# Date 2008-01-16 Time 05:16:37 PST -0800 (1200489397.90 s)
#phil __OFF__

Command line arguments: "../663.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12994
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 663

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.93, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98108
Completeness in resolution range: 0.967836
Completeness with d_max=infinity: 0.964785

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9811

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98108
Completeness in resolution range: 0.967836
Completeness with d_max=infinity: 0.964785

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2387 [2117/2144]  1906   211  10.0%
  bin  2:  4.2387 -  3.3772 [2041/2057]  1836   205  10.0%
  bin  3:  3.3772 -  2.9540 [2019/2038]  1815   204  10.1%
  bin  4:  2.9540 -  2.6856 [2000/2030]  1805   195   9.8%
  bin  5:  2.6856 -  2.4941 [1986/2005]  1786   200  10.1%
  bin  6:  2.4941 -  2.3476 [1953/1978]  1761   192   9.8%
  bin  7:  2.3476 -  2.2304 [1970/2003]  1769   201  10.2%
  bin  8:  2.2304 -  2.1336 [1958/1989]  1762   196  10.0%
  bin  9:  2.1336 -  2.0517 [1962/2004]  1766   196  10.0%
  bin 10:  2.0517 -  1.9811 [1583/1992]  1424   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_663/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:
        1.81 -     2.42: 13
        2.42 -     3.04: 2211
        3.04 -     3.66: 4700
        3.66 -     4.28: 9070
        4.28 -     4.90: 12419
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.177 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.207 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.327 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28408 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_663/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_663/model_refine_001.geo

CPU time processing inputs: 9.69


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2266   r_free= 0.2301   ksol= 0.00   Bsol= 0.00   scale= 1.009    |
|                                                                             |
| 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:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.720709                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7275 0.99   1378  154 0.2517 0.2526      6.2626      6.2192|
|  2:  4.7275 -  3.7722 0.99   1334  145 0.1775 0.1694      6.1076       6.098|
|  3:  3.7722 -  3.3012 0.99   1302  146 0.1871 0.1858       5.973      6.0674|
|  4:  3.3012 -  3.0021 0.99   1291  145 0.1881 0.2182      5.8361      5.8901|
|  5:  3.0021 -  2.7884 0.99   1281  141 0.2112 0.1919      5.7342      5.7144|
|  6:  2.7884 -  2.6249 0.99   1283  144 0.2220 0.2290      5.6929       5.684|
|  7:  2.6249 -  2.4941 0.99   1279  140 0.2300 0.2066      5.6988      5.5912|
|  8:  2.4941 -  2.3860 0.98   1264  144 0.2359 0.2420      5.6454      5.6939|
|  9:  2.3860 -  2.2944 0.98   1271  139 0.2387 0.2582      5.6059      5.6413|
| 10:  2.2944 -  2.2155 0.99   1246  142 0.2394 0.2785      5.5687      5.7507|
| 11:  2.2155 -  2.1465 0.99   1275  139 0.2423 0.2531      5.5182      5.5717|
| 12:  2.1465 -  2.0853 0.97   1243  137 0.2400 0.2420      5.4904      5.5038|
| 13:  2.0853 -  2.0305 0.99   1253  142 0.2470 0.2493      5.3908      5.3881|
| 14:  2.0305 -  1.9811 0.72    930  101 0.2578 0.2892      5.3922      5.3807|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7275  1378   154  0.82  23.62   0.88     0.82      35515.70|
|  2:  4.7275 -  3.7722  1334   145  0.89  17.06   1.00     0.95      27599.04|
|  3:  3.7722 -  3.3012  1302   146  0.89  17.33   1.03     1.01      21360.64|
|  4:  3.3012 -  3.0021  1291   145  0.89  17.80   1.04     1.02      17393.36|
|  5:  3.0021 -  2.7884  1281   141  0.86  20.57   1.03     1.01      13826.11|
|  6:  2.7884 -  2.6249  1283   144  0.86  20.68   1.05     1.02      11993.98|
|  7:  2.6249 -  2.4941  1279   140  0.86  20.85   1.05     1.04      10942.59|
|  8:  2.4941 -  2.3860  1264   144  0.84  22.80   1.06     1.03      11304.79|
|  9:  2.3860 -  2.2944  1271   139  0.83  23.61   1.09     1.03      10907.11|
| 10:  2.2944 -  2.2155  1246   142  0.82  24.96   1.10     1.04      10795.45|
| 11:  2.2155 -  2.1465  1275   139  0.83  24.22   1.12     1.06       9473.05|
| 12:  2.1465 -  2.0853  1243   137  0.84  23.40   1.12     1.09       8856.05|
| 13:  2.0853 -  2.0305  1253   142  0.82  25.33   1.12     1.07       7955.84|
| 14:  2.0305 -  1.9811   930   101  0.81  25.95   1.11     1.00       7464.29|
|alpha:            min =        0.82 max =            1.09 mean =         1.01|
|beta:             min =     7464.29 max =        35515.70 mean =     15015.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.87 mean =        21.90|
|phase err.(test): min =        0.00 max =           89.96 mean =        21.91|
|-----------------------------------------------------------------------------|

