# Date 2008-01-16 Time 06:30:52 PST -0800 (1200493852.45 s)
#phil __OFF__

Command line arguments: "../1175.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7298
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1175

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.3993, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.02225
Completeness in resolution range: 0.969897
Completeness with d_max=infinity: 0.966881

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   2.0222

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 2.02225
Completeness in resolution range: 0.969897
Completeness with d_max=infinity: 0.966881

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.3270 [2118/2142]  1905   213  10.1%
  bin  2:  4.3270 -  3.4474 [2035/2055]  1832   203  10.0%
  bin  3:  3.4474 -  3.0154 [2015/2034]  1815   200   9.9%
  bin  4:  3.0154 -  2.7414 [1997/2027]  1798   199  10.0%
  bin  5:  2.7414 -  2.5459 [1988/2007]  1787   201  10.1%
  bin  6:  2.5459 -  2.3964 [1957/1982]  1759   198  10.1%
  bin  7:  2.3964 -  2.2768 [1954/1982]  1761   193   9.9%
  bin  8:  2.2768 -  2.1780 [1964/2000]  1769   195   9.9%
  bin  9:  2.1780 -  2.0944 [1943/1985]  1750   193   9.9%
  bin 10:  2.0944 -  2.0222 [1618/1983]  1454   164  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1175/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: 0.15 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:
        1.70 -     2.34: 3
        2.34 -     2.98: 1750
        2.98 -     3.62: 4456
        3.62 -     4.26: 8931
        4.26 -     4.90: 12487
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.698 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.364 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27622 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_1175/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1175/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.3993 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4343   r_free= 0.4288   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.234477                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8260 0.99   1379  152 0.3337 0.3266      6.4661      6.3794|
|  2:  4.8260 -  3.8507 0.99   1326  150 0.3562 0.3576       6.731      6.7405|
|  3:  3.8507 -  3.3699 0.99   1298  142 0.3976 0.3470        6.62      6.5633|
|  4:  3.3699 -  3.0645 0.99   1286  145 0.4122 0.4193      6.4715      6.4057|
|  5:  3.0645 -  2.8463 0.99   1282  142 0.4535 0.4313      6.3191      6.3566|
|  6:  2.8463 -  2.6795 0.99   1293  141 0.4566 0.4594      6.2435      6.1645|
|  7:  2.6795 -  2.5459 0.99   1273  144 0.4735 0.4865      6.1994       6.226|
|  8:  2.5459 -  2.4355 0.98   1258  137 0.4899 0.4623      6.1664      6.1211|
|  9:  2.4355 -  2.3421 0.98   1263  142 0.4800 0.4820      6.0916      6.1442|
| 10:  2.3421 -  2.2616 1.00   1262  143 0.4993 0.4713      6.0948      6.0985|
| 11:  2.2616 -  2.1911 0.97   1263  136 0.5075 0.5255      6.0322      6.0723|
| 12:  2.1911 -  2.1286 0.98   1236  139 0.5025 0.5245      5.9674      5.9883|
| 13:  2.1286 -  2.0727 0.99   1282  142 0.5075 0.4825      5.8852      5.8341|
| 14:  2.0727 -  2.0222 0.74    929  104 0.4912 0.5109      5.8222      5.7943|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.8260  1379   152  0.76  28.59   0.83     0.79      51433.24|
|  2:  4.8260 -  3.8507  1326   150  0.78  28.25   0.92     0.84      73740.78|
|  3:  3.8507 -  3.3699  1298   142  0.70  35.81   0.91     0.82      79577.08|
|  4:  3.3699 -  3.0645  1286   145  0.62  42.29   0.91     0.75      75039.97|
|  5:  3.0645 -  2.8463  1282   142  0.52  50.13   0.90     0.68      63758.32|
|  6:  2.8463 -  2.6795  1293   141  0.49  52.50   0.90     0.63      58907.07|
|  7:  2.6795 -  2.5459  1273   144  0.45  55.88   0.90     0.60      55802.53|
|  8:  2.5459 -  2.4355  1258   137  0.44  56.79   0.90     0.60      52647.88|
|  9:  2.4355 -  2.3421  1263   142  0.44  57.20   0.91     0.60      49025.62|
| 10:  2.3421 -  2.2616  1262   143  0.42  58.51   0.95     0.59      44310.23|
| 11:  2.2616 -  2.1911  1263   136  0.40  60.20   0.90     0.57      43219.61|
| 12:  2.1911 -  2.1286  1236   139  0.39  60.45   0.90     0.57      40144.04|
| 13:  2.1286 -  2.0727  1282   142  0.37  62.10   0.91     0.55      34949.38|
| 14:  2.0727 -  2.0222   929   104  0.40  60.03   0.92     0.51      27038.31|
|alpha:            min =        0.51 max =            0.84 mean =         0.65|
|beta:             min =    27038.31 max =        79577.08 mean =     54205.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.18|
|phase err.(test): min =        0.00 max =           89.99 mean =        50.11|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.446612              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.481   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.888148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.697   (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 |  1.698 -  2.019:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.019 -  2.339:        1 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.339 -  2.659:       56 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.659 -  2.979:     1694 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.979 -  3.299:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.299 -  3.619:     2593 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.619 -  3.940:     4610 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.940 -  4.260:     4321 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.260 -  4.580:     5671 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.580 -  4.900:     6816 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.698 |       0.151 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    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: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4343   r_free= 0.4288   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.234477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4267   r_free= 0.4220   ksol= 0.30   Bsol= 80.00   scale= 0.943   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.41,-0.69,3.35,-0.00,0.00,0.00); trace/3= 1.03                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.225827                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.742895              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.046830              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.344   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4267      final r-factor (work) = 0.2955          |
| start r-factor (free) = 0.4220      final r-factor (free) = 0.3185          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0408 = 5.74 * 0.50 * 6.2258 + 1.00 * 0.1637                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5059 = 5.74 * 0.50 * 6.0597 + 1.00 * 0.1058                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2955      final r-factor (work) = 0.2647          |
| start r-factor (free) = 0.3185      final r-factor (free) = 0.3248          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3495 = 1.05 * 1.00 * 6.0597 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1657 = 1.05 * 1.00 * 5.8724 + 1.00 * 0.0183                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.41  18.96    None  None   None       |
|    all(noH): 2823   0      0.00    112.41  18.96    None  None   None       |
|    Sol.    : 438    0      0.00    112.41  44.57    None  None   None       |
|    Mac.    : 2385   0      0.00    91.67   14.26    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 -  11.242: 1200   |   5:    56.207 -  67.449:   81        |
|      1:    11.242 -  22.483:  862   |   6:    67.449 -  78.690:   45        |
|      2:    22.483 -  33.724:  331   |   7:    78.690 -  89.932:   21        |
|      3:    33.724 -  44.966:  173   |   8:    89.932 - 101.173:    6        |
|      4:    44.966 -  56.207:  100   |   9:   101.173 - 112.415:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2647 r_free = 0.3248             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2644 r_free = 0.3247             target_work(ml) = 5.882         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2644   r_free= 0.3247   ksol= 0.30   Bsol= 80.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.41,-0.69,3.35,-0.00,0.00,0.00); trace/3= 1.03                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.882366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2634   r_free= 0.3242   ksol= 0.34   Bsol= 97.69   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,-1.12,0.86,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.883118                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.704533              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.550   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.305148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.395  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2634      final r-factor (work) = 0.1837          |
