# Date 2008-01-16 Time 04:54:19 PST -0800 (1200488059.36 s)
#phil __OFF__

Command line arguments: "../509.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4296
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 509

-------------------------------------------------------------------------------
  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: (69.8988, 46.2261, 85.5261, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.97157
Completeness in resolution range: 0.973463
Completeness with d_max=infinity: 0.970425

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9716

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: (69.8988, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.97157
Completeness in resolution range: 0.973463
Completeness with d_max=infinity: 0.970425

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.2185 [2108/2132]  1898   210  10.0%
  bin  2:  4.2185 -  3.3610 [2034/2054]  1829   205  10.1%
  bin  3:  3.3610 -  2.9398 [2003/2022]  1802   201  10.0%
  bin  4:  2.9398 -  2.6727 [1988/2018]  1793   195   9.8%
  bin  5:  2.6727 -  2.4821 [1979/1998]  1781   198  10.0%
  bin  6:  2.4821 -  2.3364 [1963/1988]  1761   202  10.3%
  bin  7:  2.3364 -  2.2197 [1949/1977]  1756   193   9.9%
  bin  8:  2.2197 -  2.1234 [1953/1989]  1759   194   9.9%
  bin  9:  2.1234 -  2.0419 [1929/1971]  1737   192  10.0%
  bin 10:  2.0419 -  1.9716 [1683/1974]  1514   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_509/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 36
        2.42 -     3.04: 2230
        3.04 -     3.66: 4786
        3.66 -     4.28: 9175
        4.28 -     4.90: 12496
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.944 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  2.026 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  2.049 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.067 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28718 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_509/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_509/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 69.89875 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3732   r_free= 0.3708   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.151397                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7050 0.99   1378  152 0.3124 0.3063       6.422      6.3841|
|  2:  4.7050 -  3.7542 0.99   1314  147 0.3036 0.2794      6.5875      6.5154|
|  3:  3.7542 -  3.2854 0.99   1294  143 0.3261 0.3092      6.4936      6.5755|
|  4:  3.2854 -  2.9877 0.99   1281  146 0.3413 0.3784      6.3584      6.3915|
|  5:  2.9877 -  2.7750 0.99   1286  142 0.3858 0.3493      6.2331      6.1654|
|  6:  2.7750 -  2.6123 0.99   1276  140 0.3894 0.4106      6.1651      6.1397|
|  7:  2.6123 -  2.4821 0.99   1274  139 0.3999 0.3871      6.1134      6.0799|
|  8:  2.4821 -  2.3745 0.98   1246  142 0.4125 0.4304      6.0894      6.1111|
|  9:  2.3745 -  2.2834 0.98   1265  139 0.4124 0.4213      6.0299      6.0243|
| 10:  2.2834 -  2.2049 1.00   1254  143 0.4123 0.4208      5.9937      6.0038|
| 11:  2.2049 -  2.1362 0.97   1255  133 0.4285 0.4334      5.9555      5.9957|
| 12:  2.1362 -  2.0753 0.98   1241  142 0.4314 0.4244      5.9237      5.9087|
| 13:  2.0753 -  2.0208 0.99   1269  140 0.4281 0.4151      5.8109      5.7687|
| 14:  2.0208 -  1.9716 0.79    997  111 0.4599 0.4284      5.8115      5.7063|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.7050  1378   152  0.77  28.15   0.86     0.80      49733.91|
|  2:  4.7050 -  3.7542  1314   147  0.81  25.65   0.96     0.91      61971.51|
|  3:  3.7542 -  3.2854  1294   143  0.75  30.82   0.99     0.93      64536.11|
|  4:  3.2854 -  2.9877  1281   146  0.70  35.23   0.99     0.90      59014.48|
|  5:  2.9877 -  2.7750  1286   142  0.64  40.43   0.96     0.85      48060.10|
|  6:  2.7750 -  2.6123  1276   140  0.63  41.14   0.97     0.84      42485.62|
|  7:  2.6123 -  2.4821  1274   139  0.62  42.49   0.97     0.83      38893.51|
|  8:  2.4821 -  2.3745  1246   142  0.60  44.02   1.00     0.82      36979.81|
|  9:  2.3745 -  2.2834  1265   139  0.60  43.83   0.98     0.81      33734.28|
| 10:  2.2834 -  2.2049  1254   143  0.59  45.05   1.02     0.82      31500.61|
| 11:  2.2049 -  2.1362  1255   133  0.58  46.15   1.02     0.84      29798.30|
| 12:  2.1362 -  2.0753  1241   142  0.58  45.78   1.04     0.84      26866.02|
| 13:  2.0753 -  2.0208  1269   140  0.57  46.78   1.02     0.83      23051.75|
| 14:  2.0208 -  1.9716   997   111  0.59  45.40   1.02     0.79      18719.49|
|alpha:            min =        0.79 max =            0.93 mean =         0.84|
|beta:             min =    18719.49 max =        64536.11 mean =     40927.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.65|
|phase err.(work): min =        0.00 max =           89.99 mean =        39.83|
|phase err.(test): min =        0.00 max =           89.97 mean =        39.86|
|-----------------------------------------------------------------------------|

============================== 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 = 6.088207              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.512   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.075121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.923   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       29 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      212 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2018 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1906 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2880 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4704 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4471 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5708 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6788 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.257 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3732   r_free= 0.3708   ksol= 0.00   Bsol= 0.00   scale= 0.960    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.151397                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3590   r_free= 0.3564   ksol= 0.33   Bsol= 30.85   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,2.21,-0.59,0.00,-0.00,-0.00); trace/3= -0.46                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.136197                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.198947              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.466   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.557861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.836   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3590      final r-factor (work) = 0.2186          |
| start r-factor (free) = 0.3564      final r-factor (free) = 0.2460          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1143 = 5.20 * 0.50 * 6.1352 + 1.00 * 0.1659                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3641 = 5.20 * 0.50 * 5.8778 + 1.00 * 0.0849                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2186      final r-factor (work) = 0.2003          |
| start r-factor (free) = 0.2460      final r-factor (free) = 0.2574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2849 = 0.56 * 1.00 * 5.8778 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1560 = 0.56 * 1.00 * 5.6377 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.30   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    80.30   17.48    None  None   None       |
|    Sol.    : 438    0      7.25    80.30   40.04    None  None   None       |
|    Mac.    : 2385   0      0.00    74.73   13.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.030:  591   |   5:    40.151 -  48.181:  120        |
|      1:     8.030 -  16.060: 1246   |   6:    48.181 -  56.211:   99        |
|      2:    16.060 -  24.091:  423   |   7:    56.211 -  64.241:   43        |
|      3:    24.091 -  32.121:  153   |   8:    64.241 -  72.272:   17        |