============================== 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 = 3.579402              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.095   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.373081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.636   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      198 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2013 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1853 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2847 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4664 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4406 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5655 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6764 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.152 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2266   r_free= 0.2301   ksol= 0.00   Bsol= 0.00   scale= 1.009    |
|                                                                             |
| 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:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.720709                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2057   r_free= 0.2078   ksol= 0.32   Bsol= 39.26   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-2.78,-0.24,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.681571                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.169102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.260   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.511   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2057      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.2078      final r-factor (free) = 0.1510          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2505 = 3.17 * 0.50 * 5.7369 + 1.00 * 0.1602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6024 = 3.17 * 0.50 * 5.3908 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1510      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9913 = 0.18 * 1.00 * 5.3908 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9798 = 0.18 * 1.00 * 5.1611 + 1.00 * 0.0366                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.42   16.41    None  None   None       |
|    all(noH): 2823   0      0.00    69.42   16.41    None  None   None       |
|    Sol.    : 438    0      5.70    62.49   36.99    None  None   None       |
|    Mac.    : 2385   0      0.00    69.42   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:     0.000 -   6.942:  227   |   5:    34.712 -  41.654:  109        |
|      1:     6.942 -  13.885: 1497   |   6:    41.654 -  48.597:   86        |
|      2:    13.885 -  20.827:  531   |   7:    48.597 -  55.539:   65        |
|      3:    20.827 -  27.770:  143   |   8:    55.539 -  62.482:   31        |
|      4:    27.770 -  34.712:  132   |   9:    62.482 -  69.424:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1203 r_free = 0.1520             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1198 r_free = 0.1517             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1517   ksol= 0.32   Bsol= 39.26   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-2.78,-0.24,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.163350                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1502   ksol= 0.32   Bsol= 41.54   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.73,-1.45,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.158646                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.817464              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.279  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.212694              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.506   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1502      final r-factor (free) = 0.1477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7498 = 1.82 * 0.50 * 5.1608 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7158 = 1.82 * 0.50 * 5.1246 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1477      final r-factor (free) = 0.1484          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2002 = 0.21 * 1.00 * 5.1246 + 1.00 * 0.1102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0918 = 0.21 * 1.00 * 5.1004 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    67.63   16.58    None  None   None       |
|    all(noH): 2823   0      1.93    67.63   16.58    None  None   None       |
|    Sol.    : 438    0      5.02    67.09   37.10    None  None   None       |
|    Mac.    : 2385   0      1.93    67.63   12.81    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:     1.933 -   8.503:  585   |   5:    34.782 -  41.352:  108        |
|      1:     8.503 -  15.073: 1290   |   6:    41.352 -  47.921:   89        |
|      2:    15.073 -  21.642:  390   |   7:    47.921 -  54.491:   91        |
|      3:    21.642 -  28.212:  128   |   8:    54.491 -  61.061:   30        |
|      4:    28.212 -  34.782:  105   |   9:    61.061 -  67.630:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1484             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1485             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1485   ksol= 0.32   Bsol= 41.54   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.73,-1.45,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1483   ksol= 0.32   Bsol= 41.54   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.43,-1.48,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.103701                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.289741              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.228  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.759244              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.591  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1483      final r-factor (free) = 0.1494          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3483 = 1.29 * 0.50 * 5.1008 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3453 = 1.29 * 0.50 * 5.1088 + 1.00 * 0.0508                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1494      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8858 = 0.76 * 1.00 * 5.1088 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8859 = 0.76 * 1.00 * 5.1069 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    79.77   16.88    None  None   None       |
|    all(noH): 2823   0      0.79    79.77   16.88    None  None   None       |
|    Sol.    : 438    0      5.51    71.19   38.72    None  None   None       |
|    Mac.    : 2385   0      0.79    79.77   12.87    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:     0.788 -   8.686:  701   |   5:    40.277 -  48.175:  117        |
|      1:     8.686 -  16.584: 1294   |   6:    48.175 -  56.072:   87        |
|      2:    16.584 -  24.481:  331   |   7:    56.072 -  63.970:   42        |
|      3:    24.481 -  32.379:  118   |   8:    63.970 -  71.868:   18        |
|      4:    32.379 -  40.277:  109   |   9:    71.868 -  79.766:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1513             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1514             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1514   ksol= 0.32   Bsol= 41.54   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.43,-1.48,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.113899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1513   ksol= 0.32   Bsol= 44.07   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.21,-1.37,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.113483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.659561              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.791  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.160408              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.858  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1047          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8427 = 2.66 * 0.50 * 5.1075 + 1.00 * 0.0508                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8420 = 2.66 * 0.50 * 5.0964 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1047      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1507          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8260 = 0.16 * 1.00 * 5.0964 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8250 = 0.16 * 1.00 * 5.0999 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    77.54   16.28    None  None   None       |
|    all(noH): 2823   0      1.71    77.54   16.28    None  None   None       |
|    Sol.    : 438    0      5.90    69.80   36.41    None  None   None       |
|    Mac.    : 2385   0      1.71    77.54   12.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.711 -   9.294:  861   |   5:    39.625 -  47.208:  108        |
|      1:     9.294 -  16.877: 1185   |   6:    47.208 -  54.791:   82        |
|      2:    16.877 -  24.459:  289   |   7:    54.791 -  62.374:   24        |
|      3:    24.459 -  32.042:  128   |   8:    62.374 -  69.957:    8        |
