# Date 2008-01-16 Time 05:58:08 PST -0800 (1200491888.27 s)
#phil __OFF__

Command line arguments: "../951.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1667
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 951

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.8686, 86.39, 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: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 2.00123
Completeness in resolution range: 0.959916
Completeness with d_max=infinity: 0.956915

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   2.0012

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.8686, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 2.00123
Completeness in resolution range: 0.959916
Completeness with d_max=infinity: 0.956915

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1032 -  4.2818 [2137/2165]  1925   212   9.9%
  bin  2:  4.2818 -  3.4115 [2055/2074]  1847   208  10.1%
  bin  3:  3.4115 -  2.9841 [2039/2059]  1836   203  10.0%
  bin  4:  2.9841 -  2.7129 [2016/2041]  1818   198   9.8%
  bin  5:  2.7129 -  2.5194 [2010/2029]  1806   204  10.1%
  bin  6:  2.5194 -  2.3715 [1971/2016]  1778   193   9.8%
  bin  7:  2.3715 -  2.2531 [1976/2010]  1776   200  10.1%
  bin  8:  2.2531 -  2.1553 [1989/2024]  1786   203  10.2%
  bin  9:  2.1553 -  2.0726 [1975/2004]  1785   190   9.6%
  bin 10:  2.0726 -  2.0012 [1421/1985]  1273   148  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_951/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:
        1.59 -     2.25: 7
        2.25 -     2.92: 1432
        2.92 -     3.58: 4407
        3.58 -     4.24: 9046
        4.24 -     4.90: 13004
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.592 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.847 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.972 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.978 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27891 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_951/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_951/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.8686 86.39 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 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3903   r_free= 0.3748   ksol= 0.00   Bsol= 0.00   scale= 0.922    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.194021                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7756 0.99   1386  154 0.3206 0.3400      6.4447      6.4169|
|  2:  4.7756 -  3.8106 0.99   1349  147 0.3223 0.3359      6.6867      6.6782|
|  3:  3.8106 -  3.3348 0.99   1313  153 0.3542 0.3160      6.5549      6.4762|
|  4:  3.3348 -  3.0326 0.99   1309  139 0.3723 0.3407      6.4215      6.3213|
|  5:  3.0326 -  2.8167 0.99   1293  144 0.4054 0.3893      6.2849      6.3064|
|  6:  2.8167 -  2.6516 0.98   1292  143 0.4171 0.3839      6.1988      6.0826|
|  7:  2.6516 -  2.5194 0.99   1290  145 0.4218 0.3629      6.1697      6.0374|
|  8:  2.5194 -  2.4102 0.98   1276  144 0.4370 0.4141      6.1044      6.1011|
|  9:  2.4102 -  2.3178 0.98   1285  138 0.4397 0.4448      6.0561      6.1176|
| 10:  2.3178 -  2.2381 0.97   1260  142 0.4382 0.4154      6.0429      6.0051|
| 11:  2.2381 -  2.1683 0.99   1261  142 0.4381 0.3886      5.9863      5.9551|
| 12:  2.1683 -  2.1065 0.98   1268  137 0.4401 0.4670      5.9335      5.9742|
| 13:  2.1065 -  2.0512 0.97   1254  142 0.4388 0.4006      5.8299      5.7911|
| 14:  2.0512 -  2.0012 0.62    794   89 0.4189 0.4384      5.7592      5.7522|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7756  1386   154  0.74  30.36   0.84     0.77      56722.91|
|  2:  4.7756 -  3.8106  1349   147  0.79  27.22   0.93     0.85      67494.78|
|  3:  3.8106 -  3.3348  1313   153  0.73  32.49   0.94     0.87      68573.87|
|  4:  3.3348 -  3.0326  1309   139  0.70  35.93   0.93     0.84      59474.04|
|  5:  3.0326 -  2.8167  1293   144  0.63  41.66   0.93     0.80      49427.25|
|  6:  2.8167 -  2.6516  1292   143  0.62  42.12   0.93     0.79      41363.84|
|  7:  2.6516 -  2.5194  1290   145  0.61  42.85   0.95     0.78      37922.63|
|  8:  2.5194 -  2.4102  1276   144  0.58  46.12   0.95     0.77      37648.74|
|  9:  2.4102 -  2.3178  1285   138  0.56  47.33   0.94     0.75      36527.38|
| 10:  2.3178 -  2.2381  1260   142  0.56  47.79   0.96     0.75      34464.32|
| 11:  2.2381 -  2.1683  1261   142  0.56  47.57   0.97     0.78      31738.61|
| 12:  2.1683 -  2.1065  1268   137  0.55  48.44   0.98     0.77      29959.18|
| 13:  2.1065 -  2.0512  1254   142  0.52  50.44   0.95     0.75      26526.11|
| 14:  2.0512 -  2.0012   794    89  0.53  50.02   0.98     0.70      21912.11|
|alpha:            min =        0.70 max =            0.87 mean =         0.79|
|beta:             min =    21912.11 max =        68573.87 mean =     43726.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.94 mean =        41.76|
|phase err.(test): min =        0.00 max =           89.79 mean =        41.80|
|-----------------------------------------------------------------------------|

============================== 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 = 7.655815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.571   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.170567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.868   (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 |  1.592 -  1.923:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.923 -  2.254:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.254 -  2.584:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.584 -  2.915:     1410 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.915 -  3.246:     1870 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.246 -  3.577:     2537 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.577 -  3.908:     4622 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.908 -  4.238:     4424 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.238 -  4.569:     5919 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.569 -  4.900:     7085 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.592 |       0.194 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    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 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3903   r_free= 0.3748   ksol= 0.00   Bsol= 0.00   scale= 0.922    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.194021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3771   r_free= 0.3632   ksol= 0.29   Bsol= 38.41   scale= 0.953   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,5.16,-1.87,0.00,-0.00,-0.00); trace/3= 0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.176275                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.008790              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.390   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598180              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.791   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3771      final r-factor (work) = 0.2656          |
| start r-factor (free) = 0.3632      final r-factor (free) = 0.2921          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8148 = 7.01 * 0.50 * 6.1778 + 1.00 * 0.1654                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0108 = 7.01 * 0.50 * 5.9627 + 1.00 * 0.1152                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2656      final r-factor (work) = 0.2425          |
| start r-factor (free) = 0.2921      final r-factor (free) = 0.3001          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5729 = 0.60 * 1.00 * 5.9627 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4937 = 0.60 * 1.00 * 5.8147 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.90   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    89.90   17.22    None  None   None       |
|    Sol.    : 438    0      2.78    89.90   38.49    None  None   None       |
|    Mac.    : 2385   0      0.00    80.15   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.990:  894   |   5:    44.952 -  53.942:   91        |
|      1:     8.990 -  17.981: 1048   |   6:    53.942 -  62.933:   64        |
|      2:    17.981 -  26.971:  386   |   7:    62.933 -  71.923:   32        |
|      3:    26.971 -  35.962:  173   |   8:    71.923 -  80.913:    9        |
