak=    3.228 closest distance to " O   HOH Z 171 " =    4.007
peak=    3.228 closest distance to " N   VAL A 265 " =    1.216
peak=    3.226 closest distance to " CB  ALA A 291 " =    1.256
peak=    3.226 closest distance to " OD2 ASP A 286 " =    3.269
peak=    3.223 closest distance to " CB  ALA A 248 " =    0.984
peak=    3.219 closest distance to " O   HOH Z 261 " =    1.733
peak=    3.216 closest distance to " O   HOH Z 305 " =    3.730
peak=    3.216 closest distance to " CG BARG A 102 " =    1.792
peak=    3.215 closest distance to " O   HOH Z  48 " =    1.655
peak=    3.209 closest distance to " O   HOH Z 116 " =    3.185
peak=    3.209 closest distance to " CB  ARG A 139 " =    0.998
peak=    3.209 closest distance to " NH2BARG A 145 " =    2.185
peak=    3.209 closest distance to " N   ASN A 127 " =    1.327
peak=    3.206 closest distance to " CG2 ILE A 234 " =    0.909
peak=    3.204 closest distance to " O   HOH Z  97 " =    2.338
peak=    3.197 closest distance to " O   TYR A 116 " =    1.366
peak=    3.197 closest distance to " CB  ALA A   1 " =    4.957
peak=    3.192 closest distance to " OD1 ASN A 301 " =    1.648
peak=    3.192 closest distance to " O   HOH Z 174 " =    2.472
peak=    3.191 closest distance to " N   PHE A 130 " =    1.236
peak=    3.188 closest distance to " CB  GLN A 103 " =    0.855
peak=    3.186 closest distance to " O   HOH Z 419 " =    1.949
peak=    3.184 closest distance to " CG2 THR A 221 " =    1.162
peak=    3.183 closest distance to " CA  GLN A  94 " =    0.746
peak=    3.183 closest distance to " CZ2 TRP A 179 " =    1.751
peak=    3.176 closest distance to " CA  ASP A 140 " =    1.357
peak=    3.173 closest distance to " CB  MET A  47 " =    0.967
peak=    3.172 closest distance to " CA  ASP A 191 " =    1.250
peak=    3.165 closest distance to " O   HOH Z 251 " =    1.570
peak=    3.163 closest distance to " CA  ALA A 233 " =    1.509
peak=    3.163 closest distance to " O   HOH Z  68 " =    2.039
peak=    3.162 closest distance to " CG  ARG A 219 " =    1.070
peak=    3.159 closest distance to " CA  ALA A 291 " =    0.742
peak=    3.159 closest distance to " O   HOH Z 116 " =    1.784
peak=    3.157 closest distance to " CE1 HIS A  81 " =    1.677
peak=    3.157 closest distance to " CD1AILE A 234 " =    0.857
peak=    3.156 closest distance to " CB  ALA A 242 " =    1.028
peak=    3.150 closest distance to " CA  ARG A 102 " =    1.104
peak=    3.150 closest distance to " OE2 GLU A  53 " =    2.043
peak=    3.149 closest distance to " OG  SER A 245 " =    1.673
peak=    3.147 closest distance to " CG  GLU A  53 " =    1.824
peak=    3.141 closest distance to " O   HOH Z  10 " =    1.777
peak=    3.141 closest distance to " CD1 ILE A 199 " =    1.044
peak=    3.137 closest distance to " CG1 ILE A  49 " =    1.580
peak=    3.133 closest distance to " O  BHOH Z  74 " =    1.360
peak=    3.133 closest distance to " O   HOH Z 357 " =    2.120
peak=    3.129 closest distance to " O   ALA A 158 " =    1.221
peak=    3.126 closest distance to " OD2 ASP A  50 " =    3.219
peak=    3.124 closest distance to " O   HOH Z 286 " =    2.262
peak=    3.122 closest distance to " O   HOH Z  20 " =    1.402
peak=    3.119 closest distance to " O   HOH Z 425 " =    1.265
peak=    3.111 closest distance to " O   HOH Z 295 " =    1.523
peak=    3.102 closest distance to " CG BARG A 275 " =    1.372
peak=    3.101 closest distance to " O   HOH Z 156 " =    2.655
peak=    3.096 closest distance to " O   HOH Z  85 " =    2.323
