# Date 2008-01-16 Time 04:18:25 PST -0800 (1200485905.24 s)
#phil __OFF__

Command line arguments: "../258.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17184
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 258

-------------------------------------------------------------------------------
  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: (69.1963, 45.9914, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, 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: (69.1963, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.829 1.96208
Completeness in resolution range: 0.96412
Completeness with d_max=infinity: 0.96114

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8290
                             d_min =   1.9621

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: (69.1963, 45.9914, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.829 1.96208
Completeness in resolution range: 0.96412
Completeness with d_max=infinity: 0.96114

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8295 -  4.1982 [2142/2166]  1924   218  10.2%
  bin  2:  4.1982 -  3.3448 [2042/2062]  1841   201   9.8%
  bin  3:  3.3448 -  2.9257 [2022/2041]  1820   202  10.0%
  bin  4:  2.9257 -  2.6599 [1995/2025]  1793   202  10.1%
  bin  5:  2.6599 -  2.4702 [2006/2025]  1807   199   9.9%
  bin  6:  2.4702 -  2.3251 [1984/2009]  1783   201  10.1%
  bin  7:  2.3251 -  2.2091 [1960/1988]  1766   194   9.9%
  bin  8:  2.2091 -  2.1132 [1968/2004]  1772   196  10.0%
  bin  9:  2.1132 -  2.0320 [1946/1988]  1755   191   9.8%
  bin 10:  2.0320 -  1.9621 [1524/2010]  1369   155  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_258/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.63 -     2.29: 33
        2.29 -     2.94: 1649
        2.94 -     3.59: 4608
        3.59 -     4.25: 9406
        4.25 -     4.90: 13142
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.632 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.720 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.761 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.823 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28833 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_258/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_258/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 = 69.19625 45.9914 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4178   r_free= 0.4093   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.227918                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8295 -  4.6824 0.99   1390  152 0.3448 0.3341      6.4985      6.4725|
|  2:  4.6824 -  3.7361 0.99   1330  152 0.3432 0.3169      6.6995      6.6431|
|  3:  3.7361 -  3.2696 0.99   1299  143 0.3872 0.3596      6.6275      6.6511|
|  4:  3.2696 -  2.9733 0.99   1308  145 0.3943 0.4030      6.4609      6.5035|
|  5:  2.9733 -  2.7616 0.99   1286  145 0.4467 0.3865      6.3204      6.2715|
|  6:  2.7616 -  2.5997 0.99   1290  141 0.4436 0.4741      6.2318      6.1688|
|  7:  2.5997 -  2.4702 0.99   1282  144 0.4497 0.4392      6.1849      6.1078|
|  8:  2.4702 -  2.3631 0.98   1270  136 0.4622 0.4847      6.1488      6.2025|
|  9:  2.3631 -  2.2724 0.98   1262  144 0.4569 0.4677      6.0915      6.1339|
| 10:  2.2724 -  2.1943 1.00   1286  143 0.4608 0.4612      6.0725      6.0269|
| 11:  2.1943 -  2.1259 0.97   1252  137 0.4523 0.4782      5.9863      6.0564|
| 12:  2.1259 -  2.0653 0.98   1250  144 0.4720 0.4509      5.9604      5.9786|
| 13:  2.0653 -  2.0110 0.99   1277  133 0.4648 0.4477      5.8446       5.811|
| 14:  2.0110 -  1.9621 0.66    848  100 0.4983 0.4532      5.8774      5.7526|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8295 -  4.6824  1390   152  0.73  31.39   0.84     0.78      61095.25|
|  2:  4.6824 -  3.7361  1330   152  0.76  29.69   0.94     0.87      81962.63|
|  3:  3.7361 -  3.2696  1299   143  0.68  36.97   0.96     0.87      87032.98|
|  4:  3.2696 -  2.9733  1308   145  0.61  42.74   0.96     0.81      80420.10|
|  5:  2.9733 -  2.7616  1286   145  0.54  48.89   0.94     0.74      63449.64|
|  6:  2.7616 -  2.5997  1290   141  0.53  49.45   0.92     0.72      54977.88|
|  7:  2.5997 -  2.4702  1282   144  0.51  51.28   0.97     0.70      51161.85|
|  8:  2.4702 -  2.3631  1270   136  0.48  53.55   0.95     0.68      48774.96|
|  9:  2.3631 -  2.2724  1262   144  0.48  53.93   0.96     0.67      45608.07|
| 10:  2.2724 -  2.1943  1286   143  0.48  54.10   0.99     0.68      40606.27|
| 11:  2.1943 -  2.1259  1252   137  0.46  55.23   1.00     0.70      39066.39|
| 12:  2.1259 -  2.0653  1250   144  0.47  54.75   1.00     0.71      34763.85|
| 13:  2.0653 -  2.0110  1277   133  0.46  55.46   0.99     0.70      29533.06|
| 14:  2.0110 -  1.9621   848   100  0.51  51.39   1.00     0.70      22975.81|
|alpha:            min =        0.67 max =            0.87 mean =         0.74|
|beta:             min =    22975.81 max =        87032.98 mean =     53974.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.48|
|phase err.(test): min =        0.00 max =           89.91 mean =        47.41|
|-----------------------------------------------------------------------------|

============================== 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 = 11.310971             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.277   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.426124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.031   (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 |  1.632 -  1.959:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.959 -  2.286:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.286 -  2.612:       76 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.612 -  2.939:     1573 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.939 -  3.266:     1955 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.266 -  3.593:     2653 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.593 -  3.920:     4832 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.920 -  4.246:     4574 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.246 -  4.573:     5969 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.573 -  4.900:     7173 |
|-----------------------------------------------------------------------------|
|-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 |        0.181 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.632 |       0.494 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    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: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4178   r_free= 0.4093   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.227918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4058   r_free= 0.3981   ksol= 0.34   Bsol= 22.75   scale= 0.956   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,2.97,-1.78,0.00,-0.00,-0.00); trace/3= -0.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.216754                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.446832              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.053   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.787169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.832   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4058      final r-factor (work) = 0.2777          |
| start r-factor (free) = 0.3981      final r-factor (free) = 0.3118          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5362 = 9.45 * 0.50 * 6.2148 + 1.00 * 0.1813                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6068 = 9.45 * 0.50 * 6.0299 + 1.00 * 0.1251                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2777      final r-factor (work) = 0.2515          |
| start r-factor (free) = 0.3118      final r-factor (free) = 0.3261          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7525 = 0.79 * 1.00 * 6.0299 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6218 = 0.79 * 1.00 * 5.8533 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.10  17.95    None  None   None       |
|    all(noH): 2823   0      0.00    100.10  17.95    None  None   None       |
|    Sol.    : 438    0      4.56    100.10  39.46    None  None   None       |