|      4:    32.042 -  39.625:  133   |   9:    69.957 -  77.539:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1058 r_free = 0.1507             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1057 r_free = 0.1507             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1507   ksol= 0.32   Bsol= 44.07   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.21,-1.37,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095630                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1508   ksol= 0.32   Bsol= 44.07   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.07,-1.25,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095832                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.701559              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.997  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.269429              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.966  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1057      final r-factor (work) = 0.1051          |
| start r-factor (free) = 0.1508      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9546 = 2.70 * 0.50 * 5.1006 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9457 = 2.70 * 0.50 * 5.0936 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1051      final r-factor (work) = 0.1049          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3793 = 0.27 * 1.00 * 5.0936 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3799 = 0.27 * 1.00 * 5.0950 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    77.77   16.18    None  None   None       |
|    all(noH): 2823   0      1.29    77.77   16.18    None  None   None       |
|    Sol.    : 438    0      5.88    69.72   36.49    None  None   None       |
|    Mac.    : 2385   0      1.29    77.77   12.45    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:     1.289 -   8.937:  812   |   5:    39.528 -  47.175:  113        |
|      1:     8.937 -  16.584: 1215   |   6:    47.175 -  54.823:   84        |
|      2:    16.584 -  24.232:  303   |   7:    54.823 -  62.471:   24        |
|      3:    24.232 -  31.880:  129   |   8:    62.471 -  70.118:    8        |
|      4:    31.880 -  39.528:  130   |   9:    70.118 -  77.766:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1049 r_free = 0.1520             target_work(ml) = 5.097         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1049 r_free = 0.1520             target_work(ml) = 5.097         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1520   ksol= 0.32   Bsol= 44.07   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.07,-1.25,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097334                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7275 0.99   1378  154 0.0987 0.1251      5.3687      5.5118|
|  2:  4.7275 -  3.7722 0.99   1334  145 0.0842 0.1091      5.4233      5.6072|
|  3:  3.7722 -  3.3012 0.99   1302  146 0.1007 0.1502       5.439      5.8632|
|  4:  3.3012 -  3.0021 0.99   1291  145 0.1136 0.1467       5.417      5.5528|
|  5:  3.0021 -  2.7884 0.99   1281  141 0.1229 0.1698      5.2773      5.5273|
|  6:  2.7884 -  2.6249 0.99   1283  144 0.1117 0.1719      5.1621      5.3865|
|  7:  2.6249 -  2.4941 0.99   1279  140 0.1162 0.1576      5.1089      5.3478|
|  8:  2.4941 -  2.3860 0.98   1264  144 0.1078 0.1682      5.0098      5.3035|
|  9:  2.3860 -  2.2944 0.98   1271  139 0.1080 0.1721      4.9777      5.2896|
| 10:  2.2944 -  2.2155 0.99   1246  142 0.1029 0.1602      4.9104      5.1269|
| 11:  2.2155 -  2.1465 0.99   1275  139 0.1067 0.1742      4.8948      5.2484|
| 12:  2.1465 -  2.0853 0.97   1243  137 0.1007 0.1571       4.819       5.122|
| 13:  2.0853 -  2.0305 0.99   1253  142 0.1032 0.1690      4.7423      5.0509|
| 14:  2.0305 -  1.9811 0.72    930  101 0.0973 0.1630      4.6134      4.8728|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7275  1378   154  0.94   8.85   0.98     0.95       6715.15|
|  2:  4.7275 -  3.7722  1334   145  0.95   7.69   1.02     1.01       8726.66|
|  3:  3.7722 -  3.3012  1302   146  0.94  10.95   1.02     1.01       9902.51|
|  4:  3.3012 -  3.0021  1291   145  0.93  12.93   1.00     0.99       9816.28|
|  5:  3.0021 -  2.7884  1281   141  0.90  15.21   0.99     0.96       7651.20|
|  6:  2.7884 -  2.6249  1283   144  0.91  14.89   0.98     0.95       6511.50|
|  7:  2.6249 -  2.4941  1279   140  0.91  14.78   0.99     0.96       5611.15|
|  8:  2.4941 -  2.3860  1264   144  0.92  14.01   0.99     0.97       4788.45|
|  9:  2.3860 -  2.2944  1271   139  0.92  14.33   1.00     0.98       4530.17|
| 10:  2.2944 -  2.2155  1246   142  0.91  14.38   1.00     0.96       3991.47|
| 11:  2.2155 -  2.1465  1275   139  0.90  15.76   1.00     0.96       4076.98|
| 12:  2.1465 -  2.0853  1243   137  0.92  13.89   1.00     0.99       3560.56|
| 13:  2.0853 -  2.0305  1253   142  0.91  15.08   1.01     1.00       3100.34|
| 14:  2.0305 -  1.9811   930   101  0.92  13.61   0.98     0.95       2310.98|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2310.98 max =         9902.51 mean =      5912.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.25|
|phase err.(test): min =        0.00 max =           89.30 mean =        12.84|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1521   ksol= 0.32   Bsol= 44.03   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-1.91,-1.09,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097306                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1049   r_free= 0.1521   ksol= 0.32   Bsol= 44.03   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-1.91,-1.09,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097306                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7275 0.99   1378  154 0.0987 0.1252      5.3684      5.5118|
|  2:  4.7275 -  3.7722 0.99   1334  145 0.0843 0.1091      5.4235      5.6072|
|  3:  3.7722 -  3.3012 0.99   1302  146 0.1007 0.1503      5.4391      5.8633|
|  4:  3.3012 -  3.0021 0.99   1291  145 0.1136 0.1467      5.4169      5.5528|
|  5:  3.0021 -  2.7884 0.99   1281  141 0.1228 0.1697      5.2772       5.527|
|  6:  2.7884 -  2.6249 0.99   1283  144 0.1117 0.1720       5.162      5.3864|
|  7:  2.6249 -  2.4941 0.99   1279  140 0.1162 0.1576      5.1089      5.3479|
|  8:  2.4941 -  2.3860 0.98   1264  144 0.1078 0.1682      5.0098      5.3033|
|  9:  2.3860 -  2.2944 0.98   1271  139 0.1080 0.1722      4.9777      5.2897|
| 10:  2.2944 -  2.2155 0.99   1246  142 0.1029 0.1602      4.9104      5.1268|
| 11:  2.2155 -  2.1465 0.99   1275  139 0.1067 0.1742      4.8948      5.2483|
| 12:  2.1465 -  2.0853 0.97   1243  137 0.1007 0.1571      4.8189       5.122|
| 13:  2.0853 -  2.0305 0.99   1253  142 0.1032 0.1690      4.7422      5.0505|
| 14:  2.0305 -  1.9811 0.72    930  101 0.0973 0.1630      4.6134      4.8729|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7275  1378   154  0.94   8.85   0.98     0.96       6707.41|
|  2:  4.7275 -  3.7722  1334   145  0.95   7.69   1.02     1.01       8725.57|
|  3:  3.7722 -  3.3012  1302   146  0.94  10.96   1.02     1.01       9904.18|
|  4:  3.3012 -  3.0021  1291   145  0.93  12.93   1.01     0.99       9814.23|
|  5:  3.0021 -  2.7884  1281   141  0.90  15.21   0.99     0.97       7649.69|
|  6:  2.7884 -  2.6249  1283   144  0.91  14.89   0.99     0.96       6510.08|
|  7:  2.6249 -  2.4941  1279   140  0.91  14.78   0.99     0.96       5610.72|
|  8:  2.4941 -  2.3860  1264   144  0.92  14.01   1.00     0.98       4787.65|
|  9:  2.3860 -  2.2944  1271   139  0.92  14.33   1.01     0.98       4530.21|
| 10:  2.2944 -  2.2155  1246   142  0.91  14.38   1.00     0.97       3991.22|
| 11:  2.2155 -  2.1465  1275   139  0.90  15.76   1.00     0.97       4076.43|
| 12:  2.1465 -  2.0853  1243   137  0.92  13.89   1.01     0.99       3559.53|
| 13:  2.0853 -  2.0305  1253   142  0.91  15.08   1.02     1.01       3099.59|
| 14:  2.0305 -  1.9811   930   101  0.92  13.61   0.99     0.95       2311.04|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2311.04 max =         9904.18 mean =      5911.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.25|
|phase err.(test): min =        0.00 max =           89.30 mean =        12.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.24    77.72   16.14    None  None   None       |
|    all(noH): 2823   0      1.24    77.72   16.14    None  None   None       |
|    Sol.    : 438    0      5.83    69.67   36.44    None  None   None       |
|    Mac.    : 2385   0      1.24    77.72   12.41    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:     1.244 -   8.891:  812   |   5:    39.482 -  47.130:  113        |
|      1:     8.891 -  16.539: 1215   |   6:    47.130 -  54.777:   84        |
|      2:    16.539 -  24.187:  303   |   7:    54.777 -  62.425:   24        |
|      3:    24.187 -  31.834:  129   |   8:    62.425 -  70.073:    8        |
|      4:    31.834 -  39.482:  130   |   9:    70.073 -  77.721:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 283         
Filter by distance & map next to the model:
   mapped sites are within: 0.516 - 4.694
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 278 from: 283
   mapped sites are within: 0.712 - 4.694