peak=    3.095 closest distance to " CB  ALA A 227 " =    1.106
peak=    3.083 closest distance to " OG  SER A  62 " =    2.861
peak=    3.071 closest distance to " O   HOH Z 327 " =    1.559
peak=    3.068 closest distance to " ND2 ASN A 110 " =    1.563
peak=    3.056 closest distance to " O   HOH Z 383 " =    1.683
peak=    3.051 closest distance to " CA  GLY A 211 " =    1.304
peak=    3.041 closest distance to " O   TRP A 274 " =    1.849

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.987 - 5.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 211
   mapped sites are within: 0.987 - 5.878

peak=   -4.667 closest distance to " CD  ARG A  14 " =    3.443
peak=   -4.645 closest distance to " CD  GLN A  58 " =    1.009
peak=   -4.473 closest distance to " O   HOH Z 266 " =    5.467
peak=   -4.448 closest distance to " CD  ARG A 156 " =    2.059
peak=   -4.421 closest distance to " O   VAL A  67 " =    2.706
peak=   -4.377 closest distance to " CG1 VAL A 112 " =    2.617
peak=   -4.322 closest distance to " CB  PRO A 243 " =    2.678
peak=   -4.268 closest distance to " C   HIS A 108 " =    1.105
peak=   -4.261 closest distance to " O   HOH Z 231 " =    2.354
peak=   -4.251 closest distance to " O   HOH Z 196 " =    2.085
peak=   -4.179 closest distance to " O   HOH Z  10 " =    1.512
peak=   -4.157 closest distance to " CD2 TYR A 293 " =    1.976
peak=   -4.113 closest distance to " O   HOH Z 198 " =    1.958
peak=   -4.102 closest distance to " O   HOH Z  73 " =    2.427
peak=   -4.075 closest distance to " OE1 GLN A 223 " =    2.095
peak=   -4.068 closest distance to " CD1 LEU A 101 " =    2.428
peak=   -4.055 closest distance to " CG2 ILE A  49 " =    2.760
peak=   -4.043 closest distance to " CG1 VAL A 250 " =    2.693
peak=   -4.042 closest distance to " O   ILE A 109 " =    2.620
peak=   -4.024 closest distance to " O   HOH Z 377 " =    2.135
peak=   -3.998 closest distance to " CE2 PHE A  61 " =    2.630
peak=   -3.984 closest distance to " OXT GLY A 302 " =    2.968
peak=   -3.975 closest distance to " CZ3 TRP A 179 " =    1.211
peak=   -3.956 closest distance to " OG  SER A  97 " =    2.257
peak=   -3.952 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.944 closest distance to " O   PRO A 198 " =    1.340
peak=   -3.941 closest distance to " N   ALA A  43 " =    2.574
peak=   -3.928 closest distance to " OG BSER A 134 " =    1.308
peak=   -3.859 closest distance to " CG1 VAL A 112 " =    2.804
peak=   -3.839 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.820 closest distance to " CA  VAL A  67 " =    3.014
peak=   -3.797 closest distance to " O   HOH Z 185 " =    2.345
peak=   -3.795 closest distance to " O   HOH Z 394 " =    1.533
peak=   -3.774 closest distance to " OD1 ASN A 148 " =    1.497
peak=   -3.762 closest distance to " O   HOH Z 290 " =    1.256
peak=   -3.750 closest distance to " CD  GLN A 223 " =    1.268
peak=   -3.743 closest distance to " NE2 GLN A 194 " =    1.951
peak=   -3.741 closest distance to " O   SER A 210 " =    1.918
peak=   -3.722 closest distance to " CD1 PHE A  59 " =    2.022
peak=   -3.691 closest distance to " CA  GLY A 241 " =    3.340
peak=   -3.678 closest distance to " CE  MET A 105 " =    2.420
peak=   -3.647 closest distance to " ND2 ASN A  45 " =    1.837
peak=   -3.645 closest distance to " CG  PRO A 243 " =    1.807
peak=   -3.633 closest distance to " CE3 TRP A 150 " =    2.276
peak=   -3.629 closest distance to " CG  ARG A  66 " =    2.467
peak=   -3.622 closest distance to " CD1 ILE A 151 " =    2.439