|    Mac.    : 2385   0      0.00    76.32   14.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.010:  950   |   5:    50.048 -  60.058:   93        |
|      1:    10.010 -  20.019: 1038   |   6:    60.058 -  70.067:   32        |
|      2:    20.019 -  30.029:  374   |   7:    70.067 -  80.077:   15        |
|      3:    30.029 -  40.038:  191   |   8:    80.077 -  90.086:    0        |
|      4:    40.038 -  50.048:  129   |   9:    90.086 - 100.096:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2515 r_free = 0.3261             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2513 r_free = 0.3263             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2513   r_free= 0.3263   ksol= 0.34   Bsol= 22.75   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,2.97,-1.78,0.00,-0.00,-0.00); trace/3= -0.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.870564                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2492   r_free= 0.3218   ksol= 0.33   Bsol= 43.85   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.09,-0.95,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.860328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.240640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.390  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.194054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.799  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2492      final r-factor (work) = 0.1839          |
| start r-factor (free) = 0.3218      final r-factor (free) = 0.2324          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4577 = 5.24 * 0.50 * 5.8514 + 1.00 * 0.1251                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1220 = 5.24 * 0.50 * 5.7429 + 1.00 * 0.0738                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1839      final r-factor (work) = 0.1651          |
| start r-factor (free) = 0.2324      final r-factor (free) = 0.2110          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1285 = 0.19 * 1.00 * 5.7429 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0779 = 0.19 * 1.00 * 5.5165 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    87.36   16.94    None  None   None       |
|    all(noH): 2823   0      1.47    87.36   16.94    None  None   None       |
|    Sol.    : 438    0      6.48    87.36   38.25    None  None   None       |
|    Mac.    : 2385   0      1.47    76.44   13.02    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:     1.473 -  10.061:  994   |   5:    44.415 -  53.003:  115        |
|      1:    10.061 -  18.650: 1082   |   6:    53.003 -  61.592:   59        |
|      2:    18.650 -  27.238:  277   |   7:    61.592 -  70.180:    9        |
|      3:    27.238 -  35.827:  158   |   8:    70.180 -  78.769:    5        |
|      4:    35.827 -  44.415:  123   |   9:    78.769 -  87.357:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1651 r_free = 0.2110             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1650 r_free = 0.2105             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1650   r_free= 0.2105   ksol= 0.33   Bsol= 43.85   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-0.09,-0.95,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.470398                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1645   r_free= 0.2089   ksol= 0.32   Bsol= 43.85   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.68,-0.95,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.462950                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.388592              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.852   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208138              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.373  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1645      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.2089      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6617 = 2.39 * 0.50 * 5.5162 + 1.00 * 0.0738                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4599 = 2.39 * 0.50 * 5.3624 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1759      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1235 = 0.21 * 1.00 * 5.3624 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0992 = 0.21 * 1.00 * 5.2453 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    85.12   16.82    None  None   None       |
|    all(noH): 2823   0      0.86    85.12   16.82    None  None   None       |
|    Sol.    : 438    0      3.34    85.12   39.19    None  None   None       |
|    Mac.    : 2385   0      0.86    78.32   12.71    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:     0.857 -   9.283:  854   |   5:    42.987 -  51.413:  123        |
|      1:     9.283 -  17.709: 1224   |   6:    51.413 -  59.839:   76        |
|      2:    17.709 -  26.135:  270   |   7:    59.839 -  68.265:   24        |
|      3:    26.135 -  34.561:  129   |   8:    68.265 -  76.691:    8        |
|      4:    34.561 -  42.987:  113   |   9:    76.691 -  85.117:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1258 r_free = 0.1703             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1256 r_free = 0.1703             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1703   ksol= 0.32   Bsol= 43.85   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.68,-0.95,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.226153                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1257   r_free= 0.1699   ksol= 0.32   Bsol= 43.85   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.34,-1.10,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.225089                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.109246              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.303  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.559697              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.498  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5891 = 2.11 * 0.50 * 5.2469 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5271 = 2.11 * 0.50 * 5.1884 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9114 = 0.56 * 1.00 * 5.1884 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8867 = 0.56 * 1.00 * 5.1419 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.17    87.54   17.08    None  None   None       |
|    all(noH): 2823   0      0.17    87.54   17.08    None  None   None       |
|    Sol.    : 438    0      3.15    87.54   40.70    None  None   None       |
|    Mac.    : 2385   0      0.17    86.97   12.74    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:     0.170 -   8.907:  786   |   5:    43.854 -  52.591:  102        |
|      1:     8.907 -  17.644: 1292   |   6:    52.591 -  61.328:   69        |
|      2:    17.644 -  26.381:  273   |   7:    61.328 -  70.065:   44        |
|      3:    26.381 -  35.117:  120   |   8:    70.065 -  78.801:   10        |
|      4:    35.117 -  43.854:  121   |   9:    78.801 -  87.538:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1586             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1586             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1586   ksol= 0.32   Bsol= 43.85   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.34,-1.10,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1585   ksol= 0.32   Bsol= 43.85   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.34,-0.97,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139597                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.588805              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.626  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.503543              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.287  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1400 = 1.59 * 0.50 * 5.1419 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1298 = 1.59 * 0.50 * 5.1357 + 1.00 * 0.0500                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5948 = 0.50 * 1.00 * 5.1357 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5922 = 0.50 * 1.00 * 5.1302 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.16    88.39   16.95    None  None   None       |