| start r-factor (free) = 0.3242      final r-factor (free) = 0.2413          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.7410 = 7.70 * 0.50 * 5.8758 + 1.00 * 0.1058                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2336 = 7.70 * 0.50 * 5.7514 + 1.00 * 0.0775                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1837      final r-factor (work) = 0.1663          |
| start r-factor (free) = 0.2413      final r-factor (free) = 0.2157          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7733 = 0.31 * 1.00 * 5.7514 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6982 = 0.31 * 1.00 * 5.5269 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    110.52  18.16    None  None   None       |
|    all(noH): 2823   0      0.79    110.52  18.16    None  None   None       |
|    Sol.    : 438    0      3.24    110.52  44.27    None  None   None       |
|    Mac.    : 2385   0      0.79    90.59   13.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.791 -  11.764: 1376   |   5:    55.655 -  66.628:   83        |
|      1:    11.764 -  22.737:  822   |   6:    66.628 -  77.601:   41        |
|      2:    22.737 -  33.709:  220   |   7:    77.601 -  88.574:   20        |
|      3:    33.709 -  44.682:  156   |   8:    88.574 -  99.547:    5        |
|      4:    44.682 -  55.655:   96   |   9:    99.547 - 110.519:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1663 r_free = 0.2157             target_work(ml) = 5.476         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1662 r_free = 0.2154             target_work(ml) = 5.475         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1662   r_free= 0.2154   ksol= 0.34   Bsol= 97.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,-1.12,0.86,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.474675                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1665   r_free= 0.2146   ksol= 0.34   Bsol= 89.68   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.52,-0.03,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.475207                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.057909              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.715  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.090391              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.811  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1665      final r-factor (work) = 0.1392          |
| start r-factor (free) = 0.2146      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5315 = 3.06 * 0.50 * 5.5293 + 1.00 * 0.0775                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3287 = 3.06 * 0.50 * 5.4001 + 1.00 * 0.0722                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1392      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.7004 = 3.09 * 1.00 * 5.4001 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.3759 = 3.09 * 1.00 * 5.2944 + 1.00 * 0.0140                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.84  18.01    None  None   None       |
|    all(noH): 2823   0      0.00    114.84  18.01    None  None   None       |
|    Sol.    : 438    0      4.54    114.84  45.80    None  None   None       |
|    Mac.    : 2385   0      0.00    97.58   12.91    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 -  11.484: 1385   |   5:    57.418 -  68.902:   86        |
|      1:    11.484 -  22.967:  861   |   6:    68.902 -  80.386:   39        |
|      2:    22.967 -  34.451:  181   |   7:    80.386 -  91.869:   20        |
|      3:    34.451 -  45.935:  125   |   8:    91.869 - 103.353:    6        |
|      4:    45.935 -  57.418:  116   |   9:   103.353 - 114.837:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1804             target_work(ml) = 5.281         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1300 r_free = 0.1803             target_work(ml) = 5.281         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1803   ksol= 0.34   Bsol= 89.68   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.52,-0.03,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.280862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1803   ksol= 0.34   Bsol= 89.68   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.52,-0.03,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.280747                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.642742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.427  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.349856              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.578   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1302      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1803      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0676 = 2.64 * 0.50 * 5.2941 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0174 = 2.64 * 0.50 * 5.2561 + 1.00 * 0.0722                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1725          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3647 = 2.35 * 1.00 * 5.2561 + 1.00 * 0.0138                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3006 = 2.35 * 1.00 * 5.2287 + 1.00 * 0.0139                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.03  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    123.03  17.62    None  None   None       |
|    Sol.    : 438    0      4.93    123.03  45.08    None  None   None       |
|    Mac.    : 2385   0      0.00    102.88  12.58    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 -  12.303: 1584   |   5:    61.515 -  73.818:   70        |
|      1:    12.303 -  24.606:  715   |   6:    73.818 -  86.121:   25        |
|      2:    24.606 -  36.909:  173   |   7:    86.121 -  98.424:   14        |
|      3:    36.909 -  49.212:  132   |   8:    98.424 - 110.727:    7        |
|      4:    49.212 -  61.515:  101   |   9:   110.727 - 123.030:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1213 r_free = 0.1725             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1725             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1725   ksol= 0.34   Bsol= 89.68   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.49,-1.52,-0.03,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220826                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1724   ksol= 0.33   Bsol= 78.40   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-1.17,0.27,-0.00,0.00,0.00); trace/3= -0.68                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220613                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.396022              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.896  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.947  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1210      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1724      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9529 = 3.40 * 0.50 * 5.2301 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9230 = 3.40 * 0.50 * 5.2038 + 1.00 * 0.0868                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2923 = 0.25 * 1.00 * 5.2038 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2878 = 0.25 * 1.00 * 5.2012 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    112.48  16.40    None  None   None       |
|    all(noH): 2823   0      0.45    112.48  16.40    None  None   None       |
|    Sol.    : 438    0      4.90    112.48  40.26    None  None   None       |
|    Mac.    : 2385   0      0.45    89.65   12.01    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:     0.455 -  11.658: 1544   |   5:    56.470 -  67.672:   53        |
|      1:    11.658 -  22.861:  754   |   6:    67.672 -  78.875:   17        |
|      2:    22.861 -  34.064:  177   |   7:    78.875 -  90.078:   13        |
|      3:    34.064 -  45.267:  155   |   8:    90.078 - 101.281:    4        |