peak=   -3.620 closest distance to " O   HOH Z  71 " =    2.268
peak=   -3.618 closest distance to " CG  GLU A 277 " =    1.160
peak=   -3.614 closest distance to " N   THR A  52 " =    1.697
peak=   -3.612 closest distance to " O   HOH Z 372 " =    2.364
peak=   -3.596 closest distance to " CG  ARG A 269 " =    2.413
peak=   -3.593 closest distance to " ND2 ASN A 249 " =    2.468
peak=   -3.591 closest distance to " O   HOH Z 348 " =    2.227
peak=   -3.590 closest distance to " CB  PHE A 192 " =    2.039
peak=   -3.582 closest distance to " O   HOH Z 211 " =    1.573
peak=   -3.579 closest distance to " ND2 ASN A  45 " =    1.204
peak=   -3.571 closest distance to " CB  ALA A 248 " =    2.310
peak=   -3.560 closest distance to " CB  ASN A  39 " =    2.404
peak=   -3.559 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.556 closest distance to " NE2 GLN A  11 " =    1.781
peak=   -3.548 closest distance to " CB  ALA A 291 " =    2.398
peak=   -3.546 closest distance to " O   PHE A 218 " =    1.510
peak=   -3.545 closest distance to " O   ALA A  10 " =    1.702
peak=   -3.538 closest distance to " CA  GLY A 241 " =    2.361
peak=   -3.534 closest distance to " CG2 VAL A 189 " =    2.200
peak=   -3.525 closest distance to " O   HOH Z 114 " =    3.136
peak=   -3.522 closest distance to " NH2AARG A 275 " =    5.347
peak=   -3.520 closest distance to " O   HOH Z   6 " =    2.296
peak=   -3.511 closest distance to " O   HOH Z 166 " =    1.873
peak=   -3.507 closest distance to " CB  ALA A  43 " =    2.618
peak=   -3.501 closest distance to " O   PRO A 163 " =    2.095
peak=   -3.496 closest distance to " NE2 GLN A  88 " =    1.895
peak=   -3.493 closest distance to " CA  GLY A 203 " =    2.437
peak=   -3.477 closest distance to " O   ALA A  34 " =    2.390
peak=   -3.476 closest distance to " CG  HIS A  86 " =    1.113
peak=   -3.472 closest distance to " CZ  TYR A 169 " =    1.797
peak=   -3.471 closest distance to " O   VAL A 189 " =    2.680
peak=   -3.466 closest distance to " CB  ASP A 132 " =    2.340
peak=   -3.462 closest distance to " NH2 ARG A  79 " =    1.533
peak=   -3.458 closest distance to " C   LEU A 143 " =    1.116
peak=   -3.445 closest distance to " CG1AVAL A  41 " =    2.702
peak=   -3.442 closest distance to " O   HOH Z 357 " =    2.084
peak=   -3.440 closest distance to " OD1 ASP A 171 " =    1.583
peak=   -3.437 closest distance to " CG2 ILE A 263 " =    2.309
peak=   -3.437 closest distance to " N   ALA A 248 " =    1.664
peak=   -3.434 closest distance to " O   HOH Z 102 " =    1.489
peak=   -3.431 closest distance to " CZ  PHE A 155 " =    1.244
peak=   -3.418 closest distance to " O   HOH Z 429 " =    2.187
peak=   -3.410 closest distance to " CG  PHE A 283 " =    2.638
peak=   -3.409 closest distance to " O   HOH Z 353 " =    2.205
peak=   -3.407 closest distance to " O   HOH Z 351 " =    1.510
peak=   -3.406 closest distance to " O   HOH Z 407 " =    3.088
peak=   -3.404 closest distance to " O   HOH Z 393 " =    1.399
peak=   -3.402 closest distance to " O   HOH Z 128 " =    2.634
peak=   -3.398 closest distance to " CG1 VAL A 125 " =    1.950
peak=   -3.397 closest distance to " O   HOH Z 216 " =    1.280
peak=   -3.394 closest distance to " CD  ARG A 195 " =    5.130
peak=   -3.383 closest distance to " CB  TRP A  85 " =    2.571
peak=   -3.382 closest distance to " CG  GLU A  53 " =    1.575
peak=   -3.380 closest distance to " CE BMET A  47 " =    1.729
peak=   -3.376 closest distance to " O   HOH Z 264 " =    1.794