peak=    5.573 closest distance to " O   HOH Z 126 " =    1.894
peak=    5.479 closest distance to " NH2 ARG A  56 " =    2.224
peak=    5.250 closest distance to " CB  SER A  63 " =    1.177
peak=    5.236 closest distance to " CB  ARG A 275 " =    0.910
peak=    5.041 closest distance to " CB  GLN A 223 " =    1.435
peak=    4.987 closest distance to " O   HOH Z 142 " =    1.697
peak=    4.853 closest distance to " O   HOH Z 236 " =    1.943
peak=    4.810 closest distance to " C   PRO A 198 " =    1.453
peak=    4.752 closest distance to " CB  GLN A 183 " =    1.178
peak=    4.750 closest distance to " NE2 GLN A  11 " =    1.102
peak=    4.740 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.633 closest distance to " O   HOH Z 232 " =    2.372
peak=    4.557 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.556 closest distance to " O   HOH Z  15 " =    2.245
peak=    4.509 closest distance to " O   HOH Z  78 " =    1.699
peak=    4.432 closest distance to " CB  ASN A 148 " =    1.712
peak=    4.425 closest distance to " O   HOH Z 298 " =    1.899
peak=    4.419 closest distance to " O   HOH Z 193 " =    1.845
peak=    4.369 closest distance to " CB  ARG A  79 " =    1.313
peak=    4.350 closest distance to " OD1 ASN A  69 " =    2.591
peak=    4.304 closest distance to " O   HOH Z 234 " =    3.650
peak=    4.302 closest distance to " CB  TYR A 169 " =    0.741
peak=    4.260 closest distance to " O   HOH Z 427 " =    2.867
peak=    4.258 closest distance to " O   HOH Z 369 " =    2.097
peak=    4.247 closest distance to " O   HOH Z 158 " =    3.064
peak=    4.206 closest distance to " CB  LEU A 228 " =    1.077
peak=    4.196 closest distance to " ND2 ASN A 187 " =    1.505
peak=    4.189 closest distance to " O   HOH Z 303 " =    2.018
peak=    4.157 closest distance to " O   HOH Z 403 " =    1.655
peak=    4.133 closest distance to " O   HOH Z 144 " =    2.192
peak=    4.118 closest distance to " O   HOH Z  54 " =    1.738
peak=    4.093 closest distance to " O   HOH Z 272 " =    1.904
peak=    4.089 closest distance to " O   HOH Z 344 " =    3.150
peak=    4.087 closest distance to " CA  ASN A 215 " =    1.177
peak=    4.060 closest distance to " O   HOH Z 346 " =    1.743
peak=    4.037 closest distance to " CB  VAL A 265 " =    1.289
peak=    4.030 closest distance to " O   HOH Z  40 " =    1.686
peak=    4.030 closest distance to " O   HOH Z  66 " =    2.093
peak=    4.018 closest distance to " O   HOH Z  10 " =    1.842
peak=    4.013 closest distance to " CB  ARG A 190 " =    1.689
peak=    4.012 closest distance to " CB  GLU A 128 " =    1.028
peak=    3.994 closest distance to " OG ASER A 258 " =    3.084
peak=    3.965 closest distance to " CB  SER A   3 " =    1.310
peak=    3.947 closest distance to " O   HOH Z  61 " =    1.606
peak=    3.942 closest distance to " CG2 VAL A 257 " =    0.899
peak=    3.935 closest distance to " O   SER A  87 " =    2.280
peak=    3.933 closest distance to " O   HOH Z 245 " =    1.317
peak=    3.929 closest distance to " O   HOH Z  21 " =    1.771
peak=    3.914 closest distance to " O   HOH Z 389 " =    1.883
peak=    3.905 closest distance to " O   HOH Z 250 " =    1.413
peak=    3.895 closest distance to " CD2 TRP A 179 " =    1.366
peak=    3.894 closest distance to " O   HOH Z 392 " =    3.111
peak=    3.875 closest distance to " CA  ALA A  21 " =    1.218
peak=    3.875 closest distance to " O   HOH Z 189 " =    2.128
peak=    3.871 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.869 closest distance to " O   HOH Z  93 " =    2.564
peak=    3.861 closest distance to " O   HOH Z 203 " =    1.753
peak=    3.851 closest distance to " O   HOH Z  43 " =    1.901
peak=    3.846 closest distance to " CG  PRO A 243 " =    1.063
peak=    3.843 closest distance to " OD2 ASP A 286 " =    2.838
peak=    3.841 closest distance to " O   HOH Z  44 " =    1.886
peak=    3.834 closest distance to " O   HOH Z 423 " =    1.914
peak=    3.825 closest distance to " CB  TRP A 179 " =    1.330
peak=    3.824 closest distance to " O   HOH Z  61 " =    1.507
peak=    3.815 closest distance to " CB  TYR A 169 " =    0.857
peak=    3.811 closest distance to " O   HOH Z 368 " =    1.958
peak=    3.791 closest distance to " O   HOH Z 425 " =    1.893
peak=    3.774 closest distance to " O   HOH Z 132 " =    2.502
peak=    3.770 closest distance to " CG  ARG A  66 " =    2.585
peak=    3.763 closest distance to " O   HOH Z 327 " =    1.660
peak=    3.755 closest distance to " O   HOH Z 402 " =    1.449
peak=    3.754 closest distance to " O   HOH Z 248 " =    1.694
peak=    3.751 closest distance to " CB  ASP A 140 " =    0.871
peak=    3.748 closest distance to " O   HOH Z   9 " =    2.095
peak=    3.746 closest distance to " NZ  LYS A 117 " =    3.315
peak=    3.746 closest distance to " CZ  PHE A 218 " =    1.026
peak=    3.741 closest distance to " O   HOH Z  19 " =    2.398
peak=    3.737 closest distance to " CE  LYS A  76 " =    0.903
peak=    3.732 closest distance to " CG  PRO A  90 " =    1.080
peak=    3.728 closest distance to " CG2 ILE A 120 " =    1.143
peak=    3.720 closest distance to " ND2 ASN A 110 " =    1.802
peak=    3.707 closest distance to " CD1 ILE A 106 " =    0.885
peak=    3.697 closest distance to " CB  GLU A 277 " =    3.494
peak=    3.693 closest distance to " O   HOH Z 407 " =    2.472
peak=    3.685 closest distance to " CA  THR A 264 " =    0.912
peak=    3.673 closest distance to " O   HOH Z 193 " =    2.039
peak=    3.667 closest distance to " CB  ALA A 291 " =    1.364
peak=    3.665 closest distance to " NH1AARG A 145 " =    1.168
peak=    3.658 closest distance to " CB  VAL A 202 " =    1.524
peak=    3.657 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.656 closest distance to " O   HOH Z 371 " =    3.179
peak=    3.651 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.633 closest distance to " O   HOH Z 291 " =    1.549
peak=    3.632 closest distance to " O   HOH Z 193 " =    1.631
peak=    3.631 closest distance to " O   HOH Z 175 " =    2.163
peak=    3.631 closest distance to " CG1BVAL A  72 " =    1.581
peak=    3.631 closest distance to " O   HOH Z 214 " =    2.018
peak=    3.619 closest distance to " O   HOH Z   1 " =    2.010
peak=    3.615 closest distance to " O   HOH Z 148 " =    3.257
peak=    3.605 closest distance to " O   HOH Z 426 " =    1.518
peak=    3.604 closest distance to " O   HOH Z 213 " =    1.651
peak=    3.603 closest distance to " O   HOH Z 128 " =    2.058
peak=    3.599 closest distance to " O   HOH Z  97 " =    1.930
peak=    3.593 closest distance to " CB  SER A 212 " =    1.101
peak=    3.588 closest distance to " CB  ILE A 120 " =    1.261
peak=    3.587 closest distance to " CA  THR A 221 " =    0.991
peak=    3.578 closest distance to " CB  SER A 216 " =    0.787
peak=    3.575 closest distance to " CG2 THR A 221 " =    1.169
peak=    3.572 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.570 closest distance to " O   HOH Z 199 " =    1.507
peak=    3.568 closest distance to " O   HOH Z 417 " =    3.185
peak=    3.564 closest distance to " O   HOH Z 250 " =    1.854
peak=    3.560 closest distance to " CD  ARG A 159 " =    0.712
peak=    3.557 closest distance to " CB  SER A  26 " =    1.579
peak=    3.552 closest distance to " CB  ARG A 139 " =    0.985
peak=    3.545 closest distance to " O   HOH Z 173 " =    1.908
peak=    3.543 closest distance to " O   HOH Z 172 " =    3.538
peak=    3.538 closest distance to " NH2BARG A 145 " =    2.027
peak=    3.532 closest distance to " CD1 LEU A 300 " =    1.278
peak=    3.532 closest distance to " O   MET A 105 " =    1.824
peak=    3.528 closest distance to " O   HOH Z  85 " =    2.209
peak=    3.527 closest distance to " O   HOH Z 305 " =    3.657
peak=    3.505 closest distance to " CA  ALA A  84 " =    1.335
peak=    3.502 closest distance to " O   TRP A 274 " =    1.879
peak=    3.499 closest distance to " CG2 ILE A  20 " =    1.509
peak=    3.498 closest distance to " O   HOH Z 126 " =    2.125
peak=    3.491 closest distance to " CG  PRO A 198 " =    1.239
peak=    3.488 closest distance to " O   HOH Z 295 " =    1.522
peak=    3.488 closest distance to " CD2 LEU A 297 " =    0.827
peak=    3.488 closest distance to " O   HOH Z 368 " =    3.572
peak=    3.484 closest distance to " CB  ASN A 224 " =    1.095
peak=    3.484 closest distance to " O   HOH Z 329 " =    3.798
peak=    3.482 closest distance to " O   HOH Z  59 " =    2.060
peak=    3.463 closest distance to " OG BSER A 164 " =    2.315
peak=    3.460 closest distance to " O   HOH Z 128 " =    2.202
peak=    3.459 closest distance to " N   ARG A 156 " =    1.278
peak=    3.456 closest distance to " CG  GLN A  77 " =    2.004
peak=    3.450 closest distance to " O   HOH Z 337 " =    3.665
peak=    3.449 closest distance to " O   HOH Z 187 " =    2.279