|      4:    32.121 -  40.151:  126   |   9:    72.272 -  80.302:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2003 r_free = 0.2574             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2000 r_free = 0.2569             target_work(ml) = 5.651         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2000   r_free= 0.2569   ksol= 0.33   Bsol= 30.85   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,2.21,-0.59,0.00,-0.00,-0.00); trace/3= -0.46                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.650989                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1971   r_free= 0.2530   ksol= 0.33   Bsol= 38.64   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.16,-1.40,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.639191                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.299894              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.154   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.146182              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.884  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1971      final r-factor (work) = 0.1416          |
| start r-factor (free) = 0.2530      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3936 = 3.30 * 0.50 * 5.6418 + 1.00 * 0.0849                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1370 = 3.30 * 0.50 * 5.5037 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1416      final r-factor (work) = 0.1313          |
| start r-factor (free) = 0.1896      final r-factor (free) = 0.1745          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8155 = 0.15 * 1.00 * 5.5037 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7825 = 0.15 * 1.00 * 5.3073 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.79    75.80   16.76    None  None   None       |
|    all(noH): 2823   0      1.79    75.80   16.76    None  None   None       |
|    Sol.    : 438    0      6.56    74.25   37.82    None  None   None       |
|    Mac.    : 2385   0      1.79    75.80   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.787 -   9.188:  758   |   5:    38.792 -  46.193:   97        |
|      1:     9.188 -  16.589: 1237   |   6:    46.193 -  53.594:   96        |
|      2:    16.589 -  23.990:  319   |   7:    53.594 -  60.995:   39        |
|      3:    23.990 -  31.391:  121   |   8:    60.995 -  68.396:   13        |
|      4:    31.391 -  38.792:  136   |   9:    68.396 -  75.798:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1313 r_free = 0.1745             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1745             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1745   ksol= 0.33   Bsol= 38.64   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.16,-1.40,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.265686                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1742   ksol= 0.32   Bsol= 39.61   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.18,-1.44,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.262669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.016388              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.233  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.249604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.065  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4068 = 2.02 * 0.50 * 5.3072 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3036 = 2.02 * 0.50 * 5.2082 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3067 = 0.25 * 1.00 * 5.2082 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2908 = 0.25 * 1.00 * 5.1418 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    78.05   16.74    None  None   None       |
|    all(noH): 2823   0      1.06    78.05   16.74    None  None   None       |
|    Sol.    : 438    0      5.64    74.78   38.36    None  None   None       |
|    Mac.    : 2385   0      1.06    78.05   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.061 -   8.759:  690   |   5:    39.553 -  47.251:  107        |
|      1:     8.759 -  16.458: 1301   |   6:    47.251 -  54.950:   94        |
|      2:    16.458 -  24.156:  324   |   7:    54.950 -  62.648:   38        |
|      3:    24.156 -  31.855:  131   |   8:    62.648 -  70.347:   15        |
|      4:    31.855 -  39.553:  118   |   9:    70.347 -  78.045:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1552             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1552             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1552   ksol= 0.32   Bsol= 39.61   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.18,-1.44,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134787                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1551   ksol= 0.32   Bsol= 39.61   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.43,-1.47,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.134133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.652265              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.166  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.218794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.505  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3003 = 1.65 * 0.50 * 5.1415 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2826 = 1.65 * 0.50 * 5.1221 + 1.00 * 0.0510                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1533      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2502 = 1.22 * 1.00 * 5.1221 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2362 = 1.22 * 1.00 * 5.1093 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    87.19   17.04    None  None   None       |
|    all(noH): 2823   0      0.25    87.19   17.04    None  None   None       |
|    Sol.    : 438    0      6.13    80.04   40.09    None  None   None       |
|    Mac.    : 2385   0      0.25    87.19   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.248 -   8.942:  802   |   5:    43.720 -  52.414:  109        |
|      1:     8.942 -  17.637: 1273   |   6:    52.414 -  61.109:   69        |
|      2:    17.637 -  26.331:  275   |   7:    61.109 -  69.803:   33        |
|      3:    26.331 -  35.025:  125   |   8:    69.803 -  78.497:   17        |
|      4:    35.025 -  43.720:  117   |   9:    78.497 -  87.192:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1542             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1542             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1542   ksol= 0.32   Bsol= 39.61   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.43,-1.47,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114415                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1541   ksol= 0.32   Bsol= 42.84   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.30,-1.27,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113776                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.192761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.242  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.657690              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6534 = 2.19 * 0.50 * 5.1099 + 1.00 * 0.0510                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6515 = 2.19 * 0.50 * 5.1027 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1061      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4677 = 1.66 * 1.00 * 5.1027 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4618 = 1.66 * 1.00 * 5.0988 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.59   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    95.59   16.96    None  None   None       |
|    Sol.    : 438    0      6.00    86.50   40.18    None  None   None       |
|    Mac.    : 2385   0      0.00    95.59   12.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.559:  988   |   5:    47.795 -  57.354:   95        |
|      1:     9.559 -  19.118: 1167   |   6:    57.354 -  66.913:   45        |
|      2:    19.118 -  28.677:  230   |   7:    66.913 -  76.471:   22        |
|      3:    28.677 -  38.236:  131   |   8:    76.471 -  86.030:   10        |