|      4:    45.267 -  56.470:  105   |   9:   101.281 - 112.484:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1661             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1661             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1661   ksol= 0.33   Bsol= 78.40   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-1.17,0.27,-0.00,0.00,0.00); trace/3= -0.68                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188779                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8260 0.99   1379  152 0.1017 0.1371      5.4182      5.5669|
|  2:  4.8260 -  3.8507 0.99   1326  150 0.0848 0.1136      5.4503      5.6633|
|  3:  3.8507 -  3.3699 0.99   1298  142 0.1071 0.1508      5.4932      5.8472|
|  4:  3.3699 -  3.0645 0.99   1286  145 0.1258 0.1655      5.4904      5.6471|
|  5:  3.0645 -  2.8463 0.99   1282  142 0.1457 0.1873      5.4055      5.6204|
|  6:  2.8463 -  2.6795 0.99   1293  141 0.1294 0.2185      5.2944       5.579|
|  7:  2.6795 -  2.5459 0.99   1273  144 0.1364 0.1710      5.2405      5.4115|
|  8:  2.5459 -  2.4355 0.98   1258  137 0.1257 0.1727      5.1357      5.3954|
|  9:  2.4355 -  2.3421 0.98   1263  142 0.1218 0.1733      5.0727      5.2956|
| 10:  2.3421 -  2.2616 1.00   1262  143 0.1200 0.1873      5.0053      5.2815|
| 11:  2.2616 -  2.1911 0.97   1263  136 0.1205 0.1845      4.9839      5.2549|
| 12:  2.1911 -  2.1286 0.98   1236  139 0.1189 0.1831      4.9421      5.2682|
| 13:  2.1286 -  2.0727 0.99   1282  142 0.1222 0.1940      4.8401      5.1369|
| 14:  2.0727 -  2.0222 0.74    929  104 0.1094 0.1710      4.6821      4.9439|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.8260  1379   152  0.94   9.82   0.96     0.94       8152.25|
|  2:  4.8260 -  3.8507  1326   150  0.95   8.43   0.99     0.98       9650.13|
|  3:  3.8507 -  3.3699  1298   142  0.93  11.43   1.01     1.00      10813.77|
|  4:  3.3699 -  3.0645  1286   145  0.91  14.35   1.00     0.98      11124.37|
|  5:  3.0645 -  2.8463  1282   142  0.89  16.97   1.00     0.96       9524.29|
|  6:  2.8463 -  2.6795  1293   141  0.89  17.54   0.98     0.95       8489.06|
|  7:  2.6795 -  2.5459  1273   144  0.89  17.37   0.99     0.96       7304.86|
|  8:  2.5459 -  2.4355  1258   137  0.90  16.21   0.98     0.96       5981.05|
|  9:  2.4355 -  2.3421  1263   142  0.91  15.78   0.99     0.95       5378.35|
| 10:  2.3421 -  2.2616  1262   143  0.90  15.96   0.99     0.95       4700.36|
| 11:  2.2616 -  2.1911  1263   136  0.89  17.18   0.98     0.93       4671.96|
| 12:  2.1911 -  2.1286  1236   139  0.90  16.36   0.99     0.99       4492.69|
| 13:  2.1286 -  2.0727  1282   142  0.89  16.82   0.98     0.95       3615.60|
| 14:  2.0727 -  2.0222   929   104  0.92  13.95   0.95     0.92       2525.25|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2525.25 max =        11124.37 mean =      7007.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.83|
|phase err.(test): min =        0.00 max =           88.85 mean =        14.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1660   ksol= 0.32   Bsol= 67.41   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-1.02,0.44,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188749                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1660   ksol= 0.32   Bsol= 67.41   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.98,-1.02,0.44,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188749                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.8260 0.99   1379  152 0.1011 0.1369      5.4136      5.5644|
|  2:  4.8260 -  3.8507 0.99   1326  150 0.0842 0.1127      5.4449      5.6559|
|  3:  3.8507 -  3.3699 0.99   1298  142 0.1068 0.1509      5.4907      5.8478|
|  4:  3.3699 -  3.0645 0.99   1286  145 0.1260 0.1656      5.4926      5.6477|
|  5:  3.0645 -  2.8463 0.99   1282  142 0.1461 0.1879      5.4082      5.6234|
|  6:  2.8463 -  2.6795 0.99   1293  141 0.1295 0.2189      5.2966      5.5809|
|  7:  2.6795 -  2.5459 0.99   1273  144 0.1366 0.1712      5.2422      5.4134|
|  8:  2.5459 -  2.4355 0.98   1258  137 0.1258 0.1728      5.1366      5.3959|
|  9:  2.4355 -  2.3421 0.98   1263  142 0.1218 0.1731      5.0732      5.2952|
| 10:  2.3421 -  2.2616 1.00   1262  143 0.1202 0.1876      5.0062      5.2829|
| 11:  2.2616 -  2.1911 0.97   1263  136 0.1205 0.1847      4.9847      5.2555|
| 12:  2.1911 -  2.1286 0.98   1236  139 0.1189 0.1833      4.9425       5.269|
| 13:  2.1286 -  2.0727 0.99   1282  142 0.1222 0.1941      4.8404       5.137|
| 14:  2.0727 -  2.0222 0.74    929  104 0.1095 0.1711      4.6823      4.9438|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.8260  1379   152  0.94   9.77   0.96     0.94       8090.55|
|  2:  4.8260 -  3.8507  1326   150  0.95   8.38   1.00     0.98       9566.29|
|  3:  3.8507 -  3.3699  1298   142  0.93  11.35   1.01     1.01      10739.12|
|  4:  3.3699 -  3.0645  1286   145  0.91  14.37   1.00     0.98      11149.63|
|  5:  3.0645 -  2.8463  1282   142  0.89  17.00   1.00     0.97       9560.56|
|  6:  2.8463 -  2.6795  1293   141  0.89  17.58   0.98     0.96       8529.91|
|  7:  2.6795 -  2.5459  1273   144  0.89  17.39   0.99     0.96       7328.75|
|  8:  2.5459 -  2.4355  1258   137  0.90  16.22   0.99     0.96       5989.14|
|  9:  2.4355 -  2.3421  1263   142  0.91  15.79   1.00     0.95       5381.33|
| 10:  2.3421 -  2.2616  1262   143  0.90  15.97   0.99     0.96       4704.30|
| 11:  2.2616 -  2.1911  1263   136  0.89  17.20   0.98     0.94       4679.53|
| 12:  2.1911 -  2.1286  1236   139  0.90  16.37   1.00     0.99       4499.57|
| 13:  2.1286 -  2.0727  1282   142  0.89  16.83   0.98     0.96       3618.44|
| 14:  2.0727 -  2.0222   929   104  0.92  13.95   0.96     0.93       2525.05|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2525.05 max =        11149.63 mean =      7002.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.83|
|phase err.(test): min =        0.00 max =           88.93 mean =        14.16|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.478)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.44    112.47  16.38    None  None   None       |
|    all(noH): 2823   0      0.44    112.47  16.38    None  None   None       |
|    Sol.    : 438    0      4.89    112.47  40.25    None  None   None       |
|    Mac.    : 2385   0      0.44    89.64   12.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.441 -  11.644: 1544   |   5:    56.455 -  67.658:   53        |
|      1:    11.644 -  22.847:  754   |   6:    67.658 -  78.861:   17        |
|      2:    22.847 -  34.050:  177   |   7:    78.861 -  90.064:   13        |
|      3:    34.050 -  45.252:  155   |   8:    90.064 - 101.267:    4        |
|      4:    45.252 -  56.455:  105   |   9:   101.267 - 112.470:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.451 - 4.793
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 310
   mapped sites are within: 0.750 - 4.793

peak=    5.703 closest distance to " CB  GLN A 223 " =    1.471
peak=    5.125 closest distance to " O   HOH Z 111 " =    2.033
peak=    5.046 closest distance to " O   HOH Z 232 " =    2.183
peak=    4.993 closest distance to " CZ  PHE A 218 " =    1.121
peak=    4.960 closest distance to " CG  PRO A  54 " =    1.393
peak=    4.802 closest distance to " CB  ARG A 190 " =    1.510
peak=    4.679 closest distance to " O   HOH Z 369 " =    2.038
peak=    4.595 closest distance to " CB  GLN A 183 " =    1.304
peak=    4.593 closest distance to " CG  PRO A 213 " =    1.206
peak=    4.494 closest distance to " CB  SER A  63 " =    1.230
peak=    4.398 closest distance to " ND2 ASN A 187 " =    1.495
peak=    4.339 closest distance to " O   HOH Z 298 " =    2.043
peak=    4.324 closest distance to " NH1AARG A 145 " =    1.375
peak=    4.281 closest distance to " CB  VAL A 202 " =    1.616
peak=    4.251 closest distance to " O   PRO A 198 " =    1.574
peak=    4.246 closest distance to " CG  PRO A 198 " =    1.303
peak=    4.244 closest distance to " O   HOH Z  15 " =    2.214
peak=    4.221 closest distance to " CD  ARG A 269 " =    0.924
peak=    4.219 closest distance to " CB  ARG A  79 " =    1.318
peak=    4.193 closest distance to " CB  TRP A 266 " =    1.023
peak=    4.175 closest distance to " NE2 GLN A  11 " =    1.055
peak=    4.173 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.159 closest distance to " CB  ASP A 124 " =    0.775
peak=    4.152 closest distance to " O   HOH Z 188 " =    2.940
peak=    4.147 closest distance to " CB  GLU A 277 " =    3.812
peak=    4.140 closest distance to " O   HOH Z 287 " =    2.192
peak=    4.121 closest distance to " O   HOH Z 126 " =    1.567
peak=    4.108 closest distance to " O   HOH Z 368 " =    2.173
peak=    4.104 closest distance to " CD  LYS A 166 " =    1.336
peak=    4.094 closest distance to " O   HOH Z  21 " =    1.851
peak=    4.092 closest distance to " CB  ARG A 275 " =    0.986