peak=    3.433 closest distance to " O   HOH Z 433 " =    1.753
peak=    3.430 closest distance to " O   HOH Z 185 " =    1.744
peak=    3.425 closest distance to " O   HOH Z 280 " =    2.970
peak=    3.425 closest distance to " CB  MET A  40 " =    0.875
peak=    3.423 closest distance to " O   HOH Z  71 " =    2.285
peak=    3.421 closest distance to " CG  GLN A  58 " =    2.663
peak=    3.413 closest distance to " CZ2 TRP A 179 " =    1.727
peak=    3.412 closest distance to " CA  ALA A  51 " =    0.903
peak=    3.406 closest distance to " N   ASN A  39 " =    1.236
peak=    3.402 closest distance to " CD BLYS A 290 " =    1.209
peak=    3.400 closest distance to " O   HOH Z 188 " =    2.044
peak=    3.400 closest distance to " CA  ASP A 140 " =    1.128
peak=    3.398 closest distance to " O   HOH Z 227 " =    2.144
peak=    3.394 closest distance to " OE1 GLU A   2 " =    2.212
peak=    3.391 closest distance to " O   HOH Z 234 " =    1.782
peak=    3.387 closest distance to " O   HOH Z 345 " =    3.365
peak=    3.383 closest distance to " O   HOH Z  49 " =    2.175
peak=    3.380 closest distance to " O   HOH Z 144 " =    1.848
peak=    3.376 closest distance to " O   HOH Z 423 " =    2.997
peak=    3.374 closest distance to " CA  ALA A 291 " =    0.882
peak=    3.372 closest distance to " CB  GLN A 278 " =    0.856
peak=    3.370 closest distance to " O   HOH Z 366 " =    3.240
peak=    3.368 closest distance to " CA  ILE A  33 " =    1.441
peak=    3.364 closest distance to " O   HOH Z 298 " =    2.615
peak=    3.363 closest distance to " O   HOH Z 209 " =    2.354
peak=    3.361 closest distance to " CB  ALA A 248 " =    1.407
peak=    3.359 closest distance to " CA  ASP A 162 " =    1.029
peak=    3.358 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.353 closest distance to " O   HOH Z 133 " =    1.446
peak=    3.351 closest distance to " NH2 ARG A 156 " =    1.093
peak=    3.350 closest distance to " O   HOH Z 258 " =    1.698
peak=    3.349 closest distance to " CA  ALA A 233 " =    1.241
peak=    3.346 closest distance to " CD  ARG A  66 " =    2.450
peak=    3.343 closest distance to " O   HOH Z 273 " =    2.648
peak=    3.341 closest distance to " O   HOH Z 411 " =    3.872
peak=    3.340 closest distance to " O   HOH Z 281 " =    4.036
peak=    3.335 closest distance to " O   HOH Z 261 " =    2.161
peak=    3.334 closest distance to " CG  LYS A  76 " =    0.981
peak=    3.332 closest distance to " O   HOH Z 219 " =    1.998
peak=    3.331 closest distance to " CD2 LEU A 255 " =    1.374
peak=    3.331 closest distance to " O   HOH Z 406 " =    1.579
peak=    3.330 closest distance to " CA  ARG A  36 " =    1.010
peak=    3.325 closest distance to " O   HOH Z 265 " =    2.303
peak=    3.316 closest distance to " O   HOH Z 286 " =    2.278
peak=    3.315 closest distance to " O   HOH Z 227 " =    1.581
peak=    3.313 closest distance to " O   HOH Z 383 " =    1.689
peak=    3.307 closest distance to " CB  GLN A  88 " =    1.196
peak=    3.303 closest distance to " O   HOH Z 410 " =    1.953
peak=    3.298 closest distance to " CE1 TYR A 186 " =    1.311
peak=    3.298 closest distance to " CB  SER A 141 " =    0.978
peak=    3.298 closest distance to " ND1 HIS A  86 " =    1.798
peak=    3.297 closest distance to " O   ALA A   1 " =    1.651
peak=    3.287 closest distance to " CA  ASN A 176 " =    1.241
peak=    3.285 closest distance to " CB  GLU A  46 " =    0.997
peak=    3.279 closest distance to " O   HOH Z 411 " =    1.711
peak=    3.274 closest distance to " CA  MET A  40 " =    1.082
peak=    3.265 closest distance to " O   HOH Z 209 " =    2.429
peak=    3.263 closest distance to " ND1 HIS A  81 " =    1.666
peak=    3.262 closest distance to " O   HOH Z 163 " =    1.777
peak=    3.262 closest distance to " O   HOH Z 299 " =    4.477
peak=    3.262 closest distance to " O   HOH Z 419 " =    1.918
peak=    3.262 closest distance to " CE BLYS A 290 " =    1.116
peak=    3.259 closest distance to " CA  SER A  87 " =    0.988
peak=    3.259 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.259 closest distance to " O   HOH Z 421 " =    1.663
peak=    3.259 closest distance to " CB  ALA A   1 " =    4.694
peak=    3.258 closest distance to " CG1 ILE A 151 " =    0.948
peak=    3.255 closest distance to " O   HOH Z 435 " =    1.914
peak=    3.253 closest distance to " O   HOH Z 391 " =    2.972
peak=    3.252 closest distance to " O   HOH Z 163 " =    1.837
peak=    3.247 closest distance to " CA  ASN A 217 " =    1.272
peak=    3.247 closest distance to " O   HOH Z 180 " =    2.155
peak=    3.243 closest distance to " O   HOH Z 213 " =    2.074
peak=    3.243 closest distance to " CB  MET A  47 " =    1.090
peak=    3.241 closest distance to " O   HOH Z  88 " =    3.103
peak=    3.239 closest distance to " CB  ALA A 242 " =    0.896
peak=    3.239 closest distance to " CB  ALA A 114 " =    1.245
peak=    3.236 closest distance to " O   HOH Z 166 " =    3.825
peak=    3.233 closest distance to " O   ALA A 165 " =    1.456
peak=    3.231 closest distance to " CD  LYS A 166 " =    1.214
peak=    3.230 closest distance to " O   HOH Z 359 " =    1.477
peak=    3.229 closest distance to " CG  GLU A 277 " =    2.250
peak=    3.225 closest distance to " CB  GLN A  89 " =    1.260
peak=    3.223 closest distance to " CD  LYS A 119 " =    1.385
peak=    3.222 closest distance to " CB  ASN A 142 " =    1.030
peak=    3.221 closest distance to " CB  THR A  31 " =    1.693
peak=    3.217 closest distance to " CB  THR A 157 " =    1.100
peak=    3.217 closest distance to " NH1BARG A 145 " =    1.237
peak=    3.208 closest distance to " O   HOH Z 341 " =    1.913
peak=    3.207 closest distance to " O   HOH Z 108 " =    2.464
peak=    3.207 closest distance to " N   PHE A 130 " =    1.365
peak=    3.206 closest distance to " NE2 GLN A  77 " =    3.226
peak=    3.202 closest distance to " O   HOH Z 171 " =    2.111
peak=    3.200 closest distance to " O   HOH Z 358 " =    3.777
peak=    3.198 closest distance to " CD1 ILE A 263 " =    1.326
peak=    3.194 closest distance to " CB  ASN A 215 " =    1.146
peak=    3.193 closest distance to " O   HOH Z 302 " =    1.996
peak=    3.193 closest distance to " CG  PRO A 213 " =    1.000
peak=    3.191 closest distance to " CD  ARG A  36 " =    1.005
peak=    3.190 closest distance to " CB  THR A 294 " =    1.657
peak=    3.187 closest distance to " CG  GLN A  11 " =    1.506
peak=    3.187 closest distance to " NH2AARG A 190 " =    1.154
peak=    3.186 closest distance to " O   HOH Z 126 " =    1.670
peak=    3.183 closest distance to " O   HOH Z  44 " =    3.293
peak=    3.182 closest distance to " CG BARG A 275 " =    1.432
peak=    3.181 closest distance to " CB  HIS A 108 " =    0.824
peak=    3.177 closest distance to " CA  ALA A 158 " =    1.181
peak=    3.175 closest distance to " O   HOH Z 279 " =    2.106
peak=    3.173 closest distance to " CB  ALA A  34 " =    1.036
peak=    3.173 closest distance to " CB  VAL A 126 " =    1.077
peak=    3.162 closest distance to " ND2 ASN A 301 " =    1.570
peak=    3.159 closest distance to " O   HOH Z 133 " =    2.542
peak=    3.158 closest distance to " CA  MET A 105 " =    0.934
peak=    3.158 closest distance to " CB  ASN A 110 " =    1.120
peak=    3.153 closest distance to " CD1AILE A 234 " =    0.998
peak=    3.153 closest distance to " CB  ALA A   9 " =    1.521
peak=    3.152 closest distance to " O   HOH Z 374 " =    2.611
peak=    3.146 closest distance to " O   HOH Z 263 " =    1.712
peak=    3.145 closest distance to " NH2AARG A 190 " =    1.865
peak=    3.135 closest distance to " O   HOH Z 267 " =    2.051
peak=    3.128 closest distance to " N   SER A 135 " =    1.266
peak=    3.124 closest distance to " CB  ARG A 259 " =    1.913
peak=    3.121 closest distance to " O   HOH Z 357 " =    1.779
peak=    3.115 closest distance to " O   GLY A  57 " =    2.616
peak=    3.104 closest distance to " CG  GLN A  89 " =    1.521
peak=    3.102 closest distance to " CD2 HIS A  81 " =    1.197
peak=    3.100 closest distance to " CG  GLN A 278 " =    1.280
peak=    3.100 closest distance to " OD1BASN A 224 " =    2.323
peak=    3.092 closest distance to " CD  ARG A 219 " =    1.137
peak=    3.092 closest distance to " O   ALA A   1 " =    1.450
peak=    3.087 closest distance to " CB  LEU A 255 " =    0.771
peak=    3.079 closest distance to " CB  SER A  62 " =    1.254
peak=    3.075 closest distance to " CA  GLY A  80 " =    0.715
peak=    3.075 closest distance to " O   HOH Z 409 " =    3.003
peak=    3.058 closest distance to " O   HOH Z 371 " =    1.754
peak=    3.055 closest distance to " O   HOH Z  49 " =    2.686
peak=    3.054 closest distance to " O   HOH Z 336 " =    1.769
peak=    3.045 closest distance to " CB  TYR A 116 " =    0.815
peak=    3.044 closest distance to " O   SER A  26 " =    1.932