|    all(noH): 2823   0      0.16    88.39   16.95    None  None   None       |
|    Sol.    : 438    0      4.70    87.75   40.46    None  None   None       |
|    Mac.    : 2385   0      0.16    88.39   12.64    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:     0.165 -   8.987:  836   |   5:    44.276 -  53.098:  102        |
|      1:     8.987 -  17.809: 1258   |   6:    53.098 -  61.920:   66        |
|      2:    17.809 -  26.631:  267   |   7:    61.920 -  70.742:   41        |
|      3:    26.631 -  35.454:  122   |   8:    70.742 -  79.564:   11        |
|      4:    35.454 -  44.276:  114   |   9:    79.564 -  88.387:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1565             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1566             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1566   ksol= 0.32   Bsol= 43.85   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-2.34,-0.97,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131387                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8295 -  4.6824 0.99   1390  152 0.0973 0.1213      5.3545      5.4974|
|  2:  4.6824 -  3.7361 0.99   1330  152 0.0833 0.1139      5.4228      5.6265|
|  3:  3.7361 -  3.2696 0.99   1299  143 0.1068 0.1490      5.4835      5.8446|
|  4:  3.2696 -  2.9733 0.99   1308  145 0.1216 0.1627      5.4396      5.5842|
|  5:  2.9733 -  2.7616 0.99   1286  145 0.1301 0.1707      5.3148      5.5291|
|  6:  2.7616 -  2.5997 0.99   1290  141 0.1182 0.1998      5.1893      5.4904|
|  7:  2.5997 -  2.4702 0.99   1282  144 0.1260 0.1561       5.157      5.3043|
|  8:  2.4702 -  2.3631 0.98   1270  136 0.1167 0.1635      5.0582       5.321|
|  9:  2.3631 -  2.2724 0.98   1262  144 0.1146 0.1709      5.0188      5.2599|
| 10:  2.2724 -  2.1943 1.00   1286  143 0.1100 0.1728        4.94      5.1924|
| 11:  2.1943 -  2.1259 0.97   1252  137 0.1115 0.1727      4.9369      5.2464|
| 12:  2.1259 -  2.0653 0.98   1250  144 0.1131 0.1708      4.8811      5.2179|
| 13:  2.0653 -  2.0110 0.99   1277  133 0.1126 0.1813      4.7828      5.0651|
| 14:  2.0110 -  1.9621 0.66    848  100 0.0945 0.1574      4.6371       4.862|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8295 -  4.6824  1390   152  0.94   8.71   0.98     0.96       6515.74|
|  2:  4.6824 -  3.7361  1330   152  0.96   7.61   1.03     1.02       8732.44|
|  3:  3.7361 -  3.2696  1299   143  0.94  11.15   1.04     1.03      10316.22|
|  4:  3.2696 -  2.9733  1308   145  0.92  13.22   1.01     1.00       9844.74|
|  5:  2.9733 -  2.7616  1286   145  0.91  15.19   1.01     0.99       8002.72|
|  6:  2.7616 -  2.5997  1290   141  0.90  15.72   0.99     0.96       6710.94|
|  7:  2.5997 -  2.4702  1282   144  0.90  15.56   0.99     0.96       6012.74|
|  8:  2.4702 -  2.3631  1270   136  0.91  14.77   1.00     0.98       5080.76|
|  9:  2.3631 -  2.2724  1262   144  0.92  14.59   1.01     0.98       4824.19|
| 10:  2.2724 -  2.1943  1286   143  0.90  15.38   1.00     0.97       4246.25|
| 11:  2.1943 -  2.1259  1252   137  0.90  15.87   1.00     0.96       4339.31|
| 12:  2.1259 -  2.0653  1250   144  0.91  15.75   1.02     1.01       4008.13|
| 13:  2.0653 -  2.0110  1277   133  0.91  15.78   1.01     0.99       3299.75|
| 14:  2.0110 -  1.9621   848   100  0.93  13.34   0.99     0.96       2474.17|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2474.17 max =        10316.22 mean =      6146.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.71|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1566   ksol= 0.32   Bsol= 43.84   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.27,-0.81,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1566   ksol= 0.32   Bsol= 43.84   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.27,-0.81,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.131342                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8295 -  4.6824 0.99   1390  152 0.0973 0.1214      5.3553      5.4983|
|  2:  4.6824 -  3.7361 0.99   1330  152 0.0833 0.1138      5.4232      5.6265|
|  3:  3.7361 -  3.2696 0.99   1299  143 0.1068 0.1490      5.4836      5.8447|
|  4:  3.2696 -  2.9733 0.99   1308  145 0.1216 0.1628      5.4396      5.5842|
|  5:  2.9733 -  2.7616 0.99   1286  145 0.1301 0.1706      5.3146      5.5288|
|  6:  2.7616 -  2.5997 0.99   1290  141 0.1181 0.1996      5.1889      5.4895|
|  7:  2.5997 -  2.4702 0.99   1282  144 0.1260 0.1561      5.1569      5.3044|
|  8:  2.4702 -  2.3631 0.98   1270  136 0.1167 0.1635      5.0581      5.3208|
|  9:  2.3631 -  2.2724 0.98   1262  144 0.1147 0.1707      5.0188      5.2592|
| 10:  2.2724 -  2.1943 1.00   1286  143 0.1100 0.1730      4.9399      5.1934|
| 11:  2.1943 -  2.1259 0.97   1252  137 0.1115 0.1727      4.9371      5.2464|
| 12:  2.1259 -  2.0653 0.98   1250  144 0.1130 0.1709       4.881      5.2182|
| 13:  2.0653 -  2.0110 0.99   1277  133 0.1126 0.1811      4.7824      5.0638|
| 14:  2.0110 -  1.9621 0.66    848  100 0.0945 0.1572      4.6361      4.8609|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8295 -  4.6824  1390   152  0.94   8.72   0.98     0.96       6527.10|
|  2:  4.6824 -  3.7361  1330   152  0.96   7.62   1.03     1.02       8740.96|
|  3:  3.7361 -  3.2696  1299   143  0.94  11.15   1.04     1.04      10317.26|
|  4:  3.2696 -  2.9733  1308   145  0.92  13.22   1.02     1.00       9842.35|
|  5:  2.9733 -  2.7616  1286   145  0.91  15.18   1.01     0.99       7995.40|
|  6:  2.7616 -  2.5997  1290   141  0.90  15.71   0.99     0.97       6705.76|
|  7:  2.5997 -  2.4702  1282   144  0.91  15.56   1.00     0.96       6009.34|
|  8:  2.4702 -  2.3631  1270   136  0.91  14.77   1.00     0.99       5078.49|
|  9:  2.3631 -  2.2724  1262   144  0.92  14.59   1.01     0.99       4823.66|
| 10:  2.2724 -  2.1943  1286   143  0.90  15.38   1.01     0.97       4247.90|
| 11:  2.1943 -  2.1259  1252   137  0.90  15.87   1.01     0.97       4342.15|
| 12:  2.1259 -  2.0653  1250   144  0.91  15.75   1.02     1.02       4008.93|
| 13:  2.0653 -  2.0110  1277   133  0.91  15.77   1.01     1.00       3295.59|
| 14:  2.0110 -  1.9621   848   100  0.93  13.31   1.00     0.97       2466.81|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2466.81 max =        10317.26 mean =      6146.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.71|
|phase err.(test): min =        0.00 max =           89.05 mean =        13.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.444)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.16    88.38   16.95    None  None   None       |
|    all(noH): 2823   0      0.16    88.38   16.95    None  None   None       |
|    Sol.    : 438    0      4.70    87.75   40.46    None  None   None       |
|    Mac.    : 2385   0      0.16    88.38   12.63    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:     0.162 -   8.984:  836   |   5:    44.273 -  53.095:  102        |
|      1:     8.984 -  17.806: 1258   |   6:    53.095 -  61.917:   66        |
|      2:    17.806 -  26.628:  267   |   7:    61.917 -  70.739:   41        |
|      3:    26.628 -  35.450:  122   |   8:    70.739 -  79.561:   11        |
|      4:    35.450 -  44.273:  114   |   9:    79.561 -  88.383:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.671 - 4.621
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 299
   mapped sites are within: 0.706 - 4.621

peak=    6.398 closest distance to " NE2 GLN A  11 " =    1.247
peak=    6.353 closest distance to " O   HOH Z 142 " =    1.968
peak=    5.874 closest distance to " O   HOH Z 126 " =    2.068
peak=    5.638 closest distance to " O   HOH Z 375 " =    1.298
peak=    5.576 closest distance to " CG  PRO A  54 " =    1.313
peak=    5.373 closest distance to " O   HOH Z 417 " =    1.841
peak=    5.338 closest distance to " O   HOH Z 287 " =    1.886
peak=    5.289 closest distance to " NH2 ARG A  56 " =    2.083
peak=    5.288 closest distance to " O   HOH Z 236 " =    1.473
peak=    5.192 closest distance to " O   HOH Z 423 " =    1.641
peak=    5.132 closest distance to " CB  ARG A 275 " =    0.950
peak=    5.075 closest distance to " O   HOH Z 427 " =    2.242
peak=    5.028 closest distance to " CB  PRO A  54 " =    1.027
peak=    4.962 closest distance to " O   HOH Z   9 " =    1.279