peak=   -3.375 closest distance to " O   HOH Z 103 " =    1.858
peak=   -3.371 closest distance to " ND2 ASN A 187 " =    1.585
peak=   -3.370 closest distance to " O   HOH Z 177 " =    1.763
peak=   -3.369 closest distance to " O   HOH Z 193 " =    1.697
peak=   -3.360 closest distance to " OD2 ASP A 191 " =    1.501
peak=   -3.360 closest distance to " C   THR A 264 " =    1.378
peak=   -3.360 closest distance to " OG BSER A 134 " =    1.975
peak=   -3.359 closest distance to " OD1 ASP A 191 " =    1.679
peak=   -3.354 closest distance to " O   HOH Z 295 " =    1.583
peak=   -3.354 closest distance to " O   HOH Z 174 " =    2.580
peak=   -3.348 closest distance to " O   HOH Z 292 " =    4.730
peak=   -3.346 closest distance to " OE1 GLN A  88 " =    1.044
peak=   -3.344 closest distance to " O   HOH Z  51 " =    1.932
peak=   -3.343 closest distance to " CG1BVAL A  41 " =    2.690
peak=   -3.331 closest distance to " O   HOH Z  60 " =    1.879
peak=   -3.329 closest distance to " O   HOH Z 389 " =    1.922
peak=   -3.325 closest distance to " O   SER A  62 " =    2.280
peak=   -3.325 closest distance to " CG2 THR A 178 " =    2.344
peak=   -3.323 closest distance to " CD  ARG A 139 " =    1.644
peak=   -3.321 closest distance to " O   HOH Z 265 " =    2.454
peak=   -3.315 closest distance to " O   HOH Z 368 " =    1.797
peak=   -3.313 closest distance to " NH2 ARG A 159 " =    2.390
peak=   -3.313 closest distance to " O   HOH Z   6 " =    1.502
peak=   -3.313 closest distance to " O   HOH Z  13 " =    1.740
peak=   -3.309 closest distance to " CD  ARG A  79 " =    1.175
peak=   -3.307 closest distance to " O   SER A 135 " =    1.437
peak=   -3.307 closest distance to " C   SER A 206 " =    1.540
peak=   -3.293 closest distance to " O   ALA A 161 " =    1.775
peak=   -3.291 closest distance to " NE2 GLN A  88 " =    1.151
peak=   -3.290 closest distance to " O   HOH Z  38 " =    1.581
peak=   -3.289 closest distance to " CB  ASP A 286 " =    2.191
peak=   -3.285 closest distance to " CB  PHE A  16 " =    2.488
peak=   -3.284 closest distance to " O   HOH Z 106 " =    1.974
peak=   -3.279 closest distance to " O   HOH Z 171 " =    2.110
peak=   -3.277 closest distance to " N   ALA A 226 " =    2.068
peak=   -3.273 closest distance to " CZ  PHE A  59 " =    1.754
peak=   -3.266 closest distance to " OE1 GLN A 183 " =    1.581
peak=   -3.265 closest distance to " CA  GLY A 133 " =    2.365
peak=   -3.261 closest distance to " O   HOH Z 421 " =    3.358
peak=   -3.257 closest distance to " CE3 TRP A 274 " =    2.472
peak=   -3.255 closest distance to " O   HOH Z 111 " =    1.816
peak=   -3.252 closest distance to " O   PRO A 198 " =    1.719
peak=   -3.251 closest distance to " CD1 LEU A   5 " =    2.537
peak=   -3.247 closest distance to " O   GLY A  17 " =    1.143
peak=   -3.237 closest distance to " O   HOH Z 236 " =    1.533
peak=   -3.236 closest distance to " O   HOH Z 311 " =    3.800
peak=   -3.235 closest distance to " O   HOH Z 275 " =    1.538
peak=   -3.225 closest distance to " O   HOH Z  78 " =    1.874
peak=   -3.225 closest distance to " O   HOH Z 426 " =    1.639
peak=   -3.223 closest distance to " CG  MET A 105 " =    0.987
peak=   -3.221 closest distance to " CD  PRO A 213 " =    2.149
peak=   -3.218 closest distance to " C   GLY A 262 " =    2.085
peak=   -3.216 closest distance to " O   HOH Z 435 " =    2.771
peak=   -3.212 closest distance to " O   VAL A 189 " =    1.677
peak=   -3.212 closest distance to " O   HOH Z 174 " =    3.832