peak=    4.080 closest distance to " O   HOH Z  19 " =    2.469
peak=    4.060 closest distance to " CG2 THR A 221 " =    0.969
peak=    4.056 closest distance to " CD  ARG A 159 " =    0.805
peak=    4.049 closest distance to " CD1 LEU A 300 " =    1.260
peak=    4.046 closest distance to " O   HOH Z 412 " =    3.877
peak=    4.039 closest distance to " O   HOH Z 425 " =    1.384
peak=    4.031 closest distance to " O   HOH Z 261 " =    1.885
peak=    4.026 closest distance to " CB  GLU A 128 " =    0.979
peak=    3.992 closest distance to " CB  GLU A 152 " =    1.200
peak=    3.986 closest distance to " O   HOH Z 265 " =    2.142
peak=    3.981 closest distance to " O   TYR A 116 " =    1.326
peak=    3.977 closest distance to " O   HOH Z 214 " =    2.167
peak=    3.966 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.958 closest distance to " O   HOH Z 234 " =    3.891
peak=    3.935 closest distance to " CB  ASN A 187 " =    2.040
peak=    3.907 closest distance to " O   HOH Z 133 " =    2.719
peak=    3.880 closest distance to " CB  ASN A 148 " =    1.471
peak=    3.870 closest distance to " CB  TYR A 169 " =    0.803
peak=    3.869 closest distance to " CB  LEU A 228 " =    1.073
peak=    3.850 closest distance to " O   HOH Z 427 " =    3.278
peak=    3.844 closest distance to " CB  ASP A 140 " =    0.883
peak=    3.827 closest distance to " CB  VAL A 265 " =    1.336
peak=    3.825 closest distance to " CG  PRO A 243 " =    1.068
peak=    3.809 closest distance to " CB  ALA A   9 " =    1.657
peak=    3.805 closest distance to " O   SER A  87 " =    2.268
peak=    3.804 closest distance to " O   HOH Z  40 " =    1.936
peak=    3.804 closest distance to " O   HOH Z 383 " =    2.002
peak=    3.800 closest distance to " CG BARG A 275 " =    1.411
peak=    3.799 closest distance to " CA  ARG A 195 " =    1.205
peak=    3.797 closest distance to " CA  ALA A 160 " =    0.990
peak=    3.794 closest distance to " CD2 TRP A 179 " =    1.273
peak=    3.792 closest distance to " CA  TYR A  30 " =    1.041
peak=    3.791 closest distance to " O   HOH Z 192 " =    2.139
peak=    3.782 closest distance to " O   HOH Z 303 " =    2.164
peak=    3.769 closest distance to " CA  ASP A 191 " =    0.869
peak=    3.764 closest distance to " CB  LEU A  83 " =    0.793
peak=    3.751 closest distance to " CE  LYS A  76 " =    0.870
peak=    3.748 closest distance to " O   HOH Z 285 " =    2.367
peak=    3.742 closest distance to " O   HOH Z  49 " =    0.983
peak=    3.739 closest distance to " CB  ASN A  39 " =    0.896
peak=    3.736 closest distance to " CA  MET A 105 " =    1.007
peak=    3.735 closest distance to " CB  ASN A 142 " =    0.942
peak=    3.731 closest distance to " O   HOH Z 361 " =    3.777
peak=    3.724 closest distance to " CZ  PHE A  38 " =    1.263
peak=    3.721 closest distance to " CA  ALA A  51 " =    0.866
peak=    3.721 closest distance to " O   HOH Z 406 " =    1.695
peak=    3.717 closest distance to " O   HOH Z 158 " =    3.039
peak=    3.716 closest distance to " CG2AVAL A 121 " =    2.344
peak=    3.702 closest distance to " O   HOH Z 213 " =    1.976
peak=    3.701 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.699 closest distance to " NH2 ARG A 156 " =    1.147
peak=    3.690 closest distance to " N   ASN A  39 " =    1.337
peak=    3.675 closest distance to " CG  ARG A 138 " =    1.162
peak=    3.674 closest distance to " CA  ALA A 295 " =    1.083
peak=    3.668 closest distance to " O   HOH Z 346 " =    1.552
peak=    3.664 closest distance to " O  BHOH Z 338 " =    2.339
peak=    3.664 closest distance to " CB  SER A 212 " =    1.185
peak=    3.656 closest distance to " CA  ARG A  36 " =    1.213
peak=    3.651 closest distance to " O   HOH Z 294 " =    1.521
peak=    3.647 closest distance to " O   HOH Z 180 " =    2.055
peak=    3.638 closest distance to " O   HOH Z  78 " =    1.592
peak=    3.635 closest distance to " CG  MET A 185 " =    1.231
peak=    3.634 closest distance to " CD ALYS A 290 " =    0.996
peak=    3.631 closest distance to " O   HOH Z 316 " =    3.185
peak=    3.630 closest distance to " CB  ALA A 104 " =    0.785
peak=    3.621 closest distance to " O   ALA A 165 " =    1.407
peak=    3.608 closest distance to " CB  ALA A 248 " =    1.097
peak=    3.596 closest distance to " NZ  LYS A 117 " =    3.225
peak=    3.593 closest distance to " O   MET A 105 " =    1.821
peak=    3.591 closest distance to " CB  GLN A  89 " =    1.202
peak=    3.589 closest distance to " O   HOH Z 183 " =    1.405
peak=    3.582 closest distance to " CD  ARG A  66 " =    2.299
peak=    3.581 closest distance to " CB  PRO A  90 " =    1.208
peak=    3.578 closest distance to " O   HOH Z 271 " =    2.692
peak=    3.574 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.573 closest distance to " CA  ALA A 154 " =    0.984
peak=    3.570 closest distance to " O   HOH Z 272 " =    1.917
peak=    3.560 closest distance to " CG AARG A 275 " =    1.168
peak=    3.559 closest distance to " O   HOH Z 148 " =    3.391
peak=    3.553 closest distance to " CA  MET A  40 " =    1.222
peak=    3.546 closest distance to " O   HOH Z 359 " =    1.676
peak=    3.543 closest distance to " CB  GLN A  88 " =    1.195
peak=    3.540 closest distance to " O   HOH Z 116 " =    1.845
peak=    3.538 closest distance to " CA  GLY A 241 " =    0.847
peak=    3.536 closest distance to " O   HOH Z  80 " =    1.797
peak=    3.536 closest distance to " O   HOH Z 171 " =    3.971
peak=    3.535 closest distance to " CB  ALA A 242 " =    0.836
peak=    3.534 closest distance to " CG2 VAL A 257 " =    0.793
peak=    3.533 closest distance to " OD1 ASN A  69 " =    2.658
peak=    3.532 closest distance to " OE1 GLN A  11 " =    2.084
peak=    3.529 closest distance to " NH2AARG A 275 " =    3.516
peak=    3.529 closest distance to " O   HOH Z 403 " =    1.585
peak=    3.523 closest distance to " O   HOH Z 193 " =    2.294
peak=    3.522 closest distance to " O   HOH Z 197 " =    2.803
peak=    3.518 closest distance to " O   HOH Z 176 " =    1.615
peak=    3.517 closest distance to " O   HOH Z 193 " =    1.774
peak=    3.511 closest distance to " CB  SER A   3 " =    1.652
peak=    3.498 closest distance to " CG1 VAL A 153 " =    0.993
peak=    3.497 closest distance to " O   HOH Z 353 " =    2.673
peak=    3.495 closest distance to " O   ASN A 209 " =    1.319
peak=    3.491 closest distance to " CA  GLU A 152 " =    0.949
peak=    3.490 closest distance to " O   HOH Z 172 " =    3.918
peak=    3.482 closest distance to " O   HOH Z 147 " =    1.770
peak=    3.478 closest distance to " CG  GLU A  37 " =    0.978
peak=    3.475 closest distance to " CA  SER A  87 " =    0.964
peak=    3.470 closest distance to " CD1 LEU A  96 " =    0.750
peak=    3.469 closest distance to " CA  VAL A 125 " =    1.295
peak=    3.461 closest distance to " CB  SER A 141 " =    1.075
peak=    3.459 closest distance to " O   HOH Z  88 " =    1.916
peak=    3.446 closest distance to " O   HOH Z 128 " =    2.276
peak=    3.445 closest distance to " CD2 LEU A 255 " =    1.743
peak=    3.431 closest distance to " N   ARG A 156 " =    1.413
peak=    3.427 closest distance to " CB  TYR A 116 " =    0.890
peak=    3.424 closest distance to " CG1BVAL A  72 " =    1.864
peak=    3.421 closest distance to " CA  TYR A 116 " =    1.404
peak=    3.416 closest distance to " O   HOH Z  97 " =    2.020
peak=    3.413 closest distance to " O   HOH Z  88 " =    3.806
peak=    3.412 closest distance to " CG  LEU A 167 " =    1.212
peak=    3.412 closest distance to " CB  ILE A 120 " =    1.203
peak=    3.400 closest distance to " O   HOH Z 326 " =    2.429
peak=    3.398 closest distance to " CA  ASP A 162 " =    1.031
peak=    3.395 closest distance to " NE  ARG A  79 " =    1.131
peak=    3.395 closest distance to " CB  ALA A  34 " =    1.007
peak=    3.395 closest distance to " O   HOH Z 227 " =    1.821
peak=    3.395 closest distance to " O   HOH Z  61 " =    1.639
peak=    3.394 closest distance to " O   HOH Z 313 " =    1.866
peak=    3.389 closest distance to " CB  ALA A   1 " =    4.793
peak=    3.383 closest distance to " O   THR A 182 " =    1.454
peak=    3.381 closest distance to " O   ALA A 158 " =    1.261
peak=    3.380 closest distance to " CA  THR A 221 " =    0.913
peak=    3.379 closest distance to " CG2 ILE A 120 " =    1.087
peak=    3.379 closest distance to " O   HOH Z 313 " =    1.615
peak=    3.377 closest distance to " NE2 GLN A  77 " =    3.574
peak=    3.377 closest distance to " OG BSER A 164 " =    2.459
peak=    3.376 closest distance to " O   HOH Z  63 " =    1.483