|      4:    35.962 -  44.952:  125   |   9:    80.913 -  89.904:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2425 r_free = 0.3001             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2423 r_free = 0.2995             target_work(ml) = 5.819         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2423   r_free= 0.2995   ksol= 0.29   Bsol= 38.41   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,5.16,-1.87,0.00,-0.00,-0.00); trace/3= 0.38                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.819466                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2398   r_free= 0.2961   ksol= 0.33   Bsol= 67.05   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,1.45,-0.99,0.00,-0.00,-0.00); trace/3= -0.43                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.812336                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.661507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.472   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.536660              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.520   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2398      final r-factor (work) = 0.1696          |
| start r-factor (free) = 0.2961      final r-factor (free) = 0.2086          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5657 = 5.66 * 0.50 * 5.8114 + 1.00 * 0.1152                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1554 = 5.66 * 0.50 * 5.6801 + 1.00 * 0.0764                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1511          |
| start r-factor (free) = 0.2086      final r-factor (free) = 0.1936          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0614 = 0.54 * 1.00 * 5.6801 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9215 = 0.54 * 1.00 * 5.4228 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    91.26   17.30    None  None   None       |
|    all(noH): 2823   0      0.36    91.26   17.30    None  None   None       |
|    Sol.    : 438    0      4.67    88.29   41.53    None  None   None       |
|    Mac.    : 2385   0      0.36    91.26   12.84    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:     0.362 -   9.451: 1007   |   5:    45.809 -  54.898:   99        |
|      1:     9.451 -  18.540: 1085   |   6:    54.898 -  63.987:   79        |
|      2:    18.540 -  27.630:  258   |   7:    63.987 -  73.077:   32        |
|      3:    27.630 -  36.719:  137   |   8:    73.077 -  82.166:   16        |
|      4:    36.719 -  45.809:  105   |   9:    82.166 -  91.256:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1511 r_free = 0.1936             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1509 r_free = 0.1935             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1509   r_free= 0.1935   ksol= 0.33   Bsol= 67.05   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,1.45,-0.99,0.00,-0.00,-0.00); trace/3= -0.43                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.389745                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.1933   ksol= 0.33   Bsol= 67.05   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-0.23,-0.89,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.387438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.479089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.063  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.737002              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.905  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1506      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1933      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5123 = 3.48 * 0.50 * 5.4244 + 1.00 * 0.0764                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3089 = 3.48 * 0.50 * 5.3088 + 1.00 * 0.0740                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9238 = 0.74 * 1.00 * 5.3088 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8630 = 0.74 * 1.00 * 5.2261 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.59   17.04    None  None   None       |
|    all(noH): 2823   0      0.00    97.59   17.04    None  None   None       |
|    Sol.    : 438    0      4.72    95.30   42.07    None  None   None       |
|    Mac.    : 2385   0      0.00    97.59   12.44    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 -   9.759: 1126   |   5:    48.795 -  58.554:   95        |
|      1:     9.759 -  19.518: 1059   |   6:    58.554 -  68.314:   65        |
|      2:    19.518 -  29.277:  201   |   7:    68.314 -  78.073:   28        |
|      3:    29.277 -  39.036:  129   |   8:    78.073 -  87.832:   10        |
|      4:    39.036 -  48.795:  106   |   9:    87.832 -  97.591:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1670             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1669             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1669   ksol= 0.33   Bsol= 67.05   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-0.23,-0.89,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1669   ksol= 0.33   Bsol= 69.54   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-0.70,-0.68,-0.00,-0.00,-0.00); trace/3= -1.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212545                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.933979              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.852  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.643892              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.310  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7415 = 2.93 * 0.50 * 5.2267 + 1.00 * 0.0740                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6913 = 2.93 * 0.50 * 5.1926 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3547 = 0.64 * 1.00 * 5.1926 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3430 = 0.64 * 1.00 * 5.1749 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.73  16.66    None  None   None       |
|    all(noH): 2823   0      0.00    101.73  16.66    None  None   None       |
|    Sol.    : 438    0      3.28    96.62   41.11    None  None   None       |
|    Mac.    : 2385   0      0.00    101.73  12.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.173: 1260   |   5:    50.863 -  61.035:   94        |
|      1:    10.173 -  20.345:  958   |   6:    61.035 -  71.208:   47        |
|      2:    20.345 -  30.518:  208   |   7:    71.208 -  81.380:   20        |
|      3:    30.518 -  40.690:  118   |   8:    81.380 -  91.553:    7        |
|      4:    40.690 -  50.863:  107   |   9:    91.553 - 101.726:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1634             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1634             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1634   ksol= 0.33   Bsol= 69.54   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-0.70,-0.68,-0.00,-0.00,-0.00); trace/3= -1.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.173843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1633   ksol= 0.32   Bsol= 66.03   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-0.70,-0.41,-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: 5.173815                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.939594              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.771  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.267261              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.960  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0929 = 1.94 * 0.50 * 5.1753 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0849 = 1.94 * 0.50 * 5.1791 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5741 = 1.27 * 1.00 * 5.1791 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5735 = 1.27 * 1.00 * 5.1782 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.89  16.44    None  None   None       |
|    all(noH): 2823   0      0.00    103.89  16.44    None  None   None       |
|    Sol.    : 438    0      4.55    97.23   41.00    None  None   None       |
|    Mac.    : 2385   0      0.00    103.89  11.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.389: 1363   |   5:    51.946 -  62.335:   94        |
|      1:    10.389 -  20.779:  871   |   6:    62.335 -  72.725:   43        |
|      2:    20.779 -  31.168:  200   |   7:    72.725 -  83.114:   16        |
|      3:    31.168 -  41.557:  119   |   8:    83.114 -  93.503:    6        |
|      4:    41.557 -  51.946:  107   |   9:    93.503 - 103.892:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1643             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1643             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1643   ksol= 0.32   Bsol= 66.03   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-0.70,-0.41,-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: 5.181099                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7756 0.99   1386  154 0.0989 0.1303      5.3849      5.5331|