peak=   -3.211 closest distance to " CG1 VAL A 265 " =    2.508
peak=   -3.208 closest distance to " O   HOH Z 126 " =    1.962
peak=   -3.204 closest distance to " CB  ALA A 114 " =    2.533
peak=   -3.203 closest distance to " CG  LEU A  83 " =    2.044
peak=   -3.203 closest distance to " CZ  PHE A  38 " =    1.982
peak=   -3.203 closest distance to " CA  PRO A 243 " =    2.444
peak=   -3.195 closest distance to " O   HOH Z 252 " =    3.861
peak=   -3.192 closest distance to " O   SER A  95 " =    1.705
peak=   -3.192 closest distance to " N   SER A 276 " =    1.407
peak=   -3.189 closest distance to " CE3 TRP A  70 " =    1.746
peak=   -3.183 closest distance to " O   TYR A 186 " =    1.792
peak=   -3.181 closest distance to " OD2 ASP A 270 " =    1.176
peak=   -3.175 closest distance to " O   HOH Z 292 " =    1.824
peak=   -3.175 closest distance to " CD2 TYR A 247 " =    2.420
peak=   -3.171 closest distance to " NE2 GLN A 223 " =    1.552
peak=   -3.171 closest distance to " OD1 ASN A 173 " =    1.407
peak=   -3.170 closest distance to " O   HOH Z 359 " =    3.025
peak=   -3.168 closest distance to " O   HOH Z  52 " =    1.613
peak=   -3.168 closest distance to " O   HOH Z 191 " =    5.878
peak=   -3.163 closest distance to " CB  TYR A  15 " =    2.252
peak=   -3.160 closest distance to " O   HOH Z 166 " =    1.570
peak=   -3.158 closest distance to " O   HOH Z 116 " =    1.444
peak=   -3.140 closest distance to " O   HOH Z 322 " =    1.710
peak=   -3.139 closest distance to " O   SER A 276 " =    1.669
peak=   -3.137 closest distance to " O   HOH Z 139 " =    3.013
peak=   -3.134 closest distance to " CD  PRO A 243 " =    2.160
peak=   -3.132 closest distance to " O   HOH Z 262 " =    2.811
peak=   -3.132 closest distance to " O   HOH Z 323 " =    1.531
peak=   -3.126 closest distance to " O   HOH Z 156 " =    3.572
peak=   -3.126 closest distance to " O   HOH Z 234 " =    4.303
peak=   -3.124 closest distance to " C   ALA A 158 " =    1.394
peak=   -3.124 closest distance to " CD1 TRP A  70 " =    1.063
peak=   -3.124 closest distance to " O   HOH Z 357 " =    2.260
peak=   -3.123 closest distance to " CG2 VAL A 189 " =    1.907
peak=   -3.122 closest distance to " OD2 ASP A 171 " =    1.794
peak=   -3.120 closest distance to " NE2 GLN A 278 " =    1.645
peak=   -3.120 closest distance to " CD2 HIS A 207 " =    2.331
peak=   -3.112 closest distance to " O   GLN A 240 " =    2.541
peak=   -3.111 closest distance to " CB  ALA A  10 " =    2.259
peak=   -3.109 closest distance to " O   ALA A 292 " =    2.077
peak=   -3.108 closest distance to " O   HOH Z 278 " =    1.704
peak=   -3.107 closest distance to " ND2 ASN A  60 " =    1.285
peak=   -3.103 closest distance to " OG BSER A 210 " =    2.064
peak=   -3.095 closest distance to " OD1 ASN A 301 " =    2.011
peak=   -3.089 closest distance to " O   HOH Z 317 " =    2.220
peak=   -3.074 closest distance to " O   HOH Z 283 " =    5.449
peak=   -3.073 closest distance to " O   HOH Z 145 " =    2.866
peak=   -3.069 closest distance to " CG  ASN A 148 " =    2.420
peak=   -3.068 closest distance to " O   GLY A  80 " =    2.592
peak=   -3.064 closest distance to " O   HOH Z 139 " =    4.873
peak=   -3.064 closest distance to " CD1 ILE A 199 " =    2.554
peak=   -3.060 closest distance to " CA  HIS A  86 " =    2.322
peak=   -3.058 closest distance to " CG2BVAL A  41 " =    2.089
peak=   -3.052 closest distance to " CA  GLY A 241 " =    2.890
peak=   -3.046 closest distance to " O   TRP A  92 " =    1.942