|      4:    38.236 -  47.795:  132   |   9:    86.030 -  95.589:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1058 r_free = 0.1536             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1058 r_free = 0.1536             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1536   ksol= 0.32   Bsol= 42.84   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-2.30,-1.27,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.100115                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7050 0.99   1378  152 0.0977 0.1216      5.3654      5.4983|
|  2:  4.7050 -  3.7542 0.99   1314  147 0.0815 0.1117      5.4082       5.612|
|  3:  3.7542 -  3.2854 0.99   1294  143 0.1013 0.1503      5.4482      5.8454|
|  4:  3.2854 -  2.9877 0.99   1281  146 0.1157 0.1537      5.4196      5.5582|
|  5:  2.9877 -  2.7750 0.99   1286  142 0.1219 0.1750      5.2771       5.536|
|  6:  2.7750 -  2.6123 0.99   1276  140 0.1092 0.1680      5.1549      5.3791|
|  7:  2.6123 -  2.4821 0.99   1274  139 0.1194 0.1503      5.1166      5.3249|
|  8:  2.4821 -  2.3745 0.98   1246  142 0.1087 0.1716      5.0104      5.3452|
|  9:  2.3745 -  2.2834 0.98   1265  139 0.1087 0.1632      4.9799      5.2147|
| 10:  2.2834 -  2.2049 1.00   1254  143 0.1026 0.1710       4.906      5.2163|
| 11:  2.2049 -  2.1362 0.97   1255  133 0.1067 0.1676      4.9038      5.2293|
| 12:  2.1362 -  2.0753 0.98   1241  142 0.1056 0.1680      4.8438      5.2048|
| 13:  2.0753 -  2.0208 0.99   1269  140 0.1055 0.1719      4.7642       5.046|
| 14:  2.0208 -  1.9716 0.79    997  111 0.1014 0.1654      4.6484      4.8859|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.7050  1378   152  0.94   8.86   0.98     0.95       6703.21|
|  2:  4.7050 -  3.7542  1314   147  0.95   7.67   1.03     1.01       8708.05|
|  3:  3.7542 -  3.2854  1294   143  0.94  10.82   1.04     1.03       9919.29|
|  4:  3.2854 -  2.9877  1281   146  0.93  12.83   1.01     1.00       9688.73|
|  5:  2.9877 -  2.7750  1286   142  0.91  15.01   1.00     0.97       7689.53|
|  6:  2.7750 -  2.6123  1276   140  0.91  14.91   0.99     0.97       6503.13|
|  7:  2.6123 -  2.4821  1274   139  0.91  15.20   0.99     0.96       5718.64|
|  8:  2.4821 -  2.3745  1246   142  0.92  13.82   0.99     0.97       4634.22|
|  9:  2.3745 -  2.2834  1265   139  0.92  14.26   1.01     0.98       4555.04|
| 10:  2.2834 -  2.2049  1254   143  0.91  14.16   1.00     0.96       3922.41|
| 11:  2.2049 -  2.1362  1255   133  0.90  16.04   1.00     0.97       4196.60|
| 12:  2.1362 -  2.0753  1241   142  0.92  14.57   1.01     1.00       3714.33|
| 13:  2.0753 -  2.0208  1269   140  0.91  15.23   1.00     0.99       3224.72|
| 14:  2.0208 -  1.9716   997   111  0.92  14.04   0.98     0.95       2493.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2493.91 max =         9919.29 mean =      5916.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.33|
|phase err.(test): min =        0.00 max =           89.26 mean =        12.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1537   ksol= 0.32   Bsol= 43.93   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.17,-1.11,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.100647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1537   ksol= 0.32   Bsol= 43.93   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.17,-1.11,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.100647                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.7050 0.99   1378  152 0.0971 0.1238      5.3648      5.4948|
|  2:  4.7050 -  3.7542 0.99   1314  147 0.0824 0.1116      5.4124      5.6081|
|  3:  3.7542 -  3.2854 0.99   1294  143 0.1017 0.1494      5.4487      5.8413|
|  4:  3.2854 -  2.9877 0.99   1281  146 0.1157 0.1536      5.4199      5.5633|
|  5:  2.9877 -  2.7750 0.99   1286  142 0.1222 0.1742      5.2788      5.5319|
|  6:  2.7750 -  2.6123 0.99   1276  140 0.1091 0.1678      5.1548      5.3815|
|  7:  2.6123 -  2.4821 0.99   1274  139 0.1196 0.1509      5.1181      5.3257|
|  8:  2.4821 -  2.3745 0.98   1246  142 0.1085 0.1721      5.0108      5.3456|
|  9:  2.3745 -  2.2834 0.98   1265  139 0.1088 0.1630      4.9809      5.2178|
| 10:  2.2834 -  2.2049 1.00   1254  143 0.1023 0.1712      4.9059      5.2183|
| 11:  2.2049 -  2.1362 0.97   1255  133 0.1065 0.1675      4.9034      5.2284|
| 12:  2.1362 -  2.0753 0.98   1241  142 0.1054 0.1680      4.8432      5.2045|
| 13:  2.0753 -  2.0208 0.99   1269  140 0.1053 0.1719      4.7639      5.0464|
| 14:  2.0208 -  1.9716 0.79    997  111 0.1015 0.1648       4.648      4.8855|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.7050  1378   152  0.94   8.78   0.98     0.95       6672.02|
|  2:  4.7050 -  3.7542  1314   147  0.95   7.66   1.03     1.02       8669.97|
|  3:  3.7542 -  3.2854  1294   143  0.94  10.80   1.04     1.03       9900.84|
|  4:  3.2854 -  2.9877  1281   146  0.93  12.84   1.02     1.01       9702.19|
|  5:  2.9877 -  2.7750  1286   142  0.91  15.02   1.01     0.98       7692.19|
|  6:  2.7750 -  2.6123  1276   140  0.91  14.92   1.00     0.97       6513.41|
|  7:  2.6123 -  2.4821  1274   139  0.91  15.21   1.00     0.96       5729.01|
|  8:  2.4821 -  2.3745  1246   142  0.92  13.83   1.00     0.98       4644.17|
|  9:  2.3745 -  2.2834  1265   139  0.92  14.30   1.02     0.99       4566.29|
| 10:  2.2834 -  2.2049  1254   143  0.91  14.17   1.01     0.97       3927.46|
| 11:  2.2049 -  2.1362  1255   133  0.90  16.05   1.01     0.97       4197.48|
| 12:  2.1362 -  2.0753  1241   142  0.92  14.58   1.02     1.00       3714.01|
| 13:  2.0753 -  2.0208  1269   140  0.91  15.23   1.01     1.00       3225.76|
| 14:  2.0208 -  1.9716   997   111  0.92  14.04   0.99     0.96       2493.54|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2493.54 max =         9900.84 mean =      5914.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.33|
|phase err.(test): min =        0.00 max =           89.18 mean =        12.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.553)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.59   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    95.59   16.96    None  None   None       |
|    Sol.    : 438    0      6.00    86.51   40.18    None  None   None       |
|    Mac.    : 2385   0      0.00    95.59   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.562:  988   |   5:    47.798 -  57.357:   95        |
|      1:     9.562 -  19.121: 1167   |   6:    57.357 -  66.916:   45        |
|      2:    19.121 -  28.680:  230   |   7:    66.916 -  76.474:   22        |
|      3:    28.680 -  38.239:  131   |   8:    76.474 -  86.033:   10        |
|      4:    38.239 -  47.798:  132   |   9:    86.033 -  95.592:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.417 - 4.622
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 292
   mapped sites are within: 0.750 - 4.622

peak=    6.267 closest distance to " NE2 GLN A  11 " =    1.219
peak=    5.931 closest distance to " O   HOH Z 126 " =    1.893
peak=    5.833 closest distance to " O   HOH Z 144 " =    1.712
peak=    5.558 closest distance to " CG  PRO A  54 " =    1.250
peak=    5.493 closest distance to " NH2 ARG A  56 " =    2.136
peak=    5.120 closest distance to " CB  ARG A 275 " =    0.920
peak=    5.039 closest distance to " CG  PRO A 213 " =    1.254
peak=    4.932 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.920 closest distance to " CB  SER A  63 " =    1.186
peak=    4.802 closest distance to " CB  GLN A 223 " =    1.544
peak=    4.733 closest distance to " O   HOH Z 369 " =    2.233
peak=    4.725 closest distance to " O   HOH Z  78 " =    1.755
peak=    4.685 closest distance to " O   HOH Z 209 " =    2.205
peak=    4.679 closest distance to " CB  GLN A 183 " =    1.220
peak=    4.624 closest distance to " CB  PRO A  54 " =    0.957
peak=    4.613 closest distance to " O   HOH Z 427 " =    2.733
peak=    4.510 closest distance to " C   PRO A 198 " =    1.446
peak=    4.468 closest distance to " O   HOH Z 193 " =    1.783
peak=    4.443 closest distance to " O   HOH Z 236 " =    1.420
peak=    4.428 closest distance to " O   HOH Z   9 " =    2.313
peak=    4.417 closest distance to " O   HOH Z 298 " =    1.839
peak=    4.413 closest distance to " O   HOH Z 287 " =    1.954
peak=    4.342 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.336 closest distance to " O   HOH Z 303 " =    2.240