|  2:  4.7756 -  3.8106 0.99   1349  147 0.0844 0.1043      5.4173      5.5927|
|  3:  3.8106 -  3.3348 0.99   1313  153 0.1039 0.1493      5.4592      5.8516|
|  4:  3.3348 -  3.0326 0.99   1309  139 0.1264 0.1651      5.4902       5.652|
|  5:  3.0326 -  2.8167 0.99   1293  144 0.1408 0.1878      5.3891      5.5834|
|  6:  2.8167 -  2.6516 0.98   1292  143 0.1319 0.2014      5.2806      5.5039|
|  7:  2.6516 -  2.5194 0.99   1290  145 0.1289 0.1782      5.2023      5.4159|
|  8:  2.5194 -  2.4102 0.98   1276  144 0.1219 0.1793      5.1242      5.3692|
|  9:  2.4102 -  2.3178 0.98   1285  138 0.1187 0.1899      5.0666      5.3905|
| 10:  2.3178 -  2.2381 0.97   1260  142 0.1177 0.1811      5.0217      5.2407|
| 11:  2.2381 -  2.1683 0.99   1261  142 0.1207 0.1861      4.9758      5.2995|
| 12:  2.1683 -  2.1065 0.98   1268  137 0.1140 0.1775      4.9223      5.2036|
| 13:  2.1065 -  2.0512 0.97   1254  142 0.1193 0.1813      4.8377      5.1241|
| 14:  2.0512 -  2.0012 0.62    794   89 0.1119 0.1864      4.7308      4.9947|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7756  1386   154  0.94   9.26   0.96     0.94       7351.99|
|  2:  4.7756 -  3.8106  1349   147  0.95   7.82   1.00     0.98       8645.13|
|  3:  3.8106 -  3.3348  1313   153  0.94  11.09   1.01     1.01      10108.26|
|  4:  3.3348 -  3.0326  1309   139  0.91  14.37   1.00     0.97      11071.50|
|  5:  3.0326 -  2.8167  1293   144  0.89  17.27   0.99     0.96       9454.83|
|  6:  2.8167 -  2.6516  1292   143  0.89  17.10   0.98     0.95       8100.07|
|  7:  2.6516 -  2.5194  1290   145  0.90  16.38   0.98     0.95       6788.22|
|  8:  2.5194 -  2.4102  1276   144  0.90  16.53   0.98     0.95       6125.04|
|  9:  2.4102 -  2.3178  1285   138  0.90  16.25   0.98     0.93       5432.68|
| 10:  2.3178 -  2.2381  1260   142  0.90  16.59   0.97     0.93       5000.51|
| 11:  2.2381 -  2.1683  1261   142  0.89  17.10   0.97     0.93       4628.22|
| 12:  2.1683 -  2.1065  1268   137  0.91  15.79   0.98     0.96       4354.29|
| 13:  2.1065 -  2.0512  1254   142  0.89  17.31   0.97     0.96       3786.40|
| 14:  2.0512 -  2.0012   794    89  0.90  16.12   0.94     0.90       2924.47|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     2924.47 max =        11071.50 mean =      6839.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        14.82|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1641   ksol= 0.32   Bsol= 67.57   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.54,-0.14,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.181272                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1641   ksol= 0.32   Bsol= 67.57   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,-0.54,-0.14,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.181272                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7756 0.99   1386  154 0.0990 0.1304      5.3861      5.5351|
|  2:  4.7756 -  3.8106 0.99   1349  147 0.0846 0.1045      5.4191      5.5942|
|  3:  3.8106 -  3.3348 0.99   1313  153 0.1040 0.1494        5.46      5.8519|
|  4:  3.3348 -  3.0326 0.99   1309  139 0.1263 0.1652        5.49      5.6521|
|  5:  3.0326 -  2.8167 0.99   1293  144 0.1407 0.1878      5.3884      5.5829|
|  6:  2.8167 -  2.6516 0.98   1292  143 0.1318 0.2010        5.28      5.5027|
|  7:  2.6516 -  2.5194 0.99   1290  145 0.1289 0.1784       5.202      5.4165|
|  8:  2.5194 -  2.4102 0.98   1276  144 0.1219 0.1792      5.1242      5.3685|
|  9:  2.4102 -  2.3178 0.98   1285  138 0.1186 0.1898      5.0667      5.3905|
| 10:  2.3178 -  2.2381 0.97   1260  142 0.1177 0.1812      5.0219      5.2415|
| 11:  2.2381 -  2.1683 0.99   1261  142 0.1206 0.1862      4.9758      5.2995|
| 12:  2.1683 -  2.1065 0.98   1268  137 0.1139 0.1776      4.9223      5.2044|
| 13:  2.1065 -  2.0512 0.97   1254  142 0.1194 0.1812      4.8377      5.1238|
| 14:  2.0512 -  2.0012 0.62    794   89 0.1119 0.1862      4.7304      4.9937|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7756  1386   154  0.94   9.29   0.96     0.94       7375.81|
|  2:  4.7756 -  3.8106  1349   147  0.95   7.84   1.00     0.98       8674.39|
|  3:  3.8106 -  3.3348  1313   153  0.94  11.12   1.02     1.01      10135.48|
|  4:  3.3348 -  3.0326  1309   139  0.91  14.38   1.00     0.98      11070.63|
|  5:  3.0326 -  2.8167  1293   144  0.89  17.26   1.00     0.97       9441.33|
|  6:  2.8167 -  2.6516  1292   143  0.89  17.09   0.98     0.96       8087.78|
|  7:  2.6516 -  2.5194  1290   145  0.90  16.37   0.99     0.96       6782.98|
|  8:  2.5194 -  2.4102  1276   144  0.90  16.54   0.99     0.95       6125.05|
|  9:  2.4102 -  2.3178  1285   138  0.90  16.25   0.99     0.94       5434.72|
| 10:  2.3178 -  2.2381  1260   142  0.90  16.60   0.98     0.94       5002.62|
| 11:  2.2381 -  2.1683  1261   142  0.89  17.11   0.98     0.94       4630.15|
| 12:  2.1683 -  2.1065  1268   137  0.91  15.80   0.99     0.97       4356.97|
| 13:  2.1065 -  2.0512  1254   142  0.89  17.31   0.98     0.97       3784.85|
| 14:  2.0512 -  2.0012   794    89  0.90  16.11   0.96     0.91       2920.02|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2920.02 max =        11070.63 mean =      6844.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.83|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.90  16.44    None  None   None       |
|    all(noH): 2823   0      0.00    103.90  16.44    None  None   None       |
|    Sol.    : 438    0      4.55    97.23   41.00    None  None   None       |
|    Mac.    : 2385   0      0.00    103.90  11.93    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 -  10.392: 1363   |   5:    51.949 -  62.338:   94        |
|      1:    10.392 -  20.781:  871   |   6:    62.338 -  72.728:   43        |
|      2:    20.781 -  31.171:  200   |   7:    72.728 -  83.117:   16        |
|      3:    31.171 -  41.560:  119   |   8:    83.117 -  93.506:    6        |
|      4:    41.560 -  51.949:  107   |   9:    93.506 - 103.895:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.679 - 4.740
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.739 - 4.740

peak=    6.009 closest distance to " O   HOH Z 111 " =    2.295
peak=    5.634 closest distance to " CB  GLN A 223 " =    1.386
peak=    5.403 closest distance to " O   HOH Z 210 " =    1.054
peak=    5.242 closest distance to " CG  PRO A  54 " =    1.350
peak=    5.009 closest distance to " CB  SER A  63 " =    1.271
peak=    4.917 closest distance to " O   HOH Z 232 " =    2.332
peak=    4.853 closest distance to " CB  ARG A 190 " =    1.734
peak=    4.767 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.748 closest distance to " CG  PRO A 198 " =    1.229
peak=    4.709 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.704 closest distance to " CB  PRO A  54 " =    0.896
peak=    4.689 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.679 closest distance to " C   PRO A 198 " =    1.536
peak=    4.653 closest distance to " CG  PRO A 280 " =    0.807
peak=    4.632 closest distance to " CB  GLN A 183 " =    1.321
peak=    4.568 closest distance to " CB  GLU A 128 " =    1.128
peak=    4.514 closest distance to " O   HOH Z 134 " =    1.660
peak=    4.388 closest distance to " NH2 ARG A 156 " =    1.173
peak=    4.375 closest distance to " O   HOH Z  15 " =    2.160
peak=    4.366 closest distance to " CZ  PHE A 218 " =    1.107
peak=    4.358 closest distance to " O   HOH Z 298 " =    1.995
peak=    4.317 closest distance to " O   HOH Z  44 " =    2.319
peak=    4.294 closest distance to " O   HOH Z  43 " =    1.992
peak=    4.276 closest distance to " O   HOH Z 234 " =    3.818
peak=    4.256 closest distance to " O   HOH Z 403 " =    1.729
peak=    4.228 closest distance to " O   HOH Z 189 " =    2.491
peak=    4.227 closest distance to " O   HOH Z 133 " =    2.474
peak=    4.200 closest distance to " CD  ARG A 269 " =    0.965
peak=    4.196 closest distance to " O   HOH Z 265 " =    2.086
peak=    4.188 closest distance to " OD1 ASN A  69 " =    2.581
peak=    4.185 closest distance to " O   HOH Z 369 " =    2.274
peak=    4.181 closest distance to " CG1 ILE A  33 " =    1.216
peak=    4.176 closest distance to " CB  ARG A  79 " =    1.392
peak=    4.169 closest distance to " C   ILE A 106 " =    1.873
peak=    4.150 closest distance to " CB  TYR A 169 " =    0.860