peak=    4.953 closest distance to " O   HOH Z  65 " =    1.004
peak=    4.922 closest distance to " CG  PRO A 213 " =    1.319
peak=    4.909 closest distance to " O   HOH Z 112 " =    1.296
peak=    4.829 closest distance to " O   HOH Z  63 " =    1.609
peak=    4.656 closest distance to " CG2 VAL A 257 " =    0.863
peak=    4.610 closest distance to " O   HOH Z  78 " =    1.590
peak=    4.603 closest distance to " CG  PRO A  90 " =    1.176
peak=    4.597 closest distance to " O   HOH Z 371 " =    2.124
peak=    4.595 closest distance to " CB  GLN A 223 " =    1.513
peak=    4.579 closest distance to " O   HOH Z 232 " =    2.332
peak=    4.560 closest distance to " CB  SER A  63 " =    1.233
peak=    4.448 closest distance to " O   HOH Z 209 " =    2.206
peak=    4.447 closest distance to " CB  ASN A 148 " =    1.390
peak=    4.442 closest distance to " O   HOH Z 298 " =    1.887
peak=    4.382 closest distance to " CG  ARG A  66 " =    2.443
peak=    4.373 closest distance to " OG BSER A 164 " =    2.184
peak=    4.371 closest distance to " O   HOH Z 427 " =    1.160
peak=    4.353 closest distance to " O   HOH Z 371 " =    1.818
peak=    4.352 closest distance to " O   HOH Z 380 " =    1.782
peak=    4.346 closest distance to " O   HOH Z 419 " =    2.477
peak=    4.331 closest distance to " O   SER A  87 " =    2.342
peak=    4.322 closest distance to " CA  TYR A  30 " =    0.935
peak=    4.312 closest distance to " CB  GLN A 183 " =    1.185
peak=    4.305 closest distance to " CG  TRP A 179 " =    2.185
peak=    4.189 closest distance to " O   HOH Z 327 " =    1.697
peak=    4.189 closest distance to " CG  PRO A 198 " =    1.256
peak=    4.182 closest distance to " O   HOH Z   1 " =    1.686
peak=    4.169 closest distance to " O   HOH Z 272 " =    1.816
peak=    4.167 closest distance to " CB  ARG A 190 " =    1.674
peak=    4.163 closest distance to " O   HOH Z 193 " =    1.702
peak=    4.139 closest distance to " ND2 ASN A 187 " =    1.572
peak=    4.137 closest distance to " O   HOH Z 316 " =    3.000
peak=    4.130 closest distance to " O   HOH Z 425 " =    2.001
peak=    4.115 closest distance to " CB  ARG A  79 " =    1.364
peak=    4.109 closest distance to " O   HOH Z  44 " =    1.771
peak=    4.039 closest distance to " CB  VAL A 265 " =    1.264
peak=    4.023 closest distance to " O   HOH Z  97 " =    1.999
peak=    4.018 closest distance to " CB  GLU A 152 " =    1.279
peak=    4.013 closest distance to " O   HOH Z   9 " =    1.963
peak=    4.012 closest distance to " CG  PRO A 243 " =    1.115
peak=    4.009 closest distance to " NZ  LYS A 117 " =    2.847
peak=    4.000 closest distance to " O   HOH Z 346 " =    1.625
peak=    3.996 closest distance to " O   HOH Z 203 " =    1.808
peak=    3.993 closest distance to " O   HOH Z 365 " =    2.638
peak=    3.969 closest distance to " O   HOH Z 132 " =    2.176
peak=    3.967 closest distance to " CB  SER A   3 " =    1.225
peak=    3.963 closest distance to " O   HOH Z 144 " =    2.131
peak=    3.956 closest distance to " O   HOH Z 425 " =    1.336
peak=    3.947 closest distance to " O   HOH Z 250 " =    1.530
peak=    3.945 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.941 closest distance to " NZ  LYS A 119 " =    2.575
peak=    3.926 closest distance to " O   HOH Z 368 " =    3.589
peak=    3.923 closest distance to " CB  GLU A 277 " =    3.493
peak=    3.907 closest distance to " O   HOH Z 124 " =    1.290
peak=    3.905 closest distance to " CB  GLU A 128 " =    0.985
peak=    3.893 closest distance to " O   HOH Z 394 " =    1.680
peak=    3.876 closest distance to " CD  ARG A 159 " =    0.747
peak=    3.851 closest distance to " O   HOH Z  61 " =    1.673
peak=    3.837 closest distance to " CB  THR A  31 " =    1.618
peak=    3.833 closest distance to " O   HOH Z 405 " =    1.399
peak=    3.831 closest distance to " O   HOH Z  61 " =    1.441
peak=    3.828 closest distance to " CE  LYS A 119 " =    1.212
peak=    3.822 closest distance to " O  BHOH Z  74 " =    1.378
peak=    3.817 closest distance to " O   HOH Z 158 " =    2.765
peak=    3.814 closest distance to " OD1 ASN A  69 " =    2.463
peak=    3.811 closest distance to " O   HOH Z   3 " =    2.019
peak=    3.810 closest distance to " O   HOH Z   1 " =    1.800
peak=    3.807 closest distance to " O   HOH Z 146 " =    1.640
peak=    3.804 closest distance to " O   HOH Z 222 " =    2.329
peak=    3.792 closest distance to " O   HOH Z 362 " =    2.075
peak=    3.789 closest distance to " O   HOH Z 234 " =    3.545
peak=    3.788 closest distance to " OG BSER A  99 " =    2.354
peak=    3.788 closest distance to " O   HOH Z  93 " =    2.101
peak=    3.787 closest distance to " O   HOH Z 437 " =    1.831
peak=    3.781 closest distance to " O   HOH Z 128 " =    2.075
peak=    3.768 closest distance to " NH1BARG A 145 " =    1.288
peak=    3.765 closest distance to " O   HOH Z 344 " =    3.186
peak=    3.746 closest distance to " CB  ILE A 120 " =    1.339
peak=    3.734 closest distance to " CB  TRP A 266 " =    1.115
peak=    3.732 closest distance to " CA  ASN A 215 " =    1.073
peak=    3.732 closest distance to " CB  SER A  26 " =    1.677
peak=    3.730 closest distance to " O   HOH Z   2 " =    1.615
peak=    3.722 closest distance to " NH1AARG A 145 " =    1.180
peak=    3.711 closest distance to " CE  LYS A  76 " =    0.864
peak=    3.694 closest distance to " CB  VAL A 202 " =    1.563
peak=    3.656 closest distance to " CD2 LEU A 297 " =    1.012
peak=    3.640 closest distance to " CG1 ILE A  33 " =    1.247
peak=    3.635 closest distance to " O   HOH Z 403 " =    1.297
peak=    3.633 closest distance to " O   HOH Z 389 " =    1.661
peak=    3.624 closest distance to " CA  ALA A  84 " =    1.229
peak=    3.616 closest distance to " O   HOH Z 286 " =    2.199
peak=    3.605 closest distance to " O   HOH Z 109 " =    2.401
peak=    3.604 closest distance to " CB  THR A 157 " =    1.121
peak=    3.597 closest distance to " CB  ARG A 139 " =    1.046
peak=    3.597 closest distance to " CB  LYS A 117 " =    1.212
peak=    3.594 closest distance to " O   HOH Z 357 " =    1.876
peak=    3.588 closest distance to " CB  SER A  62 " =    1.268
peak=    3.580 closest distance to " NH2AARG A 190 " =    1.765
peak=    3.579 closest distance to " O   HOH Z 139 " =    1.094
peak=    3.575 closest distance to " O   HOH Z 130 " =    2.264
peak=    3.573 closest distance to " CG2 ILE A 120 " =    1.139
peak=    3.564 closest distance to " CB  TRP A 179 " =    1.251
peak=    3.563 closest distance to " O   HOH Z 214 " =    2.363
peak=    3.563 closest distance to " O   HOH Z 368 " =    1.984
peak=    3.561 closest distance to " CB  ASN A 187 " =    1.003
peak=    3.561 closest distance to " C   PRO A 198 " =    1.472
peak=    3.560 closest distance to " CA  ALA A 299 " =    0.929
peak=    3.553 closest distance to " CB  SER A 216 " =    0.780
peak=    3.541 closest distance to " O   HOH Z 305 " =    3.462
peak=    3.534 closest distance to " OG  SER A  62 " =    2.891
peak=    3.531 closest distance to " CD BLYS A 290 " =    1.198
peak=    3.530 closest distance to " O   HOH Z 227 " =    1.933
peak=    3.524 closest distance to " CZ  PHE A 218 " =    1.047
peak=    3.521 closest distance to " O   HOH Z 336 " =    1.848
peak=    3.520 closest distance to " O   HOH Z 422 " =    2.554
peak=    3.519 closest distance to " CB  ALA A 114 " =    1.430
peak=    3.519 closest distance to " O   HOH Z 419 " =    1.661
peak=    3.516 closest distance to " O   HOH Z 189 " =    2.009
peak=    3.514 closest distance to " CD2 TRP A 179 " =    1.316
peak=    3.512 closest distance to " CB  ASN A  39 " =    0.874
peak=    3.510 closest distance to " O   HOH Z 423 " =    1.905
peak=    3.510 closest distance to " N   GLN A 278 " =    1.152
peak=    3.503 closest distance to " N   GLU A   2 " =    1.409
peak=    3.497 closest distance to " CA  PHE A 283 " =    1.285
peak=    3.497 closest distance to " O   HOH Z  59 " =    2.139
peak=    3.497 closest distance to " O   HOH Z 290 " =    1.071
peak=    3.493 closest distance to " O   HOH Z 390 " =    2.297
peak=    3.491 closest distance to " CG1BVAL A  72 " =    1.361
peak=    3.485 closest distance to " O   HOH Z 386 " =    3.007