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.578 - 5.284
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 216
   mapped sites are within: 0.759 - 5.284

peak=   -4.748 closest distance to " O   HOH Z 266 " =    4.738
peak=   -4.579 closest distance to " CB  PRO A 243 " =    2.601
peak=   -4.479 closest distance to " O   VAL A  67 " =    2.730
peak=   -4.452 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.389 closest distance to " C   HIS A 108 " =    1.112
peak=   -4.333 closest distance to " O   HOH Z 290 " =    1.226
peak=   -4.270 closest distance to " SG  CYS A 254 " =    3.372
peak=   -4.266 closest distance to " CG  GLN A 223 " =    1.837
peak=   -4.185 closest distance to " CA  VAL A  67 " =    2.755
peak=   -4.178 closest distance to " CB  ALA A 161 " =    2.579
peak=   -4.149 closest distance to " O   HOH Z 389 " =    1.817
peak=   -4.115 closest distance to " O   HOH Z 372 " =    2.396
peak=   -4.046 closest distance to " O   HOH Z 198 " =    2.136
peak=   -4.043 closest distance to " CZ3 TRP A 179 " =    1.184
peak=   -3.989 closest distance to " CD  GLN A  58 " =    1.034
peak=   -3.985 closest distance to " CG  ASP A 231 " =    0.793
peak=   -3.985 closest distance to " CD  ARG A 139 " =    1.474
peak=   -3.979 closest distance to " O   HOH Z 435 " =    2.823
peak=   -3.916 closest distance to " O   HOH Z 353 " =    2.139
peak=   -3.904 closest distance to " OG BSER A 134 " =    1.220
peak=   -3.869 closest distance to " CG1 VAL A 112 " =    2.765
peak=   -3.834 closest distance to " O   HOH Z 377 " =    2.160
peak=   -3.827 closest distance to " N   ALA A  43 " =    2.506
peak=   -3.823 closest distance to " O   HOH Z 185 " =    2.302
peak=   -3.820 closest distance to " CG  PHE A 283 " =    2.721
peak=   -3.818 closest distance to " O   HOH Z 126 " =    1.871
peak=   -3.812 closest distance to " CD1 PHE A  59 " =    1.862
peak=   -3.806 closest distance to " CZ  PHE A  59 " =    1.546
peak=   -3.806 closest distance to " O   HOH Z  10 " =    1.512
peak=   -3.802 closest distance to " O   HOH Z 211 " =    1.786
peak=   -3.784 closest distance to " O   HOH Z 114 " =    3.170
peak=   -3.782 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.766 closest distance to " ND2 ASN A  45 " =    1.602
peak=   -3.756 closest distance to " O   PRO A 198 " =    1.291
peak=   -3.751 closest distance to " OXT GLY A 302 " =    2.711
peak=   -3.742 closest distance to " CB  ALA A 291 " =    2.238
peak=   -3.740 closest distance to " O   PRO A 163 " =    2.037
peak=   -3.737 closest distance to " N   GLN A  58 " =    1.555
peak=   -3.731 closest distance to " CG2 ILE A 263 " =    2.276
peak=   -3.726 closest distance to " CG1 VAL A 112 " =    2.886
peak=   -3.720 closest distance to " CB  ASN A  39 " =    2.237
peak=   -3.714 closest distance to " O   HOH Z 198 " =    1.215
peak=   -3.706 closest distance to " CD2 PHE A 192 " =    2.073
peak=   -3.704 closest distance to " CD1 LEU A 101 " =    2.361
peak=   -3.701 closest distance to " O   HOH Z 311 " =    3.616
peak=   -3.697 closest distance to " O   HOH Z 407 " =    3.032
peak=   -3.672 closest distance to " CZ  TYR A 169 " =    1.690
peak=   -3.669 closest distance to " O   HOH Z 351 " =    1.456
peak=   -3.665 closest distance to " CB  PRO A 163 " =    2.508
peak=   -3.663 closest distance to " NH1 ARG A 195 " =    2.537
peak=   -3.662 closest distance to " SG ACYS A 201 " =    1.890
peak=   -3.661 closest distance to " CD2 LEU A 300 " =    2.927
peak=   -3.660 closest distance to " CD1 LEU A 228 " =    2.233
peak=   -3.650 closest distance to " OD1 ASP A 171 " =    1.637
peak=   -3.635 closest distance to " OG  SER A  97 " =    2.174
peak=   -3.631 closest distance to " O   HOH Z 231 " =    2.222
peak=   -3.621 closest distance to " CE2 PHE A 218 " =    2.464
peak=   -3.615 closest distance to " N   SER A 212 " =    1.985
peak=   -3.612 closest distance to " NH2AARG A 275 " =    5.284
peak=   -3.580 closest distance to " O   HOH Z 313 " =    1.932
peak=   -3.578 closest distance to " O   ARG A 145 " =    1.602
peak=   -3.575 closest distance to " O   HOH Z 196 " =    1.976
peak=   -3.563 closest distance to " CD1 LEU A 297 " =    2.296
peak=   -3.553 closest distance to " CB  ALA A 291 " =    2.343
peak=   -3.540 closest distance to " CB  ASP A 286 " =    2.159
peak=   -3.535 closest distance to " O   HOH Z  43 " =    1.634
peak=   -3.531 closest distance to " C   ALA A 158 " =    1.272
peak=   -3.502 closest distance to " N   ALA A 248 " =    1.624
peak=   -3.486 closest distance to " CG1 VAL A 112 " =    2.588
peak=   -3.486 closest distance to " CA  GLY A 241 " =    3.010
peak=   -3.476 closest distance to " CG  ASP A 132 " =    2.290
peak=   -3.475 closest distance to " OG BSER A 134 " =    1.739
peak=   -3.474 closest distance to " O   ALA A 161 " =    1.640
peak=   -3.437 closest distance to " ND2 ASN A  45 " =    1.055
peak=   -3.435 closest distance to " CG  ARG A 269 " =    2.300
peak=   -3.431 closest distance to " C   MET A 188 " =    1.420
peak=   -3.429 closest distance to " O   HOH Z  52 " =    1.284
peak=   -3.429 closest distance to " O   SER A  95 " =    1.513
peak=   -3.426 closest distance to " CE  MET A 105 " =    2.254
peak=   -3.420 closest distance to " CA  GLY A 133 " =    2.020
peak=   -3.414 closest distance to " O   HOH Z 298 " =    1.267
peak=   -3.409 closest distance to " CA  GLY A 203 " =    2.300
peak=   -3.405 closest distance to " CA  GLY A  98 " =    1.917
peak=   -3.402 closest distance to " OG  SER A   3 " =    1.638
peak=   -3.400 closest distance to " O   HOH Z  13 " =    1.493
peak=   -3.397 closest distance to " N   ASP A 286 " =    2.387
peak=   -3.393 closest distance to " O   HOH Z 385 " =    2.025
peak=   -3.393 closest distance to " OD2 ASP A 171 " =    2.278
peak=   -3.391 closest distance to " CB  TYR A  15 " =    2.198
peak=   -3.389 closest distance to " C   LEU A 143 " =    1.052
peak=   -3.388 closest distance to " O   HOH Z 395 " =    5.220
peak=   -3.383 closest distance to " O   HOH Z 385 " =    1.945
peak=   -3.383 closest distance to " OG  SER A  62 " =    1.486
peak=   -3.381 closest distance to " CB  ALA A 248 " =    2.351
peak=   -3.380 closest distance to " CD1 ILE A 239 " =    2.108
peak=   -3.377 closest distance to " NH2 ARG A  79 " =    1.959
peak=   -3.373 closest distance to " O   SER A 135 " =    1.482
peak=   -3.364 closest distance to " N   ALA A 226 " =    2.027
peak=   -3.359 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -3.355 closest distance to " O   GLY A 196 " =    1.081
peak=   -3.354 closest distance to " OG  SER A  26 " =    1.141
peak=   -3.346 closest distance to " O   VAL A 189 " =    2.567
peak=   -3.343 closest distance to " O   HOH Z   6 " =    1.472
peak=   -3.342 closest distance to " CB  ALA A 248 " =    2.094
peak=   -3.334 closest distance to " CG  PHE A 283 " =    2.648