peak=    4.149 closest distance to " CA  ALA A  51 " =    0.999
peak=    4.143 closest distance to " CB  LEU A 228 " =    1.094
peak=    4.083 closest distance to " CB  GLU A 277 " =    3.743
peak=    4.072 closest distance to " CB  GLU A 152 " =    1.139
peak=    4.068 closest distance to " O   HOH Z  20 " =    1.745
peak=    4.067 closest distance to " O   HOH Z 402 " =    1.520
peak=    4.053 closest distance to " O   HOH Z  40 " =    1.906
peak=    4.046 closest distance to " CG  PRO A 243 " =    1.185
peak=    4.045 closest distance to " O   HOH Z 368 " =    2.107
peak=    4.037 closest distance to " CA  ALA A  21 " =    1.376
peak=    4.028 closest distance to " O   HOH Z  80 " =    1.735
peak=    4.005 closest distance to " CA  ARG A  36 " =    1.135
peak=    3.998 closest distance to " O   HOH Z  68 " =    2.034
peak=    3.997 closest distance to " O   HOH Z  97 " =    2.042
peak=    3.995 closest distance to " CB  VAL A 202 " =    1.572
peak=    3.990 closest distance to " O   HOH Z 433 " =    1.431
peak=    3.986 closest distance to " O   HOH Z 412 " =    3.644
peak=    3.980 closest distance to " O   HOH Z 423 " =    1.867
peak=    3.967 closest distance to " CG2BVAL A  41 " =    0.864
peak=    3.953 closest distance to " CA  ALA A 160 " =    0.881
peak=    3.935 closest distance to " O   HOH Z 352 " =    1.895
peak=    3.930 closest distance to " CA  ARG A 195 " =    1.198
peak=    3.924 closest distance to " CD1 LEU A 300 " =    1.202
peak=    3.920 closest distance to " O   HOH Z  21 " =    1.813
peak=    3.918 closest distance to " CB  ASN A 148 " =    1.386
peak=    3.913 closest distance to " O   HOH Z 418 " =    1.532
peak=    3.904 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.887 closest distance to " CB  SER A   3 " =    1.329
peak=    3.885 closest distance to " O   HOH Z 108 " =    2.921
peak=    3.876 closest distance to " O   ASN A  74 " =    1.633
peak=    3.875 closest distance to " NZ  LYS A 117 " =    3.204
peak=    3.874 closest distance to " CA  PRO A  54 " =    1.356
peak=    3.874 closest distance to " O   HOH Z 126 " =    1.518
peak=    3.849 closest distance to " O   HOH Z 374 " =    2.784
peak=    3.838 closest distance to " CD  LYS A 166 " =    1.330
peak=    3.825 closest distance to " CG  ARG A  66 " =    2.552
peak=    3.807 closest distance to " O   HOH Z 128 " =    2.149
peak=    3.794 closest distance to " O   THR A 251 " =    1.209
peak=    3.791 closest distance to " O   HOH Z 126 " =    2.027
peak=    3.780 closest distance to " CA  ASN A 176 " =    1.782
peak=    3.773 closest distance to " CD1 LEU A  96 " =    0.754
peak=    3.771 closest distance to " CD2 LEU A 297 " =    0.900
peak=    3.770 closest distance to " O   HOH Z  78 " =    1.633
peak=    3.768 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.756 closest distance to " NH2BARG A 145 " =    2.186
peak=    3.754 closest distance to " CG2 THR A 221 " =    1.130
peak=    3.750 closest distance to " O   HOH Z 280 " =    3.000
peak=    3.747 closest distance to " CB  ASP A 140 " =    0.897
peak=    3.747 closest distance to " O   HOH Z  44 " =    1.858
peak=    3.737 closest distance to " O   HOH Z 357 " =    2.087
peak=    3.736 closest distance to " NE2 GLN A  11 " =    0.994
peak=    3.733 closest distance to " CB  SER A 141 " =    1.013
peak=    3.731 closest distance to " O   HOH Z 287 " =    1.988
peak=    3.712 closest distance to " O   HOH Z 362 " =    3.576
peak=    3.710 closest distance to " O   HOH Z 245 " =    1.328
peak=    3.709 closest distance to " O   HOH Z 279 " =    2.240
peak=    3.708 closest distance to " O   HOH Z 316 " =    3.089
peak=    3.707 closest distance to " CB  ALA A 291 " =    1.298
peak=    3.700 closest distance to " O   HOH Z 383 " =    2.161
peak=    3.700 closest distance to " O   HOH Z 426 " =    1.535
peak=    3.691 closest distance to " CB  ARG A  79 " =    0.923
peak=    3.687 closest distance to " O   HOH Z  19 " =    1.852
peak=    3.686 closest distance to " CB  MET A  40 " =    0.852
peak=    3.686 closest distance to " ND2 ASN A 249 " =    2.036
peak=    3.682 closest distance to " CA  THR A 221 " =    0.959
peak=    3.680 closest distance to " O   SER A  87 " =    2.214
peak=    3.678 closest distance to " O   ALA A 165 " =    1.375
peak=    3.677 closest distance to " O   HOH Z  59 " =    2.485
peak=    3.663 closest distance to " N   ASN A  39 " =    1.347
peak=    3.662 closest distance to " O   HOH Z 147 " =    1.775
peak=    3.662 closest distance to " CE  LYS A  76 " =    0.811
peak=    3.659 closest distance to " O   HOH Z  63 " =    1.891
peak=    3.656 closest distance to " O   HOH Z 303 " =    2.207
peak=    3.654 closest distance to " CZ  PHE A 192 " =    0.915
peak=    3.651 closest distance to " CA  GLU A 152 " =    0.851
peak=    3.643 closest distance to " O   HOH Z 163 " =    1.591
peak=    3.642 closest distance to " CA  ASP A 191 " =    0.839
peak=    3.641 closest distance to " O   HOH Z 421 " =    1.711
peak=    3.640 closest distance to " N   ILE A  33 " =    1.055
peak=    3.616 closest distance to " O   HOH Z 180 " =    2.239
peak=    3.615 closest distance to " O   HOH Z  30 " =    1.397
peak=    3.611 closest distance to " O   HOH Z 174 " =    2.375
peak=    3.605 closest distance to " CG2 VAL A 257 " =    0.895
peak=    3.604 closest distance to " O   HOH Z 346 " =    1.577
peak=    3.603 closest distance to " OG BSER A 164 " =    2.435
peak=    3.602 closest distance to " O   HOH Z 425 " =    1.320
peak=    3.596 closest distance to " O   HOH Z 193 " =    1.887
peak=    3.595 closest distance to " O   HOH Z 196 " =    1.156
peak=    3.591 closest distance to " CE1 TYR A 186 " =    1.308
peak=    3.589 closest distance to " CB  SER A  62 " =    0.803
peak=    3.588 closest distance to " O   HOH Z 406 " =    1.611
peak=    3.587 closest distance to " O   HOH Z 132 " =    2.778
peak=    3.584 closest distance to " O   HOH Z 261 " =    1.769
peak=    3.582 closest distance to " O   HOH Z 214 " =    2.489
peak=    3.571 closest distance to " O   HOH Z 391 " =    2.995
peak=    3.568 closest distance to " O   HOH Z 158 " =    3.008
peak=    3.565 closest distance to " O   HOH Z 371 " =    3.208
peak=    3.560 closest distance to " CB  TYR A 116 " =    1.038
peak=    3.556 closest distance to " O   HOH Z 427 " =    3.061
peak=    3.548 closest distance to " CG1 VAL A 153 " =    1.105
peak=    3.544 closest distance to " O   HOH Z 291 " =    1.502
peak=    3.533 closest distance to " O   THR A 220 " =    1.136
peak=    3.527 closest distance to " O   HOH Z 344 " =    3.160
peak=    3.526 closest distance to " O   HOH Z 403 " =    1.405
peak=    3.526 closest distance to " CD  ARG A 159 " =    0.833
peak=    3.526 closest distance to " ND2 ASN A 187 " =    1.489
peak=    3.521 closest distance to " O   ALA A 158 " =    1.238
peak=    3.520 closest distance to " CB  LEU A  83 " =    0.855
peak=    3.517 closest distance to " OG BSER A 134 " =    2.885
peak=    3.516 closest distance to " CD BLYS A 290 " =    0.962
peak=    3.515 closest distance to " O   HOH Z 411 " =    1.720
peak=    3.511 closest distance to " CG2 VAL A  78 " =    0.972
peak=    3.511 closest distance to " CD2 TRP A 179 " =    1.326
peak=    3.508 closest distance to " CA  LYS A 117 " =    1.230
peak=    3.507 closest distance to " OD2 ASP A 286 " =    2.872
peak=    3.507 closest distance to " CZ  PHE A  38 " =    1.272
peak=    3.504 closest distance to " O   HOH Z 345 " =    1.678
peak=    3.500 closest distance to " CA  SER A  87 " =    1.066
peak=    3.500 closest distance to " CG2 VAL A 197 " =    1.151
peak=    3.497 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.497 closest distance to " OD2 ASP A 298 " =    3.896
peak=    3.494 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.492 closest distance to " NH1AARG A 145 " =    1.219
peak=    3.488 closest distance to " CA  THR A 221 " =    1.425
peak=    3.487 closest distance to " O   HOH Z 247 " =    1.413
peak=    3.482 closest distance to " NZ  LYS A 166 " =    3.142
peak=    3.481 closest distance to " CD1 ILE A 106 " =    0.894
peak=    3.475 closest distance to " CA  ASP A 162 " =    1.198
peak=    3.473 closest distance to " O   HOH Z 272 " =    1.903
peak=    3.467 closest distance to " O   HOH Z 250 " =    1.456
peak=    3.466 closest distance to " CB  VAL A 265 " =    1.211
peak=    3.464 closest distance to " O   HOH Z  49 " =    1.902
peak=    3.453 closest distance to " CA  ALA A 295 " =    1.121
peak=    3.447 closest distance to " O   HOH Z 155 " =    3.371
peak=    3.446 closest distance to " CG  GLU A  37 " =    0.891