peak=    3.481 closest distance to " OE2 GLU A  53 " =    2.090
peak=    3.478 closest distance to " NE2 GLN A  73 " =    3.618
peak=    3.473 closest distance to " CB  LEU A 228 " =    1.067
peak=    3.472 closest distance to " O   HOH Z 371 " =    3.095
peak=    3.470 closest distance to " O   HOH Z 403 " =    1.616
peak=    3.469 closest distance to " O   HOH Z  88 " =    2.557
peak=    3.467 closest distance to " CB  TYR A 169 " =    0.727
peak=    3.467 closest distance to " O   HOH Z  10 " =    1.732
peak=    3.464 closest distance to " O   HOH Z  88 " =    2.421
peak=    3.462 closest distance to " O   HOH Z 423 " =    1.687
peak=    3.459 closest distance to " O   HOH Z 391 " =    2.847
peak=    3.459 closest distance to " O   HOH Z  44 " =    2.911
peak=    3.453 closest distance to " O   HOH Z 329 " =    3.824
peak=    3.452 closest distance to " O   HOH Z 257 " =    2.120
peak=    3.444 closest distance to " O   HOH Z 166 " =    1.419
peak=    3.441 closest distance to " N   HIS A  86 " =    1.793
peak=    3.440 closest distance to " O   HOH Z  32 " =    1.857
peak=    3.439 closest distance to " O   HOH Z 245 " =    1.341
peak=    3.434 closest distance to " CB  ALA A 114 " =    0.915
peak=    3.430 closest distance to " O   HOH Z 175 " =    2.056
peak=    3.426 closest distance to " OD1BASN A 224 " =    2.201
peak=    3.425 closest distance to " CB  GLN A  89 " =    1.368
peak=    3.417 closest distance to " CD  ARG A 138 " =    0.706
peak=    3.414 closest distance to " CB  LEU A 300 " =    0.968
peak=    3.412 closest distance to " CE1 TYR A 186 " =    1.297
peak=    3.411 closest distance to " O   HOH Z 153 " =    1.607
peak=    3.408 closest distance to " CG2BVAL A  41 " =    0.718
peak=    3.405 closest distance to " O   HOH Z  68 " =    2.199
peak=    3.400 closest distance to " CB  GLN A  88 " =    1.227
peak=    3.392 closest distance to " O   HOH Z 244 " =    1.721
peak=    3.392 closest distance to " O   HOH Z 421 " =    2.094
peak=    3.391 closest distance to " CG  LEU A 167 " =    1.212
peak=    3.385 closest distance to " O   HOH Z   6 " =    2.023
peak=    3.380 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.376 closest distance to " O   ASN A  74 " =    1.451
peak=    3.374 closest distance to " O   HOH Z 291 " =    1.501
peak=    3.371 closest distance to " CB  SER A 212 " =    1.177
peak=    3.364 closest distance to " CB  ALA A  34 " =    1.251
peak=    3.362 closest distance to " CB  ALA A   1 " =    4.621
peak=    3.360 closest distance to " CA  MET A 105 " =    0.901
peak=    3.360 closest distance to " O   HOH Z 145 " =    2.421
peak=    3.359 closest distance to " CB  LYS A 290 " =    1.360
peak=    3.359 closest distance to " N   ASN A  39 " =    1.194
peak=    3.358 closest distance to " CB  SER A  99 " =    1.016
peak=    3.357 closest distance to " NE2 GLN A  58 " =    3.944
peak=    3.355 closest distance to " O   HOH Z 359 " =    1.319
peak=    3.352 closest distance to " CA  ALA A 129 " =    1.259
peak=    3.347 closest distance to " O  BHOH Z 338 " =    2.387
peak=    3.345 closest distance to " O   HOH Z 345 " =    3.233
peak=    3.345 closest distance to " O   HOH Z 302 " =    1.452
peak=    3.344 closest distance to " N   ARG A 156 " =    1.315
peak=    3.340 closest distance to " O   HOH Z 151 " =    1.466
peak=    3.339 closest distance to " CG AARG A 275 " =    1.050
peak=    3.337 closest distance to " N   PHE A 130 " =    1.200
peak=    3.333 closest distance to " O   HOH Z  17 " =    1.752
peak=    3.330 closest distance to " O   HOH Z  92 " =    1.151
peak=    3.328 closest distance to " CA  ASN A 127 " =    1.023
peak=    3.328 closest distance to " CB  LYS A 290 " =    1.057
peak=    3.328 closest distance to " O   HOH Z 119 " =    4.321
peak=    3.325 closest distance to " O   HOH Z  40 " =    2.047
peak=    3.323 closest distance to " O   HOH Z 373 " =    1.460
peak=    3.323 closest distance to " CA  ILE A 234 " =    0.972
peak=    3.315 closest distance to " CD  LYS A 166 " =    1.332
peak=    3.313 closest distance to " O   HOH Z 173 " =    2.060
peak=    3.312 closest distance to " CB  ALA A  21 " =    1.961
peak=    3.312 closest distance to " O   HOH Z 193 " =    1.631
peak=    3.296 closest distance to " O   HOH Z 116 " =    2.775
peak=    3.294 closest distance to " O   HOH Z  80 " =    1.942
peak=    3.293 closest distance to " O   HOH Z 272 " =    2.056
peak=    3.290 closest distance to " CB  ASP A 140 " =    0.822
peak=    3.289 closest distance to " O   HOH Z 406 " =    1.562
peak=    3.288 closest distance to " O   HOH Z 392 " =    1.177
peak=    3.285 closest distance to " O   HOH Z  90 " =    2.090
peak=    3.282 closest distance to " O   HOH Z 193 " =    2.002
peak=    3.280 closest distance to " O   HOH Z  59 " =    1.369
peak=    3.276 closest distance to " ND2 ASN A 249 " =    0.824
peak=    3.275 closest distance to " O   PRO A 198 " =    1.247
peak=    3.275 closest distance to " O   HOH Z  24 " =    1.779
peak=    3.275 closest distance to " O   ARG A 145 " =    1.762
peak=    3.272 closest distance to " O   HOH Z 402 " =    1.432
peak=    3.254 closest distance to " O   HOH Z 411 " =    3.783
peak=    3.253 closest distance to " O   HOH Z 126 " =    1.416
peak=    3.252 closest distance to " O   HOH Z 213 " =    1.953
peak=    3.251 closest distance to " O   HOH Z 298 " =    2.529
peak=    3.248 closest distance to " CG2 THR A 221 " =    1.223
peak=    3.246 closest distance to " O   HOH Z 128 " =    1.943
peak=    3.241 closest distance to " CB  MET A 188 " =    1.653
peak=    3.241 closest distance to " O   HOH Z 426 " =    1.887
peak=    3.239 closest distance to " O   HOH Z  21 " =    1.719
peak=    3.237 closest distance to " CB  SER A 276 " =    1.185
peak=    3.235 closest distance to " NZ  LYS A 117 " =    1.345
peak=    3.234 closest distance to " CD  PRO A 243 " =    1.608
peak=    3.232 closest distance to " NE2 GLN A 278 " =    3.374
peak=    3.229 closest distance to " O   HOH Z 180 " =    2.200
peak=    3.228 closest distance to " O   HOH Z 181 " =    2.139
peak=    3.225 closest distance to " CG1 ILE A 151 " =    1.039
peak=    3.224 closest distance to " CB  TYR A 116 " =    0.927
peak=    3.221 closest distance to " O   HOH Z 301 " =    1.900
peak=    3.220 closest distance to " O   HOH Z 214 " =    3.826
peak=    3.215 closest distance to " N   CYS A 260 " =    0.772
peak=    3.214 closest distance to " O   HOH Z 334 " =    1.399
peak=    3.213 closest distance to " CA  ARG A 102 " =    1.127
peak=    3.211 closest distance to " CG2 VAL A 197 " =    1.012
peak=    3.210 closest distance to " CG  MET A 113 " =    0.967
peak=    3.208 closest distance to " O   HOH Z 337 " =    3.504
peak=    3.204 closest distance to " CG  GLU A 277 " =    2.003
peak=    3.201 closest distance to " CA  ALA A  21 " =    1.094
peak=    3.200 closest distance to " O   PRO A  90 " =    1.659
peak=    3.199 closest distance to " N   ALA A   1 " =    2.223
peak=    3.180 closest distance to " CA  ALA A 158 " =    1.188
peak=    3.179 closest distance to " N   TYR A 116 " =    1.545
peak=    3.172 closest distance to " O   HOH Z 213 " =    1.470
peak=    3.170 closest distance to " N   SER A 134 " =    1.377
peak=    3.168 closest distance to " CB  PHE A 130 " =    0.912
peak=    3.166 closest distance to " CB  ASN A 142 " =    0.999
peak=    3.165 closest distance to " O   HOH Z 189 " =    2.299
peak=    3.163 closest distance to " CA  ARG A 195 " =    1.267
peak=    3.157 closest distance to " N   SER A  97 " =    0.871
peak=    3.157 closest distance to " CB  ASN A 215 " =    1.026
peak=    3.156 closest distance to " CG2 VAL A 232 " =    0.826
peak=    3.151 closest distance to " O   HOH Z 432 " =    1.868
peak=    3.151 closest distance to " SD AMET A  47 " =    1.142
peak=    3.149 closest distance to " O   HOH Z  94 " =    1.829
peak=    3.147 closest distance to " O   HOH Z 283 " =    2.344
peak=    3.146 closest distance to " CE AMET A  47 " =    1.290
peak=    3.145 closest distance to " O   HOH Z 407 " =    2.191
peak=    3.139 closest distance to " CB  HIS A 108 " =    0.772
peak=    3.134 closest distance to " O   HOH Z  89 " =    2.082
peak=    3.133 closest distance to " O   HOH Z  59 " =    2.347