peak=    4.331 closest distance to " O   HOH Z 203 " =    1.778
peak=    4.322 closest distance to " ND2 ASN A 187 " =    1.419
peak=    4.320 closest distance to " CG  ARG A  66 " =    2.489
peak=    4.289 closest distance to " O   HOH Z 419 " =    2.200
peak=    4.249 closest distance to " CB  GLU A 152 " =    1.303
peak=    4.244 closest distance to " NZ  LYS A 117 " =    3.119
peak=    4.237 closest distance to " O   HOH Z 234 " =    3.583
peak=    4.225 closest distance to " O   HOH Z  63 " =    1.472
peak=    4.217 closest distance to " CA  TYR A  30 " =    0.915
peak=    4.213 closest distance to " CB  ARG A  79 " =    1.405
peak=    4.205 closest distance to " O   HOH Z 144 " =    2.222
peak=    4.205 closest distance to " OG BSER A 164 " =    2.237
peak=    4.199 closest distance to " CB  GLU A 128 " =    1.050
peak=    4.184 closest distance to " OG ASER A 258 " =    3.054
peak=    4.168 closest distance to " O   HOH Z  61 " =    1.693
peak=    4.160 closest distance to " O   HOH Z  78 " =    2.101
peak=    4.144 closest distance to " O   HOH Z   1 " =    1.954
peak=    4.144 closest distance to " CB  SER A   3 " =    1.290
peak=    4.131 closest distance to " CB  VAL A 265 " =    1.368
peak=    4.126 closest distance to " O   HOH Z 368 " =    1.922
peak=    4.095 closest distance to " CG  PRO A  90 " =    1.080
peak=    4.089 closest distance to " O   HOH Z  44 " =    1.752
peak=    4.073 closest distance to " OD1 ASN A  69 " =    2.644
peak=    4.047 closest distance to " O   HOH Z 371 " =    1.782
peak=    4.021 closest distance to " O   HOH Z 272 " =    1.812
peak=    4.014 closest distance to " O   HOH Z 344 " =    3.176
peak=    4.006 closest distance to " CG2 VAL A 257 " =    0.813
peak=    3.989 closest distance to " O   HOH Z 158 " =    2.987
peak=    3.985 closest distance to " CB  ARG A 139 " =    1.039
peak=    3.969 closest distance to " CB  LEU A 228 " =    1.098
peak=    3.962 closest distance to " O   SER A  87 " =    2.186
peak=    3.925 closest distance to " O   HOH Z 425 " =    1.273
peak=    3.911 closest distance to " O   HOH Z 405 " =    1.144
peak=    3.911 closest distance to " CB  TYR A 169 " =    0.759
peak=    3.901 closest distance to " CG1 ILE A  33 " =    1.244
peak=    3.894 closest distance to " O   HOH Z   3 " =    1.910
peak=    3.883 closest distance to " CG  PRO A 198 " =    1.197
peak=    3.878 closest distance to " O   HOH Z 189 " =    2.025
peak=    3.875 closest distance to " O   HOH Z 250 " =    1.469
peak=    3.864 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.858 closest distance to " O   HOH Z 423 " =    1.381
peak=    3.851 closest distance to " O   HOH Z 368 " =    3.617
peak=    3.842 closest distance to " O   HOH Z  66 " =    2.210
peak=    3.841 closest distance to " CE  LYS A  76 " =    0.833
peak=    3.837 closest distance to " CB  ARG A 190 " =    1.625
peak=    3.817 closest distance to " O   HOH Z   1 " =    1.680
peak=    3.804 closest distance to " O   HOH Z 128 " =    2.110
peak=    3.797 closest distance to " NH1BARG A 145 " =    1.267
peak=    3.791 closest distance to " O   HOH Z  40 " =    2.014
peak=    3.781 closest distance to " O   HOH Z 289 " =    1.640
peak=    3.775 closest distance to " O   HOH Z 132 " =    2.301
peak=    3.771 closest distance to " O   HOH Z 380 " =    1.623
peak=    3.766 closest distance to " O   HOH Z  43 " =    1.801
peak=    3.764 closest distance to " CB  TRP A 179 " =    1.316
peak=    3.762 closest distance to " O   HOH Z 437 " =    1.651
peak=    3.760 closest distance to " N   PHE A 130 " =    1.247
peak=    3.740 closest distance to " O   HOH Z  59 " =    1.603
peak=    3.737 closest distance to " CA  ASN A 215 " =    1.172
peak=    3.695 closest distance to " O   HOH Z 286 " =    2.371
peak=    3.693 closest distance to " O   HOH Z 353 " =    2.586
peak=    3.684 closest distance to " O   HOH Z  61 " =    1.494
peak=    3.683 closest distance to " CB  GLU A 277 " =    3.489
peak=    3.683 closest distance to " O   HOH Z 133 " =    2.585
peak=    3.681 closest distance to " O   HOH Z 175 " =    2.227
peak=    3.675 closest distance to " CD2 TRP A 179 " =    1.360
peak=    3.666 closest distance to " O   HOH Z 407 " =    2.253
peak=    3.665 closest distance to " O   HOH Z 263 " =    2.383
peak=    3.662 closest distance to " CD2 LEU A 297 " =    0.966
peak=    3.651 closest distance to " CA  ALA A  21 " =    1.092
peak=    3.642 closest distance to " CB  SER A 216 " =    0.799
peak=    3.633 closest distance to " O   HOH Z 392 " =    3.024
peak=    3.628 closest distance to " CD BLYS A 290 " =    1.249
peak=    3.625 closest distance to " O   HOH Z 371 " =    2.917
peak=    3.617 closest distance to " CB  THR A 157 " =    1.101
peak=    3.616 closest distance to " O   HOH Z 207 " =    1.682
peak=    3.615 closest distance to " CA  THR A 264 " =    0.823
peak=    3.605 closest distance to " O   HOH Z  10 " =    1.780
peak=    3.601 closest distance to " O   HOH Z 214 " =    2.151
peak=    3.599 closest distance to " OD2 ASP A 286 " =    2.720
peak=    3.597 closest distance to " O   HOH Z 327 " =    1.661
peak=    3.588 closest distance to " O   HOH Z 193 " =    1.838
peak=    3.586 closest distance to " O   HOH Z 403 " =    1.636
peak=    3.578 closest distance to " ND1 HIS A  86 " =    1.807
peak=    3.576 closest distance to " OD1BASN A 224 " =    2.253
peak=    3.574 closest distance to " OG  SER A  62 " =    2.883
peak=    3.572 closest distance to " NH2BARG A 145 " =    2.020
peak=    3.569 closest distance to " CG  PRO A 243 " =    1.089
peak=    3.567 closest distance to " O   HOH Z  93 " =    2.209
peak=    3.560 closest distance to " NH1AARG A 145 " =    1.135
peak=    3.536 closest distance to " O   HOH Z 128 " =    2.049
peak=    3.536 closest distance to " O   HOH Z 402 " =    1.408
peak=    3.530 closest distance to " CA  ALA A 233 " =    0.931
peak=    3.529 closest distance to " O   HOH Z 357 " =    1.853
peak=    3.526 closest distance to " CB  ALA A  34 " =    1.094
peak=    3.522 closest distance to " O   MET A 105 " =    1.824
peak=    3.522 closest distance to " CA  MET A  40 " =    1.103
peak=    3.522 closest distance to " O   HOH Z 172 " =    3.107
peak=    3.520 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.513 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.503 closest distance to " O   HOH Z 391 " =    2.948
peak=    3.503 closest distance to " CB  THR A  31 " =    1.761
peak=    3.498 closest distance to " CB  TRP A 266 " =    1.043
peak=    3.494 closest distance to " O   HOH Z 128 " =    2.014
peak=    3.489 closest distance to " CB  TYR A 116 " =    0.815
peak=    3.488 closest distance to " CG2 THR A 221 " =    1.148
peak=    3.488 closest distance to " O   HOH Z 305 " =    3.486
peak=    3.486 closest distance to " O   HOH Z 291 " =    1.573
peak=    3.485 closest distance to " O   HOH Z 245 " =    1.281
peak=    3.480 closest distance to " NH2AARG A 190 " =    1.936
peak=    3.479 closest distance to " O   HOH Z  97 " =    2.009
peak=    3.477 closest distance to " O   HOH Z 417 " =    3.571
peak=    3.471 closest distance to " O   HOH Z 292 " =    1.712
peak=    3.470 closest distance to " O   HOH Z 389 " =    1.773
peak=    3.469 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.467 closest distance to " O   HOH Z 153 " =    1.678
peak=    3.467 closest distance to " CB  GLN A  89 " =    1.409
peak=    3.458 closest distance to " CB  VAL A 202 " =    1.596
peak=    3.457 closest distance to " O   HOH Z 126 " =    1.495
peak=    3.450 closest distance to " CA  PHE A 283 " =    1.299
peak=    3.449 closest distance to " OE1 GLN A  11 " =    2.110
peak=    3.444 closest distance to " CB  SER A  26 " =    1.583
peak=    3.443 closest distance to " O   HOH Z 219 " =    2.295
peak=    3.442 closest distance to " O   HOH Z 146 " =    1.664
peak=    3.436 closest distance to " O   HOH Z 365 " =    2.744
peak=    3.430 closest distance to " O   HOH Z  89 " =    2.134
peak=    3.429 closest distance to " O   HOH Z 411 " =    3.787
peak=    3.423 closest distance to " CG  LEU A 167 " =    1.202
peak=    3.418 closest distance to " O   HOH Z 290 " =    0.929