peak=    3.376 closest distance to " CA  ARG A 139 " =    1.234
peak=    3.375 closest distance to " CB  ASN A 187 " =    1.050
peak=    3.372 closest distance to " O   HOH Z 290 " =    1.193
peak=    3.371 closest distance to " O   PRO A 213 " =    1.476
peak=    3.371 closest distance to " CB  ARG A 138 " =    1.057
peak=    3.367 closest distance to " CB  ALA A  43 " =    0.919
peak=    3.362 closest distance to " OG BSER A 134 " =    2.888
peak=    3.361 closest distance to " O   HOH Z 417 " =    3.299
peak=    3.359 closest distance to " OD1 ASN A 217 " =    1.533
peak=    3.359 closest distance to " O   HOH Z  44 " =    2.109
peak=    3.354 closest distance to " CA  ALA A 100 " =    1.025
peak=    3.350 closest distance to " O   ASN A  74 " =    1.560
peak=    3.345 closest distance to " O   THR A 251 " =    1.307
peak=    3.345 closest distance to " O   HOH Z 422 " =    2.718
peak=    3.345 closest distance to " CA  SER A  26 " =    0.928
peak=    3.344 closest distance to " O   HOH Z  98 " =    1.650
peak=    3.342 closest distance to " OG  SER A  22 " =    2.840
peak=    3.342 closest distance to " O   HOH Z 250 " =    1.416
peak=    3.342 closest distance to " CA  GLU A  46 " =    0.807
peak=    3.341 closest distance to " CA  ALA A 291 " =    0.844
peak=    3.338 closest distance to " CB  THR A  82 " =    1.324
peak=    3.338 closest distance to " O   HOH Z 141 " =    1.662
peak=    3.337 closest distance to " O   HOH Z 248 " =    1.685
peak=    3.336 closest distance to " O   HOH Z   1 " =    2.323
peak=    3.335 closest distance to " CB  ALA A 291 " =    1.099
peak=    3.334 closest distance to " O   HOH Z 130 " =    2.156
peak=    3.332 closest distance to " N   ARG A 190 " =    1.170
peak=    3.330 closest distance to " CB  TRP A 150 " =    1.431
peak=    3.328 closest distance to " CB  MET A  40 " =    0.763
peak=    3.326 closest distance to " O   HOH Z 142 " =    1.668
peak=    3.320 closest distance to " CB  TRP A 179 " =    1.435
peak=    3.313 closest distance to " CA  ALA A 233 " =    1.536
peak=    3.312 closest distance to " O   HOH Z 285 " =    1.976
peak=    3.310 closest distance to " O   HOH Z 234 " =    1.835
peak=    3.310 closest distance to " O   HOH Z 403 " =    1.430
peak=    3.309 closest distance to " NE2 HIS A 207 " =    1.194
peak=    3.308 closest distance to " O   HOH Z 146 " =    2.232
peak=    3.303 closest distance to " CG2 VAL A 197 " =    1.179
peak=    3.303 closest distance to " CD1 ILE A 106 " =    0.838
peak=    3.303 closest distance to " CA  THR A 264 " =    0.830
peak=    3.303 closest distance to " O   HOH Z 184 " =    1.625
peak=    3.298 closest distance to " O   ASP A 124 " =    1.236
peak=    3.297 closest distance to " CB  GLN A 103 " =    0.868
peak=    3.294 closest distance to " O   HOH Z 423 " =    1.853
peak=    3.294 closest distance to " O   HOH Z   9 " =    2.035
peak=    3.291 closest distance to " OG  SER A 245 " =    1.771
peak=    3.287 closest distance to " OG  SER A  28 " =    1.611
peak=    3.281 closest distance to " N   PHE A 130 " =    1.252
peak=    3.278 closest distance to " ND1 HIS A  86 " =    1.687
peak=    3.275 closest distance to " CA  GLY A  98 " =    1.175
peak=    3.273 closest distance to " CB  GLN A 205 " =    1.052
peak=    3.271 closest distance to " O   HOH Z  10 " =    1.884
peak=    3.269 closest distance to " OD2 ASP A 200 " =    1.230
peak=    3.268 closest distance to " CA  ASN A 215 " =    1.126
peak=    3.267 closest distance to " CZ  PHE A 192 " =    0.984
peak=    3.263 closest distance to " O   HOH Z  59 " =    2.331
peak=    3.261 closest distance to " N   ASN A 127 " =    1.325
peak=    3.257 closest distance to " CA  ARG A 102 " =    1.161
peak=    3.251 closest distance to " O   HOH Z 174 " =    2.359
peak=    3.251 closest distance to " CG  GLN A  11 " =    1.381
peak=    3.250 closest distance to " CB  ASN A 285 " =    0.929
peak=    3.248 closest distance to " O   THR A 220 " =    1.155
peak=    3.248 closest distance to " CB  ASP A 298 " =    1.215
peak=    3.247 closest distance to " O   HOH Z  28 " =    1.828
peak=    3.246 closest distance to " CG2 THR A 220 " =    0.898
peak=    3.245 closest distance to " ND1 HIS A  81 " =    1.702
peak=    3.245 closest distance to " O   ASN A 284 " =    1.717
peak=    3.241 closest distance to " O   HOH Z 124 " =    2.074
peak=    3.236 closest distance to " N   CYS A 260 " =    0.816
peak=    3.234 closest distance to " CG2 ILE A 234 " =    0.971
peak=    3.232 closest distance to " CG  PHE A 204 " =    0.905
peak=    3.230 closest distance to " O   THR A 251 " =    1.931
peak=    3.227 closest distance to " CA  TYR A  30 " =    1.051
peak=    3.226 closest distance to " O   HOH Z 102 " =    1.310
peak=    3.217 closest distance to " CG1 ILE A  33 " =    1.257
peak=    3.216 closest distance to " O   HOH Z 134 " =    2.757
peak=    3.215 closest distance to " CA  ASN A 127 " =    1.100
peak=    3.214 closest distance to " ND2 ASN A 249 " =    0.824
peak=    3.210 closest distance to " O   HOH Z 371 " =    3.207
peak=    3.204 closest distance to " CB  LEU A  96 " =    1.340
peak=    3.203 closest distance to " O   HOH Z  68 " =    1.808
peak=    3.201 closest distance to " CG  LYS A  76 " =    1.019
peak=    3.199 closest distance to " CB  PHE A 155 " =    0.814
peak=    3.197 closest distance to " CA  ILE A 106 " =    0.844
peak=    3.195 closest distance to " NH2BARG A 145 " =    2.207
peak=    3.192 closest distance to " O   HOH Z 391 " =    2.990
peak=    3.191 closest distance to " CB  ALA A 100 " =    1.320
peak=    3.190 closest distance to " O   HOH Z 106 " =    4.126
peak=    3.189 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.188 closest distance to " NZ  LYS A  48 " =    1.385
peak=    3.188 closest distance to " O   HOH Z  85 " =    2.265
peak=    3.187 closest distance to " CB  PRO A 243 " =    1.322
peak=    3.186 closest distance to " CA  GLY A 211 " =    1.315
peak=    3.183 closest distance to " O   HOH Z 403 " =    1.996
peak=    3.180 closest distance to " CG  MET A 185 " =    1.038
peak=    3.178 closest distance to " CB  LYS A 117 " =    1.115
peak=    3.172 closest distance to " CA  ASN A 217 " =    1.319
peak=    3.169 closest distance to " O   HOH Z 166 " =    3.731
peak=    3.166 closest distance to " CD  ARG A  66 " =    2.858
peak=    3.162 closest distance to " O   HOH Z 203 " =    1.805
peak=    3.159 closest distance to " ND2 ASN A 249 " =    1.965
peak=    3.147 closest distance to " CA  GLY A 267 " =    1.018
peak=    3.147 closest distance to " CE  MET A 113 " =    1.811
peak=    3.147 closest distance to " CA  ASP A 124 " =    0.820
peak=    3.141 closest distance to " CE1 HIS A 115 " =    0.926
peak=    3.139 closest distance to " O   HOH Z 409 " =    2.963
peak=    3.135 closest distance to " CB  MET A  47 " =    0.942
peak=    3.135 closest distance to " O   HOH Z 327 " =    1.935
peak=    3.131 closest distance to " O   HOH Z 128 " =    2.424
peak=    3.127 closest distance to " O   HOH Z 394 " =    4.005
peak=    3.125 closest distance to " CB  ASN A 215 " =    1.150
peak=    3.125 closest distance to " O   THR A 294 " =    1.286
peak=    3.119 closest distance to " O   ASP A 191 " =    1.487
peak=    3.118 closest distance to " CA  ALA A  21 " =    1.189
peak=    3.117 closest distance to " CB  LEU A 300 " =    0.935
peak=    3.112 closest distance to " N   VAL A 126 " =    1.435
peak=    3.108 closest distance to " O   HOH Z  68 " =    1.988
peak=    3.105 closest distance to " O   HOH Z 299 " =    4.587
peak=    3.104 closest distance to " CB  MET A 113 " =    1.868
peak=    3.101 closest distance to " CD  LYS A 193 " =    2.020
peak=    3.099 closest distance to " CB  ARG A 156 " =    1.108
peak=    3.089 closest distance to " CE3 TRP A 150 " =    1.081
peak=    3.089 closest distance to " CB  ALA A 114 " =    0.862
peak=    3.089 closest distance to " CZ3 TRP A  85 " =    0.947
peak=    3.084 closest distance to " CB  SER A 210 " =    0.831
peak=    3.084 closest distance to " O   HOH Z 256 " =    1.547
peak=    3.075 closest distance to " CG  ARG A 159 " =    0.889
peak=    3.069 closest distance to " CA  GLN A 223 " =    0.973
peak=    3.065 closest distance to " CG BARG A 102 " =    1.910
peak=    3.057 closest distance to " O   HOH Z 180 " =    2.055
peak=    3.054 closest distance to " CB  SER A 216 " =    0.871
peak=    3.053 closest distance to " CA  LEU A  83 " =    1.560
peak=    3.032 closest distance to " O   HOH Z 364 " =    2.700
peak=    3.032 closest distance to " O   HOH Z 211 " =    0.999
peak=    3.030 closest distance to " O   HOH Z 394 " =    1.826

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 239         