================= 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    :  0.3780 0.3708   6.159121e+00   6.136080e+00
   1_bss:  0.3642 0.3579   6.140250e+00   6.114658e+00
   1_xyz:  0.2264 0.2501   5.717800e+00   5.803336e+00
   1_adp:  0.2052 0.2547   5.662418e+00   5.823950e+00
   1_occ:  0.2050 0.2550   5.662286e+00   5.825089e+00
   2_bss:  0.2020 0.2524   5.653676e+00   5.818825e+00
   2_xyz:  0.1487 0.1912   5.374836e+00   5.573129e+00
   2_adp:  0.1409 0.1813   5.324088e+00   5.522096e+00
   2_occ:  0.1408 0.1811   5.323017e+00   5.521094e+00
   3_bss:  0.1407 0.1804   5.320776e+00   5.517896e+00
   3_xyz:  0.1230 0.1657   5.215985e+00   5.433270e+00
   3_adp:  0.1189 0.1656   5.198570e+00   5.430006e+00
   3_occ:  0.1188 0.1656   5.198622e+00   5.430170e+00
   4_bss:  0.1187 0.1654   5.198298e+00   5.430128e+00
   4_xyz:  0.1143 0.1634   5.171929e+00   5.416417e+00
   4_adp:  0.1135 0.1612   5.163669e+00   5.407942e+00
   4_occ:  0.1134 0.1613   5.163725e+00   5.408294e+00
   5_bss:  0.1133 0.1606   5.161961e+00   5.404841e+00
   5_xyz:  0.1105 0.1614   5.153925e+00   5.408083e+00
   5_adp:  0.1104 0.1615   5.152845e+00   5.409268e+00
   5_occ:  0.1103 0.1615   5.152886e+00   5.409379e+00
   5_bss:  0.1102 0.1613   5.152944e+00   5.409441e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.310  58.105  -3.592  -0.061   4.050  -0.000   0.000   0.000
   1_xyz:  0.310  58.105  -3.592  -0.061   4.050  -0.000   0.000   0.000
   1_adp:  0.310  58.105  -3.592  -0.061   4.050  -0.000   0.000   0.000
   1_occ:  0.310  58.105  -3.592  -0.061   4.050  -0.000   0.000   0.000
   2_bss:  0.333  75.221  -2.906  -1.164   0.772  -0.000   0.000   0.000
   2_xyz:  0.333  75.221  -2.906  -1.164   0.772  -0.000   0.000   0.000
   2_adp:  0.333  75.221  -2.906  -1.164   0.772  -0.000   0.000   0.000
   2_occ:  0.333  75.221  -2.906  -1.164   0.772  -0.000   0.000   0.000
   3_bss:  0.335  73.781  -2.565  -1.493   0.080  -0.000   0.000   0.000
   3_xyz:  0.335  73.781  -2.565  -1.493   0.080  -0.000   0.000   0.000
   3_adp:  0.335  73.781  -2.565  -1.493   0.080  -0.000   0.000   0.000
   3_occ:  0.335  73.781  -2.565  -1.493   0.080  -0.000   0.000   0.000
   4_bss:  0.329  70.298  -2.219  -1.427   0.022  -0.000   0.000   0.000
   4_xyz:  0.329  70.298  -2.219  -1.427   0.022  -0.000   0.000   0.000
   4_adp:  0.329  70.298  -2.219  -1.427   0.022  -0.000   0.000   0.000
   4_occ:  0.329  70.298  -2.219  -1.427   0.022  -0.000   0.000   0.000
   5_bss:  0.324  66.071  -2.004  -1.316   0.092  -0.000   0.000   0.000
   5_xyz:  0.324  66.071  -2.004  -1.316   0.092  -0.000   0.000   0.000
   5_adp:  0.324  66.071  -2.004  -1.316   0.092  -0.000   0.000   0.000
   5_occ:  0.324  66.071  -2.004  -1.316   0.092  -0.000   0.000   0.000
   5_bss:  0.320  63.475  -1.749  -1.113   0.271  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.715 0.6361  0.7921    40204.814
   1_bss:  39.523 0.6486  0.8140    37049.400
   1_xyz:  24.940 0.8128  0.9722    16141.607
   1_adp:  25.792 0.8031  0.9596    17001.957
   1_occ:  25.839 0.8025  0.9586    17032.482
   2_bss:  25.319 0.8084  0.9271    16700.139
   2_xyz:  18.437 0.8759  0.9710     9444.377
   2_adp:  17.014 0.8896  0.9682     8529.871
   2_occ:  16.985 0.8898  0.9683     8509.853
   3_bss:  16.876 0.8908  0.9616     8428.391
   3_xyz:  15.077 0.9061  0.9703     7072.137
   3_adp:  14.931 0.9076  0.9605     6965.967
   3_occ:  14.934 0.9076  0.9604     6964.412
   4_bss:  14.926 0.9077  0.9647     6963.895
   4_xyz:  14.593 0.9104  0.9679     6740.928