peak=    3.445 closest distance to " O   HOH Z 132 " =    3.371
peak=    3.444 closest distance to " O   HOH Z 109 " =    2.470
peak=    3.431 closest distance to " O   HOH Z 130 " =    2.271
peak=    3.431 closest distance to " NE2 HIS A 115 " =    1.002
peak=    3.426 closest distance to " OE1 GLN A  11 " =    1.960
peak=    3.424 closest distance to " O   HOH Z 173 " =    2.340
peak=    3.422 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.417 closest distance to " ND1 HIS A  81 " =    1.639
peak=    3.412 closest distance to " N   CYS A 260 " =    0.814
peak=    3.411 closest distance to " O   HOH Z 142 " =    1.515
peak=    3.402 closest distance to " C   GLY A  80 " =    1.070
peak=    3.395 closest distance to " CB  THR A 157 " =    1.132
peak=    3.392 closest distance to " O   HOH Z  88 " =    3.555
peak=    3.389 closest distance to " CB  ASN A 142 " =    1.144
peak=    3.386 closest distance to " O   HOH Z 185 " =    1.769
peak=    3.382 closest distance to " CB  GLN A 103 " =    0.911
peak=    3.377 closest distance to " CB  ASN A 187 " =    1.186
peak=    3.371 closest distance to " O   HOH Z 437 " =    1.358
peak=    3.367 closest distance to " CG2 ILE A 120 " =    1.002
peak=    3.358 closest distance to " O   TRP A 274 " =    1.849
peak=    3.351 closest distance to " CG  GLN A  58 " =    2.642
peak=    3.351 closest distance to " CB  SER A  28 " =    1.073
peak=    3.350 closest distance to " CA  ASN A 215 " =    1.153
peak=    3.348 closest distance to " O   HOH Z 197 " =    1.983
peak=    3.334 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.329 closest distance to " CB  ARG A 139 " =    0.886
peak=    3.328 closest distance to " N   GLY A  98 " =    1.195
peak=    3.323 closest distance to " CD  ARG A  66 " =    2.466
peak=    3.322 closest distance to " CA  VAL A 125 " =    1.209
peak=    3.322 closest distance to " CB  ARG A 269 " =    0.793
peak=    3.321 closest distance to " CB  ALA A  71 " =    1.310
peak=    3.321 closest distance to " O   HOH Z  66 " =    2.086
peak=    3.316 closest distance to " C   TYR A 214 " =    1.505
peak=    3.316 closest distance to " CB  ALA A 248 " =    1.281
peak=    3.315 closest distance to " CB  ILE A 120 " =    1.301
peak=    3.313 closest distance to " CG2 ILE A  20 " =    1.337
peak=    3.312 closest distance to " O   HOH Z 102 " =    1.255
peak=    3.306 closest distance to " N   ASN A 127 " =    1.250
peak=    3.306 closest distance to " O   HOH Z 145 " =    2.330
peak=    3.305 closest distance to " O   HOH Z  48 " =    1.910
peak=    3.304 closest distance to " CG  LEU A 167 " =    1.122
peak=    3.299 closest distance to " CG2 THR A  29 " =    1.427
peak=    3.298 closest distance to " O   HOH Z 128 " =    2.208
peak=    3.297 closest distance to " CB  SER A 212 " =    1.092
peak=    3.295 closest distance to " OH  TYR A  30 " =    1.239
peak=    3.293 closest distance to " O   HOH Z 336 " =    1.675
peak=    3.291 closest distance to " CA  GLN A  88 " =    1.278
peak=    3.291 closest distance to " O   HOH Z  47 " =    1.175
peak=    3.289 closest distance to " CA  LEU A  83 " =    1.403
peak=    3.289 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.287 closest distance to " O   HOH Z 365 " =    2.901
peak=    3.286 closest distance to " OE1 GLU A   2 " =    2.053
peak=    3.283 closest distance to " CB  ASN A 285 " =    0.891
peak=    3.278 closest distance to " OG1 THR A 294 " =    2.471
peak=    3.277 closest distance to " O   HOH Z 125 " =    3.806
peak=    3.276 closest distance to " O   HOH Z 419 " =    3.010
peak=    3.269 closest distance to " O   HOH Z  97 " =    2.507
peak=    3.268 closest distance to " O   HOH Z 281 " =    4.740
peak=    3.264 closest distance to " O   HOH Z 148 " =    3.264
peak=    3.259 closest distance to " CB  MET A  47 " =    0.937
peak=    3.259 closest distance to " CB  SER A 216 " =    0.861
peak=    3.255 closest distance to " CG AARG A 275 " =    1.128
peak=    3.254 closest distance to " CA  ILE A 106 " =    0.847
peak=    3.254 closest distance to " O   HOH Z 387 " =    2.679
peak=    3.252 closest distance to " O   HOH Z 423 " =    3.359
peak=    3.249 closest distance to " NH1 ARG A 269 " =    0.750
peak=    3.246 closest distance to " O   HOH Z 193 " =    1.693
peak=    3.244 closest distance to " O   HOH Z 258 " =    2.112
peak=    3.242 closest distance to " O   HOH Z 171 " =    3.929
peak=    3.240 closest distance to " CB  PRO A 198 " =    1.050
peak=    3.239 closest distance to " O   HOH Z 294 " =    1.555
peak=    3.237 closest distance to " CA  MET A 105 " =    1.060
peak=    3.237 closest distance to " NZ ALYS A 290 " =    1.053
peak=    3.235 closest distance to " O   HOH Z 327 " =    2.322
peak=    3.234 closest distance to " O   ASP A 124 " =    1.259
peak=    3.230 closest distance to " N   ASN A 252 " =    1.254
peak=    3.230 closest distance to " O   HOH Z 295 " =    1.478
peak=    3.226 closest distance to " CA  ASP A 140 " =    1.225
peak=    3.223 closest distance to " O   HOH Z 353 " =    2.816
peak=    3.223 closest distance to " O   HOH Z 250 " =    1.591
peak=    3.221 closest distance to " CB  PHE A  16 " =    0.989
peak=    3.219 closest distance to " NZ  LYS A 117 " =    1.764
peak=    3.216 closest distance to " OG  SER A 245 " =    1.640
peak=    3.216 closest distance to " O   HOH Z   1 " =    2.732
peak=    3.214 closest distance to " O   HOH Z  54 " =    1.627
peak=    3.213 closest distance to " CD  ARG A 195 " =    0.927
peak=    3.212 closest distance to " CA  VAL A  41 " =    0.873
peak=    3.211 closest distance to " CB  SER A 273 " =    0.849
peak=    3.210 closest distance to " CA  ASN A 217 " =    1.320
peak=    3.204 closest distance to " O   HOH Z 227 " =    1.579
peak=    3.204 closest distance to " CB  TYR A 169 " =    0.828
peak=    3.204 closest distance to " CA  ALA A 100 " =    1.108
peak=    3.203 closest distance to " N   ARG A 190 " =    1.020
peak=    3.202 closest distance to " O   HOH Z 261 " =    1.625
peak=    3.200 closest distance to " N   ASP A 132 " =    1.160
peak=    3.200 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.196 closest distance to " CD1AILE A 234 " =    0.874
peak=    3.196 closest distance to " O   HOH Z 386 " =    2.320
peak=    3.195 closest distance to " CD1 LEU A 222 " =    0.764
peak=    3.192 closest distance to " CG2 THR A 220 " =    0.756
peak=    3.192 closest distance to " CG1 ILE A  49 " =    1.575
peak=    3.188 closest distance to " O   GLY A  57 " =    2.682
peak=    3.184 closest distance to " O   HOH Z 227 " =    1.649
peak=    3.181 closest distance to " O   HOH Z 150 " =    1.537
peak=    3.179 closest distance to " CA  ALA A 291 " =    0.865
peak=    3.178 closest distance to " CB  PRO A 243 " =    1.245
peak=    3.178 closest distance to " O   ALA A 242 " =    1.173
peak=    3.176 closest distance to " O   HOH Z 394 " =    1.662
peak=    3.167 closest distance to " CA  GLY A 196 " =    1.035
peak=    3.167 closest distance to " CG1BVAL A  72 " =    1.814
peak=    3.167 closest distance to " O   HOH Z 176 " =    1.501
peak=    3.166 closest distance to " CA  ARG A 102 " =    1.176
peak=    3.163 closest distance to " O   HOH Z 359 " =    1.408
peak=    3.163 closest distance to " O   HOH Z 416 " =    3.021
peak=    3.160 closest distance to " CA  ALA A  84 " =    1.323
peak=    3.159 closest distance to " CB  PHE A 204 " =    0.953
peak=    3.158 closest distance to " OG  SER A  97 " =    3.598
peak=    3.147 closest distance to " CA  ALA A 233 " =    1.643
peak=    3.146 closest distance to " O   HOH Z 299 " =    4.497
peak=    3.142 closest distance to " OH  TYR A 116 " =    1.131
peak=    3.141 closest distance to " O   HOH Z 417 " =    3.063
peak=    3.140 closest distance to " O   HOH Z 325 " =    2.165
peak=    3.138 closest distance to " NE2 GLN A  58 " =    3.949
peak=    3.137 closest distance to " OD2 ASP A 200 " =    1.303
peak=    3.134 closest distance to " O   HOH Z  85 " =    2.105
peak=    3.132 closest distance to " O   GLN A 278 " =    1.316
peak=    3.130 closest distance to " O   HOH Z 156 " =    2.624
peak=    3.127 closest distance to " CB  ALA A 100 " =    1.341
peak=    3.126 closest distance to " CB  ALA A   9 " =    1.573
peak=    3.125 closest distance to " CA  GLU A  46 " =    0.860
peak=    3.122 closest distance to " CA  GLN A 223 " =    0.877
peak=    3.120 closest distance to " O   HOH Z 128 " =    1.776
peak=    3.119 closest distance to " O   HOH Z 121 " =    3.783
peak=    3.115 closest distance to " CB  ASN A 148 " =    1.971
peak=    3.115 closest distance to " O   HOH Z  10 " =    1.807