peak=    3.418 closest distance to " O   HOH Z 409 " =    2.538
peak=    3.416 closest distance to " O   HOH Z 135 " =    1.704
peak=    3.415 closest distance to " CD  PRO A 243 " =    1.486
peak=    3.411 closest distance to " O   HOH Z 388 " =    1.928
peak=    3.409 closest distance to " O   HOH Z  88 " =    2.587
peak=    3.409 closest distance to " O   HOH Z  64 " =    2.076
peak=    3.408 closest distance to " CA  ASP A 162 " =    1.094
peak=    3.407 closest distance to " O   HOH Z  21 " =    1.747
peak=    3.399 closest distance to " O   ARG A 145 " =    1.780
peak=    3.396 closest distance to " O   HOH Z 271 " =    2.333
peak=    3.396 closest distance to " CB  SER A  62 " =    1.230
peak=    3.395 closest distance to " O   HOH Z 435 " =    1.904
peak=    3.394 closest distance to " O   HOH Z   6 " =    1.962
peak=    3.393 closest distance to " O   HOH Z 284 " =    2.904
peak=    3.392 closest distance to " O   HOH Z 183 " =    1.343
peak=    3.391 closest distance to " CB  ALA A   1 " =    4.622
peak=    3.389 closest distance to " O   HOH Z 298 " =    2.513
peak=    3.388 closest distance to " O   HOH Z 403 " =    1.279
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.340
peak=    3.382 closest distance to " O   HOH Z 426 " =    1.688
peak=    3.375 closest distance to " CB  SER A 212 " =    1.003
peak=    3.371 closest distance to " O   HOH Z 345 " =    3.375
peak=    3.368 closest distance to " CB  LYS A 117 " =    1.202
peak=    3.367 closest distance to " O   HOH Z 303 " =    1.705
peak=    3.361 closest distance to " OG  SER A  22 " =    2.753
peak=    3.360 closest distance to " NE2 GLN A  73 " =    3.578
peak=    3.356 closest distance to " CZ  PHE A 218 " =    0.999
peak=    3.354 closest distance to " O   HOH Z 359 " =    1.357
peak=    3.346 closest distance to " OE2 GLU A  53 " =    2.069
peak=    3.341 closest distance to " O   HOH Z  44 " =    3.071
peak=    3.341 closest distance to " O   HOH Z 189 " =    2.200
peak=    3.335 closest distance to " CD2 LEU A 255 " =    1.494
peak=    3.335 closest distance to " O   HOH Z 432 " =    1.736
peak=    3.329 closest distance to " CB  LYS A 290 " =    1.415
peak=    3.326 closest distance to " O  BHOH Z 338 " =    2.353
peak=    3.320 closest distance to " CB  ALA A 114 " =    1.472
peak=    3.317 closest distance to " CA  ALA A  84 " =    1.346
peak=    3.316 closest distance to " O   HOH Z 261 " =    2.232
peak=    3.314 closest distance to " O   HOH Z 227 " =    1.758
peak=    3.314 closest distance to " O   HOH Z 266 " =    3.168
peak=    3.314 closest distance to " CB  ASN A  39 " =    0.849
peak=    3.313 closest distance to " O   HOH Z 337 " =    3.646
peak=    3.309 closest distance to " O   HOH Z   2 " =    1.325
peak=    3.298 closest distance to " O   HOH Z 124 " =    1.332
peak=    3.294 closest distance to " O   HOH Z 108 " =    2.236
peak=    3.292 closest distance to " ND1 HIS A  81 " =    1.558
peak=    3.286 closest distance to " O   HOH Z 422 " =    2.632
peak=    3.284 closest distance to " O   HOH Z 173 " =    1.885
peak=    3.284 closest distance to " CA  ALA A 158 " =    1.149
peak=    3.282 closest distance to " O   HOH Z  55 " =    2.242
peak=    3.275 closest distance to " CB  ILE A 120 " =    1.395
peak=    3.271 closest distance to " CB  LEU A 300 " =    0.891
peak=    3.271 closest distance to " CB  SER A 273 " =    0.795
peak=    3.269 closest distance to " O   HOH Z 417 " =    1.066
peak=    3.264 closest distance to " O   HOH Z 394 " =    1.552
peak=    3.262 closest distance to " CB  THR A 279 " =    1.752
peak=    3.262 closest distance to " CG2 ILE A 120 " =    1.158
peak=    3.261 closest distance to " CB  ALA A 291 " =    1.426
peak=    3.256 closest distance to " CA  LEU A 101 " =    1.495
peak=    3.253 closest distance to " CG  GLN A  77 " =    2.429
peak=    3.248 closest distance to " O   HOH Z  47 " =    1.793
peak=    3.248 closest distance to " CB  LEU A 143 " =    1.107
peak=    3.247 closest distance to " CG AARG A 275 " =    1.067
peak=    3.242 closest distance to " CD  ARG A  79 " =    2.321
peak=    3.239 closest distance to " O   HOH Z 433 " =    1.744
peak=    3.238 closest distance to " N   ASN A 127 " =    1.243
peak=    3.226 closest distance to " CB  SER A  62 " =    0.763
peak=    3.225 closest distance to " CB  ASP A 140 " =    0.937
peak=    3.225 closest distance to " CA  ILE A 234 " =    1.007
peak=    3.225 closest distance to " CA  ALA A  51 " =    0.927
peak=    3.219 closest distance to " CB  GLN A  88 " =    1.240
peak=    3.212 closest distance to " O   HOH Z 211 " =    2.818
peak=    3.212 closest distance to " N   ARG A 156 " =    1.263
peak=    3.210 closest distance to " CG1BVAL A  72 " =    1.389
peak=    3.208 closest distance to " O   HOH Z 336 " =    2.002
peak=    3.205 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.202 closest distance to " CB  ALA A 248 " =    0.927
peak=    3.198 closest distance to " O   HOH Z 217 " =    1.411
peak=    3.197 closest distance to " O   HOH Z 112 " =    1.129
peak=    3.196 closest distance to " O   HOH Z 144 " =    1.881
peak=    3.195 closest distance to " CB  MET A  47 " =    1.257
peak=    3.190 closest distance to " O   HOH Z  40 " =    2.016
peak=    3.187 closest distance to " CA  ASN A  74 " =    1.297
peak=    3.181 closest distance to " O   HOH Z 109 " =    2.582
peak=    3.180 closest distance to " O   HOH Z  88 " =    2.491
peak=    3.178 closest distance to " O   HOH Z  30 " =    1.542
peak=    3.173 closest distance to " CG2 THR A 294 " =    1.710
peak=    3.172 closest distance to " O   HOH Z  85 " =    2.187
peak=    3.171 closest distance to " CB  HIS A 108 " =    0.795
peak=    3.166 closest distance to " O   HOH Z 258 " =    2.211
peak=    3.166 closest distance to " CB  ASN A 142 " =    0.939
peak=    3.165 closest distance to " CA  SER A  32 " =    1.644
peak=    3.165 closest distance to " NH1 ARG A  14 " =    1.213
peak=    3.164 closest distance to " O   GLY A  57 " =    2.567
peak=    3.161 closest distance to " O   HOH Z 325 " =    3.682
peak=    3.160 closest distance to " O   HOH Z 213 " =    2.145
peak=    3.160 closest distance to " CB  SER A 276 " =    1.069
peak=    3.157 closest distance to " CG  MET A 185 " =    1.271
peak=    3.156 closest distance to " CG  GLN A  89 " =    1.473
peak=    3.156 closest distance to " O   HOH Z 374 " =    2.537
peak=    3.155 closest distance to " O   HOH Z 110 " =    1.661
peak=    3.154 closest distance to " CG2 VAL A 197 " =    1.131
peak=    3.154 closest distance to " N   CYS A 260 " =    0.864
peak=    3.152 closest distance to " CA  ARG A 102 " =    1.126
peak=    3.151 closest distance to " O   HOH Z 329 " =    3.698
peak=    3.150 closest distance to " CB  LEU A 255 " =    0.790
peak=    3.150 closest distance to " O   HOH Z 133 " =    1.435
peak=    3.148 closest distance to " O   HOH Z 411 " =    1.688
peak=    3.148 closest distance to " O   HOH Z 302 " =    1.584
peak=    3.139 closest distance to " CB  TRP A 179 " =    1.409
peak=    3.135 closest distance to " CA  ALA A 291 " =    0.899
peak=    3.130 closest distance to " CB  ASN A 110 " =    1.085
peak=    3.130 closest distance to " O   HOH Z  50 " =    1.602
peak=    3.125 closest distance to " CG  MET A 113 " =    1.135
peak=    3.118 closest distance to " CB  ARG A 138 " =    0.865
peak=    3.118 closest distance to " CA  ALA A 299 " =    0.890
peak=    3.117 closest distance to " CA  ALA A 248 " =    1.205
peak=    3.117 closest distance to " N   GLN A 278 " =    1.148
peak=    3.116 closest distance to " CB  VAL A 126 " =    1.145
peak=    3.113 closest distance to " O   HOH Z  43 " =    2.720
peak=    3.106 closest distance to " O   HOH Z 188 " =    1.930
peak=    3.099 closest distance to " O   HOH Z  71 " =    2.361
peak=    3.098 closest distance to " O   HOH Z 423 " =    1.743
peak=    3.098 closest distance to " CD2 HIS A  81 " =    1.077
peak=    3.097 closest distance to " OG  SER A  62 " =    2.974
peak=    3.096 closest distance to " NZ  LYS A 119 " =    1.234
peak=    3.095 closest distance to " CG1 VAL A 189 " =    1.851
peak=    3.092 closest distance to " CG  GLN A 240 " =    3.427