Filter by distance & map next to the model:
   mapped sites are within: 0.592 - 5.965
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 237 from: 239
   mapped sites are within: 0.773 - 5.965

peak=   -4.727 closest distance to " CB  PRO A 243 " =    2.660
peak=   -4.716 closest distance to " CG1 VAL A 112 " =    2.599
peak=   -4.457 closest distance to " CD  GLN A  58 " =    0.919
peak=   -4.456 closest distance to " CG1 VAL A 250 " =    2.748
peak=   -4.400 closest distance to " O   HOH Z 211 " =    1.043
peak=   -4.376 closest distance to " O   HOH Z  73 " =    2.443
peak=   -4.260 closest distance to " CA  GLY A 241 " =    3.227
peak=   -4.231 closest distance to " O   PRO A 198 " =    1.352
peak=   -4.220 closest distance to " O   HOH Z 290 " =    1.204
peak=   -4.213 closest distance to " CD  ARG A 156 " =    2.196
peak=   -4.181 closest distance to " CD  ARG A  14 " =    3.406
peak=   -4.144 closest distance to " N   ALA A  43 " =    2.667
peak=   -4.140 closest distance to " O   HOH Z 411 " =    5.628
peak=   -4.104 closest distance to " CZ3 TRP A 179 " =    1.146
peak=   -4.097 closest distance to " O   HOH Z 114 " =    0.957
peak=   -4.069 closest distance to " O   HOH Z 377 " =    0.940
peak=   -4.049 closest distance to " O   VAL A  67 " =    2.689
peak=   -4.038 closest distance to " CD1 PHE A 130 " =    2.336
peak=   -3.984 closest distance to " CE2 PHE A  61 " =    2.665
peak=   -3.977 closest distance to " CD2 TYR A 293 " =    2.008
peak=   -3.964 closest distance to " O   HOH Z 183 " =    1.215
peak=   -3.957 closest distance to " O   HOH Z 196 " =    2.322
peak=   -3.946 closest distance to " O   HOH Z  10 " =    1.548
peak=   -3.942 closest distance to " O   HOH Z 394 " =    1.576
peak=   -3.940 closest distance to " CE2 TYR A  30 " =    2.807
peak=   -3.925 closest distance to " O   HOH Z 128 " =    2.743
peak=   -3.901 closest distance to " OE1 GLN A 223 " =    2.131
peak=   -3.897 closest distance to " CG  LEU A 101 " =    2.491
peak=   -3.860 closest distance to " O   HOH Z  43 " =    1.346
peak=   -3.856 closest distance to " CG  ARG A 269 " =    2.399
peak=   -3.854 closest distance to " O   HOH Z 232 " =    1.847
peak=   -3.847 closest distance to " CG  MET A 105 " =    1.002
peak=   -3.813 closest distance to " O   HOH Z 166 " =    1.746
peak=   -3.811 closest distance to " O   HOH Z  38 " =    1.154
peak=   -3.792 closest distance to " O   ILE A 109 " =    2.636
peak=   -3.780 closest distance to " CD1 LEU A 101 " =    2.473
peak=   -3.778 closest distance to " O   HOH Z 377 " =    1.772
peak=   -3.777 closest distance to " C   ALA A 158 " =    1.419
peak=   -3.765 closest distance to " O   HOH Z 133 " =    1.231
peak=   -3.762 closest distance to " OG  SER A  97 " =    2.305
peak=   -3.761 closest distance to " OD1 ASN A 148 " =    1.445
peak=   -3.751 closest distance to " NE2 GLN A  11 " =    1.385
peak=   -3.748 closest distance to " CA  VAL A  67 " =    2.905
peak=   -3.745 closest distance to " CD1 PHE A  59 " =    2.043
peak=   -3.736 closest distance to " O   HOH Z 216 " =    1.047
peak=   -3.720 closest distance to " CD  GLN A 223 " =    1.208
peak=   -3.682 closest distance to " O   HOH Z  60 " =    1.323
peak=   -3.676 closest distance to " C   HIS A 108 " =    1.103
peak=   -3.669 closest distance to " O   HOH Z  51 " =    1.367
peak=   -3.668 closest distance to " CG  LYS A 193 " =    2.619
peak=   -3.656 closest distance to " CB  ALA A 129 " =    2.460
peak=   -3.649 closest distance to " ND2 ASN A  45 " =    2.107
peak=   -3.643 closest distance to " O   HOH Z  37 " =    2.069
peak=   -3.636 closest distance to " O   HOH Z 368 " =    1.769
peak=   -3.630 closest distance to " CA  ASP A 298 " =    1.132
peak=   -3.614 closest distance to " C   ASN A 285 " =    2.537
peak=   -3.614 closest distance to " SG  CYS A 254 " =    3.247
peak=   -3.589 closest distance to " CB  ALA A  10 " =    2.224
peak=   -3.588 closest distance to " CB  ALA A  43 " =    2.721
peak=   -3.588 closest distance to " O   HOH Z 150 " =    2.181
peak=   -3.576 closest distance to " CD  GLN A  88 " =    0.774
peak=   -3.571 closest distance to " CG1 VAL A 265 " =    2.340
peak=   -3.571 closest distance to " CG  HIS A  86 " =    1.189
peak=   -3.571 closest distance to " NH2 ARG A  79 " =    1.597
peak=   -3.566 closest distance to " CG1 VAL A 112 " =    2.772
peak=   -3.564 closest distance to " CE BMET A  47 " =    2.054
peak=   -3.562 closest distance to " O   HOH Z 393 " =    1.265
peak=   -3.556 closest distance to " O   ALA A  10 " =    1.705
peak=   -3.554 closest distance to " N   ASP A 171 " =    2.443
peak=   -3.547 closest distance to " CG2 ILE A  49 " =    2.811
peak=   -3.545 closest distance to " O   HOH Z 275 " =    1.888
peak=   -3.543 closest distance to " O   HOH Z   6 " =    1.338
peak=   -3.541 closest distance to " CE3 TRP A  70 " =    1.934
peak=   -3.538 closest distance to " CD  ARG A  79 " =    1.167
peak=   -3.533 closest distance to " CG2 VAL A 189 " =    2.200
peak=   -3.522 closest distance to " O   SER A 210 " =    1.962
peak=   -3.520 closest distance to " OH  TYR A 247 " =    1.795
peak=   -3.517 closest distance to " O   HOH Z 264 " =    1.753
peak=   -3.516 closest distance to " CD  GLN A  55 " =    0.869
peak=   -3.511 closest distance to " O   HOH Z 359 " =    2.999
peak=   -3.492 closest distance to " O   HOH Z 351 " =    1.644
peak=   -3.489 closest distance to " NH2AARG A 275 " =    5.555
peak=   -3.487 closest distance to " O   HOH Z  99 " =    0.872
peak=   -3.486 closest distance to " O   HOH Z 111 " =    1.774
peak=   -3.481 closest distance to " CA  GLY A 241 " =    2.373
peak=   -3.470 closest distance to " O   HOH Z  52 " =    1.440
peak=   -3.467 closest distance to " O   HOH Z 438 " =    3.216
peak=   -3.466 closest distance to " N   THR A  18 " =    1.293
peak=   -3.461 closest distance to " OD1 ASP A 171 " =    1.632
peak=   -3.459 closest distance to " O   HOH Z 177 " =    1.772
peak=   -3.459 closest distance to " CG1 VAL A 125 " =    1.970
peak=   -3.455 closest distance to " O   PRO A 163 " =    2.122
peak=   -3.451 closest distance to " CG  LEU A  83 " =    2.080
peak=   -3.449 closest distance to " O   HOH Z 145 " =    0.902
peak=   -3.446 closest distance to " O   HOH Z 185 " =    2.427
peak=   -3.441 closest distance to " OE1 GLN A  88 " =    1.123
peak=   -3.438 closest distance to " CG  ARG A 219 " =    2.890
peak=   -3.436 closest distance to " O   GLN A  94 " =    2.229
peak=   -3.435 closest distance to " O   HOH Z 175 " =    4.078
peak=   -3.432 closest distance to " NE2 GLN A 240 " =    1.809
peak=   -3.425 closest distance to " CB  ALA A   7 " =    2.407
peak=   -3.418 closest distance to " CD  GLN A  11 " =    0.838
peak=   -3.412 closest distance to " O   HOH Z 407 " =    3.582
peak=   -3.409 closest distance to " O   HOH Z 198 " =    1.140
peak=   -3.408 closest distance to " O   HOH Z 389 " =    2.134
peak=   -3.404 closest distance to " OD1 ASP A 191 " =    1.546
peak=   -3.401 closest distance to " CG2 THR A 178 " =    2.384
peak=   -3.400 closest distance to " CB  TRP A  85 " =    2.531
peak=   -3.399 closest distance to " NE2 GLN A 103 " =    1.868
peak=   -3.395 closest distance to " O   ALA A  34 " =    2.708
peak=   -3.393 closest distance to " O   HOH Z 156 " =    3.449
peak=   -3.393 closest distance to " OD2 ASP A 171 " =    1.950
peak=   -3.389 closest distance to " CB  ALA A 291 " =    2.525
peak=   -3.386 closest distance to " N   THR A  52 " =    1.593
peak=   -3.384 closest distance to " CA  GLY A 133 " =    2.341
peak=   -3.370 closest distance to " OG BSER A 134 " =    1.567
peak=   -3.368 closest distance to " CG  GLU A  53 " =    1.572
peak=   -3.366 closest distance to " O   HOH Z 426 " =    1.680
peak=   -3.364 closest distance to " O   HOH Z  60 " =    2.571
peak=   -3.364 closest distance to " O   HOH Z 234 " =    4.599
peak=   -3.362 closest distance to " CG  ARG A  66 " =    2.275
peak=   -3.360 closest distance to " CG1AVAL A  41 " =    2.808
peak=   -3.352 closest distance to " CB  ALA A   9 " =    2.496
peak=   -3.350 closest distance to " ND2 ASN A 249 " =    2.434
peak=   -3.350 closest distance to " C   LEU A 143 " =    1.229
peak=   -3.349 closest distance to " O   SER A 271 " =    2.247
peak=   -3.347 closest distance to " O   HOH Z 193 " =    1.748
peak=   -3.340 closest distance to " N   THR A 264 " =    1.377
peak=   -3.337 closest distance to " O   HOH Z 313 " =    1.142
peak=   -3.335 closest distance to " CE3 TRP A 150 " =    2.258
peak=   -3.326 closest distance to " O   GLY A 211 " =    1.430
peak=   -3.320 closest distance to " O   HOH Z 372 " =    2.576