peak=    3.115 closest distance to " O   THR A 251 " =    1.985
peak=    3.114 closest distance to " CA  GLU A 152 " =    1.464
peak=    3.113 closest distance to " CB  GLN A  89 " =    1.165
peak=    3.103 closest distance to " CZ3 TRP A  85 " =    0.935
peak=    3.102 closest distance to " ND2 ASN A 249 " =    0.887
peak=    3.091 closest distance to " O   VAL A  72 " =    3.210
peak=    3.087 closest distance to " ND2 ASN A 301 " =    1.597
peak=    3.086 closest distance to " CA  THR A 264 " =    0.868
peak=    3.085 closest distance to " N   TYR A  15 " =    0.809
peak=    3.077 closest distance to " OG  SER A  62 " =    2.976
peak=    3.076 closest distance to " NH2AARG A 275 " =    3.470
peak=    3.062 closest distance to " CB  ALA A 104 " =    0.739
peak=    3.045 closest distance to " NE1 TRP A 266 " =    1.372
peak=    3.042 closest distance to " CZ2 TRP A 179 " =    1.809
peak=    3.040 closest distance to " O   HOH Z 251 " =    1.557
peak=    3.035 closest distance to " OD2 ASP A 298 " =    3.623
peak=    3.033 closest distance to " O   HOH Z 271 " =    2.149
peak=    3.015 closest distance to " O   HOH Z 271 " =    2.522

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.888 - 5.960
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 217
   mapped sites are within: 0.888 - 5.960

peak=   -4.623 closest distance to " O   HOH Z 266 " =    4.998
peak=   -4.393 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.328 closest distance to " CG1 VAL A 250 " =    2.711
peak=   -4.248 closest distance to " O   HOH Z   5 " =    1.615
peak=   -4.119 closest distance to " CD  GLN A 223 " =    1.307
peak=   -4.112 closest distance to " C   HIS A 108 " =    1.099
peak=   -4.061 closest distance to " OG  SER A  97 " =    2.218
peak=   -4.056 closest distance to " OXT GLY A 302 " =    2.945
peak=   -4.041 closest distance to " CB  PRO A 243 " =    2.702
peak=   -4.037 closest distance to " O   VAL A  67 " =    2.630
peak=   -4.010 closest distance to " O   HOH Z 166 " =    1.685
peak=   -3.992 closest distance to " O   HOH Z 196 " =    2.447
peak=   -3.992 closest distance to " CD1 PHE A 130 " =    2.386
peak=   -3.978 closest distance to " O   HOH Z 283 " =    2.198
peak=   -3.963 closest distance to " O   PRO A 163 " =    2.221
peak=   -3.954 closest distance to " O   HOH Z  52 " =    1.684
peak=   -3.954 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.952 closest distance to " O   HOH Z 292 " =    4.603
peak=   -3.940 closest distance to " CD  GLN A  58 " =    1.072
peak=   -3.910 closest distance to " CE2 TYR A  30 " =    2.675
peak=   -3.906 closest distance to " CG1 VAL A 112 " =    2.607
peak=   -3.905 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.880 closest distance to " O   HOH Z  13 " =    1.714
peak=   -3.865 closest distance to " CD  ARG A  14 " =    3.422
peak=   -3.864 closest distance to " CD1 PHE A  59 " =    1.916
peak=   -3.861 closest distance to " O   HOH Z 348 " =    2.268
peak=   -3.834 closest distance to " OD1 ASN A 148 " =    1.530
peak=   -3.818 closest distance to " N   ALA A  43 " =    2.650
peak=   -3.814 closest distance to " CH2 TRP A 179 " =    1.213
peak=   -3.803 closest distance to " CD1 LEU A 101 " =    2.533
peak=   -3.797 closest distance to " CG  ARG A  66 " =    2.477
peak=   -3.790 closest distance to " O   HOH Z 394 " =    1.552
peak=   -3.784 closest distance to " O   HOH Z 353 " =    2.313
peak=   -3.778 closest distance to " NH2 ARG A  66 " =    1.802
peak=   -3.774 closest distance to " ND2 ASN A  45 " =    1.830
peak=   -3.771 closest distance to " O   HOH Z 377 " =    2.101
peak=   -3.741 closest distance to " O   ILE A 109 " =    2.657
peak=   -3.740 closest distance to " CB  ASP A 132 " =    2.428
peak=   -3.717 closest distance to " O   HOH Z 377 " =    1.250
peak=   -3.701 closest distance to " CA  GLY A 203 " =    2.323
peak=   -3.696 closest distance to " O   HOH Z 185 " =    2.408
peak=   -3.696 closest distance to " O   HOH Z 290 " =    1.164
peak=   -3.692 closest distance to " C   SER A 206 " =    1.553
peak=   -3.692 closest distance to " NE1 TRP A 266 " =    2.303
peak=   -3.686 closest distance to " C   ASN A 285 " =    2.443
peak=   -3.679 closest distance to " O   HOH Z  19 " =    2.171
peak=   -3.677 closest distance to " CG  ASP A 231 " =    0.888
peak=   -3.652 closest distance to " CB  ALA A  10 " =    2.134
peak=   -3.642 closest distance to " O   HOH Z 372 " =    2.519
peak=   -3.628 closest distance to " CD  ARG A 139 " =    1.581
peak=   -3.625 closest distance to " ND2 ASN A 187 " =    1.679
peak=   -3.625 closest distance to " O   HOH Z 407 " =    3.580
peak=   -3.605 closest distance to " CG  GLU A  53 " =    1.447
peak=   -3.598 closest distance to " CB  ASN A  39 " =    2.274
peak=   -3.593 closest distance to " O   HOH Z 166 " =    1.890
peak=   -3.589 closest distance to " CG2 ILE A 263 " =    2.354
peak=   -3.587 closest distance to " O   HOH Z  71 " =    1.656
peak=   -3.576 closest distance to " O   HOH Z 150 " =    1.844
peak=   -3.574 closest distance to " OE1 GLN A 223 " =    2.079
peak=   -3.565 closest distance to " CA  GLY A 133 " =    2.354
peak=   -3.552 closest distance to " N   SER A 276 " =    1.502
peak=   -3.547 closest distance to " OD1 ASP A 191 " =    1.643
peak=   -3.545 closest distance to " OG  SER A  62 " =    1.664
peak=   -3.538 closest distance to " O   ALA A  10 " =    1.742
peak=   -3.532 closest distance to " CG2 ILE A  49 " =    2.739
peak=   -3.529 closest distance to " ND2 ASN A  45 " =    1.103
peak=   -3.528 closest distance to " O   HOH Z 210 " =    0.904
peak=   -3.526 closest distance to " CG  PRO A 243 " =    1.771
peak=   -3.520 closest distance to " CE2 PHE A  61 " =    2.577
peak=   -3.518 closest distance to " O   HOH Z 165 " =    1.930
peak=   -3.517 closest distance to " CD2 TYR A 293 " =    1.979
peak=   -3.512 closest distance to " OG BSER A 210 " =    2.146
peak=   -3.495 closest distance to " O   SER A 210 " =    1.969
peak=   -3.494 closest distance to " O   HOH Z 150 " =    1.188
peak=   -3.493 closest distance to " SG ACYS A 201 " =    1.123
peak=   -3.487 closest distance to " O   HOH Z 252 " =    4.050
peak=   -3.483 closest distance to " OD2 ASP A 171 " =    1.842
peak=   -3.481 closest distance to " O   VAL A  67 " =    2.837
peak=   -3.474 closest distance to " O   HOH Z 234 " =    4.388
peak=   -3.469 closest distance to " O   ALA A  34 " =    2.467
peak=   -3.465 closest distance to " O   PHE A 218 " =    1.484
peak=   -3.455 closest distance to " O   HOH Z   6 " =    1.491
peak=   -3.451 closest distance to " O   HOH Z  90 " =    1.869
peak=   -3.447 closest distance to " C   LEU A 143 " =    1.167
peak=   -3.436 closest distance to " O   HOH Z 118 " =    3.589
peak=   -3.433 closest distance to " C   ALA A 158 " =    1.319
peak=   -3.427 closest distance to " O   HOH Z 106 " =    2.019
peak=   -3.425 closest distance to " O   HOH Z 197 " =    2.112
peak=   -3.422 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.422 closest distance to " O   HOH Z 111 " =    1.980
peak=   -3.422 closest distance to " CB  PHE A 192 " =    1.972
peak=   -3.419 closest distance to " CB  ALA A 291 " =    2.409
peak=   -3.406 closest distance to " NE2 GLN A 103 " =    1.817
peak=   -3.405 closest distance to " OD1 ASN A 187 " =    1.594
peak=   -3.405 closest distance to " C   THR A 279 " =    1.120
peak=   -3.403 closest distance to " O   HOH Z 275 " =    1.579
peak=   -3.395 closest distance to " C   ASN A 187 " =    1.915
peak=   -3.389 closest distance to " O   HOH Z  11 " =    1.906
peak=   -3.388 closest distance to " NH2AARG A 275 " =    5.414
peak=   -3.385 closest distance to " CD  PRO A 213 " =    2.245
peak=   -3.381 closest distance to " CE3 TRP A 150 " =    2.066
peak=   -3.379 closest distance to " CG2 VAL A 189 " =    2.241
peak=   -3.378 closest distance to " CE BMET A  47 " =    2.288
peak=   -3.377 closest distance to " O   HOH Z 426 " =    1.708
peak=   -3.376 closest distance to " OG BSER A 134 " =    1.311
peak=   -3.373 closest distance to " O   HOH Z 393 " =    1.543
peak=   -3.372 closest distance to " C   ARG A  79 " =    2.654
peak=   -3.371 closest distance to " O   ALA A   1 " =    1.999
peak=   -3.368 closest distance to " CH2 TRP A 177 " =    2.005
peak=   -3.368 closest distance to " ND2 ASN A 249 " =    2.440
peak=   -3.357 closest distance to " O   ALA A 160 " =    1.506
peak=   -3.356 closest distance to " OG BSER A 134 " =    1.910
peak=   -3.349 closest distance to " O   HOH Z 198 " =    2.330
peak=   -3.348 closest distance to " ND2BASN A 224 " =    1.848