peak=    3.086 closest distance to " CG BARG A 102 " =    1.767
peak=    3.082 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.070 closest distance to " CA  ARG A  36 " =    1.020
peak=    3.061 closest distance to " O   HOH Z 286 " =    2.300
peak=    3.054 closest distance to " CA  MET A 105 " =    0.969
peak=    3.054 closest distance to " CA  ALA A 233 " =    1.655
peak=    3.049 closest distance to " O   HOH Z  59 " =    1.936
peak=    3.038 closest distance to " O  BHOH Z  74 " =    1.412

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.772 - 5.551
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 210
   mapped sites are within: 0.772 - 5.551

peak=   -4.683 closest distance to " O   HOH Z 377 " =    2.020
peak=   -4.625 closest distance to " O   HOH Z 266 " =    4.668
peak=   -4.610 closest distance to " CB  PRO A 243 " =    2.564
peak=   -4.573 closest distance to " CD  ARG A 156 " =    2.019
peak=   -4.495 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.390 closest distance to " CG  GLN A 223 " =    1.891
peak=   -4.335 closest distance to " SG  CYS A 254 " =    3.381
peak=   -4.278 closest distance to " OG BSER A 134 " =    1.228
peak=   -4.230 closest distance to " CG1 VAL A 112 " =    2.821
peak=   -4.194 closest distance to " O   PRO A 198 " =    1.304
peak=   -4.108 closest distance to " O   HOH Z 231 " =    2.190
peak=   -4.082 closest distance to " O   HOH Z 372 " =    2.458
peak=   -4.057 closest distance to " O   VAL A  67 " =    2.668
peak=   -4.035 closest distance to " N   GLN A  58 " =    1.586
peak=   -4.003 closest distance to " O   HOH Z 198 " =    1.916
peak=   -4.000 closest distance to " O   HOH Z 313 " =    1.900
peak=   -3.970 closest distance to " O   SER A 135 " =    1.455
peak=   -3.950 closest distance to " CD1 LEU A 255 " =    2.882
peak=   -3.938 closest distance to " O   HOH Z 102 " =    1.595
peak=   -3.933 closest distance to " CB  ASN A  39 " =    2.261
peak=   -3.930 closest distance to " CZ  PHE A  59 " =    1.468
peak=   -3.883 closest distance to " CE2 TYR A  30 " =    2.756
peak=   -3.879 closest distance to " O   VAL A  67 " =    2.771
peak=   -3.862 closest distance to " O   HOH Z 351 " =    1.572
peak=   -3.861 closest distance to " ND2 ASN A  45 " =    1.041
peak=   -3.860 closest distance to " CA  GLY A  98 " =    1.843
peak=   -3.858 closest distance to " CB  ALA A 291 " =    2.129
peak=   -3.848 closest distance to " ND2 ASN A  45 " =    1.560
peak=   -3.842 closest distance to " O   HOH Z  13 " =    1.520
peak=   -3.831 closest distance to " O   HOH Z 290 " =    1.210
peak=   -3.828 closest distance to " OXT GLY A 302 " =    2.820
peak=   -3.820 closest distance to " CG  PHE A 283 " =    2.605
peak=   -3.815 closest distance to " O   HOH Z 389 " =    1.886
peak=   -3.814 closest distance to " OD1 ASN A 187 " =    1.575
peak=   -3.785 closest distance to " O   HOH Z 407 " =    3.004
peak=   -3.784 closest distance to " CB  TYR A  15 " =    2.155
peak=   -3.770 closest distance to " O   ARG A 145 " =    1.578
peak=   -3.766 closest distance to " O   HOH Z 185 " =    2.122
peak=   -3.762 closest distance to " O   PRO A 163 " =    1.929
peak=   -3.728 closest distance to " OD2 ASP A 191 " =    1.457
peak=   -3.728 closest distance to " N   ASP A 286 " =    2.408
peak=   -3.724 closest distance to " CD1 PHE A  59 " =    1.960
peak=   -3.716 closest distance to " O   HOH Z  43 " =    1.785
peak=   -3.715 closest distance to " CD1 LEU A 228 " =    2.077
peak=   -3.706 closest distance to " CB  ALA A 161 " =    2.494
peak=   -3.706 closest distance to " O   HOH Z 263 " =    2.910
peak=   -3.692 closest distance to " CA  GLY A 203 " =    2.188
peak=   -3.682 closest distance to " O   HOH Z 298 " =    1.196
peak=   -3.667 closest distance to " CD  ARG A 139 " =    1.533
peak=   -3.664 closest distance to " O   ALA A 161 " =    1.577
peak=   -3.650 closest distance to " O   PRO A 198 " =    1.264
peak=   -3.647 closest distance to " CB  PHE A 192 " =    1.902
peak=   -3.641 closest distance to " OD1 ASP A 191 " =    1.898
peak=   -3.637 closest distance to " CE  MET A 105 " =    2.205
peak=   -3.631 closest distance to " O   SER A  95 " =    1.458
peak=   -3.623 closest distance to " CG  ASP A 231 " =    0.772
peak=   -3.606 closest distance to " CZ  TYR A 169 " =    1.675
peak=   -3.600 closest distance to " O   HOH Z 385 " =    1.891
peak=   -3.588 closest distance to " OD1 ASP A 191 " =    1.476
peak=   -3.586 closest distance to " CB  ALA A 248 " =    1.987
peak=   -3.584 closest distance to " CZ3 TRP A 179 " =    1.222
peak=   -3.574 closest distance to " O   HOH Z 152 " =    4.990
peak=   -3.571 closest distance to " C   LEU A 143 " =    1.096
peak=   -3.567 closest distance to " O   PRO A 243 " =    2.531
peak=   -3.563 closest distance to " OD1 ASP A 171 " =    1.544
peak=   -3.553 closest distance to " N   ALA A 248 " =    1.537
peak=   -3.552 closest distance to " OD2 ASP A 171 " =    2.124
peak=   -3.547 closest distance to " NH2 ARG A  79 " =    1.968
peak=   -3.545 closest distance to " O   HOH Z 211 " =    1.561
peak=   -3.543 closest distance to " O   HOH Z 193 " =    2.058
peak=   -3.541 closest distance to " CB  ALA A 291 " =    2.292
peak=   -3.506 closest distance to " O   HOH Z 198 " =    1.529
peak=   -3.503 closest distance to " O   SER A  22 " =    2.439
peak=   -3.494 closest distance to " O   HOH Z  24 " =    1.291
peak=   -3.492 closest distance to " O   HOH Z  63 " =    1.853
peak=   -3.483 closest distance to " O   HOH Z  51 " =    1.232
peak=   -3.481 closest distance to " CG2 THR A 178 " =    2.154
peak=   -3.480 closest distance to " NH2BARG A 275 " =    1.793
peak=   -3.479 closest distance to " O   VAL A 189 " =    2.499
peak=   -3.478 closest distance to " CA  GLY A 133 " =    1.942
peak=   -3.477 closest distance to " O   HOH Z 126 " =    1.878
peak=   -3.471 closest distance to " CG  GLN A  58 " =    1.185
peak=   -3.455 closest distance to " O   VAL A 174 " =    2.196
peak=   -3.454 closest distance to " CD1 LEU A 101 " =    2.247
peak=   -3.453 closest distance to " OG  SER A  97 " =    2.047
peak=   -3.447 closest distance to " O   HOH Z 393 " =    3.463
peak=   -3.447 closest distance to " CB  PHE A 208 " =    2.212
peak=   -3.443 closest distance to " CB  ASP A 132 " =    2.340
peak=   -3.441 closest distance to " ND2 ASN A  69 " =    1.542
peak=   -3.440 closest distance to " O   HOH Z 131 " =    4.054
peak=   -3.435 closest distance to " OG  SER A  87 " =    1.277
peak=   -3.427 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.423 closest distance to " CB  ALA A   7 " =    2.042
peak=   -3.423 closest distance to " ND2 ASN A 187 " =    1.547
peak=   -3.422 closest distance to " C   ALA A 158 " =    1.294
peak=   -3.405 closest distance to " CD2 LEU A 237 " =    2.657
peak=   -3.404 closest distance to " OG  SER A 245 " =    1.277
peak=   -3.402 closest distance to " CB  ALA A 248 " =    2.299
peak=   -3.401 closest distance to " O   HOH Z 140 " =    1.795
peak=   -3.391 closest distance to " O   HOH Z  60 " =    2.295
peak=   -3.390 closest distance to " CB  CYS A 254 " =    2.248
peak=   -3.389 closest distance to " OG BSER A 134 " =    1.550
peak=   -3.389 closest distance to " OE1 GLN A 183 " =    1.417
peak=   -3.365 closest distance to " O   HOH Z  60 " =    1.979
peak=   -3.363 closest distance to " CE2 PHE A 218 " =    2.393
peak=   -3.363 closest distance to " CB  PRO A 163 " =    2.402
peak=   -3.361 closest distance to " CG1 VAL A 268 " =    2.398
peak=   -3.358 closest distance to " O   HOH Z 266 " =    4.525
peak=   -3.356 closest distance to " CG  MET A 105 " =    0.947
peak=   -3.356 closest distance to " CG2 VAL A 189 " =    1.966
peak=   -3.354 closest distance to " NH2AARG A 275 " =    5.215
peak=   -3.351 closest distance to " OD1 ASN A 148 " =    1.591
peak=   -3.347 closest distance to " O   HOH Z 165 " =    2.180
peak=   -3.347 closest distance to " CG1 VAL A 230 " =    1.948
peak=   -3.339 closest distance to " O   SER A 146 " =    1.049
peak=   -3.330 closest distance to " CG  GLN A  88 " =    0.813
peak=   -3.329 closest distance to " O   HOH Z  11 " =    1.838
peak=   -3.322 closest distance to " O   HOH Z 114 " =    2.904