peak=   -3.320 closest distance to " CA  GLY A 203 " =    2.524
peak=   -3.316 closest distance to " CD2 HIS A 207 " =    2.287
peak=   -3.312 closest distance to " CB  ASP A 286 " =    2.168
peak=   -3.306 closest distance to " O   HOH Z 106 " =    2.057
peak=   -3.303 closest distance to " NE2 GLN A 194 " =    1.950
peak=   -3.302 closest distance to " O   HOH Z 298 " =    2.623
peak=   -3.297 closest distance to " CG  GLN A  58 " =    1.180
peak=   -3.293 closest distance to " CG  GLU A 277 " =    1.184
peak=   -3.284 closest distance to " ND2 ASN A  69 " =    1.702
peak=   -3.282 closest distance to " O   HOH Z 113 " =    2.277
peak=   -3.282 closest distance to " O   SER A 276 " =    1.817
peak=   -3.278 closest distance to " CE1 PHE A 225 " =    2.132
peak=   -3.276 closest distance to " O   HOH Z 421 " =    3.379
peak=   -3.275 closest distance to " O   HOH Z 348 " =    2.250
peak=   -3.275 closest distance to " CB  ASP A 132 " =    2.312
peak=   -3.271 closest distance to " O   HOH Z 396 " =    2.208
peak=   -3.266 closest distance to " CD  GLN A  88 " =    1.040
peak=   -3.264 closest distance to " OD1 ASN A 173 " =    1.521
peak=   -3.263 closest distance to " SG BCYS A 201 " =    0.972
peak=   -3.260 closest distance to " O   HOH Z 252 " =    3.883
peak=   -3.255 closest distance to " O   HOH Z  78 " =    1.993
peak=   -3.251 closest distance to " CG  PRO A 163 " =    2.030
peak=   -3.250 closest distance to " O   HOH Z 357 " =    2.035
peak=   -3.249 closest distance to " CZ  PHE A  38 " =    2.032
peak=   -3.249 closest distance to " N   ALA A 248 " =    1.811
peak=   -3.249 closest distance to " OH  TYR A 247 " =    2.243
peak=   -3.249 closest distance to " O   HOH Z 435 " =    2.598
peak=   -3.249 closest distance to " ND2 ASN A  60 " =    1.392
peak=   -3.246 closest distance to " O   HOH Z 136 " =    2.402
peak=   -3.244 closest distance to " CB  PHE A  16 " =    2.533
peak=   -3.243 closest distance to " O   ARG A  24 " =    2.171
peak=   -3.242 closest distance to " O   HOH Z 275 " =    1.649
peak=   -3.240 closest distance to " CG  ARG A 269 " =    2.071
peak=   -3.226 closest distance to " O   HOH Z 265 " =    2.455
peak=   -3.224 closest distance to " O   HOH Z 189 " =    2.174
peak=   -3.224 closest distance to " O   HOH Z  82 " =    2.064
peak=   -3.222 closest distance to " CE  MET A 105 " =    2.332
peak=   -3.221 closest distance to " O   GLN A 240 " =    2.665
peak=   -3.220 closest distance to " CG  TRP A 266 " =    1.869
peak=   -3.219 closest distance to " OD2 ASP A  50 " =    2.275
peak=   -3.217 closest distance to " O   HOH Z 357 " =    1.913
peak=   -3.210 closest distance to " CD1 LEU A  83 " =    2.731
peak=   -3.209 closest distance to " N   ALA A 226 " =    2.109
peak=   -3.209 closest distance to " O   HOH Z 150 " =    1.378
peak=   -3.208 closest distance to " O   HOH Z  71 " =    2.334
peak=   -3.208 closest distance to " O   HOH Z 236 " =    1.371
peak=   -3.208 closest distance to " O   HOH Z  70 " =    2.186
peak=   -3.207 closest distance to " ND2 ASN A  60 " =    4.154
peak=   -3.206 closest distance to " CG1 VAL A 112 " =    2.853
peak=   -3.201 closest distance to " CD1 LEU A   5 " =    2.574
peak=   -3.201 closest distance to " N   GLY A  35 " =    1.552
peak=   -3.200 closest distance to " O   HOH Z  19 " =    2.129
peak=   -3.198 closest distance to " C   ALA A 165 " =    1.994
peak=   -3.195 closest distance to " O   HOH Z 111 " =    1.645
peak=   -3.194 closest distance to " OD1 ASN A 173 " =    1.336
peak=   -3.194 closest distance to " OE1 GLN A  88 " =    0.854
peak=   -3.191 closest distance to " NE1 TRP A 266 " =    2.265
peak=   -3.191 closest distance to " CG  PRO A 243 " =    1.843
peak=   -3.188 closest distance to " O   HOH Z 317 " =    2.218
peak=   -3.186 closest distance to " ND2 ASN A  45 " =    1.261
peak=   -3.185 closest distance to " O   HOH Z 371 " =    1.635
peak=   -3.184 closest distance to " CG2 THR A 221 " =    2.266
peak=   -3.178 closest distance to " CG2BVAL A  41 " =    2.107
peak=   -3.176 closest distance to " CB  ASP A 132 " =    2.343
peak=   -3.170 closest distance to " O   ALA A  34 " =    2.151
peak=   -3.168 closest distance to " CD2 TYR A 293 " =    2.170
peak=   -3.165 closest distance to " CD2 PHE A 225 " =    1.221
peak=   -3.157 closest distance to " O   HOH Z  65 " =    0.885
peak=   -3.150 closest distance to " O   HOH Z 413 " =    5.375
peak=   -3.145 closest distance to " O   HOH Z 409 " =    4.575
peak=   -3.144 closest distance to " C   GLY A  13 " =    0.910
peak=   -3.144 closest distance to " CB  PRO A  54 " =    2.551
peak=   -3.143 closest distance to " C   MET A 188 " =    1.413
peak=   -3.137 closest distance to " CG1 VAL A  67 " =    2.731
peak=   -3.137 closest distance to " O   HOH Z 191 " =    5.965
peak=   -3.136 closest distance to " CA  VAL A 268 " =    2.882
peak=   -3.134 closest distance to " O   GLY A 196 " =    1.284
peak=   -3.133 closest distance to " O   HOH Z 413 " =    0.970
peak=   -3.130 closest distance to " C   ARG A  79 " =    2.621
peak=   -3.122 closest distance to " CG1 VAL A  78 " =    2.793
peak=   -3.116 closest distance to " CZ  PHE A 155 " =    1.273
peak=   -3.110 closest distance to " CB  ALA A 100 " =    2.075
peak=   -3.110 closest distance to " O   HOH Z 259 " =    4.211
peak=   -3.109 closest distance to " CD2 PHE A  59 " =    2.479
peak=   -3.098 closest distance to " O   VAL A 125 " =    2.332
peak=   -3.095 closest distance to " O   HOH Z 323 " =    1.345
peak=   -3.092 closest distance to " ND2 ASN A 187 " =    1.614
peak=   -3.087 closest distance to " O   HOH Z 390 " =    2.210
peak=   -3.075 closest distance to " O   HOH Z 292 " =    1.694
peak=   -3.074 closest distance to " O   HOH Z  51 " =    1.340
peak=   -3.072 closest distance to " CD  GLN A  73 " =    0.773
peak=   -3.072 closest distance to " OG BSER A 134 " =    1.990
peak=   -3.059 closest distance to " O   HOH Z 399 " =    2.212
peak=   -3.058 closest distance to " O   HOH Z 340 " =    1.589
peak=   -3.055 closest distance to " CD  PRO A 243 " =    2.157
peak=   -3.053 closest distance to " NH2 ARG A  66 " =    2.258
peak=   -3.052 closest distance to " O   HOH Z  44 " =    1.051
peak=   -3.050 closest distance to " OD1 ASN A 301 " =    1.971
peak=   -3.047 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.047 closest distance to " O   HOH Z 251 " =    5.146
peak=   -3.046 closest distance to " CD1 TRP A  70 " =    1.115
peak=   -3.043 closest distance to " O   HOH Z 109 " =    1.104
peak=   -3.038 closest distance to " CB  PRO A 163 " =    2.567
peak=   -3.019 closest distance to " O   HOH Z 290 " =    1.008
peak=   -3.002 closest distance to " CG2 VAL A 189 " =    1.935

================= 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    :  0.4343 0.4288   6.234477e+00   6.218654e+00
   1_bss:  0.4267 0.4220   6.225827e+00   6.208553e+00
   1_xyz:  0.2955 0.3185   5.941447e+00   6.001164e+00
   1_adp:  0.2647 0.3248   5.882960e+00   6.022332e+00
   1_occ:  0.2644 0.3247   5.882366e+00   6.022476e+00
   2_bss:  0.2634 0.3242   5.883118e+00   6.021618e+00
   2_xyz:  0.1837 0.2413   5.567982e+00   5.769346e+00
   2_adp:  0.1663 0.2157   5.475516e+00   5.676159e+00
   2_occ:  0.1662 0.2154   5.474675e+00   5.675769e+00
   3_bss:  0.1665 0.2146   5.475207e+00   5.674288e+00
   3_xyz:  0.1392 0.1847   5.325975e+00   5.540905e+00
   3_adp:  0.1301 0.1804   5.281016e+00   5.510838e+00
   3_occ:  0.1300 0.1803   5.280862e+00   5.510787e+00
   4_bss:  0.1302 0.1803   5.280747e+00   5.510905e+00
   4_xyz:  0.1232 0.1747   5.236686e+00   5.477600e+00
   4_adp:  0.1213 0.1725   5.220794e+00   5.464480e+00
   4_occ:  0.1212 0.1725   5.220826e+00   5.464701e+00
   5_bss:  0.1210 0.1724   5.220613e+00   5.464565e+00
   5_xyz:  0.1163 0.1699   5.196681e+00   5.453005e+00
   5_adp:  0.1172 0.1661   5.188849e+00   5.434120e+00
   5_occ:  0.1171 0.1661   5.188779e+00   5.434275e+00
   5_bss:  0.1171 0.1660   5.188749e+00   5.434306e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  80.000   0.414  -0.687   3.351  -0.000   0.000   0.000
   1_xyz:  0.300  80.000   0.414  -0.687   3.351  -0.000   0.000   0.000
   1_adp:  0.300  80.000   0.414  -0.687   3.351  -0.000   0.000   0.000
   1_occ:  0.300  80.000   0.414  -0.687   3.351  -0.000   0.000   0.000
   2_bss:  0.339  97.695  -0.857  -1.118   0.858  -0.000   0.000   0.000
   2_xyz:  0.339  97.695  -0.857  -1.118   0.858  -0.000   0.000   0.000
   2_adp:  0.339  97.695  -0.857  -1.118   0.858  -0.000   0.000   0.000
   2_occ:  0.339  97.695  -0.857  -1.118   0.858  -0.000   0.000   0.000