   4_adp:  14.374 0.9122  0.9616     6628.606
   4_occ:  14.377 0.9122  0.9615     6630.550
   5_bss:  14.329 0.9126  0.9660     6556.098
   5_xyz:  14.370 0.9123  0.9661     6614.920
   5_adp:  14.370 0.9123  0.9579     6610.144
   5_occ:  14.370 0.9124  0.9577     6609.587
   5_bss:  14.372 0.9123  0.9650     6610.195
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6617e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6617e-01
   1_xyz:   1.272  0.010  0.079 15.164  0.005  4.115   8.6277e-02
   1_adp:   1.272  0.010  0.079 15.164  0.005  4.115   8.6277e-02
   1_occ:   1.272  0.010  0.079 15.164  0.005  4.115   8.6277e-02
   2_bss:   1.272  0.010  0.079 15.164  0.005  4.115   8.6277e-02
   2_xyz:   1.049  0.007  0.075 14.634  0.004  4.131   6.1195e-02
   2_adp:   1.049  0.007  0.075 14.634  0.004  4.131   6.1195e-02
   2_occ:   1.049  0.007  0.075 14.634  0.004  4.131   6.1195e-02
   3_bss:   1.049  0.007  0.075 14.634  0.004  4.131   6.1195e-02
   3_xyz:   1.059  0.009  0.079 14.638  0.004  4.140   6.5535e-02
   3_adp:   1.059  0.009  0.079 14.638  0.004  4.140   6.5535e-02
   3_occ:   1.059  0.009  0.079 14.638  0.004  4.140   6.5535e-02
   4_bss:   1.059  0.009  0.079 14.638  0.004  4.140   6.5535e-02
   4_xyz:   1.082  0.010  0.082 14.603  0.004  4.118   7.0751e-02
   4_adp:   1.082  0.010  0.082 14.603  0.004  4.118   7.0751e-02
   4_occ:   1.082  0.010  0.082 14.603  0.004  4.118   7.0751e-02
   5_bss:   1.082  0.010  0.082 14.603  0.004  4.118   7.0751e-02
   5_xyz:   1.117  0.011  0.086 14.674  0.004  4.122   7.6589e-02
   5_adp:   1.117  0.011  0.086 14.674  0.004  4.122   7.6589e-02
   5_occ:   1.117  0.011  0.086 14.674  0.004  4.122   7.6589e-02
   5_bss:   1.117  0.011  0.086 14.674  0.004  4.122   7.6589e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.619   2.4386e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.619   2.4386e-01
   1_xyz:   8.896  0.053  0.321 83.770  0.047  2.200   1.1377e-01
   1_adp:   8.896  0.053  0.321 83.770  0.047  2.200   1.1377e-01
   1_occ:   8.896  0.053  0.321 83.770  0.047  2.200   1.1377e-01
   2_bss:   8.896  0.053  0.321 83.770  0.047  2.200   1.1377e-01
   2_xyz:   7.208  0.036  0.230 83.777  0.052  2.337   4.7943e-02
   2_adp:   7.208  0.036  0.230 83.777  0.052  2.337   4.7943e-02
   2_occ:   7.208  0.036  0.230 83.777  0.052  2.337   4.7943e-02
   3_bss:   7.208  0.036  0.230 83.777  0.052  2.337   4.7943e-02
   3_xyz:   7.819  0.047  0.250 82.756  0.038  2.370   4.3987e-02
   3_adp:   7.819  0.047  0.250 82.756  0.038  2.370   4.3987e-02
   3_occ:   7.819  0.047  0.250 82.756  0.038  2.370   4.3987e-02
   4_bss:   7.819  0.047  0.250 82.756  0.038  2.370   4.3987e-02
   4_xyz:   7.841  0.050  0.281 83.309  0.040  2.352   5.0709e-02
   4_adp:   7.841  0.050  0.281 83.309  0.040  2.352   5.0709e-02
   4_occ:   7.841  0.050  0.281 83.309  0.040  2.352   5.0709e-02
   5_bss:   7.841  0.050  0.281 83.309  0.040  2.352   5.0709e-02
   5_xyz:   7.966  0.059  0.295 82.024  0.037  2.349   6.5194e-02
   5_adp:   7.966  0.059  0.295 82.024  0.037  2.349   6.5194e-02
   5_occ:   7.966  0.059  0.295 82.024  0.037  2.349   6.5194e-02
   5_bss:   7.966  0.059  0.295 82.024  0.037  2.349   6.5194e-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:  79.96   0.00  17.42  74.09   0.00  13.14  79.96   4.67  40.73
   1_occ:  79.96   0.00  17.42  74.09   0.00  13.14  79.96   4.67  40.73
   2_bss:  79.96   0.00  17.42  74.09   0.00  13.14  79.96   4.67  40.73
   2_xyz:  79.96   0.00  17.42  74.09   0.00  13.14  79.96   4.67  40.73