peak=   -3.331 closest distance to " CB  LEU A  83 " =    2.377
peak=   -3.331 closest distance to " NH2 ARG A  79 " =    1.641
peak=   -3.329 closest distance to " N   THR A 235 " =    1.308
peak=   -3.326 closest distance to " CB  GLN A  11 " =    1.771
peak=   -3.325 closest distance to " OD1 ASP A 191 " =    1.541
peak=   -3.321 closest distance to " O   LEU A 101 " =    2.892
peak=   -3.315 closest distance to " NZ  LYS A 119 " =    3.528
peak=   -3.312 closest distance to " O   HOH Z  38 " =    1.634
peak=   -3.309 closest distance to " CG  GLU A 277 " =    1.190
peak=   -3.306 closest distance to " CG  ARG A  66 " =    2.382
peak=   -3.304 closest distance to " O   HOH Z  76 " =    1.883
peak=   -3.302 closest distance to " CG1 VAL A 230 " =    2.077
peak=   -3.296 closest distance to " CZ3 TRP A 274 " =    1.115
peak=   -3.295 closest distance to " CB  PHE A 208 " =    2.236
peak=   -3.294 closest distance to " O   HOH Z 244 " =    2.054
peak=   -3.294 closest distance to " O   LYS A 117 " =    1.680
peak=   -3.294 closest distance to " OD1 ASN A 148 " =    1.600
peak=   -3.287 closest distance to " O   HOH Z 166 " =    1.509
peak=   -3.287 closest distance to " CG2 THR A 178 " =    2.235
peak=   -3.284 closest distance to " CB  CYS A 201 " =    2.661
peak=   -3.284 closest distance to " OG BSER A 210 " =    2.232
peak=   -3.281 closest distance to " N   THR A 157 " =    1.549
peak=   -3.280 closest distance to " O   HOH Z  11 " =    1.703
peak=   -3.274 closest distance to " O   PHE A 218 " =    1.661
peak=   -3.274 closest distance to " CB  ASP A 132 " =    2.364
peak=   -3.268 closest distance to " OE2 GLU A   2 " =    1.741
peak=   -3.268 closest distance to " O   HOH Z 322 " =    1.641
peak=   -3.261 closest distance to " ND2 ASN A 187 " =    1.462
peak=   -3.259 closest distance to " O   HOH Z 111 " =    2.288
peak=   -3.251 closest distance to " OG1 THR A 178 " =    1.275
peak=   -3.251 closest distance to " N   PHE A  59 " =    2.100
peak=   -3.250 closest distance to " CG  GLU A 152 " =    0.784
peak=   -3.250 closest distance to " O   MET A  40 " =    2.745
peak=   -3.248 closest distance to " CD1 TYR A 247 " =    2.784
peak=   -3.242 closest distance to " CD2 PHE A  61 " =    2.466
peak=   -3.241 closest distance to " CD2 LEU A 237 " =    2.694
peak=   -3.234 closest distance to " O   GLN A 240 " =    1.932
peak=   -3.233 closest distance to " N   GLN A 122 " =    1.439
peak=   -3.232 closest distance to " O   PRO A  90 " =    1.835
peak=   -3.229 closest distance to " O   HOH Z 414 " =    1.613
peak=   -3.228 closest distance to " O   HOH Z 417 " =    2.491
peak=   -3.227 closest distance to " OD2 ASP A  50 " =    2.356
peak=   -3.227 closest distance to " O   HOH Z 174 " =    2.422
peak=   -3.225 closest distance to " O   HOH Z 317 " =    2.430
peak=   -3.221 closest distance to " NE2 GLN A 278 " =    1.740
peak=   -3.219 closest distance to " OE1 GLN A  88 " =    1.261
peak=   -3.212 closest distance to " OE1 GLN A 223 " =    1.838
peak=   -3.211 closest distance to " O   GLY A 211 " =    1.456
peak=   -3.208 closest distance to " O   HOH Z 323 " =    1.353
peak=   -3.206 closest distance to " OXT GLY A 302 " =    3.293
peak=   -3.205 closest distance to " O   VAL A 153 " =    2.306
peak=   -3.205 closest distance to " CD  GLN A  88 " =    0.759
peak=   -3.198 closest distance to " CG  GLU A 152 " =    2.390
peak=   -3.195 closest distance to " CA  GLY A 241 " =    2.760
peak=   -3.195 closest distance to " O   TRP A  92 " =    1.636
peak=   -3.194 closest distance to " OD1 ASN A 176 " =    1.312
peak=   -3.194 closest distance to " C   GLN A 205 " =    1.927
peak=   -3.190 closest distance to " CD  LYS A 289 " =    2.525
peak=   -3.189 closest distance to " CG1 VAL A  78 " =    3.229
peak=   -3.187 closest distance to " O   HOH Z 193 " =    1.962
peak=   -3.185 closest distance to " O   HOH Z  60 " =    2.403
peak=   -3.173 closest distance to " O   TRP A  70 " =    1.570
peak=   -3.171 closest distance to " O   HOH Z  73 " =    2.300
peak=   -3.169 closest distance to " N   GLY A  23 " =    2.326
peak=   -3.164 closest distance to " O   ALA A  51 " =    1.409
peak=   -3.161 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.161 closest distance to " O   VAL A 174 " =    1.996
peak=   -3.160 closest distance to " CG  MET A 105 " =    0.973
peak=   -3.157 closest distance to " O   HOH Z  91 " =    1.616
peak=   -3.150 closest distance to " NH2BARG A 275 " =    2.026
peak=   -3.149 closest distance to " CG2 THR A 221 " =    2.249
peak=   -3.144 closest distance to " O   HOH Z 262 " =    2.796
peak=   -3.143 closest distance to " C   TRP A 274 " =    1.463
peak=   -3.143 closest distance to " O   HOH Z 148 " =    1.853
peak=   -3.140 closest distance to " CZ  ARG A 259 " =    0.859
peak=   -3.136 closest distance to " CG  TRP A 266 " =    1.867
peak=   -3.130 closest distance to " O   LEU A 167 " =    1.514
peak=   -3.130 closest distance to " O   HOH Z 348 " =    1.873
peak=   -3.128 closest distance to " O   LYS A 289 " =    2.904
peak=   -3.124 closest distance to " O   HOH Z 361 " =    3.458
peak=   -3.123 closest distance to " ND2 ASN A  60 " =    1.539
peak=   -3.117 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.110 closest distance to " O   HOH Z 148 " =    3.248
peak=   -3.109 closest distance to " CB  TRP A  85 " =    2.523
peak=   -3.106 closest distance to " O   HOH Z 241 " =    1.382
peak=   -3.105 closest distance to " CE  LYS A  76 " =    2.877
peak=   -3.102 closest distance to " O   GLY A  80 " =    2.515
peak=   -3.086 closest distance to " O   HOH Z  41 " =    2.524
peak=   -3.085 closest distance to " O   HOH Z 436 " =    1.353
peak=   -3.081 closest distance to " NE2 GLN A  88 " =    1.772
peak=   -3.078 closest distance to " CZ  PHE A 130 " =    0.983
peak=   -3.078 closest distance to " O   HOH Z 351 " =    1.349
peak=   -3.076 closest distance to " O   HOH Z 295 " =    1.544
peak=   -3.074 closest distance to " O   HOH Z 210 " =    1.104
peak=   -3.071 closest distance to " O   HOH Z 137 " =    1.504
peak=   -3.062 closest distance to " CG1 VAL A 197 " =    2.176
peak=   -3.060 closest distance to " CE  LYS A  76 " =    2.696
peak=   -3.055 closest distance to " O   HOH Z 184 " =    1.794
peak=   -3.052 closest distance to " O   HOH Z 200 " =    3.396
peak=   -3.051 closest distance to " O   ALA A 292 " =    1.983
peak=   -3.050 closest distance to " O   HOH Z 407 " =    3.164
peak=   -3.045 closest distance to " O   HOH Z 281 " =    2.658
peak=   -3.041 closest distance to " O   HOH Z 234 " =    4.089
peak=   -3.040 closest distance to " CG  GLU A 152 " =    1.435
peak=   -3.032 closest distance to " NH2 ARG A  66 " =    5.198
peak=   -3.028 closest distance to " OD1AASN A 224 " =    1.756
peak=   -3.015 closest distance to " O   HOH Z 175 " =    4.360