   3_bss:  0.343  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   3_xyz:  0.343  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   3_adp:  0.343  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   3_occ:  0.343  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   4_bss:  0.338  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   4_xyz:  0.338  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   4_adp:  0.338  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   4_occ:  0.338  89.684  -1.487  -1.519  -0.033  -0.000  -0.000  -0.000
   5_bss:  0.325  78.404  -1.127  -1.175   0.267  -0.000   0.000   0.000
   5_xyz:  0.325  78.404  -1.127  -1.175   0.267  -0.000   0.000   0.000
   5_adp:  0.325  78.404  -1.127  -1.175   0.267  -0.000   0.000   0.000
   5_occ:  0.325  78.404  -1.127  -1.175   0.267  -0.000   0.000   0.000
   5_bss:  0.317  67.409  -0.977  -1.018   0.440  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.174 0.5183  0.6536    54205.784
   1_bss:  49.495 0.5258  0.6946    52646.929
   1_xyz:  32.815 0.7271  0.9255    26640.088
   1_adp:  34.315 0.7089  0.8978    28665.421
   1_occ:  34.332 0.7087  0.8973    28672.600
   2_bss:  34.240 0.7098  0.8565    28605.496
   2_xyz:  23.925 0.8215  0.9605    14730.233
   2_adp:  20.572 0.8565  0.9747    11758.711
   2_occ:  20.560 0.8565  0.9745    11738.356
   3_bss:  20.503 0.8570  0.9529    11683.336
   3_xyz:  17.284 0.8872  0.9667     8764.128
   3_adp:  16.579 0.8935  0.9555     8186.101
   3_occ:  16.572 0.8936  0.9554     8178.594
   4_bss:  16.584 0.8934  0.9553     8185.162
   4_xyz:  15.807 0.9002  0.9604     7599.180
   4_adp:  15.473 0.9032  0.9519     7426.959
   4_occ:  15.475 0.9032  0.9517     7425.960
   5_bss:  15.474 0.9032  0.9629     7419.041
   5_xyz:  15.230 0.9052  0.9647     7240.210
   5_adp:  14.762 0.9092  0.9595     7012.359
   5_occ:  14.763 0.9092  0.9594     7007.874
   5_bss:  14.765 0.9092  0.9643     7002.739
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6367e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6367e-01
   1_xyz:   1.440  0.011  0.090 15.273  0.006  4.118   1.0579e-01
   1_adp:   1.440  0.011  0.090 15.273  0.006  4.118   1.0579e-01
   1_occ:   1.440  0.011  0.090 15.273  0.006  4.118   1.0579e-01
   2_bss:   1.440  0.011  0.090 15.273  0.006  4.118   1.0579e-01
   2_xyz:   1.177  0.010  0.083 14.960  0.005  4.140   7.7494e-02
   2_adp:   1.177  0.010  0.083 14.960  0.005  4.140   7.7494e-02
   2_occ:   1.177  0.010  0.083 14.960  0.005  4.140   7.7494e-02
   3_bss:   1.177  0.010  0.083 14.960  0.005  4.140   7.7494e-02
   3_xyz:   1.090  0.010  0.080 14.871  0.004  4.118   7.2169e-02
   3_adp:   1.090  0.010  0.080 14.871  0.004  4.118   7.2169e-02
   3_occ:   1.090  0.010  0.080 14.871  0.004  4.118   7.2169e-02
   4_bss:   1.090  0.010  0.080 14.871  0.004  4.118   7.2169e-02
   4_xyz:   1.099  0.010  0.081 14.785  0.004  4.125   7.2166e-02
   4_adp:   1.099  0.010  0.081 14.785  0.004  4.125   7.2166e-02
   4_occ:   1.099  0.010  0.081 14.785  0.004  4.125   7.2166e-02
   5_bss:   1.099  0.010  0.081 14.785  0.004  4.125   7.2166e-02
   5_xyz:   1.193  0.012  0.087 14.897  0.004  4.118   8.6789e-02
   5_adp:   1.193  0.012  0.087 14.897  0.004  4.118   8.6789e-02
   5_occ:   1.193  0.012  0.087 14.897  0.004  4.118   8.6789e-02
   5_bss:   1.193  0.012  0.087 14.897  0.004  4.118   8.6789e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.698   2.4555e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.698   2.4555e-01
   1_xyz:   9.745  0.059  0.325 85.463  0.052  2.088   9.4278e-02
   1_adp:   9.745  0.059  0.325 85.463  0.052  2.088   9.4278e-02
   1_occ:   9.745  0.059  0.325 85.463  0.052  2.088   9.4278e-02
   2_bss:   9.745  0.059  0.325 85.463  0.052  2.088   9.4278e-02
   2_xyz:   7.537  0.055  0.269 84.622  0.043  2.296   7.2335e-02
   2_adp:   7.537  0.055  0.269 84.622  0.043  2.296   7.2335e-02
   2_occ:   7.537  0.055  0.269 84.622  0.043  2.296   7.2335e-02
   3_bss:   7.537  0.055  0.269 84.622  0.043  2.296   7.2335e-02
   3_xyz:   8.103  0.049  0.255 82.369  0.039  2.311   7.2653e-02
   3_adp:   8.103  0.049  0.255 82.369  0.039  2.311   7.2653e-02
   3_occ:   8.103  0.049  0.255 82.369  0.039  2.311   7.2653e-02
   4_bss:   8.103  0.049  0.255 82.369  0.039  2.311   7.2653e-02
   4_xyz:   8.213  0.046  0.257 82.713  0.041  2.393   4.6948e-02
   4_adp:   8.213  0.046  0.257 82.713  0.041  2.393   4.6948e-02
   4_occ:   8.213  0.046  0.257 82.713  0.041  2.393   4.6948e-02
   5_bss:   8.213  0.046  0.257 82.713  0.041  2.393   4.6948e-02
   5_xyz:   8.111  0.053  0.284 83.266  0.039  2.363   5.8135e-02
   5_adp:   8.111  0.053  0.284 83.266  0.039  2.363   5.8135e-02
   5_occ:   8.111  0.053  0.284 83.266  0.039  2.363   5.8135e-02
   5_bss:   8.111  0.053  0.284 83.266  0.039  2.363   5.8135e-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: 112.41   0.00  18.96  91.67   0.00  14.26 112.41   0.00  44.57
   1_occ: 112.41   0.00  18.96  91.67   0.00  14.26 112.41   0.00  44.57
   2_bss: 112.41   0.00  18.96  91.67   0.00  14.26 112.41   0.00  44.57
   2_xyz: 112.41   0.00  18.96  91.67   0.00  14.26 112.41   0.00  44.57
   2_adp: 110.52   0.79  18.16  90.59   0.79  13.36 110.52   3.24  44.27
   2_occ: 110.52   0.79  18.16  90.59   0.79  13.36 110.52   3.24  44.27
   3_bss: 110.52   0.79  18.16  90.59   0.79  13.36 110.52   3.24  44.27
   3_xyz: 110.52   0.79  18.16  90.59   0.79  13.36 110.52   3.24  44.27
   3_adp: 114.84   0.00  18.01  97.58   0.00  12.91 114.84   4.54  45.80
   3_occ: 114.84   0.00  18.01  97.58   0.00  12.91 114.84   4.54  45.80
   4_bss: 114.84   0.00  18.01  97.58   0.00  12.91 114.84   4.54  45.80
   4_xyz: 114.84   0.00  18.01  97.58   0.00  12.91 114.84   4.54  45.80
   4_adp: 123.03   0.00  17.62 102.88   0.00  12.58 123.03   4.93  45.08
   4_occ: 123.03   0.00  17.62 102.88   0.00  12.58 123.03   4.93  45.08
   5_bss: 123.03   0.00  17.62 102.88   0.00  12.58 123.03   4.93  45.08
   5_xyz: 123.03   0.00  17.62 102.88   0.00  12.58 123.03   4.93  45.08
   5_adp: 112.48   0.45  16.40  89.65   0.45  12.01 112.48   4.90  40.26
   5_occ: 112.48   0.45  16.40  89.65   0.45  12.01 112.48   4.90  40.26
   5_bss: 112.47   0.44  16.38  89.64   0.44  12.00 112.47   4.89  40.25
------------------------------------------------------------------------
 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:    1.766    0.013    0.358
   1_adp:    1.766    0.013    0.358
   1_occ:    1.766    0.013    0.358
   2_bss:    1.766    0.013    0.358
   2_xyz:    1.419    0.028    0.523
   2_adp:    1.419    0.028    0.523
   2_occ:    1.419    0.028    0.523
   3_bss:    1.419    0.028    0.523
   3_xyz:    1.351    0.021    0.602
   3_adp:    1.351    0.021    0.602
   3_occ:    1.351    0.021    0.602
   4_bss:    1.351    0.021    0.602
   4_xyz:    1.265    0.070    0.620
   4_adp:    1.265    0.070    0.620
   4_occ:    1.265    0.070    0.620
   5_bss:    1.265    0.070    0.620
   5_xyz:    1.296    0.059    0.631
   5_adp:    1.296    0.059    0.631
   5_occ:    1.296    0.059    0.631
   5_bss:    1.296    0.059    0.631
------------------------------------------------------------------------

CPU time actual refinement: 338.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1175/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_1175/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1175/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1175/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1175/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.56 
  Macro-tasks:
    bulk solvent and scale       = 66.56  
    individual site refinement   = 124.11 
    weights calculation          = 28.83  
    collect and process          = 6.59   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.21 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 97.01  
    alpha_beta                      = 8.39   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 104.38 
    fmodel                         = 9.79   
    r_factors                      = 0.35   
    phase_errors                   = 10.96  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 234.12 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.829 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    609 calls, 96.57 s
gradients_fft:          554 calls, 92.00 s

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

# Date 2008-01-16 Time 06:36:44 PST -0800 (1200494204.48 s)
Start R-work = 0.4343, R-free = 0.4288 (no bulk solvent and anisotropic scale)
Final R-work = 0.1348, R-free = 0.1809 (no bulk solvent and anisotropic scale)

Start R-work = 0.4267, R-free = 0.4220
Final R-work = 0.1171, R-free = 0.1660