   2_adp:  80.27   1.14  17.09  74.46   1.14  12.80  80.27   5.44  40.43
   2_occ:  80.27   1.14  17.09  74.46   1.14  12.80  80.27   5.44  40.43
   3_bss:  80.27   1.14  17.09  74.46   1.14  12.80  80.27   5.44  40.43
   3_xyz:  80.27   1.14  17.09  74.46   1.14  12.80  80.27   5.44  40.43
   3_adp:  90.35   0.00  17.38  90.00   0.00  12.70  90.35   5.30  42.84
   3_occ:  90.35   0.00  17.38  90.00   0.00  12.70  90.35   5.30  42.84
   4_bss:  90.35   0.00  17.38  90.00   0.00  12.70  90.35   5.30  42.84
   4_xyz:  90.35   0.00  17.38  90.00   0.00  12.70  90.35   5.30  42.84
   4_adp:  91.74   0.00  16.92  91.74   0.00  12.42  90.93   4.67  41.43
   4_occ:  91.74   0.00  16.92  91.74   0.00  12.42  90.93   4.67  41.43
   5_bss:  91.74   0.00  16.92  91.74   0.00  12.42  90.93   4.67  41.43
   5_xyz:  91.74   0.00  16.92  91.74   0.00  12.42  90.93   4.67  41.43
   5_adp:  92.65   0.00  16.72  92.65   0.00  12.21  91.57   4.40  41.24
   5_occ:  92.65   0.00  16.72  92.65   0.00  12.21  91.57   4.40  41.24
   5_bss:  92.65   0.00  16.72  92.65   0.00  12.22  91.57   4.41  41.24
------------------------------------------------------------------------
 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:    1.435    0.012    0.373
   1_adp:    1.435    0.012    0.373
   1_occ:    1.435    0.012    0.373
   2_bss:    1.435    0.012    0.373
   2_xyz:    1.201    0.033    0.446
   2_adp:    1.201    0.033    0.446
   2_occ:    1.201    0.033    0.446
   3_bss:    1.201    0.033    0.446
   3_xyz:    1.180    0.017    0.498
   3_adp:    1.180    0.017    0.498
   3_occ:    1.180    0.017    0.498
   4_bss:    1.180    0.017    0.498
   4_xyz:    1.261    0.012    0.514
   4_adp:    1.261    0.012    0.514
   4_occ:    1.261    0.012    0.514
   5_bss:    1.261    0.012    0.514
   5_xyz:    1.377    0.051    0.528
   5_adp:    1.377    0.051    0.528
   5_occ:    1.377    0.051    0.528
   5_bss:    1.377    0.051    0.528
------------------------------------------------------------------------

CPU time actual refinement: 338.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_691/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_691/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_691/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_691/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_691/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.44 
  Macro-tasks:
    bulk solvent and scale       = 46.39  
    individual site refinement   = 140.58 
    weights calculation          = 28.69  
    collect and process          = 6.60   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.38 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 104.71 
    alpha_beta                      = 8.04   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.28 
    fmodel                         = 7.34   
    r_factors                      = 0.26   
    phase_errors                   = 11.15  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 250.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.702 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    657 calls, 104.37 s
gradients_fft:          602 calls, 100.86 s

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

# Date 2008-01-16 Time 05:25:38 PST -0800 (1200489938.83 s)
Start R-work = 0.3780, R-free = 0.3708 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1768 (no bulk solvent and anisotropic scale)

Start R-work = 0.3642, R-free = 0.3579
Final R-work = 0.1102, R-free = 0.1613