================= 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    :  0.2266 0.2301   5.720709e+00   5.740975e+00
   1_bss:  0.2057 0.2078   5.681571e+00   5.682152e+00
   1_xyz:  0.1300 0.1510   5.219048e+00   5.345673e+00
   1_adp:  0.1203 0.1520   5.166453e+00   5.359310e+00
   1_occ:  0.1198 0.1517   5.163350e+00   5.356703e+00
   2_bss:  0.1196 0.1502   5.158646e+00   5.348810e+00
   2_xyz:  0.1120 0.1477   5.115076e+00   5.331053e+00
   2_adp:  0.1091 0.1484   5.104488e+00   5.335105e+00
   2_occ:  0.1090 0.1485   5.104264e+00   5.335273e+00
   3_bss:  0.1088 0.1483   5.103701e+00   5.334760e+00
   3_xyz:  0.1099 0.1494   5.113429e+00   5.343364e+00
   3_adp:  0.1087 0.1513   5.113806e+00   5.353027e+00
   3_occ:  0.1086 0.1514   5.113899e+00   5.353331e+00
   4_bss:  0.1085 0.1513   5.113483e+00   5.352832e+00
   4_xyz:  0.1047 0.1520   5.095260e+00   5.353071e+00
   4_adp:  0.1058 0.1507   5.095536e+00   5.346586e+00
   4_occ:  0.1057 0.1507   5.095630e+00   5.346852e+00
   5_bss:  0.1057 0.1508   5.095832e+00   5.347059e+00
   5_xyz:  0.1051 0.1517   5.097005e+00   5.354218e+00
   5_adp:  0.1049 0.1520   5.097282e+00   5.356898e+00
   5_occ:  0.1049 0.1520   5.097334e+00   5.356975e+00
   5_bss:  0.1049 0.1521   5.097306e+00   5.356935e+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:  0.321  39.256  -3.134  -2.776  -0.242  -0.000  -0.000  -0.000
   1_xyz:  0.321  39.256  -3.134  -2.776  -0.242  -0.000  -0.000  -0.000
   1_adp:  0.321  39.256  -3.134  -2.776  -0.242  -0.000  -0.000  -0.000
   1_occ:  0.321  39.256  -3.134  -2.776  -0.242  -0.000  -0.000  -0.000
   2_bss:  0.324  41.538  -3.063  -2.733  -1.451  -0.000  -0.000  -0.000
   2_xyz:  0.324  41.538  -3.063  -2.733  -1.451  -0.000  -0.000  -0.000
   2_adp:  0.324  41.538  -3.063  -2.733  -1.451  -0.000  -0.000  -0.000
   2_occ:  0.324  41.538  -3.063  -2.733  -1.451  -0.000  -0.000  -0.000
   3_bss:  0.322  41.538  -2.763  -2.434  -1.483  -0.000  -0.000  -0.000
   3_xyz:  0.322  41.538  -2.763  -2.434  -1.483  -0.000  -0.000  -0.000
   3_adp:  0.322  41.538  -2.763  -2.434  -1.483  -0.000  -0.000  -0.000
   3_occ:  0.322  41.538  -2.763  -2.434  -1.483  -0.000  -0.000  -0.000
   4_bss:  0.322  44.074  -2.525  -2.207  -1.371  -0.000  -0.000  -0.000
   4_xyz:  0.322  44.074  -2.525  -2.207  -1.371  -0.000  -0.000  -0.000
   4_adp:  0.322  44.074  -2.525  -2.207  -1.371  -0.000  -0.000  -0.000
   4_occ:  0.322  44.074  -2.525  -2.207  -1.371  -0.000  -0.000  -0.000
   5_bss:  0.325  44.074  -2.376  -2.068  -1.247  -0.000  -0.000  -0.000
   5_xyz:  0.325  44.074  -2.376  -2.068  -1.247  -0.000  -0.000  -0.000
   5_adp:  0.325  44.074  -2.376  -2.068  -1.247  -0.000  -0.000  -0.000
   5_occ:  0.325  44.074  -2.376  -2.068  -1.247  -0.000  -0.000  -0.000
   5_bss:  0.324  44.029  -2.204  -1.907  -1.090  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  21.903 0.8469  1.0115    15015.077
   1_bss:  20.098 0.8624  0.9573    11536.790
   1_xyz:  13.038 0.9230  0.9906     5913.057
   1_adp:  13.377 0.9201  0.9896     6007.071
   1_occ:  13.323 0.9205  0.9896     5953.824
   2_bss:  13.168 0.9216  0.9774     5852.670
   2_xyz:  12.762 0.9249  0.9774     5649.102
   2_adp:  12.875 0.9240  0.9732     5652.195
   2_occ:  12.877 0.9240  0.9731     5651.126
   3_bss:  12.870 0.9240  0.9798     5648.039
   3_xyz:  13.013 0.9230  0.9789     5756.386
   3_adp:  13.214 0.9214  0.9728     5842.023
   3_occ:  13.219 0.9214  0.9727     5845.755
   4_bss:  13.211 0.9215  0.9796     5841.478
   4_xyz:  13.201 0.9215  0.9799     5850.129
   4_adp:  13.051 0.9226  0.9759     5792.200
   4_occ:  13.059 0.9226  0.9758     5795.057
   5_bss:  13.064 0.9225  0.9808     5800.390
   5_xyz:  13.158 0.9219  0.9804     5889.791
   5_adp:  13.207 0.9215  0.9751     5911.356
   5_occ:  13.213 0.9215  0.9751     5912.468
   5_bss:  13.212 0.9215  0.9793     5911.273
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6017e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6017e-01
   1_xyz:   1.010  0.007  0.075 15.116  0.004  4.109   6.0514e-02
   1_adp:   1.010  0.007  0.075 15.116  0.004  4.109   6.0514e-02
   1_occ:   1.010  0.007  0.075 15.116  0.004  4.109   6.0514e-02
   2_bss:   1.010  0.007  0.075 15.116  0.004  4.109   6.0514e-02
   2_xyz:   0.973  0.007  0.075 15.109  0.004  4.118   5.8940e-02
   2_adp:   0.973  0.007  0.075 15.109  0.004  4.118   5.8940e-02
   2_occ:   0.973  0.007  0.075 15.109  0.004  4.118   5.8940e-02
   3_bss:   0.973  0.007  0.075 15.109  0.004  4.118   5.8940e-02
   3_xyz:   0.892  0.005  0.069 14.854  0.004  4.117   5.0797e-02
   3_adp:   0.892  0.005  0.069 14.854  0.004  4.117   5.0797e-02
   3_occ:   0.892  0.005  0.069 14.854  0.004  4.117   5.0797e-02
   4_bss:   0.892  0.005  0.069 14.854  0.004  4.117   5.0797e-02
   4_xyz:   1.028  0.008  0.078 15.180  0.004  4.118   6.4843e-02
   4_adp:   1.028  0.008  0.078 15.180  0.004  4.118   6.4843e-02
   4_occ:   1.028  0.008  0.078 15.180  0.004  4.118   6.4843e-02
   5_bss:   1.028  0.008  0.078 15.180  0.004  4.118   6.4843e-02
   5_xyz:   1.028  0.008  0.079 15.154  0.004  4.118   6.5364e-02
   5_adp:   1.028  0.008  0.079 15.154  0.004  4.118   6.5364e-02
   5_occ:   1.028  0.008  0.079 15.154  0.004  4.118   6.5364e-02
   5_bss:   1.028  0.008  0.079 15.154  0.004  4.118   6.5364e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_xyz:   6.943  0.046  0.290 85.168  0.030  2.304   5.1109e-02
   1_adp:   6.943  0.046  0.290 85.168  0.030  2.304   5.1109e-02
   1_occ:   6.943  0.046  0.290 85.168  0.030  2.304   5.1109e-02
   2_bss:   6.943  0.046  0.290 85.168  0.030  2.304   5.1109e-02
   2_xyz:   6.738  0.040  0.241 83.773  0.043  2.308   4.5200e-02
   2_adp:   6.738  0.040  0.241 83.773  0.043  2.308   4.5200e-02
   2_occ:   6.738  0.040  0.241 83.773  0.043  2.308   4.5200e-02
   3_bss:   6.738  0.040  0.241 83.773  0.043  2.308   4.5200e-02
   3_xyz:   6.544  0.040  0.220 83.262  0.037  2.381   3.1815e-02
   3_adp:   6.544  0.040  0.220 83.262  0.037  2.381   3.1815e-02
   3_occ:   6.544  0.040  0.220 83.262  0.037  2.381   3.1815e-02
   4_bss:   6.544  0.040  0.220 83.262  0.037  2.381   3.1815e-02
   4_xyz:   6.735  0.040  0.250 82.984  0.037  2.286   4.9466e-02
   4_adp:   6.735  0.040  0.250 82.984  0.037  2.286   4.9466e-02
   4_occ:   6.735  0.040  0.250 82.984  0.037  2.286   4.9466e-02
   5_bss:   6.735  0.040  0.250 82.984  0.037  2.286   4.9466e-02
   5_xyz:   6.927  0.039  0.253 83.276  0.039  2.259   5.1364e-02
   5_adp:   6.927  0.039  0.253 83.276  0.039  2.259   5.1364e-02
   5_occ:   6.927  0.039  0.253 83.276  0.039  2.259   5.1364e-02
   5_bss:   6.927  0.039  0.253 83.276  0.039  2.259   5.1364e-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:  69.42   0.00  16.41  69.42   0.00  12.63  62.49   5.70  36.99
   1_occ:  69.42   0.00  16.41  69.42   0.00  12.63  62.49   5.70  36.99
   2_bss:  69.42   0.00  16.41  69.42   0.00  12.63  62.49   5.70  36.99
   2_xyz:  69.42   0.00  16.41  69.42   0.00  12.63  62.49   5.70  36.99
   2_adp:  67.63   1.93  16.58  67.63   1.93  12.81  67.09   5.02  37.10
   2_occ:  67.63   1.93  16.58  67.63   1.93  12.81  67.09   5.02  37.10
   3_bss:  67.63   1.93  16.58  67.63   1.93  12.81  67.09   5.02  37.10
   3_xyz:  67.63   1.93  16.58  67.63   1.93  12.81  67.09   5.02  37.10
   3_adp:  79.77   0.79  16.88  79.77   0.79  12.87  71.19   5.51  38.72
   3_occ:  79.77   0.79  16.88  79.77   0.79  12.87  71.19   5.51  38.72
   4_bss:  79.77   0.79  16.88  79.77   0.79  12.87  71.19   5.51  38.72
   4_xyz:  79.77   0.79  16.88  79.77   0.79  12.87  71.19   5.51  38.72
   4_adp:  77.54   1.71  16.28  77.54   1.71  12.58  69.80   5.90  36.41
   4_occ:  77.54   1.71  16.28  77.54   1.71  12.58  69.80   5.90  36.41
   5_bss:  77.54   1.71  16.28  77.54   1.71  12.58  69.80   5.90  36.41
   5_xyz:  77.54   1.71  16.28  77.54   1.71  12.58  69.80   5.90  36.41
   5_adp:  77.77   1.29  16.18  77.77   1.29  12.45  69.72   5.88  36.49
   5_occ:  77.77   1.29  16.18  77.77   1.29  12.45  69.72   5.88  36.49
   5_bss:  77.72   1.24  16.14  77.72   1.24  12.41  69.67   5.83  36.44
------------------------------------------------------------------------
 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:    0.656    0.008    0.184
   1_adp:    0.656    0.008    0.184
   1_occ:    0.656    0.008    0.184
   2_bss:    0.656    0.008    0.184
   2_xyz:    0.584    0.006    0.205
   2_adp:    0.584    0.006    0.205
   2_occ:    0.584    0.006    0.205
   3_bss:    0.584    0.006    0.205
   3_xyz:    0.703    0.006    0.211
   3_adp:    0.703    0.006    0.211
   3_occ:    0.703    0.006    0.211
   4_bss:    0.703    0.006    0.211
   4_xyz:    0.841    0.009    0.217
   4_adp:    0.841    0.009    0.217
   4_occ:    0.841    0.009    0.217
   5_bss:    0.841    0.009    0.217
   5_xyz:    1.001    0.014    0.221
   5_adp:    1.001    0.014    0.221
   5_occ:    1.001    0.014    0.221
   5_bss:    1.001    0.014    0.221
------------------------------------------------------------------------

CPU time actual refinement: 323.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_663/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_663/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_663/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_663/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_663/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.10 
  Macro-tasks:
    bulk solvent and scale       = 37.34  
    individual site refinement   = 129.62 
    weights calculation          = 29.82  
    collect and process          = 6.57   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 203.48 
  Micro-tasks:
    mask                            = 0.59   
    f_calc                          = 103.57 
    alpha_beta                      = 8.15   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 111.58 
    fmodel                         = 6.47   
    r_factors                      = 0.25   
    phase_errors                   = 11.02  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 243.06 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.629 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    645 calls, 103.22 s
gradients_fft:          590 calls,  98.35 s

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

# Date 2008-01-16 Time 05:22:13 PST -0800 (1200489733.97 s)
Start R-work = 0.2266, R-free = 0.2301 (no bulk solvent and anisotropic scale)
Final R-work = 0.1299, R-free = 0.1721 (no bulk solvent and anisotropic scale)

Start R-work = 0.2057, R-free = 0.2078
Final R-work = 0.1049, R-free = 0.1521