peak=   -3.346 closest distance to " O   HOH Z 264 " =    1.797
peak=   -3.346 closest distance to " CE  MET A  93 " =    1.380
peak=   -3.345 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.344 closest distance to " O   VAL A 189 " =    2.657
peak=   -3.343 closest distance to " O   HOH Z 128 " =    2.538
peak=   -3.337 closest distance to " CG  MET A 105 " =    0.895
peak=   -3.337 closest distance to " CE3 TRP A 274 " =    2.512
peak=   -3.336 closest distance to " CG1 VAL A  78 " =    2.695
peak=   -3.333 closest distance to " CZ  PHE A  38 " =    1.968
peak=   -3.333 closest distance to " O   HOH Z 236 " =    1.494
peak=   -3.322 closest distance to " O   HOH Z 311 " =    3.740
peak=   -3.322 closest distance to " O   HOH Z  38 " =    1.465
peak=   -3.321 closest distance to " O   HOH Z 275 " =    1.869
peak=   -3.309 closest distance to " CA  GLY A 241 " =    3.150
peak=   -3.307 closest distance to " CD  GLN A  88 " =    0.889
peak=   -3.304 closest distance to " O   HOH Z 350 " =    1.903
peak=   -3.304 closest distance to " O   HOH Z 177 " =    1.757
peak=   -3.303 closest distance to " O   ASP A  27 " =    2.162
peak=   -3.299 closest distance to " CD2 PHE A  59 " =    2.529
peak=   -3.297 closest distance to " CB  ALA A   9 " =    2.647
peak=   -3.295 closest distance to " O   HOH Z 117 " =    4.508
peak=   -3.295 closest distance to " ND2 ASN A  69 " =    1.622
peak=   -3.293 closest distance to " CB  ALA A 291 " =    2.286
peak=   -3.289 closest distance to " CB  ALA A  43 " =    2.613
peak=   -3.285 closest distance to " CD2 PHE A  61 " =    2.017
peak=   -3.285 closest distance to " N   ALA A 226 " =    2.098
peak=   -3.283 closest distance to " CD  ARG A 195 " =    5.091
peak=   -3.282 closest distance to " O   HOH Z  43 " =    1.496
peak=   -3.271 closest distance to " CZ  TYR A 169 " =    1.822
peak=   -3.263 closest distance to " O   HOH Z 414 " =    1.598
peak=   -3.263 closest distance to " CD1 LEU A 228 " =    2.379
peak=   -3.259 closest distance to " NH2 ARG A 159 " =    2.359
peak=   -3.255 closest distance to " CD2 LEU A 300 " =    2.932
peak=   -3.255 closest distance to " O   GLY A 118 " =    2.225
peak=   -3.254 closest distance to " O   HOH Z 283 " =    5.960
peak=   -3.253 closest distance to " O   HOH Z 200 " =    1.455
peak=   -3.252 closest distance to " O   HOH Z 298 " =    2.724
peak=   -3.249 closest distance to " O   SER A 276 " =    1.702
peak=   -3.247 closest distance to " OH  TYR A 169 " =    1.045
peak=   -3.244 closest distance to " NE2 GLN A 194 " =    1.893
peak=   -3.244 closest distance to " OD2 ASP A 171 " =    2.363
peak=   -3.244 closest distance to " CB  PRO A 163 " =    2.643
peak=   -3.237 closest distance to " CD  LYS A 289 " =    2.448
peak=   -3.237 closest distance to " O   HOH Z 102 " =    1.543
peak=   -3.234 closest distance to " CG  ARG A 269 " =    2.356
peak=   -3.233 closest distance to " O   HOH Z 423 " =    2.393
peak=   -3.229 closest distance to " ND2 ASN A  60 " =    1.796
peak=   -3.228 closest distance to " O   HOH Z  37 " =    1.860
peak=   -3.226 closest distance to " CB  PHE A  16 " =    2.583
peak=   -3.224 closest distance to " N   LYS A 289 " =    1.499
peak=   -3.223 closest distance to " O   HOH Z 145 " =    1.999
peak=   -3.221 closest distance to " O   HOH Z 136 " =    1.982
peak=   -3.217 closest distance to " O   HOH Z  91 " =    1.999
peak=   -3.215 closest distance to " CZ  PHE A  59 " =    1.976
peak=   -3.210 closest distance to " N   THR A  52 " =    1.623
peak=   -3.207 closest distance to " CD1 ILE A 151 " =    2.344
peak=   -3.205 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.204 closest distance to " NE2 GLN A  88 " =    1.849
peak=   -3.202 closest distance to " N   THR A 235 " =    1.312
peak=   -3.199 closest distance to " CD2 PHE A 225 " =    1.294
peak=   -3.195 closest distance to " CB  ALA A 131 " =    2.152
peak=   -3.189 closest distance to " CG1 VAL A 125 " =    2.065
peak=   -3.189 closest distance to " O   HOH Z 232 " =    1.604
peak=   -3.185 closest distance to " OD1 ASN A  39 " =    2.281
peak=   -3.184 closest distance to " CG  GLU A 277 " =    1.184
peak=   -3.177 closest distance to " O   HOH Z 265 " =    2.305
peak=   -3.176 closest distance to " CD1 TRP A 179 " =    1.084
peak=   -3.174 closest distance to " CG  LEU A  83 " =    2.039
peak=   -3.172 closest distance to " CB  TRP A  85 " =    2.428
peak=   -3.172 closest distance to " O   HOH Z 396 " =    1.776
peak=   -3.167 closest distance to " O   HOH Z 191 " =    5.733
peak=   -3.161 closest distance to " O   HOH Z 301 " =    2.356
peak=   -3.157 closest distance to " CG  TRP A 266 " =    1.860
peak=   -3.156 closest distance to " CG  ARG A 219 " =    2.642
peak=   -3.155 closest distance to " CG1 VAL A 112 " =    2.898
peak=   -3.153 closest distance to " CG2BVAL A  41 " =    1.581
peak=   -3.152 closest distance to " CD  GLN A  58 " =    1.016
peak=   -3.144 closest distance to " O   HOH Z 171 " =    2.116
peak=   -3.142 closest distance to " O   HOH Z  77 " =    1.969
peak=   -3.142 closest distance to " CD1 LEU A 167 " =    2.124
peak=   -3.139 closest distance to " CA  GLY A  98 " =    2.186
peak=   -3.138 closest distance to " O   HOH Z  78 " =    1.819
peak=   -3.136 closest distance to " CB  GLN A  11 " =    1.745
peak=   -3.136 closest distance to " CD2 LEU A 222 " =    2.068
peak=   -3.135 closest distance to " OH  TYR A 247 " =    1.762
peak=   -3.127 closest distance to " NH2 ARG A  66 " =    4.037
peak=   -3.125 closest distance to " N   ALA A 248 " =    1.667
peak=   -3.125 closest distance to " O   HOH Z  17 " =    1.522
peak=   -3.120 closest distance to " O   HOH Z 174 " =    2.141
peak=   -3.116 closest distance to " O   HOH Z 134 " =    2.327
peak=   -3.116 closest distance to " CA  VAL A 197 " =    1.049
peak=   -3.114 closest distance to " ND2 ASN A  60 " =    1.596
peak=   -3.098 closest distance to " OE2 GLU A 152 " =    2.275
peak=   -3.096 closest distance to " O   HOH Z 417 " =    2.719
peak=   -3.086 closest distance to " O   HOH Z 281 " =    2.406
peak=   -3.082 closest distance to " O   HOH Z 171 " =    2.172
peak=   -3.081 closest distance to " N   GLN A  58 " =    1.513
peak=   -3.080 closest distance to " OE1 GLN A  88 " =    1.140
peak=   -3.071 closest distance to " O   HOH Z 111 " =    3.864
peak=   -3.071 closest distance to " O   HOH Z 259 " =    2.026
peak=   -3.067 closest distance to " CG  PRO A 163 " =    2.358
peak=   -3.056 closest distance to " O   HOH Z 380 " =    4.612
peak=   -3.020 closest distance to " O   HOH Z 357 " =    2.070

================= 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    :  0.3903 0.3748   6.194021e+00   6.159604e+00
   1_bss:  0.3771 0.3632   6.176275e+00   6.138772e+00
   1_xyz:  0.2656 0.2921   5.873940e+00   5.951725e+00
   1_adp:  0.2425 0.3001   5.820553e+00   5.966374e+00
   1_occ:  0.2423 0.2995   5.819466e+00   5.965411e+00
   2_bss:  0.2398 0.2961   5.812336e+00   5.959392e+00
   2_xyz:  0.1696 0.2086   5.479418e+00   5.654117e+00
   2_adp:  0.1511 0.1936   5.390441e+00   5.587362e+00
   2_occ:  0.1509 0.1935   5.389745e+00   5.586824e+00
   3_bss:  0.1506 0.1933   5.387438e+00   5.581737e+00
   3_xyz:  0.1259 0.1715   5.245105e+00   5.473840e+00
   3_adp:  0.1209 0.1670   5.212088e+00   5.447270e+00
   3_occ:  0.1209 0.1669   5.211818e+00   5.447078e+00
   4_bss:  0.1213 0.1669   5.212545e+00   5.446712e+00
   4_xyz:  0.1154 0.1641   5.179575e+00   5.424284e+00
   4_adp:  0.1142 0.1634   5.173857e+00   5.420459e+00
   4_occ:  0.1141 0.1634   5.173843e+00   5.420828e+00
   5_bss:  0.1140 0.1633   5.173815e+00   5.420841e+00
   5_xyz:  0.1152 0.1636   5.180733e+00   5.423558e+00
   5_adp:  0.1151 0.1643   5.181030e+00   5.426110e+00
   5_occ:  0.1150 0.1643   5.181099e+00   5.426404e+00
   5_bss:  0.1149 0.1641   5.181272e+00   5.426617e+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:  0.293  38.412  -2.151   5.159  -1.871   0.000  -0.000  -0.000
   1_xyz:  0.293  38.412  -2.151   5.159  -1.871   0.000  -0.000  -0.000
   1_adp:  0.293  38.412  -2.151   5.159  -1.871   0.000  -0.000  -0.000
   1_occ:  0.293  38.412  -2.151   5.159  -1.871   0.000  -0.000  -0.000
   2_bss:  0.327  67.047  -1.755   1.449  -0.992   0.000  -0.000  -0.000
   2_xyz:  0.327  67.047  -1.755   1.449  -0.992   0.000  -0.000  -0.000
   2_adp:  0.327  67.047  -1.755   1.449  -0.992   0.000  -0.000  -0.000
   2_occ:  0.327  67.047  -1.755   1.449  -0.992   0.000  -0.000  -0.000
   3_bss:  0.327  67.047  -1.846  -0.233  -0.894  -0.000  -0.000  -0.000
   3_xyz:  0.327  67.047  -1.846  -0.233  -0.894  -0.000  -0.000  -0.000