peak=   -3.320 closest distance to " O   HOH Z 234 " =    3.865
peak=   -3.314 closest distance to " O   HOH Z 213 " =    1.403
peak=   -3.312 closest distance to " O   HOH Z  93 " =    2.036
peak=   -3.310 closest distance to " N   ALA A  43 " =    2.596
peak=   -3.309 closest distance to " O   HOH Z 191 " =    5.551
peak=   -3.309 closest distance to " CB  TRP A  85 " =    2.418
peak=   -3.307 closest distance to " O   HOH Z 103 " =    1.698
peak=   -3.306 closest distance to " CA  ASP A  27 " =    2.424
peak=   -3.305 closest distance to " NE  ARG A  36 " =    1.897
peak=   -3.305 closest distance to " O   HOH Z 250 " =    1.446
peak=   -3.304 closest distance to " NH1 ARG A 195 " =    2.639
peak=   -3.299 closest distance to " O   GLY A  80 " =    2.412
peak=   -3.296 closest distance to " OD1 ASN A 176 " =    1.308
peak=   -3.295 closest distance to " CD  LYS A 289 " =    2.339
peak=   -3.295 closest distance to " O   HOH Z  52 " =    1.369
peak=   -3.291 closest distance to " O   ALA A 180 " =    1.294
peak=   -3.290 closest distance to " CB  ALA A 131 " =    1.922
peak=   -3.287 closest distance to " O   HOH Z 388 " =    2.068
peak=   -3.286 closest distance to " OE1 GLN A 223 " =    1.994
peak=   -3.286 closest distance to " O   HOH Z 282 " =    1.293
peak=   -3.280 closest distance to " N   THR A 157 " =    1.472
peak=   -3.276 closest distance to " O   HOH Z  90 " =    2.512
peak=   -3.275 closest distance to " O   HOH Z 166 " =    1.298
peak=   -3.272 closest distance to " O   HOH Z 236 " =    1.972
peak=   -3.268 closest distance to " CB  ILE A  33 " =    2.803
peak=   -3.267 closest distance to " NH1AARG A 275 " =    1.781
peak=   -3.266 closest distance to " N   SER A 212 " =    1.960
peak=   -3.262 closest distance to " O   ALA A  51 " =    1.307
peak=   -3.260 closest distance to " CB  ASP A 132 " =    2.206
peak=   -3.260 closest distance to " O   HOH Z 111 " =    2.335
peak=   -3.254 closest distance to " C   PRO A  90 " =    1.504
peak=   -3.253 closest distance to " CE3 TRP A 274 " =    2.283
peak=   -3.252 closest distance to " O   HOH Z 166 " =    2.155
peak=   -3.252 closest distance to " CE1 TYR A 169 " =    2.506
peak=   -3.249 closest distance to " CE3 TRP A 123 " =    1.274
peak=   -3.248 closest distance to " O   MET A  40 " =    2.728
peak=   -3.243 closest distance to " O   ALA A  10 " =    1.684
peak=   -3.239 closest distance to " O   HOH Z 353 " =    2.131
peak=   -3.232 closest distance to " O   THR A 220 " =    1.848
peak=   -3.231 closest distance to " O   HOH Z 359 " =    3.297
peak=   -3.227 closest distance to " CG  TRP A 266 " =    1.856
peak=   -3.218 closest distance to " O   HOH Z 351 " =    1.682
peak=   -3.212 closest distance to " CB  ASP A 286 " =    2.195
peak=   -3.212 closest distance to " NE2 GLN A 278 " =    1.723
peak=   -3.195 closest distance to " O   HOH Z 324 " =    2.049
peak=   -3.195 closest distance to " O   TRP A  70 " =    1.488
peak=   -3.193 closest distance to " CD2 PHE A  61 " =    2.195
peak=   -3.192 closest distance to " N   THR A 235 " =    1.324
peak=   -3.190 closest distance to " OG  SER A  62 " =    1.704
peak=   -3.190 closest distance to " O   ASN A 249 " =    1.487
peak=   -3.189 closest distance to " OE1 GLN A 194 " =    1.649
peak=   -3.184 closest distance to " CE  MET A  93 " =    1.201
peak=   -3.183 closest distance to " ND2 ASN A  39 " =    1.417
peak=   -3.183 closest distance to " SG ACYS A 201 " =    1.726
peak=   -3.182 closest distance to " N   PHE A  59 " =    1.861
peak=   -3.177 closest distance to " CD2 PHE A 225 " =    1.111
peak=   -3.177 closest distance to " O   ASP A 162 " =    2.161
peak=   -3.176 closest distance to " CG1 VAL A 197 " =    2.084
peak=   -3.175 closest distance to " CA  TRP A 274 " =    1.502
peak=   -3.168 closest distance to " O   HOH Z  38 " =    1.761
peak=   -3.167 closest distance to " CB  ALA A  51 " =    1.844
peak=   -3.167 closest distance to " OH  TYR A 214 " =    1.265
peak=   -3.165 closest distance to " CE  LYS A  76 " =    2.852
peak=   -3.164 closest distance to " O   HOH Z 414 " =    1.904
peak=   -3.162 closest distance to " O   HOH Z 137 " =    1.463
peak=   -3.157 closest distance to " O   HOH Z 137 " =    1.426
peak=   -3.154 closest distance to " O   HOH Z 147 " =    1.842
peak=   -3.148 closest distance to " C   LYS A  76 " =    1.715
peak=   -3.141 closest distance to " O   HOH Z 256 " =    1.383
peak=   -3.137 closest distance to " CG2 ILE A 263 " =    2.246
peak=   -3.135 closest distance to " O   ALA A  34 " =    2.467
peak=   -3.134 closest distance to " CA  ASN A 127 " =    1.409
peak=   -3.134 closest distance to " OD2 ASP A  50 " =    1.497
peak=   -3.120 closest distance to " CA  GLY A  57 " =    2.115
peak=   -3.116 closest distance to " O   HOH Z 288 " =    1.423
peak=   -3.115 closest distance to " CZ2 TRP A 274 " =    0.997
peak=   -3.115 closest distance to " OG  SER A  97 " =    1.693
peak=   -3.106 closest distance to " OE2 GLU A 152 " =    1.122
peak=   -3.103 closest distance to " CB  ASP A 286 " =    1.763
peak=   -3.101 closest distance to " C   MET A 188 " =    1.457
peak=   -3.096 closest distance to " O   HOH Z 298 " =    2.439
peak=   -3.091 closest distance to " O   HOH Z 111 " =    4.607
peak=   -3.082 closest distance to " CB  ALA A 244 " =    2.007
peak=   -3.078 closest distance to " CG  GLU A   2 " =    2.071
peak=   -3.067 closest distance to " CB  ASN A  39 " =    2.040
peak=   -3.060 closest distance to " CD2 TYR A 293 " =    1.932
peak=   -3.059 closest distance to " O   ASN A 127 " =    2.197
peak=   -3.058 closest distance to " CD  GLN A  77 " =    1.592
peak=   -3.041 closest distance to " O   HOH Z 323 " =    1.409
peak=   -3.032 closest distance to " OD1 ASP A 200 " =    1.399
peak=   -3.016 closest distance to " CD  GLN A 223 " =    1.395

================= 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    :  0.3732 0.3708   6.151397e+00   6.137267e+00
   1_bss:  0.3590 0.3564   6.136197e+00   6.110093e+00
   1_xyz:  0.2186 0.2460   5.702313e+00   5.798536e+00
   1_adp:  0.2003 0.2574   5.652430e+00   5.837272e+00
   1_occ:  0.2000 0.2569   5.650989e+00   5.836031e+00
   2_bss:  0.1971 0.2530   5.639191e+00   5.824410e+00
   2_xyz:  0.1416 0.1896   5.338346e+00   5.563399e+00
   2_adp:  0.1313 0.1745   5.266341e+00   5.483019e+00
   2_occ:  0.1311 0.1745   5.265686e+00   5.482922e+00
   3_bss:  0.1313 0.1742   5.262669e+00   5.477694e+00
   3_xyz:  0.1166 0.1580   5.156724e+00   5.381613e+00
   3_adp:  0.1133 0.1552   5.134806e+00   5.366580e+00
   3_occ:  0.1132 0.1552   5.134787e+00   5.366878e+00
   4_bss:  0.1132 0.1551   5.134133e+00   5.366329e+00
   4_xyz:  0.1104 0.1533   5.116041e+00   5.355098e+00
   4_adp:  0.1090 0.1542   5.114402e+00   5.361224e+00
   4_occ:  0.1089 0.1542   5.114415e+00   5.361448e+00
   5_bss:  0.1088 0.1541   5.113776e+00   5.360715e+00
   5_xyz:  0.1061 0.1534   5.101138e+00   5.359302e+00
   5_adp:  0.1058 0.1536   5.100022e+00   5.359921e+00
   5_occ:  0.1058 0.1536   5.100115e+00   5.360183e+00
   5_bss:  0.1058 0.1537   5.100647e+00   5.359961e+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:  0.332  30.854  -3.003   2.205  -0.589   0.000  -0.000  -0.000
   1_xyz:  0.332  30.854  -3.003   2.205  -0.589   0.000  -0.000  -0.000
   1_adp:  0.332  30.854  -3.003   2.205  -0.589   0.000  -0.000  -0.000
   1_occ:  0.332  30.854  -3.003   2.205  -0.589   0.000  -0.000  -0.000
   2_bss:  0.325  38.635  -2.805  -1.159  -1.399  -0.000  -0.000  -0.000
   2_xyz:  0.325  38.635  -2.805  -1.159  -1.399  -0.000  -0.000  -0.000
   2_adp:  0.325  38.635  -2.805  -1.159  -1.399  -0.000  -0.000  -0.000
   2_occ:  0.325  38.635  -2.805  -1.159  -1.399  -0.000  -0.000  -0.000
   3_bss:  0.320  39.610  -2.742  -2.181  -1.440  -0.000  -0.000  -0.000
   3_xyz:  0.320  39.610  -2.742  -2.181  -1.440  -0.000  -0.000  -0.000
   3_adp:  0.320  39.610  -2.742  -2.181  -1.440  -0.000  -0.000  -0.000
   3_occ:  0.320  39.610  -2.742  -2.181  -1.440  -0.000  -0.000  -0.000
   4_bss:  0.320  39.610  -2.700  -2.425  -1.473  -0.000  -0.000  -0.000
   4_xyz:  0.320  39.610  -2.700  -2.425  -1.473  -0.000  -0.000  -0.000