peak=    3.132 closest distance to " O   HOH Z 189 " =    2.572
peak=    3.131 closest distance to " CB  ASP A 124 " =    0.883
peak=    3.130 closest distance to " O   HOH Z 434 " =    1.158
peak=    3.129 closest distance to " NH2BARG A 190 " =    1.472
peak=    3.120 closest distance to " O   HOH Z 128 " =    1.529
peak=    3.117 closest distance to " NH2BARG A 145 " =    1.940
peak=    3.116 closest distance to " O   HOH Z 135 " =    1.641
peak=    3.104 closest distance to " O   HOH Z 433 " =    1.804
peak=    3.100 closest distance to " O   HOH Z 383 " =    1.798
peak=    3.100 closest distance to " O   HOH Z  85 " =    2.309
peak=    3.098 closest distance to " O   HOH Z 365 " =    1.534
peak=    3.095 closest distance to " N   ASN A 127 " =    1.346
peak=    3.092 closest distance to " O   HOH Z 130 " =    3.226
peak=    3.088 closest distance to " CA  SER A  87 " =    1.060
peak=    3.077 closest distance to " CB  GLU A 175 " =    0.885
peak=    3.072 closest distance to " CB  ARG A 138 " =    0.712
peak=    3.071 closest distance to " O   HOH Z  50 " =    1.541
peak=    3.070 closest distance to " O   HOH Z 172 " =    2.485
peak=    3.065 closest distance to " ND1 HIS A  81 " =    1.584
peak=    3.064 closest distance to " CA  ALA A  51 " =    0.954
peak=    3.052 closest distance to " O   HOH Z 247 " =    1.173
peak=    3.049 closest distance to " O   HOH Z 125 " =    2.371
peak=    3.049 closest distance to " NZ  LYS A 119 " =    1.347
peak=    3.044 closest distance to " CG  LYS A  76 " =    0.924
peak=    3.035 closest distance to " O   HOH Z 153 " =    3.689

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.677 - 5.860
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.772 - 5.860

peak=   -4.334 closest distance to " C   HIS A 108 " =    1.192
peak=   -4.323 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.305 closest distance to " O   HOH Z 377 " =    1.969
peak=   -4.264 closest distance to " CG  GLN A  58 " =    1.017
peak=   -4.189 closest distance to " O   PRO A 198 " =    1.225
peak=   -4.159 closest distance to " O   VAL A  67 " =    2.533
peak=   -4.146 closest distance to " CB  PRO A 243 " =    2.599
peak=   -4.126 closest distance to " OG BSER A 134 " =    1.409
peak=   -4.109 closest distance to " SG  CYS A 254 " =    3.403
peak=   -4.081 closest distance to " O   HOH Z 266 " =    4.788
peak=   -4.075 closest distance to " CD1 LEU A 255 " =    2.809
peak=   -4.032 closest distance to " O   HOH Z 185 " =    2.083
peak=   -4.023 closest distance to " O   HOH Z 198 " =    1.611
peak=   -4.010 closest distance to " CE  MET A 105 " =    2.361
peak=   -4.000 closest distance to " O   HOH Z 290 " =    1.014
peak=   -3.989 closest distance to " CG  PHE A 283 " =    2.589
peak=   -3.985 closest distance to " O   HOH Z 372 " =    2.547
peak=   -3.968 closest distance to " CG2 ILE A  20 " =    2.944
peak=   -3.957 closest distance to " CG  GLN A 223 " =    1.734
peak=   -3.956 closest distance to " O   HOH Z  65 " =    1.096
peak=   -3.937 closest distance to " OD2 ASP A 191 " =    1.403
peak=   -3.931 closest distance to " N   GLN A  58 " =    1.580
peak=   -3.929 closest distance to " CA  GLY A  98 " =    1.696
peak=   -3.919 closest distance to " O   HOH Z 351 " =    1.593
peak=   -3.881 closest distance to " CB  ALA A 248 " =    2.102
peak=   -3.847 closest distance to " O   HOH Z 389 " =    1.984
peak=   -3.827 closest distance to " CB  ASN A  39 " =    2.289
peak=   -3.810 closest distance to " O   HOH Z 317 " =    1.450
peak=   -3.807 closest distance to " CB  ALA A 291 " =    2.147
peak=   -3.799 closest distance to " CZ  PHE A  59 " =    1.361
peak=   -3.787 closest distance to " O   ASP A 191 " =    1.915
peak=   -3.782 closest distance to " OG  SER A   3 " =    1.597
peak=   -3.780 closest distance to " O   SER A  22 " =    2.470
peak=   -3.778 closest distance to " CG1 VAL A 112 " =    2.891
peak=   -3.777 closest distance to " CB  PHE A 192 " =    1.865
peak=   -3.736 closest distance to " O   HOH Z 231 " =    2.075
peak=   -3.726 closest distance to " O   HOH Z 427 " =    1.771
peak=   -3.722 closest distance to " CD1 ILE A 239 " =    2.548
peak=   -3.715 closest distance to " O   SER A 135 " =    1.433
peak=   -3.710 closest distance to " O   HOH Z  13 " =    1.660
peak=   -3.709 closest distance to " CZ2 TRP A 274 " =    0.957
peak=   -3.706 closest distance to " O   ALA A 161 " =    1.545
peak=   -3.688 closest distance to " CD2 TYR A 293 " =    1.835
peak=   -3.680 closest distance to " ND2 ASN A  45 " =    1.070
peak=   -3.674 closest distance to " CD2 PHE A 225 " =    1.205
peak=   -3.656 closest distance to " CB  ILE A  33 " =    2.850
peak=   -3.655 closest distance to " O   HOH Z 313 " =    1.716
peak=   -3.651 closest distance to " O   HOH Z 211 " =    1.625
peak=   -3.651 closest distance to " O   PHE A 218 " =    1.413
peak=   -3.650 closest distance to " O   HOH Z 407 " =    2.862
peak=   -3.645 closest distance to " O   PRO A 198 " =    1.242
peak=   -3.635 closest distance to " O   SER A  95 " =    1.392
peak=   -3.635 closest distance to " N   ALA A  43 " =    2.448
peak=   -3.627 closest distance to " N   THR A 157 " =    1.417
peak=   -3.603 closest distance to " O   ARG A 145 " =    1.441
peak=   -3.601 closest distance to " CA  GLY A 133 " =    1.918
peak=   -3.595 closest distance to " CD1 LEU A 101 " =    2.175
peak=   -3.590 closest distance to " CB  ALA A  43 " =    2.290
peak=   -3.581 closest distance to " O   HOH Z 213 " =    1.388
peak=   -3.574 closest distance to " O   HOH Z  60 " =    1.825
peak=   -3.574 closest distance to " CB  ALA A   7 " =    1.979
peak=   -3.568 closest distance to " CG1 VAL A 268 " =    2.386
peak=   -3.558 closest distance to " O   HOH Z  37 " =    1.675
peak=   -3.553 closest distance to " OE1 GLN A  88 " =    1.157
peak=   -3.528 closest distance to " OE1 GLN A 183 " =    1.459
peak=   -3.524 closest distance to " O   HOH Z 412 " =    5.860
peak=   -3.519 closest distance to " O   HOH Z  24 " =    1.217
peak=   -3.515 closest distance to " NE2 GLN A 278 " =    1.628
peak=   -3.514 closest distance to " O   HOH Z 250 " =    1.306
peak=   -3.511 closest distance to " O   HOH Z 152 " =    4.955
peak=   -3.505 closest distance to " O   ALA A  10 " =    1.707
peak=   -3.502 closest distance to " O   HOH Z 131 " =    4.147
peak=   -3.499 closest distance to " CB  TYR A  15 " =    2.158
peak=   -3.497 closest distance to " O   HOH Z 298 " =    1.177
peak=   -3.494 closest distance to " CZ  TYR A 169 " =    1.672
peak=   -3.491 closest distance to " O   HOH Z  52 " =    1.319
peak=   -3.488 closest distance to " O   HOH Z 377 " =    0.954
peak=   -3.480 closest distance to " O   HOH Z  90 " =    2.246
peak=   -3.477 closest distance to " OD1 ASN A 148 " =    1.583
peak=   -3.477 closest distance to " OD2 ASP A 171 " =    2.085
peak=   -3.477 closest distance to " O   HOH Z 102 " =    1.558
peak=   -3.473 closest distance to " CE2 PHE A 218 " =    2.317
peak=   -3.472 closest distance to " N   MET A 188 " =    1.944
peak=   -3.460 closest distance to " NH1AARG A 275 " =    1.847
peak=   -3.459 closest distance to " O   VAL A 189 " =    2.534
peak=   -3.452 closest distance to " CE3 TRP A 179 " =    1.271
peak=   -3.449 closest distance to " C   ALA A 158 " =    1.706
peak=   -3.449 closest distance to " O   HOH Z 348 " =    2.214
peak=   -3.447 closest distance to " N   GLN A 122 " =    1.330
peak=   -3.442 closest distance to " CA  GLY A  57 " =    2.119
peak=   -3.437 closest distance to " NE  ARG A  36 " =    1.921
peak=   -3.431 closest distance to " CE2 TYR A  30 " =    2.679
peak=   -3.431 closest distance to " CG  PRO A 243 " =    1.556
peak=   -3.430 closest distance to " O   VAL A 197 " =    1.582
peak=   -3.426 closest distance to " O   HOH Z 166 " =    1.224
peak=   -3.423 closest distance to " N   ALA A 248 " =    1.572
peak=   -3.421 closest distance to " O   HOH Z 298 " =    2.409
peak=   -3.414 closest distance to " O   HOH Z 140 " =    1.475
peak=   -3.406 closest distance to " N   ASN A 127 " =    1.458
peak=   -3.403 closest distance to " CE3 TRP A 274 " =    2.279
peak=   -3.401 closest distance to " O   HOH Z 134 " =    3.850
peak=   -3.393 closest distance to " O   HOH Z  15 " =    1.497
peak=   -3.383 closest distance to " OG  SER A  87 " =    1.365