   3_adp:  0.327  67.047  -1.846  -0.233  -0.894  -0.000  -0.000  -0.000
   3_occ:  0.327  67.047  -1.846  -0.233  -0.894  -0.000  -0.000  -0.000
   4_bss:  0.328  69.537  -1.724  -0.699  -0.678  -0.000  -0.000  -0.000
   4_xyz:  0.328  69.537  -1.724  -0.699  -0.678  -0.000  -0.000  -0.000
   4_adp:  0.328  69.537  -1.724  -0.699  -0.678  -0.000  -0.000  -0.000
   4_occ:  0.328  69.537  -1.724  -0.699  -0.678  -0.000  -0.000  -0.000
   5_bss:  0.323  66.035  -1.481  -0.699  -0.414  -0.000  -0.000  -0.000
   5_xyz:  0.323  66.035  -1.481  -0.699  -0.414  -0.000  -0.000  -0.000
   5_adp:  0.323  66.035  -1.481  -0.699  -0.414  -0.000  -0.000  -0.000
   5_occ:  0.323  66.035  -1.481  -0.699  -0.414  -0.000  -0.000  -0.000
   5_bss:  0.324  67.572  -1.221  -0.539  -0.143  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.768 0.6243  0.7876    43725.337
   1_bss:  40.981 0.6321  0.8050    40707.578
   1_xyz:  30.931 0.7479  0.9214    23505.354
   1_adp:  31.683 0.7388  0.8992    24382.050
   1_occ:  31.649 0.7392  0.8994    24322.878
   2_bss:  31.122 0.7452  0.8864    23822.410
   2_xyz:  20.548 0.8554  0.9763    11091.594
   2_adp:  18.640 0.8742  0.9776     9662.410
   2_occ:  18.621 0.8744  0.9777     9650.757
   3_bss:  18.478 0.8757  0.9603     9527.404
   3_xyz:  15.961 0.8983  0.9712     7499.429
   3_adp:  15.276 0.9045  0.9641     7171.284
   3_occ:  15.270 0.9046  0.9640     7169.815
   4_bss:  15.275 0.9045  0.9631     7176.508
   4_xyz:  14.795 0.9084  0.9650     6808.751
   4_adp:  14.690 0.9095  0.9569     6780.121
   4_occ:  14.694 0.9095  0.9568     6784.718
   5_bss:  14.696 0.9095  0.9627     6784.054
   5_xyz:  14.717 0.9094  0.9620     6799.164
   5_adp:  14.764 0.9090  0.9523     6834.937
   5_occ:  14.766 0.9090  0.9522     6839.295
   5_bss:  14.772 0.9090  0.9602     6843.422
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6540e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6540e-01
   1_xyz:   1.524  0.012  0.094 15.787  0.005  4.119   1.1515e-01
   1_adp:   1.524  0.012  0.094 15.787  0.005  4.119   1.1515e-01
   1_occ:   1.524  0.012  0.094 15.787  0.005  4.119   1.1515e-01
   2_bss:   1.524  0.012  0.094 15.787  0.005  4.119   1.1515e-01
   2_xyz:   1.171  0.009  0.079 15.022  0.004  4.113   7.6410e-02
   2_adp:   1.171  0.009  0.079 15.022  0.004  4.113   7.6410e-02
   2_occ:   1.171  0.009  0.079 15.022  0.004  4.113   7.6410e-02
   3_bss:   1.171  0.009  0.079 15.022  0.004  4.113   7.6410e-02
   3_xyz:   1.121  0.010  0.081 14.899  0.004  4.123   7.3996e-02
   3_adp:   1.121  0.010  0.081 14.899  0.004  4.123   7.3996e-02
   3_occ:   1.121  0.010  0.081 14.899  0.004  4.123   7.3996e-02
   4_bss:   1.121  0.010  0.081 14.899  0.004  4.123   7.3996e-02
   4_xyz:   1.102  0.010  0.081 14.907  0.004  4.116   7.3886e-02
   4_adp:   1.102  0.010  0.081 14.907  0.004  4.116   7.3886e-02
   4_occ:   1.102  0.010  0.081 14.907  0.004  4.116   7.3886e-02
   5_bss:   1.102  0.010  0.081 14.907  0.004  4.116   7.3886e-02
   5_xyz:   1.014  0.008  0.076 14.627  0.003  4.116   6.2215e-02
   5_adp:   1.014  0.008  0.076 14.627  0.003  4.116   6.2215e-02
   5_occ:   1.014  0.008  0.076 14.627  0.003  4.116   6.2215e-02
   5_bss:   1.014  0.008  0.076 14.627  0.003  4.116   6.2215e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.592   2.4382e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.592   2.4382e-01
   1_xyz:  11.961  0.088  0.418 88.053  0.043  2.066   1.1286e-01
   1_adp:  11.961  0.088  0.418 88.053  0.043  2.066   1.1286e-01
   1_occ:  11.961  0.088  0.418 88.053  0.043  2.066   1.1286e-01
   2_bss:  11.961  0.088  0.418 88.053  0.043  2.066   1.1286e-01
   2_xyz:   7.871  0.059  0.256 89.144  0.048  2.239   6.9996e-02
   2_adp:   7.871  0.059  0.256 89.144  0.048  2.239   6.9996e-02
   2_occ:   7.871  0.059  0.256 89.144  0.048  2.239   6.9996e-02
   3_bss:   7.871  0.059  0.256 89.144  0.048  2.239   6.9996e-02
   3_xyz:   8.150  0.054  0.245 81.548  0.031  2.277   6.0023e-02
   3_adp:   8.150  0.054  0.245 81.548  0.031  2.277   6.0023e-02
   3_occ:   8.150  0.054  0.245 81.548  0.031  2.277   6.0023e-02
   4_bss:   8.150  0.054  0.245 81.548  0.031  2.277   6.0023e-02
   4_xyz:   8.114  0.048  0.278 81.531  0.033  2.336   5.8492e-02
   4_adp:   8.114  0.048  0.278 81.531  0.033  2.336   5.8492e-02
   4_occ:   8.114  0.048  0.278 81.531  0.033  2.336   5.8492e-02
   5_bss:   8.114  0.048  0.278 81.531  0.033  2.336   5.8492e-02
   5_xyz:   7.434  0.043  0.235 81.015  0.031  2.379   4.4427e-02
   5_adp:   7.434  0.043  0.235 81.015  0.031  2.379   4.4427e-02
   5_occ:   7.434  0.043  0.235 81.015  0.031  2.379   4.4427e-02
   5_bss:   7.434  0.043  0.235 81.015  0.031  2.379   4.4427e-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:  89.90   0.00  17.22  80.15   0.00  13.32  89.90   2.78  38.49
   1_occ:  89.90   0.00  17.22  80.15   0.00  13.32  89.90   2.78  38.49
   2_bss:  89.90   0.00  17.22  80.15   0.00  13.32  89.90   2.78  38.49
   2_xyz:  89.90   0.00  17.22  80.15   0.00  13.32  89.90   2.78  38.49
   2_adp:  91.26   0.36  17.30  91.26   0.36  12.84  88.29   4.67  41.53
   2_occ:  91.26   0.36  17.30  91.26   0.36  12.84  88.29   4.67  41.53
   3_bss:  91.26   0.36  17.30  91.26   0.36  12.84  88.29   4.67  41.53
   3_xyz:  91.26   0.36  17.30  91.26   0.36  12.84  88.29   4.67  41.53
   3_adp:  97.59   0.00  17.04  97.59   0.00  12.44  95.30   4.72  42.07
   3_occ:  97.59   0.00  17.04  97.59   0.00  12.44  95.30   4.72  42.07
   4_bss:  97.59   0.00  17.04  97.59   0.00  12.44  95.30   4.72  42.07
   4_xyz:  97.59   0.00  17.04  97.59   0.00  12.44  95.30   4.72  42.07
   4_adp: 101.73   0.00  16.66 101.73   0.00  12.17  96.62   3.28  41.11
   4_occ: 101.73   0.00  16.66 101.73   0.00  12.17  96.62   3.28  41.11
   5_bss: 101.73   0.00  16.66 101.73   0.00  12.17  96.62   3.28  41.11
   5_xyz: 101.73   0.00  16.66 101.73   0.00  12.17  96.62   3.28  41.11
   5_adp: 103.89   0.00  16.44 103.89   0.00  11.93  97.23   4.55  41.00
   5_occ: 103.89   0.00  16.44 103.89   0.00  11.93  97.23   4.55  41.00
   5_bss: 103.90   0.00  16.44 103.90   0.00  11.93  97.23   4.55  41.00
------------------------------------------------------------------------
 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:    1.587    0.023    0.417
   1_adp:    1.587    0.023    0.417
   1_occ:    1.587    0.023    0.417
   2_bss:    1.587    0.023    0.417
   2_xyz:    1.185    0.036    0.543
   2_adp:    1.185    0.036    0.543
   2_occ:    1.185    0.036    0.543
   3_bss:    1.185    0.036    0.543
   3_xyz:    1.313    0.044    0.608
   3_adp:    1.313    0.044    0.608
   3_occ:    1.313    0.044    0.608
   4_bss:    1.313    0.044    0.608
   4_xyz:    1.273    0.071    0.631
   4_adp:    1.273    0.071    0.631
   4_occ:    1.273    0.071    0.631
   5_bss:    1.273    0.071    0.631
   5_xyz:    1.266    0.091    0.638
   5_adp:    1.266    0.091    0.638
   5_occ:    1.266    0.091    0.638
   5_bss:    1.266    0.091    0.638
------------------------------------------------------------------------

CPU time actual refinement: 328.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_951/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_951/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_951/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_951/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_951/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.43 
  Macro-tasks:
    bulk solvent and scale       = 37.56  
    individual site refinement   = 130.14 
    weights calculation          = 28.57  
    collect and process          = 6.53   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 202.91 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 105.35 
    alpha_beta                      = 8.22   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.87 
    fmodel                         = 6.52   
    r_factors                      = 0.24   
    phase_errors                   = 10.80  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 248.22 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.677 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    665 calls, 104.96 s
gradients_fft:          610 calls, 100.61 s

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

# Date 2008-01-16 Time 06:03:49 PST -0800 (1200492229.92 s)
Start R-work = 0.3903, R-free = 0.3748 (no bulk solvent and anisotropic scale)
Final R-work = 0.1321, R-free = 0.1787 (no bulk solvent and anisotropic scale)

Start R-work = 0.3771, R-free = 0.3632
Final R-work = 0.1149, R-free = 0.1641