   4_adp:  0.320  39.610  -2.700  -2.425  -1.473  -0.000  -0.000  -0.000
   4_occ:  0.320  39.610  -2.700  -2.425  -1.473  -0.000  -0.000  -0.000
   5_bss:  0.319  42.837  -2.451  -2.302  -1.270  -0.000  -0.000  -0.000
   5_xyz:  0.319  42.837  -2.451  -2.302  -1.270  -0.000  -0.000  -0.000
   5_adp:  0.319  42.837  -2.451  -2.302  -1.270  -0.000  -0.000  -0.000
   5_occ:  0.319  42.837  -2.451  -2.302  -1.270  -0.000  -0.000  -0.000
   5_bss:  0.320  43.933  -2.276  -2.175  -1.105  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  39.837 0.6476  0.8444    40929.370
   1_bss:  38.478 0.6614  0.8450    36891.213
   1_xyz:  23.757 0.8263  0.9977    15661.325
   1_adp:  25.027 0.8123  0.9852    16878.498
   1_occ:  24.987 0.8126  0.9851    16808.554
   2_bss:  24.415 0.8185  0.9474    16175.259
   2_xyz:  17.829 0.8814  0.9914     8876.088
   2_adp:  15.892 0.8993  0.9983     7711.147
   2_occ:  15.885 0.8993  0.9982     7698.168
   3_bss:  15.769 0.9002  0.9869     7602.943
   3_xyz:  13.812 0.9161  0.9916     6188.538
   3_adp:  13.465 0.9191  0.9877     6018.156
   3_occ:  13.469 0.9191  0.9876     6017.347
   4_bss:  13.454 0.9192  0.9850     6011.008
   4_xyz:  13.211 0.9213  0.9858     5869.775
   4_adp:  13.328 0.9204  0.9799     5925.162
   4_occ:  13.331 0.9204  0.9798     5928.199
   5_bss:  13.315 0.9205  0.9871     5918.510
   5_xyz:  13.267 0.9209  0.9868     5917.831
   5_adp:  13.281 0.9208  0.9799     5913.994
   5_occ:  13.286 0.9207  0.9798     5916.770
   5_bss:  13.289 0.9207  0.9857     5914.769
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6587e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6587e-01
   1_xyz:   1.214  0.010  0.079 15.024  0.005  4.105   8.4932e-02
   1_adp:   1.214  0.010  0.079 15.024  0.005  4.105   8.4932e-02
   1_occ:   1.214  0.010  0.079 15.024  0.005  4.105   8.4932e-02
   2_bss:   1.214  0.010  0.079 15.024  0.005  4.105   8.4932e-02
   2_xyz:   0.986  0.006  0.071 14.461  0.004  4.111   5.6154e-02
   2_adp:   0.986  0.006  0.071 14.461  0.004  4.111   5.6154e-02
   2_occ:   0.986  0.006  0.071 14.461  0.004  4.111   5.6154e-02
   3_bss:   0.986  0.006  0.071 14.461  0.004  4.111   5.6154e-02
   3_xyz:   0.923  0.005  0.068 14.547  0.004  4.110   5.2791e-02
   3_adp:   0.923  0.005  0.068 14.547  0.004  4.110   5.2791e-02
   3_occ:   0.923  0.005  0.068 14.547  0.004  4.110   5.2791e-02
   4_bss:   0.923  0.005  0.068 14.547  0.004  4.110   5.2791e-02
   4_xyz:   0.911  0.005  0.068 14.379  0.004  4.110   5.1049e-02
   4_adp:   0.911  0.005  0.068 14.379  0.004  4.110   5.1049e-02
   4_occ:   0.911  0.005  0.068 14.379  0.004  4.110   5.1049e-02
   5_bss:   0.911  0.005  0.068 14.379  0.004  4.110   5.1049e-02
   5_xyz:   0.972  0.006  0.072 14.569  0.004  4.110   5.7007e-02
   5_adp:   0.972  0.006  0.072 14.569  0.004  4.110   5.7007e-02
   5_occ:   0.972  0.006  0.072 14.569  0.004  4.110   5.7007e-02
   5_bss:   0.972  0.006  0.072 14.569  0.004  4.110   5.7007e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3814e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3814e-01
   1_xyz:   7.995  0.055  0.382 87.330  0.039  2.170   7.8312e-02
   1_adp:   7.995  0.055  0.382 87.330  0.039  2.170   7.8312e-02
   1_occ:   7.995  0.055  0.382 87.330  0.039  2.170   7.8312e-02
   2_bss:   7.995  0.055  0.382 87.330  0.039  2.170   7.8312e-02
   2_xyz:   6.714  0.042  0.210 81.817  0.041  2.314   6.1060e-02
   2_adp:   6.714  0.042  0.210 81.817  0.041  2.314   6.1060e-02
   2_occ:   6.714  0.042  0.210 81.817  0.041  2.314   6.1060e-02
   3_bss:   6.714  0.042  0.210 81.817  0.041  2.314   6.1060e-02
   3_xyz:   6.754  0.046  0.208 84.997  0.036  2.319   5.2077e-02
   3_adp:   6.754  0.046  0.208 84.997  0.036  2.319   5.2077e-02
   3_occ:   6.754  0.046  0.208 84.997  0.036  2.319   5.2077e-02
   4_bss:   6.754  0.046  0.208 84.997  0.036  2.319   5.2077e-02
   4_xyz:   6.215  0.036  0.207 84.393  0.040  2.322   3.4148e-02
   4_adp:   6.215  0.036  0.207 84.393  0.040  2.322   3.4148e-02
   4_occ:   6.215  0.036  0.207 84.393  0.040  2.322   3.4148e-02
   5_bss:   6.215  0.036  0.207 84.393  0.040  2.322   3.4148e-02
   5_xyz:   6.254  0.038  0.228 84.254  0.035  2.284   4.1752e-02
   5_adp:   6.254  0.038  0.228 84.254  0.035  2.284   4.1752e-02
   5_occ:   6.254  0.038  0.228 84.254  0.035  2.284   4.1752e-02
   5_bss:   6.254  0.038  0.228 84.254  0.035  2.284   4.1752e-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:  80.30   0.00  17.48  74.73   0.00  13.34  80.30   7.25  40.04
   1_occ:  80.30   0.00  17.48  74.73   0.00  13.34  80.30   7.25  40.04
   2_bss:  80.30   0.00  17.48  74.73   0.00  13.34  80.30   7.25  40.04
   2_xyz:  80.30   0.00  17.48  74.73   0.00  13.34  80.30   7.25  40.04
   2_adp:  75.80   1.79  16.76  75.80   1.79  12.90  74.25   6.56  37.82
   2_occ:  75.80   1.79  16.76  75.80   1.79  12.90  74.25   6.56  37.82
   3_bss:  75.80   1.79  16.76  75.80   1.79  12.90  74.25   6.56  37.82
   3_xyz:  75.80   1.79  16.76  75.80   1.79  12.90  74.25   6.56  37.82
   3_adp:  78.05   1.06  16.74  78.05   1.06  12.77  74.78   5.64  38.36
   3_occ:  78.05   1.06  16.74  78.05   1.06  12.77  74.78   5.64  38.36
   4_bss:  78.05   1.06  16.74  78.05   1.06  12.77  74.78   5.64  38.36
   4_xyz:  78.05   1.06  16.74  78.05   1.06  12.77  74.78   5.64  38.36
   4_adp:  87.19   0.25  17.04  87.19   0.25  12.80  80.04   6.13  40.09
   4_occ:  87.19   0.25  17.04  87.19   0.25  12.80  80.04   6.13  40.09
   5_bss:  87.19   0.25  17.04  87.19   0.25  12.80  80.04   6.13  40.09
   5_xyz:  87.19   0.25  17.04  87.19   0.25  12.80  80.04   6.13  40.09
   5_adp:  95.59   0.00  16.96  95.59   0.00  12.69  86.50   6.00  40.18
   5_occ:  95.59   0.00  16.96  95.59   0.00  12.69  86.50   6.00  40.18
   5_bss:  95.59   0.00  16.96  95.59   0.00  12.70  86.51   6.00  40.18
------------------------------------------------------------------------
 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:    1.460    0.012    0.366
   1_adp:    1.460    0.012    0.366
   1_occ:    1.460    0.012    0.366
   2_bss:    1.460    0.012    0.366
   2_xyz:    0.968    0.028    0.457
   2_adp:    0.968    0.028    0.457
   2_occ:    0.968    0.028    0.457
   3_bss:    0.968    0.028    0.457
   3_xyz:    0.941    0.051    0.501
   3_adp:    0.941    0.051    0.501
   3_occ:    0.941    0.051    0.501
   4_bss:    0.941    0.051    0.501
   4_xyz:    1.063    0.058    0.515
   4_adp:    1.063    0.058    0.515
   4_occ:    1.063    0.058    0.515
   5_bss:    1.063    0.058    0.515
   5_xyz:    1.172    0.066    0.525
   5_adp:    1.172    0.066    0.525
   5_occ:    1.172    0.066    0.525
   5_bss:    1.172    0.066    0.525
------------------------------------------------------------------------

CPU time actual refinement: 336.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_509/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_509/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_509/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_509/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_509/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.48 
  Macro-tasks:
    bulk solvent and scale       = 38.70  
    individual site refinement   = 141.91 
    weights calculation          = 29.04  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.32 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 108.03 
    alpha_beta                      = 8.06   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 118.31 
    fmodel                         = 6.58   
    r_factors                      = 0.20   
    phase_errors                   = 11.04  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 255.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.693 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    669 calls, 107.67 s
gradients_fft:          614 calls, 104.12 s

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

# Date 2008-01-16 Time 05:00:09 PST -0800 (1200488409.23 s)
Start R-work = 0.3732, R-free = 0.3708 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1726 (no bulk solvent and anisotropic scale)

Start R-work = 0.3590, R-free = 0.3564
Final R-work = 0.1058, R-free = 0.1537