peak=   -3.379 closest distance to " CG  MET A 105 " =    0.921
peak=   -3.375 closest distance to " ND2 ASN A 187 " =    1.423
peak=   -3.373 closest distance to " O   HOH Z 263 " =    3.013
peak=   -3.372 closest distance to " O   ALA A  51 " =    1.210
peak=   -3.372 closest distance to " ND2 ASN A  45 " =    1.934
peak=   -3.366 closest distance to " CB  ALA A 248 " =    2.249
peak=   -3.362 closest distance to " O   HOH Z 339 " =    1.782
peak=   -3.356 closest distance to " O   ALA A 180 " =    1.104
peak=   -3.347 closest distance to " O   ASP A 162 " =    2.119
peak=   -3.344 closest distance to " OE2 GLU A 152 " =    1.087
peak=   -3.342 closest distance to " O   HOH Z  11 " =    1.798
peak=   -3.341 closest distance to " ND2 ASN A 252 " =    1.794
peak=   -3.341 closest distance to " O   HOH Z  63 " =    2.197
peak=   -3.338 closest distance to " CB  ALA A 291 " =    2.227
peak=   -3.337 closest distance to " O   HOH Z 191 " =    5.579
peak=   -3.336 closest distance to " CE BMET A  47 " =    1.133
peak=   -3.332 closest distance to " O   PRO A 163 " =    1.182
peak=   -3.330 closest distance to " O   ALA A   1 " =    1.591
peak=   -3.327 closest distance to " CG1 VAL A 230 " =    2.025
peak=   -3.318 closest distance to " O   ALA A  34 " =    2.356
peak=   -3.304 closest distance to " CE  LYS A  76 " =    2.787
peak=   -3.301 closest distance to " CB  PRO A 163 " =    2.460
peak=   -3.297 closest distance to " ND2 ASN A  39 " =    1.344
peak=   -3.290 closest distance to " CB  ASP A 132 " =    2.367
peak=   -3.289 closest distance to " OG  SER A  63 " =    1.170
peak=   -3.287 closest distance to " O   TRP A  70 " =    1.387
peak=   -3.278 closest distance to " CG  ASP A 231 " =    0.772
peak=   -3.278 closest distance to " CG2 ILE A 263 " =    2.290
peak=   -3.277 closest distance to " CB  TRP A  85 " =    2.344
peak=   -3.275 closest distance to " O   TYR A 186 " =    1.518
peak=   -3.270 closest distance to " CA  GLY A 203 " =    2.311
peak=   -3.268 closest distance to " OG  SER A  87 " =    1.633
peak=   -3.266 closest distance to " OG BSER A 134 " =    1.578
peak=   -3.263 closest distance to " CD2 LEU A 237 " =    2.720
peak=   -3.263 closest distance to " CB  ALA A 131 " =    2.013
peak=   -3.262 closest distance to " O   MET A  40 " =    2.739
peak=   -3.260 closest distance to " O   HOH Z 388 " =    2.125
peak=   -3.260 closest distance to " O   HOH Z 134 " =    3.316
peak=   -3.259 closest distance to " C   ALA A 114 " =    2.215
peak=   -3.251 closest distance to " CE3 TRP A 123 " =    1.662
peak=   -3.250 closest distance to " OD1 ASP A 171 " =    1.532
peak=   -3.247 closest distance to " O   HOH Z 345 " =    1.952
peak=   -3.245 closest distance to " O   HOH Z 114 " =    2.905
peak=   -3.243 closest distance to " O   LEU A 101 " =    2.277
peak=   -3.242 closest distance to " N   PRO A 163 " =    1.607
peak=   -3.242 closest distance to " CG2 VAL A 296 " =    1.843
peak=   -3.241 closest distance to " N   SER A 212 " =    1.969
peak=   -3.241 closest distance to " NH2 ARG A  79 " =    2.147
peak=   -3.240 closest distance to " O   GLU A 152 " =    1.428
peak=   -3.240 closest distance to " O   HOH Z  28 " =    1.945
peak=   -3.230 closest distance to " O   SER A 146 " =    1.076
peak=   -3.229 closest distance to " O   HOH Z 385 " =    1.946
peak=   -3.229 closest distance to " CB  GLN A  55 " =    1.283
peak=   -3.228 closest distance to " CG2 ILE A 151 " =    2.553
peak=   -3.224 closest distance to " O   GLN A 144 " =    1.353
peak=   -3.218 closest distance to " NE2 GLN A 194 " =    2.830
peak=   -3.206 closest distance to " O   HOH Z 438 " =    1.286
peak=   -3.205 closest distance to " CA  ASP A 298 " =    1.106
peak=   -3.202 closest distance to " O   ILE A  49 " =    1.665
peak=   -3.197 closest distance to " OE1 GLU A 277 " =    2.125
peak=   -3.196 closest distance to " CB  ASP A  27 " =    2.342
peak=   -3.194 closest distance to " O   HOH Z 158 " =    1.994
peak=   -3.194 closest distance to " O   HOH Z 165 " =    2.375
peak=   -3.192 closest distance to " CB  ALA A 114 " =    2.489
peak=   -3.187 closest distance to " CD  LYS A 289 " =    2.385
peak=   -3.186 closest distance to " O   HOH Z 309 " =    2.397
peak=   -3.180 closest distance to " O   HOH Z 187 " =    1.897
peak=   -3.177 closest distance to " OXT GLY A 302 " =    2.917
peak=   -3.176 closest distance to " O   VAL A 125 " =    2.179
peak=   -3.174 closest distance to " CB  CYS A 201 " =    2.466
peak=   -3.166 closest distance to " CD2 LEU A 237 " =    2.320
peak=   -3.162 closest distance to " N   PHE A  59 " =    1.829
peak=   -3.156 closest distance to " OG  SER A 245 " =    1.342
peak=   -3.149 closest distance to " CG2 THR A 178 " =    2.142
peak=   -3.147 closest distance to " CD1 PHE A  59 " =    1.991
peak=   -3.145 closest distance to " CD1 TRP A 179 " =    1.161
peak=   -3.145 closest distance to " O   PRO A 163 " =    1.783
peak=   -3.140 closest distance to " O   GLN A 240 " =    1.914
peak=   -3.139 closest distance to " O   HOH Z 383 " =    0.919
peak=   -3.131 closest distance to " O   THR A 220 " =    1.793
peak=   -3.117 closest distance to " O   HOH Z  51 " =    1.189
peak=   -3.117 closest distance to " C   MET A 188 " =    1.565
peak=   -3.115 closest distance to " OD1 ASP A 200 " =    1.389
peak=   -3.110 closest distance to " CB  ALA A 244 " =    2.027
peak=   -3.107 closest distance to " O   VAL A 174 " =    2.145
peak=   -3.103 closest distance to " CG1 VAL A 197 " =    2.092
peak=   -3.102 closest distance to " O   HOH Z 111 " =    2.395
peak=   -3.100 closest distance to " O   HOH Z  93 " =    2.075
peak=   -3.085 closest distance to " O   HOH Z 236 " =    2.008
peak=   -3.061 closest distance to " OG1 THR A  82 " =    1.826
peak=   -3.041 closest distance to " O   HOH Z  89 " =    2.818
peak=   -3.023 closest distance to " O   ALA A 180 " =    0.971
peak=   -3.020 closest distance to " CB  SER A 210 " =    1.172

================= 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    :  0.4178 0.4093   6.227918e+00   6.214293e+00
   1_bss:  0.4058 0.3981   6.216754e+00   6.194604e+00
   1_xyz:  0.2777 0.3118   5.917877e+00   5.996157e+00
   1_adp:  0.2515 0.3261   5.871028e+00   6.027927e+00
   1_occ:  0.2513 0.3263   5.870564e+00   6.027743e+00
   2_bss:  0.2492 0.3218   5.860328e+00   6.018169e+00
   2_xyz:  0.1839 0.2324   5.567099e+00   5.755338e+00
   2_adp:  0.1651 0.2110   5.471790e+00   5.668433e+00
   2_occ:  0.1650 0.2105   5.470398e+00   5.667324e+00
   3_bss:  0.1645 0.2089   5.462950e+00   5.658673e+00
   3_xyz:  0.1323 0.1759   5.270053e+00   5.487926e+00
   3_adp:  0.1258 0.1703   5.226641e+00   5.451177e+00
   3_occ:  0.1256 0.1703   5.226153e+00   5.450594e+00
   4_bss:  0.1257 0.1699   5.225089e+00   5.448909e+00
   4_xyz:  0.1152 0.1590   5.153306e+00   5.386390e+00
   4_adp:  0.1124 0.1586   5.139915e+00   5.381148e+00
   4_occ:  0.1123 0.1586   5.139792e+00   5.381060e+00
   5_bss:  0.1123 0.1585   5.139597e+00   5.380811e+00
   5_xyz:  0.1112 0.1568   5.132361e+00   5.374345e+00
   5_adp:  0.1107 0.1565   5.131337e+00   5.374863e+00
   5_occ:  0.1107 0.1566   5.131387e+00   5.374980e+00
   5_bss:  0.1106 0.1566   5.131342e+00   5.374875e+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:  0.340  22.745  -1.562   2.973  -1.782   0.000  -0.000  -0.000
   1_xyz:  0.340  22.745  -1.562   2.973  -1.782   0.000  -0.000  -0.000
   1_adp:  0.340  22.745  -1.562   2.973  -1.782   0.000  -0.000  -0.000
   1_occ:  0.340  22.745  -1.562   2.973  -1.782   0.000  -0.000  -0.000
   2_bss:  0.332  43.847  -2.028  -0.095  -0.947  -0.000  -0.000  -0.000
   2_xyz:  0.332  43.847  -2.028  -0.095  -0.947  -0.000  -0.000  -0.000
   2_adp:  0.332  43.847  -2.028  -0.095  -0.947  -0.000  -0.000  -0.000
   2_occ:  0.332  43.847  -2.028  -0.095  -0.947  -0.000  -0.000  -0.000
   3_bss:  0.320  43.847  -2.488  -1.680  -0.951  -0.000  -0.000  -0.000
   3_xyz:  0.320  43.847  -2.488  -1.680  -0.951  -0.000  -0.000  -0.000
   3_adp:  0.320  43.847  -2.488  -1.680  -0.951  -0.000  -0.000  -0.000
   3_occ:  0.320  43.847  -2.488  -1.680  -0.951  -0.000  -0.000  -0.000
   4_bss:  0.320  43.847  -2.796  -2.337  -1.099  -0.000  -0.000  -0.000
   4_xyz:  0.320  43.847  -2.796  -2.337  -1.099  -0.000  -0.000  -0.000
   4_adp:  0.320  43.847  -2.796  -2.337  -1.099  -0.000  -0.000  -0.000
   4_occ:  0.320  43.847  -2.796  -2.337  -1.099  -0.000  -0.000  -0.000
   5_bss:  0.320  43.847  -2.685  -2.337  -0.969  -0.000  -0.000  -0.000
   5_xyz:  0.320  43.847  -2.685  -2.337  -0.969  -0.000  -0.000  -0.000
   5_adp:  0.320  43.847  -2.685  -2.337  -0.969  -0.000  -0.000  -0.000
   5_occ:  0.320  43.847  -2.685  -2.337  -0.969  -0.000  -0.000  -0.000
   5_bss:  0.320  43.844  -2.555  -2.270  -0.815  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.474 0.5538  0.7408    53975.785
   1_bss:  46.420 0.5650  0.7511    50351.885
   1_xyz:  32.080 0.7358  0.9379    26468.293
   1_adp:  34.063 0.7122  0.9121    29102.346
   1_occ:  34.087 0.7119  0.9111    29089.471
   2_bss:  33.286 0.7206  0.8952    27848.038
   2_xyz:  22.992 0.8316  0.9917    14002.779
   2_adp:  20.159 0.8607  1.0074    11557.014
   2_occ:  20.124 0.8609  1.0072    11493.815
   3_bss:  19.836 0.8634  0.9837    11168.131
   3_xyz:  16.187 0.8963  0.9983     7812.412
   3_adp:  15.324 0.9040  0.9961     7319.533
   3_occ:  15.314 0.9041  0.9960     7303.880
   4_bss:  15.271 0.9044  0.9831     7276.440
   4_xyz:  13.960 0.9151  0.9892     6336.584
   4_adp:  13.821 0.9163  0.9871     6258.045
   4_occ:  13.821 0.9163  0.9870     6254.771
   5_bss:  13.816 0.9164  0.9900     6252.710
   5_xyz:  13.666 0.9177  0.9890     6146.572
   5_adp:  13.672 0.9177  0.9844     6146.006
   5_occ:  13.678 0.9177  0.9843     6146.594
   5_bss:  13.676 0.9177  0.9884     6146.391
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8133e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8133e-01
   1_xyz:   1.538  0.011  0.101 15.514  0.007  4.104   1.2511e-01
   1_adp:   1.538  0.011  0.101 15.514  0.007  4.104   1.2511e-01
   1_occ:   1.538  0.011  0.101 15.514  0.007  4.104   1.2511e-01
   2_bss:   1.538  0.011  0.101 15.514  0.007  4.104   1.2511e-01
   2_xyz:   1.115  0.008  0.080 14.833  0.005  4.106   7.3772e-02
   2_adp:   1.115  0.008  0.080 14.833  0.005  4.106   7.3772e-02
   2_occ:   1.115  0.008  0.080 14.833  0.005  4.106   7.3772e-02
   3_bss:   1.115  0.008  0.080 14.833  0.005  4.106   7.3772e-02
   3_xyz:   0.953  0.006  0.069 14.656  0.004  4.109   5.5603e-02
   3_adp:   0.953  0.006  0.069 14.656  0.004  4.109   5.5603e-02
   3_occ:   0.953  0.006  0.069 14.656  0.004  4.109   5.5603e-02
   4_bss:   0.953  0.006  0.069 14.656  0.004  4.109   5.5603e-02
   4_xyz:   0.957  0.006  0.072 14.622  0.004  4.107   5.5256e-02
   4_adp:   0.957  0.006  0.072 14.622  0.004  4.107   5.5256e-02
   4_occ:   0.957  0.006  0.072 14.622  0.004  4.107   5.5256e-02
   5_bss:   0.957  0.006  0.072 14.622  0.004  4.107   5.5256e-02
   5_xyz:   0.902  0.005  0.067 14.464  0.004  4.107   5.0008e-02
   5_adp:   0.902  0.005  0.067 14.464  0.004  4.107   5.0008e-02
   5_occ:   0.902  0.005  0.067 14.464  0.004  4.107   5.0008e-02
   5_bss:   0.902  0.005  0.067 14.464  0.004  4.107   5.0008e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.632   2.3800e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.632   2.3800e-01
   1_xyz:   9.512  0.070  0.390 82.680  0.057  2.078   8.4839e-02
   1_adp:   9.512  0.070  0.390 82.680  0.057  2.078   8.4839e-02
   1_occ:   9.512  0.070  0.390 82.680  0.057  2.078   8.4839e-02
   2_bss:   9.512  0.070  0.390 82.680  0.057  2.078   8.4839e-02
   2_xyz:   7.185  0.056  0.254 85.612  0.037  2.273   1.4489e-01
   2_adp:   7.185  0.056  0.254 85.612  0.037  2.273   1.4489e-01
   2_occ:   7.185  0.056  0.254 85.612  0.037  2.273   1.4489e-01
   3_bss:   7.185  0.056  0.254 85.612  0.037  2.273   1.4489e-01
   3_xyz:   6.733  0.038  0.199 82.826  0.030  2.341   6.4173e-02
   3_adp:   6.733  0.038  0.199 82.826  0.030  2.341   6.4173e-02
   3_occ:   6.733  0.038  0.199 82.826  0.030  2.341   6.4173e-02
   4_bss:   6.733  0.038  0.199 82.826  0.030  2.341   6.4173e-02
   4_xyz:   6.701  0.033  0.216 84.382  0.041  2.317   4.5028e-02
   4_adp:   6.701  0.033  0.216 84.382  0.041  2.317   4.5028e-02
   4_occ:   6.701  0.033  0.216 84.382  0.041  2.317   4.5028e-02
   5_bss:   6.701  0.033  0.216 84.382  0.041  2.317   4.5028e-02
   5_xyz:   6.746  0.040  0.208 84.979  0.037  2.357   3.1613e-02
   5_adp:   6.746  0.040  0.208 84.979  0.037  2.357   3.1613e-02
   5_occ:   6.746  0.040  0.208 84.979  0.037  2.357   3.1613e-02
   5_bss:   6.746  0.040  0.208 84.979  0.037  2.357   3.1613e-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: 100.10   0.00  17.95  76.32   0.00  14.00 100.10   4.56  39.46
   1_occ: 100.10   0.00  17.95  76.32   0.00  14.00 100.10   4.56  39.46
   2_bss: 100.10   0.00  17.95  76.32   0.00  14.00 100.10   4.56  39.46
   2_xyz: 100.10   0.00  17.95  76.32   0.00  14.00 100.10   4.56  39.46
   2_adp:  87.36   1.47  16.94  76.44   1.47  13.02  87.36   6.48  38.25
   2_occ:  87.36   1.47  16.94  76.44   1.47  13.02  87.36   6.48  38.25
   3_bss:  87.36   1.47  16.94  76.44   1.47  13.02  87.36   6.48  38.25
   3_xyz:  87.36   1.47  16.94  76.44   1.47  13.02  87.36   6.48  38.25
   3_adp:  85.12   0.86  16.82  78.32   0.86  12.71  85.12   3.34  39.19
   3_occ:  85.12   0.86  16.82  78.32   0.86  12.71  85.12   3.34  39.19
   4_bss:  85.12   0.86  16.82  78.32   0.86  12.71  85.12   3.34  39.19
   4_xyz:  85.12   0.86  16.82  78.32   0.86  12.71  85.12   3.34  39.19
   4_adp:  87.54   0.17  17.08  86.97   0.17  12.74  87.54   3.15  40.70
   4_occ:  87.54   0.17  17.08  86.97   0.17  12.74  87.54   3.15  40.70
   5_bss:  87.54   0.17  17.08  86.97   0.17  12.74  87.54   3.15  40.70
   5_xyz:  87.54   0.17  17.08  86.97   0.17  12.74  87.54   3.15  40.70
   5_adp:  88.39   0.16  16.95  88.39   0.16  12.64  87.75   4.70  40.46
   5_occ:  88.39   0.16  16.95  88.39   0.16  12.64  87.75   4.70  40.46
   5_bss:  88.38   0.16  16.95  88.38   0.16  12.63  87.75   4.70  40.46
------------------------------------------------------------------------
 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:    1.596    0.032    0.427
   1_adp:    1.596    0.032    0.427
   1_occ:    1.596    0.032    0.427
   2_bss:    1.596    0.032    0.427
   2_xyz:    1.387    0.042    0.563
   2_adp:    1.387    0.042    0.563
   2_occ:    1.387    0.042    0.563
   3_bss:    1.387    0.042    0.563
   3_xyz:    1.279    0.095    0.639
   3_adp:    1.279    0.095    0.639
   3_occ:    1.279    0.095    0.639
   4_bss:    1.279    0.095    0.639
   4_xyz:    1.283    0.085    0.662
   4_adp:    1.283    0.085    0.662
   4_occ:    1.283    0.085    0.662
   5_bss:    1.283    0.085    0.662
   5_xyz:    1.348    0.090    0.672
   5_adp:    1.348    0.090    0.672
   5_occ:    1.348    0.090    0.672
   5_bss:    1.348    0.090    0.672
------------------------------------------------------------------------

CPU time actual refinement: 329.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_258/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_258/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_258/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_258/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_258/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.91 
  Macro-tasks:
    bulk solvent and scale       = 43.52  
    individual site refinement   = 132.30 
    weights calculation          = 28.98  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.43 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 102.92 
    alpha_beta                      = 8.13   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 111.29 
    fmodel                         = 7.31   
    r_factors                      = 0.22   
    phase_errors                   = 10.81  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 243.85 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.667 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    642 calls, 102.65 s
gradients_fft:          587 calls,  97.91 s

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

# Date 2008-01-16 Time 04:24:07 PST -0800 (1200486247.39 s)
Start R-work = 0.4178, R-free = 0.4093 (no bulk solvent and anisotropic scale)
Final R-work = 0.1351, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.4058, R-free = 0.3981
Final R-work = 0.1106, R-free = 0.1566